nextera rapid capture enrichment guide 15037436 f

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Part # 15037436 Rev. FJanuary 2014

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Nextera Rapid Capture Enrichment Guide

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Nextera RapidCapture EnrichmentGuide v

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Nextera RapidCapture EnrichmentGuide vii

RevisionHistory

Part# Revision Date Description of Change15037436 F January

2014 Added Nextera Rapid Capture Exome Enrichment 8 rxn 3 plex,8rxn6plex, and 8rxn9plex kits. Revised the following sectionsregarding these kits: Protocol Introduction First PCR Amplification Kit Contents Index SequencesMake DNA Stock Plate

Modified description of existing exome and expanded exome kits todenote the reactions and plexity of each kit

Changed the following plate names to clarify library vs. sample: NES (Nextera Enrichment Sample Plate) is now NEL (NexteraEnrichment Library Plate)

NLS (Nextera Library Sample Plate) is now NIL (Nextera IndexLibrary Plate)

AddedDNA Input Recommendations for an optional cleanup stepfollowed by requantitation of DNA samples

Added references to BaseSpace for organizing samples, libraries, pools,and runs

Removed Low-Plex Pooling Guidelines which are now available in aNextera Rapid Capture Enrichment Low-Plex Pooling Guidelines TechNote

Moved content from the Sequencing section to Quantify Libraries andthe Nextera Rapid Capture Enrichment support pages on the Illuminawebsite

Corrected the 8 Reaction - Oligos box configuration

viii Part # 15037436 Rev. F

Part# Revision Date Description of Change15037436 E November

2013 Added guidance on EDTA to DNA Input Recommendations Added training and qPCR information to Additional Resources Renamed the EUC to EUC and LTF Added Nextera Rapid Capture Exome Enrichment (8 Samples) Kit.Revised the following sections regarding this kit: Protocol Introduction First PCR Amplification Kit Contents Index SequencesMake DNA Stock Plate

Corrected the 96 Samples - Box 2 configuration15037436 D August

2013Providing eight Index 2 (i5) adapters in Box 3 of the Nextera RapidCapture Custom Enrichment Kits (288 Samples). Revised the followingsections regarding the additional indices:Nextera Rapid Capture Custom Enrichment Kits (288 Samples) Low-Plex Pooling Guidelines Index Sequences

15037436 C June 2013 Appended Enrichment to product name15037436 B May 2013 Added Nextera Rapid Capture Custom Kit information

Changed protocol for small-size capture panels Reorganized Getting Started content and move some topics to theAppendix

Replaced Best Practices with reference to content on the Illuminawebsite

Removed recommendation for a paired-end 76 cycle sequencing run15037436 A February

2013Initial Release

Nextera RapidCapture EnrichmentGuide ix

Table ofContents

Revision History viiTable of Contents ixList of Tables xi

Chapter 1 Overview 1Introduction 2DNA Input Recommendations 3Additional Resources 4

Chapter 2 Protocol 7Introduction 8Sample Prep Workflow 10Tagment Genomic DNA 11Clean Up Tagmented DNA 14First PCR Amplification 18First PCR Clean Up 22First Hybridization 26First Capture 31Second Hybridization 36Second Capture 39Capture Sample Clean Up 44Second PCR Amplification 47Second PCR Clean Up 50Validate Library 53

Appendix A Supporting Information 55Introduction 56Acronyms 57Kit Contents 59Consumables and Equipment 86Index Sequences 90DNA Quantitation 92

Index 99

Technical Assistance 101

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Nextera RapidCapture EnrichmentGuide xi

List of Tables

Table 1 DNA Libraries for Enrichment 28Table 2 Nextera Rapid Capture Enrichment Acronyms 57Table 3 Nextera Rapid Capture Exome Enrichment Kits 59Table 4 Nextera Rapid Capture Expanded Exome Enrichment Kits 59Table 5 Nextera Rapid Capture Custom Enrichment Kits 60Table 6 User-Supplied Consumables 86Table 7 User-Supplied Equipment 88Table 8 Nextera Rapid Capture Enrichment Index Adapter Sequences 91Table 9 Concentrations of Lambda DNA 94Table 10 Illumina General Contact Information 101Table 11 Illumina Customer Support Telephone Numbers 101

xii Part # 15037436 Rev. F

Chapter1

Nextera RapidCapture EnrichmentGuide 1

Chapter 1 Overview

Overview

Introduction 2DNA Input Recommendations 3Additional Resources 4

Overview

2 Part # 15037436 Rev. F

Introduction

This protocol explains how to prepare up to 96 indexed, paired-end libraries, followed byenrichment using exome or custom probe panels and reagents provided in an IlluminaNextera Rapid Capture Exome, Expanded Exome, or Custom Enrichment kit, forsubsequent cluster generation and DNA sequencing. The goal of this protocol is to fragmentand add adapter sequences onto template DNA to generate indexed sequencing librariesthat can be carried through enrichment for targeted resequencing applications.The Nextera Rapid Capture Enrichment protocol offers:} Fast and easy sample preparation

Prepare up to 96 enriched libraries in approximately 1.5 days, includingapproximately 5 hours of hands-on time

High throughput, automation-friendly procedures with no fragmentationbottlenecks

} Low DNA input and excellent data quality Excellent data quality with low input of 50 ng Access precious samples with no affect on performance Ability to archive samples for subsequent analysis

} High enrichment rates, low duplicates, and exceptional coverage uniformity Efficient use of sequencing and reliable variant calling Reduced hands-on time with the most cost-effective, high-throughput workflow

DNAInputRecom

mendations


DNA InputRecommendations

Nextera Rapid Capture Enrichment library preparation uses an enzymatic DNAfragmentation step and thus can be more sensitive to DNA input compared to mechanicalfragmentation methods. The ultimate success of enrichment strongly depends on using anaccurately quantified amount of input DNA. Therefore, accurate quantitation of the gDNAis essential.Illumina recommends quantifying the starting gDNA using a fluorometric-based methodspecific for double-stranded DNA (dsDNA) such as QuantiFluor and running samples intriplicate to obtain more confident measurements.} Avoid methods that measure total nucleic acid content (e.g. nanodrop or other UV

absorbance methods)} Common contaminants, such as ssDNA, RNA, and oligos, are not substrates for the

Nextera Rapid Capture Enrichment assay} Make sure that the starting DNA does not contain more than 1mM EDTA and is free

of organic contaminants, such as phenol and ethanol. For more information, see DNAQuantitation on page 92.

} DNA samples can contain substances that interfere with the Nextera tagmentationreaction and result in unexpected library insert sizes. Therefore, Illumina recommendsan optional sample cleanup, followed by requantifying the DNA samples, prior tobeginning library preparation. The additional cleanup makes sure that the conditionsare optimal for Nextera Rapid Capture Enrichment library preparation.

The Nextera Rapid Capture Enrichment protocol has been optimized for 50 ng of totalgDNA. A higher mass input of gDNA can result in incomplete tagmentation and largerinsert sizes, which can affect enrichment performance. A lower mass input of gDNA or lowquality gDNA in the tagmentation reaction can generate smaller than expected insert sizes.Smaller inserts can be lost during subsequent cleanup steps and result in lower diversity.

To minimize gDNA sample input variability into the tagmentation step, Illumina stronglyrecommends a two-step method of gDNA normalization. After the initial quantification,gDNA samples are first normalized to 10 ng/ul. Samples are then requantified using asimilar fluorometric-based method and normalized to a final 5 ng/ul.

Overview

4 Part # 15037436 Rev. F

AdditionalResources

The following resources are available for Nextera Rapid Capture Enrichment protocolguidance and sample tracking. Access these and other resources on the Illumina website atsupport.illumina.com/sequencing/kits.ilmn. Then, select Nextera Rapid Capture Exomeand Expanded Exome Enrichment Kits Support or Nextera Rapid Capture CustomEnrichment Kits Support.

Resource Description

Training Illustrates elements of the Nextera Rapid Capture Enrichmentprocess. Viewing these videos is recommended for new andless experienced users before starting sample preparation. Click Training on Nextera Rapid Capture Exome andExpanded Exome Enrichment Kits Support or

Click Training on Nextera Rapid Capture CustomEnrichment Kits Support

Best Practices Provides best practices specific to this protocol. Review thesebest practices before starting sample preparation. Topicsinclude: Consistency Handling Magnetic Beads Avoiding Cross-ContaminationWashing During SPB Clean-Up Freeze/thawing for Small Number of Samples Preventing PCR Product Contamination Click Best Practices on Nextera Rapid Capture Exome andExpanded Exome Enrichment Kits Support or

Click Best Practices on Nextera Rapid Capture CustomEnrichment Kits Support

AdditionalResources



Nextera Rapid CaptureEnrichment Experienced UserCard and Lab Tracking Form(part # 15037437)

Provides protocol instructions, but with less detail than what isprovided in this user guide. New or less experienced usersare advised to follow this user guide and not the EUC andLTF. Click Documentation & Literature on Nextera RapidCapture Exome and Expanded Exome EnrichmentKits Support or

Click Documentation & Literature on Nextera RapidCapture Custom Enrichment Kits Support

Illumina Experiment Manager(IEM)

Enables you to create and edit appropriate sample sheets forIllumina sequencers and analysis software and recordparameters for your sample plate.To download the software: Click Downloads on Nextera Rapid Capture Exome andExpanded Exome Enrichment Kits Support or

Click Downloads on Nextera Rapid Capture CustomEnrichment Kits Support

To download the documentation: Click Documentation & Literature on Nextera RapidCapture Exome and Expanded Exome EnrichmentKits Support or


BaseSpace Sequencing data analysis tool that also enables you toorganize samples, libraries, pools, and run in a singleenvironment.For more information on BaseSpace and BaseSpacedocumentation see,support.illumina.com/sequencing/sequencing_software/basespace.ilmn

Overview

6 Part # 15037436 Rev. F


Nextera Rapid CaptureEnrichment Low-Plex PoolingGuidelines Tech Note

Provides pooling guidelines and dual indexing strategies forNextera Rapid Capture Enrichmentlibrary preparation. Click Documentation & Literature on Nextera RapidCapture Exome and Expanded Exome EnrichmentKits Support or


Sequencing Library qPCRQuantification Guide (part #11322363)

Describes a qPCR method for quantifying sequencing bysynthesis (SBS) libraries generated using the Illumina samplepreparation protocols. Click Documentation & Literature on Nextera RapidCapture Exome and Expanded Exome EnrichmentKits Support or


Chapter2


Chapter 2 Protocol

Protocol

Introduction 8Sample Prep Workflow 10Tagment Genomic DNA 11Clean Up Tagmented DNA 14First PCR Amplification 18First PCR Clean Up 22First Hybridization 26First Capture 31Second Hybridization 36Second Capture 39Capture Sample Clean Up 44Second PCR Amplification 47Second PCR Clean Up 50Validate Library 53

Protoc

ol

8 Part # 15037436 Rev. F

Introduction

This chapter describes the Nextera Rapid Capture Enrichment protocol.} Review Best Practices before proceeding. See Additional Resources on page 4 for

information on how to access Nextera Rapid Capture Enrichment Best Practices on theIllumina website.

} Review Appendix A Supporting Information to confirm your kit contents and makesure that you have obtained all of the requisite equipment and consumables.

} Follow the protocols in the order shown, using the specified volumes and incubationparameters.

} If you are pooling, record information about your samples before beginning librarypreparation for later use in data analysis. Do one of the following:

Use IEM to create and edit sample sheets for Illumina sequencers and analysissoftware. See Additional Resources on page 4 for information on how todownload IEM software and documentation from the Illumina website.

Use BaseSpace to organize samples, libraries, pools, and a run for Illuminasequencers and analysis software. See Additional Resources on page 4 forinformation on how to access BaseSpace or download BaseSpacedocumentation from the Illumina website.

Include a common index in each column to facilitate pipetting operations whendispensing indexed adapters and pooling indexed libraries. See Additional Resourceson page 4 for information on how to download the Nextera Rapid CaptureEnrichment Low-Plex Pooling Guidelines Tech Note.

Introduction


Nextera Rapid Capture Enrichment kits support the following reactions andplexity. For more information on the kit configurations, see Kit Contents on page 59.

Samples EnrichmentReactions

Plexity

8 8 1

24 8 3

48 8 6

72 8 9

24 2 12

48 4 12

96 8 12

288 24 12

Protoc

ol

10 Part # 15037436 Rev. F

Sample PrepWorkflow

The following diagram illustrates the workflow using a Nextera Rapid Capture Enrichmentkit. Safe stopping points are marked between steps.

Figure 1 Nextera Rapid Capture Enrichment Workflow

TagmentG

enomicDNA


TagmentGenomicDNA

This process tagments (tags and fragments) the gDNA by the Nextera transposome. TheNextera transposome simultaneously fragments the gDNA and adds adapter sequences tothe ends, allowing amplification by PCR in subsequent processes.

Consumables

Item Quantity Storage Supplied By

Sample Purification Beads (SPB) 1 tube 2C to 8C Illumina

Stop Tagment Buffer (ST) 1 tube 15C to 30C Illumina

Tagment DNA Buffer (TD) 1 tube -15C to -25C Illumina

Tagment DNA Enzyme (TDE1) 1 tube -15C to -25C Illumina

96-well MIDI plate 1 15C to 30C User

gDNA (5 ng/l) 50 ng -15C to -25C User

Microseal 'B' adhesive seals 2 15C to 30C User

RNase/DNase-free eight-tubestrips and caps(for multi-sample processing)

3 15C to 30C User

RNase/DNase-free reagentreservoir(for multi-sample processing)

1 15C to 30C User

Tris-HCl 10 mM, pH 8.5 As needed 15C to 30C User

Preparation} Remove the Tagment DNA Buffer, Tagment DNA Enzyme 1, and gDNA from -15C to

-25C storage and thaw on ice. After thawing, make sure that all reagents are adequately mixed. Gently invert the

tubes 35 times, followed by a brief spin in a microcentrifuge.

Protoc

ol

12 Part # 15037436 Rev. F

} Remove the Sample Purification Beads from 2C to 8C storage and let stand to bring toroom temperature.

} Make sure that the Stop Tagment Buffer has no precipitate. If there is precipitate, vortexuntil all particulates are resuspended.

} For multi-sample processing: Use a multichannel pipette. Distribute the Stop Tagment Buffer, Tagment DNA Buffer, and Tagment DNA

Enzyme 1 into separate eight-tube strips, dispensing equal volumes into each of thewells.

Pour the Sample Purification Beads into a multichannel reagent reservoir.} Place a MIDI plate insert on the microheating system.} Pre-heat the microheating system to 58C.} Label a new 96-well MIDI plate NLT (Nextera Library Tagment) with a smudge

resistant pen.} Use IEM to determine the index primers to be used or BaseSpace to organize your

samples, libraries, pools, and run. For more information, see Additional Resources onpage 4.

