A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
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DOI：
10.4161/fly.19695
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发表时间：
2012-04-01
期刊：
影响因子：
1.2
通讯作者：
Ruden, Douglas M.
中科院分区：
文献类型：
--
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
我们描述了一种新的计算机程序，SnpEff，用于快速分类基因组序列中变异的影响。一旦基因组被测序，SnpEff根据它们的基因组位置注释变体并预测编码效果。注释的基因组位置包括内含子、非翻译区、上游、下游、剪接位点或基因间区域。可以预测编码效应，例如同义或非同义氨基酸替换、起始密码子获得或丢失、终止密码子获得或丢失或移码。在此，SnpEff的使用通过在类似于117 Mb的独特序列中注释类似于356，660个候选SNP来说明，所述独特序列代表在黑腹果蝇w（1118）; iso-2; iso-3菌株和参考y（1）; cn（1）bw（1）sp（1）菌株之间类似于1/305核苷酸的取代率。我们发现，近似15，842个SNP是同义的，近似4，467个SNP是非同义的（N/S近似0.28）。其余的SNP属于其他类别，例如5 'UTR中的终止密码子增加（38个SNP）、终止密码子丢失（8个SNP）和起始密码子增加（297个SNP）。我们发现，正如预期的那样，SNP频率与重组频率成比例（即，在染色体臂的中间最高）。我们还发现，黑腹果蝇中的起始-增益或终止-丢失SNP通常导致在其他果蝇物种中保守的N-末端或C-末端氨基酸的添加。看来5'和3' UTR是遗传变异的储存库，在果蝇属的进化过程中改变蛋白质的末端。随着基因组测序变得越来越便宜和常规，SnpEff使全基因组测序数据的快速分析能够由单个实验室进行。
We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on their genomic locations and predicts coding effects. Annotated genomic locations include intronic, untranslated region, upstream, downstream, splice site, or intergenic regions. Coding effects such as synonymous or non-synonymous amino acid replacement, start codon gains or losses, stop codon gains or losses, or frame shifts can be predicted. Here the use of SnpEff is illustrated by annotating similar to 356,660 candidate SNPs in similar to 117 Mb unique sequences, representing a substitution rate of similar to 1/305 nucleotides, between the Drosophila melanogaster w(1118); iso-2; iso-3 strain and the reference y(1); cn(1) bw(1) sp(1) strain. We show that similar to 15,842 SNPs are synonymous and similar to 4,467 SNPs are non-synonymous (N/S similar to 0.28). The remaining SNPs are in other categories, such as stop codon gains (38 SNPs), stop codon losses (8 SNPs), and start codon gains (297 SNPs) in the 5'UTR. We found, as expected, that the SNP frequency is proportional to the recombination frequency (i.e., highest in the middle of chromosome arms). We also found that start-gain or stop-lost SNPs in Drosophila melanogaster often result in additions of N-terminal or C-terminal amino acids that are conserved in other Drosophila species. It appears that the 5' and 3'UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus. As genome sequencing is becoming inexpensive and routine, SnpEff enables rapid analyses of whole-genome sequencing data to be performed by an individual laboratory.