The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Demographic history and rare allele sharing among human populations
Open accessAbstract
High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2–4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ∼1,000 sequenced chromosomes per population, whereas ∼2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence.
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Citations
Cites
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
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MethodResultInfluentialSelf-citationSequencing of 50 Human Exomes Reveals Adaptation to High Altitude
Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z. X. P., Pool, J. E., Xu, X., Jiang, H., Vinckenbosch, N., Korneliussen, T. S., et al. (2010) · Science · doi:10.1126/science.1190371 · Cited by 1,611 · cited 1×
“We developmethods to precisely estimate SFSs from high-throughput sequencing data and use this information to estimate demographic parameters for a detailed Out-of-Africa demographic model by using ∂a∂i (6), a software package that uses diffusion approximation to calculate expected SFSs across multiple populations (6,…”
MethodSelf-citationAssessing the evolutionary impact of amino acid mutations in the human genome.
Boyko, A. R., Williamson, S. H., Indap, A. R., Degenhardt, J. D., Hernandez, R. D., Lohmueller, K. E., Adams, M. D., Schmidt, S., Sninsky, J. J., Sunyaev, S. R., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000083 · Cited by 628
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Cited by
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711
ANGSD: Analysis of Next Generation Sequencing Data
Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014) · BMC Bioinformatics · doi:10.1186/s12859-014-0356-4 · Cited by 2,982
Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program
Taliun, D., Harris, D. N., Kessler, M. D., Carlson, J., Szpiech, Z. A., Torres, R., Taliun, S. A. G., Corvelo, A., Gogarten, S. M., Kang, H. M., et al. (2021) · Nature · doi:10.1038/s41586-021-03205-y · Cited by 2,213
Self-citationGERAD1 Consortium, Pardiñas, A. F., CRESTAR Consortium, Holmans, P., Pocklington, A. J., Escott-Price, V., Ripke, S., Carrera, N., Legge, S. E., Bishop, S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0059-2 · Cited by 1,552
Self-citationEvolution and functional impact of rare coding variation from deep sequencing of human exomes
Tennessen, J. A., Bigham, A. W., O’Connor, T. D., Fu, W., Kenny, E. E., Gravel, S., McGee, S., Do, R., Liu, X., Jun, G., et al. (2012) · Science · doi:10.1126/science.1219240 · Cited by 1,613
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Metadata
- Authors
- Gravel, S., Henn, B. M., Gutenkunst, R. N., Indap, A. R., Marth, G. T., Clark, A. G., Yu, F., Gibbs, R. A., The 1000 Genomes Project, Bustamante, C. D., Altshuler, D. L., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., Collins, F. S., De La Vega, F. M., Donnelly, P., Egholm, M., Flicek, P., Gabriel, S. B., Gibbs, R. A., Knoppers, B. M., Lander, E. S., Lehrach, H., Mardis, E. R., McVean, G. A., Nickerson, D. A., Peltonen, L., Schafer, A. J., Sherry, S. T., Wang, J., Wilson, R. K., Gibbs, R. A., Deiros, D., Metzker, M., Muzny, D., Reid, J., Wheeler, D., Wang, J., Li, J., Jian, M., Li, G., Li, R., Liang, H., Tian, G., Wang, B., Wang, J., Wang, W., Yang, H., Zhang, X., Zheng, H., Lander, E. S., Altshuler, D. L., Ambrogio, L., Bloom, T., Cibulskis, K., Fennell, T. J., Gabriel, S. B., Jaffe, D. B., Shefler, E., Sougnez, C. L., Bentley, D. R., Gormley, N., Humphray, S., Kingsbury, Z., Koko-Gonzales, P., Stone, J., McKernan, K. J., Costa, G. L., Ichikawa, J. K., Lee, C. C., Sudbrak, R., Lehrach, H., Borodina, T. A., Dahl, A., Davydov, A. N., Marquardt, P., Mertes, F., Nietfeld, W., Rosenstiel, P., Schreiber, S., Soldatov, A. V., Timmermann, B., Tolzmann, M., Egholm, M., Affourtit, J., Ashworth, D., Attiya, S., Bachorski, M., Buglione, E., Burke, A., Caprio, A., Celone, C., Clark, S., Conners, D., Desany, B., Gu, L., Guccione, L., Kao, K., Kebbel, A., Knowlton, J., Labrecque, M., McDade, L., Mealmaker, C., Minderman, M., Nawrocki, A., Niazi, F., Pareja, K., Ramenani, R., Riches, D., Song, W., Turcotte, C., Wang, S., Mardis, E. R., Wilson, R. K., Dooling, D., Fulton, L., Fulton, R., Weinstock, G., Durbin, R. M., Burton, J., Carter, D. M., Churcher, C., Coffey, A., Cox, A., Palotie, A., Quail, M., Skelly, T., Stalker, J., Swerdlow, H. P., Turner, D., De Witte, A., Giles, S., Gibbs, R. A., Wheeler, D., Bainbridge, M., Challis, D., Sabo, A., Yu, F., Yu, J., Wang, J., Fang, X., Guo, X., Li, R., Li, Y., Luo, R., Tai, S., Wu, H., Zheng, H., Zheng, X., Zhou, Y., Li, G., Wang, J., Yang, H., Marth, G. T., Garrison, E. P., Huang, W., Indap, A., Kural, D., Lee, W.-P., Leong, W. F., Quinlan, A. R., Stewart, C., Stromberg, M. P., Ward, A. N., Wu, J., Lee, C., Mills, R. E., Shi, X., Daly, M. J., DePristo, M. A., Altshuler, D. L., Ball, A. D., Banks, E., Bloom, T., Browning, B. L., Cibulskis, K., Fennell, T. J., Garimella, K. V., Grossman, S. R., Handsaker, R. E., Hanna, M., Hartl, C., Jaffe, D. B., Kernytsky, A. M., Korn, J. M., Li, H., Maguire, J. R., McCarroll, S. A., McKenna, A., Nemesh, J. C., Philippakis, A. A., Poplin, R. E., Price, A., Rivas, M. A., Sabeti, P. C., Schaffner, S. F., Shefler, E., Shlyakhter, I. A., Cooper, D. N., Ball, E. V., Mort, M., Phillips, A. D., Stenson, P. D., Sebat, J., Makarov, V., Ye, K., Yoon, S. C., Bustamante, C. D., Clark, A. G., Boyko, A., Degenhardt, J., Gravel, S., Gutenkunst, R. N., Kaganovich, M., Keinan, A., Lacroute, P., Ma, X., Reynolds, A., Clarke, L., Flicek, P., Cunningham, F., Herrero, J., Keenen, S., Kulesha, E., Leinonen, R., McLaren, W. M., Radhakrishnan, R., Smith, R. E., Zalunin, V., Zheng-Bradley, X., Korbel, J. O., Stütz, A. M., Humphray, S., Bauer, M., Cheetham, R. K., Cox, T., Eberle, M., James, T., Kahn, S., Murray, L., Chakravarti, A., Ye, K., De La Vega, F. M., Fu, Y., Hyland, F. C. L., Manning, J. M., McLaughlin, S. F., Peckham, H. E., Sakarya, O., Sun, Y. A., Tsung, E. F., Batzer, M. A., Konkel, M. K., Walker, J. A., Sudbrak, R., Albrecht, M. W., Amstislavskiy, V. S., Herwig, R., Parkhomchuk, D. V., Sherry, S. T., Agarwala, R., Khouri, H. M., Morgulis, A. O., Paschall, J. E., Phan, L. D., Rotmistrovsky, K. E., Sanders, R. D., Shumway, M. F., Xiao, C., McVean, G. A., Auton, A., Iqbal, Z., Lunter, G., Marchini, J. L., Moutsianas, L., Myers, S., Tumian, A., Desany, B., Knight, J., Winer, R., Craig, D. W., Beckstrom-Sternberg, S. M., Christoforides, A., Kurdoglu, A. A., Pearson, J. V., Sinari, S. A., Tembe, W. D., Haussler, D., Hinrichs, A. S., Katzman, S. J., Kern, A., Kuhn, R. M., Przeworski, M., Hernandez, R. D., Howie, B., Kelley, J. L., Melton, S. C., Abecasis, G. R., Li, Y., Anderson, P., Blackwell, T., Chen, W., Cookson, W. O., Ding, J., Kang, H. M., Lathrop, M., Liang, L., Moffatt, M. F., Scheet, P., Sidore, C., Snyder, M., Zhan, X., Zöllner, S., Awadalla, P., Casals, F., Idaghdour, Y., Keebler, J., Stone, E. A., Zilversmit, M., Jorde, L., Xing, J., Eichler, E. E., Aksay, G., Alkan, C., Hajirasouliha, I., Hormozdiari, F., Kidd, J. M., Sahinalp, S. C., Sudmant, P. H., Mardis, E. R., Chen, K., Chinwalla, A., Ding, L., Koboldt, D. C., McLellan, M. D., Dooling, D., Weinstock, G., Wallis, J. W., Wendl, M. C., Zhang, Q., Durbin, R. M., Albers, C. A., Ayub, Q., Balasubramaniam, S., Barrett, J. C., Carter