Bolognini, Davide Halgren, Alma Lou, Runyang Raveane, Alessandro Rocha, Joana Guarracino, Andrea Soranzo, Nicole Chin, Chen-Shan Garrison, Erik Sudmant, Peter
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The adoption of agriculture triggered a rapid shift towards starch-rich diets in human populations1. Amylase genes facilitate starch digestion, and increased amylase copy number has been observed in some modern human populations with high-starch intake2, although evidence of recent selection is lacking3,4. Here, using 94 long-read haplotype-resolve...
Yao, Michael Daniels, Jason Grosvenor, Luke Morrill, Valerie Feinberg, Jason Bakulski, Kelly Piven, Joseph Hazlett, Heather Shen, Mark Newschaffer, Craig
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BACKGROUND: Common genetic variation has been shown to account for a large proportion of ASD heritability. Polygenic scores generated for autism spectrum disorder (ASD-PGS) using the most recent discovery data, however, explain less variance than expected, despite reporting significant associations with ASD and other ASD-related traits. Here, we in...
Orcales, Faye Kumar, Sugandh Bui, Audrey Johnson, Chandler Liu, Jared Huang, Zhi-Ming Liao, Wilson
Psoriasis is a chronic, immune-mediated inflammatory skin disease associated with a polygenic mode of inheritance. There are few studies that explore the association of a psoriasis Polygenic Risk Score (PRS) with patient clinical characteristics, and to our knowledge there are no studies examining psoriasis PRS associations across different ethnici...
Metayer, Catherine Spector, Logan G Scheurer, Michael E Jeon, Soyoung Scott, Rodney J Takagi, Masatoshi Clavel, Jacqueline Manabe, Atsushi Ma, Xiaomei Hailu, Elleni M
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BackgroundPrenatal folate supplementation has been consistently associated with a reduced risk of childhood acute lymphoblastic leukemia (ALL). Previous germline genetic studies examining the one carbon (folate) metabolism pathway were limited in sample size, scope, and population diversity and led to inconclusive results.MethodsWe evaluated whethe...
Koka, Hela Zhou, Weiyin McMaster, Mary Bai, Jiwei Luo, Wen Klein, Alyssa Zhang, Tongwu Hua, Xing Li, Xin Wang, Difei
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Chordoma is a rare bone cancer with variable clinical outcomes. Here, we recruited 184 sporadic chordoma patients from the US and Canada and collected their clinical and treatment data. The average age at diagnosis was 45.5 years (Range 5-78) and the chordoma site distribution was 49.2% clivus, 26.2% spinal, and 24.0% sacral. Most patients (97.5%) ...
Talwar, James V Klie, Adam Pagadala, Meghana S Carter, Hannah
SummaryHarmonizing variant indexing and allele assignments across datasets is crucial for data integrity in cross-dataset studies such as multi-cohort genome-wide association studies, meta-analyses, and the development, validation, and application of polygenic risk scores. Ensuring this indexing and allele consistency is a laborious, time-consuming...
Yang, Hui Wang, Xinzhi Blanco-Gómez, Adrián He, Li García-Sancha, Natalia Corchado-Cobos, Roberto Pérez-Baena, Manuel Jiménez-Navas, Alejandro Wang, Pin Inman, Jamie
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BACKGROUND: Deeper insights into ERBB2-driven cancers are essential to develop new treatment approaches for ERBB2+ breast cancers (BCs). We employed the Collaborative Cross (CC) mouse model to unearth genetic factors underpinning Erbb2-driven mammary tumour development and metastasis. METHODS: 732 F1 hybrid female mice between FVB/N MMTV-Erbb2 and ...
Akdeniz, Bayram Frei, Oleksandr Shadrin, Alexey Vetrov, Dmitry Kropotov, Dmitry Hovig, Eivind Andreassen, Ole Dale, Anders
Genome-wide association studies (GWAS) implicate broad genomic loci containing clusters of highly correlated genetic variants. Finemapping techniques can select and prioritize variants within each GWAS locus which are more likely to have a functional influence on the trait. Here, we present a novel method, Finemap-MiXeR, for finemapping causal vari...
Hervoso, Jonatan L Amoah, Kofi Dodson, Jack Choudhury, Mudra Bhattacharya, Arjun Quinones-Valdez, Giovanni Pasaniuc, Bogdan Xiao, Xinshu
Recent studies have highlighted the essential role of RNA splicing, a key mechanism of alternative RNA processing, in establishing connections between genetic variations and disease. Genetic loci influencing RNA splicing variations show considerable influence on complex traits, possibly surpassing those affecting total gene expression. Dysregulated...
Verma, Anurag Huffman, Jennifer E Rodriguez, Alex Conery, Mitchell Liu, Molei Ho, Yuk-Lam Kim, Youngdae Heise, David A Guare, Lindsay Panickan, Vidul Ayakulangara
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One of the justifiable criticisms of human genetic studies is the underrepresentation of participants from diverse populations. Lack of inclusion must be addressed at-scale to identify causal disease factors and understand the genetic causes of health disparities. We present genome-wide associations for 2068 traits from 635,969 participants in the ...