Ancestry inference in complex admixtures via variable-length markov chain linkage models

Journal of Computational Biology

Volumn 20, Issue 3, 2013, Pages 199-211

  Rodriguez, Jesse M ^a,b   Bercovici, Sivan ^a   Elmore, Megan ^a   Batzoglou, Serafim ^a  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

ancestry inference; FHMM; population genetics; VLMC

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER SIMULATION; GENE LINKAGE DISEQUILIBRIUM; GENE POOL; GENEALOGY; GENETIC LINKAGE; GENETICS; HAPLOTYPE; HUMAN; METHODOLOGY; PROBABILITY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENE POOL; GENEALOGY AND HERALDRY; GENETIC LINKAGE; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MARKOV CHAINS; MODELS, GENETIC;

EID: 84874685634     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2012.0088     Document Type: Article

References (27)

1. Alkan, C., Coe, B.P., and Eichler, E.E. 2011. Genome structural variation discovery and genotyping. Nature reviews. Genetics 12, 363-376.
2. Altshuler, D.M., Gibbs, R.A., Peltonen, L., 2010. et al. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52-58.
3. Baye, T.M., and Wilke, R.A. 2010 Mapping genes that predict treatment outcome in admixed populations. The Pharmacogenomics Journal 10, 465-477.
4. Bercovici, S., and Geiger, D. 2009. Inferring ancestries efficiently in admixed populations with linkage disequilibrium. Journal of Computational Biology : A Journal of Computational Molecular Cell Biology 16, 1141-50.
5. Browning S.R., and Browning, B.L. 2007. Rapid and accurate haplotype phasing and missing-data inference for wholegenome association studies by use of localized haplotype clustering. The American Journal of Human Genetics 81, 1084-1097, 2007.
6. Ghahramani, Z., Jordan, M.I., and Smyth, P. 1997. Factorial hidden Markov models. In Machine Learning. MIT Press, Cambridge, MA.
7. Gravel, S., Henn, B.M., Gutenkunst, R.N., et al. 2011. Demographic history and rare allele sharing among human populations. Proceedings of the National Academy of Sciences 108, 11983-11988.
8. Haldane J.B.S. 1919. The combination of linkage values, and the calculation of distance between the loci of linked factors. J Genet 8, 299-309, 1919.
9. Henn, B.M., Botigué, L.R., Gravel, S. et al. 2012. Genomic Ancestry of North Africans supports back-to-Africa migrations. PLoS Genet 8, e1002397.
10. Hinch, A.G., Tandon, A., Patterson, N., et al. 2011. The landscape of recombination in African Americans. Nature 476, 170-175.
11. Jakobsson, M., Scholz, S.W., Scheet, P., et al. 2008. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451, 998-1003.
12. Long, J.C. 1991. The genetic structure of admixed population. Genetics 127, 417-428.
13. Pasaniuc, B., Sankararaman, S., Kimmel, G., and Halperin, E. 2009. Inference of locus-specific ancestry in closely related populations. Bioinformatics (Oxford, England) 25, i213-21.
14. Pasaniuc, B., Zaitlen, N., Lettre, G., et al. 2011. Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium. PLoS genetics 7, e1001371.
15. Patterson, N., Hattangadi, N., Lane, B. et al. 2004. Methods for high-density admixture mapping of disease genes. American Journal of Human Genetics 74, 979-1000.
16. Pool, J.E., and Nielsen, R. 2009. Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics 181, 711-719.
17. Price, A.L., Tandon, A., Patterson, N., et al. 2009. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet 5, e1000519.
18. Rabiner, L.R. 1989. A tutorial on hidden Markov models and selected applications in speech recognition. In Proceedings of the IEEE, 257-286.
19. Ron, D., Singer, Y., and Tishby, N., 1995. On the learnability and usage of acyclic probabilistic finite automata. In Journal of Computer and System Sciences 31-40.
20. Rosenberg, N.A., Li, L.M., Ward, R., and Pritchard, J.K. 2003. Informativeness of genetic markers for inference of ancestry. The American Journal of Human Genetics 73, 1402-1422.
21. Sankararaman, S., Sridhar, S., Kimmel, G., and Halperin, E. 2008. Estimating local ancestry in admixed populations. Journal of Human Genetics February, 290-303.
22. Seldin, M.F., Pasaniuc, B., and Price, A.L. 2011. New approaches to disease mapping in admixed populations. Nature reviews. Genetics 12, 523-8.
23. Sundquist, A., Fratkin, E., Do, C.B., and Batzoglou, S. 2008. Effect of genetic divergence in identifying ancestral origin using HAPAA. Genome research 18, 676-82.
24. Tang, H., Coram, M., Wang, P., et al. 2006. Reconstructing genetic ancestry blocks in admixed individuals. American Journal of Human Genetics 79, 1-12.
25. Tian, C., Hinds, D.A., Shigeta, R., et al. 2006. A genomewide single-nucleotide polymorphism panel with high ancestry information for african american admixture mapping. The American Journal of Human Genetics 79, 640-649.
26. Wegmann, D., Kessner, D.E., Veeramah, K.R., et al. 2011. Recombination rates in admixed individuals identified by ancestry-based inference. Nature Genetics 43, 847-853.
27. Winkler, C.A., Nelson, G.W., and Smith, M.W. Admixture mapping comes of age. Annual Review of Genomics and Human Genetics 11, 65-89.