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7. Mitochondrial gene organization and expression in petunia male fertile and sterile plants

Author

Hanson, M.R., Wilson, R.K., Bentolila, S., Kohler, R.H., and Chen, H.C.

Subjects
Plant mitochondria -- Research, Cytoplasmic male sterility -- Research, Petunia -- Research, Biological sciences
Abstract

Details regarding gene structure and expression of the petunia CMS-associated fused gene (pcf) locus and its fertile homologues in Petunia, are reported. The cytoplasmic male sterility (CMS)-associated region of Petunia seem to carry novel recombinant genes, possibly created by unusual spontaneous recombination events. Restorer genes may occur due to recognition of a sequence in the DNA, RNA or protein product of a novel mitochondrial gene.

Published
1999

8. Nickel-base alloys for severe environments

Author

Wilson, R.K., Flower, H.L., Hack, G.A.J., and Isobe, S.

Subjects
Nickel alloys -- Research -- Methods, Isostatic pressing -- Methods -- Research
Abstract

New sizes and product forms of mechanically alloyed nickel-base superalloys are suitable for industrial applications requiring high strength and resistance to corrosion at elevated temperatures. Inconel alloys MA754 and MA758 […]

Published
1996

9. Correction: Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation (Molecular Psychiatry, (2018), 10.1038/s41380-018-0112-7)

Author

Bis, J.C. (Joshua), Jian, X. (Xueqiu), Kunkle, B.W. (Brian W.), Chen, Y. (Yuning), Hamilton-Nelson, K.L. (Kara L.), Bush, W.S. (William S.), Salerno, W.J. (William J.), Lancour, D. (Daniel), Ma, Y. (Yiyi), Renton, A. (Alan), Marcora, E. (Edoardo), Farrell, J.J. (John J.), Zhao, Y. (Yi), Qu, L. (Liming), Ahmad, S. (Shahzad), Amin, N. (Najaf), Amouyel, P. (Philippe), Beecham, G.W., Below, J.E. (Jennifer E.), Campion, D. (Dominique), Cantwell, L.B. (Laura B.), Charbonnier, C. (Camille), Chung, J. (Jaeyoon), Crane, P.K. (Paul K.), Crane, L.M.A., Cupples, L.A. (L. Adrienne), Dartigues, J.-F., Debette, S. (Stéphanie), Deleuze, J.-F. (Jean-François), Fulton, L. (Lucinda), Gabriel, S.B. (Stacey), Genin, E. (Emmanuelle), Gibbs, R.A. (Richard), Goate, A. (Alison), Grenier-Boley, B. (Benjamin), Gupta, N. (Namrata), Haines, J.L. (Jonathan), Havulinna, A.S. (Aki), Helisalmi, S. (Seppo), Hiltunen, M. (Mikko), Howrigan, D.P. (Daniel P.), Ikram, M.A. (Arfan), Kaprio, J. (Jaakko), Konrad, J. (Jan), Kuzma, A. (Amanda), Lander, E.S. (Eric), Lathrop, M. (Mark), Lehtimäki, T. (Terho), Lin, H. (Honghuang), Mattila, K. (Kari), Mayeux, R. (Richard), Muzny, D. (Donna), Nasser, W. (Waleed), Neale, B.M. (Benjamin), Nho, K. (Kwangsik), Nicolas, G. (Gaël), Patel, D. (Devanshi), Kunkle, B. (Brian), Perola, M. (Markus), Psaty, B.M. (Bruce), Quenez, O. (Olivier), Rajabli, F. (Farid), Redon, R. (Richard), Reitz, C. (Christiane), Remes, A. (Anne), Salomaa, V. (Veikko), Sarnowski, C., Schmidt, H. (Helena), Schmidt, M. (Michael), Schmidt, R. (Reinhold), Soininen, H. (H.), Thornton, T.A. (Timothy A.), Tosto, G. (G.), Tzourio, C. (Christophe), Lee, S.J. (Sven) van der, Duijn, C.M. (Cornelia) van, Valladares, O. (Otto), Vardarajan, B.N. (Badri), Wang, L.S. (Li-San), Wang, W. (Weixin), Wijsman, E. (Ellen), Wilson, R.K. (Richard K.), Witten, D. (Daniela), Worley, K.C. (Kim C.), Zhang, X. (Xiaoling), Bellenguez, C. (Céline), Lambert, J.-C. (J.), Kurki, M.I. (Mitja I.), Palotie, A. (Aarno), Daly, M.J. (Mark), Boerwinkle, E.A. (Eric), Lunetta, K.L. (Kathryn), DeStefano, A.L. (Anita), Martin, E.R., Schellenberg, G.D. (Gerard), Seshadri, S. (Sudha), Naj, A.C. (Adam C.), Fornage, M. (Myriam), Farrer, L.A. (Lindsay), Bis, J.C. (Joshua), Jian, X. (Xueqiu), Kunkle, B.W. (Brian W.), Chen, Y. (Yuning), Hamilton-Nelson, K.L. (Kara L.), Bush, W.S. (William S.), Salerno, W.J. (William J.), Lancour, D. (Daniel), Ma, Y. (Yiyi), Renton, A. (Alan), Marcora, E. (Edoardo), Farrell, J.J. (John J.), Zhao, Y. (Yi), Qu, L. (Liming), Ahmad, S. (Shahzad), Amin, N. (Najaf), Amouyel, P. (Philippe), Beecham, G.W., Below, J.E. (Jennifer E.), Campion, D. (Dominique), Cantwell, L.B. (Laura B.), Charbonnier, C. (Camille), Chung, J. (Jaeyoon), Crane, P.K. (Paul K.), Crane, L.M.A., Cupples, L.A. (L. Adrienne), Dartigues, J.-F., Debette, S. (Stéphanie), Deleuze, J.-F. (Jean-François), Fulton, L. (Lucinda), Gabriel, S.B. (Stacey), Genin, E. (Emmanuelle), Gibbs, R.A. (Richard), Goate, A. (Alison), Grenier-Boley, B. (Benjamin), Gupta, N. (Namrata), Haines, J.L. (Jonathan), Havulinna, A.S. (Aki), Helisalmi, S. (Seppo), Hiltunen, M. (Mikko), Howrigan, D.P. (Daniel P.), Ikram, M.A. (Arfan), Kaprio, J. (Jaakko), Konrad, J. (Jan), Kuzma, A. (Amanda), Lander, E.S. (Eric), Lathrop, M. (Mark), Lehtimäki, T. (Terho), Lin, H. (Honghuang), Mattila, K. (Kari), Mayeux, R. (Richard), Muzny, D. (Donna), Nasser, W. (Waleed), Neale, B.M. (Benjamin), Nho, K. (Kwangsik), Nicolas, G. (Gaël), Patel, D. (Devanshi), Kunkle, B. (Brian), Perola, M. (Markus), Psaty, B.M. (Bruce), Quenez, O. (Olivier), Rajabli, F. (Farid), Redon, R. (Richard), Reitz, C. (Christiane), Remes, A. (Anne), Salomaa, V. (Veikko), Sarnowski, C., Schmidt, H. (Helena), Schmidt, M. (Michael), Schmidt, R. (Reinhold), Soininen, H. (H.), Thornton, T.A. (Timothy A.), Tosto, G. (G.), Tzourio, C. (Christophe), Lee, S.J. (Sven) van der, Duijn, C.M. (Cornelia) van, Valladares, O. (Otto), Vardarajan, B.N. (Badri), Wang, L.S. (Li-San), Wang, W. (Weixin), Wijsman, E. (Ellen), Wilson, R.K. (Richard K.), Witten, D. (Daniela), Worley, K.C. (Kim C.), Zhang, X. (Xiaoling), Bellenguez, C. (Céline), Lambert, J.-C. (J.), Kurki, M.I. (Mitja I.), Palotie, A. (Aarno), Daly, M.J. (Mark), Boerwinkle, E.A. (Eric), Lunetta, K.L. (Kathryn), DeStefano, A.L. (Anita), Martin, E.R., Schellenberg, G.D. (Gerard), Seshadri, S. (Sudha), Naj, A.C. (Adam C.), Fornage, M. (Myriam), and Farrer, L.A. (Lindsay)

Abstract

Following publication, the authors noticed that ‘Laura Cantwell’, ‘Otto Valladares’, and ‘Li-San Wang’ were inadvertently omitted from the author list. These authors have now been added to the author list in 21st, 77th, and 79th position, respectively. This has been corrected in both the PDF and HTML versions of the article.

