U.S. patent application number 14/992023 was filed with the patent office on 2016-04-28 for control nucleic acids for multiple parameters.
The applicant listed for this patent is Roche Molecular Systems, Inc.. Invention is credited to Meike Eickhoff, Ellen Fiss, Joachim Glaubitz, Niclas Hitziger, Stephen Will, Dirk Zimmerman.
Application Number | 20160115529 14/992023 |
Document ID | / |
Family ID | 46577667 |
Filed Date | 2016-04-28 |
United States Patent
Application |
20160115529 |
Kind Code |
A1 |
Eickhoff; Meike ; et
al. |
April 28, 2016 |
CONTROL NUCLEIC ACIDS FOR MULTIPLE PARAMETERS
Abstract
The present invention concerns the amplification of at least a
first and a second target nucleic acid that may be present in at
least one fluid sample using an internal control nucleic acid for
qualitative and/or quantitative purposes.
Inventors: |
Eickhoff; Meike; (Rotkreuz,
CH) ; Fiss; Ellen; (Albany, CA) ; Glaubitz;
Joachim; (Sins, CH) ; Hitziger; Niclas;
(Lucerne, CH) ; Will; Stephen; (Oakland, CA)
; Zimmerman; Dirk; (Zug, CH) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Roche Molecular Systems, Inc. |
Pleasanton |
CA |
US |
|
|
Family ID: |
46577667 |
Appl. No.: |
14/992023 |
Filed: |
January 11, 2016 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14079155 |
Nov 13, 2013 |
9234250 |
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14992023 |
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13192317 |
Jul 27, 2011 |
8609340 |
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14079155 |
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61368979 |
Jul 29, 2010 |
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Current U.S.
Class: |
435/6.12 |
Current CPC
Class: |
C12Q 2600/156 20130101;
C12Q 1/6851 20130101; C12Q 1/6883 20130101; C12Q 1/708 20130101;
C12Q 1/706 20130101; C12Q 1/703 20130101; C12Q 1/707 20130101; C12Q
2565/50 20130101; C12Q 1/6851 20130101; C12Q 2521/107 20130101;
C12Q 2545/101 20130101; C12Q 2563/107 20130101 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68 |
Claims
1. A process for isolating and simultaneously amplifying at least a
first and a second target nucleic acid that may be present in one
or more samples, the process comprising the steps of: a) adding an
internal control nucleic acid to each of the one or more samples;
b) combining a solid support material and the one or more samples
in one or more vessels for a period of time, under conditions
sufficient to permit nucleic acids comprising the target nucleic
acids and the internal control nucleic acid to be immobilized on
the solid support material; c) isolating the solid support material
from the other material present in the samples in a separation
station; d) purifying the target nucleic acids in the separation
station and washing the solid support material one or more times
with a wash buffer; e) contacting the purified target nucleic acids
and the purified internal control nucleic acid with one or more
amplification reagents, comprising at least one distinct set of
primers for each of the target nucleic acids and for the internal
control nucleic acid in at least two reaction vessels, wherein at
least a first reaction vessel comprises at least the first target
nucleic acid, and at least a second reaction vessel comprises at
least the second target nucleic acid, and wherein the second target
nucleic acid is absent from the first reaction vessel; f)
incubating in the reaction vessels the purified target nucleic
acids and the purified internal control nucleic acid with the one
or more amplification reagents for a period of time, under
conditions sufficient for an amplification reaction indicative of
the presence or absence of the target nucleic acids to occur; and
g) detecting and measuring signals generated by the amplification
products of the target nucleic acids and being proportional to the
concentration of the target nucleic acids, and detecting and
measuring a signal generated by the internal control nucleic acid;
wherein the conditions for amplification and detection in steps d)
to g) are identical for the at least first and second purified
target nucleic acids and the internal control nucleic acid, and
wherein the sequence of the internal control nucleic acid is
identical for the at least first and second purified target nucleic
acids.
2. The process according to claim 1, wherein the presence of an
amplification product of the internal control nucleic acid is
indicative of an amplification occurring in the reaction mixture
even in the absence of amplification products for one or more of
the target nucleic acids.
3. The process according to claim 1, further comprising the
following step: h) determining the quantity of one or more of the
target nucleic acids.
4. The process according to claim 1, wherein the amplification
reagents comprise a polymerase with reverse transcriptase activity,
the process further comprising between step e) and step f) the step
of incubating in the reaction vessels the purified nucleic acids
with the one or more amplification reagents for a period of time
and under conditions suitable for transcription of RNA by the
polymerase with reverse transcriptase activity to occur.
5. The process according to claim 1, wherein the internal control
nucleic acid is DNA.
6. The process according to claim 1, wherein the internal control
nucleic acid is RNA.
7. The process according to claim 1, wherein the internal control
nucleic acid is an armored nucleic acid.
8. The process according to claim 1, wherein the sequence of the
internal control nucleic acid is different from the sequences of
the other nucleic acids present in the one or more samples.
9. The process according to claim 1, wherein the sequence of the
internal control nucleic acid is derived from a naturally occurring
genome.
10. The process according to claim 1, wherein the sequence of the
internal control nucleic acid is scrambled.
11. The process according to claim 1, wherein the internal control
nucleic acid has a melting temperature from 50.degree. C. to
90.degree. C.
12. The process according to claim 1, wherein the internal control
nucleic acid has a length of up to 500 bases.
13. The process according to claim 1, wherein the sequence of the
internal control nucleic acid has a GC content of 30% to 70%.
14. The process according to claim 1, wherein the internal control
nucleic acid has a concentration between LOD and 20.times.LOD.
15. The process according to claim 1, wherein the internal control
nucleic acid has a concentration between 20.times.LOD and
5000.lamda.LOD.
16. The process according to claim 1, wherein more than one
internal control nucleic acid is added in step a), but only one of
the internal control nucleic acids is amplified in step f).
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] The present application claims the benefit of U.S.
Provisional Application No. 61/368,979 filed on Jul. 29, 2010. The
present application is a continuation of U.S. Non-provisional
application Ser. No. 14/079,155 filed on Nov. 13, 2013, which is a
continuation of U.S. Non-provisional application Ser. No.
13/192,317 filed on Jul. 27, 2011 (issued as U.S. Pat. No.
8,609,340 on Dec. 17, 2013), which claims the benefit of U.S.
Provisional Application No. 61/368,979 filed on Jul. 29, 2010. The
entire disclosures of the above-referenced prior applications are
hereby incorporated herein by reference in their entirety.
FIELD OF THE INVENTION
[0002] The present invention belongs to the field of in-vitro
diagnostics. Within this field, it particularly concerns the
amplification of at least a first and a second target nucleic acid
that may be present in at least one fluid sample using an internal
control nucleic acid for qualitative and/or quantitative
purposes.
BACKGROUND OF THE INVENTION
[0003] In the field of molecular diagnostics, the amplification of
nucleic acids from numerous sources has been of considerable
significance. Examples for diagnostic applications of nucleic acid
amplification and detection are the detection of viruses such as
Human Papilloma Virus (HPV), West Nile Virus (WNV) or the routine
screening of blood donations for the presence of Human
Immunodeficiency Virus (HIV), Hepatitis-B (HBV) and/or C Virus
(HCV). Furthermore, said amplification techniques are suitable for
bacterial targets such as mycobacteria, or the analysis of oncology
markers.
[0004] The most prominent and widely-used amplification technique
is Polymerase Chain Reaction (PCR). Other amplification reactions
comprise, among others, the Ligase Chain Reaction, Polymerase
Ligase Chain Reaction, Gap-LCR, Repair Chain Reaction, 3 SR, NASBA,
Strand Displacement Amplification (SDA), Transcription Mediated
Amplification (TMA), and Q.beta.-amplification. Automated systems
for PCR-based analysis often make use of real-time detection of
product amplification during the PCR process in the same reaction
vessel. Key to such methods is the use of modified oligonucleotides
carrying reporter groups or labels.
[0005] It has been shown that amplification and detection of more
than one target nucleic acid in the same vessel is possible. This
method is commonly termed "multiplex" amplification and requires
different labels for distinction if real-time detection is
performed.
[0006] It is mostly desirable or even mandatory in the field of
clinical nucleic acid diagnostics to control the respective
amplification using control nucleic acids with a known sequence,
for qualitative (performance control) and/or quantitative
(determination of the quantity of a target nucleic using the
control as a reference) purposes. Given the diversity especially of
diagnostic targets, comprising prokaryotic, eukaryotic as well as
viral nucleic acids, and given the diversity between different
types of nucleic acids such as RNA and DNA, control nucleic acids
are usually designed in a specific manner. In brief, these controls
usually resemble the target nucleic acid for which they serve as
control in order to mimic their properties during the process. This
circumstance applies for both qualitative and quantitative assays.
In case multiple parameters are to be detected in a single or in
parallel experiments, usually different controls resembling
different target nucleic acids are employed, such as e.g. in
Swanson et al. (J. Clin. Microbiol., (2004), 42, pp. 1863-1868).
Stocher et al. (J. Virol. Meth. (2003), 108, pp. 1-8) discloses a
control nucleic acid in which multiple virus-specific competitive
controls are comprised on the same DNA molecule.
[0007] The present invention provides a controlled amplification
method using a different approach that displays various
advantages.
SUMMARY OF THE INVENTION
[0008] The present invention provides a process for isolating and
simultaneously amplifying at least a first and a second target
nucleic acid that may be present in one or more samples, the
process comprising the steps of: [0009] a) adding an internal
control nucleic acid to each of the one or more samples; [0010] b)
combining a solid support material and the one or more samples in
one or more vessels for a period of time, under conditions
sufficient to permit nucleic acids comprising the target nucleic
acids and the internal control nucleic acid to be immobilized on
the solid support material; [0011] c) isolating the solid support
material from the other material present in the samples in a
separation station; [0012] d) purifying the target nucleic acids in
the separation station and washing the solid support material one
or more times with a wash buffer; [0013] e) contacting the purified
target nucleic acids and the purified internal control nucleic acid
with one or more amplification reagents, comprising at least one
distinct set of primers for each of the target nucleic acids and
for the internal control nucleic acid in at least two reaction
vessels, wherein at least a first reaction vessel comprises at
least the first target nucleic acid, and at least a second reaction
vessel comprises at least the second target nucleic acid, and
wherein the second target nucleic acid is absent from the first
reaction vessel; [0014] f) incubating in the reaction vessels the
purified target nucleic acids and the purified internal control
nucleic acid with the one or more amplification reagents for a
period of time, under conditions sufficient for an amplification
reaction indicative of the presence or absence of the target
nucleic acids to occur; and [0015] g) detecting and measuring
signals generated by the amplification products of the target
nucleic acids and being proportional to the concentration of the
target nucleic acids, and detecting and measuring a signal
generated by the internal control nucleic acid; wherein the
conditions for amplification and detection in steps d) to g) are
identical for the at least first and second purified target nucleic
acids and the internal control nucleic acid, and wherein the
sequence of the internal control nucleic acid is identical for the
at least first and second purified target nucleic acids.
[0016] The invention further provides wherein the presence of an
amplification product of the internal control nucleic acid is
indicative of an amplification occurring in the reaction mixture
even in the absence of amplification products for one or more of
the target nucleic acids, in an embodiment further comprising the
following step: [0017] h) determining the quantity of one or more
of the target nucleic acids.
[0018] The invention further provides a process wherein the
amplification reagents comprise a polymerase with reverse
transcriptase activity, the process further comprising between step
e) and step f) the step of incubating in the reaction vessels the
purified nucleic acids with the one or more amplification reagents
for a period of time and under conditions suitable for
transcription of RNA by the polymerase with reverse transcriptase
activity to occur.
[0019] The invention provides an embodiment wherein the internal
control nucleic acid is DNA, wherein the internal control nucleic
acid is RNA, and further, wherein the internal control nucleic acid
is an armored nucleic acid. Further, the invention provides wherein
the sequence of the internal control nucleic acid is different from
the sequences of the other nucleic acids present in the one or more
samples, wherein the sequence of the internal control nucleic acid
is derived from a naturally occurring genome, wherein the sequence
of the internal control nucleic acid is scrambled, wherein the
internal control nucleic acid has a melting temperature from
50.degree. C. to 90.degree. C., and wherein the internal control
nucleic acid has a length of up to 500 bases. Further provided is
the process wherein the sequence of the internal control nucleic
acid has a GC content of 30% to 70%, wherein the internal control
nucleic acid has a concentration between LOD and 20.times.LOD, and
wherein the internal control nucleic acid has a concentration
between 20.times.LOD and 5000.times.LOD. In another embodiment, the
more than one internal control nucleic acid is added in step a),
but only one of the internal control nucleic acids is amplified in
step f).
DESCRIPTION OF THE INVENTION
[0020] The present invention provides a method for the controlled
amplification of at least a first and a second target nucleic acid
that may be present in a fluid sample.
[0021] In a first aspect, the invention relates to a process for
isolating and simultaneously amplifying at least a first and a
second target nucleic acid that may be present in one or more fluid
samples, said process comprising the automated steps of: [0022] a.
adding an internal control nucleic acid to each of said fluid
samples [0023] b. combining together a solid support material and
said one or more fluid samples in one or more vessels for a period
of time and under conditions sufficient to permit nucleic acids
comprising the target nucleic acids and the internal control
nucleic acid to be immobilized on the solid support material [0024]
c. isolating the solid support material from the other material
present in the fluid samples in a separation station [0025] d.
purifying the nucleic acids in said separation station and washing
the solid support material one or more times with a wash buffer
[0026] e. contacting the purified target nucleic acids and the
purified internal control nucleic acid with one or more
amplification reagents comprising at least one distinct set of
primers for each of said target nucleic acids and for said internal
control nucleic acid in at least two reaction vessels, wherein at
least a first reaction vessel comprises at least said first target
nucleic acid and at least a second reaction vessel comprises at
least said second target nucleic acid and wherein the second target
nucleic acid is absent from the first reaction vessel [0027] f.
incubating in said reaction vessel said purified target nucleic
acids and said purified internal control nucleic acid with said one
or more amplification reagents for a period of time and under
conditions sufficient for an amplification reaction indicative of
the presence or absence of said target nucleic acids to occur
[0028] g. detecting and measuring signals generated by the
amplification products of said target nucleic acids and being
proportional to the concentration of said target nucleic acids, and
detecting and measuring a signal generated by said internal control
nucleic acid, wherein the conditions for amplification and
detection in steps d. to g. are identical for said at least first
and second purified target nucleic acids and said internal control
nucleic acid, and wherein the sequence of said internal control
nucleic acid is identical for said at least first and second
purified target nucleic acids.
[0029] The present invention allows for the development of
simultaneous assays on a plurality of parameters and/or nucleic
acid types while using the same internal control nucleic acid
sequence for said different parameters and/or nucleic acid types.
Therefore, it contributes to reducing the overall complexity of the
corresponding experiments on various levels: For instance, only one
internal control nucleic acid sequence has to be designed and added
to the respective amplification mixes, thus saving the time and
costs for designing and synthesizing or buying multiple control
nucleic acid sequences. The assay or assays can be streamlined, and
the risk of handling errors is reduced. In addition, the more
different control nucleic acid sequences are employed in one assay
or parallel assays carried out simultaneously under the same
conditions, the more complex it may result to adjust the respective
conditions. Moreover, with a single control suitable for a
plurality of nucleic acids, said control can be dispensed from a
single source e.g. into different vessels containing said different
target nucleic acids. Within the scope of the invention, the single
control nucleic acid sequence may also serve as a qualitative and
as a quantitative control.
[0030] As a further advantage of the method described above, the
testing of a particular biological sample for other nucleic acids
in possible subsequent experiments need not involve another sample
preparation procedure with the addition of a different internal
control nucleic acid, since the control used in the invention can
be used to control the amplification of different nucleic acids.
Thus, once an internal control nucleic acid has been added, other
parameters may be tested in the same sample under the same
conditions.
[0031] The internal control nucleic acid can be competitive,
non-competitive or partially competitive.
[0032] A competitive internal control nucleic acid carries
essentially the same primer binding sites as the target and thus
competes for the same primers with the target. While this principle
allows a good mimicry of the respective target nucleic acid due to
their similar structure, it can lower the amplification efficiency
with regard to the target nucleic acid or acids and thus lead to a
less sensitive assay.
[0033] A non-competitive internal control nucleic acid has
different primer binding sites than the target and thus binds to
different primers. Advantages of such a setup comprise, among
others, the fact that the single amplification events of the
different nucleic acids in the reaction mixture can take place
independently from each other without any competition effects.
Thus, no adverse effects occur regarding the limit of detection of
the assay as can be the case in a competitive setup.
[0034] Finally, in an amplification using a partially competitive
setup the respective control nucleic acid and at least one of the
target nucleic acids compete for the same primers, while at least
one other target nucleic acid binds to different primers.
[0035] The fact that the method described above involves a distinct
set of primers for each of said target nucleic acids and for said
internal control nucleic acid renders the method considerably
flexible. In this non-competitive setup it is not necessary to
introduce target-specific binding sites into the control nucleic
acid as in the case of a competitive setup, and the drawbacks of a
competitive setup as mentioned above are avoided. In a
non-competitive setup, the internal control nucleic acid has a
sequence different from any target sequences, in order not to
compete for their primers and/or probes. For example, the sequence
of the internal control nucleic acid can be different from the
other nucleic acid sequences in the fluid sample. As an example, if
the fluid sample is derived from a human, the internal control
nucleic acid may not have a sequence which also endogenously occurs
within humans. The difference in sequence should thus be at least
significant enough to not allow the binding of primers and/or
probes to the respective endogenous nucleic acid or acids under
stringent conditions and thus render the setup competitive. In
order to avoid such interference, the sequence of the internal
control nucleic acid used in the invention can be derived from a
source different from the origin of the fluid sample. For example,
it is derived from a naturally occurring genome, for example a
plant genome, or from a grape genome. In an embodiment, a nucleic
acid derived from a naturally occurring genome is scrambled. As
known in the art, "scrambling" means introducing base mutations in
a sequence to a certain extent. For example, the sequence of the
internal control nucleic acid used in the invention is
substantially altered with respect to the naturally occurring gene
it is derived from.
[0036] The process comprising the automated steps mentioned above
also displays various additional advantages:
[0037] It has been a challenge in the prior art that the number of
different target nucleic acids in a multiplex assay carried out in
a single reaction vessel is limited by the number of appropriate
labels. In a real-time PCR assay, for example, the potential
overlap of fluorochrome spectra has a great impact on assay
performance (risk of false positive results, lower precision etc.)
Therefore, the respective fluorophores have to be carefully
selected and spectrally well separated in order to assure the
desired performance of a diagnostic test. Typically, the number of
different usable fluorophores corresponds to a single-digit number
of PCR instrument fluorescence channels.
[0038] In contrast, in the process described supra, the internally
controlled amplification of at least a first and a second target
nucleic acid takes place in at least two different reaction
vessels, allowing for the simultaneous amplification of a higher
number of different target nucleic acids, since signals in
different reaction vessels can be detected independently from each
other. Still, within the scope of the present invention are
embodiments wherein in one or more of the multiple reaction vessels
multiplex reactions are performed, thereby multiplying the number
of targets that may be amplified simultaneously and under the same
conditions. In such embodiments, the internal control nucleic acid
serves as a control for the different target nucleic acids within a
vessel as well as different target nucleic acids in different
vessel.
[0039] Thus, one aspect of the invention relates to the process
described supra, wherein at least two target nucleic acids are
amplified in the same reaction vessel.
[0040] For example, it may be preferred to amplify the first, but
not the second target nucleic acid in the first reaction vessel and
only the second, but not the first target nucleic acid in the
second reaction vessel, e.g. depending on the sample and/or the
target nucleic acid or acids in question.
[0041] Therefore, a further embodiment of the invention is the
process described above, wherein the first target nucleic acid is
absent from the second reaction vessel.
[0042] Especially if a fluid sample is suspected to contain target
nucleic acids from different organisms, or even the different
organisms as such, or if it is not clear which of the different
nucleic acids or organisms may be present in said sample, an
advantageous embodiment of the invention is the process described
above, wherein the first target nucleic acid and the second target
nucleic acid are from different organisms.
[0043] A further aspect of the invention is the process described
above, wherein the first and/or the second target nucleic acid is a
non-viral nucleic acid.
[0044] Also, an aspect of the invention is the process described
supra, wherein the first and/or the second target nucleic acid is a
bacterial nucleic acid.
[0045] As described before, the method described above is useful
for qualitatively or quantitatively controlling the amplification
of at least a first and a second target nucleic acid.
[0046] Qualitative detection of a nucleic acid in a biological
sample is crucial e.g. for recognizing an infection of an
individual. Thereby, one important requirement for an assay for
detection of a microbial infection is that false-negative or
false-positive results be avoided, since such results would almost
inevitably lead to severe consequences with regard to treatment of
the respective patient. Thus, especially in PCR-based methods, a
qualitative internal control nucleic acid is added to the detection
mix. Said control is particularly important for confirming the
validity of a test result: At least in the case of a negative
result with regard to the respective target nucleic acid, the
qualitative internal control reaction has to perform reactive
within given settings, i.e. the qualitative internal control must
be detected, otherwise the test itself is considered to be
inoperative. However, in a qualitative setup, said qualitative
internal control does not necessarily have to be detected in case
of a positive result. For qualitative tests, it is especially
important that the sensitivity of the reaction is guaranteed and
therefore strictly controlled As a consequence, the concentration
of the qualitative internal control must be relatively low so that
even in a situation e.g. of slight inhibition the qualitative
internal control is not be detected and therefore the test is
invalidated.