ProcedureNOTEMake sure that the reaction is assembled in the order described for optimal kit performance.It is not necessary to assemble the reaction on ice.

1 Perform the following steps to normalize your gDNA samples:a Quantify your gDNA samples using a fluorometric method such as QuantiFluor or

Qubit.b Normalize your gDNA samples in Tris-HCl 10 mM, pH 8.5 to 10 ng/l.c Requantify the 10 ng/l normalized sample using the same fluorometric

quantification method.d Based on the quantification, further dilute your gDNA samples in Tris-HCl 10 mM,

pH 8.5 to a final volume of 10 l at 5 ng/l (50 ng total).

2 Add 10 l gDNA at 5 ng/l (50 ng total) to each well of the new 96-well MIDI platelabeled NLT.

NOTEIt is critical to use the full amount of input DNA.

TagmentG

enomicDNA


3 Add 25 l Tagment DNA Buffer to each well of the NLT plate.

4 Add 15 l Tagment DNA Enzyme 1 to each well of the NLT plate.

5 Mix thoroughly as follows:a Seal the NLT plate with a Microseal B adhesive seal.b Shake the NLT plate on a microplate shaker at 1800rpm for 1minute.

6 Centrifuge the NLT plate at 280g for 1minute.

7 Place the sealed NLT plate on the pre-heated microheating system. Close the lid andincubate at 58C for 10minutes.

8 Remove the NLT plate from the microheating system.

9 Remove the adhesive seal from the NLT plate.

10 Add 15 l Stop Tagment Buffer to each well of the NLT plate.



13 Incubate the NLT plate at room temperature for 4 minutes.

14 Proceed to Clean Up Tagmented DNA on page 14.

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14 Part # 15037436 Rev. F

CleanUpTagmentedDNA

This process purifies the tagmented DNA from the Nextera transposome. It is critical,because the Nextera transposome can bind tightly to DNA ends and interfere withdownstream processes when it is not removed.

Consumables


Resuspension Buffer (RSB) 1 tube -15C to -25C Illumina


96-well hard-shell plate (HSP) 1 15C to 30C User

Freshly prepared 80% ethanol(EtOH)

400 l per sample 15C to 30C User


RNase/DNase-free reagentreservoirs(for multi-sample processing)

3 15C to 30C User

Preparation} Remove the Resuspension Buffer from -15C to -25C storage and thaw at room

temperature.NOTEThe Resuspension Buffer can be stored at 2C to 8C after the initial thaw.

} Review Best Practices for Handling Magnetic Beads. See Additional Resources on page 4for information on how to access Nextera Rapid Capture Enrichment Best Practices onthe Illumina website.

} Remove the Sample Purification Beads from 2Cto8C storage and bring them to roomtemperature.

CleanUp

Tagmented

DNA


} For multi-sample processing: Use a multichannel pipette. Pour the Resuspension Buffer, Sample Purification Beads, and 80% EtOH into

separate multichannel reagent reservoirs.} Label a new 96-well HSP plate NLA (Nextera Library Amplification) with a smudge

resistant pen.

Procedure1 Remove the adhesive seal from the NLT plate.

2 Add 65 l well-resuspended Sample Purification Beads to each well of the NLT plate.





7 Place the plate on the magnetic stand for 2 minutes or until the liquid is clear.

8 Using a 200 l single channel or multichannel pipette set to 130 l, remove anddiscard all of the supernatant from each well of the NLT plate.

NOTELeave the NLT plate on the magnetic stand while performing the following 80% EtOHwash steps (912).

9 With the NLT plate on the magnetic stand, slowly add 200 l freshly prepared80%EtOH to each well without disturbing the beads.

10 Incubate the NLT plate at room temperature for 30 seconds.

11 Remove and discard the 80% EtOH from each well of the NLT plate.

12 Repeat steps 911 one time for a total of two 80% EtOH washes.

13 Using a 20 l single channel or multichannel pipette, remove any remaining80%EtOH from each well of the NLT plate without disturbing the beads.

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16 Part # 15037436 Rev. F

14 With the NLT plate on the magnetic stand, incubate the plate at room temperature for10minutes to dry.

15 Remove the NLT plate from the magnetic stand.

16 Add 22.5 l Resuspension Buffer to each well of the NLT plate. Do not touch the beadswith the pipette tips.

17 Mix thoroughly as follows:a Seal the NLT plate with a Microseal B adhesive seal.b Shake the NLT plate on a microplate shaker at 1800rpm for 1minute



20 Place the NLT plate on the magnetic stand for 2 minutes or until the liquid is clear.


22 Transfer 20 l of clear supernatant from each well of the NLT plate to thecorresponding well of the new HSP plate labeled NLA. Take care not to disturb thebeads.

NOTEIllumina recommends using a 20 l single channel or multichannel pipette set to 10 l toperform two consecutive transfers of 10 l. This technique reduces sample loss bymaking sure that all of the liquid is transferred without disturbing the beads.

CleanUp

Tagmented

DNA


23 [Optional] Load 1l of the tagmentation reaction remaining in the NLT plate on anAgilent Technologies 2100 Bioanalyzer using an Agilent High Sensitivity DNA Chip.Check the size of the sample for a broad distribution of DNA fragments with a sizerange from approximately 150bp1kb.

Figure 2 Example Nextera Rapid Capture Enrichment Post-Tagmentation Library Distribution

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18 Part # 15037436 Rev. F

First PCRAmplification

This process amplifies the purified tagmented DNA via a 10-cycle PCR program. It alsoadds index 1 (i7) and index 2 (i5) sequences needed for sequencing, as well as commonadapters (P5 and P7) required for cluster generation and sequencing.

NOTESee Kit Contents on page 59 to determine which indices are provided in your Nextera RapidCapture Enrichment kit.

Consumables


Index 1 primers(i7, e.g., N701N712)

1 tube each index -15C to -25C Illumina

Index 1 Tube Caps, Orange 1 per Index 1 primertube

15C to 30C Illumina

Index 2 primers(i5, e.g., E501E508)

1 tube each index -15C to -25C Illumina

Index 2 Tube Caps, White 1 per Index 2 primertube

15C to 30C Illumina

Nextera Library AmplificationMix (NLM)

1 tube -15C to -25C Illumina

1.7 ml microcentrifuge tubes 1 per index primertube

15C to 30C User

Microseal 'A' film 1 15C to 30C User

Microseal 'B' adhesive seal 1 15C to 30C User


1 15C to 30C User

[Optional] TruSeq Index PlateFixture Kit

1 15C to 30C User

FirstPCRAm

plification


Preparation} Remove the Nextera Library Amplification Mix from -15C to -25C storage and thaw

on ice.} Remove the following from -15C to -25C storage and thaw at room temperature:

Index 1 primers (i7, N7xx) (only remove primers being used) Index 2 primers (i5, E5xx) (only remove primers being used)

NOTENextera Rapid Capture Enrichment kits are designed to work only with Index 2primers with the "E" prefix. Do not use Index 2 primers from other Nextera sampleprep kits.

} For multi-sample processing: Use a multichannel pipette. Dispense the Nextera Library Amplification Mix in equal volumes into each of the

wells of an eight-tube strip.} Pre-program the thermal cycler with the following program and save as NLM AMP:

Choose the pre-heat lid option and set to 100C 72C for 3minutes 98C for 30seconds 10 cycles of:

98C for 10seconds 60C for 30seconds 72C for 30seconds

72C for 5minutes Hold at 10C

NOTEIllumina has optimized the number of recommended PCR cycles for enrichment assaysbased on the level of pre-enrichment sample pooling and the size of the oligonucleotideset. To ensure libraries that produce high-quality sequencing results, do not add orreduce the PCR cycles.