Published
2019
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10. Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation

Author

Bis, J.C. (Joshua), Jian, X. (Xueqiu), Kunkle, B.W. (Brian W.), Chen, Y. (Yuning), Hamilton-Nelson, K.L. (Kara L.), Bush, W.S. (William S.), Salerno, W.J. (William J.), Lancour, D. (Daniel), Ma, Y. (Yiyi), Renton, A. (Alan), Marcora, E. (Edoardo), Farrell, J.J. (John J.), Zhao, Y. (Yi), Qu, L. (Liming), Ahmad, S. (Shahzad), Amin, N. (Najaf), Amouyel, P. (Philippe), Beecham, G.W., Below, J.E. (Jennifer E.), Campion, D. (Dominique), Charbonnier, C. (Camille), Chung, J. (Jaeyoon), Crane, L.M.A., Cruchaga, C. (Carlos), Cupples, L.A. (L. Adrienne), Dartigues, J.-F., Debette, S. (Stéphanie), Deleuze, J.-F. (Jean-François), Fulton, L. (Lucinda), Gabriel, S.B. (Stacey), Genin, E. (Emmanuelle), Gibbs, R.A. (Richard A.), Goate, A.M. (Alison), Grenier-Boley, B. (Benjamin), Gupta, N. (Namrata), Haines, J.L. (Jonathan), Havulinna, A.S. (Aki), Helisalmi, S. (Seppo), Hiltunen, M. (Mikko), Howrigan, D.P. (Daniel P.), Ikram, M.A. (Arfan), Kaprio, J. (Jaakko), Konrad, J. (Jan), Kuzma, A. (Amanda), Lander, E.S. (Eric), Lathrop, M. (Mark), Lehtimäki, T. (Terho), Lin, H. (Honghuang), Mattila, K. (Kari), Mayeux, R. (Richard), Muzny, D. (Donna), Nasser, W. (Waleed), Neale, B.M. (Benjamin), Nho, K. (Kwangsik), Nicolas, G. (Gaël), Patel, D. (Devanshi), Pericak-Vance, M.A. (Margaret), Perola, M. (Markus), Psaty, B.M. (Bruce M.), Quenez, O. (Olivier), Rajabli, F. (Farid), Redon, R. (Richard), Reitz, C. (Christiane), Remes, A. (Anne), Salomaa, V. (Veikko), Sarnowski, C., Schmidt, H. (Helena), Schmidt, M. (Michael), Schmidt, R. (Reinhold), Soininen, H. (H.), Thornton, T.A. (Timothy A.), Tosto, G. (G.), Tzourio, C. (Christophe), Lee, S.J. (Sven) van der, Duijn, C.M. (Cornelia) van, Vardarajan, B.N. (Badri), Wang, W. (Weixin), Wijsman, E.M. (Ellen), Wilson, R.K. (Richard K.), Witten, D. (Daniela), Worley, K.C. (Kim C.), Zhang, X. (Xiaoling), Bellenguez, C. (Céline), Lambert, J.-C. (J.), Kurki, M.I. (Mitja I.), Palotie, A. (Aarno), Daly, M. (Mark), Boerwinkle, E. (Eric), Lunetta, K.L. (Kathryn), DeStefano, A.L. (Anita), Dupuis, J. (Josée), Martin, E.R. (Eden R.), Schellenberg, G.D. (Gerard), Seshadri, S. (Sudha), Naj, A.C. (Adam C.), Fornage, M. (Myriam), Farrer, L.A. (Lindsay), Bis, J.C. (Joshua), Jian, X. (Xueqiu), Kunkle, B.W. (Brian W.), Chen, Y. (Yuning), Hamilton-Nelson, K.L. (Kara L.), Bush, W.S. (William S.), Salerno, W.J. (William J.), Lancour, D. (Daniel), Ma, Y. (Yiyi), Renton, A. (Alan), Marcora, E. (Edoardo), Farrell, J.J. (John J.), Zhao, Y. (Yi), Qu, L. (Liming), Ahmad, S. (Shahzad), Amin, N. (Najaf), Amouyel, P. (Philippe), Beecham, G.W., Below, J.E. (Jennifer E.), Campion, D. (Dominique), Charbonnier, C. (Camille), Chung, J. (Jaeyoon), Crane, L.M.A., Cruchaga, C. (Carlos), Cupples, L.A. (L. Adrienne), Dartigues, J.-F., Debette, S. (Stéphanie), Deleuze, J.-F. (Jean-François), Fulton, L. (Lucinda), Gabriel, S.B. (Stacey), Genin, E. (Emmanuelle), Gibbs, R.A. (Richard A.), Goate, A.M. (Alison), Grenier-Boley, B. (Benjamin), Gupta, N. (Namrata), Haines, J.L. (Jonathan), Havulinna, A.S. (Aki), Helisalmi, S. (Seppo), Hiltunen, M. (Mikko), Howrigan, D.P. (Daniel P.), Ikram, M.A. (Arfan), Kaprio, J. (Jaakko), Konrad, J. (Jan), Kuzma, A. (Amanda), Lander, E.S. (Eric), Lathrop, M. (Mark), Lehtimäki, T. (Terho), Lin, H. (Honghuang), Mattila, K. (Kari), Mayeux, R. (Richard), Muzny, D. (Donna), Nasser, W. (Waleed), Neale, B.M. (Benjamin), Nho, K. (Kwangsik), Nicolas, G. (Gaël), Patel, D. (Devanshi), Pericak-Vance, M.A. (Margaret), Perola, M. (Markus), Psaty, B.M. (Bruce M.), Quenez, O. (Olivier), Rajabli, F. (Farid), Redon, R. (Richard), Reitz, C. (Christiane), Remes, A. (Anne), Salomaa, V. (Veikko), Sarnowski, C., Schmidt, H. (Helena), Schmidt, M. (Michael), Schmidt, R. (Reinhold), Soininen, H. (H.), Thornton, T.A. (Timothy A.), Tosto, G. (G.), Tzourio, C. (Christophe), Lee, S.J. (Sven) van der, Duijn, C.M. (Cornelia) van, Vardarajan, B.N. (Badri), Wang, W. (Weixin), Wijsman, E.M. (Ellen), Wilson, R.K. (Richard K.), Witten, D. (Daniela), Worley, K.C. (Kim C.), Zhang, X. (Xiaoling), Bellenguez, C. (Céline), Lambert, J.-C. (J.), Kurki, M.I. (Mitja I.), Palotie, A. (Aarno), Daly, M. (Mark), Boerwinkle, E. (Eric), Lunetta, K.L. (Kathryn), DeStefano, A.L. (Anita), Dupuis, J. (Josée), Martin, E.R. (Eden R.), Schellenberg, G.D. (Gerard), Seshadri, S. (Sudha), Naj, A.C. (Adam C.), Fornage, M. (Myriam), and Farrer, L.A. (Lindsay)

Abstract

The Alzheimer’s Disease Sequencing Project (ADSP) undertook whole exome sequencing in 5,740 late-onset Alzheimer disease (AD) cases and 5,096 cognitively normal controls primarily of European ancestry (EA), among whom 218 cases and 177 controls were Caribbean Hispanic (CH). An age-, sex- and APOE based risk score and family history were used to select cases most likely to harbor novel AD risk variants and controls least likely to develop AD by age 85 years. We tested ~1.5 million single nucleotide variants (SNVs) and 50,000 insertion-deletion polymorphisms (indels) for association to AD, using multiple models considering individual variants as well as gene-based tests aggregating rare, predicted functional, and loss of function variants. Sixteen single variants and 19 genes that met criteria for significant or suggestive associations after multiple-testing correction were evaluated for replication in four independent samples; three with whole exome sequencing (2,778 cases, 7,262 contro

Published
2018
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11. Forensic analysis of Turkish elections in 2017–2018

Author

Wilson, R.K., Klimek, P., Jiménez, R., Hidalgo, M., Hinteregger, A., Thurner, S., Wilson, R.K., Klimek, P., Jiménez, R., Hidalgo, M., Hinteregger, A., and Thurner, S.

Abstract

With a majority of ‘Yes’ votes in the Constitutional Referendum of 2017, Turkey continued its drift towards an autocracy. By the will of the Turkish people, this referendum transferred practically all executive power to president Erdoğan. However, the referendum was confronted with a substantial number of allegations of electoral misconducts and irregularities, ranging from state coercion of ‘No’ supporters to the controversial validity of unstamped ballots. Here we report the results of an election forensic analysis of recent Turkish elections to clarify to what extent it is plausible that these voting irregularities were present and able to influence the outcome of the referendum. We apply statistical forensics tests to identify the specific nature of the alleged electoral malpractices. In particular, we test whether the data contains fingerprints for ballot stuffing (submission of multiple ballots per person during the vote) and voter rigging (coercion and intimidation of voters). Additionally, we perform tests to identify numerical anomalies in the election results. For the 2017 Constitutional Referendum we find systematic and highly significant statistical support for the presence of both ballot stuffing and voter rigging. In 11% of stations we find signs for ballot stuffing with a standard deviation (uncertainty of ballot stuffing probability) of 2.7% (4 sigma event). Removing such ballot-stuffing-characteristic anomalies from the data would tip the overall balance from ‘No’ to a majority of ‘Yes’ votes. The 2017 election was followed by early elections in 2018 to directly vote for a new president who would now be head of state and government. We find statistical irregularities in the 2018 presidential and parliamentary elections similar in size and direction to those in 2017. These findings validate that our results unveil systematic and potentially even fraudulent biases that require further attention in order to combat electoral malpractices.