[0047] Thus, an aspect of the invention is the process described
above, wherein the presence of an amplification product of said
internal control nucleic acid is indicative of an amplification
occurring in the reaction mixture even in the absence of
amplification products for one or more of said target nucleic
acids.
[0048] On the other hand and in addition to mere detection of the
presence or absence of a nucleic acid in a sample, it is often
important to determine the quantity of said nucleic acid. As an
example, stage and severity of a viral disease may be assessed on
the basis of the viral load. Further, monitoring of any therapy
requires information on the quantity of a pathogen present in an
individual in order to evaluate the therapy's success. For a
quantitative assay, it is necessary to introduce a quantitative
standard nucleic acid serving as a reference for determining the
absolute quantity of a target nucleic acid. Quantitation can be
effectuated either by referencing to an external calibration or by
implementing an internal quantitative standard.
[0049] In the case of an external calibration, standard curves are
created in separate reactions using known amounts of identical or
comparable nucleic acids. The absolute quantity of a target nucleic
acid is subsequently determined by comparison of the result
obtained with the analyzed sample with said standard function.
External calibration, however, has the disadvantage that a possible
extraction procedure, its varied efficacy, and the possible and
often not predictable presence of agents inhibiting the
amplification and/or detection reaction are not reflected in the
control.
[0050] This circumstance applies to any sample-related effects.
Therefore, it might be the case that a sample is judged as negative
due to an unsuccessful extraction procedure or other sample-based
factors, whereas the target nucleic acid to be detected and
quantified is actually present in the sample.
[0051] For these and other reasons, an internal control nucleic
acid added to the test reaction itself is of advantage. When
serving as a quantitative standard, said internal control nucleic
acid has at least the following two functions in a quantitative
test:
i) It monitors the validity of the reaction. ii) It serves as
reference in titer calculation thus compensating for effects of
inhibition and controlling the preparation and amplification
processes to allow a more accurate quantitation.
[0052] Therefore, in contrast to the qualitative internal control
nucleic acid in a qualitative test which must be positive only in a
target-negative reaction, the quantitative control nucleic acid in
a quantitative test has two functions: reaction control and
reaction calibration. Therefore it must be positive and valid both
in target-negative and target-positive reactions.
[0053] It further has to be suited to provide a reliable reference
value for the calculation of high nucleic acid concentrations.
Thus, the concentration of an internal quantitative control nucleic
acid needs to be relatively high.
[0054] Therefore, an aspect of the invention is the process
described above, further comprising the following step: [0055] h.
determining the quantity of one or more of said target nucleic
acids.
[0056] The internally controlled process described above requires
considerably less hands-on time and testing is much simpler to
perform than real-time PCR methods used in the prior art. The
process offers a major advantage e.g. in the field of clinical
virology as it permits parallel amplification of several viruses in
parallel experiments. The process is particularly useful in the
management of post-transplant patients, in whom frequent viral
monitoring is required. Thereby said process facilitates
cost-effective diagnosis and contributes to a decrease in the use
of antiviral agents and in viral complications and
hospitalizations. This equally applies to the field of clinical
microbiology. In general, efficiencies will be gained in faster
turnaround time and improved testing flexibility. Consequently,
this leads to a decrease in the number of tests requested on a
patient to make a diagnosis, and potentially shorter hospital stays
(e.g. if a diagnosis can be provided sooner, patients requiring
antimicrobial therapy will receive it sooner and thus recover
earlier). In addition, patients show less morbidity and therefore
cause fewer costs related to supportive therapy (e.g., intensive
care related to a delay in diagnosis of sepsis). Providing a
negative result sooner can have important implications for the
overprescription of antibiotics. For example, if a test result
obtained by the process according to the invention is able to rule
out the pathogen more quickly than with a standard real-time PCR
method, then the clinician will not be forced to use empirical
antibiotics. Alternatively, if empirical antibiotics are used, the
duration of the respective treatment can be shortened.
[0057] With respect to designing a specific test based on the
process according to the invention, the skilled artisan will
particularly, but not only, benefit from the following advantages:
[0058] a reduction in software complexity (leading to a reduced
risk of programming errors) [0059] focusing of assay development
efforts on the chemistry optimization instead of the chemistry plus
the instrument control parameters [0060] much more reliable system
since a single process is always used and the hardware can be
optimally designed to perform this protocol [0061] the skilled
artisan performing the internally controlled process described
above is provided with the flexibility to run multiple different
assays in parallel as part of the same process [0062] cost
reduction.
[0063] In the sense of the invention, "purification", "isolation"
or "extraction" of nucleic acids relate to the following: Before
nucleic acids may be analyzed in a diagnostic assay e.g. by
amplification, they typically have to be purified, isolated or
extracted from biological samples containing complex mixtures of
different components. Often, for the first steps, processes are
used which allow the enrichment of the nucleic acids. To release
the contents of cells or viral particles, they may be treated with
enzymes or with chemicals to dissolve, degrade or denature the
cellular walls or viral particles. This process is commonly
referred to as lysis. The resulting solution containing such lysed
material is referred to as lysate. A problem often encountered
during lysis is that other enzymes degrading the component of
interest, e.g. deoxyribonucleases or ribonucleases degrading
nucleic acids, come into contact with the component of interest
during the lysis procedure. These degrading enzymes may also be
present outside the cells or may have been spatially separated in
different cellular compartments prior to lysis. As the lysis takes
place, the component of interest becomes exposed to said degrading
enzymes. Other components released during this process may e.g. be
endotoxins belonging to the family of lipopolysaccharides which are
toxic to cells and can cause problems for products intended to be
used in human or animal therapy.
[0064] There is a variety of means to tackle the above-mentioned
problem. It is common to use chaotropic agents such as guanidinium
thiocyanate or anionic, cationic, zwitterionic or non-ionic
detergents when nucleic acids are intended to be set free. It is
also an advantage to use proteases which rapidly degrade the
previously described enzymes or unwanted proteins. However, this
may produce another problem as said substances or enzymes can
interfere with reagents or components in subsequent steps.
[0065] Enzymes which can be advantageously used in such lysis or
sample preparation processes mentioned above are enzymes which
cleave the amide linkages in protein substrates and which are
classified as proteases, or (interchangeably) peptidases (see
Walsh, 1979, Enzymatic Reaction Mechanisms. W. H. Freeman and
Company, San Francisco, Chapter 3). Proteases used in the prior art
comprise alkaline proteases (WO 98/04730) or acid proteases (U.S.
Pat. No. 5,386,024). A protease which has been widely used for
sample preparation in the isolation of nucleic acids in the prior
art is proteinase K from Tritirachium album (see e.g. Sambrook J.
et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N. Y., 1989) which is active
around neutral pH and belongs to a family of proteases known to the
person skilled in the art as subtilisins. Especially advantageous
for the use in lysis or sample preparation processes mentioned
above is the enzyme esperase, a robust protease that retains its
activity at both high alkalinity and at high temperatures (EP 1 201
753).
[0066] In the sample preparation steps following the lysis step,
the component of interest is further enriched. If the
non-proteinaceous components of interest are e.g. nucleic acids,
they are normally extracted from the complex lysis mixtures before
they are used in a probe-based assay.
[0067] There are several methods for the purification of nucleic
acids: [0068] sequence-dependent or biospecific methods as e.g.:
[0069] affinity chromatography [0070] hybridization to immobilized
probes [0071] sequence-independent or physico-chemical methods as
e.g.: [0072] liquid-liquid extraction with e.g. phenol-chloroform
[0073] precipitation with e.g. pure ethanol [0074] extraction with
filter paper [0075] extraction with micelle-forming agents as
cetyl-trimethyl-ammonium-bromide [0076] binding to immobilized,
intercalating dyes, e.g. acridine derivatives [0077] adsorption to
silica gel or diatomic earths [0078] adsorption to magnetic glass
particles (MGP) or organo-silane particles under chaotropic
conditions
[0079] Particularly interesting for purification purposes is the
adsorption of nucleic acids to a glass surface although other
surfaces are possible. Many procedures for isolating nucleic acids
from their natural environment have been proposed in recent years
by the use of their binding behavior to glass surfaces. If
unmodified nucleic acids are the target, a direct binding of the
nucleic acids to a material with a silica surface may be preferred
because, among other reasons, the nucleic acids do not have to be
modified, and even native nucleic acids can be bound. These
processes are described in detail by various documents. In
Vogelstein B. et al., Proc. Natl. Acad. USA 76 (1979) 615-9, for
instance, a procedure for binding nucleic acids from agarose gels
in the presence of sodium iodide to ground flint glass is proposed.
The purification of plasmid DNA from bacteria on glass dust in the
presence of sodium perchlorate is described in Marko M. A. et al.,
Anal. Biochem. 121 (1982) 382-387. In DE-A 37 34 442, the isolation
of single-stranded M13 phage DNA on glass fiber filters by
precipitating phage particles using acetic acid and lysis of the
phage particles with perchlorate is described. The nucleic acids
bound to the glass fiber filters are washed and then eluted with a
methanol-containing Tris/EDTA buffer. A similar procedure for
purifying DNA from lambda phages is described in Jakobi R. et al.,
Anal. Biochem. 175 (1988) 196-201. The procedure entails the
selective binding of nucleic acids to glass surfaces in chaotropic
salt solutions and separating the nucleic acids from contaminants
such as agarose, proteins or cell residue. To separate the glass
particles from the contaminants, the particles may be either
centrifuged or fluids are drawn through glass fiber filters. This
is a limiting step, however, that prevents the procedure from being
used to process large quantities of samples. The use of magnetic
particles to immobilize nucleic acids after precipitation by adding
salt and ethanol is more advantageous and described e.g. in
Alderton R. P. et al., S., Anal. Biochem. 201 (1992) 166-169 and
PCT GB 91/00212. In this procedure, the nucleic acids are
agglutinated along with the magnetic particles. The agglutinate is
separated from the original solvent by applying a magnetic field
and performing a wash step. After one wash step, the nucleic acids
are dissolved in a Tris buffer. This procedure has a disadvantage,
however, in that the precipitation is not selective for nucleic
acids. Rather, a variety of solid and dissolved substances are
agglutinated as well. As a result, this procedure can not be used
to remove significant quantities of any inhibitors of specific
enzymatic reactions that may be present. Magnetic, porous glass is
also commercially available that contains magnetic particles in a
porous, particular glass matrix and is covered with a layer
containing streptavidin. This product can be used to isolate
biological materials, e.g., proteins or nucleic acids, if they are
modified in a complex preparation step so that they bind covalently
to biotin. Magnetizable particular adsorbents proved to be very
efficient and suitable for automatic sample preparation.
Ferrimagnetic and ferromagnetic as well as superparamagnetic
pigments are used for this purpose. Magnetic glass particles and
methods using them are described in WO 01/37291. Particularly
useful for the nucleic acid isolation in the context of the
invention is the method according to R. Boom et al. (J Clin
Microbiol. 28 (1990), 495-503).
[0080] The term "solid support material" comprises any of the solid
materials mentioned above in connection with the immobilization of
nucleic acids, e.g. magnetic glass particles, glass fibers, glass
fiber filters, filter paper etc., while the solid support material
is not limited to these materials.
[0081] Thus, an aspect of the invention is the process described
above, wherein the solid support material comprises one or more of
the materials selected from silica, metal, metal oxides, plastic,
polymers and nucleic acids. In an embodiment of the invention, the
solid support material is magnetic glass particles.
[0082] "Immobilize", in the context of the invention, means to
capture objects such as e.g. nucleic acids in a reversible or
irreversible manner. Particularly, "immobilized on the solid
support material", means that the object or objects are associated
with the solid support material for the purpose of their separation
from any surrounding media, and can be recovered e.g. by separation
from the solid support material at a later point. In this context,
"immobilization" can e.g. comprise the adsorption of nucleic acids
to glass or other suitable surfaces of solid materials as described
supra. Moreover, nucleic acids can be "immobilized" specifically by
binding to capture probes, wherein nucleic acids are bound to
essentially complementary nucleic acids attached to a solid support
by base-pairing. In the latter case, such specific immobilization
leads to the predominant binding of target nucleic acids.
[0083] After the purification or isolation of the nucleic acids
including the target nucleic acids from their natural surroundings,
analysis may be performed e.g. via the simultaneous amplification
described supra.
[0084] "Simultaneously", in the sense of the invention, means that
two actions, such as amplifying a first and a second or more
nucleic acids, are performed at the same time and under the same
physical conditions. In one embodiment, simultaneous amplification
of the at least first and second target nucleic acids is performed
in one vessel. In another embodiment, simultaneous amplification is
performed with at least one nucleic acid in one vessel and at least
a second nucleic acid in a second vessel, at the same time and
under the same physical conditions, particularly with respect to
temperature and incubation time wherein the internal control
nucleic acid mentioned above is present each of said vessels.
[0085] The "first target nucleic acid" and the "second target
nucleic acid" are different nucleic acids.
[0086] A "fluid sample" is any fluid material that can be subjected
to a diagnostic assay targeting nucleic acids and may be derived
from a biological source. For example, said fluid sample is derived
from a human and is a body liquid. In an embodiment of the
invention, the fluid sample is human blood, urine, sputum, sweat,
swab, pipettable stool, or spinal fluid.
[0087] The term "reaction vessel" comprises, but is not limited to,
tubes or the wells of plates such as microwell, deepwell or other
types of multiwell plates, in which a reaction for the analysis of
the fluid sample such as e.g. reverse transcription or a polymerase
chain reaction takes place. The outer limits or walls of such
vessels are chemically inert such that they do not interfere with
the analytical reaction taking place within. For example, the
isolation of the nucleic acids as described above is also carried
out in a multiwell plate.
[0088] In this context, multiwell plates in analytical systems
allow parallel separation and analyzing or storage of multiple
samples. Multiwell plates may be optimized for maximal liquid
uptake, or for maximal heat transfer. A multiwell plate for use in
the context of the present invention can be optimized for
incubating or separating an analyte in an automated analyzer. For
example, the multiwell plate is constructed and arranged to contact
a magnetic device and/or a heating device.
[0089] Said multiwell plate, which is interchangeably termed
"processing plate" in the context of the invention, comprises:
[0090] a top surface comprising multiple vessels with openings at
the top arranged in rows. The vessels comprise an upper part, a
center part and a bottom part. The upper part is joined to the top
surface of the multiwell plate and comprises two longer and two
shorter sides. The center part has a substantially rectangular
cross-section with two longer sides and two shorter sides; [0091]
two opposing shorter and two opposing longer side walls and [0092]
a base, wherein said base comprises an opening constructed and
arranged to place the multiwell plate in contact with said magnetic
device and/or a heating device.
[0093] In an embodiment of the multiwell plate, adjacent vessels
within one row are joined on the longer side of said almost
rectangular shape.
[0094] For example, the multiwell plate comprises a continuous
space which is located between adjacent rows of vessels. Said
continuous space is constructed and arranged to accommodate a
plate-shaped magnetic device. In an embodiment, the bottom part of
the vessels comprises a spherical bottom. In an embodiment, the
bottom part of said vessels comprises a conical part located
between said central part and said spherical bottom.
[0095] In an embodiment, the top surface comprises ribs, wherein
said ribs surround the openings of the vessels. For example, one
shorter side of said upper part of the vessels comprises a recess,
said recess comprising a bent surface extending from the rib to the
inside of the vessel.
[0096] Furthermore, in an embodiment, the vessels comprise a
rounded inside shape.
[0097] For fixation to the processing or incubation stations, the
base may comprises a rim comprising recesses. Latch clips on a
station of an analyzer can engage with said recesses to fix the
plate on a station.
[0098] In an embodiment, the vessels comprise an essentially
constant wall thickness.
[0099] For example, the processing plate (101) in the context of
the present invention is a 1-component plate. Its top surface (110)
comprises multiple vessels (103) (FIG. 5, FIG. 6). Each vessel has
an opening (108) at the top and is closed at the bottom end (112).
The top surface (110) comprises ribs (104) which are may be
elevated relative to the top surface (110) and surround the
openings (108) of the vessels (103). This prevents contamination of
the contents of the vessels (103) with droplets of liquid that may
fall onto the top surface (110) of the plate (101). Views of an
exemplary process plate are shown in FIGS. 3 to 8.
[0100] The footprint of the processing plate (101) may comprise a
length and width of the base corresponding to ANSI SBS footprint
format. For example, the length is 127.76 mm+/-0.25 mm, and the
width is 85.48 mm+/-0.25 mm. Thus, the plate (101) has two opposing
shorter side walls (109) and two opposing longer side walls (118).
The processing plate (101) comprises form locking elements (106)
for interacting with a handler (500, FIG. 12). The processing plate
(101) can be gripped, transported and positioned quickly and safely
at high speed while maintaining the correct orientation and
position. For example, the form locking elements (106) for gripping
are located within the upper central part, for example the upper
central third of the processing plate (101). This has the advantage
that a potential distortion of the processing plate (101) has only
a minor effect on the form locking elements (106) and that the
handling of the plate (101) is more robust.
[0101] The processing plate (101) may comprise hardware-identifiers
(102) and (115). The hardware identifiers (102) and (115) are
unique for the processing plate (101) and different from hardware
identifiers of other consumables used in the same system. The
hardware identifiers (102, 115) may comprise ridges (119) and/or
recesses (125) on the side walls of the consumables, wherein said
pattern of ridges (119) and/or recesses (125) is unique for a
specific type of consumable, for example the processing plate
(101). This unique pattern is also referred to herein as a unique
"surface geometry". The hardware-identifiers (102, 115) ensure that
the user can only load the processing plate (101) into the
appropriate stacker position of an analytical instrument in the
proper orientation. On the sides of processing plate (101), guiding
elements (116) and (117) are comprised (FIG. 3, FIG. 4). They
prevent canting of the processing plate (101). The guiding elements
(116, 117) allow the user to load the processing plates (101) with
guiding elements (116, 117) as a stack into an analytical
instrument which is then transferred vertically within the
instrument in a stacker without canting of the plates.
[0102] The center part (120) of the vessels (103) has an almost
rectangular cross section (FIG. 6, FIG. 7). They are separated
along the longer side (118) of the almost rectangular shape by a
common wall (113) (FIG. 3). The row of vessels (103) formed thereby
has the advantage that despite the limited space available, they
have a large volume, for example 4 ml. Another advantage is that
because of the essentially constant wall thickness, the production
is very economical. A further advantage is that the vessels (103)
strengthen each other and, thus, a high stability of the shape can
be obtained.
[0103] Between the rows of vessels (103), a continuous space (121)
is located (FIG. 6, FIG. 7). The space (121) can accommodate
magnets (202, 203) or heating devices (128) (FIG. 11). These
magnets (202, 203) and heating devices (128) are for example solid
devices. Thus, magnetic particles (216) comprised in liquids (215)
which can be held in the vessels (103) can be separated from the
liquid (215) by exerting a magnetic field on the vessels (103) when
the magnets (202, 203) are brought into proximity of the vessels
(103). Or the contents of the vessels (103) can be incubated at an
elevated, controlled temperature when the processing plate (101) is
placed on the heating device (128). Since the magnets (202, 203) or
heating devices (128) can be solid, a high energy density can be
achieved. The almost rectangular shape of the central part (120) of
the vessels (103) (FIG. 10) also optimizes the contact between the
vessel wall (109) and a flat shaped magnet (202) or heating device
(128) by optimizing the contact surface between vessel (103) and
magnet (202) or heating device (128) and thus enhancing energy
transfer into the vessel (103).
[0104] In the area of the conical bottom (111) of the vessels, the
space (121) is even more pronounced and can accommodate further
magnets (203). The combination of the large magnets (202) in the
upper area and the smaller magnets (203) in the conical area of the
vessels allows separation of magnetic particles (216) in larger or
small volumes of liquid (215). The small magnets (203), thus, make
it easier to sequester the magnetic particles (216) during eluate
pipetting. This makes it possible to pipette the eluate with
minimal loss by reducing the dead volume of the magnetic particle
(216) pellet. Furthermore, the presence of magnetic particles (216)
in the transferred eluate is minimized.
[0105] At the upper end of the vessels (103), one of the shorter
side walls (109) of the vessel (103) comprises an reagent inlet
channel (105) which extends to the circumferential rib (104) (FIGS.
3, 4, 7). The reagents are pipetted onto the reagent inlet channel
(105) and drain off the channel (105) into the vessel (103). Thus,
contact between the pipet needle or tip (3, 4) and liquid contained
in the vessel is prevented. Furthermore, splashes resulting from
liquid being directly dispensed into another liquid (215) contained
in the vessels (103), which may cause contamination of the pipet
needle or tip (3, 4) or neighboring vessels (103) is prevented.
Sequential pipetting onto the reagent inlet channel (105) of small
volumes of reagents followed by the largest volume of another
reagent ensures that the reagents which are only added in small
amounts are drained completely into the vessel (103). Thus,
pipetting of small volumes of reagents is possible without loss of
accuracy of the test to be performed.
[0106] On the inside, on the bottom of the vessels (111, 112), the
shape becomes conical (111) and ends with a spherical bottom (112)
(FIG. 6. FIG. 7). The inside shape of the vessel (114), including
the rectangular center part (120), is rounded. The combination of
spherical bottom (112), rounded inside shape (114), conical part
(111) and refined surface of the vessels (103) leads to favorable
fluidics which facilitate an effective separation and purification
of analytes in the processing plate (101). The spherical bottom
(112) allows an essentially complete use of the separated eluate
and a reduction of dead-volume which reduces the carryover of
reagents or sample cross-contamination.
