Article
Genetics & Heredity
Seyoon Ko, Benjamin B. Chu, Daniel Peterson, Chidera Okenwa, Jeanette C. Papp, David H. Alexander, Eric M. Sobel, Hua Zhou, Kenneth L. Lange
Summary: This paper introduces an unsupervised and scalable method for selecting ancestry-informative SNP markers and estimating admixture proportions. The method, implemented in the open-source software OpenADMIXTURE, shows scalability to modern biobank datasets in simulated and real data examples.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Multidisciplinary Sciences
Nicholas W. Bateman, Christopher M. Tarney, Tamara S. Abulez, Brian L. Hood, Kelly A. Conrads, Ming Zhou, Anthony R. Soltis, Pang-Ning Teng, Amanda Jackson, Chunqiao Tian, Clifton L. Dalgard, Matthew D. Wilkerson, Michael D. Kessler, Zachary Goecker, Jeremy Loffredo, Craig D. Shriver, Hai Hu, Michele Cote, Glendon J. Parker, James Segars, Ayman Al-Hendy, John Risinger, Neil T. Phippen, Yovanni Casablanca, Kathleen M. Darcy, G. Larry Maxwell, Thomas P. Conrads, Timothy D. O'Connor
Summary: Characterization of ancestry-linked peptide variants in disease-relevant patient tissues is important for understanding the relationship between patient ancestry and disease pathogenesis. The study identifies peptide ancestry informative markers (pAIMs) to determine ancestry proportions and their correlation with patient race and genotype. The findings contribute to the understanding of the impact of ancestry on the human proteome and its relevance to uterine neoplasms.
Article
Genetics & Heredity
Samantha Boudeau, Meganathan P. Ramakodi, Yan Zhou, Jeffrey C. Liu, Camille Ragin, Rob J. Kulathinal
Summary: Researchers have identified a set of African ancestry-informative markers (AIMs) that effectively differentiate populations of African ancestry from other global populations and further identify substructure within African populations. These AIMs have shown associations with diseases in African populations. However, there is a need to better represent historically understudied populations as the current genotyping platforms lack these AIMs.
FRONTIERS IN GENETICS
(2023)
Article
Oncology
Linda Zollner, Felix Boekstegers, Carol Barahona Ponce, Dominique Scherer, Katherine Marcelain, Valentina Garate-Calderon, Melanie Waldenberger, Erik Morales, Armando Rojas, Cesar Munoz, Javier Retamales, Gonzalo De Toro, Allan Vera Kortmann, Olga Barajas, Maria Teresa Rivera, Analia Cortes, Denisse Loader, Javiera Saavedra, Lorena Gutierrez, Alejandro Ortega, Maria Enriqueta Bertran, Leonardo Bartolotti, Fernando Gabler, Monica Campos, Juan Alvarado, Fabricio Moisan, Loreto Spencer, Bruno Nervi, Daniel Carvajal, Hector Losada, Mauricio Almau, Plinio Fernandez, Jordi Olloquequi, Alice R. Carter, Juan Francisco Miquel Poblete, Bernabe Ignacio Bustos, Macarena Fuentes Guajardo, Rolando Gonzalez-Jose, Maria Catira Bortolini, Victor Acuna-Alonzo, Carla Gallo, Andres Ruiz Linares, Francisco Rothhammer, Justo Lorenzo Bermejo
Summary: There is a strong association between the proportion of Mapuche ancestry and the risk of gallbladder cancer (GBC). Mapuche ancestry has a putatively causal effect on GBC risk and gallstone disease, while showing a negative effect on BMI. These findings have significant implications for GBC prevention and future admixture mapping studies.
Article
Oncology
Pascal Belleau, Astrid Deschenes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz
Summary: The study explores the feasibility and accuracy of inferring genetic ancestry from cancer-derived data. A data synthesis framework is developed to optimize and evaluate the performance of ancestry inference based on various molecular profiles. The results demonstrate the accuracy and robustness of the inference procedure, making it possible to determine the continental-level ancestry of cancer patients.
