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1. A draft human pangenome reference

Author

Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K, Monlong, Jean, Abel, Haley J, Buonaiuto, Silvia, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M, Feng, Xiaowen, Fischer, Christian, Fulton, Robert S, Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T, Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J, Mitchell, Matthew W, Munson, Katherine M, Mwaniki, Moses Njagi, Novak, Adam M, Olsen, Hugh E, Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A, Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R, Antonacci-Fulton, Lucinda L, Baid, Gunjan, Baker, Carl A, Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E, Cook-Deegan, Robert M, Cornejo, Omar E, Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L, Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A, Giron, Carlos Garcia, Green, Richard E, Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Korbel, Jan O, Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D, Popejoy, Alice B, Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A, Rhie, Arang, Sacco, Samuel, Sanders, Ashley D, Schneider, Valerie A, Schultz, Baergen I, Shafin, Kishwar, Smith, Michael W, Sofia, Heidi J, Abou Tayoun, Ahmad N, Thibaud-Nissen, Françoise, and Tricomi, Francesca Floriana

Subjects
Biological Sciences, Genetics, 2.1 Biological and endogenous factors, 1.5 Resources and infrastructure (underpinning), Generic health relevance, Humans, Diploidy, Genome, Human, Haplotypes, Sequence Analysis, DNA, Genomics, Reference Standards, Cohort Studies, Alleles, Genetic Variation, General Science & Technology
Abstract

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Published
2023

2. Gaps and complex structurally variant loci in phased genome assemblies

Author

Porubsky, David, Vollger, Mitchell R, Harvey, William T, Rozanski, Allison N, Ebert, Peter, Hickey, Glenn, Hasenfeld, Patrick, Sanders, Ashley D, Stober, Catherine, Consortium, Human Pangenome Reference, Korbel, Jan O, Paten, Benedict, Marschall, Tobias, Eichler, Evan E, Abel, Haley J, Antonacci-Fulton, Lucinda L, Asri, Mobin, Baid, Gunjan, Baker, Carl A, Belyaeva, Anastasiya, Billis, Konstantinos, Bourque, Guillaume, Buonaiuto, Silvia, Carroll, Andrew, Chaisson, Mark JP, Chang, Pi-Chuan, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Cody, Sarah, Colonna, Vincenza, Cook, Daniel E, Cook-Deegan, Robert M, Cornejo, Omar E, Diekhans, Mark, Doerr, Daniel, Ebler, Jana, Eizenga, Jordan M, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L, Feng, Xiaowen, Fischer, Christian, Flicek, Paul, Formenti, Giulio, Frankish, Adam, Fulton, Robert S, Gao, Yan, Garg, Shilpa, Garrison, Erik, Garrison, Nanibaa’ A, Giron, Carlos Garcia, Green, Richard E, Groza, Cristian, Guarracino, Andrea, Haggerty, Leanne, Hall, Ira M, Haukness, Marina, Haussler, David, Heumos, Simon, Hoekzema, Kendra, Hourlier, Thibaut, Howe, Kerstin, Jain, Miten, Jarvis, Erich D, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P, Li, Heng, Liao, Wen-Wei, Lu, Shuangjia, Lu, Tsung-Yu, Lucas, Julian K, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, Markello, Charles, Martin, Fergal J, McCartney, Ann, McDaniel, Jennifer, Miga, Karen H, Mitchell, Matthew W, Monlong, Jean, Mountcastle, Jacquelyn, Munson, Katherine M, Mwaniki, Moses Njagi, Nattestad, Maria, Novak, Adam M, and Nurk, Sergey

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Humans, DNA, Satellite, Polymorphism, Genetic, Haplotypes, Segmental Duplications, Genomic, Sequence Analysis, DNA, Human Pangenome Reference Consortium, Medical and Health Sciences, Bioinformatics
Abstract

