Project description:This SuperSeries is composed of the following subset Series: GSE20574: Agilent 244A aCGH array for comparison of lung tumor CNA to high-throughput sequencing data GSE20578: Assessment of mutation on expression levels GSE20584: Affymetrix SNP6.0 array for comparison of lung tumor and adjacent normal to high-throughput sequencing data Refer to individual Series
Project description:<p>Whole genome sequencing was applied to tumor and adjacent normal lung tissue in an individual non-small-cell lung cancer patient. We present an analysis of somatic changes identified throughout the tumor genome, including single-nucleotide variants, copy number variants, and large-scale chromosomal rearrangements. Over 50,000 high-confidence single-nucleotide variants were identified, revealing evidence of substantial smoking-related DNA damage as well as distinct mutational pressures within the tumor resulting in uneven distribution of somatic mutations across the genome.</p>
Project description:Three different experimental approaches were evaluated for discrimination of genomic variance in and between duplicated sequences using 48 markers in duplicon regions and 17 SNPs in unique sequences previously characterized in another study. We found only the method high-throughput single sperm typing could conclusively resolve the alleles of all markers. Resulting data from single sperm analysis were also used to examine the genetic structure of duplicon markers in the human population. Single sperm typing can be a rapid, efficient and accurate method for initial screening and assessment of genetic variation and for detailed genetic analysis of duplicon markers. Keywords: Genotyping Sixty-five markers including 17 MSVs, 12 PSVs, 19 SIDs and 17 SNPs in unique sequences described in Fredman et al. were selected for study. The samples include 40 genomic DNA samples from four ethnic groups, semen samples from 11 donors, and 10 to 20 sperm from each donor except one, AB012, for whom 65 sperm were analyzed. Both genomic and sperm DNA samples were subject to multiplex amplification followed by microarray analysis. Genotypes were determined by using the Accutyping software. Semen samples were genotyped on both strands. Allele status in these samples were compared and analyzed. The single sperm typing method allowed us to identify markers residing in non-unique sequence, to analyze the detailed genetic structure of the duplicons and to learn whether different alleles are present for the duplicon sequences in the human population.