Phenomic Determinants of Genomic Variation in Autism Spectrum Disorders

Background:     Autism Spectrum Disorders (ASDs) are common, heritable neurobiologic conditions of unknown etiology confounded by significant clinical and genetic heterogeneity. Since ASDs are considered complex genetic disorders, resulting from the interaction of several genes and environmental factors, the lumping together of all cases of ASD, with no subgrouping based on phenotypic characteristics, makes the identification of contributory genes extremely difficult. The fact that autism is known to be associated with several distinct medical/genetic disorders further highlights its genetic heterogeneity. Thus, comprehensive “whole body” phenotyping and more accurate diagnostic methods are necessary to clarify the underlying co-morbidities, causes and symptoms of ASDs – inclusive of neurobehavioural, medical and morphologic traits. Array comparative genomic hybridization (array-CGH) technology has been used to rapidly screen the genome for pathogenic copy number variants (pCNVs) associated with ASD. Whilst current data suggests that pCNVs contribute to ASD pathogenesis, their role within a growing constellation of ASD microdeletion and microduplication syndromes remains poorly understood, due to  the absence of consistent, standardized and comprehensive somatic, medical and neurobehavioural phenotyping of ASD subjects. 
Objectives:     To address this, we evaluated a broad categorization of phenotypic traits (or phenomes) for 100 subjects with ADI-R/ADOS-G confirmed idiopathic ASD undergoing 1Mb BAC array-CGH. We selected 100 subjects with “complex” ASD scores of ≥3 based on criteria modified from de Vries et al. (J Med Genet 2001) for array-CGH screening for CNVs, and summarize a systematic classification of clinical features present in those individuals with and without pCNVs.
Methods:     We stratified our findings  according to CNV type (pathogenic or benign) and total CNV load and reviewed detailed prenatal, medical, developmental and multi-generation family histories, assigning subjects to specific phenotypic subgroups based on co-morbidity with; (1) Intellectual Disability (ID; IQ<70); (2) presence of prenatal (intrauterine growth retardation) and/or post-natal growth anomalies; (3) micro-/macro-cephaly; (4) epilepsy; (5) craniofacial dysmorphisms; (6) congenital physical or systemic anomalies, (7) pregnancy complications; and, (8) neonatal complications.
Results:     Array-CGH uncovered 9 different pCNVs found in 9/100 ASD subjects having complex phenotypes (ASD ± ID and/or physical anomalies) and normal routine karyotype, Fragile X, metabolic, targeted 22q11/22q13 and subtelomeric FISH findings. pCNVs included del(5)(p15.2-15.31) (2.4Mb), del(3)(p24.3) (0.1 Mb), dup(18)(p11.3)(0.9 Mb) and dup(7)(q11)(1.5 Mb). Recurrent pCNVs included del(2)(p15-16.1) (4.5 and 5.7 Mb) found in 2 unrelated subjects presenting with an ASD and ID. Deletion of 14q14.2 (0.7 Mb) and dup(15)(q11) (10 Mb) co-occurred in a niece-aunt relationship, resulting from abnormal segregation of a maternal cryptic balanced translocation. Maternally inherited del(X)(p11.22) (470 Kb) was uncovered in 2 autistic brothers with ID and cleft lip/palate. Male: female distribution of pathogenic CNVs was reduced to 1.25:1 from 3.2:1 in the original cohort. Phenotypic subgrouping confirmed greater CNV pathogenicity in subjects with microcephaly (p=0.04) and ID (p=0.02).
Conclusions:     CNVs found in individuals with ASDs signal the locations of ASD-related culprit genes, and whole genome screening coupled with extensive phenotyping including medical and morphological assessments, is an efficient and cost-effective approach to improve prediction of candidate genes and detect those of mild to moderate effect.