There has been tremendous progress in phased genome assembly production by combining long-read data with parental information or linked-read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates more than 140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 182 haploid assemblies obtained from a diversity panel of 77 unique human samples. Although trio-based approaches using HiFi are the current gold standard, chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. Importantly, the majority of assembly gaps cluster near the largest and most identical repeats (including segmental duplications [35.4%], satellite DNA [22.3%], or regions enriched in GA/AT-rich DNA [27.4%]). Consequently, 1513 protein-coding genes overlap assembly gaps in at least one haplotype, and 231 are recurrently disrupted or missing from five or more haplotypes. Furthermore, we estimate that 6-7 Mbp of DNA are misorientated per haplotype irrespective of whether trio-free or trio-based approaches are used. Of these misorientations, 81% correspond to bona fide large inversion polymorphisms in the human species, most of which are flanked by large segmental duplications. We also identify large-scale alignment discontinuities consistent with 11.9 Mbp of deletions and 161.4 Mbp of insertions per haploid genome. Although 99% of this variation corresponds to satellite DNA, we identify 230 regions of euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Such variable and incompletely assembled regions are important targets for future algorithmic development and pangenome representation.

Published
2023

3. GA4GH: International policies and standards for data sharing across genomic research and healthcare

Author

Rehm, Heidi L, Page, Angela JH, Smith, Lindsay, Adams, Jeremy B, Alterovitz, Gil, Babb, Lawrence J, Barkley, Maxmillian P, Baudis, Michael, Beauvais, Michael JS, Beck, Tim, Beckmann, Jacques S, Beltran, Sergi, Bernick, David, Bernier, Alexander, Bonfield, James K, Boughtwood, Tiffany F, Bourque, Guillaume, Bowers, Sarion R, Brookes, Anthony J, Brudno, Michael, Brush, Matthew H, Bujold, David, Burdett, Tony, Buske, Orion J, Cabili, Moran N, Cameron, Daniel L, Carroll, Robert J, Casas-Silva, Esmeralda, Chakravarty, Debyani, Chaudhari, Bimal P, Chen, Shu Hui, Cherry, J Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L, Cook-Deegan, Robert M, Courtot, Mélanie, Cunningham, Fiona, Cupak, Miro, Davies, Robert M, Denisko, Danielle, Doerr, Megan J, Dolman, Lena I, Dove, Edward S, Dursi, L Jonathan, Dyke, Stephanie OM, Eddy, James A, Eilbeck, Karen, Ellrott, Kyle P, Fairley, Susan, Fakhro, Khalid A, Firth, Helen V, Fitzsimons, Michael S, Fiume, Marc, Flicek, Paul, Fore, Ian M, Freeberg, Mallory A, Freimuth, Robert R, Fromont, Lauren A, Fuerth, Jonathan, Gaff, Clara L, Gan, Weiniu, Ghanaim, Elena M, Glazer, David, Green, Robert C, Griffith, Malachi, Griffith, Obi L, Grossman, Robert L, Groza, Tudor, Auvil, Jaime M Guidry, Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A, Hamosh, Ada, Hansen, David P, Hart, Reece K, Hartley, Dean Mitchell, Haussler, David, Hendricks-Sturrup, Rachele M, Ho, Calvin WL, Hobb, Ashley E, Hoffman, Michael M, Hofmann, Oliver M, Holub, Petr, Hsu, Jacob Shujui, Hubaux, Jean-Pierre, Hunt, Sarah E, Husami, Ammar, Jacobsen, Julius O, Jamuar, Saumya S, Janes, Elizabeth L, Jeanson, Francis, Jené, Aina, Johns, Amber L, Joly, Yann, Jones, Steven JM, Kanitz, Alexander, Kato, Kazuto, Keane, Thomas M, and Kekesi-Lafrance, Kristina

Subjects
Biological Sciences, Genetics, Human Genome, Clinical Research, Health Services, Generic health relevance, Good Health and Well Being
Abstract