Published
2018

13. Whole genome analysis of a schistosomiasis-transmitting freshwater snail

Author

Adema, C.M. (Coen M.), Hillier, L.W. (LaDeana W.), Jones, C.S. (Catherine S.), Loker, E.S. (Eric S.), Knight, M. (Matty), Minx, P. (Patrick), Oliveira, G. (Guilherme), Raghavan, N. (Nithya), Shedlock, A. (Andrew), Do Amaral, L.R. (Laurence Rodrigues), Arican-Goktas, H.D. (Halime D.), Assis, J.G. (Juliana G.), Baba, E.H. (Elio Hideo), Baron, O.L. (Olga L.), Bayne, C.J. (Christopher J.), Bickham-Wright, U. (Utibe), Biggar, K.K. (Kyle K.), Blouin, M. (Michael), Bonning, B.C. (Bryony C.), Botka, C. (Chris), Bridger, J.M. (Joanna M.), Buckley, K.M. (Katherine M.), Buddenborg, S.K. (Sarah K.), Lima Caldeira, R. (Roberta), Carleton, J. (Julia), Carvalho, O.S. (Omar S.), Castillo, M.G. (Maria G.), Chalmers, I.W. (Iain W.), Christensens, M. (Mikkel), Clifton, S. (Sandra), Cosseau, C. (Celine), Coustau, C. (Christine), Cripps, R.M. (Richard M.), Cuesta-Astroz, Y. (Yesid), Cummins, S.F. (Scott F.), DI Stephano, L. (Leon), DInguirard, N. (Nathalie), Duval, D. (David), Emrich, S. (Scott), Feschotte, C. (Cédric), Feyereisen, R. (Rene), Fitzgerald, P. (Peter), Fronick, C. (Catrina), Fulton, L. (Lucinda), Galinier, R. (Richard), Gava, S.G. (Sandra G.), Geusz, M. (Michael), Geyer, K.K. (Kathrin K.), Giraldo-Calderón, G.I. (Gloria I.), De Souza Gomes, M. (Matheus), Gordy, M.A. (Michelle A.), Gourbal, B. (Benjamin), Grunau, C. (Christoph), Hanington, P.C. (Patrick C.), Hoffmann, K.F. (Karl F.), Hughes, D. (Daniel), Humphries, J. (Judith), Jackson, D.J. (Daniel J.), Jannotti-Passos, L.K. (Liana K.), De Jesus Jeremias, W. (Wander), Jobling, S. (Susan), Kamel, B. (Bishoy), Kapusta, A. (Aurélie), Kaur, S. (Satwant), Koene, J.M. (Joris M.), Kohn, A.B. (Andrea B.), Lawson, D. (Dan), Lawton, S.P. (Scott P), Liang, D. (Di), Limpanont, Y. (Yanin), Liu, S. (Sijun), Lockyer, A.E. (Anne E.), Lovato, T.L. (TyAnna L.), Ludolf, F. (Fernanda), Magrini, V. (Vince), McManus, D.P. (Donald P.), Medina, M. (Monica), Misra, M. (Milind), Mitta, G. (Guillaume), Mkoji, G.M. (Gerald M.), Montague, M.J. (Michael J.), Montelongo, C. (Cesar), Moroz, L.L. (Leonid L.), Munoz-Torres, M.C. (Monica C.), Niazi, U. (Umar), Noble, L.R. (Leslie R.), Oliveira, F.S. (Francislon S.), Pais, F.S. (Fabiano S.), Papenfuss, A.T. (Anthony T.), Peace, R. (Rob), Pena, J.J. (Janeth J.), Pila, E.A. (Emmanuel A.), Quelais, T. (Titouan), Raney, B.J. (Brian J.), Rast, J.P. (Jonathan P.), Rollinson, D. (David), Rosse, I.C. (Izinara C.), Rotgans, B. (Bronwyn), Routledge, E.J. (Edwin J.), Ryan, K.M. (Kathryn M.), Scholte, L.L.S. (Larissa L. S.), Storey, K. (Kenneth B.), Swain, M. (Martin), Tennessen, J.A. (Jacob A.), Tomlinson, C. (Chad), Trujillo, D.L. (Damian L.), Volpi, E.V. (Emanuela V.), Walker, A.J. (Anthony J.), Wang, T. (Tianfang), Wannaporn, I. (Ittiprasert), Warren, W.C. (Wesley C.), Wu, X.-J. (Xiao-Jun), Yoshino, T.P. (Timothy P.), Yusuf, M. (Mohammed), Zhang, S.-M. (Si-Ming), Zhao, M. (Min), Wilson, R.K. (Richard K.), Adema, C.M. (Coen M.), Hillier, L.W. (LaDeana W.), Jones, C.S. (Catherine S.), Loker, E.S. (Eric S.), Knight, M. (Matty), Minx, P. (Patrick), Oliveira, G. (Guilherme), Raghavan, N. (Nithya), Shedlock, A. (Andrew), Do Amaral, L.R. (Laurence Rodrigues), Arican-Goktas, H.D. (Halime D.), Assis, J.G. (Juliana G.), Baba, E.H. (Elio Hideo), Baron, O.L. (Olga L.), Bayne, C.J. (Christopher J.), Bickham-Wright, U. (Utibe), Biggar, K.K. (Kyle K.), Blouin, M. (Michael), Bonning, B.C. (Bryony C.), Botka, C. (Chris), Bridger, J.M. (Joanna M.), Buckley, K.M. (Katherine M.), Buddenborg, S.K. (Sarah K.), Lima Caldeira, R. (Roberta), Carleton, J. (Julia), Carvalho, O.S. (Omar S.), Castillo, M.G. (Maria G.), Chalmers, I.W. (Iain W.), Christensens, M. (Mikkel), Clifton, S. (Sandra), Cosseau, C. (Celine), Coustau, C. (Christine), Cripps, R.M. (Richard M.), Cuesta-Astroz, Y. (Yesid), Cummins, S.F. (Scott F.), DI Stephano, L. (Leon), DInguirard, N. (Nathalie), Duval, D. (David), Emrich, S. (Scott), Feschotte, C. (Cédric), Feyereisen, R. (Rene), Fitzgerald, P. (Peter), Fronick, C. (Catrina), Fulton, L. (Lucinda), Galinier, R. (Richard), Gava, S.G. (Sandra G.), Geusz, M. (Michael), Geyer, K.K. (Kathrin K.), Giraldo-Calderón, G.I. (Gloria I.), De Souza Gomes, M. (Matheus), Gordy, M.A. (Michelle A.), Gourbal, B. (Benjamin), Grunau, C. (Christoph), Hanington, P.C. (Patrick C.), Hoffmann, K.F. (Karl F.), Hughes, D. (Daniel), Humphries, J. (Judith), Jackson, D.J. (Daniel J.), Jannotti-Passos, L.K. (Liana K.), De Jesus Jeremias, W. (Wander), Jobling, S. (Susan), Kamel, B. (Bishoy), Kapusta, A. (Aurélie), Kaur, S. (Satwant), Koene, J.M. (Joris M.), Kohn, A.B. (Andrea B.), Lawson, D. (Dan), Lawton, S.P. (Scott P), Liang, D. (Di), Limpanont, Y. (Yanin), Liu, S. (Sijun), Lockyer, A.E. (Anne E.), Lovato, T.L. (TyAnna L.), Ludolf, F. (Fernanda), Magrini, V. (Vince), McManus, D.P. (Donald P.), Medina, M. (Monica), Misra, M. (Milind), Mitta, G. (Guillaume), Mkoji, G.M. (Gerald M.), Montague, M.J. (Michael J.), Montelongo, C. (Cesar), Moroz, L.L. (Leonid L.), Munoz-Torres, M.C. (Monica C.), Niazi, U. (Umar), Noble, L.R. (Leslie R.), Oliveira, F.S. (Francislon S.), Pais, F.S. (Fabiano S.), Papenfuss, A.T. (Anthony T.), Peace, R. (Rob), Pena, J.J. (Janeth J.), Pila, E.A. (Emmanuel A.), Quelais, T. (Titouan), Raney, B.J. (Brian J.), Rast, J.P. (Jonathan P.), Rollinson, D. (David), Rosse, I.C. (Izinara C.), Rotgans, B. (Bronwyn), Routledge, E.J. (Edwin J.), Ryan, K.M. (Kathryn M.), Scholte, L.L.S. (Larissa L. S.), Storey, K. (Kenneth B.), Swain, M. (Martin), Tennessen, J.A. (Jacob A.), Tomlinson, C. (Chad), Trujillo, D.L. (Damian L.), Volpi, E.V. (Emanuela V.), Walker, A.J. (Anthony J.), Wang, T. (Tianfang), Wannaporn, I. (Ittiprasert), Warren, W.C. (Wesley C.), Wu, X.-J. (Xiao-Jun), Yoshino, T.P. (Timothy P.), Yusuf, M. (Mohammed), Zhang, S.-M. (Si-Ming), Zhao, M. (Min), and Wilson, R.K. (Richard K.)

