Identification of rare causal variants in sequence-based studies: methods and applications to VPS13B, a gene involved in Cohen syndrome and autism.

Abstract

Pinpointing the small number of causal variants among the abundant naturally occurring genetic variation is a difficult challenge, but a crucial one for understanding precise molecular mechanisms of disease and follow-up functional studies. We propose and investigate two complementary statistical approaches for identification of rare causal variants in sequencing studies: a backward elimination procedure based on groupwise association tests, and a hierarchical approach that can integrate sequencing data with diverse functional and evolutionary conservation annotations for individual variants. Using simulations, we show that incorporation of multiple bioinformatic predictors of deleteriousness, such as PolyPhen-2, SIFT and GERP++ scores, can improve the power to discover truly causal variants. As proof of principle, we apply the proposed methods to VPS13B, a gene mutated in the rare neurodevelopmental disorder called Cohen syndrome, and recently reported with recessive variants in autism. We identify a small set of promising candidates for causal variants, including two loss-of-function variants and a rare, homozygous probably-damaging variant that could contribute to autism risk.

• Authors: Iuliana Ionita-Laza, Marinela Capanu, Silvia De Rubeis, Kenneth McCallum, Joseph D Buxbaum
• Journal: PLoS genetics (PLoS Genet) Vol. 10 Issue 12 Pg. e1004729 (Dec 2014) ISSN: 1553-7404 [Electronic] United States
• PMID: 25502226 (Publication Type: Journal Article, Research Support, N.I.H., Extramural)

Chemical References

• ANGPTL4 protein, human
• Angiopoietin-Like Protein 4
• Angiopoietins
• VPS13B protein, human
• Vesicular Transport Proteins

Topics

• Angiopoietin-Like Protein 4
• Angiopoietins (genetics)
• Autistic Disorder (diagnosis, genetics)
• Computational Biology
• Computer Simulation
• Developmental Disabilities (diagnosis, genetics)
• Evolution, Molecular
• Fingers (abnormalities)
• Gene Frequency
• Genetic Variation
• Genome-Wide Association Study
• Humans
• Intellectual Disability (diagnosis, genetics)
• Microcephaly (diagnosis, genetics)
• Models, Genetic
• Muscle Hypotonia (diagnosis, genetics)
• Myopia (diagnosis, genetics)
• Obesity (diagnosis, genetics)
• Retinal Degeneration
• Software
• Vesicular Transport Proteins (genetics)