TransVar: a multilevel variant annotator for precision genomics

注释 生物 计算生物学 基因组学 基因亚型 遗传学 基因组 基因组DNA 基因
作者
Wanding Zhou,Tenghui Chen,Zechen Chong,Mary A. Rohrdanz,James Melott,Chris Wakefield,Jia Zeng,John N. Weinstein,Funda Meric‐Bernstam,Gordon B. Mills,Ken Chen
出处
期刊:Nature Methods [Springer Nature]
卷期号:12 (11): 1002-1003 被引量:73
标识
DOI:10.1038/nmeth.3622
摘要

One DNA sequence can code for multiple different mRNAs, and therefore many different proteins. Conversely, a variant identified at the protein or transcript level may have non-unique genomic origins. For example, EGFR:p.L747S, which mediates acquired resistance of non-small cell lung cancer to tyrosine kinase inhibitors1, can be translated from multiple genomic variants such as chr7:g.55249076_55249077delinsAG and chr7:g.55242470T>C on different isoforms defined on the human reference assembly GRCh37. One-to-many, many-to-one and many-to-many relationships among sequence variants at the genomic level and those at transcript and protein levels introduce frequent inconsistencies in current practice when vital information about the annotation process (e.g., transcript or isoform IDs) is omitted from variant identifiers. To facilitate standardization and reveal inconsistency in existing variant annotations, we have designed a novel variant annotator, TransVar, to perform three main functions supporting diverse reference genomes and transcript databases (Fig. 1a): (i) “forward annotation”, which annotates all potential effects of a genomic variant on mRNAs and proteins; (ii) “reverse annotation”, which traces an mRNA or protein variant to all potential genomic origins; and (iii) “equivalence annotation”, which, for a given protein variant, searches for alternative protein variants that have identical genomic origin but are represented based on different isoforms. Figure 1 Schematic overview of TransVar and comparison of TransVar with other tools. (a) TransVar performs forward (green arrows) and reverse annotation (pink arrows) and considers all possible mRNA transcripts or protein isoforms available in user-specified reference ... We annotated 964,132 unique single-nucleotide substitutions (SNS), 3,715 multi-nucleotide substitutions (MNS), 11,761 insertions (INS), 24,595 deletions (DEL) and 166 block substitutions (BLS) in the Catalogue of Somatic Mutations in Cancer (COSMIC v67) using TransVar, ANNOVAR2, VEP3, snpEff4, and Oncotator5, and asked whether the resulting protein identifiers (gene name, protein coordinates, and reference amino acid (AA)) match those in COSMIC. We observed comparable consistency in SNS and MNS but variable consistency in INS, DEL and BLS from different annotators (Fig. 1b, Supplementary Table 1 and Supplementary Notes). That finding can largely be attributed to a lack of standardization among variant annotations (codon or AA positions of variants) submitted to COSMIC and among conventions implemented in various annotators. Inconsistency in annotations blurred the lines of evidence for variant frequency estimation and led to inaccurate determination of variant function. TransVar revealed hidden inconsistency in these variant annotations by comprehensively outputting alternative annotations in all available transcripts in standard HGVS nomenclature, and thus resulted in greater consistency in this experiment. TransVar’s novel reverse annotation can be used to ascertain if two protein variants have identical genomic origin, thus reducing inconsistency in annotation data. It can also reveal whether or not a protein variant has non-unique genomic origins and requires caution in genetic and clinical interpretation. We reverse-annotated the protein level variants in COSMIC and found that even under the constraints imposed by the reference base or AA identity, a sizeable fraction (e.g., 11.9% of single-AA substitutions) were associated with multiple genomic variants (Supplementary Table 2), if transcripts were not specified. Among the 537 variants that were cited as clinically actionable at PersonalizedCancerTherapy.org, 78 (14.5%) (e.g., CDKN2A:p.R87P and ERBB2:p.L755_T759del) could be mapped to multiple genomic locations (Supplementary Table 3). The reverse-annotation functionality also enabled systematic genomic characterization of variants directly identified from proteomic or RNA-seq data. For example, we were able to identify in just a few minutes of compute-time the putative genomic origins of 187,464 (97.69%) protein phosphorylation sites (e.g., p.Y308/p.S473 in AKT1 and p.Y1068/p.Y1172 in EGFR) in human proteins6. Our investigation revealed frequent inconsistencies in current databases and tools and highlighted the importance of standardization. With both forward and reverse annotation enabled in TransVar, we can reveal hidden inconsistency and improve the precision of translational and clinical genomics. The source code and detailed instructions of TransVar is available at https://bitbucket.org/wanding/transvar and a web interface is at http://www.transvar.net.

科研通智能强力驱动
Strongly Powered by AbleSci AI
更新
大幅提高文件上传限制,最高150M (2024-4-1)

科研通是完全免费的文献互助平台,具备全网最快的应助速度,最高的求助完成率。 对每一个文献求助,科研通都将尽心尽力,给求助人一个满意的交代。
实时播报
刚刚
自信大白菜真实的钥匙完成签到,获得积分10
刚刚
胡峪完成签到,获得积分10
刚刚
无情山水发布了新的文献求助10
刚刚
1秒前
ccherty发布了新的文献求助10
1秒前
1秒前
小feng完成签到,获得积分10
2秒前
2秒前
laoxiaozi发布了新的文献求助10
3秒前
高大绝义发布了新的文献求助10
3秒前
星星发布了新的文献求助10
3秒前
3秒前
3秒前
4秒前
papo完成签到,获得积分10
4秒前
4秒前
不懈奋进应助如果我沉默采纳,获得30
5秒前
小马甲应助懵懂采纳,获得10
5秒前
5秒前
CipherSage应助快乐保温杯采纳,获得10
5秒前
小梦发布了新的文献求助10
5秒前
zzlark发布了新的文献求助10
6秒前
7秒前
A拉拉拉发布了新的文献求助10
7秒前
ding应助影子采纳,获得10
7秒前
所所应助Aspringin采纳,获得10
7秒前
小柒完成签到,获得积分10
8秒前
xiao_niu完成签到,获得积分10
8秒前
iye发布了新的文献求助10
8秒前
喝粥阿旺发布了新的文献求助10
8秒前
8秒前
8秒前
8秒前
8秒前
wanwan发布了新的文献求助10
9秒前
多喝水应助野菜生活采纳,获得10
10秒前
dan发布了新的文献求助10
10秒前
大饼子圆发布了新的文献求助10
10秒前
机智台灯发布了新的文献求助30
11秒前
高分求助中
Sustainability in Tides Chemistry 2000
The ACS Guide to Scholarly Communication 2000
Studien zur Ideengeschichte der Gesetzgebung 1000
TM 5-855-1(Fundamentals of protective design for conventional weapons) 1000
Pharmacogenomics: Applications to Patient Care, Third Edition 800
Ожившие листья и блуждающие цветы. Практическое руководство по содержанию богомолов [Alive leaves and wandering flowers. A practical guide for keeping praying mantises] 500
A Dissection Guide & Atlas to the Rabbit 500
热门求助领域 (近24小时)
化学 医学 生物 材料科学 工程类 有机化学 生物化学 物理 内科学 纳米技术 计算机科学 化学工程 复合材料 基因 遗传学 催化作用 物理化学 免疫学 量子力学 细胞生物学
热门帖子
关注 科研通微信公众号,转发送积分 3079871
求助须知:如何正确求助?哪些是违规求助? 2732588
关于积分的说明 7524713
捐赠科研通 2381420
什么是DOI,文献DOI怎么找? 1262876
科研通“疑难数据库(出版商)”最低求助积分说明 612123
版权声明 597460