Identification of novel candidate disease genes from de novo exonic copy number variants.

TitleIdentification of novel candidate disease genes from de novo exonic copy number variants.
Publication TypeJournal Article
Year of Publication2017
AuthorsGambin, T, Yuan, B, Bi, W, Liu, P, Rosenfeld, JA, Coban-Akdemir, Z, Pursley, AN, Nagamani, SCS, Marom, R, Golla, S, Dengle, L, Petrie, HG, Matalon, R, Emrick, L, Proud, MB, Treadwell-Deering, D, Chao, H-T, Koillinen, H, Brown, C, Urraca, N, Mostafavi, R, Bernes, S, Roeder, ER, Nugent, KM, Bader, PI, Bellus, G, Cummings, M, Northrup, H, Ashfaq, M, Westman, R, Wildin, R, Beck, AE, Immken, L, Elton, L, Varghese, S, Buchanan, E, Faivre, L, Lefebvre, M, Schaaf, CP, Walkiewicz, M, Yang, Y, Kang, S-HL, Lalani, SR, Bacino, CA, Beaudet, AL, Breman, AM, Smith, JL, Cheung, SWai, Lupski, JR, Patel, A, Shaw, CA, Stankiewicz, P
JournalGenome Med
Volume9
Issue1
Pagination83
Date Published2017 09 21
ISSN1756-994X
KeywordsCohort Studies, DNA Copy Number Variations, Exons, Genetic Diseases, Inborn, Genome, Human, Homeodomain Proteins, Humans, Intracellular Signaling Peptides and Proteins, Membrane Proteins, Neurodevelopmental Disorders, Protein Serine-Threonine Kinases, Retrospective Studies, Serine-Threonine Kinase 3, Transcription Factors, Whole Genome Sequencing
Abstract

BACKGROUND: Exon-targeted microarrays can detect small (

METHODS: We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease-associated genes were identified; the genes involved were evaluated for a potential disease association.

RESULTS: In this clinical population, among rare CNVs involving any single gene reported in 7200 patients (11%), we identified 145 de novo autosomal CNVs (117 losses and 28 intragenic gains), 257 X-linked deletion CNVs in males, and 1049 inherited autosomal CNVs (878 losses and 171 intragenic gains); 111 known disease genes were potentially disrupted by de novo autosomal or X-linked (in males) single-gene CNVs. Ninety-one genes, either recently proposed as candidate disease genes or not yet associated with diseases, were disrupted by 147 single-gene CNVs, including 37 de novo deletions and ten de novo intragenic duplications on autosomes and 100 X-linked CNVs in males. Clinical features in individuals with de novo or X-linked CNVs encompassing at most five genes (224 bp to 1.6 Mb in size) were compared to those in individuals with larger-sized deletions (up to 5 Mb in size) in the internal CMA database or loss-of-function single nucleotide variants (SNVs) detected by clinical or research whole-exome sequencing (WES). This enabled the identification of recently published genes (BPTF, NONO, PSMD12, TANGO2, and TRIP12), novel candidate disease genes (ARGLU1 and STK3), and further confirmation of disease association for two recently proposed disease genes (MEIS2 and PTCHD1). Notably, exon-targeted CMA detected several pathogenic single-exon CNVs missed by clinical WES analyses.

CONCLUSIONS: Together, these data document the efficacy of exon-targeted CMA for detection of genic and exonic CNVs, complementing and extending WES in clinical diagnostics, and the potential for discovery of novel disease genes by genome-wide assay.

DOI10.1186/s13073-017-0472-7
Alternate JournalGenome Med
PubMed ID28934986
PubMed Central IDPMC5607840
Grant List / / Wellcome Trust / United Kingdom
K12 NS098482 / NS / NINDS NIH HHS / United States
R01 NS058529 / NS / NINDS NIH HHS / United States
U54 HG006542 / HG / NHGRI NIH HHS / United States
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