[0107] The rim on the base (129) of the processing plate (101)
comprises recesses (107) for engagement with latch clips (124) on
the processing station (201) or heating device (128) or analytical
instrument (126) (FIG. 5, FIG. 9). The engagement of the latch
clips (124) with the recesses (107) allows positioning and fixation
of the processing plate (101) on the processing station (201). The
presence of the recesses (107) allows the latch force to act on the
processing plate (101) almost vertically to the base (129). Thus,
only small forces acting sideways can occur. This reduces the
occurrence of strain, and, thus, the deformation of the processing
plate (101). The vertical latch forces can also neutralize any
deformations of the processing plate (101) leading to a more
precise positioning of the spherical bottoms (111) within the
processing station (201). In general, the precise interface between
the processing plate (101) and the processing station (201) or
heating device (128) within an analyzer reduces dead-volumes and
also reduces the risk of sample cross-contamination.
[0108] A "separation station" is a device or a component of an
analytical system allowing for the isolation of the solid support
material from the other material present in the fluid sample. Such
a separation station can e.g. comprise, but is not limited to, a
centrifuge, a rack with filter tubes, a magnet, or other suitable
components. In an embodiment of the invention, the separation
station comprises one or more magnets. For example, one or more
magnets are used for the separation of magnetic particles, for
example magnetic glass particles, as a solid support. If, for
example, the fluid sample and the solid support material are
combined together in the wells of a multiwell plate, then one or
more magnets comprised by the separation station can e.g. be
contacted with the fluid sample itself by introducing the magnets
into the wells, or said one or more magnets can be brought close to
the outer walls of the wells in order to attract the magnetic
particles and subsequently separate them from the surrounding
liquid.
[0109] In an embodiment, the separation station is a device that
comprises a multiwell plate comprising vessels with an opening at
the top surface of the multiwell plate and a closed bottom. The
vessels comprise an upper part, a center part and a bottom part,
wherein the upper part is joined to the top surface of the
multiwell plate and may comprise two longer and two shorter sides.
The center part has a substantially rectangular cross-section with
two longer sides, wherein said vessels are aligned in rows. A
continuous space is located between two adjacent rows for
selectively contacting at least one magnet mounted on a fixture
with the side walls in at least two Z-positions. The device further
comprises a magnetic separation station comprising at least one
fixture. The fixture comprises at least one magnet generating a
magnetic field. A moving mechanism is present which vertically
moves said at least one fixture comprising at least one magnet at
least between first and second positions with respect to the
vessels of the multiwell plate. For example, said at least two
Z-positions of the vessels comprise the side walls and the bottom
part of said vessels. The magnetic field of said at least one
magnet may draw the magnetic particles to an inner surface of the
vessel adjacent to said at least one magnet when said at least one
magnet is in said first position. The effect of said magnetic field
is less when said at least one magnet is in said second position
than when said at least one magnet is in said first position. For
example, the fixture comprising said at least one magnet comprises
a frame. The vessels have features as described above in the
context of multiwell plate/processing plate. One such feature is
that at least a part of said vessels has a substantially
rectangular cross-section orthogonal to the axis of said
vessels.
[0110] In said first position, said at least one magnet is adjacent
to said part of said vessels. Adjacent is understood to mean either
in close proximity such as to exert a magnetic field on the
contents of the vessel, or in physical contact with the vessel.
[0111] The separation station comprises a frame to receive the
multiwell plate, and latch-clips to attach the multiwell plate. For
example, the separation station comprises two types of magnets.
This embodiment is further described below.
[0112] A second embodiment is described below, which comprises a
spring which exerts a pressure on the frame comprising the magnets
such that the magnets are pressed against the vessels of the
multiwell plate.
[0113] The first magnets may be constructed and arranged to
interact with vessels of a multiwell plate for exerting a magnetic
field on a large volume of liquid comprising magnetic particles
held in said vessels. Said second magnets may be constructed and
arranged to interact with vessels of a multiwell plate for exerting
a magnetic field on a small volume of liquid comprising magnetic
particles held in said vessels. Said first and second magnets can
be moved to different Z-positions.
[0114] Useful in the context of the present invention and said
separation station is further a method of isolating and purifying a
nucleic acid. The method comprises the steps of binding a nucleic
acid to magnetic particles in a vessel of a multiwell plate. The
vessel comprises an upper opening, a central part and a bottom
part. The bound material is then separated from unbound material
contained in a liquid when the major part of the liquid is located
above the section where the conical part of the vessel is replaced
by the central part with the rectangular shape, by moving a magnet
from a second position to a first position and, in said first
position, applying a magnetic field to the central part and,
optionally, additionally applying a magnetic field to the bottom
part of said vessel. The magnetic particles can optionally be
washed with a washing solution. A small volume of liquid, wherein
the major part of the liquid is located below the section where the
conical part of the vessel is replaced by the central part with the
rectangular shape is separated from said magnetic particles by
selectively applying a magnetic field to the bottom part of said
vessel.
[0115] Useful in the context of the present invention is also a
magnetic separation station for separating a nucleic acid bound to
magnetic particles, said separation station comprising first
magnets which are constructed and arranged to interact with vessels
of a multiwell plate for exerting a magnetic field on a large
volume of liquid comprising magnetic particles held in said
vessels, and second magnets constructed and arranged to interact
with vessels of a multiwell plate for exerting a magnetic field on
a small volume of liquid comprising magnetic particles held in said
vessels, and wherein said first and second magnets can be moved to
different Z-positions. Embodiments of the magnetic separation
station are described herein.
[0116] A first embodiment of a separation station (201) useful for
the present invention is described below. The first embodiment of
said separation station (201) comprises at least two types of
magnets (202, 203). The first, long type of magnet (202) is
constructed and arranged to fit into the space (121) of the
processing plate (101). Magnet (202), thus, exerts a magnetic field
on the liquid (215) in the vessel (103) to sequester magnetic
particles (216) on the inside of the vessel wall. This allows
separation of the magnetic particles (216) and any material bound
thereto and the liquid (215) inside the vessel (103) when a large
volume of liquid (215) is present. Magnet (202) has an elongated
structure and is constructed and arranged to interact with the
essentially rectangular central part (120) of the vessel. Thus,
magnet (202) is used when the major part of the liquid (215) is
located above the section where the conical part (111) of the
vessel (103) is replaced by the central part (120) with the
rectangular shape. As shown in FIG. 10, the construction of the
magnets (202) comprises fixtures (204, 204a) comprising magnets
(202) which fit into the space (121) between the rows of vessels
(103) in the processing plate (101). Another embodiment of magnets
(202) comprises magnets (202) arranged on fixtures (204, 204a). The
magnets (203) of the separation station (201) are smaller, and can
interact with the conical part (111) of the vessel (103). This is
shown in FIG. 10. Magnets (203) are arranged on a base (205) which
can be moved into the space (121) of the processing plate (101).
Each magnet (202, 203) is constructed to interact with two vessels
(103) in two adjacent rows. In an embodiment, the processing plate
(101) has 6 rows of 8 vessels (103). A separation station (201)
which can interact with the processing plate (101) has three
fixtures (204, 204a) comprising magnets (202) and four bases (205)
comprising magnets (203). An embodiment is also included wherein
the separation station has four magnetic fixtures (204, 204a)
comprising magnets (202) and three magnetic bases (205) comprising
magnets (203).
[0117] The magnets (202, 203) are movable. The separation station
(201) comprises a mechanism to move the fixtures (204, 204a) and
the bases (205). All fixtures (204, 204a) are interconnected by a
base (217) and are, thus, moved coordinately. All magnets (203) are
joined to one base (218) and are, thus, moved coordinately. The
mechanism for moving the magnetic plates (202) and (203) is
constructed and arranged to move the two types of magnetic plates
(202, 203) to a total of four end positions:
[0118] In FIG. 10 a-c, the magnets (203) are located in proximity
of the conical part of the vessels (103) of the processing plate
(101). This is the uppermost position of magnets (203), and is the
separation position. In this Figure, the magnets (202) are located
in the lowermost position. They are not involved in separation when
they are in this position.
[0119] In an embodiment shown in FIG. 10, the base (217) of magnets
(202) is connected to a positioning wheel (206). The base (217)
comprises a bottom end (207) which is flexibly in contact with a
connecting element (208) by a moving element (209). Said moving
element is constructed and arranged to move the connecting element
(208) along a rail (212) from one side to the other. Said moving
element (209) is fixed to the connecting element (208) with a pin
(220). Said connecting element (208) is fixed to the positioning
wheel (206) by screw (210). Connecting element (208) is also
connected to axis (211). Said connecting element (208) is a
rectangular plate. As the positioning wheel (206) moves
eccentrically, around an axis (211), such that the screw (210)
moves from a point above the eccentric axis to a point below the
eccentric axis, moving element (209) and the bottom end (207) of
the base (204) with the magnets (202) attached thereto are moved
from the uppermost position to the lowermost position. The base
(218) is mounted on a bottom part (219) and is connected, at its
lower end, with pin (213) to a moving element (214), which can be a
wheel, which interacts with the positioning wheel (206). When the
positioning wheel (206) rotates around the axis (211), wheel (214)
moves along positioning wheel (206). If the wheel (214) is located
on a section of positioning wheel (206) where the distance from the
axis (211) is short, the magnets (203) are in their lowermost
position. When wheel (214) is located on a section of positioning
wheel (206) where the distance from the axis (211) is at a maximum,
the magnets (203) are in their uppermost position. Thus, in an
embodiment of the first embodiment of the separation station, the
location of the magnets (203) is controlled by the shape of the
positioning wheel (206). When moving element (209) moves along the
central, rounded upper or lower part (212a) of rail (212), the
small type of magnets (203) are moved up and down. When the moving
element (209) is located on the side (212b) of bottom end (207) and
moves up or down, the magnets (202) are moved up- or downwards. The
positioning wheel can be rotated by any motor (224).
[0120] In an embodiment, a spring (225) is attached to the base
(222) of the separation station and the base (218) of magnets (203)
to ensure that magnets (203) are moved into the lowermost position
when they are moved downwards.
[0121] The term "pin" as used herein relates to any fixation
element, including screws or pins.
[0122] In a second embodiment, the separation station (230)
comprises at least one fixture (231) comprising at least one magnet
(232), a number of magnets equal to a number of vessels (103) in a
row (123). The separation station (230) comprises a number of
fixtures (231) equal to the number of rows (123) of the multiwell
plate (101) hereinbefore described. For example, six fixtures (231)
are mounted on the separation station (230). At least one magnet
(232) is mounted on one fixture (231). For example, the number of
magnets (232) equals the number of vessels (103) in one row (123).
For example, eight magnets (232) are mounted on one fixture (231).
For example, one type of magnet (232) is comprised on said fixture
(231). For example, the magnet (232) is mounted on one side
oriented towards the vessels with which the magnet interacts.
[0123] The fixture (231) is mounted on a base (233). For example,
said mount is flexible. The base (233) comprises springs (234)
mounted thereon. The number of springs (234) is at least one spring
per fixture (231) mounted on said base (233). The base further
comprises a chamfer (236) which limits the movement of the spring
and, consequently, the fixture (231) comprising the magnets (232).
For example, any one of said springs (234) is constructed and
arranged to interact with a fixture (231). For examples, said
spring (234) is a yoke spring. Said interaction controls the
horizontal movement of the fixtures (231). Furthermore, the
separation station (230) comprises a frame (235). The base (233)
with fixtures (231) is connected to the frame (235) by a moving
mechanism as described hereinbefore for the magnets (232) of the
first embodiment.
[0124] For example, said base (233) and fixture (231) is
constructed and arranged to move vertically (in Z-direction).
[0125] The multiwell plate (101) hereinbefore described is inserted
into the separation station (230). The fixture (231) comprising the
magnets (232) is moved vertically. Any one fixture (232) is, thus,
moved into a space (121) between two rows (123) of vessels (103).
The vertical movement brings the magnets (232) mounted on a fixture
(231) into contact with the vessels (103). The Z-position is chosen
depending on the volume of liquid (215) inside the vessels (103).
For large volumes, the magnets (232) contact the vessels (103) in a
center position (120) where the vessels (103) are of an almost
rectangular shape. For small volumes of liquid (215) where the
major part of the liquid (215) is located below the center part
(120) of the vessels (103), the magnets (232) contact the conical
part (111) of the vessels (103).
[0126] A spring is attached to the base (233) of any one frame
(231) (FIG. 9 a), b)). The spring presses the magnets (232) against
the vessels (103). This ensures a contact between magnets (232) and
vessels (103) during magnetic separation. For example, the magnet
(232) contacts the vessel (103) on the side wall (109) located
underneath the inlet (105). This has the advantage that liquid
which is added by pipetting flows over the sequestered magnetic
particles and ensures that particles are resuspended and that all
samples in all vessels are treated identically.
[0127] This embodiment is particularly suited to separate a liquid
(215) comprised in a multiwell plate (101) as hereinbefore
described, from magnetic particles (216) when different levels of
liquid (215) are contained in the vessels (103) of said multiwell
plate (101).
[0128] A "wash buffer" is a fluid that is designed to remove
undesired components, especially in a purification procedure. Such
buffers are well known in the art. In the context of the
purification of nucleic acids, the wash buffer is suited to wash
the solid support material in order to separate the immobilized
nucleic acid from any unwanted components. The wash buffer may, for
example, contain ethanol and/or chaotropic agents in a buffered
solution or solutions with an acidic pH without ethanol and/or
chaotropic agents as described above. Often the washing solution or
other solutions are provided as stock solutions which have to be
diluted before use.
[0129] The washing in the process according to the invention
requires a more or less intensive contact of the solid support
material and the nucleic acids immobilized thereon with the wash
buffer. Different methods are possible to achieve this, e.g.
shaking the wash buffer with the solid support material in or along
with the respective vessel or vessels. Another advantageous method
is aspirating and dispensing the suspension comprising wash buffer
and solid support material one or more times. This method may be
carried out using a pipet, wherein said pipet comprises a
disposable pipet tip into which said suspension is aspirated and
from which it is dispensed again. Such a pipet tip can be used
several times before being discarded and replaced. Disposable pipet
tips useful for the invention may have a volume of at least 10
.mu.l, or at least 15 .mu.l, or at least 100 .mu.l, or at least 500
.mu.l, or at least 1 ml, or about 1 ml. Pipets used in the context
of the invention can also be pipetting needles.
[0130] Thus, an aspect of the invention is the process described
above, wherein said washing in step d. comprises aspirating and
dispensing the wash buffer comprising the solid support
material.
[0131] For downstream processing of the isolated nucleic acids, it
can be advantageous to separate them from the solid support
material before subjecting them to amplification.
[0132] Therefore, an aspect of the invention is the process
described above, wherein said process further comprises in step d.
the step of eluting the purified nucleic acids from the solid
support material with an elution buffer after washing said solid
support material.
[0133] An "elution buffer" in the context of the invention is a
suitable liquid for separating the nucleic acids from the solid
support. Such a liquid may e.g. be distilled water or aqueous salt
solutions, such as e.g. Tris buffers like Tris HCl, or HEPES, or
other suitable buffers known to the skilled artisan. The pH value
of such an elution buffer can be alkaline or neutral. Said elution
buffer may contain further components such as e.g. chelators like
EDTA, which stabilizes the isolated nucleic acids by inactivation
of degrading enzymes.
[0134] The elution can be carried out at elevated temperatures,
such that an embodiment of the invention is the process described
above, wherein step d. is carried out at a temperature between
70.degree. C. and 90.degree. C., or at a temperature of 80.degree.
C.
[0135] "Amplification reagents", in the context of the invention,
are chemical or biochemical components that enable the
amplification of nucleic acids. Such reagents comprise, but are not
limited to, nucleic acid polymerases, buffers, mononucleotides such
as nucleoside triphosphates, oligonucleotides e.g. as
oligonucleotide primers, salts and their respective solutions,
detection probes, dyes, and more.
[0136] As is known in the art, a "nucleoside" is a base-sugar
combination. The base portion of the nucleoside is normally a
heterocyclic base. The two most common classes of such heterocyclic
bases are purines and pyrimidines.
[0137] "Nucleotides" are nucleosides that further include a
phosphate group covalently linked to the sugar portion of the
nucleoside. For those nucleosides that include a pentofuranosyl
sugar, the phosphate group can be linked to either the 2'-, 3'- or
5'-hydroxyl moiety of the sugar. A nucleotide is the monomeric unit
of an "oligonucleotide", which can be more generally denoted as an
"oligomeric compound", or a "polynucleotide", more generally
denoted as a "polymeric compound". Another general expression for
the aforementioned is deoxyribonucleic acid (DNA) and ribonucleic
acid (RNA).
[0138] According to the invention, an "oligomeric compound" is a
compound consisting of "monomeric units" which may be nucleotides
alone or non-natural compounds (see below), more specifically
modified nucleotides (or nucleotide analogs) or non-nucleotide
compounds, alone or combinations thereof.
[0139] "Oligonucleotides" and "modified oligonucleotides" (or
"oligonucleotide analogs") are subgroups of oligomeric compounds.
In the context of this invention, the term "oligonucleotide" refers
to components formed from a plurality of nucleotides as their
monomeric units. The phosphate groups are commonly referred to as
forming the internucleoside backbone of the oligonucleotide. The
normal linkage or backbone of RNA and DNA is a 3' to 5'
phosphodiester linkage. Oligonucleotides and modified
oligonucleotides (see below) useful for the invention may be
synthesized as principally described in the art and known to the
expert in the field. Methods for preparing oligomeric compounds of
specific sequences are known in the art, and include, for example,
cloning and restriction of appropriate sequences and direct
chemical synthesis. Chemical synthesis methods may include, for
example, the phosphotriester method described by Narang S. A. et
al., Methods in Enzymology 68 (1979) 90-98, the phosphodiester
method disclosed by Brown E. L., et al., Methods in Enzymology 68
(1979) 109-151, the phosphoramidite method disclosed in Beaucage et
al., Tetrahedron Letters 22 (1981) 1859, the H-phosphonate method
disclosed in Garegg et al., Chem. Scr. 25 (1985) 280-282 and the
solid support method disclosed in U.S. Pat. No. 4,458,066.
[0140] In the process described above, the oligonucleotides may be
chemically modified, i.e. the primer and/or the probe comprise a
modified nucleotide or a non-nucleotide compound. The probe or the
primer is then a modified oligonucleotide.
[0141] "Modified nucleotides" (or "nucleotide analogs") differ from
a natural nucleotide by some modification but still consist of a
base, a pentofuranosyl sugar, a phosphate portion, base-like,
pentofuranosyl sugar-like and phosphate-like portion or
combinations thereof. For example, a label may be attached to the
base portion of a nucleotide whereby a modified nucleotide is
obtained. A natural base in a nucleotide may also be replaced by
e.g. a 7-deazapurine whereby a modified nucleotide is obtained as
well.
[0142] A "modified oligonucleotide" (or "oligonucleotide analog"),
belonging to another specific subgroup of oligomeric compounds,
possesses one or more nucleotides and one or more modified
nucleotides as monomeric units. Thus, the term "modified
oligonucleotide" (or "oligonucleotide analog") refers to structures
that function in a manner substantially similar to oligonucleotides
and can be used interchangeably in the context of the present
invention. From a synthetical point of view, a modified
oligonucleotide (or an oligonucleotide analog) can for example be
made by chemical modification of oligonucleotides by appropriate
modification of the phosphate backbone, ribose unit or the
nucleotide bases (Uhlmann and Peyman, Chemical Reviews 90 (1990)
543; Verma S., and Eckstein F., Annu. Rev. Biochem. 67 (1998)
99-134). Representative modifications include phosphorothioate,
phosphorodithioate, methyl phosphonate, phosphotriester or
phosphoramidate inter-nucleoside linkages in place of
phosphodiester internucleoside linkages; deaza- or azapurines and
-pyrimidines in place of natural purine and pyrimidine bases,
pyrimidine bases having substituent groups at the 5 or 6 position;
purine bases having altered substituent groups at the 2, 6 or 8
positions or 7 position as 7-deazapurines; bases carrying alkyl-,
alkenyl-, alkinyl or aryl-moieties, e.g. lower alkyl groups such as
methyl, ethyl, propyl, butyl, tert-butyl, pentyl, hexyl, heptyl,
octyl, nonyl, decyl, or aryl groups like phenyl, benzyl, naphtyl;
sugars having substituent groups at, for example, their 2'
position; or carbocyclic or acyclic sugar analogs. Other
modifications consistent with the spirit of this invention are
known to those skilled in the art. Such modified oligonucleotides
(or oligonucleotide analogs) are best described as being
functionally interchangeable with, yet structurally different from,
natural oligonucleotides. In more detail, exemplary modifications
are disclosed in Verma S., and Eckstein F., Annu. Rev. Biochem. 67
(1998) 99-134 or WO 02/12263. In addition, modification can be made
wherein nucleoside units are joined via groups that substitute for
the internucleoside phosphate or sugar phosphate linkages. Such
linkages include those disclosed in Verma S., and Eckstein F.,
Annu. Rev. Biochem. 67 (1998) 99-134. When other than phosphate
linkages are utilized to link the nucleoside units, such structures
have also been described as "oligonucleosides".
[0143] A "nucleic acid" as well as the "target nucleic acid" is a
polymeric compound of nucleotides as known to the expert skilled in
the art. "Target nucleic acid" is used herein to denote a nucleic
acid in a sample which should be analyzed, i.e. the presence,
non-presence and/or amount thereof in a sample should be
determined.
[0144] The term "primer" is used herein as known to the expert
skilled in the art and refers to oligomeric compounds, primarily to
oligonucleotides, but also to modified oligonucleotides that are
able to prime DNA synthesis by a template-dependent DNA polymerase,
i.e. the 3'-end of the e.g. primer provides a free 3'-OH group
whereto further nucleotides may be attached by a template-dependent
DNA polymerase establishing 3'- to 5'-phosphodiester linkage
whereby deoxynucleoside triphosphates are used and whereby
pyrophosphate is released.
