Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes

Suganthi Balasubramanian,Daniel G Macarthur,Yao Fu,Mark Gerstein,Konrad J Karczewski,Jeremy Liu,Mike Jin,Patrick Mcgillivray,Mayur Pawashe

doi:10.1038/s41467-017-00443-5

Abstract

Variants predicted to result in the loss of function of human genes have attracted interest because of their clinical impact and surprising prevalence in healthy individuals. Here, we present ALoFT (annotation of loss-of-function transcripts), a method to annotate and predict the disease-causing potential of loss-of-function variants. Using data from Mendelian disease-gene discovery projects, we show that ALoFT can distinguish between loss-of-function variants that are deleterious as heterozygotes and those causing disease only in the homozygous state. Investigation of variants discovered in healthy populations suggests that each individual carries at least two heterozygous premature stop alleles that could potentially lead to disease if present as homozygotes. When applied to de novo putative loss-of-function variants in autism-affected families, ALoFT distinguishes between deleterious variants in patients and benign variants in unaffected siblings. Finally, analysis of somatic variants in >6500 cancer exomes shows that putative loss-of-function variants predicted to be deleterious by ALoFT are enriched in known driver genes.

Highlights

Variants predicted to result in the loss of function of human genes have attracted interest because of their clinical impact and surprising prevalence in healthy individuals
Nonsense variants in PCSK9 are associated with low low-density lipoprotein (LDL) levels[6], which prompted the active pursuit of the inhibition of PCSK9 as a potential therapeutic for hypercholesterolemia[7, 8] and led to the development of two drugs that have been recently approved by the FDA
In the context of a diploid model, it may be used to determine whether putative LoF (pLoF) variants are likely to lead to recessive or dominant disease

Summary

Introduction

Variants predicted to result in the loss of function of human genes have attracted interest because of their clinical impact and surprising prevalence in healthy individuals. We present ALoFT (annotation of loss-of-function transcripts), a method to annotate and predict the disease-causing potential of loss-of-function variants. Using data from Mendelian disease-gene discovery projects, we show that ALoFT can distinguish between loss-offunction variants that are deleterious as heterozygotes and those causing disease only in the homozygous state. Investigation of variants discovered in healthy populations suggests that each individual carries at least two heterozygous premature stop alleles that could potentially lead to disease if present as homozygotes. Analysis of somatic variants in >6500 cancer exomes shows that putative loss-of-function variants predicted to be deleterious by ALoFT are enriched in known driver genes. We validated the prediction model by applying ALoFT to known disease mutations in Mendelian diseases, autism, and cancer

Methods

Results

Conclusion