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13 results on '"Walker, Jerilyn A"'

1. An integrated map of structural variation in 2,504 human genomes.

Author

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, and Korbel JO

Subjects
Amino Acid Sequence, Genetic Predisposition to Disease, Genetics, Medical, Genetics, Population, Genome-Wide Association Study, Genomics, Genotype, Haplotypes genetics, Homozygote, Humans, Molecular Sequence Data, Mutation Rate, Polymorphism, Single Nucleotide genetics, Quantitative Trait Loci genetics, Sequence Analysis, DNA, Sequence Deletion genetics, Genetic Variation genetics, Genome, Human genetics, Physical Chromosome Mapping
Abstract

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

Published
2015
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2. Rates and patterns of great ape retrotransposition.

Author

Hormozdiari F, Konkel MK, Prado-Martinez J, Chiatante G, Herraez IH, Walker JA, Nelson B, Alkan C, Sudmant PH, Huddleston J, Catacchio CR, Ko A, Malig M, Baker C, Marques-Bonet T, Ventura M, Batzer MA, and Eichler EE

Subjects
Alu Elements genetics, Animals, Cluster Analysis, DNA Primers genetics, Genomics, Hominidae classification, Humans, Likelihood Functions, Long Interspersed Nucleotide Elements genetics, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Principal Component Analysis, Species Specificity, Genetic Variation, Genome genetics, Hominidae genetics, Phylogeny
Abstract

We analyzed 83 fully sequenced great ape genomes for mobile element insertions, predicting a total of 49,452 fixed and polymorphic Alu and long interspersed element 1 (L1) insertions not present in the human reference assembly and assigning each retrotransposition event to a different time point during great ape evolution. We used these homoplasy-free markers to construct a mobile element insertions-based phylogeny of humans and great apes and demonstrate their differential power to discern ape subspecies and populations. Within this context, we find a good correlation between L1 diversity and single-nucleotide polymorphism heterozygosity (r(2) = 0.65) in contrast to Alu repeats, which show little correlation (r(2) = 0.07). We estimate that the "rate" of Alu retrotransposition has differed by a factor of 15-fold in these lineages. Humans, chimpanzees, and bonobos show the highest rates of Alu accumulation--the latter two since divergence 1.5 Mya. The L1 insertion rate, in contrast, has remained relatively constant, with rates differing by less than a factor of three. We conclude that Alu retrotransposition has been the most variable form of genetic variation during recent human-great ape evolution, with increases and decreases occurring over very short periods of evolutionary time.

Published
2013
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3. Comparative and demographic analysis of orang-utan genomes.

Author

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, and Wilson RK

Subjects
Animals, Centromere genetics, Cerebrosides metabolism, Chromosomes, Evolution, Molecular, Female, Gene Rearrangement genetics, Genetic Speciation, Genetics, Population, Humans, Male, Phylogeny, Population Density, Population Dynamics, Species Specificity, Genetic Variation, Genome genetics, Pongo abelii genetics, Pongo pygmaeus genetics
Abstract

'Orang-utan' is derived from a Malay term meaning 'man of the forest' and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N(e)) expanded exponentially relative to the ancestral N(e) after the split, while Bornean N(e) declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

Published
2011
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5. Following the LINEs: an analysis of primate genomic variation at human-specific LINE-1 insertion sites.

Author

Vincent BJ, Myers JS, Ho HJ, Kilroy GE, Walker JA, Watkins WS, Jorde LB, and Batzer MA

Subjects
Animals, Cell Line, Gene Conversion, Gorilla gorilla genetics, Humans, Macaca mulatta genetics, Macaca nemestrina genetics, Molecular Sequence Data, Pan paniscus genetics, Pan troglodytes genetics, Polymerase Chain Reaction, Polymorphism, Genetic, Sequence Analysis, DNA, Evolution, Molecular, Genetic Variation, Long Interspersed Nucleotide Elements genetics, Phylogeny, Primates genetics
Abstract

