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Detecting Rare Variants

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Statistical Human Genetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 850))

Abstract

The limitations of genome-wide association (GWA) studies that are based on the common disease common variants (CDCV) hypothesis have motivated geneticists to test the hypothesis that rare variants contribute to the variation of common diseases, i.e., common disease/rare variants (CDRV). The newly developed high-throughput sequencing technologies have made the studies of rare variants practicable. Statistical approaches to test associations between a phenotype and rare variants are quickly developing. The central idea of these methods is to test a set of rare variants in a defined region or regions by collapsing or aggregating rare variants, thereby improving the statistical power. In this chapter, we introduce these methods as well as their applications in practice.

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References

  1. Lander ES, et al (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921

    Article  PubMed  CAS  Google Scholar 

  2. Venter JC, Adams MD, Myers EW et al (2001) The sequence of the human genome. Science 291: 1304–1351

    Article  PubMed  CAS  Google Scholar 

  3. The International HapMap Consortium (2003) The International HapMap Project. Nature 426: 789–796

    Article  Google Scholar 

  4. Frazer KA, Ballinger DG, Cox DR et al (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851–861

    Article  PubMed  CAS  Google Scholar 

  5. Chakravarti A (1999) Population genetics-making sense out of sequence. Nat Genet 21: 56–60

    Article  PubMed  CAS  Google Scholar 

  6. Lander ES (1996) The new genomics: global views of biology. Science 274: 536–539

    Article  PubMed  CAS  Google Scholar 

  7. Consortium WTCC (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661–678

    Article  Google Scholar 

  8. Gudbjartsson DF, Walters GB, Thorleifsson G et al (2008) Many sequence variants affecting diversity of adult human height. Nat Genet 40: 609–615

    Article  PubMed  CAS  Google Scholar 

  9. Lettre G, Jackson AU, Gieger C et al (2008) Identification of ten loci associated with height highlights new biological pathways in human growth. Nat Genet 40: 584–591

    Article  PubMed  CAS  Google Scholar 

  10. Weedon MN, Lango H, Lindgren CM et al (2008) Genome-wide association analysis identifies 20 loci that influence adult height. Nat Genet 40: 575–583

    Article  PubMed  CAS  Google Scholar 

  11. Easton DF et al (2007) A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer predisposition genes. Am J Hum Genet 81: 873–883

    Article  PubMed  CAS  Google Scholar 

  12. Bodmer W, Bonilla C (2008) Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 40: 695–701

    Article  PubMed  CAS  Google Scholar 

  13. Schork NJ, Murray SS, Frazer KA, Topol EJ (2009) Common vs rare allele hypotheses for complex diseases. Curr Opin Genet Dev 19: 212–219

    Article  PubMed  CAS  Google Scholar 

  14. Gorlov IP, Gorlova OY, Sunyaev SR et al (2008) Shifting paradigm of association studies, value of rare single-nucleotide polymorphisms. Am J Hum Genet 82: 100–112

    Article  PubMed  CAS  Google Scholar 

  15. Li B, Leal SM (2008) Methods for detecting associations with rare variants for common diseases, application to analysis of sequence data. Am J Hum Genet 83: 311–321

    Article  PubMed  CAS  Google Scholar 

  16. Altshuler D, Daly MJ, Lander ES (2008) Genetic mapping in human disease. Science 322: 881–888

    Article  PubMed  CAS  Google Scholar 

  17. Morgenthaler S, Thilly WG (2007) A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). Mutat Res 615: 28–56

    Article  PubMed  CAS  Google Scholar 

  18. Madsen BE, Browning SR (2009) A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic. PLoS Genet doi:10.1371/journal.pgen.1000384

    Google Scholar 

  19. Price AL et al (2010) Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 86: 832–838

    Article  PubMed  Google Scholar 

  20. Ramensky V, Bork P, Sunyaev S (2002) Human Nonsynonymous SNPs: server and survey. Nucleic Acids Res 30: 3894–3900

    Article  PubMed  CAS  Google Scholar 

  21. Adzhubei IA, Schmidt S, Peshkin L et al (2010) A method and server for predicting damaging missense mutations. Nat Methods 7: 248–249

    Article  PubMed  CAS  Google Scholar 

  22. Zhu X, Feng T, Li Y, Lu Q, Elston RC (2010) Detecting rare variants for complex traits using family and unrelated data. Genet Epidemiol 34: 171–187

    Article  PubMed  Google Scholar 

  23. Li X, Chen Y, Li J (2010) Detecting genome-wide haplotype polymorphism by combined use of mendelian constraints and local population structure. Pac Symp Biocomput 15: 348–358.

    Google Scholar 

  24. Stephens M, Donnelly P (2003) A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73: 1162–1169

    Article  PubMed  CAS  Google Scholar 

  25. Stephens M, Smith N, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978–989

    Article  PubMed  CAS  Google Scholar 

  26. Scheet P, Stephens M (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78: 629–644

    Article  PubMed  CAS  Google Scholar 

  27. Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies using localized haplotype clustering. Am J Hum Genet 81: 1084–1097

    Article  PubMed  CAS  Google Scholar 

  28. Feng T, Zhu X (2010) Genome-wide searching of rare genetic variants in WTCCC data. Hum Genet 128: 269–280

    Article  PubMed  Google Scholar 

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Correspondence to Tao Feng .

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© 2012 Springer Science+Business Media, LLC

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Feng, T., Zhu, X. (2012). Detecting Rare Variants. In: Elston, R., Satagopan, J., Sun, S. (eds) Statistical Human Genetics. Methods in Molecular Biology, vol 850. Humana Press. https://doi.org/10.1007/978-1-61779-555-8_24

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  • DOI: https://doi.org/10.1007/978-1-61779-555-8_24

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-554-1

  • Online ISBN: 978-1-61779-555-8

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