Searching PubMed for articles relevant to clinical interpretation of rare human genetic variants

TL;DR

This paper addresses the challenges in retrieving and standardizing evidence from PubMed articles for the clinical interpretation of rare human genetic variants, aiming to improve evidence sharing and query uniformity.

Contribution

It proposes methods to better extract, standardize, and share evidence from unstructured PubMed articles for clinical genetic variant interpretation.

Findings

Identified key barriers in querying variant evidence from PubMed

Developed approaches for standardizing variant annotations

Highlighted the need for collaborative evidence sharing

Abstract

Numerous challenges persist that delay clinical interpretation of human genetic variants, to name a few: (1) un- structured PubMed articles are the most abundant source of evidence, yet their variant annotations are difficult to query uniformly, (2) variants can be reported many different ways, for example as DNA sequence change or protein modification, (3) historical drift in annotations over time between various genome reference assemblies and transcript alignments, (4) no single laboratory has sufficient numbers of human samples, necessitating precompetitive efforts to share evidence for clinical interpretation.