An exome sequencing strategy to diagnose lethal autosomal recessive disorders

Sian Ellard,Matthew Johnson,Peter Turnpenny,Weijia Xie,Richard Caswell,Karen Stals,Hana Lango Allen,Emma Kivuva

doi:10.1038/ejhg.2014.120

Abstract

Rare disorders resulting in prenatal or neonatal death are genetically heterogeneous. For some conditions, affected fetuses can be diagnosed by ultrasound scan, but this is not usually possible until mid-gestation. There is often limited fetal DNA available for investigation. We investigated a strategy for diagnosing autosomal recessive lethal disorders in non-consanguineous pedigrees with multiple affected fetuses. Exome sequencing was performed to identify genes where each parent is heterozygous for a rare non-synonymous-coding or splicing variant. Putative pathogenic variants were tested for cosegregation in affected fetuses and unaffected siblings. In eight couples of European ancestry, we found on average 1.75 genes (range 0–4) where both parents were heterozygous for rare potentially deleterious variants. A proof-of-principle study detected heterozygous DYNC2H1 variants in a couple whose five fetuses had short-rib polydactyly. Prospective analysis of two couples with multiple pregnancy terminations for fetal akinesia syndrome was performed and a diagnosis was obtained in both the families. The first couple were each heterozygous for a previously reported GLE1 variant, p.Arg569His or p.Val617Met; both were inherited by their two affected fetuses. The second couple were each heterozygous for a novel RYR1 variant, c.14130-2A>G or p.Ser3074Phe; both were inherited by their three affected fetuses but not by their unaffected child. Biallelic GLE1 and RYR1 disease-causing variants have been described in other cases with fetal akinesia syndrome. We conclude that exome sequencing of parental samples can be an effective tool for diagnosing lethal recessive disorders in outbred couples. This permits early prenatal diagnosis in future pregnancies.

Highlights

Rare disorders that result in antenatal or neonatal death are both phenotypically and genetically heterogeneous
The first couple had two fetuses affected with fetal akinesia thought to result from a centronuclear or myotubular myopathy based on post-mortem muscle histopathology
We investigated two families referred to our local clinical genetics service because of a history of multiple fetuses terminated after an antenatal ultrasound scan diagnosis of fetal akinesia syndrome

Summary

Introduction

Rare disorders that result in antenatal or neonatal death are both phenotypically and genetically heterogeneous. Diagnosing lethal fetal disorders has previously been very difficult because of the large number of potential genes, the phenotypic variability associated with many known genetic causes and the challenges of defining phenotype and pathology in a mid-gestation fetus. For couples with multiple affected fetuses, most result from autosomal recessive mutations with a 25% recurrence risk for each future pregnancy. Current testing of a limited number of genes guided by phenotype often fails to achieve a molecular genetic diagnosis. Exome sequencing is a powerful tool for both disease gene identification and diagnosis of monogenic disorders. Autosomal recessive diseases can be investigated by a combination of autozygosity mapping and exome sequencing in consanguineous pedigrees to identify homozygous pathogenic variants (reviewed by Gilissen et al[1]). A novel disease gene can be revealed in a single affected individual through the detection of compound heterozygous variants.[2,3]

Methods

Results

Conclusion