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Series GSE19986 Query DataSets for GSE19986
Status Public on Jan 25, 2010
Title U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line
Organism Homo sapiens
Experiment type SNP genotyping by SNP array
Genome variation profiling by SNP array
Genome variation profiling by high throughput sequencing
Summary 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 (>100bp), 191,743 small (<21bp) 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 SNPs were reliably detected at filtering thresholds that yield greater than 99.99% sequence accuracy. Protein coding sequences were disrupted predominantly in this cancer cell line due to small indels, large deletions and translocations. In total, 512 genes were homozygously mutated, including 154 by SNVs, 178 by small indels, 145 by large microdeletions and 35 by interchromosomal translocations to reveal a highly mutated cell line genome. Of the small homozygously mutated variants, 8 SNVs and 99 indels were novel events not present in dbSNP. These data demonstrate that routine generation of broad cancer genome sequence is possible outside of genome centers. The sequence analysis of U87MG provides an unparalleled level of mutational resolution compared to any cell line to date.
 
Overall design Whole genome sequencing of the U87MG brain cancer cell line using the AB SOLiD3 sequencer and genotyping using the Illumina Human1M-Duov3 DNA Analysis BeadChip
 
Contributor(s) Nelson SF, Clark MJ
Citation(s) 20126413
Submission date Jan 21, 2010
Last update date May 15, 2019
Contact name Stanley F Nelson
E-mail(s) mjclark@ucla.edu
Phone 3108257920
Fax 3107945446
URL http://www.genetics.ucla.edu/labs/nelson/
Organization name UCLA
Department Human Genetics
Lab Nelson Lab
Street address 695 Young Dr S
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platforms (2)
GPL6984 Illumina Human1M-Duov3 DNA Analysis BeadChip (Human1M-Duov3_B)
GPL9442 AB SOLiD System 3.0 (Homo sapiens)
Samples (2)
GSM499400 U87MG-cell culture [AB SOLiD]
GSM500897 U87MG-cell culture [Illumina]
Relations
SRA SRP001699
BioProject PRJNA120147

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE19986_RAW.tar 251.0 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA
Processed data included within Sample table

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