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1. Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Author

Robert C. Green, Katrina A.B. Goddard, Gail P. Jarvik, Laura M. Amendola, Paul S. Appelbaum, Jonathan S. Berg, Barbara A. Bernhardt, Leslie G. Biesecker, Sawona Biswas, Carrie L. Blout, Kevin M. Bowling, Kyle B. Brothers, Wylie Burke, Charlisse F. Caga-anan, Arul M. Chinnaiyan, Wendy K. Chung, Ellen W. Clayton, Gregory M. Cooper, Kelly East, James P. Evans, Stephanie M. Fullerton, Levi A. Garraway, Jeremy R. Garrett, Stacy W. Gray, Gail E. Henderson, Lucia A. Hindorff, Ingrid A. Holm, Michelle Huckaby Lewis, Carolyn M. Hutter, Pasi A. Janne, Steven Joffe, David Kaufman, Bartha M. Knoppers, Barbara A. Koenig, Ian D. Krantz, Teri A. Manolio, Laurence McCullough, Jean McEwen, Amy McGuire, Donna Muzny, Richard M. Myers, Deborah A. Nickerson, Jeffrey Ou, Donald W. Parsons, Gloria M. Petersen, Sharon E. Plon, Heidi L. Rehm, J. Scott Roberts, Dan Robinson, Joseph S. Salama, Sarah Scollon, Richard R. Sharp, Brian Shirts, Nancy B. Spinner, Holly K. Tabor, Peter Tarczy-Hornoch, David L. Veenstra, Nikhil Wagle, Karen Weck, Benjamin S. Wilfond, Kirk Wilhelmsen, Susan M. Wolf, Julia Wynn, Joon-Ho Yu, Michelle Amaral, Laura Amendola, Samuel J. Aronson, Shubhangi Arora, Danielle R. Azzariti, Greg S. Barsh, E.M. Bebin, Barbara B. Biesecker, Brian L. Brown, Amber A. Burt, Peter H. Byers, Muge G. Calikoglu, Sara J. Carlson, Nizar Chahin, Kurt D. Christensen, Wendy Chung, Allison L. Cirino, Ellen Clayton, Laura K. Conlin, Greg M. Cooper, David R. Crosslin, James V. Davis, Kelly Davis, Matthew A. Deardorff, Batsal Devkota, Raymond De Vries, Pamela Diamond, Michael O. Dorschner, Noreen P. Dugan, Dmitry Dukhovny, Matthew C. Dulik, Kelly M. East, Edgar A. Rivera-Munoz, Barbara Evans, Jessica Everett, Nicole Exe, Zheng Fan, Lindsay Z. Feuerman, Kelly Filipski, Candice R. Finnila, Kristen Fishler, Bob Ghrundmeier, Karen Giles, Marian J. Gilmore, Zahra S. Girnary, Katrina Goddard, Steven Gonsalves, Adam S. Gordon, Michele C. Gornick, William M. Grady, David E. Gray, Robert Green, Robert S. Greenwood, Amanda M. Gutierrez, Paul Han, Ragan Hart, Patrick Heagerty, Naomi Hensman, Susan M. Hiatt, Patricia Himes, Fuki M. Hisama, Carolyn Y. Ho, Lily B. Hoffman-Andrews, Celine Hong, Martha J. Horike-Pyne, Sara Hull, Seema Jamal, Brian C. Jensen, Steve Joffe, Jennifer Johnston, Dean Karavite, Tia L. Kauffman, Dave Kaufman, Whitley Kelley, Jerry H. Kim, Christine Kirby, William Klein, Bartha Knoppers, Sek Won Kong, Ian Krantz, Joel B. Krier, Neil E. Lamb, Michele P. Lambert, Lan Q. Le, Matthew S. Lebo, Alexander Lee, Kaitlyn B. Lee, Niall Lennon, Michael C. Leo, Kathleen A. Leppig, Katie Lewis, Michelle Lewis, Neal I. Lindeman, Nicole Lockhart, Bob Lonigro, Edward J. Lose, Philip J. Lupo, Laura Lyman Rodriguez, Frances Lynch, Kalotina Machini, Calum MacRae, Daniel S. Marchuk, Josue N. Martinez, Aaron Masino, Heather M. McLaughlin, Carmit McMullen, Piotr A. Mieczkowski, Jeff Miller, Victoria A. Miller, Rajen Mody, Sean D. Mooney, Elizabeth G. Moore, Elissa Morris, Michael Murray, David Ng, Nelly M. Oliver, Will Parsons, Donald L. Patrick, Jeffrey Pennington, Denise L. Perry, Gloria Petersen, Sharon Plon, Katie Porter, Bradford C. Powell, Sumit Punj, Carmen Radecki Breitkopf, Robin A. Raesz-Martinez, Wendy H. Raskind, Dean A. Reigar, Jacob A. Reiss, Carla A. Rich, Carolyn Sue Richards, Christine Rini, Scott Roberts, Peggy D. Robertson, Jill O. Robinson, Marguerite E. Robinson, Myra I. Roche, Edward J. Romasko, Elisabeth A. Rosenthal, Joseph Salama, Maria I. Scarano, Jennifer Schneider, Christine E. Seidman, Bryce A. Seifert, Brian H. Shirts, Lynette M. Sholl, Javed Siddiqui, Elian Silverman, Shirley Simmons, Janae V. Simons, Debra Skinner, Elena Stoffel, Natasha T. Strande, Shamil Sunyaev, Virginia P. Sybert, Jennifer Taber, Deanne M. Taylor, Christian R. Tilley, Ashley Tomlinson, Susan Trinidad, Ellen Tsai, Peter Ubel, Eliezer M. Van Allen, Jason L. Vassy, Pankaj Vats, Victoria L. Vetter, Raymond D. Vries, Sarah A. Walser, Rebecca C. Walsh, Allison Werner-Lin, Jana Whittle, Ben Wilfond, Kirk C. Wilhelmsen, Yaping Yang, Carol Young, and Brian J. Zikmund-Fisher

