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1. The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs

Author

Shriver Mark D, Kennedy Giulia C, Parra Esteban J, Lawson Heather A, Sonpar Vibhor, Huang Jing, Akey Joshua M, and Jones Keith W

Subjects
population genomics, population genetics, microarray, genotyping, evolution, admixture, Medicine, Genetics, QH426-470
Abstract

Abstract Understanding the nature of evolutionary relationships among persons and populations is important for the efficient application of genome science to biomedical research. We have analysed 8,525 autosomal single nucleotide polymorphisms (SNPs) in 84 individuals from four populations: African-American, European-American, Chinese and Japanese. Individual relationships were reconstructed using the allele sharing distance and the neighbour-joining tree making method. Trees show clear clustering according to population, with the root branching from the African-American clade. The African-American cluster is much less star-like than European-American and East Asian clusters, primarily because of admixture. Furthermore, on the East Asian branch, all ten Chinese individuals cluster together and all ten Japanese individuals cluster together. Using positional information, we demonstrate strong correlations between inter-marker distance and both locus-specific FST (the proportion of total variation due to differentiation) levels and branch lengths. Chromosomal maps of the distribution of locus-specific branch lengths were constructed by combining these data with other published SNP markers (total of 33,704 SNPs). These maps clearly illustrate a non-uniform distribution of human genetic substructure, an instructional and useful paradigm for education and research.

Published
2004
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4. The Human Pangenome Project: a global resource to map genomic diversity

Author

Wang, Ting, Antonacci-Fulton, Lucinda, Howe, Kerstin, Lawson, Heather A, Lucas, Julian K, Phillippy, Adam M, Popejoy, Alice B, Asri, Mobin, Carson, Caryn, Chaisson, Mark JP, Chang, Xian, Cook-Deegan, Robert, Felsenfeld, Adam L, Fulton, Robert S, Garrison, Erik P, Garrison, Nanibaa’ A, Graves-Lindsay, Tina A, Ji, Hanlee, Kenny, Eimear E, Koenig, Barbara A, Li, Daofeng, Marschall, Tobias, McMichael, Joshua F, Novak, Adam M, Purushotham, Deepak, Schneider, Valerie A, Schultz, Baergen I, Smith, Michael W, Sofia, Heidi J, Weissman, Tsachy, Flicek, Paul, Li, Heng, Miga, Karen H, Paten, Benedict, Jarvis, Erich D, Hall, Ira M, Eichler, Evan E, and Haussler, David

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Genome, Human, Genomics, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, Sequence Analysis, DNA, Human Pangenome Reference Consortium, General Science & Technology
Abstract

The human reference genome is the most widely used resource in human genetics and is due for a major update. Its current structure is a linear composite of merged haplotypes from more than 20 people, with a single individual comprising most of the sequence. It contains biases and errors within a framework that does not represent global human genomic variation. A high-quality reference with global representation of common variants, including single-nucleotide variants, structural variants and functional elements, is needed. The Human Pangenome Reference Consortium aims to create a more sophisticated and complete human reference genome with a graph-based, telomere-to-telomere representation of global genomic diversity. Here we leverage innovations in technology, study design and global partnerships with the goal of constructing the highest-possible quality human pangenome reference. Our goal is to improve data representation and streamline analyses to enable routine assembly of complete diploid genomes. With attention to ethical frameworks, the human pangenome reference will contain a more accurate and diverse representation of global genomic variation, improve gene-disease association studies across populations, expand the scope of genomics research to the most repetitive and polymorphic regions of the genome, and serve as the ultimate genetic resource for future biomedical research and precision medicine.

Published
2022

5. Deciphering the impact of genomic variation on function.

Author

Engreitz, Jesse M., Lawson, Heather A., Singh, Harinder, Starita, Lea M., Hon, Gary C., Carter, Hannah, Sahni, Nidhi, Reddy, Timothy E., Lin, Xihong, Li, Yun, Munshi, Nikhil V., Chahrour, Maria H., Boyle, Alan P., Hitz, Benjamin C., Mortazavi, Ali, Craven, Mark, Mohlke, Karen L., Pinello, Luca, Wang, Ting, and Kundaje, Anshul