The L1 Ta subfamily of long interspersed elements (LINEs) consists exclusively of human-specific L1 elements. Polymerase chain reaction-based screening in nonhuman primate genomes of the orthologous sites for 249 human L1 Ta elements resulted in the recovery of various types of sequence variants for approximately 12% of these loci. Sequence analysis was employed to capture the nature of the observed variation and to determine the levels of gene conversion and insertion site homoplasy associated with LINE elements. Half of the orthologous loci differed from the predicted sizes due to localized sequence variants that occurred as a result of common mutational processes in ancestral sequences, often including regions containing simple sequence repeats. Additional sequence variation included genomic deletions that occurred upon L1 insertion, as well as successive mobile element insertions that accumulated within a single locus over evolutionary time. Parallel independent mobile element insertions at orthologous loci in distinct species may introduce homoplasy into retroelement-based phylogenetic and population genetic data. We estimate the overall frequency of parallel independent insertion events at L1 insertion sites in seven different primate species to be very low (0.52%). In addition, no cases of insertion site homoplasy involved the integration of a second L1 element at any of the loci, but rather largely involved secondary insertions of Alu elements. No independent mobile element insertion events were found at orthologous loci in the human and chimpanzee genomes. Therefore, L1 insertion polymorphisms appear to be essentially homoplasy free characters well suited for the study of population genetics and phylogenetic relationships within closely related species.

Published
2003
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6. Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms.

Author

Watkins WS, Rogers AR, Ostler CT, Wooding S, Bamshad MJ, Brassington AM, Carroll ML, Nguyen SV, Walker JA, Prasad BV, Reddy PG, Das PK, Batzer MA, and Jorde LB

Subjects
Africa, Computational Biology, Europe, Asia, Eastern, Genetics, Population methods, Humans, India, Mutagenesis, Insertional, Alu Elements genetics, Genetic Variation genetics, Polymorphism, Genetic genetics
Abstract

We examine the distribution and structure of human genetic diversity for 710 individuals representing 31 populations from Africa, East Asia, Europe, and India using 100 Alu insertion polymorphisms from all 22 autosomes. Alu diversity is highest in Africans (0.349) and lowest in Europeans (0.297). Alu insertion frequency is lowest in Africans (0.463) and higher in Indians (0.544), E. Asians (0.557), and Europeans (0.559). Large genetic distances are observed among African populations and between African and non-African populations. The root of a neighbor-joining network is located closest to the African populations. These findings are consistent with an African origin of modern humans and with a bottleneck effect in the human populations that left Africa to colonize the rest of the world. Genetic distances among all pairs of populations show a significant product-moment correlation with geographic distances (r = 0.69, P < 0.00001). F(ST), the proportion of genetic diversity attributable to population subdivision is 0.141 for Africans/E. Asians/Europeans, 0.047 for E. Asians/Indians/Europeans, and 0.090 for all 31 populations. Resampling analyses show that approximately 50 Alu polymorphisms are sufficient to obtain accurate and reliable genetic distance estimates. These analyses also demonstrate that markers with higher F(ST) values have greater resolving power and produce more consistent genetic distance estimates.

Published
2003
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7. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

Author

Warren, Wesley C, Harris, R Alan, Haukness, Marina, Fiddes, Ian T, Murali, Shwetha C, Fernandes, Jason, Dishuck, Philip C, Storer, Jessica M, Raveendran, Muthuswamy, Hillier, LaDeana W, Porubsky, David, Mao, Yafei, Gordon, David, Vollger, Mitchell R, Lewis, Alexandra P, Munson, Katherine M, DeVogelaere, Elizabeth, Armstrong, Joel, Diekhans, Mark, Walker, Jerilyn A, Tomlinson, Chad, Graves-Lindsay, Tina A, Kremitzki, Milinn, Salama, Sofie R, Audano, Peter A, Escalona, Merly, Maurer, Nicholas W, Antonacci, Francesca, Mercuri, Ludovica, Maggiolini, Flavia AM, Catacchio, Claudia Rita, Underwood, Jason G, O'Connor, David H, Sanders, Ashley D, Korbel, Jan O, Ferguson, Betsy, Kubisch, H Michael, Picker, Louis, Kalin, Ned H, Rosene, Douglas, Levine, Jon, Abbott, David H, Gray, Stanton B, Sanchez, Mar M, Kovacs-Balint, Zsofia A, Kemnitz, Joseph W, Thomasy, Sara M, Roberts, Jeffrey A, Kinnally, Erin L, Capitanio, John P, Skene, JH Pate, Platt, Michael, Cole, Shelley A, Green, Richard E, Ventura, Mario, Wiseman, Roger W, Paten, Benedict, Batzer, Mark A, Rogers, Jeffrey, and Eichler, Evan E

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, HIV/AIDS, Biotechnology, Animals, Genetic Predisposition to Disease, Genetic Variation, Genome, Humans, Macaca mulatta, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Whole Genome Sequencing, General Science & Technology
Abstract

The rhesus macaque (Macaca mulatta) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Whole-genome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.

