Roche cobas s 201 system is a high-throughput molecular diagnostics system designed to meet the needs of large-scale testing laboratories. It enables efficient and reliable testing for infectious diseases, genetic disorders, and other molecular targets. The system features advanced automation, allowing for walk-away sample processing and real-time monitoring of test progress. With its ability to perform a wide range of molecular assays, the cobas s 201 system offers versatility and flexibility for various testing needs.
Roche cobas s 201 system is a high-throughput molecular diagnostics system designed to meet the needs of large-scale testing laboratories. It enables efficient and reliable testing for infectious diseases, genetic disorders, and other molecular targets. The system features advanced automation, allowing for walk-away sample processing and real-time monitoring of test progress. With its ability to perform a wide range of molecular assays, the cobas s 201 system offers versatility and flexibility for various testing needs.
07/2008, version 1.0 1.1
Pooling Algorithms 1
Overview
The cobas s 201 system can be configured to create large pools. Large
pools contain equal aliquots from n donor samples.
n is either 24, 48, or 96.
Large pools are only used for MPX testing.
Primary Pooling
Primary Pooling for large pools is a two step process:
1 Plate Run - Pool n (MPX): Interim pools, each containing aliquots from
12 donor samples, are created in Intermediate Plate wells. In the default
configuration, the cobas s 201 system also prepares a Library Plate to save
an aliquot from each donor tube in case secondary testing is required.
2 Batch Run - Pool n (MPX): Controls are pipetted, then equal aliquots
from the Intermediate Plate wells are combined into S-tubes to create
pools containing 24 (two wells), 48 (four wells), or 96 (eight wells)
samples.
Secondary Pooling
Follow-up (secondary) testing is required if test results on a large Primary
Pool are invalid or reactive. The following Secondary Pooling options are
available:
• Repeat Batch Run - Pool n (MPX): Step 2 of the Primary Pooling
run is repeated to retest donor samples from pools with test results
that are invalid.
• Two-dimensional (2D) Pooling (MPX): A matrix of donor pools is
created where each donor sample is pipetted into a unique set of
two separate pools such that if these two pools are reactive, the
results can be attributed to a particular donor sample.
• Confirmation Pooling (MPX): Single-specimen pools are created
to confirm suspected reactive donor samples, and the remaining
samples are pooled in four-, six-, eleven-, or twelve-specimen pools
to confirm non-reactive test results.
• Resolution Pooling (MPX): Single-specimen pools are prepared to
individually test samples from invalid or reactive pools.
1.2 07/2008, version 1.0
Workflow Path
The default workflow path for testing samples in Large Pools is shown in
(Figure 1.1).
The paths in Figure 1.1 are assigned by the system. The laboratory
administrator can elect to change the default workflow path and
use for example Resolution Pooling to retest samples from reactive
or invalid pools (see Changing the Pooling Request in the cobas s 201
system Hardware and Software Reference Manual).
Figure 1.1
Workflow Path for Large Pools
Pooling Algorithms
07/2008, version 1.0 1.3
Plate Run
The Plate Run is the first step in the Primary Pooling process. Samples
that are successfully pipetted into an Intermediate Plate during the Plate
Run are scheduled for a Batch Run, the second step in the Primary Pooling
Process.
Samples with pipetting errors are scheduled for Resolution Pooling
(Figure 1.19) if they were successfully aspirated, otherwise they are eligible
for another Plate Run (Figure 1.2).
Figure 1.2
Plate Run
1.4 07/2008, version 1.0
Batch Run
The Batch Run is the second step in the Primary Pooling process. Samples
that are successfully pipetted into a Large Pool during the Batch Run are
tested for the presence of the screening analyte (Figure 1.3).
• All donor samples in the pool are reported as non-reactive if the
pool is non-reactive.
• If the pool is reactive, and it contains the expected 96, 48, or 24
samples, then donor samples in the pool are scheduled for
2D Pooling (Figure 1.4).
• If the pool is reactive, but it contains less than the planned 96, 48,
or 24 samples (due to pipetting errors), then donor samples in the
Short Pool are scheduled for Confirmation Pooling (Figure 1.18).
• Another Batch Run (a Repeat Batch Run) is scheduled if the test
result is invalid.
Samples with pipetting errors are scheduled for Resolution Pooling.
Figure 1.3
Batch Run
Pooling Algorithms
07/2008, version 1.0 1.5
2D Pooling
2D Pooling is scheduled if the test result on a Primary Pool or Repeat
Batch Pool is reactive and the pool contains the full complement (24, 48,
or 96) of donor samples.
The laboratory administrator can also elect to use 2D Pooling
instead of a Repeat Batch Run to retest an invalid Primary Pool.
2D Pooling creates a matrix of donor pools where each donor sample from
the original pool is pipetted into a unique set of two separate pools.
