Journal: Nucleic Acids Research

Article Title: Targeted resequencing of candidate genes using selector probes

doi: 10.1093/nar/gkq1005

Figure Lengend Snippet: ( a ) Mutation detection and CNV analysis of a lung cancer patient sample with matched control. Upper panel: for each position in the targeted region the number of bases called in the patient-matched normal tissue is subtracted from the number of bases called in the tumor-derived DNA, and then divided with the sum of called bases for that position in the two samples. The exons of the 28 genes are lined up after each other and genes are demarked by alternating background color. Middle panel: the inferred gene copy-number variation in the corresponding genomic loci illustrated by log2 ratios (pink line) derived from SNP array data (Affymetrix Gene Chip Mapping 250K arrays). Middle panel: the log2 ratio (pink line) of the copy-number analysis done on an Affymetrix micro array. Lower panel: the allelic ratio between the major and minor allele at each position is compared between the two samples by subtraction ( b ). A correlation plot between the Affymetrix Gene Chip log2 tumor/normal signal ratio and the log2 tumor/normal sequencing read depth ratio. ( c ) Detection of a single base pair deletion in the TP53 gene. Forward (brown) and reverse (blue) reads are aligned to a 15-bp region of the TP53 gene. Deleted bases are indicated by dashed lines. Alignment visualized in Integrative Genomic Viewer (IGV ver.1.4.2). ( d ) Detection of the same mutation in the FFPE sample from the same tumor.

Article Snippet: SNP-array experiments were performed according to the standard protocols for Affymetrix GeneChip® Mapping NspI-250K arrays (Gene Chip Mapping 500K Assay Manual (P/N 701930 Rev2.), Affymetrix Inc., Santa Clara, CA, USA) and the arrays were scanned using the GeneChip® Scanner 3000 7G.

Techniques: Mutagenesis, Derivative Assay, Microarray, Sequencing