TruSight Tumor Sample Prep Experienced User Card (15038313 B)

TruSight Tumor Sample Prep Experienced User Card (15038313 B)

TruSight Tumor Sample Preparation

Experienced User Card

FOR RESEARCH USE ONLY

Date: __________________________

Illumina Kit Lot #: __________________________

Description: ______________________________________

_________________________________________________

NOTE

Unless familiar with the protocol in the latest version of the TruSight Tumor Sample Preparation

Guide (part # 15042911), new or less experienced users are strongly advised to follow the protocol in the guide before using this Experienced User Card.

ILLUMINA PROPRIETARY

Catalog # FC-130-9004DOC

Part # 15038313 Rev. A

May 2013

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TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

Consumables

Item

Amplicon Control DNA 1 (ACD1)

Amplicon Control Oligo Pool 1 (ACP1)

Oligo Hybridization for Sequencing Reagent 3 (OHS3)

Extension Ligation Mix 3 (ELM3)

PCR Master Mix 2 (PMM2)

TruSeq DNA Polymerase 1 (TDP1)

Stringent Wash 1 (SW1)

Universal Buffer 1 (UB1)

Quality Control Primers (QCP)

TruSight Tumor Oligo Pool A (FPA)

TruSight Tumor Oligo Pool B (FPB)

Quality Control Template (QCT)

Hybridization Buffer (HT1)

Elution Buffer with Tris (EBT)

80% Ethanol

Lot Number

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Date Prepared: ______________

Page 2 of 30

Part # 15038313 Rev. A

TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

Index 1 Primers

Index Primer A701

Index Primer A702

Index Primer A703

Index Primer A704

Index Primer A705

Index Primer A706

Index Primer A707

Index Primer A708

Index Primer A709

Index Primer A710

Index Primer A711

Index Primer A712

Index 2 Primers

Index Primer A501

Index Primer A502

Index Primer A503

Index Primer A504

Index Primer A505

Index Primer A506

Index Primer A507

Index Primer A508

Lot Number

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot Number

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Lot #: _____________________

Part # 15038313 Rev. A

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TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

Qualification of DNA Extracted from FFPE Samples

During this step, a qPCR reaction will be performed to determine the amplifiability of your FFPEextracted gDNA samples. By comparing the amplifiability of FFPE DNA relative to that of the

QCT non-FFPE reference gDNA, a ΔCq value can be calculated for each sample and used to predict its performance in the TruSight Tumor Sample Preparation assay. The exact amount of

FFPE DNA input will vary according to the quality of the extracted DNA.

Estimated Time

} Total duration: 3 hours

}

Hands-on: 60 minutes

Consumables

Item

QCT (Quality Control Template)

QCP (Quality Control Primer)

Genomic DNA

KAPA SYBR FAST Master Mix

Universal (2x)

(Other qPCR mixes can be used but should be tested.)

Nuclease-free water

48 or 96-well plate

Quantity

1 tube

1 tube

As needed

1 plate

As needed

1 plate

Storage

-15° to -25°C

-15° to -25°C

-15° to -25°C

-15° to -25°C

Supplied By

Illumina

Illumina

User

User

User

User

Sample Sheet Name: ________________________________________________

Preparation

[_] 1 Remove the QCT, QCP, KAPA SYBR FAST Master Mix Universal (2x), and genomic DNA from -15° to -25°C storage and thaw at room temperature for up to 30 minutes.

Start time: _____________________ Stop time: _____________________

[_] 2 Place thawed tubes on ice.

[_] 3 If using QCT for the first time, aliquot 5 µl of QCT into different PCR strip tubes for longterm storage to avoid freeze-thawing.

Procedure

[_] 1 Add 5 µl of QCT to 495 µl of Nuclease-free water in a microfuge tube.

[_] 2 Vortex the dilution to thoroughly mix the sample.

[_] 3 Add 1 µl of QCP to 9 µl of Nuclease-free water in a microfuge tube.

NOTE

Make a larger dilution if qualifying more than one genomic DNA sample.

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Part # 15038313 Rev. A

TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

[_] 4 Vortex the dilution to thoroughly mix the sample.

[_] 5 Add 1.5 µl of Qiagen-extracted genomic DNA to 148.5 µl of Nuclease-free water in microfuge tubes to make a 100-fold dilution.

[_] 6 Vortex the dilutions to thoroughly mix the samples.