Abstract

Our genomes influence nearly every aspect of human biology—from molecular and cellular functions to phenotypes in health and disease. Studying the differences in DNA sequence between individuals (genomic variation) could reveal previously unknown mechanisms of human biology, uncover the basis of genetic predispositions to diseases, and guide the development of new diagnostic tools and therapeutic agents. Yet, understanding how genomic variation alters genome function to influence phenotype has proved challenging. To unlock these insights, we need a systematic and comprehensive catalogue of genome function and the molecular and cellular effects of genomic variants. Towards this goal, the Impact of Genomic Variation on Function (IGVF) Consortium will combine approaches in single-cell mapping, genomic perturbations and predictive modelling to investigate the relationships among genomic variation, genome function and phenotypes. IGVF will create maps across hundreds of cell types and states describing how coding variants alter protein activity, how noncoding variants change the regulation of gene expression, and how such effects connect through gene-regulatory and protein-interaction networks. These experimental data, computational predictions and accompanying standards and pipelines will be integrated into an open resource that will catalyse community efforts to explore how our genomes influence biology and disease across populations.The Impact of Genomic Variation on Function Consortium is combining single-cell mapping, genomic perturbations and predictive modelling to investigate relationships between human genomic variation, genome function and phenotypes and will provide an open resource to the community. [ABSTRACT FROM AUTHOR]

Published
2024
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9. Author Correction: Comparative and demographic analysis of orang-utan genomes

Author

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, Chris, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Fowler, Gerald R., Lunter, Gerton, Meader, Stephen, Heger, Andreas, Ponting, Chris P., Marques-Bonet, Tomas, 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, Domènec, 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., Ordoñez, Gonzalo R., López-Otín, Carlos, Vinar, Tomas, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vikas, Martins, André L., Siepel, Adam, RoyChoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thomas, 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.

Published
2022
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20. List of Contributors

Author

Aigner, Bernhard, primary, Allison, W. Ted, additional, Andreatini, Roberto, additional, Antonelli, Marta, additional, Arndt, Saskia S., additional, Austin, Amazon, additional, Brand, Cristin, additional, Bukowska, Joanna, additional, Caprariello, Andrew C., additional, Carlisle, Rachel E., additional, Chaible, Lucas M., additional, Chen, Li, additional, Chen, Mengqi, additional, Chi, Thomas, additional, Choudhury, Mohammed E., additional, Clarke, Iain J., additional, Coleman, Kristine, additional, Colpo, Gabriela D., additional, Damm, Oliver S., additional, Davis, Catherine M., additional, Davis, Erica E., additional, de Lecea, Luis, additional, de Miranda, Aline S., additional, de Souza, Diogo B., additional, Dickhout, Jeffrey G., additional, Donaldson, Paul J., additional, Donnan, Geoffrey A., additional, Emoto, Yuko, additional, Feifel, David, additional, Finzi Corat, Marcus A., additional, Frasch, Martin G., additional, Fukumura, Ryutaro, additional, Fukusato, Toshio, additional, Fuller-Jackson, John-Paul, additional, Fyffe-Maricich, Sharyl, additional, Gawronska-Kozak, Barbara, additional, Getz, Godfrey S., additional, Gondo, Yoichi, additional, Henry, Belinda A., additional, Howells, David W., additional, Jamwal, Sumit, additional, Kasahara, Jiro, additional, Katsanis, Nicholas, additional, Kemp, Matthew W., additional, Kessler, Barbara, additional, Khan, Imran, additional, King, Aileen, additional, Kinoshita, Denise, additional, Klymiuk, Nikolai, additional, Koyama, Ryuta, additional, Kretzschmar, Doris, additional, Kumar, Puneet, additional, Kuncova, Jitka, additional, Kuro, Maki, additional, Kurome, Mayuko, additional, Lardelli, Michael, additional, Lawson, Heather A., additional, Lewejohann, Lars, additional, Lim, Julie C., additional, Lyons, David M., additional, Macleod, Malcolm R., additional, Makino, Shigeru, additional, Martinez-Lage, Marta, additional, Martis, Renita M., additional, Meijer, Ellen, additional, Metz, Gerlinde A.S., additional, Miller, Robert H., additional, Miura, Yuichiro, additional, Mohammed-Ali, Zahraa, additional, Musk, Gabrielle C., additional, Nademi, Samera, additional, Nalca, Aysegul, additional, Newman, Morgan, additional, Nie, Yu, additional, Nishikawa, Noriko, additional, Nomoto, Masahiro, additional, Nordquist, Rebecca E., additional, O’Collins, Victoria E., additional, Ogawa, Masatoshi, additional, Pereira-Sampaio, Marco A., additional, Praud, Jean-Paul, additional, Quevedo, João, additional, Reardon, Catherine A., additional, Regan, Christopher P., additional, Renner, Simone, additional, Ribeiro, Fabiola M., additional, Rocha, Natalia P., additional, Rodriguez-Perales, Sandra, additional, Ruiz, Sara I., additional, Saito, Masatoshi, additional, J.B. Sampaio, Francisco, additional, Schapiro, Steven J., additional, Schatzberg, Alan F., additional, Schulkin, Jay, additional, Shamchuk, Angela L., additional, Shannon, Richard P., additional, Shen, You-Tang, additional, Shilling, Paul D., additional, Stengl, Milan, additional, Stoller, Marshall L., additional, Stürzenbaum, Stephen R., additional, Sviglerova, Jitka, additional, Taguchi, Kazumi, additional, Takahashi, Yoshihisa, additional, Tanabe, Akie, additional, Tanaka, Junya, additional, Tannenbaum, Jerrold, additional, Teixeira, Antônio L., additional, Testani, Jeffrey M., additional, Tierney, Keith B., additional, Torres-Ruiz, Raul, additional, Tsubura, Airo, additional, Tsuji, Ryosuke, additional, Tzou, David T., additional, Usuda, Haruo, additional, Valvassori, Samira S., additional, van der Staay, Franz J., additional, Varela, Roger B., additional, Verdile, Giuseppe, additional, Vorontsova, Irene, additional, Wayhart, Jessica P., additional, Weed, James L., additional, Welsh, JoEllen, additional, Werler, Steffi, additional, Wistuba, Joachim, additional, Wolf, Eckhard, additional, Wünsch, Annegret, additional, Yamamoto, Toshiyuki, additional, Yokoyama, Hironori, additional, Yoshizawa, Katsuhiko, additional, Zaidan Dagli, Maria L., additional, Zhang, Jennifer Y., additional, Zhou, Yu, additional, and Zumbrun, Elizabeth E., additional