Article
Psychiatry
Helene Choquet, Jie Yin, Eric Jorgenson
Summary: The study found significant associations between genetic ancestry and smoking behaviors in different race/ethnicity groups.
TRANSLATIONAL PSYCHIATRY
(2021)
Article
Gastroenterology & Hepatology
Alberto Queiroz Farias, Anna Curto Vilalta, Patricia Momoyo Zitelli, Gustavo Pereira, Luciana L. Goncalves, Aldo Torre, Juan Manuel Diaz, Adrian C. Gadano, Angelo Z. Mattos, Liliana S. C. Mendes, Mario R. Alvares-da-Silva, Paulo L. Bittencourt, Carlos Benitez, Claudia Alves Couto, Manuel Mendizabal, Claudio L. Toledo, Daniel F. C. Mazo, Mauricio Castillo Barradas, Eva M. Uson Raposo, P. Martin Padilla-Machaca, Adelina Zarela Lozano Miranda, Rene Male-Velazquez, Andre Castro Lyra, Milagros B. Davalos-Moscol, Jose L. Perez Hernandez, Rafael O. Ximenes, Giovanni Faria Silva, Oscar A. Beltran-Galvis, Maria S. Gonzalez Huezo, Fernando Bessone, Tarciso D. S. Rocha, Eduardo Fassio, Carlos Terra, Juan I. Marin, Patricia Sierra Casas, Carlos de la Pena-Ramirez, Ferran Aguilar Parera, Flavia Fernandes, Maria da Penha Zago-Gomes, Osvely Mendez-Guerrero, Sebastian Marciano, Angelo A. Mattos, Joao C. Oliveira, Gabriel T. S. Guerreiro, Liana Codes, Marco Arrese, Mateus J. Nardelli, Marcelo O. Silva, Renato Palma-Fernandez, Camila Alcantara, Cristina Sanchez Garrido, Jonel Trebicka, Thierry Gustot, Javier Fernandez, Joan Claria, Rajiv Jalan, Paolo Angeli, Vicente Arroyo, Richard Moreau, ACLARA Study Collaborators
Summary: This study investigated the association of genetic ancestry and race with acute-on chronic liver failure (ACLF). The results showed that Latin American patients with higher Native American genetic ancestry and Native American race were more likely to develop ACLF. This suggests that genetic ancestry and race may be associated with the risk of ACLF.
Article
Medicine, General & Internal
Elizabeth Jordan, Daniel D. Kinnamon, Garrie J. Haas, Mark Hofmeyer, Evan Kransdorf, Gregory A. Ewald, Alanna A. Morris, Anjali Owens, Brian Lowes, Douglas Stoller, W. H. Wilson Tang, Sonia Garg, Barry H. Trachtenberg, Palak Shah, Salpy V. Pamboukian, Nancy K. Sweitzer, Matthew T. Wheeler, Jane E. Wilcox, Stuart Katz, Stephen Pan, Javier Jimenez, Daniel P. Fishbein, Frank Smart, Jessica Wang, Stephen S. Gottlieb, Daniel P. Judge, Charles K. Moore, Jonathan O. Mead, Natalie Hurst, Jinwen Cao, Gordon S. Huggins, Jason Cowan, Hanyu Ni, Heidi L. Rehm, Gail P. Jarvik, Matteo Vatta, Wylie Burke, Ray E. Hershberger
Summary: This study compares the rare variant genetic architecture of dilated cardiomyopathy (DCM) among patients with DCM who are of African ancestry compared with European ancestry. The study found that African patients with DCM were less likely to have clinically actionable variants in DCM genes than those of European ancestry due to differences in genetic architecture and a lack of representation of African ancestry in clinical data sets.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2023)
Article
Genetics & Heredity
J. Ruiz-Ramirez, M. de la Puente, C. Xavier, A. Ambroa-Conde, J. Alvarez-Dios, A. Freire-Aradas, A. Mosquera-Miguel, A. Ralf, C. Amory, M. A. Katsara, T. Khellaf, M. Nothnagel, E. Y. Y. Cheung, T. E. Gross, P. M. Schneider, J. Uacyisrael, S. Oliveira, M. d. N. Klautau-Guimara, C. Carvalho-Gontijo, E. Pospiech, W. Branicki, W. Parson, M. Kayser, A. Carracedo, M. V. Lareu, C. Phillips