[_] 7 Determine the plate layout of the qPCR reaction. For 10 samples, Illumina recommends this plate layout:

A

B

C

D

E

F

1

QCT

QCT

QCT

NTC*

NTC*

NTC*

2

Sample 1

Sample 1

Sample 1

Sample 2

Sample 2

Sample 2

3

Sample 3

Sample 3

Sample 3

Sample 4

Sample 4

Sample 4

4

Sample 5

Sample 5

Sample 5

Sample 6

Sample 6

Sample 6

5

Sample 7

Sample 7

Sample 7

Sample 8

Sample 8

Sample 8

6

Sample 9

Sample 9

Sample 9

Sample 10

Sample 10

Sample 10

NTC: No template control. Illumina recommends using nuclease-free water.

[_] 8 Prepare the SYBR master mix reaction as follows. The master mix contains extra volume:

Table 1 SYBR Master Mix Reactions

Consumable

µl per well

KAPA SYBR FAST Master

Mix Universal (2x)

QCP

Nuclease-free water

5.0 µl

1.0 µl

2.0 µl

µl per plate

(48-wells)

275 µl

55 µl

110 µl

µl per plate

(96-wells)

550 µl

110 µl

220 µl

[_] 9 Mix gently but thoroughly.

[_] 10 Place the reaction mix on ice and protect it from light until use.

[_] 11 Add 8 µl of the master mix to each well of the plate. Take care to pipette accurately into the wells as small variations will affect the assay.

[_] 12 Add 2 µl of the QCT dilution, the sample dilutions, or nuclease-free water to each well of the plate. Take care to pipette accurately into the wells as small variations will affect the assay.

[_] 13 Seal the plate with the appropriate seal (depending on the instrument that you are using), taking care to avoid cross-contamination and to avoid smudging the surface of the lids.

[_] 14 Place the plate on an adapter (if needed) and centrifuge the plate to 250 xg for 1 minute.

Part # 15038313 Rev. A

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TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

[_] 15 Ensure the seal is free of any liquid or dust, place the plate on the qPCR machine in the correct orientation, then close the lid and run the following thermal profile:

Procedure

Hot Start x40

Temperature

50°C

95°C

95°C

60°C

72°C

Time

2 minutes

10 minutes

30 seconds

30 seconds

30 seconds

[_] 16 Confirm that the instrument captures images after the 72°C step.

NOTE

The Cq threshold should be set to a value that avoids inaccurate measurements due to background (100 RFU on the BioRad 396CFX System).

[_] 17 After the final step, the thermal cycler analyzes the quantified libraries. Make sure that amplification of the NTC occurs at least 10 cycles after QCT amplification.

[_] 18 Ensure that there is good amplification for the QCT and remove outliers from a triplicate group that are > 0.5 Cq different from the rest of the group.

NOTE

Four or more outliers per plate indicate technical errors.

[_] 19 Replicates exhibiting abnormal amplification curves should be excluded (see Illumina sequencing white paper, Generating Sequencing Libraries Using DNA from FFPE Samples for more details).

[_] 20 Subtract the average Cq for the QCT from the average Cq for each sample to yield the ΔCq values for each sample.

Comments

__________________________________________________________________________________

__________________________________________________________________________________

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Part # 15038313 Rev. A

TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

Hybridization of Oligo Pool

During this step, a custom pool containing upstream and downstream oligos specific to your targeted regions of interest is hybridized to your genomic DNA samples.

NOTE

Illumina does not support the use of gDNA samples giving a delta Cq value of greater than

4.

Estimated Time

}

Total duration: 14–18 hours (overnight)

}

Hands-on: 15 minutes

Consumables

Item

TruSight Tumor Sample

Preparation Oligo Pools (FPA,

FPB)

OHS3 (Oligo Hybridization for Sequencing 3)

Genomic DNA

96-well skirted PCR plate

[Optional] Adhesive aluminum foil seal if a heat sealer is not available

Troughs

Quantity

1 tube per pool

1 tube

As needed

1 plate

2 seals

As needed

Storage

-15° to -25°C

-15° to -25°C

-15° to -25°C

Supplied By

Illumina

Illumina

User

User

User

User

Preparation

[_] 1 Remove the TruSight Tumor Sample Preparation Oligo Pools (FPA, FPB) and genomic DNA from -15° to -25°C storage and thaw at room temperature for up to 30 minutes. Place thawed tubes on ice. If running Illumina-provided controls, thaw ACD1 and/or ACP1 as well.

Start time: _____________________ Stop time: _____________________

[_] 2 Set a 96-well heat block to 95°C.

Part # 15038313 Rev. A

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TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

[_] 3 Remove OHS3 from -15° to -25°C storage and thaw at room temperature. If precipitate is observed, incubate at 37°C for 10 minutes and vortex 1 minute. Repeat as needed until precipitate is no longer visible.

Start time: _____________________ Stop time: _____________________

NOTE

Using the provided controls enables Illumina Technical Support to troubleshoot in the event you need assistance. Illumina technical support recommends including control samples in your assay periodically to establish baselines and monitor overall performance.