Results for the two pools are evaluated to determine whether the donor
sample is non-reactive or whether Resolution Pooling is required
(Figure 1.4).
The number of pools in the 2D matrix depends on the size of the starting
Primary Pool:
Figure 1.4
2D Pooling
Primary Pool Size Number of 2D Pools MxN
24 4 pools of 6 specimens
6 pools of 4 specimens
4x6
48 8 pools of 6 specimens
6 pools of 8 specimens
8x6
96 Two batches each containing:
8 pools of 6 specimens
6 pools of 8 specimens
8x6
(two matrices)
1.6 07/2008, version 1.0
2D Matrix Evaluation
The evaluation of the MxN 2D pooling matrix is based on examination of
the horizontal pool results, P
H
(M), vertical pool results P
V
(N), and
interpretation of the donor results at the intersection, (R
h,
R
v
).
The diagrams on the following pages depict different 2D pooling matrix
scenarios. The circles (shown on the outside of the matrix) contain the
pool (S-tube) test results. The squares (shown on the inside of the matrix)
are the donor results that are interpreted based on the test results for the
two pools in which the donor sample was tested.
A 6x4 matrix is used in all the examples.
Figure 1.5
2D Pooling Evaluation Overview
Horizontal Result
Intersection Represents
Vertical Result
One Donor Sample
Pooling Algorithms
07/2008, version 1.0 1.7
Example 1
All 2D pools test non-reactive (-). All intersections (-,-) are interpreted as
non-reactive. All donor samples are reported as Complete, Non-Reactive
(Figure 1.6).
Example 2
One horizontal and one vertical 2D pool test reactive (+). All other 2D
pools test non-reactive (-). The donor sample at the intersection of the
reactive pools (+,+) is scheduled for Resolution Pooling. All remaining
intersections [(-,-), (+,-), (-,+)] are interpreted as non-reactive and these
donor samples are marked Complete, Non-Reactive (Figure 1.7).
Figure 1.6
2D Matrix Example 1
Figure 1.7
2D Matrix Example 2
Schedule for Resolution Pooling
1.8 07/2008, version 1.0
Example 3
One horizontal and one vertical 2D pool test invalid (I). All other 2D
pools test non-reactive (-). The donor sample at the intersection of the
invalid pools (I,I) is scheduled for Resolution Pooling. All remaining
intersections [(-,-), (I,-), (-,I)] are interpreted as non-reactive and these
donor samples are marked Complete, Non-Reactive (Figure 1.8).
Example 4
One horizontal 2D pool tests reactive (+) and one vertical 2D pool tests
invalid (I) (or vice versa). All other 2D pools test non-reactive (-). The
donor sample at the intersection of the reactive pool and invalid pool
[(+,I) or (I,+)] is scheduled for Resolution Pooling. All remaining
intersections [(-,-), (+,-), (-,+), (-,I), (I,-)] are interpreted as non-reactive
and these donor samples are marked Complete, Non-Reactive
(Figure 1.9).
Figure 1.8
2D Matrix Example 3
Schedule for Resolution Pooling
Figure 1.9
2D Matrix Example 4
Schedule for
Resolution Pooling
Pooling Algorithms
07/2008, version 1.0 1.9
Example 5
One horizontal 2D pool and two vertical 2D pools (or vice versa) test
reactive (+). All other 2D pools test non-reactive (-). The donor samples
at the (+,+) intersections are scheduled for Resolution Pooling. All
remaining intersections [(-,-), (+,-), (-,+)] are interpreted as non-reactive
and these donor samples are marked Complete, Non-Reactive
(Figure 1.10).
Example 6
One horizontal and one vertical 2D pool test reactive (+). One 2D pool (in
any direction) tests invalid (I). All other 2D pools test non-reactive (-).
The donor samples at the [(+,+), (+,I), (I,+)] intersections are scheduled
for
Resolution Pooling
. All remaining intersections [(-,-), (+,-), (-+),
(-,I), (I,-)] are interpreted as non-reactive and these donor samples are
marked Complete, Non-Reactive (Figure 1.11).
Figure 1.10
2D Matrix Example 5
Schedule for
Resolution Pooling
Figure 1.11
2D Matrix Example 6
Schedule for
Resolution Pooling
1.10 07/2008, version 1.0
Example 7
Two vertical 2D pools test reactive (+) and one horizontal 2D pool tests
invalid (I) (or vice versa). All other 2D pools test non-reactive (-). The
donor samples at the [(I,+), (+,I)] intersections are scheduled for
Resolution Pooling. All remaining intersections [(-,-), (-,+), (+,-), (-,I),
(I,-)] are interpreted as non-reactive and these donor samples are marked
Complete, Non-Reactive (Figure 1.12).
