TruSight Tumor 26 Protocol Guide (1000000001444 v01)

TruSight Tumor 26 Protocol Guide (1000000001444 v01)

TruSight Tumor 26

Protocol Guide

For Research Use Only. Not for use in diagnostic procedures.

Qualify DNA Extracted from FFPE Samples

Hybridize the Oligo Pool

Remove Unbound Oligos

Extend and Ligate Bound Oligos

Amplify Libraries

Check Library Preparation (Optional)

Clean Up Libraries

Check Libraries

Normalize Libraries

Pool Libraries

Acronyms

Technical Assistance

8

10

11

12

13

14

15

17

6

7

3

5

ILLUMINA PROPRIETARY

Document # 1000000001444 v01

January 2016

This document and its contents are proprietary to Illumina, Inc. and its affiliates ("Illumina"), and are intended solely for the contractual use of its customer in connection with the use of the product(s) described herein and for no other purpose. This document and its contents shall not be used or distributed for any other purpose and/or otherwise communicated, disclosed, or reproduced in any way whatsoever without the prior written consent of Illumina. Illumina does not convey any license under its patent, trademark, copyright, or common-law rights nor similar rights of any third parties by this document.

The instructions in this document must be strictly and explicitly followed by qualified and properly trained personnel in order to ensure the proper and safe use of the product(s) described herein. All of the contents of this document must be fully read and understood prior to using such product(s).

FAILURE TO COMPLETELY READ AND EXPLICITLY FOLLOW ALL OF THE INSTRUCTIONS CONTAINED HEREIN

MAY RESULT IN DAMAGE TO THE PRODUCT(S), INJURY TO PERSONS, INCLUDING TO USERS OR OTHERS, AND

DAMAGE TO OTHER PROPERTY.

ILLUMINA DOES NOT ASSUME ANY LIABILITY ARISING OUT OF THE IMPROPER USE OF THE PRODUCT(S)

DESCRIBED HEREIN (INCLUDING PARTS THEREOF OR SOFTWARE).

© 2016 Illumina, Inc. All rights reserved.

Illumina, 24sure, BaseSpace, BeadArray, BlueFish, BlueFuse, BlueGnome, cBot, CSPro, CytoChip, DesignStudio,

Epicentre, ForenSeq, Genetic Energy, GenomeStudio, GoldenGate, HiScan, HiSeq, HiSeq X, Infinium, iScan, iSelect,

MiSeq, MiSeqDx, MiSeq FGx, NeoPrep, NextBio, Nextera, NextSeq, Powered by Illumina, SureMDA, TruGenome,

TruSeq, TruSight, Understand Your Genome, UYG, VeraCode, verifi, VeriSeq, the pumpkin orange color, and the streaming bases design are trademarks of Illumina, Inc. and/or its affiliate(s) in the U.S. and/or other countries. All other names, logos, and other trademarks are the property of their respective owners.

Patent pending for methods performed by components in this kit.

For Research Use Only– not for any clinical or therapeutic use in humans or animals.

This product includes GoTaq® Hot Start Polymerase manufactured by Promega

Corporation for distribution by Illumina, Inc. Licensed to Promega Corporation under

U.S. Patent Nos. 5,338,671 and 5,587,287 and their corresponding foreign patents.

Qualify DNA Extracted from FFPE Samples

Preparation

1 [Optional] Make 5 µl aliquots of QCT into different PCR tube strips.

2 Place thawed tubes on ice.

Procedure

1 Add 5 µl QCT to 495 µl nuclease-free water in a microcentrifuge tube.

2 Vortex to mix.

3 Add 1 µl QCP to 9 µl nuclease-free water in a microcentrifuge tube.

4 Vortex to mix.

5 Add 1.5 µl extracted genomic DNA to 148.5 µl nuclease-free water in microcentrifuge tubes.

6 Vortex to mix.

7 Determine the plate layout of the qPCR reaction.

E

F

A

B

C

D

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

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

6

Sample 9

Sample 9

Sample 9

Sample 10

Sample 10

Sample 10

8 Prepare the SYBR master mix reaction.

Consumable

Per well

KAPA SYBR FAST qPCR Master Mix

(2X) (Universal)

Diluted QCP

Nuclease-free water

5.0 µl

1.0 µl

2.0 µl

Per 48-well plate

275 µl

55 µl

110 µl

Per 96-well plate

550 µl

110 µl

220 µl

9 Gently invert to mix.

10 Set aside on ice away from light.

11 Add 8 µl of the master mix to each well.

12 According to your plate layout, add 2 µl of the QCT dilution, the sample dilutions, or nuclease-free water to each well of the plate.