Summary: The VISAGE Enhanced Tool (ET) combines genetic markers and visible characteristics to predict ancestry and appearance. The tool uses a high-throughput sequencing assay and includes markers for differentiating Middle Eastern populations. ET can effectively differentiate different populations and their admixed backgrounds, and can be used for analyzing mixed DNA samples.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Oksana V. Vernygora, Carlos Congrains, Scott M. Geib, Julian R. Dupuis
Summary: In this study, a flexible and user-friendly tool called HiMAP2 is introduced for identifying, visualizing, and filtering phylogenetically informative loci from diverse genomic and transcriptomic resources. The tool includes features such as orthology prediction, exon extraction, and filtering of aligned exon sequences based on user-defined specifications. Additionally, HiMAP2 enables exploration of the final filtered exons through phylogenetic inference and species tree estimation. The results of marker selection can be visualized and refined using an interactive Bokeh application to generate publication-quality figures.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Genetics & Heredity
Yunyun Liu, Xiaosha Jing, Lingling Xing, Sha Liu, Jianlong Liu, Jing Cheng, Cechuan Deng, Ting Bai, Tianyu Xia, Xiang Wei, Yuan Luo, Quanfang Zhou, Qian Zhu, Hongqian Liu
Summary: The study assessed the clinical application of NIPS in low-risk pregnant women, revealing that SCA were more common than autosomal trisomy, and EICF was the most frequent USM but least predictive. Further evaluation is suggested for low-risk pregnant women with specific USMs.
FRONTIERS IN GENETICS
(2021)
Article
Oncology
Linda Zollner, Diana Torres, Ignacio Briceno, Michael Gilbert, Gabriela Torres-Mejia, Joe Dennis, Manjeet K. Bolla, Qin Wang, Ute Hamann, Justo Lorenzo Bermejo
Summary: Latin American and Hispanic women with higher Native American ancestry have a decreased risk of breast cancer, particularly in cases of familial and estrogen receptor-positive breast cancer. This unconfounded protective effect of Native American ancestry suggests potential for personalized prevention programs and further genetic studies.
BREAST CANCER RESEARCH
(2023)
Article
Medicine, General & Internal
Frances Theunissen, Loren L. Flynn, Ryan S. Anderton, P. Anthony Akkari
Summary: This article discusses the role of recent discoveries of short structural variations (SSVs) in ALS and how these findings can be applied to future clinical trials. These discoveries help reduce participant heterogeneity and improve outcomes of ALS clinical trials.
Article
Multidisciplinary Sciences
D. Truelsen, A. Freire-Aradas, M. Nazari, A. Aliferi, D. Ballard, C. Phillips, N. Morling, V Pereira, C. Borsting
Summary: The introduction of new methods in forensic genetic case work requires meticulous evaluation. The QIAseq Targeted DNA panel showed good consistency and reproducibility under different DNA input conditions, but issues were found when the input was low. Different mixture ratios in mixtures can impact the analysis results.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Xiaosha Jing, Hongqian Liu, Qian Zhu, Sha Liu, Jianlong Liu, Ting Bai, Cechuan Deng, Tianyu Xia, Yunyun Liu, Jing Cheng, Xiang Wei, Lingling Xing, Yuan Luo, Quanfang Zhou, Lin Chen, Lingping Li, Jiamin Wang
Summary: This study evaluated prenatal diagnosis methods following positive noninvasive prenatal screening (NIPS) results. The results showed that QF-PCR can quickly and accurately identify common aneuploidies, and when combined with karyotyping and CNV detection techniques, can provide more comprehensive results. In cases of sex chromosome aneuploidy (SCA) or other abnormalities, CMA and CNVseq may increase the detection rate. The addition of fluorescence in situ hybridization assay may help identify true fetal mosaicism.