Abstract

Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization's goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of Biomphalaria glabrata, a lophotrochozoan protostome, and provide timely and important information on snail biology. We describe aspects of phero-perception, stress responses, immune function and regulation of gene expression that support the persistence of B. glabrata in the field and may define this species as a suitable snail host for S. mansoni. We identify several potential targets for developing novel control measures aimed at reducing snail-mediated transmission of schistosomiasis.

Published
2017
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16. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

Author

Delaneau O., Marchini J., McVeanh G.A., Donnelly P., Lunter G., Marchini J.L., Myers, S., Gupta-Hinch, A., Iqbal, Z., Mathieson I., Rimmer, A., Xifara, D.K., Kerasidou, A., Churchhouse, C., Altshuler, D.M., Gabriel, S.B., Lander, E.S., Gupta, N., Daly, M.J., DePristo, M.A., Banks, E., Bhatia G., Carneiro, M.O., Del Angel G., Genovese G., Handsaker, R.E., Hartl, C., McCarroll, S.A., Nemesh J.C., Poplin, R.E., Schaffner, S.F., Shakir, K., Sabeti P.C., Grossman, S.R., Tabrizi, S., Tariyal, R., Li H., Reich, D., Durbin, R.M., Hurles, M.E., Balasubramaniam, S., Burton J., Danecek P., Keane, T.M., Kolb-Kokocinski, A., McCarthy, S., Stalker J., Quail, M., Ayub Q., Chen, Y., Coffey, A.J., Colonna V., Huang, N., Jostins L., Scally, A., Walter, K., Xue, Y., Zhang, Y., Blackburne, B., Lindsay, S.J., Ning, Z., Frankish, A., Harrow J., Chris, T.-S., Abecasis G.R., Kang H.M., Anderson P., Blackwell, T., Busonero F., Fuchsberger, C., Jun G., Maschio, A., Porcu, E., Sidore, C., Tan, A., Trost, M.K., Bentley, D.R., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Bauer, M., Cheetham, R.K., Cox, T., Eberle, M., Murray L., Shaw, R., Chakravarti, A., Clark, A.G., Keinan, A., Rodriguez-Flores J.L., De LaVega F.M., Degenhardt J., Eichler, E.E., Flicek P., Clarke L., Leinonen, R., Smith, R.E., Zheng-Bradley X., Beal, K., Cunningham F., Herrero J., McLaren W.M., Ritchie G.R.S., Barker J., Kelman G., Kulesha, E., Radhakrishnan, R., Roa, A., Smirnov, D., Streeter I., Toneva I., Gibbs, R.A., Dinh H., Kovar, C., Lee, S., Lewis L., Muzny, D., Reid J., Wang, M., Yu F., Bainbridge, M., Challis, D., Evani, U.S., Lu J., Nagaswamy, U., Sabo, A., Wang, Y., Yu J., Fowler G., Hale W., Kalra, D., Green, E.D., Knoppers, B.M., Korbel J.O., Rausch, T., Sttz, A.M., Lee, C., Griffin L., Hsieh, C.-H., Mills, R.E., Von Grotthuss, M., Zhang, C., Shi X., Lehrach H., Sudbrak, R., Amstislavskiy V.S., Lienhard, M., Mertes F., Sultan, M., Timmermann, B., Yaspo, M.L., Herwig, S.R., Mardis, E.R., Wilson, R.K., Fulton L., Fulton, R., Weinstock G.M., Chinwalla, A., Ding L., Dooling, D., Koboldt, D.C., McLellan, M.D., Wallis J.W., Wendl, M.C., Zhang Q., Marth G.T., Garrison, E.P., Kural, D., Lee W.-P., Leong W.F., Ward, A.N., Wu J., Zhang, M., Nickerson, D.A., Alkan, C., Hormozdiari F., Ko, A., Sudmant P.H., Schmidt J.P., Davies, C.J., Gollub J., Webster, T., Wong, B., Zhan, Y., Sherry, S.T., Xiao, C., Church, D., Ananiev V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Cohen, R., Cook, C., Garner J., Hefferon, T., Kimelman, M., Liu, C., Lopez J., Meric P., Ostapchuk, Y., Phan L., Ponomarov, S., Schneider V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang H., Wang J., Fang X., Guo X., Jian, M., Jiang H., Jin X., Li G., Li J., Li, Y., Liu X., Lu, Y., Ma X., Tai, S., Tang, M., Wang, B., Wang G., Wu H., Wu, R., Yin, Y., Zhang W., Zhao J., Zhao, M., Zheng X., Lachlan H., Fang L., Li Q., Li, Z., Lin H., Liu, B., Luo, R., Shao H., Xie, Y., Ye, C., Yu, C., Zheng H., Zhu H., Cai H., Cao H., Su, Y., Tian, Z., Yang H., Yang L., Zhu J., Cai, Z., Albrecht, M.W., Borodina, T.A., Auton, A., Yoon, S.C., Lihm J., Makarov V., Jin H., Kim W., Kim, K.C., Gottipati, S., Jones, D., Cooper, D.N., Ball, E.V., Stenson P.D., Barnes, B., Kahn, S., Ye, K., Batzer, M.A., Konkel, M.K., Walker J.A., MacArthur, D.G., Lek, M., Shriver, M.D., Bustamante, C.D., Gravel, S., Kenny, E.E., Kidd J.M., Lacroute P., Maples, B.K., Moreno-Estrada, A., Zakharia F., Henn, B., Sandoval, K., Byrnes J.K., Halperin, E., Baran, Y., Craig, D.W., Christoforides, A., Izatt, T., Kurdoglu, A.A., Sinari, S.A., Homer, N., Squire, K., Sebat J., Bafna V., Burchard, E.G., Hernandez, R.D., Gignoux, C.R., Haussler, D., Katzman, S.J., Kent W.J., Howie, B., Ruiz-Linares, A., Dermitzakis, E.T., Lappalainen, T., Devine, S.E., Maroo, A., Tallon L.J., Rosenfeld J.A., Michelson L.P., Angius, A., Cucca F., Sanna, S., Bigham, A., Jones, C., Reinier F., Lyons, R., Schlessinger, D., Awadalla P., Hodgkinson, A., Oleksyk, T.K., Martinez-Cruzado J.C., Fu, Y., Xiong, M., Jorde L., Witherspoon, D., Xing J., Browning, B.L., Hajirasouliha I., Chen, K., Albers, C.A., Gerstein, M.B., Abyzov, A., Chen J., Habegger L., Harmanci, A.O., Mu X.J., Sisu, C., Balasubramanian, S., Jin, M., Khurana, E., Clarke, D., Michaelson J.J., OSullivan, C., Barnes, K.C., Gharani, N., Toji L.H., Gerry, N., Kaye J.S., Kent, A., Mathias, R., Ossorio P.N., Parker, M., Rotimi, C.N., Royal, C.D., Tishkoff, S., Via, M., Bodmer W., Bedoya G., Yang G., You, C.J., Garcia-Montero, A., Orfao, A., Dutil J., Brooks L.D., Felsenfeld, A.L., McEwen J.E., Clemm, N.C., Guyer, M.S., Peterson J.L., Duncanson, A., Dunn, M., Peltonen L., and 1000 Genomes Project Consortium

Subjects
haplotype, genetic association, genotype, General Physics and Astronomy, Genome-wide association study, genetic analysis, gene sequence, Biology, gene frequency, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, polymorphism, Gene Frequency, single nucleotide polymorphism, Humans, chromosome, human, 1000 Genomes Project, indel mutation, genome, Alleles, Genetic association, Genetics, Whole genome sequencing, Multidisciplinary, accuracy, Genome, Human, Haplotype, allele, article, reference database, General Chemistry, Microarray Analysis, chromosome 20, Haplotypes, Human genome, microarray analysis, Imputation (genetics), Algorithms, SNP array, Genome-Wide Association Study
Abstract

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved.

Published
2014

34. IRF6 mutation screening in non‐syndromic orofacial clefting: analysis of 1521 families

Author

Leslie, E.J., primary, Koboldt, D.C., additional, Kang, C.J., additional, Ma, L., additional, Hecht, J.T., additional, Wehby, G.L., additional, Christensen, K., additional, Czeizel, A.E., additional, Deleyiannis, F.W.‐B., additional, Fulton, R.S., additional, Wilson, R.K., additional, Beaty, T.H., additional, Schutte, B.C., additional, Murray, J.C., additional, and Marazita, M.L., additional

Published
2015
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36. Investigating hookworm genomes by comparative analysis of two Ancylostoma species\ud

Author

Mitreva, M., McCarter, J.P., Arasu, P., Hawdon, J., Martin, J., Dante, M., Wylie, T., Xu, J., Stajich, J.E., Kapulkin, W., Clifton, S.W., Waterston, R.H., and Wilson, R.K.

