Discovery and genotyping of genome structural polymorphism by sequencing on a population scale

Nature Genetics

Volumn 43, Issue 3, 2011, Pages 269-276

  Handsaker, Robert E ^a,b   Korn, Joshua M ^a,b   Nemesh, James ^a,b   McCarroll, Steven A ^a,b,c  

^a HARVARD MEDICAL SCHOOL   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c Stanley Center for Psychiatric Research   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALLELE; ARTICLE; CLINICAL EVALUATION; GENE DELETION; GENE LOCATION; GENE SEQUENCE; GENETIC HETEROGENEITY; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; POPULATION GENETICS; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; BAYES THEOREM; GENETICS, POPULATION; GENOME, HUMAN; GENOTYPE; HUMANS; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 79952194317     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.768     Document Type: Article

References (26)

1. - 1000 Genomes Project Consortium et al. A map of human genome variation from population scale sequencing. Nature 467, 1061-1073 (2010).
2. Ye, K., Schulz, M.H., Long, Q., Apweiler, R. & Ning, Z. 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 (2009).
3. Lam, H.Y. et al. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat. Biotechnol. 28, 47-55 (2010).
4. Korbel, J.O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420-426 (2007). (Pubitemid 47614521)
5. Korbel, J.O. et al. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol. 10, R23 (2009).
6. Chen, K. et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods 6, 677-681 (2009).
7. Chiang, D.Y. et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods 6, 99-103 (2009).
8. Yoon, S., Xuan, Z., Makarov, V., Ye, K. & Sebat, J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 19, 1586-1592 (2009).
9. Alkan, C. et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet. 41, 1061-1067 (2009).
10. Mills, R.E. et al. Mapping copy number variation by population scale sequencing. Nature published online, doi:1:10.1038/nature09708 (3 February 2011).
11. McCarroll, S.A. et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet. 40, 1166-1174 (2008).
12. Conrad, D.F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704-712 (2010).
13. Tuzun, E. et al. Fine-scale structural variation of the human genome. Nat. Genet. 37, 727-732 (2005). (Pubitemid 41754889)
14. Iskow, R.C. et al. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 141, 1253-1261 (2010).
15. Huang, C.R. et al. Mobile interspersed repeats are major structural variants in the human genome. Cell 141, 1171-1182 (2010).
16. Mills, R.E. et al. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 16, 1182-1190 (2006). (Pubitemid 44320405)
17. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595 (2010).
18. Marchini, J., Howie, B., Myers, S., McVean, G. & Donnelly, P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39, 906-913 (2007). (Pubitemid 47014502)
19. Li, Y., Willer, C., Sanna, S. & Abecasis, G. Genotype imputation. Annu. Rev. Genomics Hum. Genet. 10, 387-406 (2009).
20. Browning, B.L. & Browning, S.R. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am. J. Hum. Genet. 84, 210-223 (2009).
21. Coin, L.J. et al. cnvHap: an integrative population and haplotype-based multiplatform model of SNPs and CNVs. Nat. Methods 7, 541-546 (2010).
22. International HapMap3 Consortium et al. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52-58 (2010).
23. International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320 (2005).
24. McCarroll, S.A. et al. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat. Genet. 40, 1107-1112 (2008).
25. Willer, C.J. et al. Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nat. Genet. 41, 25-34 (2009).
26. Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851-1858 (2008).