Published
2020

8. Rates and patterns of great ape retrotransposition

Author

Great Ape Genome Project, Hormozdiari, Fereydoun, Konkel, Miriam K., Prado-Martinez, Javier, Chiatante, Giorgia, Herraez, Irene Hernando, Walker, Jerilyn A., Nelson, Benjamin, Alkan, Can, Sudmant, Peter H., Huddleston, John, Catacchio, Claudia R., Ko, Arthur, Malig, Maika, Baker, Carl, Marques-Bonet, Tomas, Ventura, Mario, Batzer, Mark A., and Eichler, Evan E.

Published
2013

9. Papio Baboon Species Indicative Alu Elements

Author

Walker, Jerilyn A., Jordan, Vallmer E., Steely, Cody J., Beckstrom, Thomas O., McDaniel, Cullen L., St Romain, Corey P., Bennett, Emily C., Robichaux, Arianna, Clement, Brooke N., Konkel, Miriam K., Baboon Genome Analysis Consortium, Marquès i Bonet, Tomàs, 1975, and Batzer, Mark A.

Subjects
Male, 0106 biological sciences, 0301 basic medicine, Genotype, population genomics, Population, Alu element, Evolutionary biology, DNA, Mitochondrial, 010603 evolutionary biology, 01 natural sciences, Identity by descent, Population genomics, Sexual Behavior, Animal, 03 medical and health sciences, Gene Frequency, Alu Elements, Phylogenetics, biology.animal, Genetics, Animals, Retrotransposon, education, Ecology, Evolution, Behavior and Systematics, education.field_of_study, Phylogenetic tree, biology, retrotransposon, evolutionary biology, Genetic Variation, Pedigree, 030104 developmental biology, Genetic marker, Female, Papio, Research Article, Baboon
Abstract

The genus of Papio (baboon) has six recognized species separated into Northern and Southern clades, each comprised of three species distributed across the African continent. Geographic origin and phenotypic variants such as coat color and body size have commonly been used to identify different species. The existence of multiple hybrid zones, both ancient and current, have complicated efforts to characterize the phylogeny of Papio baboons. More recently, mitochondrial DNA (mtDNA) and Y-chromosome genetic markers have been utilized for species identification with particular focus on the hybrid zones. Alu elements accumulate in a random manner and are a novel source of identical by descent variation with known ancestral states for inferring population genetic and phylogenetic relationships. As part of the Baboon Genome Analysis Consortium, we assembled an Alu insertion polymorphism database of nearly 500 Papio-lineage specific insertions representing all six species and performed population structure and phylogenetic analyses. In this study, we have selected a subset of 48 species indicative Alu insertions and demonstrate their utility as genetic systems for the identification of baboon species within Papio. Individual elements from the panel are easy to genotype and can be used in a hierarchical fashion based on the original level of uncertainty. This Alu-48 panel should serve as a valuable tool during the maintenance of pedigree records in captive populations and assist in the forensic identification of fossils and potential hybrids in the wild.

Published
2017
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10. An integrated map of structural variation in 2,504 human genomes

