Genome wide snp array 6

The proband's DNA was collected, sequenced, and analyzed as part of a larger study developing a targeted multi‐disorder high‐throughput sequencing assay. The methods have been detailed previously (Delio et al. 2015). In brief, ~10 mL of whole blood was collected from the patient and genomic DNA was purified using the Puregene Genomic DNA Purification kit (Gentra, Minneapolis, MN, USA). Next, all coding, untranslated regions (UTR) and flanking intronic regions of 650 known disease‐associated genes were targeted. Within this panel there were 154 cardiac disease‐associated genes (listed in Table S1). Targeted capture‐sequencing was done using the Roche‐NimbleGen EZ SeqCapV3 capture system and sequenced on the Illumina Hiseq 2500 Rapid Run platform. Sequence reads were analyzed using a custom in‐house generated analytical pipeline (Delio et al. 2015). We sequenced eight controls and one HapMap sample to assess the precision of the panel in identifying known variants. Samples were analyzed for copy number variation using the Affymetrix Genome Wide SNP Array 6.0. Sanger sequencing was used to confirm mutations. All mutations discovered were subsequently validated in a CLIA‐approved commercial laboratory.

DNA of 19 papillary bladder tumours (500 ng each) was investigated for chromosomal alterations and copy number changes with array-based comparative genomic hybridization (aCGH) using Genome-Wide SNP Array 6.0 (Affymetrix, Munich/Germany) according to manufacturer’s protocol. Array chips were scanned with GeneChip Scanner 3000 7G. Hybridization was performed at the IZKF Z3 Core Unit Genomics of the Institute of Human Genetics in Erlangen. Data analysis was performed with Genotyping Console (Affymetrix). Tumour DNAs were compared with DNAs from 167 anonymous healthy controls, which were provided by the IZKF Z3 Core Unit Genomics.

METABRIC and TCGA used Affymetrix Genome-Wide SNP array 6.0 to derive somatic copy number variations (CNVs). METABRIC preprocessing identified somatic CNV segments in tumors using the HMM-Dosage method [63 (link)]. A similar patient-by-gene matrix was created with TCGA data using normalized circular binary segmentation [64 (link)] files for each patient. A mean log2 ratio per segment was assigned to each genic and intergenic region within the segment according to METABRIC annotation. METABRIC used the Illumina HT-12v3 platform in gene expression analysis. Pre-processing included spatial artifact correction, summarization, and normalization of log2 intensities with bead-array and BASH R packages [65 (link), 66 (link)]. In TCGA, normalized mRNA expression counts were derived from the TCGA Level 3 RNAseqV2 expression data. Illumina HiSeq 2000 was used to create the TCGA transcriptional data.