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- Study Description
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Important Links and Information
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- Instructions for requestors
- Data Use Certification (DUC) Agreement
- Talking Glossary of Genetic Terms
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.
- Study Design:
- Tumor vs. Matched-Normal
- Study Type:
- Mixed
- Cross-Sectional
- Tumor vs. Matched-Normal
- Total number of consented subjects: 10
- Subject Sample Telemetry Report (SSTR)
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- Authorized Access
- Publicly Available Data
- Link to other NCBI resources related to this study
- Study Inclusion/Exclusion Criteria
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.
- Molecular Data
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Type Source Platform Number of Oligos/SNPs SNP Batch Id Comment Targeted DNA Sequencing Illumina MiSeq N/A N/A - Selected Publications
- Diseases/Traits Related to Study (MeSH terms)
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- Study Attribution
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Principal Investigator
- Sameek Roychowdhury, MD, PhD. The Ohio State University, Columbus, OH, USA.
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Funding Source
- MRSG-12-194-01-TBG (Prostate Cancer Foundation). American Cancer Society, Atlanta, GA, USA.
- UM1HG006508-01A1 (Young Investigator Award). Fore Cancer Research, Pelotonia, Columbus, OH, USA.
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Principal Investigator