Setup Index Primers1 Vortex the index primer tubes for 5seconds.

2 Centrifuge the index primer tubes to 600g for 5seconds. Use empty 1.7 mlmicrocentrifuge tubes as tube adapters for the microcentrifuge.

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20 Part # 15037436 Rev. F

3 Arrange the index primers in a rack on ice (i.e. the TruSeq Index Plate Fixture) usingthe following arrangement:a Arrange the Index 1 Primer tubes (orange caps) vertically, aligned with columns

1-12.b Arrange the Index 2 Primer tubes (white caps) horizontally, aligned with rows A-H.

Figure 3 Example: Index Plate Fixture Setup

A Index 1 Primer tubes (orange caps)B Index 2 Primer tubes (white caps)C NLA plate

NOTEThe number of available Index 2 primers is dependent on the Nextera RapidCapture Enrichment kit that you are using. See Kit Contents on page 59 todetermine which indices are provided in your kit.

FirstPCRAm

plification


ProcedureNOTEWhen pooling libraries before enrichment, it is recommended to pool libraries so all Index 1(i7) indices are unique. Choose Index 1 and Index 2 primers for PCR accordingly. SeeAdditional Resources on page 4 for information on how to download the Nextera Rapid CaptureEnrichment Low-Plex Pooling Guidelines Tech Note.

1 Add 5 l Index 1 primer to each well of the NLA plate.

2 Add 5 l Index 2 primer to each well of the NLA plate.

3 Add 20 l Nextera Library Amplification Mix to each well of the NLA plate.

4 Mix thoroughly as follows:a Seal the NLA plate with a Microseal A film.b Shake the NLA plate on a microplate shaker at 1200rpm for 1minute

5 Centrifuge the NLA plate at 280 g for 1 minute.

6 Place the sealed NLA plate on the pre-programmed thermal cycler. Close the lid, thenselect and run the NLM AMP program.a Choose the pre-heat lid option and set to 100Cb 72C for 3minutesc 98C for 30secondsd 10 cycles of:


e 72C for 5minutesf Hold at 10C

SAFESTOPPINGPOINTIf you do not plan to proceed immediately to First PCR Clean Up on page 22, the NLA platecan remain on the thermocycler overnight. If you are stopping, replace the Microseal 'A' witha Microseal 'B' adhesive seal and store the NLA plate at 2C to 8C for up to two days.

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22 Part # 15037436 Rev. F

First PCRCleanUp

This process uses Sample Purification Beads to purify the library DNA and removeunwanted products.

Consumables


Resuspension Buffer (RSB) 1 tube 2C to 8C Illumina


96-well HSP plate 1 15C to 30C User





RNase/DNase-free reagentreservoirs(for multi-sample processing)

3 15C to 30C User

Preparation} Review Best Practices for Handling Magnetic Beads. See Additional Resources on page 4

for information on how to access Nextera Rapid Capture Enrichment Best Practices onthe Illumina website.

} Remove the Resuspension Buffer and Sample Purification Beads from 2Cto8Cstorage and bring them to room temperature.

} For multi-sample processing: Use a multichannel pipette. Pour the Resuspension Buffer, Sample Purification Beads, and 80% EtOH into

separate multichannel reagent reservoirs.} Label a new 96-well MIDI plate NLC (Nextera Library Clean Up) with a smudge

resistant pen.

FirstPCRClean

Up


} Label a new 96-well HSP plate NIL (Nextera Index Library) with a smudge resistantpen.

Procedure1 Remove the NLA plate from the thermocycler and centrifuge to 280 g for 1 minute.

2 Remove the adhesive seal from the NLA plate.

3 Transfer 50 l of clear supernatant from each well of the NLA plate to thecorresponding well of the new 96-well MIDI plate labeled NLC.

4 Vortex the Sample Purification Beads until the beads are well dispersed.

5 Add 90 l well-resuspended Sample Purification Beads to each well of the NLC plate.

6 Mix thoroughly as follows:a Seal the NLC plate with a Microseal B adhesive seal.b Shake the NLC plate on a microplate shaker at 1800rpm for 1minute.

7 Incubate the NLC plate at room temperature for 10 minutes.

8 Centrifuge the NLC plate at 280 g for 1 minute.

9 Remove the adhesive seal from the NLC plate.

10 Place the NLC plate on the magnetic stand for 2 minutes or until the liquid is clear.

11 Carefully remove and discard all of the supernatant from each well of the NLC plate.NOTELeave the NLC plate on the magnetic stand while performing the following 80% EtOHwash steps (1215).

12 With the NLC plate on the magnetic stand, slowly add 200 l freshly prepared 80%EtOH to each well without disturbing the beads.

13 Incubate the NLC plate at room temperature for 30 seconds.

14 Remove and discard the 80% EtOH from each well of the NLC plate.

15 Repeat steps 12 and 14 one time for a total of two 80% EtOH washes.

16 Using a 20 l single channel or multichannel pipette, remove any remaining80%EtOH from each well of the NLC plate without disturbing the beads.

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24 Part # 15037436 Rev. F

17 Let the NLC plate stand at room temperature for 10 minutes to dry on the magneticstand.

18 Remove the NLC plate from the magnetic stand.

19 Add 27 l Resuspension Buffer to each well of the NLC plate. Do not touch the beadswith the pipette tips.

20 Mix thoroughly as follows:a Seal the NLC plate with a Microseal B adhesive seal.b Shake the NLC plate on a microplate shaker at 1800rpm for 1minute.

21 Incubate the NLC plate at room temperature for 2 minutes.

22 Centrifuge the NLC plate at 280g for 1minute.

23 Remove the adhesive seal from the NLC plate.

24 Place the NLC plate on the magnetic stand for 2 minutes or until the liquid is clear.

25 Transfer 25 l of clear supernatant from each well of the NLC plate to thecorresponding well of the new HSP plate labeled NIL. Take care not to disturb thebeads.

NOTEIllumina recommends using a 20 l single channel or multichannel pipette set to 12.5 lto perform two consecutive transfers of 12.5 l. This technique reduces sample loss bymaking sure that all of the liquid is transferred without disturbing the beads.

26 Quantify the library in the NIL plate using a fluorometric method. See DNAQuantitation on page 92 for an example protocol using the Promega QuantiFluormethod.

27 [Optional] Load 1l of the library on an Agilent Technologies 2100 Bioanalyzer usingan Agilent DNA 1000 Chip. Check the size of the library for a distribution of DNAfragments with a size range from approximately 150bp1kb.

FirstPCRClean

Up


Figure 4 Example Nextera Rapid Capture Enrichment Post-PCR, Pre-Enriched LibraryDistribution

NOTEThe sample peak must not be significantly shifted compared to the example shown inFigure 4, although traces can differ depending on sample quality. A larger peakdistribution (>350 bp) can be indicative of >50 ng gDNA input going into tagmentationand can result in lower on-target reads. Conversely, a smaller sample peak distribution(

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26 Part # 15037436 Rev. F

FirstHybridization

This process mixes the DNA library with capture probes to targeted regions of interest. Therecommended hybridization time makes sure that targeted regions bind to the captureprobes thoroughly. This process also describes how to combine multiple libraries withdifferent indices into a single pool before enrichment.

