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Title: Comparison of custom capture for targeted next generation DNA sequencing      
citations:
25528188
description:
Targeted, capture-based DNA sequencing is an economical way to sequence a customized region of the genome. Several targeted sequencing kits are available, but the efficacies of these kits have not been compared. We appraised four targeted DNA technologies for next generation sequencing, considering on-target sequencing, uniformity, and single nucleotide variation and copy number variation discovery. The technologies which utilized sonication to fragment genomic material showed impressive uniformity of capture. The other two had shorter preparation times, but sacrificed uniformity. One of those technologies, which needs transposase to fragment genomic material, has a weakness that requires all samples be pooled and the final one, which uses restriction enzyme digestion, is limited depending on restriction enzymes digest sites. Naturally, all technologies showed some concordance for calling SNVs, the kits that used restriction enzymes or transposase missed several SNVs, due, in large part, to lack of coverage. All technologies showed high integrity for copy number variant calling when compared to SNP arrays. This study aids laboratories in their decision of the proper technology to use for their intended applications.
Identifier:
phs000811.v1.p1
accesstypes:
download
enclave
landingpage: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000811.v1.p1
authentication: simpleLogin
none
authorization:
none
duaIndividual
name:
Neoplasms
DNA
Genome
affiliations:
The Ohio State University, Columbus, OH, USA
name:
Sameek Roychowdhury, MD, PhD
roles:
Principal Investigator
affiliations:
American Cancer Society, Atlanta, GA, USA
name:
MRSG-12-194-01-TBG (Prostate Cancer Foundation)
roles:
Funding Source
affiliations:
Fore Cancer Research, Pelotonia, Columbus, OH, USA
name:
UM1HG006508-01A1 (Young Investigator Award)
roles:
Funding Source
performedBy:
TitleNameInstitute Principal InvestigatorSameek Roychowdhury, MD, PhDThe Ohio State University, Columbus, OH, USA Funding SourceMRSG-12-194-01-TBG (Prostate Cancer Foundation)American Cancer Society, Atlanta, GA, USA Funding SourceUM1HG006508-01A1 (Young Investigator Award)Fore Cancer Research, Pelotonia, Columbus, OH, USA
downloadURL: https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=DUC&view_pdf&stacc=phs000811.v1.p1
Identifier:
phs000811.v1.p1_policy
name:
Data Use Certificate
Identifier:
1
name:
General Research Use
alternateIdentifiers:
yes
selectionCriteria:

We used matched six pairs of tumor and normal samples, where tumor purity was at least 60%. We also used one cell and its matched B-lymphoblastoid cell line. We used two well-characterized cancer cell lines.

dateReleased:
10-03-2014
version:
phs000811.v1.p1
dateModified:
01-06-2015
abbreviation:
NHGRI
name:
National Human Genome Research Institute
ID:
0
name:
dbGaP