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

Published
2021

4. A draft human pangenome reference

Author

Liao, Wen Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi Chuan, Cody, Sarah, Cook, Daniel E., Cook-Deegan, Robert M., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A., Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kenny, Eimear E., Koenig, Barbara A., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Koren, Sergey, Lee, Ho Joon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D., Popejoy, Alice B., Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Walenz, Brian, Wood, Jonathan M.D., Zimin, Aleksey V., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Wang, Ting, Jarvis, Erich D., Miga, Karen H., Garrison, Erik, Marschall, Tobias, Hall, Ira M., Li, Heng, Paten, Benedict, Liao, Wen Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi Chuan, Cody, Sarah, Cook, Daniel E., Cook-Deegan, Robert M., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A., Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kenny, Eimear E., Koenig, Barbara A., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Koren, Sergey, Lee, Ho Joon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D., Popejoy, Alice B., Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Walenz, Brian, Wood, Jonathan M.D., Zimin, Aleksey V., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Wang, Ting, Jarvis, Erich D., Miga, Karen H., Garrison, Erik, Marschall, Tobias, Hall, Ira M., Li, Heng, and Paten, Benedict

Abstract

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals 1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Published
2023

8. GA4GH: International policies and standards for data sharing across genomic research and healthcare

Author

Abigail Wexner Research Institute, Academy of Finland, Medical Research Future Fund, BioBank Japan, Canada Foundation for Innovation, Canadian Institutes of Health Research, European Commission, German Research Foundation, Genome Canada, Google, Howard Hughes Medical Institute, Instituto de Salud Carlos III, Japan Agency for Medical Research and Development, Mayo Clinic, Fundación la Caixa, Ministère de l'Économie et de l'Innovation (Québec), Monarch Initiative, National Human Genome Research Institute (US), National University of Singapore, Agency for Science, Technology and Research A*STAR (Singapore), National Health and Medical Research Council (Australia), National Institutes of Health (US), National Institute of General Medical Sciences (US), Swiss Institute of Bioinformatics, State Secretariat for Education, Research and Innovation (Switzerland), Terry Fox Research Institute, Canada Research Chairs, European Molecular Biology Laboratory, Ministry of Research, Innovation and Science (Ontario), Ontario Genomics Institute, Natural Sciences and Engineering Research Council of Canada, Wellcome Trust, National Taiwan University, Rehm, Heidi L., Page, Angela, Smith, Lindsay, Adams, Jeremy B., Alterovitz, Gil, Babb, Lawrence J., Barkley, Maxmillian P., Baudis, Michael, Beauvais, Michael J. S., Beck, Tim, Beckmann, Jacques S., Varma, Susheel, Vears, Danya F., Viner, Coby, Voisin, Craig, Wagner, Alex H., Wallace, Susan E., Walsh, Brian P., Williams, Marc S., Winkler, Eva C., Brudno, Michael, Kelleher, Jerome, Wold, Barbara J., Wood, Grant M., Woolley, J. Patrick, Yamasaki, Chisato, Yates, Andrew D., Yung, Christina K., Zass, Lyndon J., Zaytseva, Ksenia, Zhang, Junjun, Goodhand, Peter, Kerry, Giselle, Brush,Matthew H., North, Kathryn, Birney, Ewan, Bujold, David, Burdett, Tony, Buske, Orion J., Cabili, Moran N., Cameron, Daniel L., Carroll, Robert J., Casas-Silva, Esmeralda, Khor, Seik-Soon, Chakravarty, Debyani, Chaudhari, Bimal P., Chen, Shu Hui, Cherry, J. Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L., Cook-Deegan, Robert M., Courtot, Melanie, Cunningham, Fiona, Knoppers, Bartha M., Cupak, Miro, Davies, Robert M., Denisko, Danielle, Doerr, Megan J., Dolman, Lena I., Dove, Edward S., Dursi, Lewis Jonathan, Dyke, Stephanie O. M., Eddy, James A., Eilbeck, Karen, Konopko, Melissa A., Ellrott, Kyle P., Fairley, Susan, Fakhro, Khalid A., Firth, Helen V., Fitzsimons, Michael S., Fiume, Marc, Flicek, Paul, Fore, Ian M., Freeberg, Mallory A., Freimuth, Robert R., Kosaki, Kenjiro, Fromont, Lauren A., Fuerth, Jonathan, Gaff, Clara L., Gan, Weiniu, Ghanaim, Elena M., Glazer, David, Green, Robert C., Griffith, Malachi, Griffith, Obi L., Grossman, Robert L., Kuba, Martin, Groza, Tudor, Guidry Auvil, Jaime M., Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A., Hamosh, Ada, Hansen, David P., Hart, Reece K., Hartley, Dean Mitchell, Haussler, David, Lawson, Jonathan, Hendricks-Sturrup, Rachele M., Ho, Calvin W. L., Hobb, Ashley E., Hoffman, Michael M., Hofmann, Oliver M., Holub, Petr, Shujui Hsu, Jacob, Hubaux, Jean-Pierre, Hunt, Sarah E., Husami, Ammar, Leinonen, Rasko, Jacobsen, Julius O., Jamuar, Saumya S., Janes, Elizabeth L., Jeanson, Francis, Jene, Aina, Johns, Amber L., Joly, Yann, Jones, Steven J. M., Kanitz, Alexander, Kato, Kazuto, Li, Stephanie, Keane, Thomas M., Kekesi-Lafrance, Kristina, Beltran, Sergi, Lin, Michael F., Linden, Mikael, Liu, Xianglin, Udara Liyanage, Isuru, López, Javier, Lucassen, Anneke M., Lukowski, Michael, Mann, Alice L., Marshall, John, Mattioni, Michele, Bernick, David, Metke-Jiménez, Alejandro, Middleton, Anna, Milne, Richard J., Molnár-Gábor, Fruzsina, Mulder, Nicola, Muñoz-Torres, Mónica C., Nag, Rishi, Nakagawa, Hidewaki, Nasir, Jamal, Navarro, Arcadi, Bernier, Alexander, Nelson, Tristan H., Niewielska, Ania, Nisselle, Amy, Niu, Jeffrey, Nyrönen, Tommi H., O’Connor, Brian D., Oesterle, Sabine, Ogishima, Soichi, Wang, Vivian Ota, Paglione, Laura A. D., Bonfield, James K., Palumbo, Emilio, Parkinson, Helen E., Philippakis, Anthony A., Pizarro, Angel D., Prlic, Andreas, Rambla, Jordi, Rendon, Augusto, Rider, Renee A., Robinson, Peter N., Rodarmer, Kurt W., Boughtwood, Tiffany F., Lyman Rodríguez, Laura, Rubin, Alan F., Rueda, Manuel, Rushton, Gregory A., Ryan, Rosalyn S., Saunders, Gary I., Schuilenburg, Helen, Schwede, Torsten, Scollen, Serena, Senf, Alexander, Bourque, Guillaume, Sheffield, Nathan C., Skantharajah, Neerjah, Smith, Albert V., Sofia, Heidi J., Spalding, Dylan, Spurdle, Amanda B., Stark, Zornitza, Stein, Lincoln D., Suematsu, Makoto, Tan, Patrick, Bowers, Sarion R., Tedds, Jonathan A., Thomson, Alastair A., Thorogood, Adrian, Tickle, Timothy L., Tokunaga, Katsushi, Törnroos,Juha, Torrents, David, Upchurch, Sean, Valencia, Alfonso, Valls Guimera, Roman, Brookes, Anthony J., Vamathevan, Jessica, Abigail Wexner Research Institute, Academy of Finland, Medical Research Future Fund, BioBank Japan, Canada Foundation for Innovation, Canadian Institutes of Health Research, European Commission, German Research Foundation, Genome Canada, Google, Howard Hughes Medical Institute, Instituto de Salud Carlos III, Japan Agency for Medical Research and Development, Mayo Clinic, Fundación la Caixa, Ministère de l'Économie et de l'Innovation (Québec), Monarch Initiative, National Human Genome Research Institute (US), National University of Singapore, Agency for Science, Technology and Research A*STAR (Singapore), National Health and Medical Research Council (Australia), National Institutes of Health (US), National Institute of General Medical Sciences (US), Swiss Institute of Bioinformatics, State Secretariat for Education, Research and Innovation (Switzerland), Terry Fox Research Institute, Canada Research Chairs, European Molecular Biology Laboratory, Ministry of Research, Innovation and Science (Ontario), Ontario