13 Centrifuge at 250 × g for 1 minute.

TruSight Tumor 26 Protocol Guide

3

14 Place on the qPCR machine, close the lid, and run the following program.

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

15 Make sure that amplification of the NTC occurs at least 10 cycles after QCT amplification.

16 Remove outliers from a triplicate group that are > 0.5 Cq different from the rest of the group.

17 Exclude replicates exhibiting abnormal amplification curves.

18 Subtract the average Cq for the QCT from the average Cq for each sample to yield the

ΔCq values for each sample.

4

Document # 1000000001444 v01

Hybridize the Oligo Pool

WARNING

This set of reagents contains formamide, an aliphatic amide that is a probable reproductive toxin. Personal injury can occur through inhalation, ingestion, skin contact, and eye contact. Wear protective equipment, including eye protection, gloves, and laboratory coat. Handle used reagents as chemical waste and discard in accordance

with the governmental safety standards for your region. For environmental, health, and safety information, see the SDS for this kit at support.illumina.com/sds.html

.

Preparation

1 Place thawed tubes on ice.

2 Preheat a 96-well heat block to 95°C.

3 Label a new 96-well PCR plate "HYP_Plate_ID".

Procedure

1 Dilute 10 µl of genomic DNA extracted from FFPE samples according to the following table.

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

2 Add 10 µl diluted sample to the left half of the plate.

3 Add 10 µl diluted sample to the right half of the plate.

4 Add 5 µl FPA to the left half of the plate.

5 Add 5 µl FPB to the right half of the plate.

6 Add 35 µl OHS3. Gently pipette to mix.

7 Seal with a heat sealer or foil seal.

8 Centrifuge at 1000 × g at 20°C for 1 minute.

9 Place on the heat block and incubate for 1 minute.

10 Reduce the heat block to 40°C, and incubate for 14–18 hours.

TruSight Tumor 26 Protocol Guide

5

Remove Unbound Oligos

WARNING

This set of reagents contains formamide, an aliphatic amide that is a probable reproductive toxin. Personal injury can occur through inhalation, ingestion, skin contact, and eye contact. Wear protective equipment, including eye protection, gloves, and laboratory coat. Handle used reagents as chemical waste and discard in accordance

with the governmental safety standards for your region. For environmental, health, and safety information, see the SDS for this kit at support.illumina.com/sds.html

.

WARNING

This set of reagents contains ß-mercaptoethanol. Perform the following procedure in a hood or well-ventilated area.

Preparation

1 Assemble the filter plate assembly unit in the following order, from top to bottom:

Lid, Filter Plate, Adapter Collar, and midi plate.

2 Label the filter plate assembly unit FPU.

3 Prewash the FPU membrane.

4 Preheat the incubator to 37°C.

5 After the overnight incubation, confirm that the heat block has cooled to 40˚C.

Procedure

1 Centrifuge at 1000 × g at 20°C for 1 minute.

2 Transfer the entire volume to the corresponding wells of the FPU.

3 Centrifuge at 2400 × g at 20°C for 5 minutes.

4 Wash the FPU.

5 Repeat the wash.

6 Discard waste, and then reassemble the FPU.

7 Add 45 µl UB1 to each well containing sample.

8 Centrifuge at 2400 × g for 5 minutes.

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Document # 1000000001444 v01

Extend and Ligate Bound Oligos

Procedure

1 Add 45 µl ELM3 to each well containing sample.

2 Seal with a foil seal, and then cover with the lid.

3 Incubate in the preheated 37°C incubator for 45 minutes.

4 During incubation, prepare the IAP.

TruSight Tumor 26 Protocol Guide

7

Amplify Libraries

Preparation

1 Add 20 µl of 10 N NaOH to 3.98 ml sterile water.

2 Save the following program as PCR AMP on a thermal cycler with a heated lid.

}

Choose the preheat lid option and set to 100°C

}

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

Procedure

1 Arrange the index primers in the TruSeq Index Plate Fixture, as follows.

} Index 1 (i7) adapters (A701–A712) in columns 1–12

}

Index 2 (i5) adapters (A501–A508) in rows A–H

2 Label a new 96-well PCR plate IAP and place on the TruSeq Index Plate Fixture.

3 Using a multichannel pipette, add 9 µl of each Index 1 (i7) adapter down each column. Replace cap on each i7 adapter tube with a new orange cap.