NOTE

The control ACP1 is specific for Homo sapiens and will not work with DNA from other species.

Procedure

[_] 1 Label a new 96-well PCR plate "HYP_Plate_ID".

[_] 2 Dilute 10 µl of genomic DNA extracted from FFPE samples. Use the table below to determine the fold dilution required for each calculated delta Cq:

Delta Cq

Dilution

-2.5 to -1.5

16x

-1.5 to -0.5

8x

-0.5 to 0.5

4x

0.5 to 1.5

2x

1.5 to 4

No dilution

NOTE

If preparing libraries from the control DNA in parallel with FFPE DNA samples, dilute 5 µl of ACD1 with 45 µl of TE Buffer. Add 10 µl to each of two control wells for FPA and FPB, and/or two control wells for ACP1.

[_] 3 Add 10 µl of each sample as prepared in step 2 to wells on the left half of the HYP plate, starting with column 1. Then, repeat this process on the right half of the HYP plate, starting with column 7.

[_] 4 Using a multichannel pipette, add 5 µl of oligo pool 1 (FPA) to all sample-containing wells on the left half of the HYP plate. Then, add 5 µl of oligo pool 2 (FPB) to all samplecontaining wells on the right half of the HYP plate. Change tips after each column to avoid contamination.

NOTE

If preparing libraries from ACD1, add 5 µl of FPA to one control well and 5 µl of FPB to the second control well. If preparing libraries using ACP1, add 5 µl of ACP1 to two additional control wells of ACD1.

[_] 5 Using a multichannel pipette, add 35 µl of OHS3 to each sample in the HYP plate. Gently pipette up and down 3–5 times to mix. Change tips after each column to avoid contamination.

NOTE

Ensure any crystals or precipitate in OHS3 have dissolved after following procedure described in Preparation step 3 .

[_] 6 Seal the HYP plate with a heat sealer (Illumina recommends the Agilent PlateLoc Thermal

Microplate Sealer). If a heat sealer is not available use an aluminum foil seal. Centrifuge at

1,000 xg at 20°C for 1 minute.

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Part # 15038313 Rev. A

TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

[_] 7 Place the HYP plate in the pre-heated block at 95°C and incubate for 1 minute.

[_] 8 Change the temperature of the same heat block to 40°C, and incubate for 14–18 hours.

Start time: _____________________ Stop time: _____________________

NOTE

Moving the plate from the 95°C heat block to another pre-heated block set to 40°C will adversely affect hybridization.

Comments

__________________________________________________________________________________

__________________________________________________________________________________

Part # 15038313 Rev. A

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TruSight Tumor Sample Preparation

Experienced User Card

Page 10 of 30

Part # 15038313 Rev. A

TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

Removal of Unbound Oligos

This process removes unbound oligos from genomic DNA using a filter capable of size selection.

Two wash steps using SW1 ensure complete removal of unbound oligos. A third wash step using UB1 removes residual SW1 and prepares samples for the extension-ligation step.

Estimated Time

} Total duration: 20 minutes

}

Hands-on: 20 minutes

Consumables

Item

ELM3 (thawed in preparation for

Extension-Ligation)

SW1 (Stringent Wash 1)

UB1 (Universal Buffer 1)

Filter plate with lid

Adapter collar (reusable)

MIDI plate

Troughs

Quantity

1 tube

1 tube

1 tube

1 plate

1 plate

1 plate

As needed

Storage

-15° to -25°C

2° to 8°C

2° to 8°C

Supplied By

Illumina

Illumina

Illumina

Illumina

Illumina

User

User

Preparation

[_] 1 Remove ELM3 from -15° to -25°C storage and thaw at room temperature.

[_] 2 Remove SW1 and UB1 from 2° to 8°C storage and set aside at room temperature.

[_] 3 Assemble the filter plate assembly unit in the order from top to bottom: Lid, Filter Plate,

Adapter Collar, and MIDI plate. Label the filter plate assembly unit FPU (Filter Plate Unit).

[_] 4 Pre-wash the FPU plate membrane as follows:

[_] a Using a multichannel pipette, add 50 µl of SW1 to each well.

[_] b Cover the FPU plate with the filter plate lid and keep it covered during each centrifugation step.

[_] c Centrifuge the FPU at 2,400 xg at 20°C for 5 minutes.

[_] 5 Pre-heat incubator (not heat block) to 37°C.

Procedure

[_] 1 After the overnight incubation, confirm the heat block has cooled to 40˚C.

NOTE

If the heat block fails to cool to 40˚C overnight, library preparation will need to be repeated.

Part # 15038313 Rev. A

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TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

[_] 2 Remove the HYP plate from the heat block and centrifuge at 1,000 xg at 20°C for 1 minute to collect condensation.