Example 8
All 2D pools test invalid (I) or are rejected by the user. The entire grid is
invalid. All donor samples are scheduled for (repeat) 2D Pooling
(Figure 1.13).
A repeat 2D Pool is only available when all 2D pools are invalid.
Figure 1.12
2D Matrix Example 7
Schedule for
Resolution Pooling
Figure 1.13
2D Matrix Example 8
Pooling Algorithms
07/2008, version 1.0 1.11
Example 9
One horizontal 2D pool tests reactive (+). There is no corresponding
reactive test for a vertical 2D pool. All other 2D pools test non-reactive (-).
The donor samples at the (+,-) intersections are scheduled for Resolution
Pooling. All remaining intersections, (-,-), are interpreted as non-reactive
and these donor samples are marked Complete, Non-Reactive
(Figure 1.14).
Example 10
One vertical 2D pool tests reactive (+). There is no corresponding reactive
test for a horizontal 2D pool. All other 2D pools test non-reactive (-). The
donor samples at the (-,+) intersections are scheduled for Resolution
Pooling. All remaining intersections, (-,-), are interpreted as non-reactive
and these donor samples are marked Complete, Non-Reactive
(Figure 1.15).
Figure 1.14
2D Matrix Example 9
Schedule for Resolution Pooling
Figure 1.15
2D Matrix Example 10
Schedule for Resolution Pooling
1.12 07/2008, version 1.0
Example 11
One horizontal 2D pool tests invalid (I). There is no corresponding invalid
test for a vertical 2D pool. All other 2D pools test non-reactive (-). The
donor samples at the (I,-) intersections are scheduled for Resolution
Pooling. All remaining intersections, (-,-), are interpreted as non-reactive
and these donor samples are marked Complete, Non-Reactive
(Figure 1.16).
Example 12
One vertical 2D pool tests invalid (I). There is no corresponding invalid
test for a horizontal 2D pool. All other 2D pools test non-reactive (-). The
donor samples at the (-,I) intersections are scheduled for Resolution
Pooling. All remaining intersections, (-,-), are interpreted as non-reactive
and these donor samples are marked Complete, Non-Reactive
(Figure 1.17).
Figure 1.16
2D Matrix Example 11
Schedule for Resolution Pooling
Figure 1.17
2D Matrix Example 12
Schedule for Resolution Pooling
Pooling Algorithms
07/2008, version 1.0 1.13
Confirmation Pooling
Confirmation Pooling is scheduled instead of 2D Pooling if a reactive
Primary Pool contains fewer than the expected number of samples due to
pipetting error(s).
The laboratory administrator can also elect to use Confirmation
Pooling instead of 2D Pooling. However, once 2D Pooling has been
initiated the 2D Pooling algorithm must be followed to completion.
Confirmation Pooling allows some samples to be tested individually (e.g.,
to confirm positive serology test results). The potentially reactive donor
samples are identified before Confirmation Pooling begins (see Exclude
Donors tab in the cobas s 201 system Hardware and Software Reference
Manual). These samples are pipetted into single-specimen pools. The
remaining samples are pipetted into smaller pools. All the pools are tested
for the presence of the screening analyte (Figure 1.18).
• The donor sample is reported as non-reactive if a single-specimen
pool is non-reactive.
• All donor samples in the pool are reported as non-reactive if a
multi-specimen pool is non-reactive.
• The donor sample is reported as reactive if a single-specimen pool
is reactive.
• All donor samples in the pool are scheduled for testing in
Resolution Pooling (Figure 1.19) if a multi-specimen pool is
reactive.
• Confirmation Pooling can be repeated if the test result is invalid.
Figure 1.18
Confirmation Pooling
1.14 07/2008, version 1.0
Resolution Pooling
Resolution Pooling is scheduled for samples with pipetting errors during
the Primary Pooling run and for samples in a reactive Confirmation Pool
or a reactive 2D Pool. Each Resolution Pool contains an aliquot of a single
donor sample.
The laboratory administrator can also elect to use Resolution
Pooling to resolve invalid or reactive results.
Resolution Pools are tested for the presence of the screening analyte(s)
(Figure 1.19).
• The donor sample is reported as non-reactive if the Resolution Pool
is non-reactive.
• The donor sample is reported as reactive if the Resolution Pool is
reactive.
• The donor sample must be included in another Resolution Pool if
the Resolution Pool is invalid.
Figure 1.19
Resolution Pooling
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Roche cobas s 201 system is a high-throughput molecular diagnostics system designed to meet the needs of large-scale testing laboratories. It enables efficient and reliable testing for infectious diseases, genetic disorders, and other molecular targets. The system features advanced automation, allowing for walk-away sample processing and real-time monitoring of test progress. With its ability to perform a wide range of molecular assays, the cobas s 201 system offers versatility and flexibility for various testing needs.
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