Genomics Institute, Natural Sciences and Engineering Research Council of Canada, Wellcome Trust, National Taiwan University, Rehm, Heidi L., Page, Angela, Smith, Lindsay, Adams, Jeremy B., Alterovitz, Gil, Babb, Lawrence J., Barkley, Maxmillian P., Baudis, Michael, Beauvais, Michael J. S., Beck, Tim, Beckmann, Jacques S., Varma, Susheel, Vears, Danya F., Viner, Coby, Voisin, Craig, Wagner, Alex H., Wallace, Susan E., Walsh, Brian P., Williams, Marc S., Winkler, Eva C., Brudno, Michael, Kelleher, Jerome, Wold, Barbara J., Wood, Grant M., Woolley, J. Patrick, Yamasaki, Chisato, Yates, Andrew D., Yung, Christina K., Zass, Lyndon J., Zaytseva, Ksenia, Zhang, Junjun, Goodhand, Peter, Kerry, Giselle, Brush,Matthew H., North, Kathryn, Birney, Ewan, Bujold, David, Burdett, Tony, Buske, Orion J., Cabili, Moran N., Cameron, Daniel L., Carroll, Robert J., Casas-Silva, Esmeralda, Khor, Seik-Soon, Chakravarty, Debyani, Chaudhari, Bimal P., Chen, Shu Hui, Cherry, J. Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L., Cook-Deegan, Robert M., Courtot, Melanie, Cunningham, Fiona, Knoppers, Bartha M., Cupak, Miro, Davies, Robert M., Denisko, Danielle, Doerr, Megan J., Dolman, Lena I., Dove, Edward S., Dursi, Lewis Jonathan, Dyke, Stephanie O. M., Eddy, James A., Eilbeck, Karen, Konopko, Melissa A., Ellrott, Kyle P., Fairley, Susan, Fakhro, Khalid A., Firth, Helen V., Fitzsimons, Michael S., Fiume, Marc, Flicek, Paul, Fore, Ian M., Freeberg, Mallory A., Freimuth, Robert R., Kosaki, Kenjiro, Fromont, Lauren A., Fuerth, Jonathan, Gaff, Clara L., Gan, Weiniu, Ghanaim, Elena M., Glazer, David, Green, Robert C., Griffith, Malachi, Griffith, Obi L., Grossman, Robert L., Kuba, Martin, Groza, Tudor, Guidry Auvil, Jaime M., Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A., Hamosh, Ada, Hansen, David P., Hart, Reece K., Hartley, Dean Mitchell, Haussler, David, Lawson, Jonathan, Hendricks-Sturrup, Rachele M., Ho, Calvin W. L., Hobb, Ashley E., Hoffman, Michael M., Hofmann, Oliver M., Holub, Petr, Shujui Hsu, Jacob, Hubaux, Jean-Pierre, Hunt, Sarah E., Husami, Ammar, Leinonen, Rasko, Jacobsen, Julius O., Jamuar, Saumya S., Janes, Elizabeth L., Jeanson, Francis, Jene, Aina, Johns, Amber L., Joly, Yann, Jones, Steven J. M., Kanitz, Alexander, Kato, Kazuto, Li, Stephanie, Keane, Thomas M., Kekesi-Lafrance, Kristina, Beltran, Sergi, Lin, Michael F., Linden, Mikael, Liu, Xianglin, Udara Liyanage, Isuru, López, Javier, Lucassen, Anneke M., Lukowski, Michael, Mann, Alice L., Marshall, John, Mattioni, Michele, Bernick, David, Metke-Jiménez, Alejandro, Middleton, Anna, Milne, Richard J., Molnár-Gábor, Fruzsina, Mulder, Nicola, Muñoz-Torres, Mónica C., Nag, Rishi, Nakagawa, Hidewaki, Nasir, Jamal, Navarro, Arcadi, Bernier, Alexander, Nelson, Tristan H., Niewielska, Ania, Nisselle, Amy, Niu, Jeffrey, Nyrönen, Tommi H., O’Connor, Brian D., Oesterle, Sabine, Ogishima, Soichi, Wang, Vivian Ota, Paglione, Laura A. D., Bonfield, James K., Palumbo, Emilio, Parkinson, Helen E., Philippakis, Anthony A., Pizarro, Angel D., Prlic, Andreas, Rambla, Jordi, Rendon, Augusto, Rider, Renee A., Robinson, Peter N., Rodarmer, Kurt W., Boughtwood, Tiffany F., Lyman Rodríguez, Laura, Rubin, Alan F., Rueda, Manuel, Rushton, Gregory A., Ryan, Rosalyn S., Saunders, Gary I., Schuilenburg, Helen, Schwede, Torsten, Scollen, Serena, Senf, Alexander, Bourque, Guillaume, Sheffield, Nathan C., Skantharajah, Neerjah, Smith, Albert V., Sofia, Heidi J., Spalding, Dylan, Spurdle, Amanda B., Stark, Zornitza, Stein, Lincoln D., Suematsu, Makoto, Tan, Patrick, Bowers, Sarion R., Tedds, Jonathan A., Thomson, Alastair A., Thorogood, Adrian, Tickle, Timothy L., Tokunaga, Katsushi, Törnroos,Juha, Torrents, David, Upchurch, Sean, Valencia, Alfonso, Valls Guimera, Roman, Brookes, Anthony J., and Vamathevan, Jessica

