Roche cobas s 201 system User manual

Brand: Roche

Model: cobas s 201 system

Type: User manual

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

(M), vertical pool results P

(N), and

interpretation of the donor results at the intersection, (R

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

Roche cobas s 201 system User manual

Roche cobas s 201 system User manual

Roche cobas s 201 system User manual

Related papers

Other documents