3 Cancer Cell lines on 2 sequencers


This website is intended to be a companion to the manuscript currently on BioRxiv, to host some important files (also accessible elsewhere) and present additional figures and reports.

Manuscript

The manuscript is accessible on BioRxiV

Pipeline

The cell lines were processed through NYGC’s Somatic Pipeline, summarized here:

Data availability

The raw data will be accessible on dbGAP and we will update this website as soon as possible.

The somatic variant files, obtained from the high-coverage data are accessible below (or directly in Variants.HighCoverage.tar.gz 140MB):

Cell lineSNV/indel CNV SV SV high confidence
COLO-829 (HiSeqX)VCF BED bedpebedpe
COLO-829 (NovaSeq)VCF BED bedpebedpe
HCC-1143 (HiSeqX)VCF BED bedpebedpe
HCC-1143 (NovaSeq)VCF BED bedpebedpe
HCC-1187 (HiSeqX)VCF BED bedpebedpe
HCC-1187 (NovaSeq)VCF BED bedpebedpe

The somatic variant files obtained from downsampled 40X/80X coverage are accessible below (or directly in Variants.Downsampled.tar.gz 89MB):

Cell lineSNV/indelCNV SV SV high confidence
COLO-829 (HiSeqX)VCFBED bedpe bedpe
COLO-829 (NovaSeq)VCFBED bedpe bedpe
HCC-1143 (HiSeqX)VCFBED bedpe bedpe
HCC-1143 (NovaSeq)VCFBED bedpe bedpe
HCC-1187 (HiSeqX)VCFBED bedpe bedpe
HCC-1187 (NovaSeq)VCFBEDbedpe bedpe

QC report

The QC report is accessible via the NYGC’s Outpost interface. In addition the individual reports are in the table below (soon)

Cell lineReport
COLO-829 (HiSeqX)HTML
COLO-829 (NovaSeq)HTML
HCC-1143 (HiSeqX)HTML
HCC-1143 (NovaSeq)HTML
HCC-1187 (HiSeqX)HTML
HCC-1187 (NovaSeq)HTML

Related work

Related to the deep sequencing of cancer cell lines in HiSeqX and NovaSeq, we tested the new kit for NovaSeq, producing 2x250bp reads. We sequenced HCC-1143 (and matched normal HCC-1143-BL) and the well-characterized CEU HapMap trio (NA12878, NA12891, and NA12892).

The poster will be presented at CSHL Biology of Genomes conference on Friday, May 9th 2019 by Minita Shah and Molly Johnson and is accessible below.

Germline and somatic variant calling with NovaSeqTM 6000 2x250bp reads

Authors: Minita Shah, Marta Byrska-Bishop, Wayne E. Clarke, Molly Johnson, Kanika Arora, Rashesh Sanghvi, Uday Evani, Kshithija Nagulapalli, Michael C. Zody, Soren Germer, Jade Carter, Giuseppe Narzisi, Nicolas Robine

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