Consumables


One of the following,depending on the kit you areusing: Coding Exome Oligos (CEX) Expanded Exome Oligos(EEX)

Rapid Capture Oligos (RCO)


Enrichment HybridizationBuffer (EHB)





2 15C to 30C User

[Optional] Amicon Ultra-0.5centrifugal filter unit(0.5 ml, 30 kDa)

1perpooledsample 15C to 30C User

Preparation} Remove the following from -15Cto-25C storage and thaw them at room temperature:

Enrichment Hybridization Buffer

FirstHybridization


One of the following, depending on the kit you are using: Coding Exome Oligos Expanded Exome Oligos Rapid Capture Oligos

} For multi-sample processing: Use a multichannel pipette. Distribute the Coding Exome Oligos, Expanded Exome Oligos, or Rapid Capture

Oligos and Enrichment Hybridization Buffer into separate eight-tube strips,dispensing equal volumes into each of the wells.

} Remove the NIL plate from -15 to -25C storage, if it was stored at the conclusion ofFirst PCR Clean Up and thaw on ice. Centrifuge the thawed NIL plate at 280 g for 1 minute. Remove the adhesive seal from the thawed NIL plate.

} Pre-program the thermal cycler with the following program and save as NRC HYB:a Choose the pre-heat lid option and set to 100Cb 95C for 10minutesc 18 cycles of 1 minute incubations, starting at 94C, then decreasing 2C per cycled 58C for forever

} Label a new 96-well HSP plate NEH1 (Nextera Enrichment Hyb 1) with a smudgeresistant pen.

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28 Part # 15037436 Rev. F

Pool LibrariesNOTEPooling is not performed with the Nextera Rapid Capture Exome Enrichment Kit(8rxn1plex).

1 Reference Table 1 for the amount of DNA library to use for enrichment. Illuminarecommends using 500ng of each DNA library, quantified by QuantiFluor. See DNAInput Recommendations on page 3.

LibraryPoolComplexity

TotalDNALibraryMass(ng)

LibraryPoolComplexity

TotalDNALibraryMass(ng)

1-plex 500 7-plex 3500

2-plex 1000 8-plex 4000

3-plex 1500 9-plex 4500

4-plex 2000 10-plex 5000

5-plex 2500 11-plex 5500

6-plex 3000 12-plex 6000

Table 1 DNA Libraries for Enrichment

If you are pooling libraries, combine 500 ng of each DNA library. If the total volume is greater than 40l, concentrate the pooled sample. Use either

a vacuum concentrator or Amicon Ultra-0.5 centrifugal filter unit (0.5 ml, 30 kDa)according to the manufacturer's instructions. If you are using a vacuum concentrator, Illumina recommends concentrating

samples with a no heat and medium drying rate setting. If you are using an Amicon Ultra-0.5 centrifugal filter unit (0.5 ml, 30 kDa), it is

not required to pre-rinse the device before use. Most of the volume filtersthrough in 5 minutes, but up to 30 minutes can be required, depending on thestarting volume.

If the pooled sample volume after concentrating is less than 40 l, bring thevolume up to 40 l with Resuspension Buffer.

FirstHybridization


For Nextera Rapid Capture Custom Enrichment projects, Illumina recommendsavoiding low levels of sample multiplexing (for example, < 6-plex) for a smallcapture target size (for example, < 2 Mb). The final enriched sample yield could beinsufficient for clustering and subsequent sequencing.

2 The recommended pre-enrichment pooling strategy is to pool libraries so that eachcontains a unique Index 1/i7 index. With this pooling approach, samples can besequenced using a single index read workflow.If Index1/i7 indices are not unique, make sure that libraries with different Index 2/i5indices are included. With this approach, sequence samples using a dual index readworkflow.For more information, see the Nextera Rapid Capture Enrichment Low-Plex PoolingGuidelines Tech Note. See Additional Resources on page 4 for information on how todownload the tech note.

Procedure1 Thoroughly vortex the Enrichment Hybridization Buffer tube until the solution is

completely resuspended. Visually make sure that no crystal structures are present.NOTEIf crystals and cloudiness are observed, vortex the Enrichment Hybridization Buffer tubeuntil it is clear.

2 Add the following reagents in the order listed to each well of the new 96-well HSPplate labeled NEH1:

Reagent Volume (l)DNA library sample or library pool from NIL plate 40Enrichment Hybridization Buffer 50Coding Exome Oligos,Expanded Exome Oligos, orRapid Capture Oligos

10

Total Volume per Sample 100

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30 Part # 15037436 Rev. F

3 Mix thoroughly as follows:a Seal the NEH1 plate with a Microseal B adhesive seal. Make sure that the plate is

tightly sealed to prevent potential evaporation. Use an adhesive seal roller to applyforce to the seal and make sure that the seal is secured.

b Shake the NEH1 plate on a microplate shaker at 1200 rpm for 1 minute.

4 Centrifuge the NEH1 plate at 280 g for 1 minute.

5 Place the sealed NEH1 plate on the pre-programmed thermal cycler. Close the lid, thenselect and run the NRC HYB program.a Choose the pre-heat lid option and set to 100Cb 95C for 10minutesc 18 cycles of 1 minute incubations, starting at 94C, then decreasing 2C per cycled 58C for foreverIncubate the plate at the 58C holding temperature for at least 90 minutes and up to amaximum of 24 hours. Do not remove the plate from 58C incubation until you areready to proceed to First Capture on page 31.

FirstCapture


FirstCapture

This process uses streptavidin beads to capture probes hybridized to the targeted regions ofinterest. Two heated wash procedures remove non-specific binding from the beads. Theenriched library is then eluted from the beads and prepared for a second round ofhybridization.

Consumables


2N NaOH (HP3) 1 tube -15C to -25C Illumina

Elute Target Buffer 2 (ET2) 1 tube 2C to 8C Illumina

Enrichment Elution Buffer 1 (EE1) 1 tube -15C to -25C Illumina

Enrichment Wash Solution (EWS) 1 tube -15C to -25C Illumina

Streptavidin Magnetic Beads (SMB) 1 tube 2C to 8C Illumina

1.7 ml microcentrifuge tube 1 15C to 30C User




Preparation} Remove the 2N NaOH, Enrichment Elution Buffer 1, and Enrichment Wash Solution

from -15Cto-25C storage and thaw at room temperature.} Remove the Elute Target Buffer 2 and Streptavidin Magnetic Beads from 2Cto8C

storage and let stand at room temperature.NOTEMake sure that you use the Streptavidin Magnetic Beads (2 ml tube) and not the SamplePurification Beads (15 ml tube) for this procedure.

} Pre-heat the microheating system to 50C.

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32 Part # 15037436 Rev. F

} Label a new 96-well MIDI plate NEW1 (Nextera Enrichment Wash 1) with a smudgeresistant pen.

} Label a new 96-well HSP plate NEH2 (Nextera Enrichment Hyb 2) with a smudgeresistant pen.

First Bind1 Remove the NEH1 plate from the thermal cycler.


3 Remove the adhesive seal from the NEH1 plate. Take care when removing the seal toavoid spilling the contents of the wells.

4 Transfer the entire contents (~100 l) from each well of the NEH1 plate to thecorresponding well of the new 96-well MIDI plate labeled NEW1.

NOTEIf an overnight First Hybridization was performed, it is normal to see a small degree ofsample loss. However, if the sample loss is greater than 15%, Illumina does notrecommend proceeding with the sample preparation. Poor sealing or not heating the lidcan cause this amount of loss.

5 Vortex the Streptavidin Magnetic Beads tube until the beads are well dispersed, thenadd 250l well-mixed Streptavidin Magnetic Beads to the wells of the NEW1 plate.