Subjects
parasitic diseases
Abstract

Background\ud \ud Hookworms, infecting over one billion people, are the mostly closely related major human parasites to the model nematode Caenorhabditis elegans. Applying genomics techniques to these species, we analyzed 3,840 and 3,149 genes from Ancylostoma caninum and A. ceylanicum.\ud \ud Results\ud \ud Transcripts originated from libraries representing infective L3 larva, stimulated L3, arrested L3, and adults. Most genes are represented in single stages including abundant transcripts like hsp-20 in infective L3 and vit-3 in adults. Over 80% of the genes have homologs in C. elegans, and nearly 30% of these were with observable RNA interference phenotypes. Homologies were identified to nematode-specific and clade V specific gene families. To study the evolution of hookworm genes, 574 A. caninum / A. ceylanicum orthologs were identified, all of which were found to be under purifying selection with distribution ratios of nonsynonymous to synonymous amino acid substitutions similar to that reported for C. elegans / C. briggsae orthologs. The phylogenetic distance between A. caninum and A. ceylanicum is almost identical to that for C. elegans / C. briggsae.\ud \ud Conclusion\ud \ud The genes discovered should substantially accelerate research toward better understanding of the parasites' basic biology as well as new therapies including vaccines and novel anthelmintics.\ud

Published
2005

37. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

Author

Bradley Shaffer, H. (H), Minx, P. (Patrick), Warren, D.E. (Daniel E.), Shedlock, A.M. (Andrew M.), Thomson, R.C. (Robert C.), Valenzuela, N. (Nicole), Abramyan, J. (John), Amemiya, C.T. (Chris T.), Badenhorst, D. (Daleen), Biggar, K.K. (Kyle K.), Borchert, G.M. (Glen M.), Botka, C.W. (Christopher W.), Bowden, R.M. (Rachel M.), Braun, E.L. (Edward L.), Bronikowski, A.M. (Anne M.), Bruneau, B.G. (Benoit G.), Buck, L.T. (Leslie T.), Capel, B. (Blanche), Castoe, T.A. (Todd A.), Czerwinski, M. (Mike), Delehaunty, K.D. (Kim D.), Edwards, S.V. (Scott V.), Fronick, C.C. (Catrina C.), Fujita, M.K. (Matthew K.), Fulton, L. (Lucinda), Graves, T.A. (Tina A.), Green, R.E. (Richard E.), Haerty, W. (Wilfried), Hariharan, R. (Ramkumar), Hernandez, O. (Omar), Hillier, L.W. (LaDeana W.), Holloway, A.K. (Alisha K.), Janes, D. (Daniel), Janzen, F.J. (Fredric J.), Kandoth, C. (Cyriac), Kong, L. (Lesheng), de Koning, A.P.J. (A.P. Jason), Li, Y. (Yang), Literman, R. (Robert), McGaugh, S.E. (Suzanne E.), Mork, L. (Lindsey), O'Laughlin, M. (Michelle), Paitz, R.T. (Ryan T.), Pollock, D.D. (David D.), Ponting, C.P. (Chris P.), Radhakrishnan, S. (Srihari), Raney, B.J. (Brian J.), Richman, J.M. (Joy M.), St John, J. (John), Schwartz, T. (Tonia), Sethuraman, A. (Arun), Spinks, P.Q. (Phillip Q.), Storey, K. (Kenneth B.), Thane, N. (Nay), Vinar, T. (Tomas), Zimmerman, L.M. (Laura M.), Warren, W.C. (Wesley C.), Mardis, E.R. (Elaine R.), Wilson, R.K. (Richard K.), Bradley Shaffer, H. (H), Minx, P. (Patrick), Warren, D.E. (Daniel E.), Shedlock, A.M. (Andrew M.), Thomson, R.C. (Robert C.), Valenzuela, N. (Nicole), Abramyan, J. (John), Amemiya, C.T. (Chris T.), Badenhorst, D. (Daleen), Biggar, K.K. (Kyle K.), Borchert, G.M. (Glen M.), Botka, C.W. (Christopher W.), Bowden, R.M. (Rachel M.), Braun, E.L. (Edward L.), Bronikowski, A.M. (Anne M.), Bruneau, B.G. (Benoit G.), Buck, L.T. (Leslie T.), Capel, B. (Blanche), Castoe, T.A. (Todd A.), Czerwinski, M. (Mike), Delehaunty, K.D. (Kim D.), Edwards, S.V. (Scott V.), Fronick, C.C. (Catrina C.), Fujita, M.K. (Matthew K.), Fulton, L. (Lucinda), Graves, T.A. (Tina A.), Green, R.E. (Richard E.), Haerty, W. (Wilfried), Hariharan, R. (Ramkumar), Hernandez, O. (Omar), Hillier, L.W. (LaDeana W.), Holloway, A.K. (Alisha K.), Janes, D. (Daniel), Janzen, F.J. (Fredric J.), Kandoth, C. (Cyriac), Kong, L. (Lesheng), de Koning, A.P.J. (A.P. Jason), Li, Y. (Yang), Literman, R. (Robert), McGaugh, S.E. (Suzanne E.), Mork, L. (Lindsey), O'Laughlin, M. (Michelle), Paitz, R.T. (Ryan T.), Pollock, D.D. (David D.), Ponting, C.P. (Chris P.), Radhakrishnan, S. (Srihari), Raney, B.J. (Brian J.), Richman, J.M. (Joy M.), St John, J. (John), Schwartz, T. (Tonia), Sethuraman, A. (Arun), Spinks, P.Q. (Phillip Q.), Storey, K. (Kenneth B.), Thane, N. (Nay), Vinar, T. (Tomas), Zimmerman, L.M. (Laura M.), Warren, W.C. (Wesley C.), Mardis, E.R. (Elaine R.), and Wilson, R.K. (Richard K.)

Abstract

Background: We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing.Results: Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented.Conclusions: Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.

Published
2013
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38. Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing

Author

Itsara, A., Peart-Vissers, L.E.L.M., Steinberg, K.M., Meyer, K.J., Zody, M.C., Koolen, D.A., de Ligt, J., Cuppen, E., Baker, C., Lee, C., Graves, T.A., Wilson, R.K., Jenkins, R.B., Veltman, J.A., Eichler, E.E., Itsara, A., Peart-Vissers, L.E.L.M., Steinberg, K.M., Meyer, K.J., Zody, M.C., Koolen, D.A., de Ligt, J., Cuppen, E., Baker, C., Lee, C., Graves, T.A., Wilson, R.K., Jenkins, R.B., Veltman, J.A., and Eichler, E.E.

Abstract

Item does not contain fulltext, Recurrent deletions have been associated with numerous diseases and genomic disorders. Few, however, have been resolved at the molecular level because their breakpoints often occur in highly copy-number-polymorphic duplicated sequences. We present an approach that uses a combination of somatic cell hybrids, array comparative genomic hybridization, and the specificity of next-generation sequencing to determine breakpoints that occur within segmental duplications. Applying our technique to the 17q21.31 microdeletion syndrome, we used genome sequencing to determine copy-number-variant breakpoints in three deletion-bearing individuals with molecular resolution. For two cases, we observed breakpoints consistent with nonallelic homologous recombination involving only H2 chromosomal haplotypes, as expected. Molecular resolution revealed that the breakpoints occurred at different locations within a 145 kbp segment of >99% identity and disrupt KANSL1 (previously known as KANSL1). In the remaining case, we found that unequal crossover occurred interchromosomally between the H1 and H2 haplotypes and that this event was mediated by a homologous sequence that was once again missing from the human reference. Interestingly, the breakpoints mapped preferentially to gaps in the current reference genome assembly, which we resolved in this study. Our method provides a strategy for the identification of breakpoints within complex regions of the genome harboring high-identity and copy-number-polymorphic segmental duplication. The approach should become particularly useful as high-quality alternate reference sequences become available and genome sequencing of individuals' DNA becomes more routine.