4 Using a multichannel pipette, add 9 µl of each Index 2 (i5) adapter across each row.

Replace the cap on each i5 adapter tube with a new white cap.

5 Prepare the PMM2/TDP1 PCR master mix.

}

For 96 reactions, add 60 µl of TDP1 to 2.58 ml of PMM2.

}

If preparing fewer reactions, use the following calculation:

Number of reactions × (0.625 µl TDP + 26.875 µl PMM2).

6 Invert 20 times to mix. Do not vortex.

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

8 Centrifuge at 2400 × g for 2 minutes.

9 Add 25 µl of 0.05 N NaOH to each containing sample. Pipette to mix.

10 Incubate at room temperature for 5 minutes.

11 During incubation, transfer 22 µl master mix to each well of the IAP plate containing index adapters.

12 Transfer samples eluted from the FPU plate to the IAP plate.

13 Centrifuge 1000 × g at for 1 minute.

14 Transfer the IAP plate to the post-amplification area.

15 On the thermal cycler, set the reaction volume to 60 µl and the temperature ramp speed to maximum.

16 Place on the preprogrammed thermal cycler and run the PCR AMP program.

8

Document # 1000000001444 v01

SAFE STOPPING POINT

If you are stopping, seal the plate and store at 2°C to 8°C for up to 2 days. Alternatively, leave on the thermal cycler overnight.

TruSight Tumor 26 Protocol Guide

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Check Library Preparation (Optional)

1 After PCR, combine 5 µl of amplified product with 15 µl of DEPC/DI H20.

2 Run on a 4% TBE agarose gel along with 100 bp ladder to confirm the presence of the 300–330 bp library product. Alternatively, the products can be run on a

Bioanalyzer.

10

Document # 1000000001444 v01

Clean Up Libraries

Preparation

1 Bring the AMPure XP beads to room temperature.

2 Prepare fresh 80% ethanol from absolute ethanol.

3 Label a new midi plate CLP_Plate_ID (Clean-up Plate).

4 Label a new 96-well PCR plate SGP (Storage Plate).

Procedure

1 Centrifuge the IAP plate at 1000 × g at 20°C for 1 minute.

2 Invert AMPure XP beads 10 times. Vortex vigorously and then invert again 10 times.

3 Add 55 µl of AMPure XP beads to each well of the CLP plate.

4 Transfer 55 µl PCR product from the IAP plate to the CLP plate.

5 Shake at 1800 rpm for 2 minutes.

6 Incubate at room temperature without shaking for 10 minutes.

7 Place on a magnetic stand and wait until the liquid is clear (~2 minutes). Keep the plate on the magnetic stand until step

11

.

8 Remove and discard the supernatant.

9 Wash 2 times with 200 µl 80% EtOH.

10 Remove residual EtOH.

11 Remove the CLP plate from the magnetic stand.

12 Air-dry the beads for 5 minutes.

13 Add 40 µl EBT to each well containing sample.

14 Shake at 1800 rpm for 5 minutes.

15 Incubate at room temperature without shaking for 2 minutes.

16 Place the plate on the magnetic stand for 2 minutes.

17 Transfer 40 µl supernatant from the CLP plate to the SGP plate.

18 Centrifuge the SGP plate at 1000 × g for 1 minute.

TruSight Tumor 26 Protocol Guide

11

Check Libraries

Procedure

1 Load 1 µl of the resuspended library on an Agilent Technologies 2100 Bioanalyzer using the Agilent DNA-1000. 

2 Check the size and purity of the sample. The expected final product is a band at

~300–330 bp.

12

Document # 1000000001444 v01

Normalize Libraries

Procedure

1 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) and record the values.