Published
2017
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22. Using Machine Learning to Evaluate Coal Geochemical Data with Respect to Dynamic Failures.

Author

Hanson, David R. and Lawson, Heather E.

Subjects
*MACHINE learning, *MINES & mineral resources, *DIMENSIONAL reduction algorithms, *HIERARCHICAL clustering (Cluster analysis), *COAL, *CLUSTER analysis (Statistics)
Abstract

Dynamic failure events have occurred in the underground coal mining industry since its inception. Recent NIOSH research has identified geochemical markers that correlate with in situ reportable dynamic event occurrence, although the causes behind this correlative relationship remain unclear. In this study, NIOSH researchers conducted machine learning analysis to examine whether a model could be constructed to assess the probability of dynamic failure occurrence based on geochemical and petrographic data. Linear regression, random forest, dimensionality reduction, and cluster analyses were applied to a catalog of dynamic failure and control data from the Pennsylvania Coal Sample Databank, cross-referenced with accident data from the Mine Safety and Health Administration (MSHA). Analyses determined that 7 of the 18 geochemical parameters that were examined had the biggest impact on model performance. Classifications based on logistic regression and random forest models attained precision values of 85.7% and 96.7%, respectively. Dimensionality reduction was used to explore patterns and groupings in the data and to search for relationships between compositional parameters. Cluster analyses were performed to determine if an algorithm could find clusters with given class memberships and to what extent misclassifications of dynamic failure status occurred. Cluster analysis using a hierarchal clustering algorithm after dimensionality reduction resulted in four clusters, with one relatively distinct dynamic failure cluster, and three clusters mostly consisting of control group members but with a small number of dynamic failure members. [ABSTRACT FROM AUTHOR]

Published
2023
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25. Internet-delivered management of pain among cancer treatment survivors (IMPACTS WF-1901).

Author

Irby, Megan, primary, Lesser, Glenn Jay, additional, Penzien, Donald, additional, Dressler, Emily Van Meter, additional, Rini, Christine, additional, Keefe, Francis, additional, Snavely, Anna, additional, Ang, Dennis, additional, Danhauer, Suzanne, additional, Brown, Mark, additional, Blackwell-Young, Caroline, additional, Boothe, Stephanie, additional, Craver, Karen, additional, Lawson, Heather, additional, Pardy, Mariana, additional, Stanfield, Bill, additional, Turner, Julie, additional, Vitolins, Mara, additional, and Weaver, Kathryn E., additional

Published
2022
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32. Improving Initial Session Attendance of Substance Abusing and Conduct Disordered Adolescents: A Controlled Study.