Published
2012

39. Initial sequencing and analysis of the human genome

Author

Univ Michigan, Sch Med, Dept Human Genet, Ann Arbor, MI 48109 USA, Univ Michigan, Sch Med, Dept Internal Med, Ann Arbor, MI 48109 USA, Whitehead Inst Biomed Res, Ctr Genome Res, Cambridge, MA 02142 USA, Sanger Ctr, Hinxton CB10 1RQ, Cambs, England, Washington Univ, Genome Sequencing Ctr, St Louis, MO 63108 USA, US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA, Baylor Coll Med, Human Genome Sequencing Ctr, Dept Mol & Human Genet, Houston, TX 77030 USA, Univ Texas, Hlth Sci Ctr, Dept Cellular & Struct Biol, San Antonio, TX 78229 USA, Yeshiva Univ Albert Einstein Coll Med, Dept Mol Genet, Bronx, NY 10461 USA, Univ Texas, Sch Med, Dept Microbiol & Mol Genet, Houston, TX 77225 USA, RIKEN, Genom Sci Ctr, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan, Genoscope, F-91057 Evry, France, CNRS, UMR 8030, F-91057 Evry, France, Genome Therapeut Corp, GTC Sequencing Ctr, Waltham, MA 02453 USA, Inst Mol Biotechnol, Dept Genome Anal, D-07745 Jena, Germany, Chinese Acad Sci, Inst Genet, Ctr Human Genome, Beijing Genom Inst, Beijing 100101, Peoples R China, So China Natl Human Genome Res Ctr, Shanghai 201203, Peoples R China, No China Natl Human Genome Res Ctr, Beijing 100176, Peoples R China, Inst Syst Biol, Multimegabase Sequencing Ctr, Seattle, WA 98105 USA, Stanford Genome Technol Ctr, Palo Alto, CA 94304 USA, Stanford Univ, Dept Genet, Sch Med, Stanford, CA 94305 USA, Stanford Univ, Stanford Human Genome Ctrr, Sch Med, Stanford, CA 94305 USA, Univ Washington, Genome Ctr, Seattle, WA 98195 USA, Keio Univ, Sch Med, Dept Biol Mol, Shinjuku Ku, Tokyo 1608582, Japan, Univ Texas, SW Med Ctr, Dallas, TX 75235 USA, Univ Oklahoma, Adv Ctr Genome Technol, Dept Chem & Biochem, Norman, OK 73019 USA, Max Planck Inst Mol Genet, D-14195 Berlin, Germany, Cold Spring Harbor Lab, Lita Annenberg Hazen Genome Ctr, Cold Spring Harbor, NY 11724 USA, GBF, German Res Ctr Biotechnol, D-38124 Braunschweig, Germany, NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA, Case Western Reserve Univ, Sch Med, Dept Genet, Cleveland, OH 44106 USA, Univ Hosp Cleveland, Cleveland, OH 44106 USA, EMBL, European Bioinformat Inst, Cambridge CB10 1SD, England, Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany, MIT, Dept Biol, Cambridge, MA 02139 USA, Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA, Univ Calif Santa Cruz, Dept Comp Sci, Santa Cruz, CA 95064 USA, Affymetrix Inc, Berkeley, CA 94710 USA, RIKEN, Yokoham Inst, Genom Sci Ctr, Genom Explorat Res Grp, Tsurumi Ku, Kanagawa 2300045, Japan, Univ Calif Santa Cruz, Dept Comp Sci, Howard Hughes Med Inst, Santa Cruz, CA 95064 USA, Univ Dublin Trinity Coll, Dept Genet, Smurfit Inst, Dublin 2, Ireland, Compaq Comp Corp, Cambridge Res Lab, Cambridge, MA 02142 USA, MIT, Genome Ctr, Cambridge, MA 02142 USA, Univ Calif Santa Cruz, Dept Math, Santa Cruz, CA 95064 USA, Univ Calif Santa Cruz, Dept Biol, Santa Cruz, CA 95064 USA, Weizmann Inst Sci, Crown Human Genet Ctr, IL-71600 Rehovot, Israel, Weizmann Inst Sci, Dept Mol Genet, IL-71600 Rehovot, Israel, Univ Oxford, Dept Human Anat & Genet, MRC, Funct Genet Unit, Oxford OX1 3QX, England, Inst Syst Biol, Seattle, WA 98105 USA, NHGRI, NIH, Bethesda, MD 20892 USA, US Dept Energy, Off Sci, Germantown, MD 20874 USA, Wellcome Trust, London NW1 2BE, England, Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J.P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J.C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R.H., Wilson, R.K., Hillier, L.W., McPherson, John D., Marra, M.A., Mardis, E.R., Fulton, L.A., Chinwalla, A.T., Pepin, K.H., Gish, W.R., Chissoe, S.L., Wendl, M.C., Delehaunty, K.D., Miner, T.L., Delehaunty, A., Kramer, J.B., Cook, L.L., Fulton, R.S., Johnson, D.L., Minx, P.J., Clifton, S.W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J.F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E.C., Frazier, M., Gibbs, R.A., Muzny, D.M., Scherer, S.E., Bouck, J.B., Sodergren, E.J., Worley, K.C., Rives, C.M., Gorrell, J.H., Metzker, M.L., Naylor, S.L., Kucherlapati, R.S., Nelson, D.L., Weinstock, G.M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H.M., Yu, J., Wang, J., Huang, G.Y., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S.Z., Davis, R.W., Federspiel, N.A., Abola, A.P., Proctor, M.J., Myers, R.M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D.R., Olson, M.V., Kaul, R., Shimizu, N., Kawasaki, K., Minoshima, S., Evans, G.A., Athanasiou, M., Schultz, R., Roe, B.A., Chen, F., Pan, H.Q., Ramser, J., Lehrach, H., Reinhardt, R., McCombie, W.R., De la Bastide, M., Dedhia, N., Blocker, H., Hornischer, K., Nordsiek, G., Agarwala, R., Aravind, L., Bailey, J.A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D.G., Burge, C.B., Cerutti, L., Chen, H.C., Church, D., Clamp, M., Copley, R.R., Doerks, T., Eddy, S.R., Eichler, E.E., Furey, T.S., Galagan, J., Gilbert, Jgr, Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W.H., Johnson, L.S., Jones, T.A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W.J., Kitts, P., Koonin, E.V., Korf, I., Kulp, D., Lancet, D., Lowe, T.M., McLysaght, A., Mikkelsen, T., Moran, J.V., Mulder, N., Pollara, V.J., Ponting, C.P., Schuler, G., Schultz, J.R., Slater, G., Smit, A.F.A., Stupka, E., Szustakowki, J., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Wallis, J., Wheeler, R., Williams, A., Wolf, Y.I., Wolfe, K.H., Yang, S.P., Yeh, R.F., Collins, F., Guyer, M.S., Peterson, J., Felsenfeld, A., Wetterstrand, K.A., Patrinos, A., Morgan, M.J., Univ Michigan, Sch Med, Dept Human Genet, Ann Arbor, MI 48109 USA, Univ Michigan, Sch Med, Dept Internal Med, Ann Arbor, MI 48109 USA, Whitehead Inst Biomed Res, Ctr Genome Res, Cambridge, MA 02142 USA, Sanger Ctr, Hinxton CB10 1RQ, Cambs, England, Washington Univ, Genome Sequencing Ctr, St Louis, MO 63108 USA, US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA, Baylor Coll Med, Human Genome Sequencing Ctr, Dept Mol & Human Genet, Houston, TX 77030 USA, Univ Texas, Hlth Sci Ctr, Dept Cellular & Struct Biol, San Antonio, TX 78229 USA, Yeshiva Univ Albert Einstein Coll Med, Dept Mol Genet, Bronx, NY 10461 USA, Univ Texas, Sch Med, Dept Microbiol & Mol Genet, Houston, TX 77225 USA, RIKEN, Genom Sci Ctr, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan, Genoscope, F-91057 Evry, France, CNRS, UMR 8030, F-91057 Evry, France, Genome Therapeut Corp, GTC Sequencing Ctr, Waltham, MA 02453 USA, Inst Mol Biotechnol, Dept Genome Anal, D-07745 Jena, Germany, Chinese Acad Sci, Inst Genet, Ctr Human Genome, Beijing Genom Inst, Beijing 100101, Peoples R China, So China Natl Human Genome Res Ctr, Shanghai 201203, Peoples R China, No China Natl Human Genome Res Ctr, Beijing 100176, Peoples R China, Inst Syst Biol, Multimegabase Sequencing Ctr, Seattle, WA 98105 USA, Stanford Genome Technol Ctr, Palo Alto, CA 94304 USA, Stanford Univ, Dept Genet, Sch Med, Stanford, CA 94305 USA, Stanford Univ, Stanford Human Genome Ctrr, Sch Med, Stanford, CA 94305 USA, Univ Washington, Genome Ctr, Seattle, WA 98195 USA, Keio Univ, Sch Med, Dept Biol Mol, Shinjuku Ku, Tokyo 1608582, Japan, Univ Texas, SW Med Ctr, Dallas, TX 75235 USA, Univ Oklahoma, Adv Ctr Genome Technol, Dept Chem & Biochem, Norman, OK 73019 USA, Max Planck Inst Mol Genet, D-14195 Berlin, Germany, Cold Spring Harbor Lab, Lita Annenberg Hazen Genome Ctr, Cold Spring Harbor, NY 11724 USA, GBF, German Res Ctr Biotechnol, D-38124 Braunschweig, Germany, NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA, Case Western Reserve Univ, Sch Med, Dept Genet, Cleveland, OH 44106 USA, Univ Hosp Cleveland, Cleveland, OH 44106 USA, EMBL, European Bioinformat Inst, Cambridge CB10 1SD, England, Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany, MIT, Dept Biol, Cambridge, MA 02139 USA, Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA, Univ Calif Santa Cruz, Dept Comp Sci, Santa Cruz, CA 95064 USA, Affymetrix Inc, Berkeley, CA 94710 USA, RIKEN, Yokoham Inst, Genom Sci Ctr, Genom Explorat Res Grp, Tsurumi Ku, Kanagawa 2300045, Japan, Univ Calif Santa Cruz, Dept Comp Sci, Howard Hughes Med Inst, Santa Cruz, CA 95064 USA, Univ Dublin Trinity Coll, Dept Genet, Smurfit Inst, Dublin 2, Ireland, Compaq Comp Corp, Cambridge Res Lab, Cambridge, MA 02142 USA, MIT, Genome Ctr, Cambridge, MA 02142 USA, Univ Calif Santa Cruz, Dept Math, Santa Cruz, CA 95064 USA, Univ Calif Santa Cruz, Dept Biol, Santa Cruz, CA 95064 USA, Weizmann Inst Sci, Crown Human Genet Ctr, IL-71600 Rehovot, Israel, Weizmann Inst Sci, Dept Mol Genet, IL-71600 Rehovot, Israel, Univ Oxford, Dept Human Anat & Genet, MRC, Funct Genet Unit, Oxford OX1 3QX, England, Inst Syst Biol, Seattle, WA 98105 USA, NHGRI, NIH, Bethesda, MD 20892 USA, US Dept Energy, Off Sci, Germantown, MD 20874 USA, Wellcome Trust, London NW1 2BE, England, Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J.P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J.C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R.H., Wilson, R.K., Hillier, L.W., McPherson, John D., Marra, M.A., Mardis, E.R., Fulton, L.A., Chinwalla, A.T., Pepin, K.H., Gish, W.R., Chissoe, S.L., Wendl, M.C., Delehaunty, K.D., Miner, T.L., Delehaunty, A., Kramer, J.B., Cook, L.L., Fulton, R.S., Johnson, D.L., Minx, P.J., Clifton, S.W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J.F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E.C., Frazier, M., Gibbs, R.A., Muzny, D.M., Scherer, S.E., Bouck, J.B., Sodergren, E.J., Worley, K.C., Rives, C.M., Gorrell, J.H., Metzker, M.L., Naylor, S.L., Kucherlapati, R.S., Nelson, D.L., Weinstock, G.M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H.M., Yu, J., Wang, J., Huang, G.Y., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S.Z., Davis, R.W., Federspiel, N.A., Abola, A.P., Proctor, M.J., Myers, R.M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D.R., Olson, M.V., Kaul, R., Shimizu, N., Kawasaki, K., Minoshima, S., Evans, G.A., Athanasiou, M., Schultz, R., Roe, B.A., Chen, F., Pan, H.Q., Ramser, J., Lehrach, H., Reinhardt, R., McCombie, W.R., De la Bastide, M., Dedhia, N., Blocker, H., Hornischer, K., Nordsiek, G., Agarwala, R., Aravind, L., Bailey, J.A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D.G., Burge, C.B., Cerutti, L., Chen, H.C., Church, D., Clamp, M., Copley, R.R., Doerks, T., Eddy, S.R., Eichler, E.E., Furey, T.S., Galagan, J., Gilbert, Jgr, Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W.H., Johnson, L.S., Jones, T.A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W.J., Kitts, P., Koonin, E.V., Korf, I., Kulp, D., Lancet, D., Lowe, T.M., McLysaght, A., Mikkelsen, T., Moran, J.V., Mulder, N., Pollara, V.J., Ponting, C.P., Schuler, G., Schultz, J.R., Slater, G., Smit, A.F.A., Stupka, E., Szustakowki, J., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Wallis, J., Wheeler, R., Williams, A., Wolf, Y.I., Wolfe, K.H., Yang, S.P., Yeh, R.F., Collins, F., Guyer, M.S., Peterson, J., Felsenfeld, A., Wetterstrand, K.A., Patrinos, A., and Morgan, M.J.