, D. M., Chen, Y., Conrad, D. F., Danecek, P., Dermitzakis, E. T., Hu, M., Huang, N., Hurles, M. E., Jin, H., Jostins, L., Keane, T. M., Le, S. Q., Lindsay, S., Long, Q., MacArthur, D. G., Montgomery, S. B., Parts, L., Stalker, J., Tyler-Smith, C., Walter, K., Zhang, Y., Gerstein, M. B., Snyder, M., Abyzov, A., Balasubramanian, S., Bjornson, R., Du, J., Grubert, F., Habegger, L., Haraksingh, R., Jee, J., Khurana, E., Lam, H. Y. K., Leng, J., Mu, X. J., Urban, A. E., Zhang, Z., Li, Y., Luo, R., Marth, G. T., Garrison, E. P., Kural, D., Quinlan, A. R., Stewart, C., Stromberg, M. P., Ward, A. N., Wu, J., Lee, C., Mills, R. E., Shi, X., McCarroll, S. A., Banks, E., DePristo, M. A., Handsaker, R. E., Hartl, C., Korn, J. M., Li, H., Nemesh, J. C., Sebat, J., Makarov, V., Ye, K., Yoon, S. C., Degenhardt, J., Kaganovich, M., Clarke, L., Smith, R. E., Zheng-Bradley, X., Korbel, J. O., Humphray, S., Cheetham, R. K., Eberle, M., Kahn, S., Murray, L., Ye, K., De La Vega, F. M., Fu, Y., Peckham, H. E., Sun, Y. A., Batzer, M. A., Konkel, M. K., Walker, J. A., Xiao, C., Iqbal, Z., Desany, B., Blackwell, T., Snyder, M., Xing, J., Eichler, E. E., Aksay, G., Alkan, C., Hajirasouliha, I., Hormozdiari, F., Kidd, J. M., Chen, K., Chinwalla, A., Ding, L., McLellan, M. D., Wallis, J. W., Hurles, M. E., Conrad, D. F., Walter, K., Zhang, Y., Gerstein, M. B., Snyder, M., Abyzov, A., Du, J., Grubert, F., Haraksingh, R., Jee, J., Khurana, E., Lam, H. Y. K., Leng, J., Mu, X. J., Urban, A. E., Zhang, Z., Gibbs, R. A., Bainbridge, M., Challis, D., Coafra, C., Dinh, H., Kovar, C., Lee, S., Muzny, D., Nazareth, L., Reid, J., Sabo, A., Yu, F., Yu, J., Marth, G. T., Garrison, E. P., Indap, A., Leong, W. F., Quinlan, A. R., Stewart, C., Ward, A. N., Wu, J., Cibulskis, K., Fennell, T. J., Gabriel, S. B., Garimella, K. V., Hartl, C., Shefler, E., Sougnez, C. L., Wilkinson, J., Clark, A. G., Gravel, S., Grubert, F., Clarke, L., Flicek, P., Smith, R. E., Zheng-Bradley, X., Sherry, S. T., Khouri, H. M., Paschall, J. E., Shumway, M. F., Xiao, C., McVean, G. A., Katzman, S. J., Abecasis, G. R., Blackwell, T., Mardis, E. R., Dooling, D., Fulton, L., Fulton, R., Koboldt, D. C., Durbin, R. M., Balasubramaniam, S., Coffey, A., Keane, T. M., MacArthur, D. G., Palotie, A., Scott, C., Stalker, J., Tyler-Smith, C., Gerstein, M. B., Balasubramanian, S., Chakravarti, A., Knoppers, B. M., Abecasis, G. R., Bustamante, C. D., Gharani, N., Gibbs, R. A., Jorde, L., Kaye, J. S., Kent, A., Li, T., McGuire, A. L., McVean, G. A., Ossorio, P. N., Rotimi, C. N., Su, Y., Toji, L. H., TylerSmith, C., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Abdallah, A., Juenger, C. R., Clemm, N. C., Collins, F. S., Duncanson, A., Green, E. D., Guyer, M. S., Peterson, J. L., Schafer, A. J., Abecasis, G. R., Altshuler, D. L., Auton, A., Brooks, L. D., Durbin, R. M., Gibbs, R. A., Hurles, M. E., & McVean, G. A.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2011-07-05
- Volume
- 108
- Issue
- 29
- Pages
- 11983-11988
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W1964547306
- Cited by
- 624
- References
- 5
- FWCI
- 27.59
- Type
- journal article
- Language
- en
- Open access
- green
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- Gravel, S., Henn, B. M., Gutenkunst, R. N., Indap, A. R., Marth, G. T., Clark, A. G., Yu, F., Gibbs, R. A., The 1000 Genomes Project, Bustamante, C. D., Altshuler, D. L., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., Collins, F. S., De La Vega, F. M., Donnelly, P., . . . McVean, G. A. (2011). Demographic history and rare allele sharing among human populations. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1019276108
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