Author

Sudmant, Peter H, Rausch, Tobias, Gardner, Eugene J, Handsaker, Robert E, Abyzov, Alexej, Huddleston, John, Zhang, Yan, Ye, Kai, Jun, Goo, Fritz, Markus Hsi-Yang, Konkel, Miriam K, Malhotra, Ankit, Stütz, Adrian M, Shi, Xinghua, Casale, Francesco Paolo, Chen, Jieming, Hormozdiari, Fereydoun, Dayama, Gargi, Chen, Ken, Malig, Maika, Chaisson, Mark JP, Walter, Klaudia, Meiers, Sascha, Kashin, Seva, Garrison, Erik, Auton, Adam, Lam, Hugo YK, Mu, Xinmeng Jasmine, Alkan, Can, Antaki, Danny, Bae, Taejeong, Cerveira, Eliza, Chines, Peter, Chong, Zechen, Clarke, Laura, Dal, Elif, Ding, Li, Emery, Sarah, Fan, Xian, Gujral, Madhusudan, Kahveci, Fatma, Kidd, Jeffrey M, Kong, Yu, Lameijer, Eric-Wubbo, McCarthy, Shane, Flicek, Paul, Gibbs, Richard A, Marth, Gabor, Mason, Christopher E, Menelaou, Androniki, Muzny, Donna M, Nelson, Bradley J, Noor, Amina, Parrish, Nicholas F, Pendleton, Matthew, Quitadamo, Andrew, Raeder, Benjamin, Schadt, Eric E, Romanovitch, Mallory, Schlattl, Andreas, Sebra, Robert, Shabalin, Andrey A, Untergasser, Andreas, Walker, Jerilyn A, Wang, Min, Yu, Fuli, Zhang, Chengsheng, Zhang, Jing, Zheng-Bradley, Xiangqun, Zhou, Wanding, Zichner, Thomas, Sebat, Jonathan, Batzer, Mark A, McCarroll, Steven A, 1000 Genomes Project Consortium, Mills, Ryan E, Gerstein, Mark B, Bashir, Ali, Stegle, Oliver, Devine, Scott E, Lee, Charles, Eichler, Evan E, and Korbel, Jan O

Subjects
Genotype, General Science & Technology, Population, Quantitative Trait Loci, Molecular Sequence Data, Mutation Rate, Medical, Genetics, 2.1 Biological and endogenous factors, Humans, Genetic Predisposition to Disease, Amino Acid Sequence, Aetiology, Polymorphism, Sequence Deletion, Genome, Human Genome, Homozygote, Genetic Variation, Genomes Project Consortium, DNA, Genomics, Single Nucleotide, Physical Chromosome Mapping, Haplotypes, Generic health relevance, Sequence Analysis, Biotechnology, Human, Genome-Wide Association Study
Abstract

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

Published
2015

11. Rates and patterns of great ape retrotransposition

Author

Hormozdiari, Fereydoun, Konkel, Miriam K, Prado-Martinez, Javier, Chiatante, Giorgia, Herraez, Irene Hernando, Walker, Jerilyn A, Nelson, Benjamin, Alkan, Can, Sudmant, Peter H, Huddleston, John, Catacchio, Claudia R, Ko, Arthur, Malig, Maika, Baker, Carl, Great Ape Genome Project, Marques-Bonet, Tomas, Ventura, Mario, Batzer, Mark A, and Eichler, Evan E

Subjects
Likelihood Functions, Principal Component Analysis, Genome, retrotransposon, Human Genome, structural variation, Genetic Variation, Hominidae, Genomics, Single Nucleotide, genetic diversity, Great Ape Genome Project, Polymerase Chain Reaction, Long Interspersed Nucleotide Elements, Species Specificity, Alu Elements, genomics, Genetics, Animals, Humans, Cluster Analysis, Polymorphism, Phylogeny, DNA Primers
Abstract

We analyzed 83 fully sequenced great ape genomes for mobile element insertions, predicting a total of 49,452 fixed and polymorphic Alu and long interspersed element 1 (L1) insertions not present in the human reference assembly and assigning each retrotransposition event to a different time point during great ape evolution. We used these homoplasy-free markers to construct a mobile element insertions-based phylogeny of humans and great apes and demonstrate their differential power to discern ape subspecies and populations. Within this context, we find a good correlation between L1 diversity and single-nucleotide polymorphism heterozygosity (r(2) = 0.65) in contrast to Alu repeats, which show little correlation (r(2) = 0.07). We estimate that the "rate" of Alu retrotransposition has differed by a factor of 15-fold in these lineages. Humans, chimpanzees, and bonobos show the highest rates of Alu accumulation--the latter two since divergence 1.5 Mya. The L1 insertion rate, in contrast, has remained relatively constant, with rates differing by less than a factor of three. We conclude that Alu retrotransposition has been the most variable form of genetic variation during recent human-great ape evolution, with increases and decreases occurring over very short periods of evolutionary time.

