Targeted Sequencing and Variant Calling

Capture was performed using SeqCap EZ Exome v2.0 (Roche Nimblegen) (n=86) and TruSeq Exome Enrichment Kit (Illumina) (n=3). Sequencing was performed using SOLiD™ 3.5 (n=8), SOLiD™ 4 (n=28), 5500xl SOLiD™ (n=12) (Life Technologies), GAIIX (n=2) and HiSeq (n=39) instruments (Illumina). Mapping to the human reference genome build hg19 was performed using BioScope v1.2 (SOLiD™ 3.5 data), BioScope v1.3 (SOLiD™ 4 data), LifeScope 2_5.1 (5500xl SOLiD™ data), bwa 0.6.2 (32 (link)) (GAIIX data), Novoalign (HiSeq data, n=40) and bwa 0.7.5a (HiSeq data, n=3). Local realignment was performed using the GATK 1.5-25 RealignerTargetCreator and IndelRealigner modules, duplicates were removed using Picard MarkDuplicates 1.29, and sorting and indexing were performed using SAMtools 0.1.8. Variant calling was conducted using the GATK 1.5-25 UnifiedGenotyper module. Variant calls were filtered to the capture target regions using BEDtools 2.16.2 (33 (link)) and bed files provided by the manufacturers. Further filtering was performed using FAVR (34 (link)). Annotation was performed using ANNOVAR (35 (link)).

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Park D.J., Tao K., Le Calvez-Kelm F., Nguyen-Dumont T., Robinot N., Hammet F., Odefrey F., Tsimiklis H., Teo Z.L., Thingholm L.B., Young E.L., Voegele C., Lonie A., Pope B.J., Roane T.C., Bell R., Hu H., S.h.a.n.k.a.r.a.c.h.a.r.y.a., Huff C.D., Ellis J., Li J., Makunin I.V., John E.M., Andrulis I.L., Terry M.B., Daly M., Buys S.S., Snyder C., Lynch H.T., Devilee P., Giles G.G., Hopper J.L., Feng B.J., Lesueur F., Tavtigian S.V., Southey M.C, & Goldgar D.E. (2014). Rare mutations in RINT1 predispose carriers to breast and Lynch Syndrome-spectrum cancers. Cancer discovery, 4(7), 804-815.

Publication 2014

SeqCap EZ Exome v2.0 TruSeq Exome Enrichment Kit SOLiD™ 4 GAIIX

Exome Further Human

Corresponding Organization : University of Utah

Other organizations : Centre International de Recherche sur le Cancer, Melbourne Bioinformatics, The University of Texas at Austin, The University of Texas MD Anderson Cancer Center, QIMR Berghofer Medical Research Institute, Cancer Prevention Institute of California, Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute, Columbia University, Fox Chase Cancer Center, Creighton University, Leiden University Medical Center, University of Melbourne, Cancer Council Victoria, Seoul National University, Inserm, École Nationale Supérieure des Mines de Paris, Institut Curie

Top 5 similar protocols

Variable analysis

independent variables

Capture method (SeqCap EZ Exome v2.0 (Roche Nimblegen), TruSeq Exome Enrichment Kit (Illumina))
Sequencing instrument (SOLiD™ 3.5, SOLiD™ 4, 5500xl SOLiD™, GAIIX, HiSeq)

dependent variables

Sequencing data
Mapped reads
Variant calls

control variables

Human reference genome build hg19
Bioinformatics tools (BioScope, LifeScope, bwa, Novoalign, GATK, Picard, SAMtools, BEDtools, FAVR, ANNOVAR)

positive controls

Not specified

negative controls

Not specified

Annotations

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