[0145] A "probe" also denotes a natural or modified
oligonucleotide. As known in the art, a probe serves the purpose to
detect an analyte or amplificate. In the case of the process
described above, probes can be used to detect the amplificates of
the target nucleic acids. For this purpose, probes typically carry
labels.
[0146] "Labels", often referred to as "reporter groups", are
generally groups that make a nucleic acid, in particular
oligonucleotides or modified oligonucleotides, as well as any
nucleic acids bound thereto distinguishable from the remainder of
the sample (nucleic acids having attached a label can also be
termed labeled nucleic acid binding compounds, labeled probes or
just probes). Exemplary labels according to the invention are
fluorescent labels, which are e.g. fluorescent dyes such as a
fluorescein dye, a rhodamine dye, a cyanine dye, and a coumarin
dye. Exemplary fluorescent dyes according to the invention are FAM,
HEX, JA270, CAL635, Coumarin343, Quasar705, Cyan500, CY5.5, LC-Red
640, LC-Red 705.
[0147] In the context of the invention, any primer and/or probe may
be chemically modified, i.e. the primer and/or the probe comprise a
modified nucleotide or a non-nucleotide compound. The probe or the
primer is then a modified oligonucleotide.
[0148] A method of nucleic acid amplification is the Polymerase
Chain Reaction (PCR) which is disclosed, among other references, in
U.S. Pat. Nos. 4,683,202, 4,683,195, 4,800,159, and 4,965,188. PCR
typically employs two or more oligonucleotide primers that bind to
a selected nucleic acid template (e.g. DNA or RNA). Primers useful
for nucleic acid analysis include oligonucleotides capable of
acting as a point of initiation of nucleic acid synthesis within
the nucleic acid sequences of the target nucleic acids. A primer
can be purified from a restriction digest by conventional methods,
or it can be produced synthetically. The primer can be
single-stranded for maximum efficiency in amplification, but the
primer can be double-stranded. Double-stranded primers are first
denatured, i.e., treated to separate the strands. One method of
denaturing double stranded nucleic acids is by heating. A
"thermostable polymerase" is a polymerase enzyme that is heat
stable, i.e., it is an enzyme that catalyzes the formation of
primer extension products complementary to a template and does not
irreversibly denature when subjected to the elevated temperatures
for the time necessary to effect denaturation of double-stranded
template nucleic acids. Generally, the synthesis is initiated at
the 3' end of each primer and proceeds in the 5' to 3' direction
along the template strand. Thermostable polymerases have e.g. been
isolated from Thermus flavus, T. ruber, T. thermophilus, T.
aquaticus, T. lacteus, T. rubens, Bacillus stearothermophilus, and
Methanothermus fervidus. Nonetheless, polymerases that are not
thermostable also can be employed in PCR assays provided the enzyme
is replenished.
[0149] If the template nucleic acid is double-stranded, it is
necessary to separate the two strands before it can be used as a
template in PCR. Strand separation can be accomplished by any
suitable denaturing method including physical, chemical or
enzymatic means. One method of separating the nucleic acid strands
involves heating the nucleic acid until it is predominately
denatured (e.g., greater than 50%, 60%, 70%, 80%, 90% or 95%
denatured). The heating conditions necessary for denaturing
template nucleic acid will depend, e.g., on the buffer salt
concentration and the length and nucleotide composition of the
nucleic acids being denatured, but typically range from about
90.degree. C. to about 105.degree. C. for a time depending on
features of the reaction such as temperature and the nucleic acid
length. Denaturation is typically performed for about 5 sec to 9
min. In order to not expose the respective polymerase like e.g. the
Z05 DNA Polymerase to such high temperatures for too long and thus
risking a loss of functional enzyme, it can be preferred to use
short denaturation steps.
[0150] In an embodiment of the invention, the denaturation step is
up to 30 sec, or up to 20 sec, or up to 10 sec, or up to 5 sec, or
about 5 sec.
[0151] If the double-stranded template nucleic acid is denatured by
heat, the reaction mixture is allowed to cool to a temperature that
promotes annealing of each primer to its target sequence on the
target nucleic acids.
[0152] The temperature for annealing can be from about 35.degree.
C. to about 70.degree. C., or about 45.degree. C. to about
65.degree. C.; or about 50.degree. C. to about 60.degree. C., or
about 55.degree. C. to about 58.degree. C. Annealing times can be
from about 10 sec to about 1 min (e.g., about 20 sec to about 50
sec; about 30 sec to about 40 sec). In this context, it can be
advantageous to use different annealing temperatures in order to
increase the inclusivity of the respective assay. In brief, this
means that at relatively low annealing temperatures, primers may
also bind to targets having single mismatches, so variants of
certain sequences can also be amplified. This can be desirable if
e.g. a certain organism has known or unknown genetic variants which
should also be detected. On the other hand, relatively high
annealing temperatures bear the advantage of providing higher
specificity, since towards higher temperatures the probability of
primer binding to not exactly matching target sequences
continuously decreases. In order to benefit from both phenomena, in
some embodiments of the invention the process described above
comprises annealing at different temperatures, for example first at
a lower, then at a higher temperature. If, e.g., a first incubation
takes place at 55.degree. C. for about 5 cycles, non-exactly
matching target sequences may be (pre-)amplified. This can be
followed e.g. by about 45 cycles at 58.degree. C., providing for
higher specificity throughout the major part of the experiment.
This way, potentially important genetic variants are not missed,
while the specificity remains relatively high.
[0153] The reaction mixture is then adjusted to a temperature at
which the activity of the polymerase is promoted or optimized,
i.e., a temperature sufficient for extension to occur from the
annealed primer to generate products complementary to the nucleic
acid to be analyzed. The temperature should be sufficient to
synthesize an extension product from each primer that is annealed
to a nucleic acid template, but should not be so high as to
denature an extension product from its complementary template
(e.g., the temperature for extension generally ranges from about
40.degree. to 80.degree. C. (e.g., about 50.degree. C. to about
70.degree. C.; about 60.degree. C.). Extension times can be from
about 10 sec to about 5 min, or about 15 sec to 2 min, or about 20
sec to about 1 min, or about 25 sec to about 35 sec. The newly
synthesized strands form a double-stranded molecule that can be
used in the succeeding steps of the reaction. The steps of strand
separation, annealing, and elongation can be repeated as often as
needed to produce the desired quantity of amplification products
corresponding to the target nucleic acids. The limiting factors in
the reaction are the amounts of primers, thermostable enzyme, and
nucleoside triphosphates present in the reaction. The cycling steps
(i.e., denaturation, annealing, and extension) can be repeated at
least once. For use in detection, the number of cycling steps will
depend, e.g., on the nature of the sample. If the sample is a
complex mixture of nucleic acids, more cycling steps will be
required to amplify the target sequence sufficient for detection.
Generally, the cycling steps are repeated at least about 20 times,
but may be repeated as many as 40, 60, or even 100 times.
[0154] Within the scope of the invention, a PCR can be carried out
in which the steps of annealing and extension are performed in the
same step (one-step PCR) or, as described above, in separate steps
(two-step PCR). Performing annealing and extension together and
thus under the same physical and chemical conditions, with a
suitable enzyme such as, for example, the Z05 DNA polymerase, bears
the advantage of saving the time for an additional step in each
cycle, and also abolishing the need for an additional temperature
adjustment between annealing and extension. Thus, the one-step PCR
reduces the overall complexity of the respective assay.
[0155] In general, shorter times for the overall amplification can
be preferred, as the time-to-result is reduced and leads to a
possible earlier diagnosis.
[0156] Other nucleic acid amplification methods to be used in the
context of the invention comprise the Ligase Chain Reaction (LCR;
Wu D. Y. and Wallace R. B., Genomics 4 (1989) 560-69; and Barany
F., Proc. Natl. Acad. Sci. USA 88 (1991) 189-193); Polymerase
Ligase Chain Reaction (Barany F., PCR Methods and Applic. 1 (1991)
5-16); Gap-LCR (WO 90/01069); Repair Chain Reaction (EP 0439182
A2), 3SR (Kwoh D. Y. et al., Proc. Natl. Acad. Sci. USA 86 (1989)
1173-1177; Guatelli J. C., et al., Proc. Natl. Acad. Sci. USA 87
(1990) 1874-1878; WO 92/08808), and NASBA (U.S. Pat. No.
5,130,238). Further, there are strand displacement amplification
(SDA), transcription mediated amplification (TMA), and
Qb-amplification (for a review see e.g. Whelen A. C. and Persing D.
H., Annu. Rev. Microbiol. 50(1996) 349-373; Abramson R. D. and
Myers T. W., Curr Opin Biotechnol 4 (1993) 41-47).
[0157] The internal control nucleic acid used in the present
invention may exhibit the following properties relating to its
sequence: [0158] a melting temperature from 55.degree. C. to
90.degree. C., or from 65.degree. C. to 85.degree. C., or from
70.degree. C. to 80.degree. C., or about 75.degree. C. [0159] a
length of up to 500 bases or base pairs, or from 50 to 300 bases or
base pairs, or from 100 to 200 bases or base pairs, or about 180
bases or base pairs [0160] a GC content from 30% to 70%, or from
40% to 60%, or about 50%.
[0161] In the context of the invention, a "sequence" is the primary
structure of a nucleic acid, i.e. the specific arrangement of the
single nucleobases of which the respective nucleic acids consists.
It has to be understood that the term "sequence" does not denote a
specific type of nucleic acid such as RNA or DNA, but applies to
both as well as to other types of nucleic acids such as e.g. PNA or
others. Where nucleobases correspond to each other, particularly in
the case of uracil (present in RNA) and thymine (present in DNA),
these bases can be considered equivalent between RNA and DNA
sequences, as well-known in the pertinent art.
[0162] Clinically relevant nucleic acids are often DNA which can be
derived e.g. from DNA viruses like e.g. Hepatitis B Virus (HBV),
Cytomegalovirus (CMV) and others, or bacteria like e.g. Chlamydia
trachomatis (CT), Neisseria gonorrhoeae (NG) and others. In such
cases, it can be advantageous to use an internal control nucleic
acid consisting of DNA, in order to reflect the target nucleic
acids properties.
[0163] Therefore, an aspect of the invention is the method
described above, wherein said internal control nucleic acid is
DNA.
[0164] On the other hand, numerous nucleic acids relevant for
clinical diagnostics are ribonucleic acids, like e.g. the nucleic
acids from RNA viruses such as for example Human Immunodeficiency
Virus (HIV), Hepatitis C Virus (HCV), the West Nile Virus (WNV),
Human Papilloma Virus (HPV), Japanese Encephalitis Virus (JEV), St.
Louis Encephalitis Virus (SLEV) and others. The present invention
can be readily applied to such nucleic acids. In this case, it can
be advantageous to use an internal control nucleic acid consisting
of RNA, in order to reflect the target nucleic acids properties. If
both RNA and DNA are to be analyzed in the process described supra,
the internal control nucleic acid can be RNA, as the internal
control nucleic acid mimics the most sensitive target of an assay
involving multiple targets, and RNA targets usually have to be more
closely controlled.
[0165] Thus, an aspect of the invention is the method described
above, wherein said internal control nucleic acid is RNA.
[0166] Since RNA is more prone to degradation than DNA due to
influences such as alkaline pH, ribonucleases etc., internal
control nucleic acids made of RNA may be provided as armored
particles. Armored particles such as especially armored RNA are
described e.g. in EP910643. In brief, the RNA, which can be
produced chemically or heterologously e.g. by bacteria such as e.g.
E. coli, is at least partially encapsulated in a viral coat
protein. The latter confers resistance of the RNA towards external
influences, in particular ribonucleases. It must be understood that
internal control DNA can also be provided as an armored particle.
Both armored RNA and DNA are useful as internal control nucleic
acids in the context of the invention. In an embodiment, RNA
control nucleic acids are armored with the MS2 coat protein in E.
coli. In a further embodiment, DNA control nucleic acids are
armored using lambda phage GT11.
[0167] Therefore, an aspect of the invention is the method
described above, wherein said internal control nucleic acid is an
armored nucleic acid.
[0168] Typically, in amplification-based nucleic acid diagnostics,
RNA templates are transcribed into DNA prior to amplification and
detection.
[0169] Hence, an aspect of the invention is the process described
above, wherein said amplification reagents comprise a polymerase
with reverse transcriptase activity, said process further
comprising between step e. and step f the step of incubating in
said reaction vessels said purified nucleic acids with said one or
more amplification reagents for a period of time and under
conditions suitable for transcription of RNA by said polymerase
with reverse transcriptase activity to occur.
[0170] A "polymerase with reverse transcriptase activity" is a
nucleic acid polymerase capable of synthesizing DNA based on an RNA
template. It is also capable of the formation of a double-stranded
DNA once the RNA has been reverse transcribed into a single strand
cDNA. In an embodiment of the invention, the polymerase with
reverse transcriptase activity is thermostable.
[0171] In an embodiment, the process according to the invention
comprises incubating a sample containing an RNA template with an
oligonucleotide primer sufficiently complementary to said RNA
template to hybridize with the latter, and a thermostable DNA
polymerase in the presence of at least all four natural or modified
deoxyribonucleoside triphosphates, in an appropriate buffer
comprising a metal ion buffer which, in an embodiment, buffers both
the pH and the metal ion concentration. This incubation is
performed at a temperature sufficient for said primer to hybridize
to said RNA template and said DNA polymerase to catalyze the
polymerization of said deoxyribonucleoside triphosphates to form a
cDNA sequence complementary to the sequence of said RNA
template.
[0172] As used herein, the term "cDNA" refers to a complementary
DNA molecule synthesized using a ribonucleic acid strand (RNA) as a
template. The RNA may e.g. be mRNA, tRNA, rRNA, or another form of
RNA, such as viral RNA. The cDNA may be single-stranded,
double-stranded or may be hydrogen-bonded to a complementary RNA
molecule as in an RNA/cDNA hybrid.
[0173] A primer suitable for annealing to an RNA template may also
be suitable for amplification by PCR. For PCR, a second primer,
complementary to the reverse transcribed cDNA strand, provides an
initiation site for the synthesis of an extension product.
[0174] In the amplification of an RNA molecule by a DNA polymerase,
the first extension reaction is reverse transcription using an RNA
template, and a DNA strand is produced. The second extension
reaction, using the DNA template, produces a double-stranded DNA
molecule. Thus, synthesis of a complementary DNA strand from an RNA
template by a DNA polymerase provides the starting material for
amplification.
[0175] Thermostable DNA polymerases can be used in a coupled,
one-enzyme reverse transcription/amplification reaction. The term
"homogeneous", in this context, refers to a two-step single
addition reaction for reverse transcription and amplification of an
RNA target. By homogeneous it is meant that following the reverse
transcription (RT) step, there is no need to open the reaction
vessel or otherwise adjust reaction components prior to the
amplification step. In a non-homogeneous RT/PCR reaction, following
reverse transcription and prior to amplification one or more of the
reaction components such as the amplification reagents are e.g.
adjusted, added, or diluted, for which the reaction vessel has to
be opened, or at least its contents have to be manipulated. Both
homogeneous and non-homogeneous embodiments are comprised by the
scope of the invention.
[0176] Reverse transcription is an important step in an RT/PCR. It
is, for example, known in the art that RNA templates show a
tendency towards the formation of secondary structures that may
hamper primer binding and/or elongation of the cDNA strand by the
respective reverse transcriptase. Thus, relatively high
temperatures for an RT reaction are advantageous with respect to
efficiency of the transcription. On the other hand, raising the
incubation temperature also implies higher specificity, i.e. the RT
primers will not anneal to sequences that exhibit mismatches to the
expected sequence or sequences. Particularly in the case of
multiple different target RNAs, it can be desirable to also
transcribe and subsequently amplify and detect sequences with
single mismatches, e.g. in the case of the possible presence of
unknown or rare substrains or subspecies of organisms in the fluid
sample.
[0177] In order to benefit from both advantages described above,
i.e. the reduction of secondary structures and the reverse
transcription of templates with mismatches, the RT incubation can
be carried out at more than one different temperature.
[0178] Therefore, an aspect of the invention is the process
described above, wherein said incubation of the polymerase with
reverse transcriptase activity is carried out at different
temperatures from 30.degree. C. to 75.degree. C., or from
45.degree. C. to 70.degree. C., or from 55.degree. C. to 65.degree.
C.
[0179] As a further important aspect of reverse transcription, long
RT steps can damage the DNA templates that may be present in the
fluid sample. If the fluid sample contains both RNA and DNA
species, it is thus favorable to keep the duration of the RT steps
as short as possible, but at the same time ensuring the synthesis
of sufficient amounts of cDNA for the subsequent amplification and
optional detection of amplificates.
[0180] Thus, an aspect of the invention is the process described
above, wherein the period of time for incubation of the polymerase
with reverse transcriptase activity is up to 30 minutes, 20
minutes, 15 minutes, 12.5 minutes, 10 minutes, 5 minutes, or 1
minute.
[0181] A further aspect of the invention is the process described
above, wherein the polymerase with reverse transcriptase activity
and comprising a mutation is selected from the group consisting of
a) a CS5 DNA polymerase [0182] b) a CS6 DNA polymerase [0183] c) a
Thermotoga maritima DNA polymerase [0184] d) a Thermus aquaticus
DNA polymerase [0185] e) a Thermus thermophilus DNA polymerase
[0186] f) a Thermus flavus DNA polymerase [0187] g) a Thermus
filiformis DNA polymerase [0188] h) a Thermus sp. sps17 DNA
polymerase [0189] i) a Thermus sp. Z05 DNA polymerase [0190] j) a
Thermotoga neapolitana DNA polymerase [0191] k) a Termosipho
africanus DNA polymerase [0192] l) a Thermus caldophilus DNA
polymerase
[0193] Particularly suitable for these requirements are enzymes
carrying a mutation in the polymerase domain that enhances their
reverse transcription efficiency in terms of a faster extension
rate.
[0194] Therefore, an aspect of the invention is the process
described above, wherein the polymerase with reverse transcriptase
activity is a polymerase comprising a mutation conferring an
improved nucleic acid extension rate and/or an improved reverse
transcriptase activity relative to the respective wildtype
polymerase.
[0195] In an embodiment, in the process described above, the
polymerase with reverse transcriptase activity is a polymerase
comprising a mutation conferring an improved reverse transcriptase
activity relative to the respective wildtype polymerase.
[0196] Polymerases carrying point mutations that render them
particularly useful in the context of the invention are disclosed
in WO 2008/046612. In particular, polymerases to be used in the
context of the present invention can be mutated DNA polymerases
comprising at least the following motif in the polymerase
domain:
[0197] T-G-R-L-S-S-X.sub.b7-X.sub.b8-P-N-L-Q-N; wherein X.sub.b7 is
an amino acid selected from S or T and wherein X.sub.b8 is an amino
acid selected from G, T, R, K, or L, wherein the polymerase
comprises 3'-5' exonuclease activity and has an improved nucleic
acid extension rate and/or an improved reverse transcription
efficiency relative to the wildtype DNA polymerase, wherein in said
wildtype DNA polymerase X.sub.b8 is an amino acid selected from D,
E or N.
[0198] One example is mutants of the thermostable DNA polymerase
from Thermus species Z05 (described e.g. in U.S. Pat. No.
5,455,170), said variations comprising mutations in the polymerase
domain as compared with the respective wildtype enzyme Z05. An
embodiment for the method according to the invention is a mutant
Z05 DNA polymerase wherein the amino acid at position 580 is
selected from the group consisting of G, T, R, K and L.
[0199] For reverse transcription using a thermostable polymerase,
Mn2+=can bes the divalent cation and is typically included as a
salt, for example, manganese chloride (MnCl2), manganese acetate
(Mn(OAc)2), or manganese sulfate (MnSO4). If MnCl2 is included in a
reaction containing 50 mM Tricine buffer, for example, the MnCl2 is
generally present at a concentration of 0.5-7.0 mM; 0.8-1.4 mM is
preferred when 200 mM of each dGTP, dATP, dUTP, and, dCTP are
utilized; and 2.5-3.5 mM MnCl2 is most preferred. Further, the use
of Mg2+ a divalent cation for reverse transcription is also in the
context of the present invention.
[0200] Since it is in the scope of the invention to
reverse-transcribe RNA target nucleic acids into cDNA while
preserving the DNA target nucleic acids so both cDNA and DNA can be
used for subsequent amplification, the internally controlled
process described above is particularly useful for the simultaneous
amplification of target nucleic acids derived from both organisms
having an RNA or organisms having a DNA genome. This advantage
considerably increases the spectrum of different organisms,
especially pathogens, that can be analyzed under identical physical
conditions.
[0201] Therefore, an aspect of the invention is the process
described above, wherein the at least two target nucleic acids
comprise RNA and DNA.
[0202] An "organism", as used herein, means any living single- or
multicellular life form. In the context of the invention, a virus
is an organism.
[0203] Especially due to an appropriate temperature optimum,
enzymes like Tth polymerase or, for example, the mutant Z05 DNA
polymerase mentioned above are suited to carry out the subsequent
step of amplification of the target nucleic acids. Exploiting the
same enzyme for both reverse transcription an amplification
contributes to the ease of carrying out the process and facilitates
its automation, since the fluid sample does not have to be
manipulated between the RT and the amplification step.
[0204] Therefore, in an embodiment, in the process described above
the same polymerase with reverse transcriptase activity is used for
reverse transcription and for the amplification in step f. For
example, the enzyme is the mutant Z05 DNA polymerase described
supra.