Published
2013

12. A map of human genome variation from population-scale sequencing

Author

Durbin, Richard M., Altshuler, David L., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Clark, Andrew G., Collins, Francis S., De La Vega, Francisco M., Donnelly, Peter, Egholm, Michael, Flicek, Paul, Gabriel, Stacey B., Gibbs, Richard A., Knoppers, Bartha M., Lander, Eric S., Lehrach, Hans, Mardis, Elaine R., McVean, Gil A., Nickerson, Debbie A., Peltonen, Leena, Schafer, Alan J., Sherry, Stephen T., Wang, Jun, Wilson, Richard K., Deiros, David, Metzker, Mike, Muzny, Donna, Reid, Jeff, Wheeler, David, Li, Jingxiang, Jian, Min, Li, Guoqing, Li, Ruiqiang, Liang, Huiqing, Tian, Geng, Wang, Bo, Wang, Jian, Wang, Wei, Yang, Huanming, Zhang, Xiuqing, Zheng, Huisong, Ambrogio, Lauren, Bloom, Toby, Cibulskis, Kristian, Fennell, Tim J., Jaffe, David B., Shefler, Erica, Sougnez, Carrie L., Gormley, Niall, Humphray, Sean, Kingsbury, Zoya, Koko-Gonzales, Paula, Stone, Jennifer, McKernan, Kevin J., Costa, Gina L., Ichikawa, Jeffry K., Lee, Clarence C., Sudbrak, Ralf, Borodina, Tatiana A., Dahl, Andreas, Davydov, Alexey N., Marquardt, Peter, Mertes, Florian, Nietfeld, Wilfiried, Rosenstiel, Philip, Schreiber, Stefan, Soldatov, Aleksey V., Timmermann, Bernd, Tolzmann, Marius, Affourtit, Jason, Ashworth, Dana, Attiya, Said, Bachorski, Melissa, Buglione, Eli, Burke, Adam, Caprio, Amanda, Celone, Christopher, Clark, Shauna, Conners, David, Desany, Brian, Gu, Lisa, Guccione, Lorri, Kao, Kalvin, Kebbel, Andrew, Knowlton, Jennifer, Labrecque, Matthew, McDade, Louise, Mealmaker, Craig, Minderman, Melissa, Nawrocki, Anne, Niazi, Faheem, Pareja, Kristen, Ramenani, Ravi, Riches, David, Song, Wanmin, Turcotte, Cynthia, Wang, Shally, Dooling, David, Fulton, Lucinda, Fulton, Robert, Weinstock, George, Burton, John, Carter, David M., Churcher, Carol, Coffey, Alison, Cox, Anthony, Palotie, Aarno, Quail, Michael, Skelly, Tom, Stalker, James, Swerdlow, Harold P., Turner, Daniel, De Witte, Anniek, Giles, Shane, Bainbridge, Matthew, Challis, Danny, Sabo, Aniko, Yu, Fuli, Yu, Jin, Fang, Xiaodong, Guo, Xiaosen, Li, Yingrui, Luo, Ruibang, Tai, Shuaishuai, Wu, Honglong, Zheng, Hancheng, Zheng, Xiaole, Zhou, Yan, Marth, Gabor T., Garrison, Erik P., Huang, Weichun, Indap, Amit, Kural, Deniz, Lee, Wan-Ping, Fung Leong, Wen, Quinlan, Aaron R., Stewart, Chip, Stromberg, Michael P., Ward, Alistair N., Wu, Jiantao, Lee, Charles, Mills, Ryan E., Shi, Xinghua, Daly, Mark J., DePristo, Mark A., Ball, Aaron D., Banks, Eric, Browning, Brian L., Garimella, Kiran V., Grossman, Sharon R., Handsaker, Robert E., Hanna, Matt, Hartl, Chris, Kernytsky, Andrew M., Korn, Joshua M., Li, Heng, Maguire, Jared R., McCarroll, Steven A., McKenna, Aaron, Nemesh, James C., Philippakis, Anthony A., Poplin, Ryan E., Price, Alkes, Rivas, Manuel A., Sabeti, Pardis C., Schaffner, Stephen F., Shlyakhter, Ilya A., Cooper, David N., Ball, Edward V., Mort, Matthew, Phillips, Andrew D., Stenson, Peter D., Sebat, Jonathan, Makarov, Vladimir, Ye, Kenny, Yoon, Seungtai C., Bustamante, Carlos D., Boyko, Adam, Degenhardt, Jeremiah, Gravel, Simon, Gutenkunst, Ryan N., Kaganovich, Mark, Keinan, Alon, Lacroute, Phil, Ma, Xin, Reynolds, Andy, Clarke, Laura, Cunningham, Fiona, Herrero, Javier, Keenen, Stephen, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Smith, Richard E., Zalunin, Vadim, Zheng-Bradley, Xiangqun, Korbel, Jan O., Stütz, Adrian M., Bauer, Markus, Keira Cheetham, R., Cox, Tony, Eberle, Michael, James, Terena, Kahn, Scott, Murray, Lisa, Ye, Kai, Fu, Yutao, Hyland, Fiona C. L., Manning, Jonathan M., McLaughlin, Stephen F., Peckham, Heather E., Sakarya, Onur, Sun, Yongming A., Tsung, Eric F., Batzer, Mark A., Konkel, Miriam K., Walker, Jerilyn A., Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Herwig, Ralf, Parkhomchuk, Dimitri V., Agarwala, Richa, Khouri, Hoda M., Morgulis, Aleksandr O., Paschall, Justin E., Phan, Lon D., Rotmistrovsky, Kirill E., Sanders, Robert D., Shumway, Martin F., Xiao, Chunlin, Auton, Adam, Iqbal, Zamin, Lunter, Gerton, Marchini, Jonathan L., Moutsianas, Loukas, Myers, Simon, Tumian, Afidalina, Knight, James, Winer, Roger, Craig, David W., Beckstrom-Sternberg, Steve M., Christoforides, Alexis, Kurdoglu, Ahmet A., Pearson, John V., Sinari, Shripad A., Tembe, Waibhav D., Haussler, David, Hinrichs, Angie S., Katzman, Sol J., Kern, Andrew, Kuhn, Robert M., Przeworski, Molly, Hernandez, Ryan D., Howie, Bryan, Kelley, Joanna L., Cord Melton, S., Li, Yun, Anderson, Paul, Blackwell, Tom, Chen, Wei, Cookson, William O., Ding, Jun, Min Kang, Hyun, Lathrop, Mark, Liang, Liming, Moffatt, Miriam F., Scheet, Paul, Sidore, Carlo, Snyder, Matthew, Zhan, Xiaowei, Zöllner, Sebastian, Awadalla, Philip, Casals, Ferran, Idaghdour, Youssef, Keebler, John, Stone, Eric A., Zilversmit, Martine, Jorde, Lynn, Xing, Jinchuan, Eichler, Evan E., Aksay, Gozde, Alkan, Can, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Kidd, Jeffrey M., Cenk Sahinalp, S., Sudmant, Peter H., Chen, Ken, Chinwalla, Asif, Ding, Li, Koboldt, Daniel C., McLellan, Mike D., Wallis, John W., Wendl, Michael C., Zhang, Qunyuan, Albers, Cornelis A., Ayub, Qasim, Balasubramaniam, Senduran, Barrett, Jeffrey C., Chen, Yuan, Conrad, Donald F., Danecek, Petr, Dermitzakis, Emmanouil T., Hu, Min, Huang, Ni, Hurles, Matt E., Jin, Hanjun, Jostins, Luke, Keane, Thomas M., Quang Le, Si, Lindsay, Sarah, Long, Quan, MacArthur, Daniel G., Montgomery, Stephen B., Parts, Leopold, Tyler-Smith, Chris, Walter, Klaudia, Zhang, Yujun, Gerstein, Mark B., Snyder, Michael, Abyzov, Alexej, Balasubramanian, Suganthi, Bjornson, Robert, Du, Jiang, Grubert, Fabian, Habegger, Lukas, Haraksingh, Rajini, Jee, Justin, Khurana, Ekta, Lam, Hugo Y. K., Leng, Jing, Jasmine Mu, Xinmeng, Urban, Alexander E., Zhang, Zhengdong, Coafra, Cristian, Dinh, Huyen, Kovar, Christie, Lee, Sandy, Nazareth, Lynne, Wilkinson, Jane, Coffey, Allison, Scott, Carol, Gharani, Neda, Kaye, Jane S., Kent, Alastair, Li, Taosha, McGuire, Amy L., Ossorio, Pilar N., Rotimi, Charles N., Su, Yeyang, Toji, Lorraine H., Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Abdallah, Assya, Juenger, Christopher R., Clemm, Nicholas C., Duncanson, Audrey, Green, Eric D., Guyer, Mark S., Peterson, Jane L., The Wellcome Trust Sanger Institute [Cambridge], Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Michigan [Ann Arbor], University of Michigan System, The 1000 Genomes Project Consortium, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., Altshuler, David, Daly, Mark J., Grossman, Sharon Rachel, Jaffe, David B., Korn, Joshua M., and Dermitzakis, Emmanouil

