Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.

TitleComparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.
Publication TypeJournal Article
Year of Publication2015
AuthorsFrankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J
JournalBMC genomics
Volume16 Suppl 8
PaginationS2
Date PublishedJun
ISSN1471-2164
Abstract

A vast amount of DNA variation is being identified by increasingly large-scale exome and genome sequencing projects. To be useful, variants require accurate functional annotation and a wide range of tools are available to this end. McCarthy et al recently demonstrated the large differences in prediction of loss-of-function (LoF) variation when RefSeq and Ensembl transcripts are used for annotation, highlighting the importance of the reference transcripts on which variant functional annotation is based.

URLhttp://www.ncbi.nlm.nih.gov/pubmed/26110515
DOI10.1186/1471-2164-16-S8-S2