Detecting structure of haplotypes and local ancestry.
| dc.contributor.author | Guan, Yongtao | |
| dc.date.accessioned | 2018-07-25T18:04:40Z | |
| dc.date.available | 2018-07-25T18:04:40Z | |
| dc.date.issued | 2014-03 | |
| dc.date.updated | 2018-07-25T18:04:38Z | |
| dc.description.abstract | We present a two-layer hidden Markov model to detect the structure of haplotypes for unrelated individuals. This allows us to model two scales of linkage disequilibrium (one within a group of haplotypes and one between groups), thereby taking advantage of rich haplotype information to infer local ancestry of admixed individuals. Our method outperforms competing state-of-the-art methods, particularly for regions of small ancestral track lengths. Applying our method to Mexican samples in HapMap3, we found two regions on chromosomes 6 and 8 that show significant departure of local ancestry from the genome-wide average. A software package implementing the methods described in this article is freely available at http://bcm.edu/cnrc/mcmcmc. | |
| dc.identifier.issn | 0016-6731 | |
| dc.identifier.issn | 1943-2631 | |
| dc.identifier.uri | ||
| dc.language | eng | |
| dc.publisher | Genetics Society of America | |
| dc.relation.ispartof | Genetics | |
| dc.relation.isversionof | 10.1534/genetics.113.160697 | |
| dc.subject | Chromosomes, Human, Pair 6 | |
| dc.subject | Chromosomes, Human, Pair 8 | |
| dc.subject | Humans | |
| dc.subject | Markov Chains | |
| dc.subject | Genomics | |
| dc.subject | Evolution, Molecular | |
| dc.subject | Phylogeny | |
| dc.subject | Haplotypes | |
| dc.subject | Linkage Disequilibrium | |
| dc.subject | Polymorphism, Single Nucleotide | |
| dc.subject | Genome, Human | |
| dc.subject | Models, Genetic | |
| dc.subject | Software | |
| dc.subject | Mexico | |
| dc.subject | Genetic Variation | |
| dc.title | Detecting structure of haplotypes and local ancestry. | |
| dc.type | Journal article | |
| duke.contributor.orcid | Guan, Yongtao|0000-0002-8055-2192 | |
| pubs.begin-page | 625 | |
| pubs.end-page | 642 | |
| pubs.issue | 3 | |
| pubs.organisational-group | School of Medicine | |
| pubs.organisational-group | Duke | |
| pubs.organisational-group | Biostatistics & Bioinformatics | |
| pubs.organisational-group | Basic Science Departments | |
| pubs.publication-status | Published | |
| pubs.volume | 196 |
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