Subjects
0301 basic medicine, Adult, Evidence-based practice, Biomedical Research, Best practice, Exploratory research, MEDLINE, Genomics, Computational biology, 030105 genetics & heredity, Bioinformatics, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Population Groups, Genetics, Medicine, Genomic medicine, Humans, Genetics(clinical), Exome, Child, Genetics (clinical), Exome sequencing, Medical education, Clinical Trials as Topic, business.industry, Genome, Human, Correction, High-Throughput Nucleotide Sequencing, Human genetics, United States, 3. Good health, National Human Genome Research Institute (U.S.), 030104 developmental biology, Cardiovascular Diseases, Evidence-Based Practice, Human genome, business, Psychology, Software
Abstract

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine.

Published
2016

2. Haplotype analysis of the internationally distributed BRCA1 c.3331_3334delCAAG founder mutation reveals a common ancestral origin in Iberia

Author

Anna Marie De Asis Tuazon, Paul Lott, Mabel Bohórquez, Jennyfer Benavides, Carolina Ramirez, Angel Criollo, Ana Estrada-Florez, Gilbert Mateus, Alejandro Velez, Jenny Carmona, Justo Olaya, Elisha Garcia, Guadalupe Polanco-Echeverry, Jacob Stultz, Carolina Alvarez, Teresa Tapia, Patricia Ashton-Prolla, Brazilian Familial Cancer Network, Ana Vega, Conxi Lazaro, Eva Tornero, Cristina Martinez-Bouzas, Mar Infante, Miguel De La Hoya, Orland Diez, Brian L. Browning, COLUMBUS Consortium, Bruce Rannala, Manuel R. Teixeira, Pilar Carvallo, Magdalena Echeverry, and Luis G. Carvajal-Carmona

Subjects
Breast cancer, Haplotype, BRCA1 c.3331_3334delCAAG, Founder mutation, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background The BRCA1 c.3331_3334delCAAG founder mutation has been reported in hereditary breast and ovarian cancer families from multiple Hispanic groups. We aimed to evaluate BRCA1 c.3331_3334delCAAG haplotype diversity in cases of European, African, and Latin American ancestry. Methods BC mutation carrier cases from Colombia (n = 32), Spain (n = 13), Portugal (n = 2), Chile (n = 10), Africa (n = 1), and Brazil (n = 2) were genotyped with the genome-wide single nucleotide polymorphism (SNP) arrays to evaluate haplotype diversity around BRCA1 c.3331_3334delCAAG. Additional Portuguese (n = 13) and Brazilian (n = 18) BC mutation carriers were genotyped for 15 informative SNPs surrounding BRCA1. Data were phased using SHAPEIT2, and identical by descent regions were determined using BEAGLE and GERMLINE. DMLE+ was used to date the mutation in Colombia and Iberia. Results The haplotype reconstruction revealed a shared 264.4-kb region among carriers from all six countries. The estimated mutation age was ~ 100 generations in Iberia and that it was introduced to South America early during the European colonization period. Conclusions Our results suggest that this mutation originated in Iberia and later introduced to Colombia and South America at the time of Spanish colonization during the early 1500s. We also found that the Colombian mutation carriers had higher European ancestry, at the BRCA1 gene harboring chromosome 17, than controls, which further supported the European origin of the mutation. Understanding founder mutations in diverse populations has implications in implementing cost-effective, ancestry-informed screening.

Published
2020
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3. Local Ancestry Inference in a Large US-Based Hispanic/Latino Study: Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

Author

Sharon R. Browning, Kelsey Grinde, Anna Plantinga, Stephanie M. Gogarten, Adrienne M. Stilp, Robert C. Kaplan, M. Larissa Avilés-Santa, Brian L. Browning, and Cathy C. Laurie

Subjects
Hispanic/Latino, local ancestry, principal components analysis, Genetics, QH426-470
Abstract

We estimated local ancestry on the autosomes and X chromosome in a large US-based study of 12,793 Hispanic/Latino individuals using the RFMix method, and we compared different reference panels and approaches to local ancestry estimation on the X chromosome by means of Mendelian inconsistency rates as a proxy for accuracy. We developed a novel and straightforward approach to performing ancestry-specific PCA after finding artifactual behavior in the results from an existing approach. Using the ancestry-specific PCA, we found significant population structure within African, European, and Amerindian ancestries in the Hispanic/Latino individuals in our study. In the African ancestral component of the admixed individuals, individuals whose grandparents were from Central America clustered separately from individuals whose grandparents were from the Caribbean, and also from reference Yoruba and Mandenka West African individuals. In the European component, individuals whose grandparents were from Puerto Rico diverged partially from other background groups. In the Amerindian ancestral component, individuals clustered into multiple different groups depending on the grandparental country of origin. Therefore, local ancestry estimation provides further insight into the complex genetic structure of US Hispanic/Latino populations, which must be properly accounted for in genotype-phenotype association studies. It also provides a basis for admixture mapping and ancestry-specific allele frequency estimation, which are useful in the identification of risk factors for disease.

Published
2016
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