Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.
复制标题
DOI：
10.1186/1471-2164-16-s8-s2
复制
发表时间：
2015
期刊：
影响因子：
4.4
通讯作者：
Harrow J
中科院分区：
文献类型：
--
作者：
Frankish A;Uszczynska B;Ritchie GR;Gonzalez JM;Pervouchine D;Petryszak R;Mudge JM;Fonseca N;Brazma A;Guigo R;Harrow J
越来越大规模的外显子组和基因组测序项目正在鉴定大量的DNA变异。为了有用，变体需要准确的功能注释，为此有各种工具可供使用。McCarthy等人最近证明了当RefSeq和Ensembl转录本用于注释时，在预测功能丧失（LoF）变异方面的巨大差异，突出了变体功能注释所基于的参考转录本的重要性。我们描述了GENCODE和RefSeq基因组中基因和转录本注释之间的相似性和差异的详细分析。我们证明GENCODE Comprehensive集合在选择性剪接、新型CDS、新型外显子方面更丰富，并且具有比RefSeq更高的基因组覆盖率，而GENCODE Basic集合与RefSeq非常相似。使用RNAseq数据，我们表明，一个基因组特有的外显子和内含子表达水平与两个基因组共有的相似。我们提出的证据表明，基因注释的差异导致变异注释的巨大差异，其中GENCODE和RefSeq被用作参考转录本，尽管这主要限于非编码转录本和UTR序列，最多约30%的LoF变异注释不一致。我们还描述了显性转录表达的调查，表明它既支持GENCODE基本集的效用，提供了一个更小的一组更高度表达的转录本，并提供了一个有用的，生物相关的过滤器，以进一步降低转录组的复杂性。选择用于变体功能注释的参考转录本确实对结果有很大影响。GENCODE Comprehensive转录本包含更多的外显子，具有更大的基因组覆盖范围，并且在基因组和外显子组数据集中捕获比RefSeq更多的变体，而GENCODE Basic集与RefSeq显示出更高程度的一致性，并且具有更少的独特特征。我们建议，GENCODE综合集具有很大的实用性，发现新的变种与功能的潜力，而GENCODE基本集更适合于应用程序，要求不太复杂的解释功能的变体。
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. 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 and has higher genomic coverage than RefSeq, while the GENCODE Basic set is very similar to RefSeq. Using RNAseq data we show that exons and introns unique to one geneset are expressed at a similar level to those common to both. We present evidence that the differences in gene annotation lead to large differences in variant annotation where GENCODE and RefSeq are used as reference transcripts, although this is predominantly confined to non-coding transcripts and UTR sequence, with at most ~30% of LoF variants annotated discordantly. We also describe an investigation of dominant transcript expression, showing that it both supports the utility of the GENCODE Basic set in providing a smaller set of more highly expressed transcripts and provides a useful, biologically-relevant filter for further reducing the complexity of the transcriptome. The reference transcripts selected for variant functional annotation do have a large effect on the outcome. The GENCODE Comprehensive transcripts contain more exons, have greater genomic coverage and capture many more variants than RefSeq in both genome and exome datasets, while the GENCODE Basic set shows a higher degree of concordance with RefSeq and has fewer unique features. We propose that the GENCODE Comprehensive set has great utility for the discovery of new variants with functional potential, while the GENCODE Basic set is more suitable for applications demanding less complex interpretation of functional variants.