[_] 3 Using a multichannel pipette set to 60 µl, transfer the entire volume of each sample onto the center of the corresponding pre-washed wells of the FPU plate. Change tips after each column to avoid cross-contamination.

[_] 4 Cover the FPU plate with the filter plate lid and centrifuge the FPU at 2,400 xg at 20°C for 5 minutes.

[_] 5 Wash the FPU plate as follows:

[_] a Using a multichannel pipette, add 50 µl of SW1 to each sample well.

[_] b Cover the FPU plate with the filter plate lid and centrifuge the FPU at 2,400 xg for 5 minutes.

[_] 6 Repeat the wash as described in the previous step.

[_] 7 Discard all the flow-through (containing formamide waste and unbound oligos) collected up to this point in an appropriate hazardous waste container, then reassemble the FPU. The same MIDI plate can be re-used for the rest of the pre-amplification process.

[_] 8 Using a multichannel pipette add 45 µl of UB1 to each sample well.

NOTE

Make sure that all liquid has drained after centrifugation. Repeat centrifugation if necessary. Any residual wash buffer may inhibit subsequent enzymatic reactions.

[_] 9 Cover the FPU plate with the filter plate lid and centrifuge the FPU at 2,400 xg for 5 minutes.

Comments

__________________________________________________________________________________

__________________________________________________________________________________

Page 12 of 30

Part # 15038313 Rev. A

TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

Extension-Ligation of Bound Oligos

This process connects the hybridized upstream and downstream oligos. A DNA polymerase extends from the upstream oligo through the targeted region, followed by ligation to the 5’ end of the downstream oligo using a DNA ligase. This results in the formation of products containing the targeted regions of interest flanked by sequences required for amplification.

Estimated Time

} Total duration: 50 minutes

}

Hands-on: 5 minutes

Consumables

Item

ELM3 (Extension-Ligation Mix 3)

Adhesive aluminum foil seal

Troughs

Quantity

1 tube

1 seal

As needed

Storage

-15° to -25°C

Supplied By

Illumina

User

User

Procedure

[_] 1 Using a multichannel pipette, add 45 µl of ELM3 to each sample well of the FPU plate.

[_] 2 Seal the FPU plate with adhesive aluminum foil, and then cover with the lid to secure the foil during incubation.

[_] 3 Incubate the entire FPU assembly in the pre-heated 37°C incubator for 45 minutes. Ensure waste is removed from bottom of the plate.

Start time: _____________________ Stop time: _____________________

[_] 4 While the FPU plate is incubating, prepare the IAP (Indexed Amplification Plate) as described in the following section.

Comments

__________________________________________________________________________________

__________________________________________________________________________________

Part # 15038313 Rev. A

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TruSight Tumor Sample Preparation

Experienced User Card

Page 14 of 30

Part # 15038313 Rev. A

TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

PCR Amplification

In this step, the extension-ligation products are amplified using primers that add index sequences for sample multiplexing (i5 and i7) as well as common adapters required for cluster generation (P5 and P7).

Estimated Time

} Total duration: ~100 minutes (depending on thermocycler)

}

Hands-on: 30 minutes

Consumables

Item

PMM2 (PCR Master Mix 2) i5 primers (A5XX) i7 primers (A7XX)

TDP1

(TruSeq DNA Polymerase 1)

Microseal 'B' adhesive film

0.05 N NaOH (freshly prepared from 10 N NaOH)

96-well skirted PCR plate

Troughs

Quantity

1 tube

1 tube per primer

1 tube per primer

1 tube

1

As needed

1 plate

As needed

Storage

-15° to -25°C

-15° to -25°C

-15° to -25°C

-15° to -25°C

Supplied By

Illumina

Illumina

Illumina

Illumina

User

User

User

User

Preparation

[_] 1 Prepare fresh 0.05 N NaOH by adding 20 µl of 10 N NaOH to 3.98 ml of sterile water.

[_] 2 Remove PMM2 and the index primers (i5 and i7) from -15° to -25°C storage and thaw on a bench at room temperature. Vortex each tube to mix and briefly centrifuge the tubes in a microcentrifuge.

[_] 3 Arrange i5 primer tubes (white caps, clear solution) vertically in the Index Plate Fixture, aligning tubes A501 through A508 with rows A through H.

[_] 4 Arrange i7 primer tubes (orange caps, yellow solution) horizontally in the Index Plate

Fixture, aligning tubes A701 through A712 with columns 1 through 12. Collect all liquid in the bottoms of the tubes by holding them in place in the rack and tapping it against the bench.

NOTE

If less than 48 samples (96 reactions) are being prepared or alternate index combinations are being employed, the Index Plate Fixture does not need to be used and the indices can be added to the appropriate wells of the IAP plate manually.

[_] 5 Label a new 96-well PCR plate IAP (Indexed Amplification Plate).

Part # 15038313 Rev. A

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TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

[_] 6 Using a multichannel pipette, add 9 µl of i5 primers (clear solution) to each column of the

IAP plate. Tips must be changed after each row to avoid index cross-contamination.

[_] 7 To avoid index cross-contamination, discard the original white caps and apply new white caps.

[_] 8 Using a multi-channel pipette, add 9 µl of i7 primers (yellow solution) to each row of the

IAP plate. Tips must be changed after each row to avoid index cross-contamination.

[_] 9 To avoid index cross-contamination, discard the original orange caps and apply new orange caps

[_] 10 For 96 reactions, add 60 µl of TDP1 to 2.58 ml of PMM2. If preparing fewer reactions, use the following calculation: # of reactions * (0.625 µl TDP + 26.875 µl PMM2). Do not pipette volumes of less than 5 µl of TDP1. Invert the PMM2/TDP1 PCR master mix 20 times to mix well. You will add this mix to the IAP plate in the next section.

NOTE

Do not vortex.

Procedure

[_] 1 When the 45-minute extension-ligation reaction is complete, remove the FPU from the incubator. Remove the aluminum foil seal and replace with the filter plate lid.

[_] 2 Centrifuge the FPU at 2,400 xg for 2 minutes.

[_] 3 Using a multichannel pipette, add 25 µl of 0.05 N NaOH to each sample well on the FPU plate. Ensure the NaOH is fully dispersed across each membrane by gently pipetting up and down if necessary.

[_] 4 Incubate the FPU plate at room temperature for 5 minutes.

Start time: _____________________ Stop time: _____________________

[_] 5 While the FPU plate is incubating, use a multichannel pipette to transfer 22 µl of the

PMM2/TDP1 PCR master mix to each well of the IAP plate containing index primers.

Change tips between samples.

[_] 6 Transfer samples eluted from the FPU plate to the IAP plate as follows:

[_] a Set a multichannel P20 pipette to 20 µl.

[_] b Pipette the contents in the first column of the FPU plate up and down 5–6 times, then transfer 20 µl from the FPU plate to the corresponding column of the IAP plate. Gently pipette up and down 5–6 times to thoroughly combine the DNA with the PCR master mix.

NOTE

Slightly tilt the FPU plate to ensure complete aspiration and to avoid air bubbles.

[_] c Transfer the remaining columns from the FPU plate to the IAP plate in a similar manner. Tips must be changed after each column to avoid index and sample crosscontamination.

[_] d After all the samples have been transferred, the waste collection MIDI plate of the FPU can be discarded. The metal adapter collar should be put away for future use.

[_] 7 Cover the IAP plate with Microseal 'B' and seal with a rubber roller.

[_] 8 Centrifuge at 1,000 xg at room temperature for 1 minute.

Page 16 of 30

Part # 15038313 Rev. A

TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

[_] 9 Transfer the IAP plate to the post-amplification area.

[_] 10 Perform PCR on a thermal cycler using the following program:

• 95°C for 3 minutes

• 27 cycles of:

— 95°C for 30 seconds

— 62°C for 30 seconds

— 72°C for 60 seconds

• 72°C for 5 minutes

• Hold at 10°C

Start time: _____________________ Stop time: _____________________

NOTE

On the PCR machine, set the reaction volume to 60 µl and the temperature ramp speed to maximum.

SAFE STOPPING POINT

If you do not plan to immediately proceed to PCR Clean-Up following the completion of

PCR, the plate can remain on the thermal cycler overnight, or store it at 2° to 8°C up to 48 hours.

Comments

__________________________________________________________________________________

__________________________________________________________________________________

Part # 15038313 Rev. A

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TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

Verify Library Preparation (Optional)

After PCR, combine 5 µl of amplified product with 15 µl of DEPC/DI H20 and run on a 4% TBE agarose gel along with 100 bp ladder to confirm the presence of the 300–330 bp library product.

If generating libraries with ACP1, the product should be present at 350–380 bp. Alternatively, the products can be run on a bioanalyzer.

Comments

__________________________________________________________________________________

__________________________________________________________________________________

Page 18 of 30

Part # 15038313 Rev. A

TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

PCR Clean-Up

This process uses AMPure XP beads to purify the PCR products from the other reaction components.

Estimated Time

} Total duration: 50 minutes

}

Hands-on: 20 minutes

Consumables

Item

EBT (Elution Buffer with Tris)

AMPure XP beads

80% Ethanol, freshly-prepared

Quantity

1 tube

440 µl per 8 samples

3.3 ml per 8 samples

Storage

Room temperature

2° to 8°C

Room temperature

Supplied By

Illumina

User

User

96-well MIDI plates

Microseal 'B' adhesive film

Troughs

2

As needed

As needed

User

User

User

Preparation

[_] 1 Bring the AMPure XP beads to room temperature.