[0205] In order not to expose the polymerase or other components of
the reaction mixture used in the context of the invention to
elevated temperatures for times longer than necessary, in an
embodiment, steps above 90.degree. C. are up to 20 sec, or up to 15
sec, or up to 10 sec, or up to 5 sec or 5 sec long. This also
reduces the time-to-result and cuts down the overall required time
of the assay.
[0206] In such a homogeneous setup, it can be of considerable
advantage to seal the reaction vessels prior to initiating the RT
and the amplification, thereby reducing the risk of contamination.
Sealing can be e.g. achieved by applying a foil that can be
transparent, a cap, or by oil added to the reaction vessels and
forming a lipophilic phase as a sealing layer at the top of the
fluid.
[0207] Thus, an aspect of the invention is the process described
above, further comprising after step e. the step of sealing the at
least two reaction vessels.
[0208] For the ease of handling and to facilitate automation, the
at least two reaction vessels can be combined in an integral
arrangement, so they can be manipulated together.
[0209] Consequently, an aspect of the invention is the process
described above, wherein the at least two reaction vessels are
combined in the same integral arrangement.
[0210] Integral arrangements can e.g. be vials or tubes reversibly
or irreversibly attached to each other or arranged in a rack. For
example, the integral arrangement is a multiwell plate.
[0211] The target of the amplification step can be an RNA/DNA
hybrid molecule. The target can be a single-stranded or
double-stranded nucleic acid. Although the most widely used PCR
procedure uses a double-stranded target, this is not a necessity.
After the first amplification cycle of a single-stranded DNA
target, the reaction mixture contains a double-stranded DNA
molecule consisting of the single-stranded target and a newly
synthesized complementary strand. Similarly, following the first
amplification cycle of an RNA/cDNA target, the reaction mixture
contains a double-stranded cDNA molecule. At this point, successive
cycles of amplification proceed as described above.
[0212] Since nucleic acid amplification, especially but not only in
the case of PCR, is very efficient if carried out as a cycling
reaction, an aspect of the invention is the process described
above, wherein the amplification reaction in step f. consists of
multiple cycling steps.
[0213] Suitable nucleic acid detection methods are known to the
expert in the field and are described in standard textbooks as
Sambrook J. et al., Molecular Cloning: A Laboratory Manual, Cold
Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y., 1989 and
Ausubel F. et al.: Current Protocols in Molecular Biology 1987, J.
Wiley and Sons, NY. There may be also further purification steps
before the nucleic acid detection step is carried out as e.g. a
precipitation step. The detection methods may include but are not
limited to the binding or intercalating of specific dyes as
ethidium bromide which intercalates into the double-stranded DNA
and changes its fluorescence thereafter. The purified nucleic acid
may also be separated by electrophoretic methods optionally after a
restriction digest and visualized thereafter. There are also
probe-based assays which exploit the oligonucleotide hybridization
to specific sequences and subsequent detection of the hybrid.
[0214] The amplified target nucleic acids can be detected during or
after the amplification reaction in order to evaluate the result of
the analysis. Particularly for detection in real time, it is
advantageous to use nucleic acid probes.
[0215] Thus, an aspect of the invention is the process described
above, wherein a cycling step comprises an amplification step and a
hybridization step, said hybridization step comprising hybridizing
the amplified nucleic acids with probes.
[0216] It can be favorable to monitor the amplification reaction in
real time, i.e. to detect the target nucleic acids and/or their
amplificates during the amplification itself.
[0217] Therefore, an aspect of the invention is the process
described above, wherein the probes are labeled with a donor
fluorescent moiety and a corresponding acceptor fluorescent
moiety.
[0218] The methods set out above can be based on Fluorescence
Resonance Energy Transfer (FRET) between a donor fluorescent moiety
and an acceptor fluorescent moiety. A representative donor
fluorescent moiety is fluorescein, and representative corresponding
acceptor fluorescent moieties include LC-Red 640, LC-Red 705, Cy5,
and Cy5.5. Typically, detection includes exciting the sample at a
wavelength absorbed by the donor fluorescent moiety and visualizing
and/or measuring the wavelength emitted by the corresponding
acceptor fluorescent moiety. In the process according to the
invention, detection can be followed by quantitating the FRET. For
example, detection is performed after each cycling step. For
example, detection is performed in real time. By using commercially
available real-time PCR instrumentation (e.g., LightCycler.TM. or
TaqMan.RTM.), PCR amplification and detection of the amplification
product can be combined in a single closed cuvette with
dramatically reduced cycling time. Since detection occurs
concurrently with amplification, the real-time PCR methods obviate
the need for manipulation of the amplification product, and
diminish the risk of cross-contamination between amplification
products. Real-time PCR greatly reduces turn-around time and is an
attractive alternative to conventional PCR techniques in the
clinical laboratory.
[0219] The following patent applications describe real-time PCR as
used in the LightCycler.TM. technology: WO 97/46707, WO 97/46714
and WO 97/46712. The LightCycler.TM. instrument is a rapid thermal
cycler combined with a microvolume fluorometer utilizing high
quality optics. This rapid thermocycling technique uses thin glass
cuvettes as reaction vessels. Heating and cooling of the reaction
chamber are controlled by alternating heated and ambient air. Due
to the low mass of air and the high ratio of surface area to volume
of the cuvettes, very rapid temperature exchange rates can be
achieved within the thermal chamber.
[0220] TaqMan.RTM. technology utilizes a single-stranded
hybridization probe labeled with two fluorescent moieties. When a
first fluorescent moiety is excited with light of a suitable
wavelength, the absorbed energy is transferred to a second
fluorescent moiety according to the principles of FRET. The second
fluorescent moiety is generally a quencher molecule. Typical
fluorescent dyes used in this format are for example, among others,
FAM, HEX, CY5, JA270, Cyan and CY5.5. During the annealing step of
the PCR reaction, the labeled hybridization probe binds to the
target nucleic acid (i.e., the amplification product) and is
degraded by the 5' to 3' exonuclease activity of the Taq or another
suitable polymerase as known by the skilled artisan, such as a
mutant Z05 polymerase, during the subsequent elongation phase. As a
result, the excited fluorescent moiety and the quencher moiety
become spatially separated from one another. As a consequence, upon
excitation of the first fluorescent moiety in the absence of the
quencher, the fluorescence emission from the first fluorescent
moiety can be detected.
[0221] In both detection formats described above, the intensity of
the emitted signal can be correlated with the number of original
target nucleic acid molecules.
[0222] As an alternative to FRET, an amplification product can be
detected using a double-stranded DNA binding dye such as a
fluorescent DNA binding dye (e.g., SYBRGREEN I.RTM. or
SYBRGOLD.RTM. (Molecular Probes)). Upon interaction with the
double-stranded nucleic acid, such fluorescent DNA binding dyes
emit a fluorescence signal after excitation with light at a
suitable wavelength. A double-stranded DNA binding dye such as a
nucleic acid intercalating dye also can be used. When
double-stranded DNA binding dyes are used, a melting curve analysis
is usually performed for confirmation of the presence of the
amplification product.
[0223] Molecular beacons in conjunction with FRET can also be used
to detect the presence of an amplification product using the
real-time PCR methods of the invention. Molecular beacon technology
uses a hybridization probe labeled with a first fluorescent moiety
and a second fluorescent moiety. The second fluorescent moiety is
generally a quencher, and the fluorescent labels are typically
located at each end of the probe. Molecular beacon technology uses
a probe oligonucleotide having sequences that permit secondary
structure formation (e.g. a hairpin). As a result of secondary
structure formation within the probe, both fluorescent moieties are
in spatial proximity when the probe is in solution. After
hybridization to the amplification products, the secondary
structure of the probe is disrupted and the fluorescent moieties
become separated from one another such that after excitation with
light of a suitable wavelength, the emission of the first
fluorescent moiety can be detected.
[0224] Thus, in a method according to the invention is the method
described above using FRET, wherein said probes comprise a nucleic
acid sequence that permits secondary structure formation, wherein
said secondary structure formation results in spatial proximity
between said first and second fluorescent moiety.
[0225] Efficient FRET can only take place when the fluorescent
moieties are in direct local proximity and when the emission
spectrum of the donor fluorescent moiety overlaps with the
absorption spectrum of the acceptor fluorescent moiety.
[0226] Thus, in an embodiment, said donor and acceptor fluorescent
moieties are within no more than 5 nucleotides of each other on
said probe.
[0227] In a further embodiment, said acceptor fluorescent moiety is
a quencher.
[0228] As described above, in the TaqMan format, during the
annealing step of the PCR reaction, the labeled hybridization probe
binds to the target nucleic acid (i.e., the amplification product)
and is degraded by the 5'- to 3'-exonuclease activity of the Taq or
another suitable polymerase as known by the skilled artisan, such
as a mutant Z05 polymerase, during the subsequent elongation
phase.
[0229] Thus, in an embodiment, in the process described above,
amplification employs a polymerase enzyme having 5'- to
3'-exonuclease activity.
[0230] It is further advantageous to carefully select the length of
the amplicon that is yielded as a result of the process described
above. Generally, relatively short amplicons increase the
efficiency of the amplification reaction. Thus, an aspect of the
invention is the process described above, wherein the amplified
fragments comprise up to 450 bases, up to 300 bases, up to 200
bases, or up to 150 bases.
[0231] The internal control nucleic acid used in the present
invention can serve as a "quantitative standard nucleic acid" which
is apt to be and used as a reference in order to quantify, i.e. to
determine the quantity of the target nucleic acids. For this
purpose, one or more quantitative standard nucleic acids undergo
all possible sample preparation steps along with the target nucleic
acids. Moreover, a quantitative standard nucleic acid is processed
throughout the method within the same reaction mixture. It must
generate, directly or indirectly, a detectable signal both in the
presence or absence of the target nucleic acid. For this purpose,
the concentration of the quantitative standard nucleic acid has to
be carefully optimized in each test in order not to interfere with
sensitivity but in order to generate a detectable signal also e.g.
at very high target concentrations. In terms of the limit of
detection (LOD, see below) of the respective assay, the
concentration range for the "quantitative standard nucleic acid" is
20-5000.times.LOD, 20-1000.times.LOD, or 20-5000.times.LOD. The
final concentration of the quantitative standard nucleic acid in
the reaction mixture is dependent on the quantitative measuring
range accomplished.
[0232] "Limit of detection" or "LOD" means the lowest detectable
amount or concentration of a nucleic acid in a sample. A low "LOD"
corresponds to high sensitivity and vice versa. The "LOD" is
usually expressed either by means of the unit "cp/ml", particularly
if the nucleic acid is a viral nucleic acid, or as IU/ml. "Cp/ml"
means "copies per milliliter" wherein a "copy" is copy of the
respective nucleic acid. IU/ml stands for "International units/ml",
referring to the WHO standard.
[0233] A widely used method for calculating an LOD is "Probit
Analysis", which is a method of analyzing the relationship between
a stimulus (dose) and the quantal (all or nothing) response. In a
typical quantal response experiment, groups of animals are given
different doses of a drug. The percent dying at each dose level is
recorded. These data may then be analyzed using Probit Analysis.
The Probit Model assumes that the percent response is related to
the log dose as the cumulative normal distribution. That is, the
log doses may be used as variables to read the percent dying from
the cumulative normal. Using the normal distribution, rather than
other probability distributions, influences the predicted response
rate at the high and low ends of possible doses, but has little
influence near the middle.
[0234] The Probit Analysis can be applied at distinct "hitrates".
As known in the art, a "hitrate" is commonly expressed in percent
[%] and indicates the percentage of positive results at a specific
concentration of an analyte. Thus for example, an LOD can be
determined at 95% hitrate, which means that the LOD is calculated
for a setting in which 95% of the valid results are positive.
[0235] In an embodiment, the process described above provides an
LOD of 1 to 100 cp/ml or 0.5 to 50 IU/ml, or 1 to 75 cp/ml or 0.5
to 30 IU/ml, or 1 to 25 cp/ml or 1 to 20 IU/ml.
[0236] With respect to some examples of possible target nucleic
acids from certain viruses, the process described above provides
the following LODs: [0237] HIV: up to 60 cp/ml, up to 50 cp/ml, up
to 40 cp/ml, up to 30 cp/ml, up to 20 cp/ml, or up to 15 cp/ml
[0238] HBV: up to 10 IU/ml, up to 7.5 IU/ml, or up to 5 IU/ml
[0239] HCV: up to 10 IU/ml, up to 7.5 IU/ml, or up to 5 IU/ml
[0240] WNV I: up to 20 cp/ml, up to 15 cp/ml, or up to 10 cp/ml
[0241] WNV II: up to 20 cp/ml, up to 15 cp/ml, up to 10 cp/ml, or
up to 5 cp/ml [0242] JEV: up to 100 cp/ml, up to 75 cp/ml, up to 50
cp/ml, or up to 30 cp/ml [0243] SLEV: up to 100 cp/ml, up to 75
cp/ml, up to 50 cp/ml, up to 25 cp/ml, or up to 10 cp/ml.
[0244] An example of how to perform calculation of quantitative
results in the TaqMan format based on an internal control nucleic
acid serving as a quantitative standard nucleic acid is described
in the following: A titer is calculated from input data of
instrument-corrected fluorescence values from an entire PCR run. A
set of samples containing a target nucleic acid and an internal
control nucleic acid serving as a quantitative standard nucleic
acid undergo PCR on a thermocycler using a specified temperature
profile. At selected temperatures and times during the PCR profile
samples are illuminated by filtered light and the filtered
fluorescence data are collected for each sample for the target
nucleic acid and the internal control nucleic acid. After a PCR run
is complete, the fluorescence readings are processed to yield one
set of dye concentration data for the internal control nucleic acid
and one set of dye concentration data for the target nucleic acid.
Each set of dye concentration data is processed in the same manner.
After several plausibility checks, the elbow values (CT) are
calculated for the internal control nucleic acid and the target
nucleic acid. The elbow value is defined as the point where the
fluorescence of the target nucleic acid or the internal control
nucleic acid crosses a predefined threshold (fluorescence
concentration). Titer determination is based on the assumptions
that the target nucleic acid and the internal control nucleic acid
are amplified with the same efficiency and that at the calculated
elbow value equal amounts of amplicon copies of target nucleic acid
and internal control nucleic acid are amplified and detected.
Therefore, the (CTQS-CTtarget) is linear to log (target conc/QS
conc). In this context, QS denotes the internal control nucleic
acid serving as a quantitative standard nucleic acid. The titer T
can then be calculated for instance by using a polynomial
calibration formula as in the following equation:
T'=10(a(CTQS-CTtarget)2+b(CTQS-CTtarget)+c)
[0245] The polynomial constants and the concentration of the
quantitative standard nucleic acid are known, therefore the only
variable in the equation is the difference (CTQS-CTtarget).
[0246] Further, in the sense of the invention, the internal control
nucleic acid can serve as a "qualitative internal control nucleic
acid". A "qualitative internal control nucleic acid" is
particularly useful for confirming the validity of the test result
of a qualitative detection assay: Even in the case of a negative
result, the qualitative internal control must be detected,
otherwise the test itself is considered to be inoperative. However,
in a qualitative setup, it does not necessarily have to be detected
in case of a positive result. As a consequence, its concentration
must be relatively low. It has to be carefully adapted to the
respective assay and its sensitivity. For example, the
concentration range for the qualitative internal nucleic acid, i.e.
the second control nucleic acid, will comprise a range of 1 copy
per reaction to 1000 copies per reaction. In relation to the
respective assay's limit of detection (LOD), its concentration is
between the LOD of an assay and the 25fold value of the LOD, or
between the LOD and 10.times.LOD. Or, it is between 2.times. and
10.times.LOD. Or, it is between 5.times. and 10.times.LOD. Or, it
is 5.times. or 10.times.LOD.
[0247] The internal control nucleic acid as used in the present
invention is not restricted to a particular sequence. It can be
advantageous to add different internal control nucleic acids to a
fluid samples, but to use only one of them for amplification e.g.
by adding only primers for one of said internal control nucleic
acids. In such embodiments, the internal control nucleic acid to be
amplified in a certain experiment can be chosen by the person
skilled in the art, thus increasing flexibility of the analysis to
be carried out. In particularly advantageous embodiments, said
different internal control nucleic acids can be comprised by a
single nucleic acid construct, e.g. a plasmid or a different
suitable nucleic acid molecule.
[0248] Therefore, an aspect of the invention is the process
described above, wherein more than one internal control nucleic
acid is added in step a., but only one of said internal control
nucleic acids is amplified in step f.
[0249] The results described above may be adulterated and, for
example, comprise false-positives, in the case of
cross-contamination with nucleic acids from sources other than the
fluid sample. In particular, amplificates of former experiments may
contribute to such undesired effects. One particular method for
minimizing the effects of cross-contamination of nucleic acid
amplification is described in U.S. Pat. No. 5,035,996. The method
involves the introduction of unconventional nucleotide bases, such
as dUTP, into the amplified product and exposing carryover products
to enzymatic and/or physicochemical treatment to render the product
DNA incapable of serving as a template for subsequent
amplifications. Enzymes for such treatments are known in the art.
For example, uracil-DNA glycosylase, also known as
uracil-N-glycosylase or UNG, will remove uracil residues from PCR
products containing that base. The enzyme treatment results in
degradation of the contaminating carryover PCR product and serves
to "sterilize" the amplification reaction.
[0250] Thus, an aspect of the invention is the process described
above, further comprising between step d) and step e) the steps of
[0251] treating the fluid sample with an enzyme under conditions in
which products from amplifications of cross-contaminating nucleic
acids from other samples are enzymatically degraded; [0252]
inactivating said enzyme.
[0253] For example, the enzyme is uracil-N-glycosylase.
[0254] In a process according to the invention, all steps are
automated. "Automated" means that the steps of a process are
suitable to be carried out with an apparatus or machine capable of
operating with little or no external control or influence by a
human being. Only the preparation steps for the method may have to
be done by hand, e.g. storage containers have to be filled and put
into place, the choice of samples has to be performed by a human
being and further steps known to the expert in the field, e.g. the
operation of a controlling computer. The apparatus or machine may
e.g. automatically add liquids, mix the samples or carry out
incubation steps at specific temperatures. Typically, such a
machine or apparatus is a robot controlled by a computer which
carries out a program in which the single steps and commands are
specified.
[0255] A further aspect of the invention is an analytical system
(440) for isolating and simultaneously amplifying at least two
target nucleic acids that may be present in a fluid sample, said
analytical system comprising the following modules: [0256] a
separation station (230) comprising a solid support material, said
separation station being constructed and arranged to separate and
purify a target nucleic acid comprised in a fluid sample [0257] an
amplification station (405) comprising at least two reaction
vessels, said reaction vessels comprising amplification reagents,
at least a first purified target nucleic acid in at least a first
reaction vessel and at least a second purified target nucleic acid
in at least a second reaction vessel, wherein the second target
nucleic acid is absent from the first reaction vessel, an internal
control nucleic acid and a polymerase with reverse transcriptase
activity, said polymerase further comprising a mutation conferring
an improved nucleic acid extension rate and/or an improved reverse
transcriptase activity relative to the respective wildtype
polymerase.
[0258] An "analytical system" is an arrangement of components such
as instruments interacting with each other with the ultimate aim to
analyze a given sample.
[0259] The advantages of said analytical system are the same as
described supra with respect to the process according to the
invention.
[0260] The analytical system (440, FIG. 11) of the present
invention is a system (440) comprising a module (401) for isolating
and/or purifying an analyte. Further, the system (440) additionally
comprises a module (403) for analyzing said analyte to obtain a
detectable signal. The detectable signal can be detected in the
same module (401, 402, 403) or, alternatively, in a separate
module. The term "module" as used herein relates to any spatially
defined location within the analyzer (400). Two modules (401, 403)
can be separated by walls, or can be in open relationship. Any one
module (401, 402, 403) can be either autonomously controlled, or
control of the module (401, 402, 403) can be shared with other
modules. For example, all modules are controlled centrally.
Transfer between modules (401, 402, 403) can be manual, or
automated. Thus, a number of different embodiments of automated
analyzers (400) are encompassed by the present invention.
[0261] The "separation station" is described supra.
[0262] An "amplification station" comprises a
temperature-controlled incubator for incubating the contents of at
least two reaction vessels. It further comprises a variety of
reaction vessels like tubes or plates, in which a reaction for the
analysis of the sample such as PCR takes place. The outer limits or
walls of such vessels are chemically inert such that they do not
interfere with the amplification reaction taking place within. For
the ease of handling and to facilitate automation, the at least two
reaction vessels can be combined in an integral arrangement, so
they can be manipulated together.
[0263] Consequently, an aspect of the invention is the analytical
system described above, wherein the at least two reaction vessels
are combined in an integral arrangement.
[0264] Integral arrangements can e.g. be vials or tubes reversibly
or irreversibly attached to each other or arranged in a rack. For
example, the integral arrangement is a multiwell plate.
[0265] For example, said multiwell plate is held in a holding
station. In an embodiment, one handler transports a multiwell
vessel from a holding station to an air-lock (460), and a second
handler transports said multiwell plate from said air-lock to said
amplification station, wherein both handlers interact with said
multiwell plate by a form-locking interaction.
[0266] In an embodiment, the analytical system is fully
automated.
[0267] In one embodiment, at least two reaction vessels combined in
an integral arrangement are transported between stations of the
system.
[0268] In a second embodiment, the purified target nucleic acid is
transferred from said separation station to said amplification
station. For example, a pipettor comprising pipets with attached
pipet tips transfers the liquid comprising the purified nucleic
acid.
[0269] In a third embodiment, the purified nucleic acid is
transferred from said separation station to a reaction vessel in an
integral arrangement held in a holding station. For example, said
reaction vessel in an integral arrangement is then transferred from
said holding station to said amplification station.
