Fine-scale mapping of copy-number alterations with massively parallel sequencing

In order to benchmark the reproducibility of Affymetrix 238K Sty arrays for detecting copy-number alterations. We performed replicate hybridizations of 3 tumor cell lines and 2 paired normal cell lines obtained from the American Type Culture Collection (ATCC). We calculated copy numbers at each SNP probeset by array pre-processing with the GISTIC algorithm (PMID: 18077431). For each SNP probeset, we calculated the median copy number across replicate arrays. The median copy number profile for each tumor cell line was segmented with the GLAD algorithm (PMID: 15381628) to partition the genome into regions of constant copy number. We compared the copy-number alterations detected by GLAD segmentation of these arrays with statistical analyses of short sequence reads obtained from the Illumina/Solexa 1G GenomeAnalyzer. Shotgun sequencing results can be found in the NCBI Short Read Archive, accession number SRP000246. Keywords: disease state analysis 77 replicates of HCC1143 (breast ductal carcinoma), 69 replicates of HCC1143BL (matched normal), 42 replicates of HCC1954 (breast ductal carcinoma), 36 replicates of HCC1954BL (matched normal), 1 replicate of NCI-H2347 (lung adenocarcinoma)

本研究旨在评测Affymetrix 238K Sty 阵列（Affymetrix 238K Sty arrays）检测拷贝数变异（copy-number alterations）的可重复性。我们对从美国典型培养物保藏中心（American Type Culture Collection, ATCC）获取的3株肿瘤细胞系与2株配对正常细胞系开展了重复杂交实验。我们通过GISTIC算法（GISTIC algorithm, PMID: 18077431）完成阵列预处理，并计算每个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）探针组的拷贝数。针对每个SNP探针组，我们计算了重复阵列间的拷贝数中位数。采用GLAD算法（GLAD algorithm, PMID: 15381628）对每株肿瘤细胞系的拷贝数中位数谱进行分段，将基因组划分为拷贝数恒定的区域。我们将通过上述阵列的GLAD分段检测得到的拷贝数变异，与从Illumina/Solexa 1G 基因组分析仪（Illumina/Solexa 1G GenomeAnalyzer）获取的短序列读段的统计分析结果进行对比。鸟枪测序结果可在美国国家生物技术信息中心短读段归档库（NCBI Short Read Archive）中获取，登录号为SRP000246。关键词：疾病状态分析；HCC1143（乳腺导管癌）77次重复实验，HCC1143BL（配对正常组织）69次重复实验，HCC1954（乳腺导管癌）42次重复实验，HCC1954BL（配对正常组织）36次重复实验，NCI-H2347（肺腺癌）1次重复实验