[_] 2 Prepare fresh 80% ethanol from absolute ethanol.

Procedure

[_] 1 Centrifuge the IAP plate at 1,000 xg at 20°C for 1 minute to collect condensation.

[_] 2 Label a new MIDI plate CLP_Plate_ID (Clean-up Plate).

[_] 3 Invert AMPure XP beads 10 times. Vortex vigorously and then invert again 10 times.

NOTE

Immediately proceed to the next step to avoid settling of the beads.

[_] 4 Using a multichannel pipette, add 55 µl of AMPure XP beads to each well of the CLP plate.

[_] 5 Using a multichannel pipette set to 60 µl, transfer 55 µl PCR product from the IAP plate to the CLP plate. Change tips between samples.

[_] 6 Seal the CLP plate with Microseal 'B'.

[_] 7 Shake the CLP plate on a microplate shaker at 1,800 rpm for 2 minutes.

[_] 8 Incubate at room temperature without shaking for 10 minutes.

Start time: _____________________ Stop time: _____________________

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Date/Time: _______________________________ Operator: _______________________________

[_] 9 Place the plate on a magnetic stand for 2 minutes or until the supernatant has cleared.

Start time: _____________________ Stop time: _____________________

[_] 10 Using a multichannel pipette set to 100 µl and with the CLP plate on the magnetic stand, carefully remove and discard the supernatant. Change tips between samples.

NOTE

Delays during this step may lead to bead clumping following removal of the supernatant. Proceed immediately to next step as soon as all supernatant is removed.

[_] 11 With the CLP plate on the magnetic stand, wash the beads with freshly prepared 80% ethanol as follows:

[_] a Add 200 µl of freshly prepared 80% ethanol to each sample well using a multichannel pipette. Avoid disturbing the beads

[_] b Incubate the plate on the magnetic stand for 30 seconds or until the supernatant appears clear.

Start time: _____________________ Stop time: _____________________

[_] c Carefully remove and discard the supernatant.

[_] 12 Repeat the 80% ethanol wash described in the previous step. Use a P20 multichannel pipette to remove excess ethanol. Aspirate all remaining ethanol using a fine tip pipette. Do not disturb or touch the beads.

[_] 13 Remove the CLP plate from the magnetic stand and allow the beads to air-dry for 5 minutes.

Start time: _____________________ Stop time: _____________________

[_] 14 Using a multichannel pipette, add 40 µl of EBT to each sample.

[_] 15 Seal the CLP plate with Microseal 'B' and shake on a microplate shaker at 1,800 rpm for 5 minutes. After shaking, if any samples are not resuspended, gently pipette up and down or lightly tap the plate on the bench to mix, then repeat this step.

Start time: _____________________ Stop time: _____________________

[_] 16 Incubate at room temperature without shaking for 2 minutes.

Start time: _____________________ Stop time: _____________________

[_] 17 Place the plate on the magnetic stand for 2 minutes.

Start time: _____________________ Stop time: _____________________

[_] 18 Label a new 96-well PCR plate SGP (Storage Plate).

[_] 19 Carefully transfer 40 µl of the supernatant from the CLP plate to the SGP plate. Change tips between samples.

[_] 20 Seal the SGP plate with Microseal 'B' and then centrifuge at 1,000 xg for 1 minute.

SAFE STOPPING POINT

After PCR-Clean Up, the SGP plate may be kept at room temperature during the upcoming library quantification and normalization steps. Once quantified samples have been normalized, the SGP plate may be stored at -20°C until ready to quantify and normalize any remaining samples.

Comments

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TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

Library Quantification

In order to achieve the highest quality of data on the Illumina MiSeq sequencing platform, it is important to create optimum cluster densities. This requires accurate quantitation of DNA libraries. Illumina recommends quantifying libraries generated from FFPE samples using the

Agilent Technologies Bioanalyzer 2100.

Quality Control

[_] 1 Load 1 µl of the re-suspended library on an Agilent Technologies 2100 Bioanalyzer using the

Agilent DNA-1000. Refer to Agilent DNA Kit Guide (Part Number G2938-90014) and Agilent

DNA 1000 Kit Quick Start Guide (Part Number G2938-90015) for complete instructions on using the Agilent Technologies 2100 Bioanalyzer.

[_] 2 Check the size and purity of the sample. The final product should be a band at ~300–330 bp as in Figure 1 . If generating libraries using ACP1, the final product will be present at ~350–

380 bp. This concentration should correlate with the relative library intensities previously observed on the agarose gel (see Verify Library Preparation (Optional) on page 18 ).