6 Mix thoroughly as follows:a Seal the NEW1 plate with a Microseal B adhesive seal.b Shake the NEW1 plate on a microplate shaker at 1200rpm for 5minutes.

7 Let the NEW1 plate stand at room temperature for 25minutes.

8 Centrifuge the NEW1 plate at 280 g for 1 minute.

9 Remove the adhesive seal from the NEW1 plate.

10 Place the NEW1 plate on the magnetic stand for 2minutes at room temperature oruntil the liquid is clear.

11 Carefully remove and discard all of the supernatant from each well of the NEW1 platewithout disturbing the beads.

12 Remove the NEW1 plate from the magnetic stand.

FirstCapture


First Wash1 Make sure that the Enrichment Wash Solution tube is at room temperature, then

thoroughly vortex the tube.NOTEIt is normal that the Enrichment Wash Solution can be cloudy after vortexing.

2 Add 200 l Enrichment Wash Solution to each well of the NEW1 plate.

3 Mix thoroughly as follows:a Seal the NEW1 plate with a Microseal B adhesive seal.b Shake the NEW1 plate on a microplate shaker at 1800rpm for 4minutes.c Remove the adhesive seal from the NEW1 plate.d Gently pipette the entire volume of each well up and down to ensure complete

resuspension of the sample.

4 Seal the NEW1 plate with a Microseal B adhesive seal.

5 Place the sealed NEW1 plate on the pre-heated microheating system. Close the lid andincubate at 50C for 30minutes.

6 Place the magnetic stand next to the microheating system for immediate access.

7 Remove the NEW1 plate from the microheating system and immediately place it on themagnetic stand for 2minutes or until the liquid is clear.


9 Immediately remove and discard all of the supernatant from each well of the NEW1plate.


11 Repeat steps 210 one time for a total of two Enrichment Wash Solution washes.

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34 Part # 15037436 Rev. F

First Elution1 Add the following reagents in the order listed in a new 1.7 ml microcentrifuge tube to

create the elution pre-mix. Multiply each volume by the number of pooled samplesbeing prepared. The volumes include an excess amount for processing multiplesamples.

Reagent Volume (l)Enrichment Elution Buffer 1 28.52N NaOH 1.5Total Volume per Sample 30

2 Vortex the elution pre-mix tube, then add 23 l of the mix to each well of the NEW1plate.




6 Carefully remove the adhesive seal from the NEW1 plate to avoid spilling the contentsof the wells.

7 Place the NEW1 plate on the magnetic stand for 2minutes or until the liquid is clear.

8 Transfer 21 l of clear supernatant from each well of the NEW1 plate to thecorresponding well of the new HSP plate labeled NEH2. Take care not to disturb thebeads.


9 Add 4 l Elute Target Buffer 2 to each well of the NEH2 plate containing samples toneutralize the elution.

FirstCapture


10 Mix thoroughly as follows:a Seal the NEH2 plate with a Microseal B adhesive seal.b Shake the NEH2 plate on a microplate shaker at 1200rpm for 1minute.


12 Store the remaining reagents as follows:a Place the Elute Target Buffer 2 and Streptavidin Magnetic Beads tubes in 2C to 8C

storage.b Place the 2N NaOH, Enrichment Elution Buffer 1, and Enrichment Wash Solution

tubes in -15Cto-25C storage.c Discard any remaining elution pre-mix.

SAFESTOPPINGPOINTIf you do not plan to proceed immediately to Second Hybridization on page 36, you can safelystop the protocol here. If you are stopping, seal the NEH2 plate with a Microseal B adhesiveseal and store it at -15Cto-25C for up to 7 days.

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36 Part # 15037436 Rev. F

SecondHybridization

This process combines the eluted DNA library from the first enrichment round withadditional capture probes to targeted regions of interest. This second hybridization isrequired to ensure high specificity of the captured regions.

Consumables


One of the following,depending on the kit you areusing: Coding Exome Oligos (CEX) Expanded Exome Oligos(EEX)

Rapid Capture Oligos (RCO)


Enrichment Hybridization(EHB) Buffer




Preparation} Remove the following from -15Cto-25C storage and thaw them at room temperature:

Enrichment Hybridization Buffer One of the following, depending on the kit you are using:

Coding Exome Oligos Expanded Exome Oligos Rapid Capture Oligos

} Remove the Resuspension Buffer from 2Cto8C storage and bring it to roomtemperature.

SecondHybridization


} Remove the NEH2 plate from -15C to -25C storage, if it was stored at the conclusionof First Capture and thaw on ice. Centrifuge the thawed NEH2 plate at 280 g for 1 minute.

Procedure1 Thoroughly vortex the Enrichment Hybridization Buffer tube until the solution is

completely resuspended. Visually make sure that no crystal structures are present.NOTEIf crystals and cloudiness are observed, vortex the Enrichment Hybridization Buffer tubeuntil it is clear.

2 Remove the adhesive seal from the NEH2 plate.

3 Add the following reagents in the order listed to each well of the NEH2 plate:

Reagent Volume (l)Resuspension Buffer 15Enrichment Hybridization Buffer 50Coding Exome Oligos,Expanded Exome Oligos, orRapid Capture Oligos

10

4 Mix thoroughly as follows:a Seal the NEH2 plate with a Microseal B adhesive seal. Make sure that the plate is

tightly sealed to prevent potential evaporation. Use an adhesive seal roller to applyforce to the seal and make sure that the seal is secured.

b Shake the NEH2 plate on a microplate shaker at 1200rpm for 1minute


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38 Part # 15037436 Rev. F

6 Place the sealed NEH2 plate on the pre-programmed thermal cycler. Close the lid, thenselect and run the NRC HYB program.a Choose the pre-heat lid option and set to 100Cb 95C for 10minutesc 18 cycles of 1 minute incubations, starting at 94C, then decreasing 2C per cycled 58C for foreverIncubate the plate at the 58C holding temperature overnight for at least 14.5 hours andup to a maximum of 24 hours. Do not remove the plate from 58C incubation until youare ready to proceed to Second Capture on page 39.

SecondCapture


SecondCapture

This process uses streptavidin beads to capture probes hybridized to the targeted regions ofinterest. Two heated wash procedures remove non-specific binding from the beads. Theenriched library is then eluted from the beads and prepared for sequencing.

NOTEThese procedures are similar to the First Capture on page 31.

Consumables


2N NaOH (HP3) 1 tube -15C to -25C Illumina

Elute Target Buffer 2 (ET2) 1 tube 2C to 8C Illumina

Enrichment Elution Buffer 1 (EE1) 1 tube -15C to -25C Illumina

Enrichment Wash Solution (EWS) 1 tube -15C to -25C Illumina

Streptavidin Magnetic Beads (SMB) 1 tube 2C to 8C Illumina

1.7 ml microcentrifuge tube 1 15C to 30C User

96-well MIDI plates 2 15C to 30C User


Preparation} Remove the 2N NaOH, Enrichment Elution Buffer 1, and Enrichment Wash Solution

from -15Cto-25C storage and thaw at room temperature.} Remove the Elute Target Buffer 2 and Streptavidin Magnetic Beads from 2Cto8C

storage and let stand at room temperature.NOTEMake sure that you use the Streptavidin Magnetic Beads (2 ml tube) and not the SamplePurification Beads (15 ml tube) for this procedure.

} Pre-heat the microheating system to 50C.

