Diagnostic Exome Sequencing to Elucidate the Genetic Basis of Likely Recessive Disorders in Consanguineous Families

Abstract

Rare, atypical, and undiagnosed autosomal-recessive disorders frequently occur in the offspring of consanguineous couples. Current routine diagnostic genetic tests fail to establish a diagnosis in many cases. We employed exome sequencing to identify the underlying molecular defects in patients with unresolved but putatively autosomal-recessive disorders in consanguineous families and postulated that the pathogenic variants would reside within homozygous regions. Fifty consanguineous families participated in the study, with a wide spectrum of clinical phenotypes suggestive of autosomal-recessive inheritance, but with no definitive molecular diagnosis. DNA samples from the patient(s), unaffected sibling(s), and the parents were genotyped with a 720K SNP array. Exome sequencing and array CGH (comparative genomic hybridization) were then performed on one affected individual per family. High-confidence pathogenic variants were found in homozygosity in known disease-causing genes in 18 families (36%) (one by array CGH and 17 by exome sequencing), accounting for the clinical phenotype in whole or in part. In the remainder of the families, no causative variant in a known pathogenic gene was identified. Our study shows that exome sequencing, in addition to being a powerful diagnostic tool, promises to rapidly expand our knowledge of rare genetic Mendelian disorders and can be used to establish more detailed causative links between mutant genotypes and clinical phenotypes.

Against all odds: blended phenotypes of three single-gene defects

“…One previous large-scale clinical WES study reported that 5% of patients with a molecular diagnosis had two underlying single-gene disorders. 5 Another study in patients from consanguineous families reported a slightly higher rate (one out of 18), 20 which may be an underestimate given the identified variants only partially explained the clinical phenotype in two families. It needs to be noted that both estimates were influenced by indication for WES as well as previous knowledge about the identified variants.…”

“…Studies of clinical WES and whole-genome sequencing have previously reported on patients with phenotypes arising from two, but not three, independent single-gene disorders. 4,5,[18][19][20] We propose that a sizeable proportion of the presumed monogenic diseases of yet unknown origin may in fact be due to clustering of several single-gene disorders. One previous large-scale clinical WES study reported that 5% of patients with a molecular diagnosis had two underlying single-gene disorders.…”

Biallelic variants in LINGO1 are associated with autosomal recessive intellectual disability, microcephaly, speech and motor delay

“…Subsequently, the variants were filtered manually using the criteria described in previous studies. 11 As an initial filter in the target region of each family, we included all homozygous exonic and splicing variants (±6 bp of the intron-exon boundary) and excluded all synonymous variants, which are not in the splicing regions. We selected variants with a minor allele frequency o0.02 in the Exome Aggregation Consortium (ExAC) (http://exac.…”

“…8 The combination of homozygosity mapping and exome sequencing is a powerful and cost-effective tool for molecular diagnosis and discovery of novel genes in families with suspected autosomal recessive disorders. [9][10][11][12][13] Using this approach, we studied two unrelated Pakistani consanguineous ID families, and identified two different homozygous missense variants in LINGO1 (leucine-rich repeat and immunoglobulin domain containing 1) that are likely to cause the intellectual disability.…”

Genome-Wide Sequencing for Prenatal Detection of Fetal Single-Gene Disorders

“…WGS and WES for Mendelian Disease Gene Discovery and Clinical Genetic Diagnosis WES, WGS, or targeted NGS sequencing of mapped candidate regions have quickly become the most widely used approaches for disease gene discovery, for which they have been highly successful (Bamshad et al 2011;Gilissen et al 2012Gilissen et al , 2014Beaulieu et al 2014;Dyment et al 2014;Makrythanasis et al 2014;Rios and Delgado 2014). This has resulted in a sharp increase in recent years in the number of Mendelian disorders for which the genetic basis is now known, from about 3000 a few years ago to a currently estimated approximately 4600 (Xue et al 2014), and this number continues to rise.…”