Figure 1 Representative DNA Sample Prep Library Size Distribution, 300–330 bp

NOTE

If >10% of the library product is present in the 150–250 bp range, we recommend repeating the PCR Clean-Up Procedure using 40 µl of product and 32 µl of AMPure XP beads.

Comments

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TruSight Tumor Sample Preparation

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TruSight Tumor Sample Preparation

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Date/Time: _______________________________ Operator: _______________________________

Library Normalization

This process normalizes the quantity of each library to ensure more equal library representation in your pooled sample.

Estimated Time

} 30 minutes

Consumables

Item

EBT (Elution Buffer with Tris)

Quantity

As needed

Storage

Room temperature

Supplied By

Illumina

MIDI plate

Microseal 'B' adhesive film

As needed

As needed

User

User

Procedure

[_] 1 From the Agilent Bioanalyzer run, determine the concentration for all samples, add all concentrations (in terms of nM) for all peaks in the 300–330 bp range (or 350–380 bp for

ACP1 libraries). The expected concentration range is 4–300 nM. Record the values.

[_] 2 Label a MIDI plate LNP_plate (Library Normalization Plate) and dilute 4 µl of all samples

>20 nM to 4 nM with the EBT buffer (e.g. if a sample is 254 nM, add 4 µl of library to 250 µl of EBT buffer to give 4 nM).

[_] 3 For any samples ≤20 nM, dilute as needed to ensure that the volume of the final 4 nM working stock is at least 20 µl.

SAFE STOPPING POINT

If you do not plan to proceed to

Library Denaturing and Pooling on page 25

and subsequent sequencing on the MiSeq after completion of

Library Normalization

, store the sealed LNP plate at -15° to -25°C for up to 7 days.

Comments

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TruSight Tumor Sample Preparation

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TruSight Tumor Sample Preparation

Experienced User Card

Date/Time: _______________________________ Operator: _______________________________

Library Denaturing and Pooling

In preparation for cluster generation and sequencing, equal volumes of normalized library are denatured, then are combined, diluted in hybridization buffer, and heat denatured prior to sequencing on the MiSeq. PhiX is used as an internal control for sequencing.

Estimated Time

} Total duration: 10 minutes

}

Hands-on: 10 minutes

Required Equipment

}

Heat block with microcentrifuge tube insert

Consumables

Item

HT1 (Hybridization buffer)

2 µl 10 nM PhiX Library

Stock 1.0 N NaOH (diluted to

0.1 N NaOH)

Laboratory-grade water

1X TE Buffer

Microcentrifuge tubes

(screwcap recommended)

PCR eight-tube strip

2.5 L Ice bucket

2 tubes

1

1

Quantity

1 tube

2 µl

Storage

-15° to -25°C

-15° to -25°C

15° to 25°C

Supplied By

Illumina

Illumina

User

User

User

User

User

User

Preparation

[_] 1 Set a heat block with a microcentrifuge tube insert to 96°C.

[_] 2 In an ice bucket, prepare an ice-bath. Place thawed HT1 in bath to chill.

[_] 3 Prepare a fresh dilution of 0.1 N NaOH by adding 100 µl stock 1 N NaOH to a microcentrifuge tube containing 900 µl laboratory-grade water.

CAUTION

Using freshly diluted NaOH is essential in order to completely denature samples for cluster generation on the MiSeq. Preparing a volume of 1 ml prevents small pipetting errors from affecting the final NaOH concentration.

[_] 4 Invert the tube several times to mix.

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TruSight Tumor Sample Preparation

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Date/Time: _______________________________ Operator: _______________________________

Prepare PhiX Control Library

[_] 1 In a microcentrifuge tube, add 2 µl of stock 10 nM PhiX library to 8 µl 1X EBT buffer to yield

10 µl of 2 nM PhiX library.

[_] 2 Add 10 µl of 0.1 N NaOH to 10 µl of 2 nM PhiX library to yield 20 µl of 1 nM PhiX library.

[_] 3 Vortex the 1 nM PhiX library briefly to mix, then spin at 280 xg for 1 minute.

[_] 4 Incubate the PhiX library for 4 minutes 30 seconds at room temperature to denature. Make sure that incubation time does not exceed a maximum of 5 minutes.

Start time: _____________________ Stop time: _____________________

[_] 5 Add 980 µl of pre-chilled HT1 to the 20 µl denatured PhiX library to make 20 pM PhiX library.

NOTE

The denatured 20 pM PhiX library can be stored up to three weeks at -15° to 25°C as singleuse aliquots. After three weeks, cluster numbers tend to decrease.

Prepare Samples for Sequencing

[_] 1 If the LNP plate was stored frozen, thaw at room temperature.