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40 Part # 15037436 Rev. F

} Label a new 96-well MIDI plate NEW2 (Nextera Enrichment Wash 2) with a smudgeresistant pen.

} Label a new 96-well MIDI plate NEC1 (Nextera Enriched Clean Up 1) with a smudgeresistant pen.

Second Bind1 Remove the NEH2 plate from the thermal cycler.

2 Centrifuge the room temperature NEH2 plate at 280 g for 1 minute.

3 Remove the adhesive seal from the NEH2 plate. Take care when removing the seal toavoid spilling the contents of the wells.

4 Transfer the entire contents (~100 l) from each well of the NEH2 plate to thecorresponding well of the new 96-well MIDI plate labeled NEW2.

NOTEIt is normal to see a small degree of sample loss after overnight hybridization. However,if the sample loss is greater than 15%, Illumina does not recommend proceeding withthe sample preparation. Poor sealing or not heating the lid can cause this amount of loss.

5 Vortex the Streptavidin Magnetic Beads tube until the beads are well dispersed, thenadd 250l well-mixed Streptavidin Magnetic Beads to the wells of the NEW2 plate.

6 Mix thoroughly as follows:a Seal the NEW2 plate with a Microseal B adhesive seal.b Shake the NEW2 plate on a microplate shaker at 1200rpm for 5minutes




10 Place the NEW2 plate on the magnetic stand for 2minutes at room temperature oruntil the liquid is clear.

11 Carefully remove and discard all of the supernatant from each well of the NEW2 platewithout disturbing the beads.


SecondCapture


SecondWash1 Make sure that the Enrichment Wash Solution tube is at room temperature, then

thoroughly vortex the tube.NOTEIt is normal that the Enrichment Wash Solution can be cloudy after vortexing.

2 Add 200 l Enrichment Wash Solution to each well of the NEW2 plate.

3 Mix thoroughly as follows:a Seal the NEW2 plate with a Microseal B adhesive seal.b Shake the NEW2 plate on a microplate shaker at 1800rpm for 4minutesc Remove the adhesive seal from the NEW2 plate.d Gently pipette the entire volume of each well up and down to ensure complete

resuspension of the sample.

4 Seal the NEW2 plate with a Microseal B adhesive seal.

5 Incubate the NEW2 plate on the pre-heated microheating system, with the lid closed, at50C for 30minutes.

6 Place the magnetic stand next to the microheating system for immediate access.

7 Remove the NEW2 plate from the microheating system and immediately place it on themagnetic stand for 2minutes or until the liquid is clear.


9 Immediately remove and discard all of the supernatant from each well of the NEW2plate.


11 Repeat steps 210 one time for a total of two Enrichment Wash Solution washes.

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42 Part # 15037436 Rev. F

Second Elution1 Add the following reagents in the order listed in a new 1.7 ml microcentrifuge tube to

create the elution pre-mix. Multiply each volume by the number of pooled samplesbeing prepared. The volumes include an excess amount for processing multiplesamples.

Reagent Volume (l)Enrichment Elution Buffer 1 28.52N NaOH 1.5Total Volume per Sample 30

2 Vortex the elution pre-mix tube, then add 23 l of the mix to each well of the NEW2plate.




6 Carefully remove the adhesive seal from the NEW2 plate to avoid spilling the contentsof the wells.

7 Place the NEW2 plate on the magnetic stand for 2minutes or until the liquid is clear.

8 Transfer 21 l of clear supernatant from each well of the NEW2 plate to thecorresponding well of the new MIDI plate labeled NEC1. Take care not to disturb thebeads.


9 Add 4 l Elute Target Buffer 2 to each well of the NEC1 plate containing samples toneutralize the elution.

SecondCapture


10 Mix thoroughly as follows:a Seal the NEC1 plate with a Microseal B adhesive seal.b Shake the NEC1 plate on a microplate shaker at 1800rpm for 1minute.

11 Centrifuge the NEC1 plate at 280 g for 1 minute.

12 Store the remaining reagents as follows:a Place the Elute Target Buffer 2 and Streptavidin Magnetic Beads tubes in 2C to 8C

storage.b Place the 2N NaOH, Enrichment Elution Buffer 1, and Enrichment Wash Solution

tubes in -15Cto-25C storage.c Discard any remaining elution pre-mix.

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44 Part # 15037436 Rev. F

Capture SampleCleanUp

This process uses Sample Purification Beads to purify the captured library before PCRamplification.

Consumables








Preparation} Remove the Resuspension Buffer and Sample Purification Beads from 2Cto8C

storage and bring them to room temperature.} Label a new 96-well HSP plate NEA (Nextera Enrichment Amplification) with a

smudge resistant pen.

Procedure1 Remove the adhesive seal from the NEC1 plate.

2 Vortex the Sample Purification Beads tube until the beads are well dispersed, then add45 l well-mixed Sample Purification Beads to each well of the NEC1 plate.


4 Incubate the NEC1 plate at room temperature for 10 minutes.


CaptureSam

pleClean

Up


6 Remove the adhesive seal from the NEC1 plate.

7 Place the NEC1 plate on the magnetic stand for 2 minutes or until the liquid is clear.

8 Remove and discard all of the supernatant from each well of the NEC1 plate.NOTELeave the NEC1 plate on the magnetic stand while performing the following 80% EtOHwash steps (912).

9 With the NEC1 plate on the magnetic stand, slowly add 200 l freshly made80%EtOH to each well without disturbing the beads.

10 Let the NEC1 plate stand at room temperature for 30seconds.

11 Remove and discard the 80% EtOH from each well of the NEC1 plate.


13 Using a 20 l single channel or multichannel pipette, remove any remaining80%EtOH from each well of the NEC1 plate without disturbing the beads.

14 Let the NEC1 plate stand at room temperature for 10 minutes to dry on the magneticstand.

15 Remove the NEC1 plate from the magnetic stand.

16 Add 27.5 l Resuspension Buffer to each well of the NEC1 plate. Do not touch thebeads with the pipette tips.



19 Centrifuge the NEC1 plate at 280g for 1minute.


21 Place the NEC1 plate on the magnetic stand for 2 minutes or until the liquid is clear.

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46 Part # 15037436 Rev. F

22 Transfer 25 l of clear supernatant from each well of the NEC1 plate to thecorresponding well of the new HSP plate labeled NEA. Take care not to disturb thebeads.


SAFESTOPPINGPOINTIf you do not plan to proceed immediately to Second PCR Amplification on page 47, you cansafely stop the protocol here. If you are stopping, seal the NEA plate with a Microseal Badhesive seal and store it at -15Cto-25C for up to 7 days.

SecondPCR

Amplification


SecondPCRAmplification

This process uses PCR to amplify the enriched DNA library for sequencing.

Consumables


Nextera EnrichmentAmplification Mix (NEM)


PCR Primer Cocktail (PPC) 1 tube -15C to -25C Illumina

Microseal 'A' film 1 15C to 30C User


Preparation} Remove the Nextera Enrichment Amplification Mix and PCR Primer Cocktail from

-15Cto-25C storage and thaw on ice. Briefly centrifuge the thawed Nextera Enrichment Amplification Mix and PCR

Primer Cocktail tubes for 5seconds.NOTEIf you do not intend to consume the Nextera Enrichment Amplification Mix and PCRPrimer Cocktail in one use, dispense the reagents into single use aliquots. Freeze thealiquots to avoid repeated freeze thaw cycles.

} Remove the NEA plate from -15C to -25C storage, if it was stored at the conclusion ofSecond Capture and thaw on ice. Centrifuge the thawed NEA plate at 280 g for 1 minute. Remove the adhesive seal from the thawed NEA plate.