2 Label a new midi plate LNP_plate (Library Normalization Plate).

3 Dilute 4 µl of all samples > 20 nM to 4 nM with the EBT buffer.

4 Dilute at least 20 µl of any samples ≤ 20 nM to 4 nM.

SAFE STOPPING POINT

If you are stopping, seal the plate and store at -25°C to -15°C for up to 7 days.

TruSight Tumor 26 Protocol Guide

13

Pool Libraries

Preparation

1 If the LNP plate was stored frozen, thaw at room temperature. When thawed, pipette to mix libraries.

2 Centrifuge at 1000 × g at 20°C for 1 minute to collect condensation.

3 Determine the libraries to be pooled.

Prepare PhiX Control Library

1 In a microcentrifuge tube, add 2 µl of 10 nM PhiX library to 8 µl 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 briefly and then centrifuge at 280 × g for 1 minute.

4 Incubate for 4.5 minutes at room temperature to denature.

5 Add 980 µl prechilled HT1 to the 20 µl denatured PhiX library to make 20 pM PhiX library.

Prepare Samples for Sequencing

1 Centrifuge at 1000 × g at 20°C for 1 minute.

2 Determine the samples to be pooled.

3 If the LNP plate was stored frozen, pipette to mix each library.

Procedure

1 Add 10 µl of 1N NaOH to 140 µl EBT buffer. Vortex to mix.

2 Transfer 5 µl of each 4 nM library from the LNP plate to its own tube in a

PCR 8-tube strip.

3 Add 15 µl NaOH/EBT solution to each 5 µl of library.

4 Incubate for 5 minutes at room temperature.

5 Label a microcentrifuge tube PAL (Pooled Amplicon Library).

6 Add 10 µl of each library/NaOH/EBT solution to the PAL tube.

7 Pipette to mix.

8 Denature and dilute pooled libraries to the loading concentration for the instrument you are using. See the denature and dilute libraries guide for your instrument.

14

Document # 1000000001444 v01

Acronyms

Acronym

FPB

FPU

HT1

HYP

IAP

LNP

OHS3

ACD1

ACP1

CLP

EBT

ELM3

FPA

PAL

PMM2

QCP

QCT

SGP

SW1

TDP1

UB1

Definition

Amplicon Control DNA 1

Amplicon Control Oligo Pool 1

Clean-up Plate

Elution Buffer with Tris

Extension Ligation Mix 3

TruSight Tumor Oligo Pool A

TruSight Tumor Oligo Pool B

Filter Plate Unit

Hybridization Buffer

HYbridization Plate

Indexed Amplification Plate

Library Normalization Plate

Oligo Hybridization for Sequencing

Reagent 3

Pooled Amplicon Library

PCR Master Mix 2

Quality Control Primers

Quality Control Template

Storage Plate

Stringent Wash 1

TruSeq DNA Polymerase 1

Universal Buffer 1

TruSight Tumor 26 Protocol Guide

15

Notes

Technical Assistance

For technical assistance, contact Illumina Technical Support.

Table 1 Illumina General Contact Information

Website

www.illumina.com

Email

[email protected]

Table 2 Illumina Customer Support Telephone Numbers

Region

North America

Australia

Austria

Belgium

China

Denmark

Finland

France

Germany

Hong Kong

Ireland

Italy

Contact Number

1.800.809.4566

1.800.775.688

0800.296575

0800.81102

400.635.9898

80882346

0800.918363

0800.911850

0800.180.8994

800960230

1.800.812949

800.874909

Region

Japan

Netherlands

New Zealand

Norway

Singapore

Spain

Sweden

Switzerland

Taiwan

United Kingdom

Other countries

Contact Number

0800.111.5011

0800.0223859

0800.451.650

800.16836

1.800.579.2745

900.812168

020790181

0800.563118

00806651752

0800.917.0041

+44.1799.534000

Safety data sheets (SDSs)—Available on the Illumina website at support.illumina.com/sds.html

.

Product documentation—Available for download in PDF from the Illumina website. Go to support.illumina.com, select a product, then select Documentation & Literature.

TruSight Tumor 26 Protocol Guide

Illumina

5200 Illumina Way

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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