ArticleMolecular biology and evolution2016
A Molecular Evolutionary Reference for the Human Variome.
Article in Molecular biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Phylogenetic tree-based amino acid sequence generation for proteomics data analysis of unknown species.Computational and structural biotechnology journal · 2025Article
- MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing.Molecular biology and evolution · 2024Article
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- The role of admixture in the rare variant contribution to inflammatory bowel disease.Genome medicine · 2023Article
- A Review of Resistance to Polymyxins and Evolving Mobile Colistin Resistance Gene (Antibiotics (Basel, Switzerland) · 2023Review
- Protein dynamics provide mechanistic insights about epistasis among common missense polymorphisms.Biophysical journal · 2023Article
- MEGA11: Molecular Evolutionary Genetics Analysis Version 11.Molecular biology and evolution · 2021Article
- Common Treatment, Common Variant: Evolutionary Prediction of Functional Pharmacogenomic Variants.Journal of personalized medicine · 2021Article
- Functional, Morphological, and Evolutionary Characterization of Hearing in Subterranean, Eusocial African Mole-Rats.Current biology : CB · 2020Article
- Article
- Genome-wide analysis indicates association between heterozygote advantage and healthy aging in humans.BMC genetics · 2019Article
- On estimating evolutionary probabilities of population variants.BMC evolutionary biology · 2019Article
- Computational enhancement of single-cell sequences for inferring tumor evolution.Bioinformatics (Oxford, England) · 2018Article
- Adaptive Landscape of Protein Variation in Human Exomes.Molecular biology and evolution · 2018Article
- Neutral Theory, Disease Mutations, and Personal Exomes.Molecular biology and evolution · 2018Article
- Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine.Current opinion in structural biology · 2015Review
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5 authors.
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Abstract
Widespread sequencing efforts are revealing unprecedented amount of genomic variation in populations. Such information is routinely used to derive consensus reference sequences and to infer positions subject to natural selection. Here, we present a new molecular evolutionary method for estimating neutral evolutionary probabilities (EPs) of each amino acid, or nucleotide state at a genomic position without using intraspecific polymorphism data. Because EPs are derived independently of population-level information, they serve as null expectations that can be used to evaluate selective forces on alleles at both polymorphic and monomorphic positions in populations. We applied this method to coding sequences in the human genome and produced a comprehensive evolutionary variome reference for all human proteins. We found that EPs accurately predict neutral and disease-associated alleles. Through an analysis of discordance between allelic EPs and their observed population frequencies, we discovered thousands of novel candidate sites for nonneutral evolution in human proteins. Many of these were validated in a joint analysis of disease-associated variants and population data. The EP method is also directly applicable to the analysis of noncoding sequences and genomic analyses of nonmodel species.
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