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48 Part # 15037436 Rev. F

} Pre-program the thermal cycler with the following program and save as AMP10 orNEM AMP12, depending on the number of PCR cycles: Choose the pre-heat lid option and set to 100C 98C for 30seconds 10 or 12 cycles of:


72C for 5minutes Hold at 10C

NOTE For large capture target sizes (for example, > 2 Mb), Illumina recommends 10 cyclesof PCR.

For small capture target sizes (for example, < 2 Mb), Illumina recommends 12 cyclesof PCR, to ensure adequate yields for clustering and sequencing.

The total target size of your Nextera Rapid Capture Enrichment pool can be found inone of the following locations: For Custom projects, see the Design Summary section of the Project Dashboard foryour Nextera Rapid Capture Custom Enrichment Project. You can accessDesignStudio through your MyIllumina account.

For Illumina pre-designed Nextera Rapid Capture Enrichment products, see theNextera Rapid Capture Enrichment data sheets. You can download Nextera RapidCapture Enrichment data sheets from the Illumina website atsupport.illumina.com/sequencing/kits.ilmn. Click Documentation & Literature on Nextera Rapid Capture Exome andExpanded Exome Enrichment Kits Support or

Click Documentation & Literature on Nextera Rapid Capture CustomEnrichment Kits Support

NOTEIllumina has optimized the number of recommended PCR cycles for enrichment assaysbased on the level of pre-enrichment sample pooling and the size of the oligonucleotideset. Do not add or reduce the cycles of PCR, because it can compromise data quality.

Procedure1 Add 5 l PCR Primer Cocktail to each well of the NEA plate.

2 Add 20 l Nextera Enrichment Amplification Mix to each well of the NEA plate.

SecondPCR

Amplification


3 Mix thoroughly as follows:a Seal the NEA plate with a Microseal A film. Use an adhesive seal roller to apply

force to the film and make sure that the film is secured.b Shake the NEA plate on a microplate shaker at 1200rpm for 1minute

4 Centrifuge the NEA plate at 280 g for 1 minute.

5 Place the sealed NEA plate on the pre-programmed thermal cycler. Close the lid, thenselect and run the NEM AMP10 or NEM AMP12 program as follows, depending onthe number of PCR cycles:a Choose the pre-heat lid option and set to 100Cb 98C for 30secondsc 10 or 12 cycles of:


d 72C for 5minutese Hold at 10C

SAFESTOPPINGPOINTIf you do not plan to proceed immediately to Second PCR Clean Up on page 50, the NEA platecan remain on the thermocycler overnight. If you are stopping, replace the Microseal 'A' filmwith a Microseal 'B' adhesive seal and store the NEA plate at 2C to 8C for up to two days.

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50 Part # 15037436 Rev. F

SecondPCRCleanUp

This process uses Sample Purification Beads to purify the enriched library and removeunwanted products.

Consumables









Preparation} Review Best Practices for Handling Magnetic Beads. See Additional Resources on page 4

for information on how to access Nextera Rapid Capture Enrichment Best Practices onthe Illumina website.

} Remove the Resuspension Buffer and Sample Purification Beads from 2Cto8Cstorage and bring them to room temperature.

} Remove the NEA plate from 2C to 8C storage, if it was stored at the conclusion ofSecond PCR Amplification and let stand to bring to room temperature.

} Label a new 96-well MIDI plate NEC2 (Nextera Enriched Clean Up 2) with a smudgeresistant pen.

} Label a new 96-well HSP plate NEL (Nextera Enrichment Library) with a smudgeresistant pen.

SecondPCR

CleanUp


Procedure1 Centrifuge the NEA plate at 280 g for 1 minute.

2 Remove the adhesive seal from the NEA plate.

3 Transfer the entire contents from each well of the NEA plate to the corresponding wellof the new 96-well MIDI plate labeled NEC2.

4 Vortex the Sample Purification Beads until the beads are well dispersed.

5 Add 90l well-mixed Sample Purification Beads to each well of the NEC2 platecontaining 50l of PCR amplified library.





10 Place the NEC2 plate on the magnetic stand at room temperature for 2minutes or untilthe liquid is clear.

11 Carefully remove and discard all of the supernatant from each well of the NEC2 plate.NOTELeave the NEC2 plate on the magnetic stand while performing the following 80% EtOHwash steps (1215).

12 With the NEC2 plate on the magnetic stand, slowly add 200l freshly prepared80%EtOH to each well without disturbing the beads.

13 Let the NEC2 plate stand at room temperature for 30 seconds.

14 Remove and discard the 80% EtOH from each well of the NEC2 plate.


16 Using a 20 l single channel or multichannel pipette, remove any remaining80%EtOH from each well of the NEC2 plate without disturbing the beads.

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52 Part # 15037436 Rev. F

17 Let the NEC2 plate stand at room temperature for 10 minutes to dry on the magneticstand.

18 Remove the NEC2 plate from the magnetic stand.

19 Add 32 l Resuspension Buffer to each well of the NEC2 plate. Do not touch the beadswith the pipette tips.



22 Centrifuge the NEC2 plate at 280g for 1minute.


24 Place the NEC2 plate on the magnetic stand for 2minutes or until the liquid is clear.

25 Transfer 30 l of clear supernatant from each well of the NEC2 plate to thecorresponding well of the new HSP plate labeled NEL. Take care not to disturb thebeads.

NOTEIllumina recommends using a 20 l single channel or multichannel pipette set to 15 l toperform two consecutive transfers of 15 l. This technique reduces sample loss bymaking sure that all of the liquid is transferred without disturbing the beads.

26 Seal the NEL plate with a Microseal B adhesive seal.SAFESTOPPINGPOINTIf you do not plan to proceed immediately to Validate Library on page 53, store the sealedNEL plate at -15C to -25C for up to 7 days. If the plate is stored for more than 7 days,requantify your library to guarantee the accuracy of your enrichment results.

ValidateLibrary


Validate Library

Illumina recommends performing the following procedures for quality control analysis andquantification of your enriched library.

Quantify LibrariesTo achieve the highest data quality on Illumina sequencing platforms, it is important tocreate optimum cluster densities across every lane of every flow cell. Optimizing clusterdensities requires accurate quantitation of DNA library templates.Quantify the post-enriched library in the NEL plate using a fluorometric method. See DNAQuantitation on page 92 for an example protocol using the Promega QuantiFluor method.

NOTEUse the following formula to convert from ng/l to nM. Assume a 400 bp library size orcalculate based on the average size of the enriched library:

(concentration in ng/l)(660 g/mol *average library size)

x 10^6 = concentration in nM

For example:15 ng/l)

(660 g/mol *400)x 10^6 = 57 nM

Alternatively, you can quantitate libraries using qPCR according to the Sequencing LibraryqPCR Quantification Guide (part # 11322363).

NOTESee Additional Resources on page 4 for information on how to download the SequencingLibrary qPCR Quantification Guide (part # 11322363) from the Illumina website.

Results can vary based on your method of quantification. When quantitation is complete,proceed to cluster generation. For cluster density information, see the cluster generationsection of the user guide for your Illumina sequencing platform. Also see the Nextera RapidCapture Enrichment requirements and compatibility information on the Illumina website.} Click Requirements & Compatibility on Nextera Rapid Capture Exome and

Expanded Exome Enrichment Kits Support or} Click Requirements & Compatibility on Nextera Rapid Capture Custom Enrichment

Kits Support

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54 Part # 15037436 Rev. F

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