Simulation of finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland

American Journal of Human Genetics

Volumn 94, Issue 5, 2014, Pages 710-720

  Wang, Sophie R ^a,b,c   Agarwala, Vineeta ^b,d,e   Flannick, Jason ^b,f   Chiang, Charleston W K ^g   Altshuler, David ^b,c,d,f   Hirschhorn, Joel N ^a,b,c  

^a BOSTON CHILDREN S HOSPITAL   (United States)

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

^c HARVARD MEDICAL SCHOOL   (United States)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^e HARVARD UNIVERSITY   (United States)

^f MASSACHUSETTS GENERAL HOSPITAL   (United States)

^g UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; BOTTLENECK POPULATION; CONTROLLED STUDY; EFFECTIVE POPULATION SIZE; EXOME; FINLAND; FOUNDER EFFECT; GENE; GENE DELETION; GENE FREQUENCY; GENE INSERTION; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HERITABILITY; HUMAN; INDEL MUTATION; MAJOR CLINICAL STUDY; MISSENSE MUTATION; NON INSULIN DEPENDENT DIABETES MELLITUS; PHENOTYPIC VARIATION; PRIORITY JOURNAL; QUANTITATIVE TRAIT; SINGLE NUCLEOTIDE POLYMORPHISM; EUROPEAN; GENETIC ASSOCIATION; GENETIC CODE; MULTIFACTORIAL INHERITANCE; POPULATION GENETICS;

COMPUTER SIMULATION; DIABETES MELLITUS, TYPE 2; EUROPEAN CONTINENTAL ANCESTRY GROUP; EXOME; FINLAND; FOUNDER EFFECT; HUMANS; MODELS, GENETIC; MULTIFACTORIAL INHERITANCE; POPULATION;

EID: 84899921864     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2014.03.019     Document Type: Article

References (35)