FRONTIERS IN GENETICS
(2022)
Editorial Material
Obstetrics & Gynecology
Jason M. Franasiak
FERTILITY AND STERILITY
(2019)
Meeting Abstract
Obstetrics & Gynecology
Brent M. Hanson, Julia G. Kim, Ashley W. Tiegs, Emily K. Osman, Shelby A. Neal, Ruth B. Lathi, Richard Thomas Scott, Jason M. Franasiak
FERTILITY AND STERILITY
(2019)
Meeting Abstract
Obstetrics & Gynecology
Emily K. Osman, Tianren Wang, Min Yang, Yiping Zhan, Caroline R. Juneau, Scott J. Morin, Emre Seli, Richard Thomas Scott, Jason M. Franasiak
FERTILITY AND STERILITY
(2019)
Meeting Abstract
Obstetrics & Gynecology
Amber M. Klimczak, Christine V. Whitehead, Shelby A. Neal, Ashley W. Tiegs, Emily K. Osman, Brent M. Hanson, Julia G. Kim, Marie D. Werner, Jason M. Franasiak, Richard Thomas Scott
FERTILITY AND STERILITY
(2019)
Meeting Abstract
Obstetrics & Gynecology
Brent M. Hanson, Julia G. Kim, Emily K. Osman, Ashley W. Tiegs, Shelby A. Neal, Ruth B. Lathi, Richard Thomas Scott, Jason M. Franasiak
FERTILITY AND STERILITY
(2019)
Meeting Abstract
Obstetrics & Gynecology
Emily K. Osman, Shelby A. Neal, Ashley W. Tiegs, Brent M. Hanson, Julia G. Kim, Jason M. Franasiak, Richard Thomas Scott
FERTILITY AND STERILITY
(2019)
Meeting Abstract
Obstetrics & Gynecology
Ashley W. Tiegs, Shelby A. Neal, Emily K. Osman, Julia G. Kim, Brent M. Hanson, Jason M. Franasiak, Richard Thomas Scott, Linnea R. Goodman
FERTILITY AND STERILITY
(2019)
Meeting Abstract
Obstetrics & Gynecology
Shelby A. Neal, Xin Tao, Li Sun, Brent M. Hanson, Julia G. Kim, Emily K. Osman, Ashley W. Tiegs, Richard Thomas Scott, Jason M. Franasiak
FERTILITY AND STERILITY
(2019)
Article
Obstetrics & Gynecology
Evelin E. Lara-Molina, Jason M. Franasiak, Diego Marin, Xin Tao, Patricia Diaz-Gimeno, Mireia Florensa, Marta Martin, Emre Seli, Antonio Pellicer
FERTILITY AND STERILITY
(2020)
Article
Genetics & Heredity
Katherine A. Green, George Patounakis, Michael P. Dougherty, Marie D. Werner, Richard T. Scott, Jason M. Franasiak
JOURNAL OF ASSISTED REPRODUCTION AND GENETICS
(2020)
Review
Obstetrics & Gynecology
Mauro Cozzolino, Jason Franasiak, Alessandra Andrisani, Guido Ambrosini, Amerigo Vitagliano
EUROPEAN JOURNAL OF OBSTETRICS & GYNECOLOGY AND REPRODUCTIVE BIOLOGY
(2020)
Article
Genetics & Heredity
Andres Reig, Jason Franasiak, Richard T. Scott, Emre Seli
JOURNAL OF ASSISTED REPRODUCTION AND GENETICS
(2020)
Editorial Material
Obstetrics & Gynecology
Amber M. Klimczak, Jason M. Franasiak
FERTILITY AND STERILITY
(2021)
Review
Obstetrics & Gynecology
Jason M. Franasiak, Diana Alecsandru, Eric J. Forman, Laura C. Gemmell, Jeffrey M. Goldberg, Natalia Llarena, Cheri Margolis, Joop Laven, Sam Schoenmakers, Emre Seli
Summary: Implantation is a critical step in human reproduction, and recurrent implantation failure can result from various factors. Literature discussing this clinical phenomenon is increasing, and there is not a universally agreed-on definition for it.
FERTILITY AND STERILITY
(2021)
Editorial Material
Obstetrics & Gynecology
Andres Reig, Jason M. Franasiak
FERTILITY AND STERILITY
(2022)