Subjects
Male, [SDV]Life Sciences [q-bio], DNA Mutational Analysis, Pilot Projects, Chromosomes, Human, Y/genetics, DNA, Mitochondrial/genetics, 0302 clinical medicine, ddc:576.5, 2. Zero hunger, Genetics, Recombination, Genetic, 0303 health sciences, Multidisciplinary, Genetics, Population/methods, Genomics, Polymorphism, Single Nucleotide/genetics, Recombination, Genetic/genetics, 3. Good health, Genetic Variation/genetics, Sequence Analysis, DNA/methods, Calibration, Female, Mutation/genetics, Genotype, Haplotypes/genetics, Biology, Instability, DNA, Mitochondrial, Polymorphism, Single Nucleotide, Article, Selection, Genetic/genetics, Factor (chord), Evolution, Molecular, 03 medical and health sciences, Table (landform), Humans, Selection, Genetic, Genetic Association Studies, 030304 developmental biology, Genotype imputation, Chromosomes, Human, Y, Genome, Human, Computational Biology, Genetic Variation, Sequence Analysis, DNA, Genomics/methods, Genetics, Population, Haplotypes, Sample Size, wide association gene-expression recombination hotspots meiotic recombination genotype imputation rare variants haplotype map nucleotide diseases common, Mutation, Genome, Human/genetics, Trinucleotide repeat expansion, Sequence Alignment, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

