Whole Exome Sequencing of Distant Relatives in Multiplex Families Implicates Rare Variants in Candidate Genes for Oral Clefts

Abstract

A dozen genes/regions have been confirmed as genetic risk factors for oral clefts in human association and linkage studies, and animal models argue even more genes may be involved. Genomic sequencing studies should identify specific causal variants and may reveal additional genes as influencing risk to oral clefts, which have a complex and heterogeneous etiology. We conducted a whole exome sequencing (WES) study to search for potentially causal variants using affected relatives drawn from multiplex cleft families. Two or three affected second, third, and higher degree relatives from 55 multiplex families were sequenced. We examined rare single nucleotide variants (SNVs) shared by affected relatives in 348 recognized candidate genes. Exact probabilities that affected relatives would share these rare variants were calculated, given pedigree structures, and corrected for the number of variants tested. Five novel and potentially damaging SNVs shared by affected distant relatives were found and confirmed by Sanger sequencing. One damaging SNV in CDH1, shared by three affected second cousins from a single family, attained statistical significance (P = 0.02 after correcting for multiple tests). Family-based designs such as the one used in this WES study offer important advantages for identifying genes likely to be causing complex and heterogeneous disorders.

Clinical exome sequencing: results from 2819 samples reflecting 1000 families

“…Published studies about the implementation of WES as a diagnostic tool have been mostly restricted to specific inbred populations or to particular highly selected groups of patients with homogeneous disease presentations. 5, 6, 7, 8, 9, 10 Here, we present the experience of 1000 consecutive WES requests in our diagnostic clinical routine setup, and validate the use of WES as a first-line diagnostics tool option for patients with a wide range of differential diagnoses or uncharacterized genetic diseases, both in inbred and outbred populations. This comprehensive study includes a highly heterogeneous cohort of 2819 samples from 1000 families referred to us for clinical WES (CentoXome), originating from 54 countries.…”

“…To date, reported WES detection rates for deleterious variants in rare disorders encompass 25–30%, but mostly focusing on highly homogenous (geographically or clinically) patient groups. 5, 6, 7, 8, 9, 27, 28, 29 Other studies that used different classification criteria and highly selected phenotypes or populations reported higher numbers, however not adhering the ACMG guidelines that are needed in a clinical setting. 10, 30 …”

Genetic factors influencing risk to orofacial clefts: today’s challenges and tomorrow’s opportunities

“…Bureau et al . 42, 43 recently showed how whole exome sequencing (WES) data in distant affected relatives (second-degree and more distant relatives) drawn from multiplex families originally recruited for linkage studies could be used to identify rare variants that modify risk to orofacial clefts. From a long list of candidate genes, this approach identified one novel variant in CHD1 shared by three affected second cousins in a single multiplex family.…”

Genetics and genomics etiology of nonsyndromic orofacial clefts

“…Exome sequencing of second‐ and third‐degree relatives of children with nonsyndromic OFC identified a shared rare damaging mutation in CDH1 (Bureau et al. ). Additional rare mutations using a targeted sequencing approach have been identified in CDH1 , suggesting that it is a nonsyndromic OFC candidate gene (Brito et al.…”