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1. Demonstrating paths for unlocking the value of cloud genomics through cross cohort analysis

Author

Nicole Deflaux, Margaret Sunitha Selvaraj, Henry Robert Condon, Kelsey Mayo, Sara Haidermota, Melissa A. Basford, Chris Lunt, Anthony A. Philippakis, Dan M. Roden, Joshua C. Denny, Anjene Musick, Rory Collins, Naomi Allen, Mark Effingham, David Glazer, Pradeep Natarajan, and Alexander G. Bick

Subjects
Science
Abstract

Abstract Recently, large scale genomic projects such as All of Us and the UK Biobank have introduced a new research paradigm where data are stored centrally in cloud-based Trusted Research Environments (TREs). To characterize the advantages and drawbacks of different TRE attributes in facilitating cross-cohort analysis, we conduct a Genome-Wide Association Study of standard lipid measures using two approaches: meta-analysis and pooled analysis. Comparison of full summary data from both approaches with an external study shows strong correlation of known loci with lipid levels (R2 ~ 83–97%). Importantly, 90 variants meet the significance threshold only in the meta-analysis and 64 variants are significant only in pooled analysis, with approximately 20% of variants in each of those groups being most prevalent in non-European, non-Asian ancestry individuals. These findings have important implications, as technical and policy choices lead to cross-cohort analyses generating similar, but not identical results, particularly for non-European ancestral populations.

Published
2023
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2. The

Author

Andrea H, Ramirez, Lina, Sulieman, David J, Schlueter, Alese, Halvorson, Jun, Qian, Francis, Ratsimbazafy, Roxana, Loperena, Kelsey, Mayo, Melissa, Basford, Nicole, Deflaux, Karthik N, Muthuraman, Karthik, Natarajan, Abel, Kho, Hua, Xu, Consuelo, Wilkins, Hoda, Anton-Culver, Eric, Boerwinkle, Mine, Cicek, Cheryl R, Clark, Elizabeth, Cohn, Lucila, Ohno-Machado, Sheri D, Schully, Brian K, Ahmedani, Maria, Argos, Robert M, Cronin, Christopher, O'Donnell, Mona, Fouad, David B, Goldstein, Philip, Greenland, Scott J, Hebbring, Elizabeth W, Karlson, Parinda, Khatri, Bruce, Korf, Jordan W, Smoller, Stephen, Sodeke, John, Wilbanks, Justin, Hentges, Stephen, Mockrin, Christopher, Lunt, Stephanie A, Devaney, Kelly, Gebo, Joshua C, Denny, Robert J, Carroll, David, Glazer, Paul A, Harris, George, Hripcsak, Anthony, Philippakis, Dan M, Roden, and Michael E, Zwick

Abstract

The

Published
2022

3. Genomic architecture of autism from comprehensive whole-genome sequence annotation

Author

Brett Trost, Bhooma Thiruvahindrapuram, Ada J.S. Chan, Worrawat Engchuan, Edward J. Higginbotham, Jennifer L. Howe, Livia O. Loureiro, Miriam S. Reuter, Delnaz Roshandel, Joe Whitney, Mehdi Zarrei, Matthew Bookman, Cherith Somerville, Rulan Shaath, Mona Abdi, Elbay Aliyev, Rohan V. Patel, Thomas Nalpathamkalam, Giovanna Pellecchia, Omar Hamdan, Gaganjot Kaur, Zhuozhi Wang, Jeffrey R. MacDonald, John Wei, Wilson W.L. Sung, Sylvia Lamoureux, Ny Hoang, Thanuja Selvanayagam, Nicole Deflaux, Melissa Geng, Siavash Ghaffari, John Bates, Edwin J. Young, Qiliang Ding, Carole Shum, Lia D'Abate, Clarrisa A. Bradley, Annabel Rutherford, Vernie Aguda, Beverly Apresto, Nan Chen, Sachin Desai, Xiaoyan Du, Matthew L.Y. Fong, Sanjeev Pullenayegum, Kozue Samler, Ting Wang, Karen Ho, Tara Paton, Sergio L. Pereira, Jo-Anne Herbrick, Richard F. Wintle, Jonathan Fuerth, Juti Noppornpitak, Heather Ward, Patrick Magee, Ayman Al Baz, Usanthan Kajendirarajah, Sharvari Kapadia, Jim Vlasblom, Monica Valluri, Joseph Green, Vicki Seifer, Morgan Quirbach, Olivia Rennie, Elizabeth Kelley, Nina Masjedi, Catherine Lord, Michael J. Szego, Ma'n H. Zawati, Michael Lang, Lisa J. Strug, Christian R. Marshall, Gregory Costain, Kristina Calli, Alana Iaboni, Afiqah Yusuf, Patricia Ambrozewicz, Louise Gallagher, David G. Amaral, Jessica Brian, Mayada Elsabbagh, Stelios Georgiades, Daniel S. Messinger, Sally Ozonoff, Jonathan Sebat, Calvin Sjaarda, Isabel M. Smith, Peter Szatmari, Lonnie Zwaigenbaum, Azadeh Kushki, Thomas W. Frazier, Jacob A.S. Vorstman, Khalid A. Fakhro, Bridget A. Fernandez, M.E. Suzanne Lewis, Rosanna Weksberg, Marc Fiume, Ryan K.C. Yuen, Evdokia Anagnostou, Neal Sondheimer, David Glazer, Dean M. Hartley, and Stephen W. Scherer

