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. 2012 Sep;9(9):855-6.
doi: 10.1038/nmeth.2147.

Evolutionary diagnosis method for variants in personal exomes

Sudhir Kumar, Maxwell Sanderford, Vanessa E Gray, Jieping Ye, Li Liu

Evolutionary diagnosis method for variants in personal exomes

Sudhir Kumar et al. Nat Methods. 2012 Sep.
No abstract available

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Conflict of interest statement

COMPETING FINANCIAL INTERESTS

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1
Performance and application of the new EvoD method. (A) Improvement in reducing the False Positive Rate, FPR, for nSNVs occurring with different population frequencies at ultra-conserved sites (Condel: black bars; PolyPhen-2:white bars). Allele frequency data for HumVar2 neutral nSNVs were retrieved from the 5,400 exome dataset. (B) The relationship of EvoD impact scores and the population frequencies of 244,272 nSNVs from the 1000 Genomes Project. Each point shows the average allele frequency for nSNVs with impact scores in increments of 5. (C) Neutrality heat maps based on EvoD predictions for homozygous (Hom.) and heterozygous (Het.) nSNVs from eight HapMap exomes that occur at ultra-, well- and less-conserved sites. Heat maps were constructed by sorting nSNVs by impact score and assigning colors from dark blue (most neutral) to red (most non-neutral) on a linear scale according to the estimated P-value.
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References

    1. Gray VE, Kukurba KR, Kumar S. Bioinformatics. 2012;336 doi: 10.1093/bioinformatics/bts. - DOI - PMC - PubMed
    1. Gonzalez-Perez A, Lopez-Bigas N. Am J Hum Genet. 2011;88:440–449. - PMC - PubMed
    1. Schmidt S, et al. Nat Methods. 2010;7:248–249. - PMC - PubMed
    1. Tennessen JA, et al. Science. 2012;337:64–69. - PMC - PubMed
    1. Ng SB, et al. Nature. 2009;461:272–276. - PMC - PubMed

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