Biomaterial Database

Complex nature of apparently balanced chromosomal rearrangements in patients with autism spectrum disorder. 2015

Anne-Claude Tabet, and Alain Verloes, and Marion Pilorge, and Elsa Delaby, and Richard Delorme, and Gudrun Nygren, and Françoise Devillard, and Marion Gérard, and Sandrine Passemard, and Delphine Héron, and Jean-Pierre Siffroi, and Aurelia Jacquette, and Andrée Delahaye, and Laurence Perrin, and Céline Dupont, and Azzedine Aboura, and Pierre Bitoun, and Mary Coleman, and Marion Leboyer, and Christopher Gillberg, and Brigitte Benzacken, and Catalina Betancur

Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France.

BACKGROUND Apparently balanced chromosomal rearrangements can be associated with an abnormal phenotype, including intellectual disability and autism spectrum disorder (ASD). Genome-wide microarrays reveal cryptic genomic imbalances, related or not to the breakpoints, in 25% to 50% of patients with an abnormal phenotype carrying a microscopically balanced chromosomal rearrangement. Here we performed microarray analysis of 18 patients with ASD carrying balanced chromosomal abnormalities to identify submicroscopic imbalances implicated in abnormal neurodevelopment. METHODS Eighteen patients with ASD carrying apparently balanced chromosomal abnormalities were screened using single nucleotide polymorphism (SNP) arrays. Nine rearrangements were de novo, seven inherited, and two of unknown inheritance. Genomic imbalances were confirmed by fluorescence in situ hybridization and quantitative PCR. RESULTS We detected clinically significant de novo copy number variants in four patients (22%), including three with de novo rearrangements and one with an inherited abnormality. The sizes ranged from 3.3 to 4.9 Mb; three were related to the breakpoint regions and one occurred elsewhere. We report a patient with a duplication of the Wolf-Hirschhorn syndrome critical region, contributing to the delineation of this rare genomic disorder. The patient has a chromosome 4p inverted duplication deletion, with a 0.5 Mb deletion of terminal 4p and a 4.2 Mb duplication of 4p16.2p16.3. The other cases included an apparently balanced de novo translocation t(5;18)(q12;p11.2) with a 4.2 Mb deletion at the 18p breakpoint, a subject with de novo pericentric inversion inv(11)(p14q23.2) in whom the array revealed a de novo 4.9 Mb deletion in 7q21.3q22.1, and a patient with a maternal inv(2)(q14.2q37.3) with a de novo 3.3 Mb terminal 2q deletion and a 4.2 Mb duplication at the proximal breakpoint. In addition, we identified a rare de novo deletion of unknown significance on a chromosome unrelated to the initial rearrangement, disrupting a single gene, RFX3. CONCLUSIONS These findings underscore the utility of SNP arrays for investigating apparently balanced chromosomal abnormalities in subjects with ASD or related neurodevelopmental disorders in both clinical and research settings.