Subjects
DNA Copy Number Variations, Autism Spectrum Disorder, Humans, Genetic Predisposition to Disease, Genomics, Autistic Disorder, General Biochemistry, Genetics and Molecular Biology
Abstract

Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG resource, which includes WGS data from 5,100 individuals with ASD and 6,212 non-ASD parents and siblings (total n = 11,312). Examining a wide variety of genetic variants in MSSNG and the Simons Simplex Collection (SSC; n = 9,205), we identified ASD-associated rare variants in 718/5,100 individuals with ASD from MSSNG (14.1%) and 350/2,419 from SSC (14.5%). Considering genomic architecture, 52% were nuclear sequence-level variants, 46% were nuclear structural variants (including copy-number variants, inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants. Our study provides a guidebook for exploring genotype-phenotype correlations in families who carry ASD-associated rare variants and serves as an entry point to the expanded studies required to dissect the etiology in the ∼85% of the ASD population that remain idiopathic.

Published
2022
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4. The All of Us Research Program: Data quality, utility, and diversity

Author

Andrea H. Ramirez, Lina Sulieman, David J. Schlueter, Alese Halvorson, Jun Qian, Francis Ratsimbazafy, Roxana Loperena, Kelsey Mayo, Melissa Basford, Nicole Deflaux, Karthik N. Muthuraman, Karthik Natarajan, Abel Kho, Hua Xu, Consuelo Wilkins, Hoda Anton-Culver, Eric Boerwinkle, Mine Cicek, Cheryl R. Clark, Elizabeth Cohn, Lucila Ohno-Machado, Sheri D. Schully, Brian K. Ahmedani, Maria Argos, Robert M. Cronin, Christopher O’Donnell, Mona Fouad, David B. Goldstein, Philip Greenland, Scott J. Hebbring, Elizabeth W. Karlson, Parinda Khatri, Bruce Korf, Jordan W. Smoller, Stephen Sodeke, John Wilbanks, Justin Hentges, Stephen Mockrin, Christopher Lunt, Stephanie A. Devaney, Kelly Gebo, Joshua C. Denny, Robert J. Carroll, David Glazer, Paul A. Harris, George Hripcsak, Anthony Philippakis, Dan M. Roden, Brian Ahmedani, Christine D. Cole Johnson, Habib Ahsan, Donna Antoine-LaVigne, Glendora Singleton, Eric Topol, Katie Baca-Motes, Steven Steinhubl, James Wade, Mark Begale, Praduman Jain, Scott Sutherland, Beth Lewis, Melissa Behringer, Ali G. Gharavi, Louise Bier, Murray H. Brilliant, Narayana Murali, Scott Joseph Hebbring, Dorothy Farrar-Edwards, Elizabeth Burnside, Marc K. Drezner, Amy Taylor, Veena Channamsetty, Wanda Montalvo, Yashoda Sharma, Carmen Chinea, Nancy Jenks, Steve Thibodeau, Beverly Wilson Holmes, Eric Schlueter, Ever Collier, Joyce Winkler, John Corcoran, Nick D’Addezio, Martha Daviglus, Robert Winn, Dan Roden, Joshua Denny, Kim Doheny, Debbie Nickerson, Evan Eichler, Gail Jarvik, Gretchen Funk, Heidi Rehm, Niall Lennon, Sekar Kathiresan, Stacey Gabriel, Richard Gibbs, Edgar M. Gil Rico, Joannie Grand, Paul Harris, Elizabeth Shenkman, William R. Hogan, Priscilla Igho-Pemu, Cliff Pollan, Milena Jorge, Sally Okun, Jordan Smoller, Shawn N. Murphy, Margaret Elizabeth Ross, Rainu Kaushal, Eboni Winford, Febe Wallace, Vik Kheterpal, Akinlolu Ojo, Francisco A. Moreno, Irving Kron, Rachele Peterson, Usha Menon, Patricia Watkins Lattimore, Noga Leviner, Juno Obedin-Maliver, Mitchell Lunn, Lynda Malik-Gagnon, Lara Mangravite, Adria Marallo, Oscar Marroquin, Shyam Visweswaran, Steven Reis, Gailen Marshall, Patrick McGovern, Deb Mignucci, John Moore, Fatima Munoz, Gregory Talavera, George T. O'Connor, Christopher O'Donnell, Greg Orr, Fornessa Randal, Andreas A. Theodorou, Eric Reiman, Mercedita Roxas-Murray, Louisa Stark, Ronnie Tepp, Alicia Zhou, Scott Topper, Rhonda Trousdale, Phil Tsao, Lisa Weidman, Scott T. Weiss, David Wellis, Jeffrey Whittle, Amanda Wilson, Stephan Zuchner, and Michael E. Zwick

Subjects
General Decision Sciences
Published
2022
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