Abstract

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

Published
2021

11. Issues in Biosecurity and Biosafety

Author

Cook-Deegan, Robert M., Berkelman, Ruth, Davidson, E. Megan, Finder, Stuart, Heitman, Elizabeth, Kelley, Maureen C., Moseley, Ray, Thomas, James C., Tilden, Samuel J., and Vangsnes, Nikki M.

Published
2005

12. Genomics Research: World Survey of Public Funding

Author

Cook-Deegan Robert M and Pohlhaus Jennifer

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Over the past two decades, genomics has evolved as a scientific research discipline. Genomics research was fueled initially by government and nonprofit funding sources, later augmented by private research and development (R&D) funding. Citizens and taxpayers of many countries have funded much of the research, and have expectations about access to the resulting information and knowledge. While access to knowledge gained from all publicly funded research is desired, access is especially important for fields that have broad social impact and stimulate public dialogue. Genomics is one such field, where public concerns are raised for reasons such as health care and insurance implications, as well as personal and ancestral identification. Thus, genomics has grown rapidly as a field, and attracts considerable interest. Results One way to study the growth of a field of research is to examine its funding. This study focuses on public funding of genomics research, identifying and collecting data from major government and nonprofit organizations around the world, and updating previous estimates of world genomics research funding, including information about geographical origins. We initially identified 89 publicly funded organizations; we requested information about each organization's funding of genomics research. Of these organizations, 48 responded and 34 reported genomics research expenditures (of those that responded but did not supply information, some did not fund such research, others could not quantify it). The figures reported here include all the largest funders and we estimate that we have accounted for most of the genomics research funding from government and nonprofit sources. Conclusion Aggregate spending on genomics research from 34 funding sources averaged around $2.9 billion in 2003 – 2006. The United States spent more than any other country on genomics research, corresponding to 35% of the overall worldwide public funding (compared to 49% US share of public health research funding for all purposes). When adjusted to genomics funding intensity, however, the United States dropped below Ireland, the United Kingdom, and Canada, as measured both by genomics research expenditure per capita and per Gross Domestic Product.

Published
2008
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