A Sample Selection Strategy for Next-Generation Sequencing

Genetic Epidemiology

Volumn 36, Issue 7, 2012, Pages 696-709

  Kang, Chul Joo ^a   Marjoram, Paul ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Coalescent; Imputation; SNP discovery

Indexed keywords

ARTICLE; GENE MAPPING; GENE SEQUENCE; GENETIC ALGORITHM; HAPLOTYPE; HUMAN; HUMAN GENOME; MEDICAL TECHNOLOGY; NEXT GENERATION SEQUENCING; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; COMPUTER SIMULATION; DIPLOIDY; GENETIC VARIATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HAPLOTYPES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMAN GENOME PROJECT; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 84867537872     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21664     Document Type: Article

References (17)

1. 1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-1073.
2. Griffiths R. 2003. The frequency spectrum of a mutation, and its age, in a general diffusion model. Theor Popul Biol 64(2):241-251.
3. Griffiths R, Marjoram P. 1996. Ancestral inference from samples of DNA sequences with recombination. J Comput Biol 3(4):479-502.
4. Griffiths R, Tavaré S. 1998. The age of a mutation in a general coalescent tree. Stoch Models 14:273-295.
5. Howie BN, Donnelly P, Marchini J. 2009. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5(6):e1000529.
6. Hudson R. 1983. Properties of a neutral allele model with intragenic recombination. Theor Popul Biol 2(23):183-201.
7. 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(3):311-321.
8. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. 2010. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 34(8):816-834.
9. Liu DJ, Leal SM. 2010. A novel adaptive method for the analysis of next-generation sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions. PLoS Genet 6(10):e1001156.
10. Madsen BE, Browning SR. 2009. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5(2):e1000384.
11. Neale BM, Rivas MA, Voight BF, Altshuler D, Devlin B, Orho-Melander M, Kathiresan S, Purcell SM, Roeder K, Daly MJ. 2011. Testing for an unusual distribution of rare variants. PLoS Genet 7(3):e1001322.
12. Patterson NJ. 2005. How old is the most recent ancestor of two copies of an allele? Genetics 169(2):1093-1104.
13. Slatkin M. 2008. A bayesian method for jointly estimating allele age and selection intensity. Genet Res 90:129-138.
14. Sokal, R, Michener, C. 1958. A statistical method for evaluating systematic relationships. Univ Kans Sci Bull (38):1409-1438.
15. Wiuf, C, Donnelly, P. 1999. Conditional genealogies and the age of a neutral mutant. Theor Pop Biol (56):183-201.
16. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, Madden PA, Heath AC, Martin NG, Montgomery GW, Goddard ME, Visscher P. 2010. Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42(7):565-569.
17. Zuk O, Hechter E, Sunyaev SR, Lander ES. 2012. The mystery of missing heritability: genetic interactions create phantom heritability. Proc Natl Acad Sci 109(4):1193-1198.