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
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
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
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
Genetics & Heredity
Guanglin He, Jing Liu, Mengge Wang, Xing Zou, Tianyue Ming, Sumin Zhu, Hui-Yuan Yeh, Chuanchao Wang, Zheng Wang, Yiping Hou
Summary: Ancestry informative markers (AIMs) with significant allele frequency differences among diverse ethnic groups are attracting interest in the forensic community for population history reconstruction. This study used the Precision ID Ancestry Panel to analyze Chinese individuals, showing its potential as a robust tool in forensic individual identification. However, limitations in discriminatory power were observed in intercontinental individuals, highlighting the need for more specific AIM sets and comprehensive population reference data validation in the future.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Biology
Khai C. Ang, Victor A. Canfield, Tiffany C. Foster, Thaddeus D. Harbaugh, Kathryn A. Early, Rachel L. Harter, Katherine P. Reid, Shou Ling Leong, Yuka Kawasawa, Dajiang Liu, John W. Hawley, Keith C. Cheng
Summary: This study focused on a Native American population with high Native American genetic ancestry, aiming to investigate the impact of this ancestry on skin color variation. The results showed that Native American genetic ancestry had the greatest effect on reducing skin pigmentation, while genetic mutations from European and African ancestries had smaller effects. However, the specific genetic variants responsible for light skin in Native American/East Asian populations remain to be identified.
Article
Biochemistry & Molecular Biology
Andrew B. Conley, Lavanya Rishishwar, Maria Ahmad, Shivam Sharma, Emily T. Norris, I. King Jordan, Leonardo Marino-Ramirez
Summary: Biobank projects generate genomic data for thousands of individuals, requiring computational methods such as genetic ancestry inference tools. Current methods do not scale to biobank-sized datasets. The Rye algorithm was developed for scalable genetic ancestry inference, outperforming existing programs in accuracy and runtime performance on a dataset from the UK Biobank. Rye utilizes principal component analysis and optimization techniques to estimate genetic ancestry at both continental and subcontinental levels.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Aline Brugnera Felkl, Eduardo Avila, Andre Zoratto Gastaldo, Catieli Gobetti Lindholz, Marcio Dorn, Clarice Sampaio Alho
Summary: Forensic DNA phenotyping (FDP) can provide valuable intelligence when conventional DNA profiling fails. The Precision ID Ancestry Panel, consisting of 165 autosomal SNPs, has been evaluated in a heterogeneous population and shown to be a useful tool for individual identification and kinship testing. Admixed- and African-derived individuals exhibit higher levels of admixture and population stratification, while European-and Amerindian-derived individuals show more genetic uniformity.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Biochemical Research Methods
Qiang Zhu, Yueyan Cao, Shu Zhang, Yuguo Huang, Yuhan Hu, Yijun Zhou, Haoyu Wang, Yufang Wang, Ji Zhang
Summary: The study showed that a highly informative InDel panel developed based on the CE platform has the potential for individual ancestry inference among Asian populations. 21 InDels with high F-ST values were selected and assembled into an ancestry informative insertion/deletion panel, enabling accurate ancestry inference among Asian populations.
Article
Cell Biology
Pradiptajati Kusuma, Murray P. Cox, Graeme Barker, Herawati Sudoyo, J. Stephen Lansing, Guy S. Jacobs
Summary: Borneo, a significant region for ancient Southeast Asian human remains and rock art, had traditional hunter-gatherer Punan communities. The connection between these communities and the present-day agriculturalist inhabitants who speak Austronesian languages and have composite genetic ancestry is unclear. By analyzing the genetic ancestry of Bornean Punan Batu, Tubu, and Aput, this study reveals deep ancestral connections and a time depth of over 7,500 years. The Punan communities largely lack the genetic signals of agricultural Borneans and demonstrate unexpected complexity in the origins and dispersal of Austronesian-expansion-related ancestry.
Article
Biochemical Research Methods
Pablo Librado, Ludovic Orlando
Summary: This article presents "Struct-f4", an automated solution for characterizing and summarizing the genetic ancestry profile of individuals, assessing their genetic affinities, identifying admixture sources, and quantifying admixture levels.
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
D. Truelsen, T. Tvedebrink, H. S. Mogensen, M. S. Farzad, M. A. Shan, N. Morling, V Pereira, C. Borsting
Summary: This study used a custom EUROFORGEN NAME panel and Precision ID Ancestry panel to sequence 1098 individuals from 14 populations. The results showed that the two panels could accurately differentiate individuals from Europe and the Middle East, while the Precision ID Ancestry panel could separate North African individuals from European and Middle Eastern individuals, with added improvement from the EUROFORGEN NAME panel. However, the separation of Middle Eastern populations from European and South-Central Asian populations remains challenging even with the use of both panels.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Soichiro Nishiyama, Kengo Sato, Ryutaro Tao
Summary: This study presents a novel approach for selecting informative markers based on binary integer programming. By combining with targeted SNP genotyping, this method allows for flexible analysis and has practical applications in large-scale problems in breeding and ecological research.
BMC BIOINFORMATICS
(2022)
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)