Clinical genetic testing for patients with autism spectrum disorders

Autism Consortium Clinical Genetics/DNA Diagnostics Collaboration

Research output: Contribution to journalArticlepeer-review

295 Scopus citations


BACKGROUND: Multiple lines of evidence indicate a strong genetic contribution to autism spectrum disorders (ASDs). Current guidelines for clinical genetic testing recommend a G-banded karyotype to detect chromosomal abnormalities and fragile X DNA testing, but guidelines for chromosomal microarray analysis have not been established. PATIENTS AND METHODS: A cohort of 933 patients received clinical genetic testing for a diagnosis of ASD between January 2006 and December 2008. Clinical genetic testing included G-banded karyotype, fragile X testing, and chromosomal microarray (CMA) to test for submicroscopic genomic deletions and duplications. Diagnostic yield of clinically significant genetic changes was compared. RESULTS: Karyotype yielded abnormal results in 19 of 852 patients (2.23% [95% confidence interval (Cl): 1.73%-2.73%]), fragile X testing was abnormal in 4 of 861 (0.46% [95% Cl: 0.36%-0.56%]), and CMA identified deletions or duplications in 154 of 848 patients (18.2% [95% Cl: 14.76%-21.64%]). CMA results for 59 of 848 patients (7.0% [95% Cl: 5.5%-8.5%]) were considered abnormal, which includes variants associated with known genomic disorders or variants of possible significance. CMA results were normal in 10 of 852 patients (1.2%) with abnormal karyotype due to balanced rearrangements or unidentified marker chromosome. CMA with whole-genome coverage and CMA with targeted genomic regions detected clinically relevant copy-number changes in 7.3% (51 of 697) and 5.3% (8 of 151) of patients, respectively, both higher than karyotype. With the exception of recurrent deletion and duplication of chromosome 16p11.2 and 15q13.2q13.3, most copynumber changes were unique or identified in only a small subset of patients. CONCLUSIONS: CMA had the highest detection rate among clinically available genetic tests for patients with ASD. Interpretation of microarray data is complicated by the presence of both novel and recurrent copy-number variants of unknown significance. Despite these limitations, CMA should be considered as part of the initial diagnostic evaluation of patients with ASD.

Original languageEnglish (US)
Pages (from-to)e727-e735
Issue number4
StatePublished - Apr 1 2010
Externally publishedYes


  • ACGH
  • ASD
  • Array CGH
  • Autism spectrum disorder
  • Language delay
  • Microdeletion
  • Microduplication
  • Neuropsychiatric disorders


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