3 Cancer Cell lines on 2 sequencers
This website is intended to be a companion to the paper published in Scientific Reports, to host some important files (also accessible elsewhere) and present additional figures and reports.
Publication
The paper is now available in Scientific Reports
Pipeline
The cell lines were processed through NYGC’s Somatic Pipeline, summarized here:
Data availability
The raw data is available on dbGAP.
The somatic variant files, obtained from the high-coverage data are accessible below (or directly in Variants.HighCoverage.tar.gz 140MB):
| Cell line | SNV/indel | CNV | SV | SV high confidence |
| COLO-829 (HiSeqX) | VCF | BED | bedpe | bedpe |
| COLO-829 (NovaSeq) | VCF | BED | bedpe | bedpe |
| HCC-1143 (HiSeqX) | VCF | BED | bedpe | bedpe |
| HCC-1143 (NovaSeq) | VCF | BED | bedpe | bedpe |
| HCC-1187 (HiSeqX) | VCF | BED | bedpe | bedpe |
| HCC-1187 (NovaSeq) | VCF | BED | bedpe | bedpe |
The somatic variant files obtained from downsampled 40X/80X coverage are accessible below (or directly in Variants.Downsampled.tar.gz 89MB):
| Cell line | SNV/indel | CNV | SV | SV high confidence |
| COLO-829 (HiSeqX) | VCF | BED | bedpe | bedpe |
| COLO-829 (NovaSeq) | VCF | BED | bedpe | bedpe |
| HCC-1143 (HiSeqX) | VCF | BED | bedpe | bedpe |
| HCC-1143 (NovaSeq) | VCF | BED | bedpe | bedpe |
| HCC-1187 (HiSeqX) | VCF | BED | bedpe | bedpe |
| HCC-1187 (NovaSeq) | VCF | BED | bedpe | bedpe |
Sample reports
Reports summarizing the results of our pipeline for each tumor-normal pair:
| Cell line | Report |
| 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