Abstract

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Published
2009

40. Genome-wide detection and characterization of positive selection in human populations

Author

Sabeti, P.C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E.H., McCarroll, S.A., Gaudet, R., Schaffner, S.F., Rotimi, C.N., Adebamowo, C.A., Ajayi, I., Aniagwu, T., Marshall, P.A., Nkwodimmah, C., Royal, C.D.M., Leppert, M.F., Dixon, M., Boudreau, A., Taillon-Miller, P., Peiffer, A., Qiu, R., Kent, A., Kato, K., Niikawa, N., Adewole, I.F., Knoppers, B.M., Foster, M.W., Clayton, E.W., Watkin, J., Xiao, M., Hardenbol, P., Muzny, D., Nazareth, L., Sodergren, E., Weinstock, G.M., Yakub, I., Birren, B.W., Wilson, R.K., Fulton, L.L., Rogers, J., Tsui, L.C., Burton, J., Leal, S.M., Carter, N.P., Clee, C.M., Griffiths, M., Jones, M.C., McLay, K., Plumb, R.W., Ross, M.T., Sims, S.K., Mak, W., Willey, D.L., Chen, Z., Pasternak, S., Han, H., Kang, L., Godbout, M., Wallenburg, J.C., L'Archevêque, P., Bellemare, G., Saeki, K., You, Q.S., Wang, H., An, D., Fu, H., Wheeler, D.A., Li, Q., Wang, Z., Wang, R., Holden, A.L., Brooks, L.D., McEwen, J.E., Tam, P.K.H., Guyer, M.S., Wang, V.O., Peterson, J.L., Shi, M., Willis, T.D., Spiegel, J., Sung, L.M., Zacharia, L.F., Collins, F.S., Kennedy, K., Nakamura, Y., Jamieson, R., Stewart, J., Yu, F., Yang, H., Zeng, C., Gao, Y., Hu, H., Hu, W., Li, C., Lin, W., Kawaguchi, T., Liu, S., Pan, H., Tang, X., Wang, J., Wang, W., Yu, J., Zhang, B., Zhang, Q., Zhao, H., Kitamoto, T., Zhou, J., Gabriel, S.B., Barry, R., Blumenstiel, B., Camargo, A., Defelice, M., Faggart, M., Goyette, M., Gupta, S., Moore, J., Morizono, T., Nguyen, H., Onofrio, R.C., Parkin, M., Roy, J., Stahl, E., Winchester, E., Ziaugra, L., Altshuler, D., Shen, Y., Yao, Z., Lander, E.S., Huang, W., Chu, X., He, Y., Jin, L., Liu, Y., Sun, W., Wang, Y., Nagashima, A., Xiong, X., Xu, L., Waye, M.M.Y., Tsui, S.K.W., Xue, H., Wong, J.T.F., Galver, L.M., Fan, J.B., Gunderson, K., Murray, S.S., Ohnishi, Y., Oliphant, A.R., Chee, M.S., Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Olivier, J.F., Phillips, M.S., Roumy, S., Sallée, C., Sekine, A., Verner, A., Hudson, T.J., Kwok, P.Y., Cai, D., Koboldt, D.C., Miller, R.D., Pawlikowska, L., Tanaka, T., Tsunoda, T., Deloukas, P., Bird, C.P., Delgado, M., Dermitzakis, E.T., Gwilliam, R., Frazer, K.A., Hunt, S., Morrison, J., Powell, D., Stranger, B.E., Whittaker, P., Bentley, D.R., Daly, M.J., De Bakker, P.I.W., Barrett, J., Chretien, Y.R., Ballinger, D.G., Maller, J., McCarroll, S., Patterson, N., Pe'Er, I., Price, A., Purcell, S., Richter, D.J., Saxena, R., Sham, P.C., Stein, L.D., Cox, D.R., Krishnan, L., Smith, A.V., Tello-Ruiz, M.K., Thorisson, G.A., Chakravarti, A., Chen, P.E., Cutler, D.J., Kashuk, C.S., Lin, S., Abecasis, G.R., Hinds, D.A., Guan, W., Li, Y., Munro, H.M., Qin, Z.S., Thomas, D.J., McVean, G., Auton, A., Bottolo, L., Cardin, N., Eyheramendy, S., Stuve, L.L., Freeman, C., Marchini, J., Myers, S., Spencer, C., Stephens, M., Donnelly, P., Cardon, L.R., Clarke, G., Evans, D.M., Morris, A.P., Gibbs, R.A., Weir, B.S., Johnson, T.A., Mullikin, J.C., Sherry, S.T., Feolo, M., Skol, A., Zhang, H., Matsuda, I., Fukushima, Y., MacEr, D.R., Belmont, J.W., Suda, E., Sabeti, P.C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E.H., McCarroll, S.A., Gaudet, R., Schaffner, S.F., Rotimi, C.N., Adebamowo, C.A., Ajayi, I., Aniagwu, T., Marshall, P.A., Nkwodimmah, C., Royal, C.D.M., Leppert, M.F., Dixon, M., Boudreau, A., Taillon-Miller, P., Peiffer, A., Qiu, R., Kent, A., Kato, K., Niikawa, N., Adewole, I.F., Knoppers, B.M., Foster, M.W., Clayton, E.W., Watkin, J., Xiao, M., Hardenbol, P., Muzny, D., Nazareth, L., Sodergren, E., Weinstock, G.M., Yakub, I., Birren, B.W., Wilson, R.K., Fulton, L.L., Rogers, J., Tsui, L.C., Burton, J., Leal, S.M., Carter, N.P., Clee, C.M., Griffiths, M., Jones, M.C., McLay, K., Plumb, R.W., Ross, M.T., Sims, S.K., Mak, W., Willey, D.L., Chen, Z., Pasternak, S., Han, H., Kang, L., Godbout, M., Wallenburg, J.C., L'Archevêque, P., Bellemare, G., Saeki, K., You, Q.S., Wang, H., An, D., Fu, H., Wheeler, D.A., Li, Q., Wang, Z., Wang, R., Holden, A.L., Brooks, L.D., McEwen, J.E., Tam, P.K.H., Guyer, M.S., Wang, V.O., Peterson, J.L., Shi, M., Willis, T.D., Spiegel, J., Sung, L.M., Zacharia, L.F., Collins, F.S., Kennedy, K., Nakamura, Y., Jamieson, R., Stewart, J., Yu, F., Yang, H., Zeng, C., Gao, Y., Hu, H., Hu, W., Li, C., Lin, W., Kawaguchi, T., Liu, S., Pan, H., Tang, X., Wang, J., Wang, W., Yu, J., Zhang, B., Zhang, Q., Zhao, H., Kitamoto, T., Zhou, J., Gabriel, S.B., Barry, R., Blumenstiel, B., Camargo, A., Defelice, M., Faggart, M., Goyette, M., Gupta, S., Moore, J., Morizono, T., Nguyen, H., Onofrio, R.C., Parkin, M., Roy, J., Stahl, E., Winchester, E., Ziaugra, L., Altshuler, D., Shen, Y., Yao, Z., Lander, E.S., Huang, W., Chu, X., He, Y., Jin, L., Liu, Y., Sun, W., Wang, Y., Nagashima, A., Xiong, X., Xu, L., Waye, M.M.Y., Tsui, S.K.W., Xue, H., Wong, J.T.F., Galver, L.M., Fan, J.B., Gunderson, K., Murray, S.S., Ohnishi, Y., Oliphant, A.R., Chee, M.S., Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Olivier, J.F., Phillips, M.S., Roumy, S., Sallée, C., Sekine, A., Verner, A., Hudson, T.J., Kwok, P.Y., Cai, D., Koboldt, D.C., Miller, R.D., Pawlikowska, L., Tanaka, T., Tsunoda, T., Deloukas, P., Bird, C.P., Delgado, M., Dermitzakis, E.T., Gwilliam, R., Frazer, K.A., Hunt, S., Morrison, J., Powell, D., Stranger, B.E., Whittaker, P., Bentley, D.R., Daly, M.J., De Bakker, P.I.W., Barrett, J., Chretien, Y.R., Ballinger, D.G., Maller, J., McCarroll, S., Patterson, N., Pe'Er, I., Price, A., Purcell, S., Richter, D.J., Saxena, R., Sham, P.C., Stein, L.D., Cox, D.R., Krishnan, L., Smith, A.V., Tello-Ruiz, M.K., Thorisson, G.A., Chakravarti, A., Chen, P.E., Cutler, D.J., Kashuk, C.S., Lin, S., Abecasis, G.R., Hinds, D.A., Guan, W., Li, Y., Munro, H.M., Qin, Z.S., Thomas, D.J., McVean, G., Auton, A., Bottolo, L., Cardin, N., Eyheramendy, S., Stuve, L.L., Freeman, C., Marchini, J., Myers, S., Spencer, C., Stephens, M., Donnelly, P., Cardon, L.R., Clarke, G., Evans, D.M., Morris, A.P., Gibbs, R.A., Weir, B.S., Johnson, T.A., Mullikin, J.C., Sherry, S.T., Feolo, M., Skol, A., Zhang, H., Matsuda, I., Fukushima, Y., MacEr, D.R., Belmont, J.W., and Suda, E.

