Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=27094764
&cmd=llinks): Failed to open stream: HTTP request failed! HTTP/1.1 429 Too Many Requests
in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 215
A somatic reference standard for cancer genome sequencing
#MMPMID27094764
Craig DW
; Nasser S
; Corbett R
; Chan SK
; Murray L
; Legendre C
; Tembe W
; Adkins J
; Kim N
; Wong S
; Baker A
; Enriquez D
; Pond S
; Pleasance E
; Mungall AJ
; Moore RA
; McDaniel T
; Ma Y
; Jones SJ
; Marra MA
; Carpten JD
; Liang WS
Sci Rep
2016[Apr]; 6
(?): 24607
PMID27094764
show ga
Large-scale multiplexed identification of somatic alterations in cancer has
become feasible with next generation sequencing (NGS). However, calibration of
NGS somatic analysis tools has been hampered by a lack of tumor/normal reference
standards. We thus performed paired PCR-free whole genome sequencing of a matched
metastatic melanoma cell line (COLO829) and normal across three lineages and
across separate institutions, with independent library preparations, sequencing,
and analysis. We generated mean mapped coverages of 99X for COLO829 and 103X for
the paired normal across three institutions. Results were combined with
previously generated data allowing for comparison to a fourth lineage on earlier
NGS technology. Aggregate variant detection led to the identification of
consensus variants, including key events that represent hallmark mutation types
including amplified BRAF V600E, a CDK2NA small deletion, a 12 kb PTEN deletion,
and a dinucleotide TERT promoter substitution. Overall, common events include
>35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected
by copy number changes. We present this reference to the community as an initial
standard for enabling quantitative evaluation of somatic mutation pipelines
across institutions.
free
free
free