[_] 2 Centrifuge the LNP plate at 1,000 xg at 20°C for 1 minute to collect condensation.

[_] 3 Determine the samples to be pooled for sequencing.

[_] 4 If the LNP plate was stored frozen, using a P200 multichannel pipette set to 40 µl, mix each library to be sequenced by pipetting up and down 3–5 times. Change tips between samples.

Library Denaturing and Pooling

When using the TruSight Tumor assay, Illumina recommends sequencing four tumor samples (8 libraries total) per run when using V2 chemistry. This process is outlined in the following steps.

If sequencing a different number of samples, adjust accordingly.

NOTE

Each sample is represented by two libraries, which are generated from the TruSight Tumor

Oligo Pools (FPA and FPB). It is critical that the FPA and FPB libraries for each sample be run together on the same flowcell in order for the MiSeq software to properly analyze the results for each sample.

NOTE

Control libraries generated from ACD1 with ACP1 must be pooled and run separately from those prepared with FPA and FPB, as they will require a longer MiSeq run of 151 cycles.

[_] 1 Add 10 µl of 1N NaOH to 140 µl EBT buffer. Vortex the solution.

[_] 2 Transfer 5 µl of each 4 nM library to be sequenced from the LNP plate to its own tube in an eight-tube PCR strip tube.

NOTE

After use, the sealed LNP plate may be stored at -15° to -25°C for up to 7 days.

[_] 3 Add 15 µl of the NaOH/EBT solution to each 5 µl of library and incubate for 5 minutes at room temperature.

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Date/Time: _______________________________ Operator: _______________________________

Start time: _____________________ Stop time: _____________________

[_] 4 Label 1 microcentrifuge tube “PAL” (Pooled Amplicon Library).

[_] 5 Add 10 µl of each library/NaOH/EBT solution (there should be 8) into the PAL tube.

[_] 6 Mix the pooled libraries well by pipetting up and down 10 times.

[_] 7 Label 1 microcentrifuge tube "DAL" (Diluted Amplicon Library).

[_] 8 In the DAL tube, mix 792 µl of HT1 with 8 µl of 20 pM PhiX library. Using the same tip, pipette up and down 3–5 times to rinse the tip and ensure complete transfer.

[_] 9 Add 8 µl from the PAL tube to the DAL tube containing HT1 and PhiX. Using the same tip, pipette up and down 3–5 times to rinse the tip and ensure complete transfer.

[_] 10 Mix DAL by vortexing the tube at top speed.

NOTE

If you would like to make and save additional DAL from the remaining 72 µl of unused

PAL for future runs, it may be stored at -15° to -25°C for up to 3 days. Longer storage may lead to sub-optimal cluster densities.

[_] 11 Centrifuge the DAL tube at 1,000 xg at 20°C for 1 minute to collect contents.

[_] 12 Incubate the DAL tube in a heat block at 96°C for 2 minutes.

Start time: _____________________ Stop time: _____________________

[_] 13 After the incubation, invert the DAL tube 1–2 times to mix. Incubate immediately in the icewater bath for 5 minutes, then transfer contents to the template position in the MiSeq reagent cartridge.

Start time: _____________________ Stop time: _____________________

NOTE

The heat denaturation and cooling steps must occur immediately before loading the DAL into the MiSeq reagent cartridge to ensure efficient template loading onto the flow cell.

[_] 14 Proceed to library sequencing as instructed in the MiSeq System User Guide.

Comments

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TruSight Tumor Sample Preparation

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Part # 15038313 Rev. A

Technical Assistance

For technical assistance, contact Illumina Technical Support.

Table 2 Illumina General Contact Information

Illumina Website

www.illumina.com

Email

[email protected]

Table 3 Illumina Customer Support Telephone Numbers

Region

North America

Austria

Belgium

Denmark

Finland

France

Germany

Ireland

Contact Number

1.800.809.4566

0800.296575

0800.81102

80882346

0800.918363

0800.911850

0800.180.8994

1.800.812949

Region

Italy

Netherlands

Norway

Spain

Sweden

Switzerland

United Kingdom

Other countries

Contact Number

800.874909

0800.0223859

800.16836

900.812168

020790181

0800.563118

0800.917.0041

+44.1799.534000

MSDSs

Material safety data sheets (MSDSs) are available on the Illumina website at www.illumina.com/msds.

Product Documentation

Product documentation in PDF is available for download from the Illumina website. Go to www.illumina.com/support, select a product, then click Documentation & Literature.

Part # 15038313 Rev. A

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Illumina

San Diego, California 92122 U.S.A.

+1.800.809.ILMN (4566)

+1.858.202.4566 (outside North America) [email protected]

www.illumina.com

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