Author

Donohue, Brad, Azrin, Nathan H., and Lawson, Heather

Abstract

Demonstrates a method of improving first session attendance in a population of conduct-disordered and substance-abusing adolescents. Results indicate that an intensive intervention involving the youth and parent was more effective in improving session attendance than a less intensive intervention that excluded the youth's involvement. Discusses implications of the study in light of the results. (Author/MKA)

Published
1998

39. Comparative and demographic analysis of orang-utan genomes

Author

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, Chris, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Fowler, Gerald R., Lunter, Gerton, Meader, Stephen, Heger, Andreas, Ponting, Chris P., Marques-Bonet, Tomas, 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, Domènec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Valle, Giuliano Della, 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., Ordoñez, Gonzalo R., López-Otín, Carlos, Vinar, Tomas, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vikas, Martins, André L., Siepel, Adam, RoyChoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thomas, 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.

Published
2011
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42. List of Contributors

Author

Aigner, Bernhard, primary, Andoh, Akira, additional, Badimon, Lina, additional, Benani, Alexandre, additional, Breckenridge, Ross A., additional, Butzke, Daniel, additional, Caprariello, Andrew V., additional, Casani, Laura, additional, Chaible, Lucas M., additional, Chen, Li, additional, Chen, Mengqi, additional, Choi, K. Yeon, additional, Choudhury, Mohammed Emamussalehin, additional, Clarke, Iain J., additional, Coleman, Kristine, additional, Daiss, John L., additional, Datiche, Frédérique, additional, Davis, Catherine M., additional, Donnan, Geoffrey A., additional, Feifel, David, additional, Fickert, Peter, additional, Finzi Corat, Marcus A., additional, Fioramonti, Xavier, additional, Fry, Christopher H., additional, Fyffe-Maricich, Sharyl, additional, Gaupel, Ann-Christin, additional, Goldberg, Steven R., additional, Gondo, Yoichi, additional, Grune, Barbara, additional, Henry, Belinda A., additional, Howells, David W., additional, Hunter, Joshua G., additional, Imanikia, Soudabeh, additional, Jabr, Rita I., additional, Kadoguchi, Naoto, additional, Kan, Lixin, additional, Kasahara, Jiro, additional, Kates, Stephen L., additional, Kemp, Matthew W., additional, Kessler, Barbara, additional, Khan, Saeed R., additional, Kinoshita, Denise, additional, Klymiuk, Nikolai, additional, Koyama, Ryuta, additional, Kretzschmar, Doris, additional, Kugler, Josephine, additional, Kuncova, Jitka, additional, Kuro, Maki, additional, Kurome, Mayuko, additional, Lardelli, Michael, additional, Lawson, Heather A., additional, Yu Lee, Edmund Chun, additional, Leloup, Corinne, additional, Lewejohann, Lars, additional, Liebsch, Manfred, additional, Lienard, Fabienne, additional, Lokensgard, James, additional, Luch, Andreas, additional, Macleod, Malcolm R., additional, McGee-Lawrence, Meghan E., additional, McGregor, Alistair, additional, Miller, Robert H., additional, Mizoguchi, Atsushi, additional, Mordan-McCombs, Sarah, additional, Musk, Gabrielle C., additional, Nalca, Aysegul, additional, Nomoto, Masahiro, additional, O’Collins, Victoria E., additional, Oelgeschläger, Michael, additional, Österreicher, Christoph H., additional, Penicaud, Luc, additional, Pollheimer, Marion J., additional, Renner, Simone, additional, Ruiz, Sara I., additional, Saito, Masatoshi, additional, Schachtele, Scott, additional, Schapiro, Steven J., additional, Schindler, Charles W., additional, Schwarz, Edward M., additional, Secreto, Frank J., additional, Seiler, Andrea, additional, Shamchuk, Angela L., additional, Shannon, Richard P., additional, Shen, You-Tang, additional, Shilling, Paul D., additional, Sittner, Dana, additional, Smith, Gideon P., additional, Stengl, Milan, additional, Stürzenbaum, Stephen R., additional, Sviglerova, Jitka, additional, Syed, Farhan A., additional, Tannenbaum, Jerrold, additional, Tenniswood, Martin, additional, Thibault, Louise, additional, Tierney, Keith B., additional, Trauner, Michael, additional, Tsubura, Airo, additional, Turner, Judith Axler, additional, Verdile, Giuseppe, additional, Vilahur, Gemma, additional, Wang, Wei-Lin Winnie, additional, Weed, James L., additional, Welsh, JoEllen, additional, Werler, Steffi, additional, Wistuba, Joachim, additional, Wolf, Eckhard, additional, Wünsch, Annegret, additional, Yamamoto, Toshiyuki, additional, Yokoyama, Hironori, additional, Yoshizawa, Katsuhiko, additional, Zaidan Dagli, Maria L., additional, Zeiss, Caroline J., additional, and Zumbrun, Elizabeth E., additional

Published
2013
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