[0270] The analytical system according to the invention further
comprises a pipetting unit. Said pipetting unit comprises at least
one pipet, or multiple pipets. In an embodiment, said multiple
pipets are combined in one or more integral arrangements, within
which the pipets can be manipulated individually. Pipets used in
the context of the invention can be pipets comprising pipet tips as
described supra. In another embodiment, the pipets are pipetting
needles.
[0271] Alternatively, a reaction vessel or arrangement of reaction
vessels used for sample preparation in the separation station and
containing the fluid comprising the purified target nucleic acids
may be transferred from the separation station to the amplification
station.
[0272] For this purpose, the analytical system according to the
invention further comprises a transfer unit, said transfer unit
comprising a robotic device, said device comprising a handler.
[0273] For the reasons set out above in the context of the process
according to the invention, the following are further aspects of
the invention: [0274] The analytical system (440) described above
wherein at least one reaction vessel comprises an RNA target
nucleic acid and a DNA target nucleic acid. [0275] The analytical
system (440) described above, wherein at least one reaction vessel
comprises an RNA target nucleic acid, and at least one other
reaction vessel comprises a DNA target nucleic acid.
[0276] For example, the analytical system (440) described above
further comprises one or more elements selected from the group
consisting of: [0277] a detection module (403) for detecting
signals evoked by an analyte [0278] a sealer (410) [0279] a storage
module (1008) for reagents and/or disposables. [0280] a control
unit (1006) for controlling system components.
[0281] A "detection module" (403) can e.g. be an optical detection
unit for detecting the result or the effect of the amplification
procedure. An optical detection unit may comprise a light source,
e.g. a xenon lamp, optics such as mirrors, lenses, optical filters,
fiber optics for guiding and filtering the light, one or more
reference channels, or a CCD camera or a different camera.
[0282] A "sealer" (410) is constructed and arranged to seal any
vessels used in connection with the analytical system according to
the invention. Such a sealer can, for example, seal tubes with
appropriate caps, or multiwell plates with foil, or other suitable
sealing materials.
[0283] A "storage module" (1008) stores the necessary reagents to
bring about a chemical or biological reaction important for
analysis of the fluid sample. It can also comprise further
components useful for the method of the invention, e.g. disposables
such as pipet tips or vessels to be used as reaction vessels within
the separation station and/or the amplification station.
[0284] For example, the analytical system according to the
invention further comprises a control unit for controlling system
components.
[0285] Such a "control unit" (1006) may comprise software for
ensuring that the different components of said analytical system
work and interact correctly and with the correct timing, e.g.
moving and manipulating components such as pipets in a coordinated
manner. The control unit may also comprise a processor running a
real-time operating system (RTOS), which is a multi-tasking
operating system intended for real-time applications. In other
words the system processor is capable of managing real-time
constraints, i.e. operational deadlines from event to system
response regardless of system load. It controls in real time that
different units within the system operate and respond correctly
according to given instructions.
[0286] In an embodiment, the present invention relates to an
analytical system (440) for processing an analyte, comprising
a. a first position comprising first receptacles (1001) in linear
arrangement comprising liquid samples (1010), a processing plate
(101) comprising receptacles (103) in n.times.m arrangement for
holding a liquid sample (1011), a first pipetting device (700)
comprising at least two pipetting units (702) in linear
arrangement, wherein said pipetting units (702) are coupled to
pipette tips (3, 4), and a tip rack (70) comprising pipette tips
(3, 4) in an a.times.(n.times.m) arrangement; b. a second position
comprising a holder (201, 128) for said processing plate (101), a
holder (330) for a multiwell plate, a holder (470) for said tip
rack (70) and a second pipetting device (35), said second pipetting
device (35) comprising pipetting units (702) in an n.times.m
arrangement for coupling to pipette tips (3, 4) (FIG. 12). The term
"holder" as used herein relates to any arrangement capable of
receiving a rack or a processing plate.
[0287] The advantages of the analytical system (440) of the present
invention are as described above for the method of the present
invention.
[0288] For example, the position of said pipetting units (702) of
the first pipetting device (700) are variable. Exemplary
embodiments of said first pipetting device (700) are described
hereinafter.
[0289] In one embodiment, the tip rack (70) comprises pipette tips
(3, 4) in an a.times.(n.times.m) arrangement. For example, a first
type (4) and a second type (3) of pipette tips are comprised in the
tip rack (70). In this embodiment, the first type of pipette tips
(4) is arranged in an n.times.m arrangement, and the second type of
pipette tips (3) is arranged in the n.times.m arrangement. In this
context, "n" denotes the number of rows and m the number of
columns, wherein n is 6 and m is 8. For example, the first type of
pipette tips (4) has a different volume than the second type of
pipette tips (3), or, the volume of the first type of pipette tips
(4) is more than 500 ul, and the volume of the second type of
pipette tips (3) is less than 500 ul. In this embodiment, a=2.
However, embodiments of the invention with more than two types of
pipette tips, and thus a>2 are also included in the present
invention.
[0290] In one aspect, the analytical system (440) of the present
invention comprises a control unit (1006) for allocating sample
types and individual tests to individual positions of said
processing plate (101). For example, said positions are separate
cells (401, 402).
[0291] In one aspect of the invention, the system additionally
comprises a transfer system (480) for transferring said process
plate (101) and said rack (70) between first (402) and second (401)
positions. Embodiments of said transfer system (480) are conveyor
belts or, one or more handler.
[0292] Furthermore, for example said pipette units of said second
pipetting device (35) are engaged to pipette tips (3, 4) which were
used in the first position (402).
[0293] An embodiment of the system (440) of the present invention
additionally comprises a third station (403) comprising a
temperature-controlled incubator for incubating said analyte with
reagents necessary to obtain a detectable signal. Further
embodiments of this system are described hereinafter.
[0294] More optimal control of the allocation of samples and tests
to the n.times.m arrangement is achieved with a first processor
(1004) which is comprised in said first position (402) to which
said control unit (1006) transfers instructions for allocating
sample types and individual tests to specific positions in the
n.times.m arrangement of vessels (103) of the process plate (101),
and a second processor (1005) which is comprised in said second
position (401) to which said control unit (1006) transfers
instructions for allocating sample types and individual tests to
specific positions in the n.times.m arrangement of vessels (103) of
the process plate.
[0295] For example, said system additionally comprises a first
processor located in said first position, and a second processor
located in said second position.
[0296] For example, said first processor (1004) controls said first
pipetting device (700) and said second processor (1005) controls
said second pipetting device (35).
[0297] All other embodiments and specific descriptions of
embodiments of the analytical system according to the invention are
those mentioned for the process according to the invention.
DESCRIPTION OF THE FIGURES
[0298] FIG. 1:
Schematic depiction of the sample preparation workflow as used in
an embodiment of the invention.
[0299] Arrows pointing down denote addition of a component or
reagent to each respective well of the deepwell plate mentioned
above, arrows pointing up their respective removal. These actions
were performed manually in steps 2, 3, 4, 21 and 22, by the process
head of the apparatus in steps 10, 14, 16, 18, and 24, and by the
reagent head of the apparatus in steps 5, 6, 7, 11, 15 and 19.
[0300] It has to be understood that the volumes used can be
adjusted flexibly within the spirit of the invention, for example
at least about up to 30% of the disclosed values. In particular, in
the case of step 2, the sample volume can be variable in order to
take into account the different types of fluid samples which may
require more or less starting material for obtaining proper
results, as known by the artisan. For example, the range is from
about 100 ul to about 850 ul. Or, it is about 100 ul, about 500 ul
or about 850 ul. For example, the volume in the respective vessels
is adjusted to an identical total volume with the diluent in step
3. For example, as in the scheme shown in FIG. 1, the total volume
adds up to about 850 ul.
[0301] FIG. 2a-g
[0302] Growth curves of the amplifications of the target nucleic
acids derived from HIV, HBV and CT carried out on a LightCycler480
(Roche Diagnostics GmbH, Mannheim, Del.) as described in Example 1.
The "Signal" indicated on the y-axis is a normalized fluorescent
signal. The x-axis shows the number of the respective PCR
cycle.
[0303] The growth curves of HIV and HBV are shown along with the
growth curves of the corresponding internal control nucleic acid.
The respective target nucleic acid curves are represented by
straight lines, the control nucleic acid curves by dotted
lines.
[0304] FIG. 2a: Qualitative HIV assay, measured in the channel for
detection of the target probe.
[0305] FIG. 2b: Qualitative HIV assay, measured in the channel for
detection of the control probe.
[0306] FIG. 2c: Quantitative HIV assay, measured in the channel for
detection of the target probe.
[0307] FIG. 2d: Quantitative HIV assay, measured in the channel for
detection of the control probe.
[0308] FIG. 2e: Quantitative HBV assay, measured in the channel for
detection of the target probe.
[0309] FIG. 2f: Quantitative HBV assay, measured in the channel for
detection of the control probe.
[0310] FIG. 2g: CT assay, measured in the channel for detection of
the target probe.
[0311] FIG. 3:
Perspective view of the processing plate.
[0312] FIG. 4:
Perspective view of the processing plate from the opposite
angle.
[0313] FIG. 5:
Top view of the processing plate.
[0314] FIG. 6:
Cross-sectional view along the longer side of the processing
plate.
[0315] FIG. 7:
A partial view of the cross-sectional view.
[0316] FIG. 8:
Perspective view of the longer side of the processing plate.
[0317] FIG. 9:
a) to d) show different views of the second embodiment of the
magnetic separation station.
[0318] FIG. 10:
(a) to (c) show a view of the first embodiment of the magnetic
separation station holding the Processing plate, with the first
type of magnets in the uppermost Z-position, and the second type of
magnets in the lowermost Z-position.
[0319] FIG. 11:
Schematic drawings of an analyzer comprising different stations,
modules or cells.
[0320] FIG. 12:
Shows an analytical system of the present invention.
[0321] FIG. 13:
Linearity of the quantitative HBV assay in EDTA plasma according to
the data in Example 2.
[0322] FIG. 14:
Linearity of the quantitative HBV assay in serum according to the
data in Example 2.
[0323] FIG. 15:
Linearity of the quantitative HCV assay in EDTA plasma according to
the data in Example 2.
[0324] FIG. 16:
Linearity of the quantitative HCV assay in serum according to the
data in Example 2.
[0325] FIG. 17:
Linearity of the quantitative HIV assay in EDTA plasma according to
the data in Example 2.
EXAMPLES
[0326] The following examples are offered to illustrate, but not to
limit the claimed invention.
Example 1
[0327] This example describes a process for isolating and
simultaneously amplifying at least a first and a second target
nucleic acid using a single generic internal control nucleic
acid.
[0328] In brief, in the depicted embodiment, realtime PCR is
carried out simultaneously and under identical conditions on a
panel of several different targets comprising bacteria (Chlamydia
trachomatis, CT) as well as a DNA virus (HBV) and an RNA virus
(HIV). All samples were processed and analyzed within the same
experiment, i.e. on the same deepwell plate (for sample
preparation) or multiwell plate (for amplification and detection),
respectively.
[0329] The following samples were prepared and subsequently
analyzed:
TABLE-US-00001 Reagent Manufacturer: HIV-1M Secondary Standard,
50'000 cp/ML Roche HBV Secondary Standard, 400 IU/ml Roche CT (DNA
POS CTL pCHL-1) Roche
[0330] Suitable standards or other types of targets are available
to the skilled artisan.
[0331] The instruments listed in the following table were used
according to the instructions of the respective manufacturer:
TABLE-US-00002 Instrument Manufacturer Hamilton Star Hamilton
Medical AG (Bonaduz, CH) Light Cycler 480 Roche Diagnostics GmbH
(Mannheim, DE) Chameleon Sealer K biosystems (Essex, UK) Compressor
K biosystems (Essex, UK)
[0332] For sample preparation the following reagents were used as
diluents:
TABLE-US-00003 Reagent Manufacturer: PreservCyt Thin Prep K3 EDTA
Plasma, PCR neg. Roche
[0333] The following dilutions were prepared in advance and stored
overnight (plasma dilutions at -60 to -90.degree. C., PreservCyt
dilutions at 2-8.degree. C.):
TABLE-US-00004 Target Concentration Matrix HBV 50 IU/ml K3 EDTA
plasma HIV-1M 100 cp/ml K3 EDTA plasma CT 2.5 fg/ml PreservCyt
[0334] Each respective sample (500 ul) and each respective specimen
diluent (350 ul) were pipetted manually into a deepwell plate,
wherein each sample was added to three different wells for
triplicate analysis. To each well containing an HIV or HBV sample,
50 ul of an internal control nucleic acid were manually added. For
the qualitative HIV assay, an RNA serving as a qualitative control
was added (100 armored particles/sample). For the quantitative HIV
assay, an RNA serving as a quantitative standard was added (500
armored particles/sample). For the quantitative HBV assay, a DNA
serving as a quantitative standard was added (1E4 copies/sample).
The sequence of said control nucleic acids was identical in all
cases and selected from the group of SEQ ID NOs 45-48.
[0335] The respective control nucleic acid was stored in the
following buffer:
TABLE-US-00005 IC/IQS - Storage Buffer Conc. or pH Tris (mM) 10
EDTA (mM) 0.1 Sodium Azide (w/v, %) 0.05 Poly rA RNA (mg/l) 20 pH
8
[0336] Sample preparation was performed on a Hamilton Star
(Hamilton, Bonaduz, CH), following the workflow according to the
scheme depicted in FIG. 1 and using the following reagents:
TABLE-US-00006 Protease reagent Conc. or pH Tris (mM) 10 EDTA (mM)
1 Calcium Chloride 5 (mM) Calcium Acetate (mM) 5 Esperase (mg/ml)
80 Glycerin (w/v, %) 50 pH 5.5
TABLE-US-00007 MGP Reagent Conc. or pH MPG Powder (mg/ml) 60 Tris
(mM) 30 Methylparaben (w/v, %) 0.1 Sodium Azide (w/v, %) 0.095 pH
8.5
TABLE-US-00008 Lysis Reagent Conc. or pH Guanidine Thiocyanate 4
(M) Sodium Citrate (mM) 50 Polydocanol (w/v, %) 5 Dithiotreitol
(w/v, %) 2 pH 5.8
TABLE-US-00009 Wash buffer Conc. or pH Sodium Citrate (mM) 7.5
Methylparaben (w/v, %) 0.1 pH 4.1
TABLE-US-00010 Elution buffer Conc. or pH Tris (mM) 30
Methylparaben (w/v, %) 0.2 pH 8.5
[0337] After the final step, the process head of the Hamilton Star
apparatus added the respective mastermixes (Mmxs) containing
amplification reagents to each well, mixed the fluids containing
the isolated nucleic acids with the Mmx and transferred each
resulting mixture to a corresponding well of a microwell plate in
which the amplification was carried out.
[0338] The following mastermixes (each consisting of the two
reagents R1 and R2) were used:
[0339] For HIV:
TABLE-US-00011 Concentration/ 50 .mu.l-PCR [.mu.M] R1 Reagent Water
(PCR grade) Mn(Ac).sub.2 * 4H.sub.2O (pH 6.1 adjusted with Acetic
Acid) 3'000 NaN3/Ri, buffered with 10 mM Tris at pH 7 [%] 0.018 R2
Reagent DMSO [%] 5.000% NaN3/Ri, buffered with 10 mM Tris at pH 7
[%] 0.027% Potassium acetate pH 7.0 110'000 Glycerol [%] 3.000%
Tricine pH 8.0 50'000 Igepal [%] 0.024% dGTP 337.5 dATP 337.5 dCTP
337.5 dUTP 675 Primers/probes selected from SEQ ID NOs 1-35
0.1-0.15 SEQ ID NO 42 0.1 SEQ ID NO 43 0.1 SEQ ID NO 44 0.1
Uracil-N-Glycosylase 10 (U/reaction) Z05-D Polymerase 40
(U/reactionn) NTQ21-46A - Aptamer 0.222 Water
[0340] For HBV:
TABLE-US-00012 Concentration/50 .mu.l-PCR R2 Reagent H20 100 %
Tricine 7.7 40 mM Tween 0.03 % (v/v) Glycerol 5 % (v/v) KOH 25.2 mM
KOAc 121.8 mM NTQ21-46A (Aptamer) 0.2625 uM dGTP 0.42 uM dATP 0.42
uM dCTP 0.42 uM dUTP 0.84 uM SEQ ID NO 36 1.2 uM SEQ ID NO 37 0.1
uM SEQ ID NO 38 1.2 uM SEQ ID NO 42 0.6 uM SEQ ID NO 43 0.6 uM SEQ
ID NO 44 0.15 uM Z05D Polymerase 35 (U/reaction)
Uracil-N-Glycosylase 2 (U/reaction) Sodium Azide 0.027 % (m/v) R1
Reagent H20 100 % MgOAc 2.5 mM MnOAc pH 6.1 2.5 mM Sodium Azide
0.018 % (m/v)
[0341] For CT:
TABLE-US-00013 Concentration/ 50 .mu.l-PCR R1 Reagent Water (PCR
grade) Mn(Ac).sub.2 (pH 6.5 in 0.002% (V/V) Glacial 2.7 mM Acetic
Acid) NaN3 0.0135% (W/V) R2 Reagent NaN3/Ri, buffered with 10 mM
Tris at pH 7 [%] 0.0315% Potassium acetate 112.4 mM Glycerol [%]
3.5% Tricine 61 mM Potassium hydroxide 28.4 mM dGTP 525 uM dATP 525
uM dCTP 525 uM dUTP 1.05 mM SEQ ID NO 39 750 nM SEQ ID NO 40 600 nM
SEQ ID NO 41 116 nM Aptamer NTQ-46A 175 nM Uracil-N-Glycosylase 5
U/reaction Z05-D Polymerase 31 U/reaction
[0342] For amplification and detection, the microwell plate was
sealed with an automated plate sealer (see above), and the plate
was transferred to a LightCycler 480 (see above).
[0343] The following PCR profile was used:
Thermo Cycling Profile
TABLE-US-00014 [0344] Program Target Acquisition Hold Ramp Rate
Analysis Name (.degree. C.) Mode (hh:mm:ss) (.degree. C./s) Cycles
Mode Pre-PCR 50 None 00:02:00 4.4 1 None 94 None 00:00:05 4.4 55
None 00:02:00 2.2 60 None 00:06:00 4.4 65 None 00:04:00 4.4 1st 95
None 00:00:05 4.4 5 Quantification Measurement 55 Single 00:00:30
2.2 2nd 91 None 00:00:05 4.4 45 Quantification Measurement 58
Single 00:00:25 2.2 Cooling 40 None 00:02:00 2.2 1 None
Detection Format (Manual)
TABLE-US-00015 [0345] Filter Combination Integration Time (sec)
435-470 1 495-525 0.5 540-580 0.5 610-645 0.5 680-700 1
[0346] The Pre-PCR program comprises initial denaturing and
incubation at 55, 60 and 65.degree. C. for reverse transcription of
RNA templates. Incubating at three temperatures combines the
advantageous effects that at lower temperatures slightly mismatched
target sequences (such as genetic variants of an organism) are also
transcribed, while at higher temperatures the formation of RNA
secondary structures is suppressed, thus leading to a more
efficient transcription.
[0347] PCR cycling is divided into two measurements, wherein both
measurements apply a one-step setup (combining annealing and
extension). The first 5 cycles at 55.degree. C. allow for an
increased inclusivity by pre-amplifying slightly mismatched target
sequences, whereas the 45 cycles of the second measurement provide
for an increased specificity by using an annealing/extension
temperature of 58.degree. C.
[0348] Using this profile on all samples comprised on the microwell
plate mentioned above, amplification and detection was achieved in
all samples, as depicted in FIG. 2. This shows that the sample
preparation prior to amplification was also successfully carried
out.
[0349] The results for the qualitative and quantitative HIV
internal controls and the quantitative HBV internal control are
depicted separately in FIG. 2 for the sake of clarity. It can be
seen that the controls were also successfully amplified in all
cases. The quantitation of the HIV and HBV targets in the
quantitative setup were calculated by comparison with the internal
control nucleic acid serving as a quantitative standard.
Example 2
[0350] The generic amplification process described hereinabove was
carried out on a variety of different target nucleic acids in
separate experiments but under identical conditions. Isolation of
the respective nucleic acid was carried out as described under
Example 1.
[0351] The respective generic internal control nucleic acid was
selected from SEQ ID NOs 45-49 and was armored RNA for RNA targets
and lambda-packaged DNA for DNA targets. For qualitative RNA
assays, 300 particles were added per sample, for quantitative RNA
assays 3000 and for all DNA assays 500.
