Lethal variants in humans: lessons learned from a large molecular autopsy cohort

Abstract

Background Molecular autopsy refers to DNA-based identification of the cause of death. Despite recent attempts to broaden its scope, the term remains typically reserved to sudden unexplained death in young adults. In this study, we aim to showcase the utility of molecular autopsy in defining lethal variants in humans. Methods We describe our experience with a cohort of 481 cases in whom the cause of premature death was investigated using DNA from the index or relatives (molecular autopsy by proxy). Molecular autopsy tool was typically exome sequencing although some were investigated using targeted approaches in the earlier stages of the study; these include positional mapping, targeted gene sequencing, chromosomal microarray, and gene panels. Results The study includes 449 cases from consanguineous families and 141 lacked family history (simplex). The age range was embryos to 18 years. A likely causal variant (pathogenic/likely pathogenic) was identified in 63.8% (307/481), a much higher yield compared to the general diagnostic yield (43%) from the same population. The predominance of recessive lethal alleles allowed us to implement molecular autopsy by proxy in 55 couples, and the yield was similarly high (63.6%). We also note the occurrence of biallelic lethal forms of typically non-lethal dominant disorders, sometimes representing a novel bona fide biallelic recessive disease trait. Forty-six disease genes with no OMIM phenotype were identified in the course of this study. The presented data support the candidacy of two other previously reported novel disease genes (FAAH2 and MSN). The focus on lethal phenotypes revealed many examples of interesting phenotypic expansion as well as remarkable variability in clinical presentation. Furthermore, important insights into population genetics and variant interpretation are highlighted based on the results. Conclusions Molecular autopsy, broadly defined, proved to be a helpful clinical approach that provides unique insights into lethal variants and the clinical annotation of the human genome.

An EHPB1L1 Nonsense Mutation Associated with Congenital Dyserythropoietic Anemia and Polymyopathy in Labrador Retriever Littermates

“…RBC morphology was not characterized further and muscles were not examined. A recent “molecular autopsy” study that included lethal variants, such as lethal malformation, still births and intrauterine fetal deaths, were identified in two families with EHBP1L1 mutations with recurrent fetal loss and non-immune hydrops fetalis [ 18 ]. The pathological changes in the organs were not described, with the exception of abnormal intestinal villi as observed in the EHBP1L1 KO mice [ 15 ].…”

EHBP1L1 Frameshift Deletion in English Springer Spaniel Dogs with Dyserythropoietic Anemia and Myopathy Syndrome (DAMS) or Neonatal Losses

“…Furthermore, two puppies that died neonatally also carried the mutant EHBP1L1 allele in a homozygous state. Previously, EHBP1L1 deficiency was only associated with neonatal death in one murine knockout model [ 34 ] and with fetal death in two human pregnancies [ 35 ].…”

“…Homozygous EHBP1L1 −/− knockout mice died neonatally and exhibited anemia and shortened small intestinal microvilli at birth [ 34 ]. In humans, homozygosity and compound homozygosity for truncating EHBP1L1 variants were reported as the cause for non-immune hydrops fetalis resulting in fetal loss in two separate consanguineous families from Saudi Arabia [ 35 ]. In our study of an ESSP dog family, the two puppies (in a litter of nine) that died shortly after birth were homozygous for the EHBP1L1 variant.…”

“…The EHBP1L1 knockout mice dying perinatally were anemic, but were not further evaluated hematologically [ 30 ]. Likewise, the two human fetal deaths related to EHBP1L1 deficiency were not examined for dyserythropoeisis or myopathy [ 35 ]. Some human CDAs can also be hemolytic [ 29 ], which, based upon the increased serum bilirubin concentrations, in comparison to that of related ESSPs, may have been present at a low grade in the ESSPs with DAMS.…”

Transcriptome analysis provides critical answers to the “variants of uncertain significance” conundrum

“…Not only can transcriptome characterization classify VUS as (likely) pathogenic, but it can also clarify variants as benign . For example, RNA data supported a variant downgrade of a likely pathogenic splice site variant at a canonical splice site (Shamseldin et al, 2021). In the case of CDH1 c.387+1G>A, various clinical laboratories initially reported the variant in multiple Hispanic/Latino patients as "likely pathogenic" on the basis of the "+1" position of the variant.…”