U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line.

PLoS Genetics
Michael James ClarkStanley F Nelson

Abstract

U87MG is a commonly studied grade IV glioma cell line that has been analyzed in at least 1,700 publications over four decades. In order to comprehensively characterize the genome of this cell line and to serve as a model of broad cancer genome sequencing, we have generated greater than 30x genomic sequence coverage using a novel 50-base mate paired strategy with a 1.4kb mean insert library. A total of 1,014,984,286 mate-end and 120,691,623 single-end two-base encoded reads were generated from five slides. All data were aligned using a custom designed tool called BFAST, allowing optimal color space read alignment and accurate identification of DNA variants. The aligned sequence reads and mate-pair information identified 35 interchromosomal translocation events, 1,315 structural variations (>100 bp), 191,743 small (<21 bp) insertions and deletions (indels), and 2,384,470 single nucleotide variations (SNVs). Among these observations, the known homozygous mutation in PTEN was robustly identified, and genes involved in cell adhesion were overrepresented in the mutated gene list. Data were compared to 219,187 heterozygous single nucleotide polymorphisms assayed by Illumina 1M Duo genotyping array to assess accuracy: 93.83% of all SNP...Continue Reading

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Methods Mentioned

BETA
genotyping
PCR
chip
pull down
deamination
Pull-Down
chromosomal aberrations
electrophoresis

Software Mentioned

ABI SOLiD
SAMtools
SeqWare LIMS
UCSC
Firecrest
Blat
Solexa
EASE
DNAA
Bustard

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