Abstract 5307: Paired analysis of matched colon normal and tumor using whole exome sequencing.
Authors: Daremipouran Mohammad , Hassanzadeh Namin Hassan , Soltani Sohaila , Devaney Joe , Frederick Wayne , Lee Edward L. , Brim Hassan , Ashktorab Hassan 
Published: August 2014

Abstract
Background: Whole Exome sequencing (WES) is a tool that is revolutionizing screening for pathogeni single nucleotide variations (SNV) in complex disorders such as cancers. Using matched normal-tumor pairs, it is possible to identify exome-wide germline and somatic variant alterations that may have an effect on disease progression or response to different interventions. The existing analysis pipelines are under continuous enhancements. In analyzing matched pairs, there is a critical assumption that the sequenced data are matched, without any quality check. Identification of germline and rare somatic variants depend on the normal sample being the qualified matched pair. Our aim was to determine if Identity By State (IBS), a genetics concept on measuring relatedness between individuals (matched tumor-normal pairs) can assess somatic landscape between individual using WES data. Materials and Methods: Genomic DNA was extracted from 8 normal-tumor pair tissues from African Americans (males n=3, females n=5) with colorectal cancer (CRC). WES was performed for identification of SNV according to manufacturer recommendations (Illumina HiScan SQ). The low quality reads were discarded and the clean reads were aligned against the human reference genome (HG19) and base quality calibration was completed using SAMTools, and GATK for variant calling and annotation. Pairs with no shared allele, one shared allele, and two shared allele assigned as IBS 0, IBS 1, and IBS 2 respectfully. Alleles in the dataset were coded using A and B and pairwise IBS was computed between all samples. Display of the IBS landscape was done using GenomeRelator. Results: The frequency of IBS from WGS data sets showed that most of the changes were IBS-1 which were heterozygous variants; i.e. AA/BB&gt;AB (somatic) or AB&gt;AA/BB (LOH). Frequency of LOH varied from 4.36% to 73.61%. Homozygous variant (i.e. IBS-0, AA&gt;BB) on the other hand was not common, from 0.00% to 4.17%. Distribution of IBS across genome for matched pairs reveals that most of the IBS were IBS-2, indicating that both alleles between matched normal and tumor were similar. Frequency of IBS-1 and IBS-0 varied amongst the samples. Sample CC1053 had the most allele changes in chr1-22, and Xq, and sample CC1054 showed the second highest allele changes in chr1,3,4,6,8,9,10,11,13, 16, 17,19,20 and 22. Conclusion: Our results showed that the SNV difference between normal-tumor matched pair is relatively small consistent with the assumption of low mutation rate in cancer. IBS approach provides the tumor contents as well as assurance in the selection of samples for sequencing using SNP data. In our samples 88% similarly was found, as shown in IBS landscape across the chromosomes. We concluded that our matched pair samples are appropriately selected and are suitable for analysis of mutation across the samples.
Citation Format: Mohammad Daremipouran, Hassan Hassanzadeh Namin, Sohaila Soltani, Joe Devaney, Wayne Frederick, Edward L. Lee, Hassan Brim, Hassan Ashktorab. Paired analysis of matched colon normal and tumor using whole exome sequencing. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5307. doi:10.1158/1538-7445.AM2013-5307