Abstract

With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia. ©2007 Nature Publishing Group.

Published
2007

41. IRF6 mutation screening in non-syndromic orofacial clefting: analysis of 1521 families.

Author

Leslie, E.J., Koboldt, D.C., Kang, C.J., Ma, L., Hecht, J.T., Wehby, G.L., Christensen, K., Czeizel, A.E., Deleyiannis, F.W.‐B., Fulton, R.S., Wilson, R.K., Beaty, T.H., Schutte, B.C., Murray, J.C., and Marazita, M.L.

Subjects
INTERFERON regulatory factors, CLEFT lip, GENETIC mutation, VAN der Woude syndrome, GENETIC polymorphisms
Abstract

Van der Woude syndrome ( VWS) is an autosomal dominant malformation syndrome characterized by orofacial clefting ( OFC) and lower lip pits. The clinical presentation of VWS is variable and can present as an isolated OFC, making it difficult to distinguish VWS cases from individuals with non-syndromic OFCs. About 70% of causal VWS mutations occur in IRF6, a gene that is also associated with non-syndromic OFCs. Screening for IRF6 mutations in apparently non-syndromic cases has been performed in several modestly sized cohorts with mixed results. In this study, we screened 1521 trios with presumed non-syndromic OFCs to determine the frequency of causal IRF6 mutations. We identified seven likely causal IRF6 mutations, although a posteriori review identified two misdiagnosed VWS families based on the presence of lip pits. We found no evidence for association between rare IRF6 polymorphisms and non-syndromic OFCs. We combined our results with other similar studies (totaling 2472 families) and conclude that causal IRF6 mutations are found in 0.24-0.44% of apparently non-syndromic OFC families. We suggest that clinical mutation screening for IRF6 be considered for certain family patterns such as families with mixed types of OFCs and/or autosomal dominant transmission. [ABSTRACT FROM AUTHOR]

Published
2016
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42. The Cemented Custom Femoral Stem - a 10 Year Review

Author

O'brien, S., primary, Wilson, R.K., additional, Hanratty, B.M., additional, Thompson, N.W., additional, Wallace, M.E., additional, Nixon, J.R., additional, Engela, D.W., additional, Orr, J.F., additional, Isaac, G.H., additional, and Beverland, D.E., additional

Published
2007
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43. Nibrin, a novel DNA double-strand break repair protein, is mutated in Nijmegen Breakage Syndrome

Author

Varon, R., Vissinga, C., Platzer, M., Cerosaletti, K.M., Chrzanowska, K.H., Saar, K., Beckman, G., Seemanová, E., Cooper, P.R., Nowak, N.J., Stumm, M., Weemaes, C.M.R., Gatti, R.A., Wilson, R.K., Digweed, M., Rosenthal, A., Sperling, K., Concannon, P., Reis, A., Varon, R., Vissinga, C., Platzer, M., Cerosaletti, K.M., Chrzanowska, K.H., Saar, K., Beckman, G., Seemanová, E., Cooper, P.R., Nowak, N.J., Stumm, M., Weemaes, C.M.R., Gatti, R.A., Wilson, R.K., Digweed, M., Rosenthal, A., Sperling, K., Concannon, P., and Reis, A.

Abstract

Item does not contain fulltext

Published
1998

44. Mutational Profiling in the Human Genome

Author

WILSON, R.K., primary, LEY, T.J., additional, COLE, F.S., additional, MILBRANDT, J.D., additional, CLIFTON, S., additional, FULTON, L., additional, FEWELL, G., additional, MINX, P., additional, SUN, H., additional, MCLELLAN, M., additional, POHL, C., additional, and MARDIS, E.R., additional

Published
2003
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45. Modification of a commercially available DNA sequencer to increase sample throughput

Author

Stuebe, E.T., primary, Steward, J.Q., additional, Chinwalia, A., additional, Cook, L.L., additional, Cook, M., additional, Fronick, B., additional, Miller, K., additional, Mullen, M.K., additional, O'Brien, D., additional, Panussis, D.A., additional, Pohl, C., additional, Snider, J.E., additional, Strong, J., additional, Williams, D., additional, Wilson, R.K., additional, Tibbets, C., additional, and Mardis, E.R., additional

Published
2000
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50. Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three Salmonella enterica serovars, Typhimurium, Typhi and Paratyphi

Author

Florea, L., Sanderson, K., Clifton, S.W., Parkhill, J., Churcher, C., Dougan, G., Wilson, R.K., Miller, W., and McClelland, M.

Abstract

The Escherichia coli K-12 genome (ECO) was compared with the sampled genomes of the sibling species Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A (collectively referred to as SAL) and the genome of the close outgroup Klebsiella pneumoniae (KPN). There are at least 160 locations where sequences of >400 bp are absent from ECO but present in the genomes of all three SAL and 394 locations where sequences are present in ECO but close homologs are absent in all SAL genomes. The 394 sequences in ECO that do not occur in SAL contain 1350 (30.6%) of the 4405 ECO genes. Of these, 1165 are missing from both SAL and KPN. Most of the 1165 genes are concentrated within 28 regions of 10-40 kb, which consist almost exclusively of such genes. Among these regions were six that included previously identified cryptic phage. A hypothetical ancestral state of genomic regions that differ between ECO and SAL can be inferred in some cases by reference to the genome structure in KPN and the more distant relative Yersinia pestis. However, many changes between ECO and SAL are concentrated in regions where all four genera have a different structure. The rate of gene insertion and deletion is sufficiently high in these regions that the ancestral state of the ECO/SAL lineage cannot be inferred from the present data. The sequencing of other closely related genomes, such as S.bongori or Citrobacter, may help in this regard.

Published
2000

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