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Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

Publication ,  Journal Article
Colonna, V; Ayub, Q; Chen, Y; Pagani, L; Luisi, P; Pybus, M; Garrison, E; Xue, Y; Tyler-Smith, C; 1000 Genomes Project Consortium, ; Auton, A ...
Published in: Genome biology
June 2014

Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes.We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively.We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.

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Published In

Genome biology

DOI

EISSN

1474-760X

ISSN

1474-7596

Publication Date

June 2014

Volume

15

Issue

6

Start / End Page

R88

Related Subject Headings

  • Sequence Analysis, DNA
  • Selection, Genetic
  • Polymorphism, Single Nucleotide
  • INDEL Mutation
  • Humans
  • Genome, Human
  • Genetic Drift
  • Gene Frequency
  • Bioinformatics
  • 08 Information and Computing Sciences
 

Citation

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Colonna, V., Ayub, Q., Chen, Y., Pagani, L., Luisi, P., Pybus, M., … McVean, G. A. (2014). Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biology, 15(6), R88. https://doi.org/10.1186/gb-2014-15-6-r88
Colonna, Vincenza, Qasim Ayub, Yuan Chen, Luca Pagani, Pierre Luisi, Marc Pybus, Erik Garrison, et al. “Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.Genome Biology 15, no. 6 (June 2014): R88. https://doi.org/10.1186/gb-2014-15-6-r88.
Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, et al. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome biology. 2014 Jun;15(6):R88.
Colonna, Vincenza, et al. “Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.Genome Biology, vol. 15, no. 6, June 2014, p. R88. Epmc, doi:10.1186/gb-2014-15-6-r88.
Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome biology. 2014 Jun;15(6):R88.

Published In

Genome biology

DOI

EISSN

1474-760X

ISSN

1474-7596

Publication Date

June 2014

Volume

15

Issue

6

Start / End Page

R88

Related Subject Headings

  • Sequence Analysis, DNA
  • Selection, Genetic
  • Polymorphism, Single Nucleotide
  • INDEL Mutation
  • Humans
  • Genome, Human
  • Genetic Drift
  • Gene Frequency
  • Bioinformatics
  • 08 Information and Computing Sciences