SeqCap EZ Prime ExomeEfficient and reliable whole-exome sequencing

ASeptember 8, 2016, BWhen using 5 μg of amplified library pool in the hybridization For Research Use Only. Not for use in diagnostic procedures.

DISCOVER MORESEQUENCE LESS

NEW SeqCap EZ Prime Exome offers comprehensive coverage and enhanced uniformity with low sequencing requirements. Based on the GRCh38/hg38 human genome assembly, the compact capture target (37 Mb) efficiently covers 98.1% of the coding regions in CCDS Rel.20A. SeqCap EZ Prime Exome also enables accurate, convenient sample tracking by targeting 340 carefully selected SNPs, increasing reliability of results.

• 40M high-quality reads per sample cover 96.3% of the primary target at 20XB

• Uniform whole-exome coverage reduces sequencing costs

• Broad coverage of medically relevant regions within the CCDS Database

• Sample-intrinsic tracking minimizes sample mix-ups without the need for spike-in ID panels

• The HyperCap Workflow with SeqCap EZ Prime Exome streamlines the production of target-enriched libraries and ensures integrated support and one-source purchasing from a single, trusted vendor

Sample Sequencing Ready Library

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2Data on file.

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

Increase sequencing efficiency• Achieve high on-target rates (close to 90%) and excellent coverage uniformity

• Cover ≥96% of target bases at ≥20X with 40M high-quality reads, starting with 100 ng of input DNA into library preparation

Cover more medically relevant genes• Discover more variants with less sequencing; 27% fewer reads yield better coverage than Supplier I’s exome panel

• Improve coverage of ACMG1, ClinVar2, CCDS, and 4589 medically relevant genes3 compared to Supplier I’s exome panel

Total duplicaterate

% on-target(Unique reads

on primarytarget)

% on-target(Unique reads

on primarytarget,

+/- 100 bp)

Fold 80base penalty

Mean targetcoverage

Median targetcoverage

% bases ≥20X % bases ≥30X

SeqCap EZ Prime Exome performance metrics

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NA12891_A

HapMap DNAsamples

NA12891_BNA12892_ANA12892_BNA18555_ANA18555_BNA18572_ANA18572_BNA18947_ANA18947_BNA19007_ANA19007_BNA19238_ANA19238_BNA19239_ANA19239_B

88.9% 1.63 55X 49X 96.3% 86.8%73.5%3.6%

90.0 90.589.5

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ACMG 59 ClinVar 4589 medicalresearch genes

CCDS Exome

Bases (%) covered at ≥20X

SeqCap EZ Prime Exome (40M reads; n=8)

Supplier I (55M reads; n=6)

93.5

90.4

87.3

88.7

87.0

Figure 1. SeqCap EZ Prime Exome yields high on-target rates and ≥20X coverage depth from only 40M reads per sample. Target-enriched libraries were prepared using 100 ng of Coriell DNA as input into the HyperCap v2.1 Workflow, with the KAPA HyperPrep Kit and SeqCap EZ Prime Exome. Pre-capture multiplex pools were prepared in duplicate (A and B); each multiplexed capture contained libraries from 8 different Coriell HapMap DNA samples. Samples were processed as described in the HyperCap User’s Guide v2.1 with a simple exome-specific modification (for details, ask your local representative for the technical note “How to… Increase sequencing efficiency with the SeqCap EZ Prime Exome”). Final libraries were sequenced on an Illumina® HiSeq® 2500 System with 2 x 101 read length and a High Output v4 Kit.

Figure 2. SeqCap EZ Prime Exome delivers better coverage of target regions with 27% less sequencing. For the Prime Exome samples, target-enriched libraries were prepared from 100 ng of Coriell DNA using the HyperCap Workflow, with the KAPA HyperPlus Kit and SeqCap EZ Prime Exome. The same workflow was followed for the other samples, using Supplier I’s probes in place of Prime Exome. Sequencing was performed using an Illumina HiSeq 2500 instrument with 2 x 101 read length using v4 chemistry. For each panel, 8 replicates were prepared; only 6 of Supplier I’s samples yielded sufficient reads.

3Data on file. For Research Use Only. Not for use in diagnostic procedures.

Track each sample with sample-intrinsic SNPsResearchers often use control spike-ins to track samples throughout NGS workflows. However, sample-handling errors can still lead to incorrect sample identification. SeqCap EZ Prime Exome targets selected SNP positions to serve as intrinsic sample identifiers that are independent of sample handling.

• Detect 340 informative SNP positions4 at an average of ≥40X with 40M reads

• Eliminate the need to manually spike in content for sample tracking

• Reduce costly identification errors, increasing reliability of results

Figure 3. SeqCap EZ Prime Exome exhibits high SNP detection sensitivity, specificity, and genotype concordance. See Figure 1 caption for experimental details.

Streamline target enrichment with the HyperCap WorkflowHyperCap delivers complex libraries by combining the high conversion rate of KAPA HyperPrep and HyperPlus Kits with Roche Target Enrichment, creating a streamlined, single-vendor-supported workflow.

• Multiplex up to 96 samples with KAPA Dual-Indexed Adapters (DI Adapters)

• Reduce workflow complexity and hands-on time with Roche Universal Blocking Oligos (UBOs), eliminating the need for adapter-matched blocking oligos

KA

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Adapter Ligation with KAPA DI Adapters

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Pre-Capture Amplification and Quantification

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Amplification and Quantification

Sequencing-readyDNA in <2 days

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Sensitivity ofSNP detection

Specificity ofSNP detection

SNP genotypeconcordance

SNP detection performance metrics at 40M reads

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NA12891_ANA12891_BNA12892_ANA12892_BNA18555_ANA18555_BNA18572_ANA18572_BNA18947_ANA18947_BNA19007_ANA19007_BNA19238_ANA19238_BNA19239_ANA19239_B

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96.3% 99.4% 98.8%

HapMap DNAsamples

Data on file.For Research Use Only. Not for use in diagnostic procedures.HYPERCAP, KAPA, and SEQCAP are trademarks of Roche. All other product names and trademarks are the property of their respective owners. © 2018 Roche Sequencing and Life Science. All rights reserved. SS507001 A404 8/18

Published by:

Roche Sequencing and Life Science 9115 Hague Road Indianapolis, IN 46256

sequencing.roche.com

Ordering information

Product Name Reactions Catalog #

SeqCap EZ Share Prime Choice XL - Prime Exome Design Name: 170907_HG38_CCDS1X_REZ_HX1 Internal Reference Number: 4000035460

24 0833309200196 08333114001384 08333122001

References

1. Kalia SS, Adelman K, Bale SJ, et al. Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics Genet Med. 2017 Feb;19(2):249 – 255.

2. https://www.ncbi.nlm.nih.gov/clinvar/

3. As selected by GeneTests™

4. Pengelly RJ, Gibson J, Andreoletti G, et al. A SNP profiling panel for sample tracking in whole-exome sequencing studies. Genome Med. 2013 Sep 27;5(9):89.

SeqCap EZ Design Share: Prime ExomeSeqCap EZ Prime Exome is part of Roche Sequencing Solutions’ Design Share Portfolio. Design Share makes it easy to access pre-designed NGS panels that are developed by Roche Sequencing Solutions or in collaboration with researchers around the world. Review the full portfolio at sequencing.roche.com/designshare.

Learn about the HyperCap Workflow—an integrated, <2-day sample preparation workflow for target-enriched NGS that combines KAPA library preparation and SeqCap target enrichment probes—at sequencing.roche.com/hypercap.

Request an evaluation:go.roche.com/designsharesample