[0352] The following PCR profile was used on all targets:
TABLE-US-00016 Target Acquisition Plateau Measure Ramp Rate
[.degree. C.] Mode [hh:mm:ss] [hh:mm:ss] [.degree. C./s] Pre-PCR
UNG-Step 50 none 00:02:00 00:00:00 2.2 UNG/Template 94 none
00:00:05 00:00:00 4.4 Denaturation RT-Step 55 none 00:02:00
00:00:00 2.2 60 none 00:06:00 00:00:00 4.4 65 none 00:04:00
00:00:00 4.4 1st 95 none 00:00:05 00:00:00 4.4 Measurement 55
single 00:00:30 00:00:08 2.2 2nd 91 none 00:00:05 00:00:00 4.4
Measurement 58 single 00:00:25 00:00:08 2.2 Cooling 40 none
00:02:00 00:00:00 2.2 Name Cycles Pre-PCR 1 1st 5 Measurement 2nd
45 Measurement Cooling 1
[0353] In detail, the following experiments were performed:
[0354] 1. Qualitative Multiplex Analysis of HBV, HCV and HIV [0355]
a. Mastermix
R1
TABLE-US-00017 [0356] Conc. in 50 ul-PCR (uM) Mn(Ac)2 * 4H2O (pH
6.1 adjusted with Acetic 3'300 Acid) NaN3/Ri, buffered with 10 mM
Tris at pH 7 0.018 pH: 6.41
R2:
TABLE-US-00018 [0357] Conc. in 50 ul-PCR Reagent (uM) DMSO (%) 5.4
NaN3/Ri, buffered with 10 mM Tris at pH 7 0.027 KOAc (pH 7.0)
120'000 Glycerol (%) 3 Tween 20 (%) 0.015 Tricine pH 8.0 60'000
NTQ21-46A - Aptamer 0.2222 Uracil-N-Glycosylase (U/uL) 0.2 dGTP
400.0 dATP 400.0 dCTP 400.0 dUTP 800.0 ZO5-D Polymerase (U/ul)* 0.9
Primers/probes selected from SEQ ID NOs 1-35 0.125-0.3 SEQ ID NO 36
0.100 SEQ ID NO 37 0.100 SEQ ID NO 38 0.150 Primers/probes selected
from SEQ ID NOs 60-76 0.050-0.250 SEQ ID NO 42 0.200 SEQ ID NO 43
0.200 SEQ ID NO 44 0.100
Analytical Sensitivity/LOD
[0358] For each detected virus (HIV-1 group M, HIV-1 group O,
HIV-2, HBV and HCV), at several concentrations/levels at and around
the anticipated LOD for EDTA-plasma. One panel per virus and
concentration was tested with at least 20 valid replicates per
concentration. The LOD was determined by PROBIT analysis (see Table
1-5).
HIV
TABLE-US-00019 [0359] TABLE 1 HIV-1 Group M Hit rates and Probit
LOD from individual panel Number of Number of Concentration
replicates positives Hit rate 32 cp/mL 21 21 100% 16 cp/mL 21 21
100% 8 cp/mL 21 21 100% 4 cp/mL 21 20 95% 2 cp/mL 21 15 71% 1 cp/mL
21 9 43% 0 cp/mL (neg. control) 12 0 0% LOD by PROBIT analysis (95%
hitrate) 4.06 cp/mL 95% confidence interval for LOD by 2.85-9.24
cp/mL PROBIT analysis
[0360] Titer of WHO Standard for HIV-1 Group M was converted to
IU/mL.
Titer ( in IV mL ) = Titer ( i n cp mL ) 0.6 ##EQU00001##
[0361] Therefore HIV-1 Group M LOD in IU/mL is
[0362] LOD by PROBIT analysis (95% hitrate): 6.77 IU/mL
[0363] 95% confidence interval for LOD by PROBIT analysis:
4.75-15.4 IU/mL
TABLE-US-00020 TABLE 2 HIV-1 Group O Hit rates and Probit LOD from
individual panel Number of Number of Concentration replicates
positives Hit rate 60 cp/mL 21 21 100% 30 cp/mL 20 20 100% 20 cp/mL
21 21 100% 14 cp/mL 21 19 90% 7 cp/mL 21 15 71% 4.5 cp/mL 21 12 57%
0 cp/mL 12 0 0% (neg. control) LOD by PROBIT analysis 14.9 cp/mL
(95% hitrate) 95% confidence interval for LOD by 10.9-31.5 cp/mL
PROBIT analysis
[0364] Titer of Primary Standard for HIV-1 Group O was reassigned
to CBER HIV-1 Group O panel; calculation factor is 0.586.
[0365] Therefore HIV-1 Group O LOD is
[0366] LOD by PROBIT analysis (95% hitrate): 8.8 cp/mL
[0367] 95% confidence interval for LOD by PROBIT analysis: 6.4-18.5
cp/mL
TABLE-US-00021 TABLE 3 HIV-2 Hit rates and Probit LOD from
individual panel Number of Number of Concentration replicates
positives Hit rate 4 cp/mL 21 21 100% 2 cp/mL 21 21 100% 1 cp/mL 21
20 95% 0.5 cp/mL 21 13 62% 0.25 cp/mL 21 13 62% 0.125 cp/mL 21 7
33% 0 cp/mL 12 0 0% (neg. control) LOD by PROBIT analysis (95%
hitrate) 1.29 cp/mL 95% confidence interval -3.11 cp/mL for LOD by
PROBIT analysis
[0368] Titer of Primary Standard for HIV-2 was reassigned to CBER
HIV-2 panel; calculation factor is 26.7.
[0369] Therefore HIV-2 LOD is
[0370] LOD by PROBIT analysis (95% hitrate): 34.44 cp/mL
[0371] 95% confidence interval for LOD by PROBIT analysis:
21.89-83.04 cp/mL
HBV
TABLE-US-00022 [0372] TABLE 4 HBV Hit rates and Probit LOD from
individual panel Number of Number of Concentration replicates
positives Hit rate 7.6 IU/mL 21 21 100% 3.8 IU/mL 21 21 100% 1.9
IU/mL 21 20 95% 0.95 IU/mL 21 14 67% 0.6 IU/mL 19 12 63% 0.4 IU/mL
21 12 57% 0 IU/mL 12 0 0% (neg. control) LOD by PROBIT analysis
2.27 IU/mL (95% hitrate) 95% confidence interval for 1.48-6.54
IU/mL LOD by PROBIT analysis
HCV
TABLE-US-00023 [0373] TABLE 5 HCV Hit rates and Probit LOD from
individual panel Number of Number of Concentration replicates
positives Hit rate 24 IU/mL 21 21 100% 12 IU/mL 21 21 100% 6 IU/mL
21 21 100% 3 IU/mL 21 17 81% 1.5 IU/mL 21 14 67% 0.75 IU/mL 21 9
43% 0 IU/mL 18 0 0% eg. control) LOD by PROBIT analysis 4.76 IU/mL
(95% hitrate) 95% confidence interval for 3.14-11.61 IU/mL LOD by
PROBIT analysis
[0374] 2. Qualitative Analysis of WNV
Mastermix
R1:
TABLE-US-00024 [0375] Conc. in Reagent 50 ul-PCR (uM) Mn(Ac)2 *
4H2O (pH 6.1 adjusted with Acetic Acid) 3'300 NaN3/Ri, buffered
with 10 mM Tris at pH 7 0.018 pH: 6.41
R2:
TABLE-US-00025 [0376] Reagent Conc. in 50 ul-PCR (uM) DMSO (%) 5.4
NaN3/Ri, buffered with 10 mM Tris at pH 7 0.027 K acetate pH 7.0
120'000 Glycerol (%) 3 Tween 20 (%) 0.015 Tricine pH 8.0 60'000
NTQ21-46A - Aptamer 0.2222 Uracil-N-Glycosylase (U/uL) 0.2 dGTP
400.0 dATP 400.0 dCTP 400.0 dUTP 800.0 ZO5-D Polymerase (U/ul)* 0.9
Primers/probes selected from SEQ ID NOs 0.08-0.4 53-59 SEQ ID NO 42
0.150 SEQ ID NO 43 0.150 SEQ ID NO 44 0.100
Analytical Sensitivity/LOD
[0377] For the viruses (WNV, SLEV and JEV) an independent panel was
prepared as a dilution series of the respective Standard including
several concentrations/levels at and around the anticipated LOD.
One panel per virus and concentration was tested with at least 20
valid replicates per concentration. The LOD was determined by
PROBIT analysis.
TABLE-US-00026 TABLE 6 WNV Hit rates and Probit LOD from individual
panel Number of Number of Concentration replicates positives Hit
rate 20 cp/mL 21 21 100% 12 cp/mL 21 21 100% 8 cp/mL 21 21 100% 5
cp/mL 21 17 81% 2.5 cp/mL 21 15 71.4% 0.5 cp/mL 21 1 4.8% 0 cp/mL
12 0 0% (neg. control) LOD by PROBIT analysis 6.57 cp/mL (95%
hitrate) 95% confidence interval for 4.74-11.03 cp/mL LOD by PROBIT
analysis
TABLE-US-00027 TABLE 7 SLEV Hit rates and Probit LOD from
individual panel Number of Number of Concentration replicates
positives Hit rate 140 cp/mL 21 21 100% 100 cp/mL 21 20 95.2% 70
cp/mL 21 20 95.2% 40 cp/mL 21 17 81.0% 20 cp/mL 21 11 52.4% 10
cp/mL 21 6 28.6% 0 cp/mL 12 0 0% (neg. control) LOD by PROBIT
analysis 78.9 cp/mL (95% hitrate) 95% confidence interval for
55.4-145.7 cp/mL LOD by PROBIT analysis
TABLE-US-00028 TABLE 8 JEV Hit rates and Probit LOD from individual
panel Number of Number of Concentration replicates positives Hit
rate 20 cp/mL 21 20 95.2% 12 cp/mL 21 20 95.2% 8 cp/mL 21 18 85.7%
5 cp/mL 21 17 81.0% 2.5 cp/mL 21 14 66.7% 0.5 cp/mL 21 2 9.52% 0
cp/mL 12 0 0% (neg. control) LOD by PROBIT analysis 13.55 cp/mL
(95% hitrate) 95% confidence interval for 8.78-27.7 cp/mL LOD by
PROBIT analysis
[0378] 3. Quantitative Analysis of HBV
Mastermix
R1:
TABLE-US-00029 [0379] Final Conc. in 50 Reagent ul-PCR (uM) Mn(Ac)2
* 4H2O (pH 6.1 adjusted with Acetic Acid) 3'300 NaN3/Ri, buffered
with 10 mM Tris at pH 7 0.018 pH: 6.41
R2:
TABLE-US-00030 [0380] Final Conc. in 50 ul-PCR Reagent (uM)
Glycerol (%, w/v) 3% Tricine 60 mM DMSO (%, v/v) 5.4% KOAc 120 mM
Tween 20 (v/v) 0.015% Aptamer NTQ21-46 A 0.222 .mu.M ZO5D
Polymerase 0.9 U/.mu.L (45 U/rxn) Uracil-N-Glycosylase 0.2 U/.mu.L
(10 U/rxn) Sodium Azide (w/v) 0.027% dCTPs 400 .mu.M dGTPs 400
.mu.M dATPs 400 .mu.M dUTPs 800 .mu.M SEQ ID NO 36 1.2 .mu.M SEQ ID
NO 37 1.2 .mu.M SEQ ID NO 50 0.6 .mu.M SEQ ID NO 51 0.6 .mu.M SEQ
ID NO 38 0.1 .mu.M SEQ ID NO 52 M
Analytical Sensitivity/LOD
[0381] Four dilution panels were prepared with HBV Secondary
Standard (representing Genotype A), i.e., two in HBV negative serum
for sample input volumes of 200 .mu.L and 500 .mu.L, and two in HBV
negative EDTA-plasma for sample input volumes of 200 .mu.L and 500
.mu.L. Each panel included 7 concentration levels at and around the
anticipated LOD. One panel per matrix was tested with .gtoreq.21
replicates per concentration level. At least 20 replicates needed
to be valid. The LOD was determined by PROBIT analysis at 95% hit
rate and by .gtoreq.95% hit rate analysis.
TABLE-US-00031 TABLE 9 LOD analysis for 200 .mu.L input volume in
EDTA-plasma.* Number of Number of Concentration replicates
positives Hit rate 25 IU/mL 41 41 100% 15 IU/mL 41 39 95.1% 10
IU/mL 41 40 97.6% 7 IU/mL 41 40 97.6% 4 IU/mL 24 20 83.3% 1 IU/mL
24 4 16.7% 0 IU/mL 24 0 0% (neg. control) LOD by PROBIT analysis
8.2 IU/mL (95% hitrate) 95% confidence interval 4.8-26.0 IU/mL for
LOD by PROBIT analysis *Additional replicates were tested to narrow
the observed 95% confidence interval.
TABLE-US-00032 TABLE 10 LOD analysis for 500 .mu.L input volume in
EDTA-plasma. Number of Number of Concentration replicates positives
Hit rate 10 IU/mL 21 21 100% 7 IU/mL 21 21 100% 4 IU/mL 21 21 100%
2.5 IU/mL 21 20 95.2% 1 IU/mL 21 14 66.7% 0.2 IU/mL 21 1 4.8% 0
IU/mL 21 0 0% (neg. control) LOD by PROBIT analysis 2.3 IU/mL (95%
hitrate) 95% confidence interval 1.6-4.2 IU/mL for LOD by PROBIT
analysis
TABLE-US-00033 TABLE 11 LOD analysis for 200 .mu.L input volume in
serum. Number of Concentration Number of replicates positives Hit
rate 25 IU/mL 21 21 100% 15 IU/mL 21 20 95.2% 10 IU/mL 21 21 100% 7
IU/mL 21 20 95.2% 4 IU/mL 21 15 71.4% 1 IU/mL 21 8 38.1% 0 IU/mL 21
0 0% (neg. control) LOD by PROBIT analysis (95% hitrate) 9.4 IU/mL
95% confidence interval for LOD by 6.2-19.0 IU/mL PROBIT
analysis
TABLE-US-00034 TABLE 12 LOD analysis for 500 .mu.L input volume in
serum. Number of Concentration Number of replicates positives Hit
rate 10 IU/mL 21 21 100% 7 IU/mL 21 21 100% 4 IU/mL 21 21 100% 2.5
IU/mL 21 16 76.2% 1 IU/mL 21 16 76.2% 0.2 IU/mL 21 7 33.3% 0 IU/mL
21 0 0% (neg. control) LOD by PROBIT analysis (95% hitrate) 4.1
IU/mL 95% confidence interval for LOD by 2.4-10.0 IU/mL PROBIT
analysis
Summary LOD:
[0382] EDTA-plasma: The PROBIT analysis at 95% hit rate resulted in
an LOD of 8.2 IU/mL for 200 .mu.L sample input volume and 2.3 IU/mL
for 500 .mu.L sample input volume for EDTA-plasma.
[0383] The 95% confidence interval range for these concentrations
was 4.8-26.0 IU/mL for 200 .mu.L sample input volume and 1.6-4.2
IU/mL for 500 .mu.L sample input volume.
[0384] Serum: The PROBIT analysis at 95% hit rate resulted in an
LOD of 9.02 IU/mL for 200 .mu.L sample input volume and 4.1 IU/mL
for 500 .mu.L sample input volume for serum.
[0385] The 95% confidence interval range for these concentrations
was 6.2-19.0 IU/mL for 200 .mu.L sample input volume and 2.4-10.0
IU/mL for 500 .mu.L sample input volume.
Linearity
[0386] One EDTA-plasma panel and one serum panel were prepared by
using HBV genotype A (provided by RMD Research Pleasanton,
linearized plasmid, pHBV-PC_ADW2). Each of the panels was analyzed
at 12 concentration levels for the determination of the expected
dynamic range (4-2E+09 IU/mL) of the assay. All concentration
levels/panel members (PM) were tested in 21 replicates.
[0387] This study was done with a sample input volume of 500 .mu.L.
The concentration levels were selected as follows: One level below
expected Lower Limit of Quantitation (LLOQ), one at expected LLOQ,
one above expected LLOQ, several concentrations at intermediates
levels, at expected Upper Limit of Quantitation (ULOQ) and one
above expected ULOQ:
PM 12-2.0E+09 IU/mL--above expected ULOQ PM 11-1.0E+09 IU/mL--at
expected ULOQ PM 10-1.0E+08 IU/mL--below expected ULOQ PM 9-1.0E+07
IU/mL--intermediate concentration level PM 8-1.0E+06
IU/mL--intermediate concentration level PM 7-1.0E+05
IU/mL--intermediate concentration level PM 6-1.0E+04
IU/mL--intermediate concentration level PM 5-1.0E+03
IU/mL--intermediate concentration level PM 6a-2.0E+02
IU/mL--intermediate concentration level (PM 6 diluted to 2.0E+02
IU/mL, used for titer assignment of serum panel) PM 4-1.0E+02
IU/mL--intermediate concentration level (also used for titer
assignment of plasma panel) PM 3-5.0E+01 IU/mL--above expected LLOQ
PM 2-1.0E+01 IU/mL--at expected LLOQ PM 1-4.0E+00 IU/mL below
expected LLOQ
[0388] For every valid sample of the linearity panel, the observed
HBV DNA titer was transformed to log 10 titer and the mean log 10
titer was calculated per concentration level.
TABLE-US-00035 TABLE 13 Linearity in EDTA Plasma Nominal Assigned
Mean Titer Titer Assigned Log 10 Titer Repli- (IU/mL) (IU/mL) Log10
Titer observed cates 4.00E+00 3.50E+00 0.54 0.52 17 1.00E+01
8.70E+00 0.94 0.91 21 5.00E+01 4.40E+01 1.64 1.69 21 1.00E+02
8.70E+01 1.94 2.04 21 1.00E+03 8.70E+02 2.94 3.01 21 1.00E+04
8.70E+03 3.94 3.9 21 1.00E+05 8.70E+04 4.94 4.88 21 1.00E+06
8.70E+05 5.94 5.87 21 1.00E+07 8.70E+06 6.94 6.92 21 1.00E+08
8.70E+07 7.94 8.01 21 1.00E+09 8.70E+08 8.94 9.04 21 2.00E+09
1.70E+09 9.24 9.38 21
[0389] A graphical depiction of this result is shown in FIG.
13.
TABLE-US-00036 TABLE 14 Linearity in Serum Nominal Assigned Mean
Titer Titer Assigned Log 10 Titer Repli- (IU/mL) (IU/mL) Log10
Titer observed cates 4.00E+00 3.30E+00 0.52 0.7 21 1.00E+01
8.30E+00 0.92 0.99 21 5.00E+01 4.10E+01 1.62 1.73 21 1.00E+02
8.30E+01 1.92 2.03 21 1.00E+03 8.30E+02 2.92 2.93 21 1.00E+04
8.30E+03 3.92 3.8 21 1.00E+05 8.30E+04 4.92 4.78 21 1.00E+06
8.30E+05 5.92 5.75 21 1.00E+07 8.30E+06 6.92 6.73 21 1.00E+08
8.30E+07 7.92 7.78 21 1.00E+09 8.30E+08 8.92 8.92 21 2.00E+09
1.70E+09 9.22 9.22 21
[0390] A graphical depiction of this result is shown in FIG.
14.
Summary Linearity:
[0391] The linear range, defined as the concentration range for
which the log 10 deviation of the mean log 10 observed titers is
within .+-.0.3 of the log 10 nominal titer was determined as:
3.5E+00 IU/mL-1.7E+09 IU/mL for EDTA-plasma and 3.3E+00
IU/mL-1.7E+09 IU/mL for serum. The Lower Limit of Quantitation was
found to be: 4.0E+00 IU/mL for EDTA-plasma and serum.
[0392] 4. Quantitative Analysis of HCV
Mastermix
R1:
TABLE-US-00037 [0393] Final Conc. in 50 Reagent ul-PCR (uM) Mn(Ac)2
* 4H2O (pH 6.1 adjusted with Acetic Acid) 3'300 NaN3/Ri, buffered
with 10 mM Tris at pH 7 0.018 pH: 6.41
R2:
TABLE-US-00038 [0394] Final Conc. in 50 Reagent ul-PCR Glycerol (%,
w/v) 3% Tricine 60 mM DMSO (%, v/v) 5.4% KOAc 120 mM Tween 20 (v/v)
0.015% NTQ21-46 A 0.222 .mu.M ZO5D 0.9 U/.mu.L (45 U/rxn) UNG 0.2
U/.mu.L (10 U/rxn) Sodium Azide (w/v) 0.027 dCTPs 400 .mu.M dGTPs
400 .mu.M dATPs 400 .mu.M dUTPs 800 .mu.M Primers/probes selected
from SEQ ID NOs 60-76 0.1 .mu.M SEQ ID NO 42 0.3 .mu.M SEQ ID NO 43
0.3 .mu.M SEQ ID NO 44 .mu.M
Analytical Sensitivity/LOD
[0395] A dilution panel was prepared with Roche HCV Secondary
Standard in HCV negative EDTA plasma and serum using a sample input
volumes of 200 .mu.L and 500 .mu.L. Each concentration level was
tested with 21 replicates. At least .gtoreq.20 replicates have to
be valid. The LOD was determined by PROBIT analysis at 95% hit rate
and by .gtoreq.95% hit rate analysis.
