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SRX1156924: Targeted sequencing of human: control normal DNA: Sample C47
1 ILLUMINA (Illumina HiSeq 2500) run: 40M spots, 8G bases, 4.9Gb downloads

Design: Targeted re-sequencing genes were chosen based upon mutation in the original whole exome pathway and additional targets related to genes that were mutated. Targeted re-sequencing libraries were prepared using the Illumina Tru-Seq kit (starting with 1ug genomic DNA) with barcodes. Libraries were pooled and capture performed with two distinct capture reagents targeting (1.2 and 3.1 Mb) (SeqCap EZ, NimbleGen [Roche]). The SeqCap EZ custom capture reagent is a solution based capture that uses isolates regions of interest from pre-prepared libraries to enable targeted capture followed by re-sequencing. Prior to library preparation, certain DNA samples without sufficient starting material were whole genome amplified (GenomePlex, Sigma). The libraries were sequenced with the Illumina HiSeq platform using 101 bp paired-end sequencing.
Submitted by: phs000913-Stanford
Study: Genomic Analysis of Mycosis Fungoides and Sézary Syndrome Identifies Recurrent Alterations in TNFR2
show Abstracthide Abstract
Mycosis Fungoides (MF) and Sezary Syndrome (Sz) comprise the majority of Cutaneous T-Cell Lymphoma (CTCL) cases and are characterized by clinical heterogeneity. This array of symptoms includes skin patches, plaques and tumors as well as blood involvement and erythroderma. Because the genetic basis of CTCL is still poorly understood, we performed whole-exome sequencing on 11 MF/Sz samples and their matched, normal control DNA. Upon analyzing this data, we distilled a list of an additional 494 genes to be sequenced at depth. The majority of these 494 genes were sequenced in the exons alone, however, for a small subset of these genes we sequenced the entire genomic locus in search of structural variation events. This 494 gene targeted resequencing effort was performed upon 72 patients with MF/Sz and their matched, normal control DNA. An additional 5 MF/Sz and matched, normal DNA samples underwent whole genome amplification (WGA) prior to library preparation... (for more see dbGaP study page.)
Sample: Non-tumor DNA sample from PBMC CD4- of a human participant in the dbGaP study "Genomic Analysis of Mycosis Fungoides and Sézary Syndrome"
SAMN03895663 • SRS1038795 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: C47
Instrument: Illumina HiSeq 2500
Strategy: WXS
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Spot descriptor:
forward102  reverse

The SRA run(s) below contain human sequence (more...)(less...)

These data are available through the dbGaP authorized access system. Request access to:

  • Study:  phs000913
  • Consent Group: HMB

Runs: 1 run, 40M spots, 8G bases, 4.9Gb
Run# of Spots# of BasesSizePublished
SRR217181340,015,8018G4.9Gb2015-09-01

ID:
1682153

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