1. L. Peltonen, A. Jalanko, and T. Varilo Molecular genetics of the Finnish disease heritage Hum. Mol. Genet. 8 1999 1913 1923
2. H.R. Nevanlinna The Finnish population structure. A genetic and genealogical study Hereditas 71 1972 195 236
3. A. de la Chapelle Disease gene mapping in isolated human populations: the example of Finland J. Med. Genet. 30 1993 857 865
4. P. Lahermo, A. Sajantila, P. Sistonen, M. Lukka, P. Aula, L. Peltonen, and M.L. Savontaus The genetic relationship between the Finns and the Finnish Saami (Lapps): analysis of nuclear DNA and mtDNA Am. J. Hum. Genet. 58 1996 1309 1322
5. A. de la Chapelle, and F.A. Wright Linkage disequilibrium mapping in isolated populations: the example of Finland revisited Proc. Natl. Acad. Sci. USA 95 1998 12416 12423
6. R.A. Kittles, M. Perola, L. Peltonen, A.W. Bergen, R.A. Aragon, M. Virkkunen, M. Linnoila, D. Goldman, and J.C. Long Dual origins of Finns revealed by Y chromosome haplotype variation Am. J. Hum. Genet. 62 1998 1171 1179
7. L. Peltonen, P. Pekkarinen, and J. Aaltonen Messages from an isolate: lessons from the Finnish gene pool Biol. Chem. Hoppe Seyler 376 1995 697 704
8. M. Hedman, V. Pimenoff, M. Lukka, P. Sistonen, and A. Sajantila Analysis of 16 Y STR loci in the Finnish population reveals a local reduction in the diversity of male lineages Forensic Sci. Int. 142 2004 37 43
9. A. Sajantila, A.H. Salem, P. Savolainen, K. Bauer, C. Gierig, and S. Pääbo Paternal and maternal DNA lineages reveal a bottleneck in the founding of the Finnish population Proc. Natl. Acad. Sci. USA 93 1996 12035 12039
10. S. Service, J. DeYoung, M. Karayiorgou, J.L. Roos, H. Pretorious, G. Bedoya, J. Ospina, A. Ruiz-Linares, A. Macedo, and J.A. Palha et al. Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies Nat. Genet. 38 2006 556 560
11. O. Zuk, S.F. Schaffner, K. Samocha, R. Do, E. Hechter, S. Kathiresan, M.J. Daly, B.M. Neale, S.R. Sunyaev, and E.S. Lander Searching for missing heritability: designing rare variant association studies Proc. Natl. Acad. Sci. USA 111 2014 E455 E464
12. T. Jonsson, J.K. Atwal, S. Steinberg, J. Snaedal, P.V. Jonsson, S. Bjornsson, H. Stefansson, P. Sulem, D. Gudbjartsson, and J. Maloney et al. A mutation in APP protects against Alzheimer's disease and age-related cognitive decline Nature 488 2012 96 99
13. J. Asimit, and E. Zeggini Rare variant association analysis methods for complex traits Annu. Rev. Genet. 44 2010 293 308
14. A.L. Price, G.V. Kryukov, P.I.W. de Bakker, S.M. Purcell, J. Staples, L.-J. Wei, and S.R. Sunyaev Pooled association tests for rare variants in exon-resequencing studies Am. J. Hum. Genet. 86 2010 832 838
15. B. Li, and S.M. Leal Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data Am. J. Hum. Genet. 83 2008 311 321
16. B.E. Madsen, and S.R. Browning A groupwise association test for rare mutations using a weighted sum statistic PLoS Genet. 5 2009 e1000384
17. M.C. Wu, S. Lee, T. Cai, Y. Li, M. Boehnke, and X. Lin Rare-variant association testing for sequencing data with the sequence kernel association test Am. J. Hum. Genet. 89 2011 82 93
18. B.M. Neale, M.A. Rivas, B.F. Voight, D. Altshuler, B. Devlin, M. Orho-Melander, S. Kathiresan, S.M. Purcell, K. Roeder, and M.J. Daly Testing for an unusual distribution of rare variants PLoS Genet. 7 2011 e1001322
19. J.K. Pritchard, and N.J. Cox The allelic architecture of human disease genes: common disease-common variant.or not? Hum. Mol. Genet. 11 2002 2417 2423
20. H. Li, and R. Durbin Fast and accurate long-read alignment with Burrows-Wheeler transform Bioinformatics 26 2010 589 595
21. M.A. DePristo, E. Banks, R. Poplin, K.V. Garimella, J.R. Maguire, C. Hartl, A.A. Philippakis, G. del Angel, M.A. Rivas, and M. Hanna et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data Nat. Genet. 43 2011 491 498
22. S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M.A.R. Ferreira, D. Bender, J. Maller, P. Sklar, P.I.W. de Bakker, M.J. Daly, and P.C. Sham PLINK: a tool set for whole-genome association and population-based linkage analyses Am. J. Hum. Genet. 81 2007 559 575
23. B.W. Lambert, J.D. Terwilliger, and K.M. Weiss ForSim: a tool for exploring the genetic architecture of complex traits with controlled truth Bioinformatics 24 2008 1821 1822
24. M.W. Nachman, and S.L. Crowell Estimate of the mutation rate per nucleotide in humans Genetics 156 2000 297 304
25. A.S. Kondrashov Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases Hum. Mutat. 21 2003 12 27
26. J.X. Sun, A. Helgason, G. Masson, S.S. Ebenesersdóttir, H. Li, S. Mallick, S. Gnerre, N. Patterson, A. Kong, D. Reich, and K. Stefansson A direct characterization of human mutation based on microsatellites Nat. Genet. 44 2012 1161 1165
27. V. Agarwala, J. Flannick, S. Sunyaev, D. Altshuler GoT2D Consortium Evaluating empirical bounds on complex disease genetic architecture Nat. Genet. 45 2013 1418 1427
28. G.V. Kryukov, A. Shpunt, J.A. Stamatoyannopoulos, and S.R. Sunyaev Power of deep, all-exon resequencing for discovery of human trait genes Proc. Natl. Acad. Sci. USA 106 2009 3871 3876
29. N. Ahituv, N. Kavaslar, W. Schackwitz, A. Ustaszewska, J. Martin, S. Hebert, H. Doelle, B. Ersoy, G. Kryukov, and S. Schmidt et al. Medical sequencing at the extremes of human body mass Am. J. Hum. Genet. 80 2007 779 791
30. A.M. Adams, and R.R. Hudson Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms Genetics 168 2004 1699 1712
31. A. Eyre-Walker Evolution in health and medicine Sackler colloquium: Genetic architecture of a complex trait and its implications for fitness and genome-wide association studies Proc. Natl. Acad. Sci. USA 107 Suppl 1 2010 1752 1756
32. I.K. Kotowski, A. Pertsemlidis, A. Luke, R.S. Cooper, G.L. Vega, J.C. Cohen, and H.H. Hobbs A spectrum of PCSK9 alleles contributes to plasma levels of low-density lipoprotein cholesterol Am. J. Hum. Genet. 78 2006 410 422
33. S. Lee, M.C. Wu, and X. Lin Optimal tests for rare variant effects in sequencing association studies Biostatistics 13 2012 762 775
34. A. Kiezun, K. Garimella, R. Do, N.O. Stitziel, B.M. Neale, P.J. McLaren, N. Gupta, P. Sklar, P.F. Sullivan, and J.L. Moran et al. Exome sequencing and the genetic basis of complex traits Nat. Genet. 44 2012 623 630
35. F. Casals, A. Hodgkinson, J. Hussin, Y. Idaghdour, V. Bruat, T. de Maillard, J.-C. Grenier, E. Gbeha, F.F. Hamdan, and S. Girard et al. Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans PLoS Genet. 9 2013 e1003815