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.

Mental retardation (MR) and multiple congenital abnormalities (MCAs) are though to arise from genetic abnormalities. Using genome-wide analysis of copy number variants (CNVs) of 318 patients with MR with unknown etiology. The authors used the Illumina HumanHap300 and HumanCNV370 BeadChips, along with Affymetrix GeneChips. One CNV in six patients overlapped a known microdeletion/duplication syndrome, another, found in eight patients, was “recently described as a new microdeletion/duplication syndrome.” Over 16% had 63 potentially pathogenic CNVs, and four “showed striking regions of loss of heterozygosity.”

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.