SNP array data for 36 acute myeloid and lymphoblastic leukemia cell lines. Homo sapiens

Copy number and LOH analysis was performed for 36 acute leukemia cell lines. All cases were genotyped with Affymetrix 250k Sty and Nsp arrays. Keywords: Acute leukemia, BCR-ABL1, cell lines, copy number analysis, loss-of-heterozygosity, genomics *** Due to privacy concerns, the primary SNP array data is no longer available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access using the Web links below. *** Overall design: All assays were performed on DNA extracted from cell lines growing in log phase under recommended conditions. All blast crisis samples were flow sorted prior to DNA extraction. SNP calls were generated using Affymetrix GTYPE. Probe intensity data was extracted and used for DNA copy number analysis using dChip, a karyotype-guided normalization algorithm (Reference normalization, Mullighan et al Nature 2007;446:758), dChip and circular binary segmentation (implemented as DNAcopy in R). To select reference chromosomes for normalization, existing cytogenetic information was curated from the literature, and karyotyping repeated for a subset of cell lines (manuscript in preparation). Prior to copy number inference, summarized, normalized SNP probe values were corrected from ploidy in triploid or tetraploid cell lines. Copy number inferences were made using a set of 50 acuteleukemia remission samples (GSE9111).

本研究对36株急性白血病细胞系开展了拷贝数与杂合性缺失（Loss-of-heterozygosity, LOH）分析。所有样本均采用Affymetrix 250k Sty和Nsp芯片进行基因分型。
关键词：急性白血病、BCR-ABL1、细胞系、拷贝数分析、杂合性缺失、基因组学
*** 鉴于隐私保护相关考量，原始单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片数据已不再提供无限制访问权限。有研究需求获取该数据的人员可通过下方网页链接申请访问权限。 ***
实验设计：所有检测均使用经推荐培养条件下处于对数生长期的细胞系提取的DNA完成。所有急变期样本均在DNA提取前通过流式细胞术分选得到。基因分型结果（SNP calls）通过Affymetrix GTYPE软件生成。探针强度数据经提取后，采用dChip软件（一种以核型为指导的标准化算法，即参考标准化法，Mullighan等，《自然》2007；446：758）、dChip软件以及环状二元分割法（在R语言中以DNAcopy包实现）开展DNA拷贝数分析。为筛选用于标准化的参考染色体，研究人员从已发表文献中整理现有细胞遗传学信息，并对部分细胞系重复进行核型分析（相关手稿待发表）。在进行拷贝数推断前，对三倍体或四倍体细胞系的汇总标准化SNP探针信号值进行倍性校正。拷贝数推断基于50例急性白血病缓解样本（GSE9111）完成。