TABLE-US-00039 TABLE 15 Hit rates and Probit with 200 .mu.L sample
process input volume for EDTA-plasma Number of Number of
Concentration replicates positives Hit rate 55 IU/mL 21 21 100% 38
IU/mL 21 21 100% 25 IU/mL 21 20 95% 12.5 IU/mL 21 19 90% 6 IU/mL 21
15 71% 3 IU/mL 21 6 29% 0 IU/mL (neg. control) 21 0 0% LOD by
PROBIT analysis (95% hitrate) 17.4 IU/mL 95% confidence interval
for LOD by PROBIT 12.1-34.3 analysis IU/mL
TABLE-US-00040 TABLE 16 Hit rates and Probit with 500 .mu.L sample
process input volume for EDTA-plasma Number of Number of
Concentration replicates positives Hit rate 22 IU/mL 21 21 100% 15
IU/mL 21 21 100% 10 IU/mL 20 20 100% 5 IU/mL 21 19 76% 2.5 IU/mL 21
15 71% 1 IU/mL 21 6 57% 0 IU/mL (neg. control) 21 0 0% LOD by
PROBIT analysis (95% hitrate) 9.0 IU/mL 95% confidence interval for
LOD by PROBIT 5.5-25.4 analysis IU/mL
TABLE-US-00041 TABLE 17 Hit rates and Probit with 200 .mu.L sample
process input volume for serum Number of Number of Concentration
replicates positives Hit rate 55 IU/mL 21 21 100% 38 IU/mL 21 21
100% 25 IU/mL 21 20 95% 12.5 IU/mL 21 18 86% 6 IU/mL 21 13 62% 3
IU/mL 21 6 29% 0 IU/mL (neg. control) 21 0 0% LOD by PROBIT
analysis (95% hitrate) 20.2 IU/mL 95% confidence interval for LOD
by PROBIT 14.0-39.3 analysis IU/mL
TABLE-US-00042 TABLE 18 Hit rates and Probit with 500 .mu.L sample
process input volume for serum Number of Number of Concentration
replicates positives Hit rate 22 IU/mL 21 21 100% 15 IU/mL 21 21
100% 10 IU/mL 21 20 95% 5 IU/mL 21 18 86% 2.5 IU/mL 21 12 57% 1
IU/mL 21 4 19% 0 IU/mL (neg. control) 21 0 0% LOD by PROBIT
analysis (95% hitrate) 8.2 IU/mL 95% confidence interval for LOD by
PROBIT 5.8-15.0 analysis IU/mL
Summary LOD:
[0396] 1. The PROBIT analysis at 95% Hit rate resulted in an LOD of
17.4 IU/mL for 200 .mu.L sample process input volume and 9.0 IU/mL
for 500 .mu.L sample process input volume for EDTA plasma. The 95%
confidence interval for these concentrations is 12.1-34.3 IU/mL for
200 .mu.L sample process input volume and 5.5-25.4 IU/mL for 500
.mu.L sample process input volume. 2. The values of the PROBIT
analysis at 95% Hit rate is 20.2 IU/mL for 200 .mu.L sample process
input volume and 8.2 IU/mL for 500 .mu.L sample process input
volume for serum. The 95% confidence interval for these
concentrations is 14.0-39.3 IU/mL for 200 .mu.L sample process
input volume and 5.8-15.0 IU/mL for 500 .mu.L sample process input
volume.
Linearity
[0397] One preparation of an EDTA-plasma panel and one preparation
of a serum panel of HCV aRNA traceable to the HCV WHO Standard were
analyzed. The linearity panels were prepared by serial dilution and
analyzed at 10 different concentrations. The study was done with
500 .mu.L sample process input volume. The concentrations were
selected as follows: One level below expected Lower Limit of
Quantification (LLoQ), one at LLoQ, one above LLOQ, several
concentrations at intermediates levels, at expected Upper Limit of
Quantification (ULoQ) and one at or above ULoQ. For all
concentrations 21 replicates were tested.
PM 1-2.0E+08 IU/mL--above expected ULoQ PM 2-1.0E+08 IU/mL--at
expected ULoQ PM 3-1.0E+07 IU/mL--below expected ULoQ PM 4-1.0E+06
IU/mL--intermediate concentration level PM 5 1.0E+05
IU/mL--intermediate concentration level PM 6-1.0E+04
IU/mL--intermediate concentration level for titer assignment PM
7-1.0E+03 IU/mL--intermediate concentration level PM 8-1.0E+02
IU/mL--above expected LLoQ PM 9-1.0E+01 IU/mL--at expected LLoQ PM
10-8.0E+00 IU/mL--below expected LLoQ
TABLE-US-00043 TABLE 19 Linearity in EDTA Plasma Nominal Assigned
Mean Titer Titer Assigned Log 10 Titer Repli- (IU/mL) (IU/mL) Log10
Titer observed cates 8.00E+00 4.87E+00 0.7 0.6 15 1.00E+01 6.09E+00
0.8 0.8 17 1.00E+02 6.09E+01 1.8 1.7 21 1.00E+03 6.09E+02 2.8 2.8
21 1.00E+04 6.09E+03 3.8 3.8 21 1.00E+05 6.09E+04 4.8 4.7 21/20
1.00E+06 6.09E+05 5.8 5.6 21/20 1.00E+07 6.09E+06 6.8 6.7 21
1.00E+08 6.09E+07 7.8 7.8/7.7 21/18 2.00E+08 1.22E+08 8.1 8
21/20
[0398] A graphical depiction of this result is shown in FIG.
15.
TABLE-US-00044 TABLE 20 Linearity in Serum Nominal Assigned Mean
Titer Titer Assigned Log 10 Titer Repli- (IU/mL) (IU/mL) Log10
Titer observed cates 8.00E+00 3.90E+00 0.6 0.7 10 1.00E+01 4.96E+00
0.7 0.7 14 1.00E+02 4.96E+01 1.7 1.6 21 1.00E+03 4.96E+02 2.7 2.8
21 1.00E+04 4.96E+03 3.7 3.7 21 1.00E+05 4.96E+04 4.7 4.7 21
1.00E+06 4.96E+05 5.7 5.7 21 1.00E+07 4.96E+06 6.7 6.7 21 1.00E+08
4.96E+07 7.7 7.7 21 2.00E+08 9.92E+07 8 8.1 21
[0399] A graphical depiction of this result is shown in FIG.
16.
Summary Linearity:
[0400] The linear range, defined as the concentration range for
which the log 10 deviation of the mean log 10 observed titers is
within .+-.0.3 of the log 10 nominal titer was determined as:
4.87E+00 IU/mL-1.22E+08 IU/mL for EDTA-plasma and 3.90E+00
IU/mL-9.92E+07 IU/mL for serum.
[0401] 5. Quantitative Analysis of HIV
Mastermix
R1:
TABLE-US-00045 [0402] Final Conc. in 50 Reagent ul-PCR (uM) Mn(Ac)2
* 4H2O (pH 6.1 adjusted with Acetic Acid) 3'300 NaN3/Ri, buffered
with 10 mM Tris at pH 7 0.018 pH: 6.41
R2:
TABLE-US-00046 [0403] Final Conc. in 50 Reagent ul-PCR Glycerol (%,
w/v) 3% Tricine 60 mM DMSO (%, v/v) 5.4% KOAc 120 mM Tween 20 (v/v)
0.02% Aptamer NTQ21-46 A 0.222 .mu.M ZO5D Polymerase 0.9 U/.mu.L
(45 U/rxn) UNG 0.2 U/.mu.L (10 U/rxn) Sodium Azide (w/v) 0.027
dCTPs 400 .mu.M dGTPs 400 .mu.M dATPs 400 .mu.M dUTPs 800 .mu.M
Primers/probes selected from SEQ ID NOs 1-35 0.1 .mu.M-0.3 .mu.M
SEQ ID NO 50 0.3 .mu.M SEQ ID NO 51 0.3 .mu.M SEQ ID NO 52
.mu.M
Analytical Sensitivity/LOD
[0404] A dilution panel was prepared with HIV-1M Secondary Standard
in HIV-1 negative EDTA plasma for sample input volumes of 200 .mu.L
and 500 .mu.L. Each concentration level was tested with 21
replicates. At least .gtoreq.20 replicates have to be valid. The
LOD was determined by PROBIT analysis at 95% hit rate and by
.gtoreq.95% hit rate analysis.
TABLE-US-00047 TABLE 21 LOD analysis for 200 .mu.L input volume in
EDTA-plasma Number of Number of Concentration replicates positives
Hit rate 200 cp/mL 21 21 100% 100 cp/mL 21 21 100% 80 cp/mL 21 21
100% 50 cp/mL 21 20 95.2% 30 cp/mL 21 18 85.7% 20 cp/mL 21 17 81.0%
10 cp/mL 21 8 38.1% 0 cp/mL (neg. control) 21 0 0% LOD by PROBIT
analysis (95% hitrate) 41.8 cp/mL 95% confidence interval for LOD
by PROBIT 30.9-74.9 analysis cp/mL
TABLE-US-00048 TABLE 22 LOD analysis for 500 .mu.L input volume
Number of Number of Concentration replicates positives Hit rate 30
cp/mL 21 21 100% 25 cp/mL 21 20 95.2% 20 cp/mL 21 21 100% 13.5
cp/mL 21 18 85.7% 9 cp/mL 21 13 61.9% 6 cp/mL 21 9 42.9% 0 cp/mL
(neg. control) 21 0 0% LOD by PROBIT analysis (95% hitrate) 18.9
cp/mL 95% confidence interval for LOD by PROBIT 14.9-29.4 analysis
cp/mL
Summary LOD
[0405] 1. The PROBIT analysis at 95% hit rate resulted in an LOD of
41.8 cp/mL for 200 .mu.L input volume and 18.9 cp/mL for 500 .mu.L
input volume. 2. The 95% confidence interval range for these
concentrations was 30.9-74.9 cp/mL for 200 .mu.L input volume and
14.9-29.4 cp/mL for 500 .mu.L input volume.
Linearity
[0406] The samples used in the Linearity/Dynamic Range/Accuracy
study consisted of a dilution panel of an HIV-1 cell culture
supernatant material, HIV-1 group M subtype B.
[0407] The linearity panel was prepared by serial dilution. This
panel was analyzed at 10 concentration levels.
[0408] The concentrations were selected as follows: One level below
expected Lower Limit of Quantitation (LLoQ), one at LLoQ, one above
LLoQ, several concentrations at intermediate levels, at expected
Upper Limit of Quantitation (ULoQ) and one above ULoQ. For all
concentrations 21 replicates were tested. The linearity study was
done with 500 .mu.L input volume):
PM 1-2.0E+07 cp/mL--above expected ULoQ PM 2-1.0E+07 cp/mL--at
expected ULoQ PM 3-1.0E+06 cp/mL--below expected ULoQ PM 4-1.0E+05
cp/mL--intermediate concentration level PM 5 3.0E+04
cp/mL--intermediate concentration level for titer assignment PM
6-1.0E+04 cp/mL--intermediate concentration level PM 7-1.0E+03
cp/mL--intermediate concentration level PM 8-1.0E+02
cp/mL--intermediate concentration level PM 9-5.0E+01 cp/mL--above
expected LLoQ PM 10-2.0E+01 cp/mL--at expected LLoQ PM 11-1.5E+01
cp/mL below expected LLoQ
TABLE-US-00049 TABLE 23 Linearity in EDTA Plasma Nominal Assigned
Mean Titer Titer Assigned Log 10 Titer Repli- (cp/mL) (cp/mL) Log10
Titer observed cates 1.50E+01 1.50E+01 1.2 1.3 21 2.00E+01 2.00E+01
1.3 1.5 21 5.00E+01 5.10E+01 1.7 1.8 21 1.00E+02 1.00E+02 2 2 21
1.00E+03 1.00E+03 3 3 21 1.00E+04 1.00E+04 4 4 21 1.00E+05 1.00E+05
5 5 21 1.00E+06 1.00E+06 6 6 21 1.00E+07 1.00E+07 7 7 21 2.00E+07
2.00E+07 7.3 7.4 21
[0409] A graphical depiction of this result is shown in FIG.
17.
Summary Linearity
[0410] The linear range, defined as the concentration range for
which the log 10 deviation of the mean log 10 observed titers is
within .+-.0.3 of the log 10 nominal titer was determined as
1.5E+01 cp/mL-2.0E+07 cp/mL
[0411] It is understood that the examples and embodiments described
herein are for illustrative purposes only and that various
modifications or changes in light thereof will be suggested to
persons skilled in the art and are to be included within the spirit
and purview of this application and scope of the appended claims.
All publications, sequence accession numbers, patents, and patent
applications cited herein are hereby incorporated by reference in
their entirety for all purposes.
Sequence CWU 1
1
76129DNAArtificial Sequenceprimer/probe 1agtgggggga catcaagcag
ccatgcaaa 29230DNAArtificial Sequenceprimer/probe 2agtgggggga
catcaagcag ccatgcaaat 30323DNAArtificial Sequenceprimer/probe
3gctttcagcc cagaagtaat acc 23425DNAArtificial Sequenceprimer/probe
4ggacacatca agcagccatg caaat 25520DNAArtificial
Sequenceprimer/probe 5agagaaccaa ggggaagtga 20628DNAArtificial
Sequenceprimer/probe 6ataatccacc tatcccagta ggagaaat
28729DNAArtificial Sequenceprimer/probe 7agtgggggga caccaggcag
caatgcaaa 29820DNAArtificial Sequenceprimer/probe 8catagcagga
actactagta 20930DNAArtificial Sequenceprimer/probe 9ggtactagta
gttcctgcta tgtcacttcc 301025DNAArtificial Sequenceprimer/probe
10ctatgtcact tccccttggt tctct 251130DNAArtificial
Sequenceprimer/probe 11ggtactagta gttcctgcta tatcacttcc
301220DNAArtificial Sequenceprimer/probe 12tccttgtctt atgtccagaa
201328DNAArtificial Sequenceprimer/probe 13tttggtcctt gtcttatgtc
cagaatgc 281428DNAArtificial Sequenceprimer/probe 14tactagtagt
tcctgctatg tcacttcc 281523DNAArtificial Sequenceprimer/probe
15tgtgttatga tggtgtttaa atc 231620DNAArtificial
Sequenceprimer/probe 16actctaaagg gttcctttgg 201733DNAArtificial
Sequenceprimer/probe 17tctgcagctt cctcattgat ggtatctttt aac
331829DNAArtificial Sequenceprimer/probe 18tcagcattat cagaaggagc
caccccaca 291932DNAArtificial Sequenceprimer/probe 19tctgcagctt
cctcattgag gtatctttta ac 322041DNAArtificial Sequenceprimer/probe
20atcctgggat taaataaaat agtaagaatg tatagcccta c 412129DNAArtificial
Sequenceprimer/probe 21accatcaatg agggaagctg cagaatggg
292226DNAArtificial Sequenceprimer/probe 22tgactctggt aactagagat
ccctca 262330DNAArtificial Sequenceprimer/probe 23tgttcaaccc
tggtatctag agatccctca 302420DNAArtificial Sequenceprimer/probe
24ggctaactag ggacccactg 202518DNAArtificial Sequenceprimer/probe
25actagggaac ccactgct 182626DNAArtificial Sequenceprimer/probe
26tcagcaagcc gagtcctgcg tcgaga 262727DNAArtificial
Sequenceprimer/probe 27ccgctaagcc gagccctttg cgtcgga
272817DNAArtificial Sequenceprimer/probe 28ggtctgaggg atctcta
172924DNAArtificial Sequenceprimer/probe 29ctgctagaga ttttccacac
tgac 243023DNAArtificial Sequenceprimer/probe 30ggctccacgc
ttgcttgctt aaa 233118DNAArtificial Sequenceprimer/probe
31ggctccacgc ttgcttgc 183231DNAArtificial Sequenceprimer/probe
32ttcccaaagc aagaagggtc ctaacagacc a 313328DNAArtificial
Sequenceprimer/probe 33tctctagcag tggcgcccga acagggac
283434DNAArtificial Sequenceprimer/probe 34accagagtca cacaacagac
gggcacacac tact 343531DNAArtificial Sequenceprimer/probe
35tcctagtcgc cgcctggtca ttcggtgttc a 313625DNAArtificial
Sequenceprimer/probe 36catgcaactt tttcacctct gccta
253727DNAArtificial Sequenceprimer/probe 37aactccacag tagctccaaa
ttcttta 273833DNAArtificial Sequenceprimer/probe 38ccaagctgtg
ccttgggtgg ctttggggca tgg 333923DNAArtificial Sequenceprimer/probe
39gggattcctg taacaacaag tca 234024DNAArtificial
Sequenceprimer/probe 40tcttccccag aacaataaga acac
244126DNAArtificial Sequenceprimer/probe 41ggcttgcaga gttctatagt
gctatg 264225DNAArtificial Sequenceprimer/probe 42ttgatagcaa
tcggctatcg actaa 254328DNAArtificial Sequenceprimer/probe
43gcttcgatac tcagtcatct cggtataa 284427DNAArtificial
Sequenceprimer/probe 44tctctcgcca tctcctaccg cattggc
2745269DNAArtificial Sequenceinternal control nucleic acid
45aattcaagct tagatctagc tttgcctgct tgatagcaat cggctatcga ctaatgactg
60tcctggcggt ctctcgccat ctcctaccgc attggctcat aggtaagctc gctgtcaccc
120agtacggagg tgccagtaga ttattagaga cagtcgccaa tcgatcgtta
taccgagatg 180actgagtatc gaagctacat tgtagccgca cataggacca
cccatcttca tgttgaaaca 240tgaggattac ccatgtggat ccaagcttg
26946235DNAArtificial Sequenceinternal control nucleic acid
46gggctgcagg tcgactctag attctaagaa tttgatgggc tttttctact aattactatt
60agtatattgc catctttaac acttagaccg aagtgtgctg aagttccagt ggccggccca
120gacctgggaa gttgcaagga cttaaacgaa tgcaagcgat catatcttga
aaaattataa 180ccagaggatc gatgaaaaaa atttcttaga gctttggatc
cccgggcgag ctccc 23547350DNAArtificial Sequenceinternal control
nucleic acid 47cgactctaga tgaagggagc cttagaacgg ggctgcgcta
gctggcatca aagtccgtca 60gagctcaacc ctccaacgag gattcctgaa tactcgaaag
tcagtgtgca gttactaaca 120acagctgctc gacctcgggg tctcgaacaa
tccatacctg ctatcgctgc cttcagacat 180acggatgggc taggaggcaa
gagctacctg tctcaacgaa ctatcggagt gggacccgat 240gaagctgtca
gcgccacttc cggcggtaag gctttaaaac gcgcccgccg gttatcacgc
300gcggggagca cagcgcggac tgacgtgctg ggaagcaccg gttaaggatc
35048470DNAArtificial Sequenceinternal control nucleic acid
48cgactctaga aactgggtag taactgcggg ggcgaatgat gcaggcttca gaaattaaac
60tcaatagtat ccggtgtctc aatctttttc gggccaggcg gcggtggacg acagacaatt
120ttacgatttt ggttccggtc acaaccgcgc catacatgtc aagaatgaag
tgggcgaacg 180ctagaaaact gacgccagca attaagtgag tcggggcgtg
gtgactccca cgtaaaaagc 240ccctaccccg caccgttacg aagtatcaaa
acgggacgcg cacgaaccga cgattggtac 300tgtataagcg gcccgacgaa
ctcaaaatcc caagtgaatc tatgaaatct acatcgcgtt 360tataatctac
ggggtgtaaa cggatgagaa ttggccaaac ggaggcacac acgcgtgcaa
420tgcgccgacc ctgagaaaag tatcatgtgc gtcggccaca ggatccccgg
47049350DNAArtificial Sequenceinternal control nucleic acid
49cgactctaga tgaagggagc cttagaacgg ggctgcgcta gctggcatca aagtccgtca
60gagctcaacc ctccaacgag gattcctgaa tactcgaaag tcagtgtgca gttactaaca
120acagctgctc gacctcgggg tctcgaacaa tccatacctg ctatcgctgc
cttcagacat 180acggatgggc taggaggcaa gagctacctg tctcaacgaa
ctatcggagt gggacccgat 240gaagctgtca gcgccacttc cggcggtaag
gctttaaaac gcgcccgccg gttatcacgc 300gcggggagca cagcgcggac
tgacgtgctg ggaagcaccg gttaaggatc 3505025DNAArtificial
Sequenceprimer/probe 50acaaccgcgc catacatgtc aagaa
255124DNAArtificial Sequenceprimer/probe 51gtcgggccgc ttatacagta
ccaa 245232DNAArtificial Sequenceprimer/probe 52gccagcaatt
aagtgagtcg gggcgtggtg ac 325352DNAArtificial Sequenceprimer/probe
53caacaaaaca gcatattgac acctgggagt agactaggag atcttctgct ct
525430DNAArtificial Sequenceprimer/probe 54tctcctagtc tttcccaggt
gtcaatatgc 305527DNAArtificial Sequenceprimer/probe 55ctgccccagg
aggactgggt taacaaa 275623DNAArtificial Sequenceprimer/probe
56tcctagtcta tcccaggtgt caa 235725DNAArtificial
Sequenceprimer/probe 57gtaagccctc agaaccgtct cggaa
255828DNAArtificial Sequenceprimer/probe 58ggactagagg ttagaggaga
ccccgagg 285928DNAArtificial Sequenceprimer/probe 59aaggactaga
ggttagagga gaccccgc 286021DNAArtificial Sequenceprimer/probe
60aaacccactc tatgtccggt c 216121DNAArtificial Sequenceprimer/probe
61gtacgccgga attgccggaa a 216221DNAArtificial Sequenceprimer/probe
62cctcaaagaa aaaccaaaag a 216326DNAArtificial Sequenceprimer/probe
63gcagaaagcg tctagccatg gcgtta 266424DNAArtificial
Sequenceprimer/probe 64gcagaaagcg tctagccatg gcgt
246521DNAArtificial Sequenceprimer/probe 65tggcgtctcc cacgcggctg g
216621DNAArtificial Sequenceprimer/probe 66ctttccccag gacctgccgg t
216725DNAArtificial Sequenceprimer/probe 67gcaagcaccc tataggcagt
accac 256824DNAArtificial Sequenceprimer/probe 68ctcgcaagca
ccctatcagg cagt 246928DNAArtificial Sequenceprimer/probe
69gcaagcaccc tatcaggcag taccacaa 287027DNAArtificial
Sequenceprimer/probe 70gcaagcaccc tatcaggcag taccaca
277124DNAArtificial Sequenceprimer/probe 71ttgccggaaa gactgggtcc
tttc 247224DNAArtificial Sequenceprimer/probe 72ttgccggaaa
gactgggtcc tttc 247324DNAArtificial Sequenceprimer/probe
73ccagcccatc ccgaaagatc ggcg 247418DNAArtificial
Sequenceprimer/probe 74tgtccggtca tttgggcg 187533DNAArtificial
Sequenceprimer/probe 75ccgggagagc catagtggtc tgcggaaccg gtg
337628DNAArtificial Sequenceprimer/probe 76tctctcgccc atctcctacc
gcattggc 28
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