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

ABSTRACT:

Background

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.

Results

We describe a detailed analysis of the similarities and differences between the gene and transcript annotation in the GENCODE and RefSeq genesets. We demonstrate that the GENCODE Comprehensive set is richer in alternative splicing, novel CDSs, novel exons an

SUBMITTER: Frankish A 

PROVIDER: S-EPMC4502323 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature