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Abstract Details

Activity Number: 468
Type: Contributed
Date/Time: Wednesday, August 1, 2012 : 8:30 AM to 10:20 AM
Sponsor: Biometrics Section
Abstract - #305424
Title: Estimating Tumor Cellularity Using Read Counts Obtained from Illumina Exome Sequencing
Author(s): Minya Pu*+ and Lei Bao and Hongying Li and Loki Natarajan and Karen Messer
Companies: University of California at San Diego and University of California at San Diego and University of California at San Diego and University of California at San Diego and University of California at San Diego
Address: 3855 Health Sciences Dr #0901, La Jolla, CA, CA 92093,
Keywords: Illumina exome sequencing ; Tumor cellularity ; Somatic variant neucleotides ; Bilateral breast tumors ; Read coverage ; Maxiumum likelihood estimates
Abstract:

Solid tumors are often a mixture of tumor and normal cells. In our study of inferring the clonality of bilateral breast tumors, 2 tumor pairs (4 total) and 2 blood samples were sequenced using next generation sequencing techniques; percent tumor cellularity of the tumors estimated by a pathologist ranged from 40% to 70%. We used read counts obtained from Illumina exome sequencing to obtain a more accurate estimate of percent cellularity along with a 95% confidence interval. In calling single neucleotide variants, we used b37 reference genome, BWA as the aligner, and GATK1.5 as the caller. Read coverage was 30X for gDNAs, and 100X or 200X for tumors with higher and lower cellularity, respectively. At each neucleotide base, we assumed that the number of alternative (different from reference) reads for germline or somatic variant neucleotides followed a Binomial distribution. Using a set of shared high confidence somatic variant calls, we show how to obtain maxiumum likelihood estimates of the percent cellularity along with a 95% confidence interval. We show how the uncertainty of the estimate depends on the number of somatic variant sites and the coverage depth.


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