April 1, 2011, The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother–father–child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10[superscript −8] per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research., Ministry of Science and Technology of the People's Republic of China (973 program no. 2011CB809200), National Natural Science Foundation (China) (30725008), National Natural Science Foundation (China) (30890032), National Natural Science Foundation (China) (30811130531), National Natural Science Foundation (China) (30221004), China (Chinese 863 program 2006AA02Z177), China (Chinese 863 program 2006AA02Z334), China (Chinese 863 program 2006AA02A302), China (Chinese 863 program 2009AA022707), National Institutes of Health (U.S.) (Grant U54HG2750), National Institutes of Health (U.S.) (Grant U01HG5208), National Institutes of Health (U.S.) (Grant U54HG3067)

Published
2010
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13. Comparative and demographic analysis of orang-utan genomes

Author

Matthew W. Hahn, Andreas Heger, Carolin Kosiol, Lisa Cook, Arindam RoyChoudhury, Arcadi Navarro, Catrina Fronick, Lin Chen, Devin P. Locke, Oliver A. Ryder, Olga Fernando, Tomas Vinar, Adam Siepel, Jian Ma, Jeremiah D. Degenhardt, Giuliano Della Valle, Brona Brejova, Oronzo Capozzi, Christie Kovar, Nicoletta Archidiacono, Lucinda Fulton, Jerilyn A. Walker, Albert J. Vilella, Domènec Farré, Julien Y. Dutheil, Xose S. Puente, Mikkel H. Schierup, Carlos Bustamante, George M. Weinstock, Lynne V. Nazareth, Can Alkan, Robert S. Fulton, Brian J. Raney, Mark A. Batzer, Tina Graves, Stephen M. J. Searle, Miriam K. Konkel, Yuko Yoshinaga, Donna M. Muzny, Mariano Rocchi, Carlos López-Otín, Bernard B. Suh, Thomas Mailund, Gonzalo R. Ordóñez, Robert Hubley, Claudio Casola, Huyen Dinh, Rui Faria, Joanne O. Nelson, Tomas Marques-Bonet, Vincent Magrini, Chris Markovic, Makedonka Mitreva, Zhengyuan Wang, Elaine R. Mardis, Arian F.A. Smit, Asger Hobolth, Javier Herrero, David Haussler, Pieter J. de Jong, Kim C. Worley, Heather Schmidt, Ryan N. Gutenkunst, Webb Miller, Yuan Chen, Richard Burhans, Gerton Lunter, Simon D. M. White, André L. Martins, Richard A. Gibbs, Wesley C. Warren, Richard K. Wilson, Patrick Minx, Elodie Gazave, Xin Ma, Daniel R. Schrider, Chris P. Ponting, Roberta Roberto, Shiaw-Pyng Yang, Víctor Quesada, Stefania Purgato, Evan E. Eichler, Andy Cree, Brygg Ullmer, Jeffrey Rogers, Fleur Darré, Robert S. Harris, Vikas Taliwal, Jeffrey M. Kidd, Craig Pohl, Aakrosh Ratan, Paul Flicek, Meritxell Oliva, Kim D. Delehaunty, LaDeana W. Hillier, Jennifer Hume, Stephen Meader, Ze Cheng, Asif T. Chinwalla, Heather A. Lawson, Gerald R. Fowler, National Human Genome Research Institute (US), National Institutes of Health (US), National Science Foundation (US), David and Lucile Packard Foundation, Cornell University, Medical Research Council (UK), European Commission, Ministerio de Ciencia e Innovación (España), Fundación Botín, Instituto Nacional de Bioinformática (España), Fundação para a Ciência e a Tecnologia (Portugal), Locke, Devin P, Hillier, Ladeana W., Warren, Wesley C., Worley, Kim C., Nazareth, Lynne V., Muzny, Donna M., Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif T., Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim D., Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda A., Fulton, Robert S., Nelson, Joanne O., Magrini, Vincent, Pohl, Craig, Graves, Tina A., Markovic, Chri, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Fowler, Gerald R., Lunter, Gerton, Meader, Stephen, Heger, Andrea, Ponting, Chris P., Marques-Bonet, Toma, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey M., Eichler, Evan E., White, Simon, Searle, Stephen, Vilella, Albert J., Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Doménec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Della Valle, Giuliano, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam K., Walker, Jerilyn A., Ullmer, Brygg, Batzer, Mark A., Smit, Arian F. A., Hubley, Robert, Casola, Claudio, Schrider, Daniel R., Hahn, Matthew W., Quesada, Victor, Puente, Xose S., Ordõez, Gonzalo R., Ĺpez-Otín, Carlo, Vinar, Toma, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vika, Martins, André L., Siepel, Adam, Roychoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thoma, Dutheil, Julien Y., Hobolth, Asger, Schierup, Mikkel H., Ryder, Oliver A., Yoshinaga, Yuko, De Jong, Pieter J., Weinstock, George M., Rogers, Jeffrey, Mardis, Elaine R., Gibbs, Richard A., and Wilson, Richard K.

