Rare copy number variants in over 100,000 European ancestry subjects reveal multiple disease associations

Yun Rose Li, Joseph T. Glessner, Bradley P. Coe, Jin Li, Maede Mohebnasab, Xiao Chang, John Connolly, Charlly Kao, Zhi Wei, Jonathan Bradfield, Cecilia Kim, Cuiping Hou, Munir Khan, Frank Mentch, Haijun Qiu, Marina Bakay, Christopher Cardinale, Maria Lemma, Debra Abrams, Andrew Bridglall-JhingoorMeckenzie Behr, Shanell Harrison, George Otieno, Alexandria Thomas, Fengxiang Wang, Rosetta Chiavacci, Lawrence Wu, Dexter Hadley, Elizabeth Goldmuntz, Josephine Elia, John Maris, Robert Grundmeier, Marcella Devoto, Brendan Keating, Michael March, Renata Pellagrino, Struan F.A. Grant, Patrick M.A. Sleiman, Mingyao Li, Evan E. Eichler, Hakon Hakonarson

Research output: Contribution to journalArticlepeer-review

42 Scopus citations


Copy number variants (CNVs) are suggested to have a widespread impact on the human genome and phenotypes. To understand the role of CNVs across human diseases, we examine the CNV genomic landscape of 100,028 unrelated individuals of European ancestry, using SNP and CGH array datasets. We observe an average CNV burden of ~650 kb, identifying a total of 11,314 deletion, 5625 duplication, and 2746 homozygous deletion CNV regions (CNVRs). In all, 13.7% are unreported, 58.6% overlap with at least one gene, and 32.8% interrupt coding exons. These CNVRs are significantly more likely to overlap OMIM genes (2.94-fold), GWAS loci (1.52-fold), and non-coding RNAs (1.44-fold), compared with random distribution (P < 1 × 10−3). We uncover CNV associations with four major disease categories, including autoimmune, cardio-metabolic, oncologic, and neurological/psychiatric diseases, and identify several drug-repurposing opportunities. Our results demonstrate robust frequency definition for large-scale rare variant association studies, identify CNVs associated with major disease categories, and illustrate the pleiotropic impact of CNVs in human disease.

Original languageEnglish (US)
Article number255
JournalNature communications
Issue number1
StatePublished - Dec 1 2020
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology
  • General Physics and Astronomy


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