Tumor tissue can acquire somatic alterations known as copy number aberrations (CNAs). The authors devised genoCN, a statistical framework to investigate CNAs (genoCNA) and copy number variations (CNVs) (genoCNV). GenoCNV can also estimate whole genome genotypes. They used data derived from a study of glioblastoma and control tissue using Illumina Human 610-Quad BeadChips. GenoCNA takes into account tissue contamination and can be used to compare normal and tumor tissue from the same individual.

Testing negative for suspected 22q11.2 deletion syndrome (DS) may just mean an atypical deletion has not been discovered especially as commercial testing with fluorescence in situ hybridization (FISH) assay only uses N25 or TUPLE1 probes. Here the authors showed that, using Illumina’s HumanCNV370-Quad BeadChips, a female and her male child were found positive for 22q11.2 DS by showing a deletion in another gene—TBX1.

The authors used complete sequencing of the protein-coding genes to find familial pancreatic patients with a germline truncating mutation in PALB2, which they posited as a predisposing factor. The protein product of PALB2 is a binding partner for the most commonly mutated pancreatic cancer gene, BRCA2. Used Infinium II Whole Genome Genotyping Assay, BeadStation software, Genome Analyzer.

The rare abnormality of a deletion of the short arm of chromosome 20 was investigated using 21 patients and five relatives. This is associated with JAG1 gene mutations and consequent Alagille syndrome (AGS), which involves various physical problems. The authors used HumanHap550 BeadChips, which have 6,846 SNP probes on 20p. Deletions extended from 20p12.3 to 20p11.21, with 75 known or predicted genes. While 11 patients had AGS only, those with “deletions that extended from the AGS-only region” had additional developmental delay and/or physical abnormalities.