Subjects
Male, Pongo abelii, Genetic Speciation, Population, Population Dynamics, Centromere, Zoology, Biology, Southeast asian, Chromosome, Genome, Chromosomes, Article, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Pongo pygmaeus, Effective population size, Cerebrosides, Species Specificity, Animals, Humans, education, Phylogeny, 030304 developmental biology, Comparative genomics, Cerebroside, Gene Rearrangement, Population Density, 0303 health sciences, education.field_of_study, Population Dynamic, Multidisciplinary, Animal, Medicine (all), Genetic Variation, Gene rearrangement, 3. Good health, Genetics, Population, Evolutionary biology, Female, Pongo pygmaeu, 030217 neurology & neurosurgery, Human
Abstract

5 páginas, 5 figuras, 2 tablas.-- This paper is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike Licence, and is freely available to all readers atwww.nature.com/nature.-- et al., ‘Orang-utan’ is derived from a Malay term meaning ‘man of the forest’ and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts., The orang-utan genome project was funded by the National Human Genome Research Institute (NHGRI), including grantsU54HG003079 (R.K.W.) and U54 HG003273 (R.A.G), with further support from National Institutes of Health R01 GM59290 (M.A.B.), PO1 AG022064 (M.A.B.), HG002385 (E.E.E.) and HG002238 (W.M.), National Science Foundation DBI-0644111 (A.S. and B.B.), David and Lucile Packard Foundation(A.S., V.T. and T.V.),CornellUniversity Provost’s Fellowship (A.L.M.), UK Medical Research Council (C.P.P., G.L., S.M. and A.H.), Marie Curie Fellowship (T.M.-B.), Ministerio de Ciencia e Innovación-Spain (MCI-Spain) and Fundación M. Botín (V.Q., X.S.P., G.R.O. and C.L.-O.), MCI-Spain BFU2006-15413-C02-01 and BFU2009-13409-C02-02 (A.N.), Spanish National Institute for Bioinformatics (INAB) and Fundação para a Ciência e a Tecnologia (Portugal), SFRH/BPD/26384/2006(R.F.) and SFRH/BD/15856/2005 (O.F.), PRIN and CEGBA (M.R., N.A. and G.D.V.), and the Commission of the European Communities IRG-224885 (T.V.), IRG-231025 (B.B.).

Published
2011
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