Genetic architecture of laterality defects revealed by whole exome sequencing

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Aberrant left-right patterning in the developing human embryo can lead to a broad spectrum of congenital malformations. The causes of most laterality defects are not known, with variants in established genes accounting for <20% of cases. We sought to characterize the genetic spectrum of these conditions by performing whole-exome sequencing of 323 unrelated laterality cases. We investigated the role of rare, predicted-damaging variation in 1726 putative laterality candidate genes derived from model organisms, pathway analyses, and human phenotypes. We also evaluated the contribution of homo/hemizygous exon deletions and gene-based burden of rare variation. A total of 28 candidate variants (26 rare predicted-damaging variants and 2 hemizygous deletions) were identified, including variants in genes known to cause heterotaxy and primary ciliary dyskinesia (ACVR2B, NODAL, ZIC3, DNAI1, DNAH5, HYDIN, MMP21), and genes without a human phenotype association, but with prior evidence for a role in embryonic laterality or cardiac development. Sanger validation of the latter variants in probands and their parents revealed no de novo variants, but apparent transmitted heterozygous (ROCK2, ISL1, SMAD2), and hemizygous (RAI2, RIPPLY1) variant patterns. Collectively, these variants account for 7.1% of our study subjects. We also observe evidence for an excess burden of rare, predicted loss-of-function variation in PXDNL and BMS1- two genes relevant to the broader laterality phenotype. These findings highlight potential new genes in the development of laterality defects, and suggest extensive locus heterogeneity and complex genetic models in this class of birth defects.

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This work was supported in part by the US National Human Genome Research Institute/National Heart Blood Lung Institute jointly funded Baylor Hopkins Center for Mendelian Genomics (UM1HG006542) and by National Institutes of Health (NIH) grants to JWB (1U54 HD083092, 5RO1 HD039056, 5RO1 HL090506, 5RO1 HL091771). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. NH is funded by a Clinical Scientist Development Award from the Doris Duke Charitable Foundation (Grant #:2013096).

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Correspondence to John W. Belmont.

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JRL holds stock ownership in 23andMe, Inc. and Lasergen, Inc., is a paid consultant for Regeneron Pharmaceuticals and is a co-inventor on multiple United States and European patents related to molecular diagnostics. The Department of Molecular and Human Genetics at Baylor College of Medicine derives revenue from molecular genetic testing offered in the Baylor Genetics Laboratories. JRL is on the Scientific Advisory Board of Baylor Genetics. JWB is a fulltime employee of Illumina Inc, but all work was performed under the listed affiliation. AHL is a fulltime employee of Regeneron Pharmaceuticals, but all analyses were performed under the listed affiliation.

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