cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data

被引：0
作者：
Evangelos Bellos
Michael R Johnson
Lachlan J M Coin
机构：
[1] Imperial College London,Department of Epidemiology and Biostatistics
[2] Department of Clinical Neurosciences Imperial College London,Department of Genomics of Common Disease
[3] Imperial College London,undefined
来源：
Genome Biology | / 13卷
关键词：
False Discovery Rate; Hide Markov Model; Copy Number Variation; Read Depth; Copy Number State;
D O I：
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摘要：
Recent advances in sequencing technologies provide the means for identifying copy number variation (CNV) at an unprecedented resolution. A single next-generation sequencing experiment offers several features that can be used to detect CNV, yet current methods do not incorporate all available signatures into a unified model. cnvHiTSeq is an integrative probabilistic method for CNV discovery and genotyping that jointly analyzes multiple features at the population level. By combining evidence from complementary sources, cnvHiTSeq achieves high genotyping accuracy and a substantial improvement in CNV detection sensitivity over existing methods, while maintaining a low false discovery rate. cnvHiTSeq is available at http://sourceforge.net/projects/cnvhitseq
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  • [1] Conrad DF(2010)Origins and functional impact of copy number variation in the human genome Nature 464 704-712
  • [2] Pinto D(2010)A new highly penetrant form of obesity due to deletions on chromosome 16p11.2 Nature 463 671-675
  • [3] Redon R(2011)Mapping copy number variation by population-scale genome sequencing Nature 470 59-65
  • [4] Feuk L(2009)Personalized copy number and segmental duplication maps using next-generation sequencing Nat Genet 41 1061-1067
  • [5] Gokcumen O(2009)Computational methods for discovering structural variation with next-generation sequencing Nat Methods 6 S13-20
  • [6] Zhang Y(2011)Discovery and genotyping of genome structural polymorphism by sequencing on a population scale Nat Genet 43 269-276
  • [7] Aerts J(2012)DELLY: structural variant discovery by integrated paired-end and split-read analysis Bioinformatics 28 i333-i339
  • [8] Andrews TD(2010)cnvHap: an integrative population and haplotype-based multiplatform model of SNPs and CNVs Nat Methods 7 541-546
  • [9] Barnes C(2009)Sensitive and accurate detection of copy number variants using read depth of coverage Genome Res 19 1586-1592
  • [10] Campbell P(2009)Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads Bioinformatics 25 2865-2871
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