Literature DB >> 25963372

Estimating the mutation load in human genomes.

Brenna M Henn1, Laura R Botigué1, Carlos D Bustamante2, Andrew G Clark3, Simon Gravel4.   

Abstract

Next-generation sequencing technology has facilitated the discovery of millions of genetic variants in human genomes. A sizeable fraction of these variants are predicted to be deleterious. Here, we review the pattern of deleterious alleles as ascertained in genome sequencing data sets and ask whether human populations differ in their predicted burden of deleterious alleles - a phenomenon known as mutation load. We discuss three demographic models that are predicted to affect mutation load and relate these models to the evidence (or the lack thereof) for variation in the efficacy of purifying selection in diverse human genomes. We also emphasize why accurate estimation of mutation load depends on assumptions regarding the distribution of dominance and selection coefficients - quantities that remain poorly characterized for current genomic data sets.

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Year:  2015        PMID: 25963372      PMCID: PMC4959039          DOI: 10.1038/nrg3931

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  82 in total

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Journal:  Am J Hum Genet       Date:  1963-09       Impact factor: 11.025

2.  The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations.

Authors:  Gabor T Marth; Eva Czabarka; Janos Murvai; Stephen T Sherry
Journal:  Genetics       Date:  2004-01       Impact factor: 4.562

3.  Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa.

Authors:  Sohini Ramachandran; Omkar Deshpande; Charles C Roseman; Noah A Rosenberg; Marcus W Feldman; L Luca Cavalli-Sforza
Journal:  Proc Natl Acad Sci U S A       Date:  2005-10-21       Impact factor: 11.205

4.  Characteristics of neutral and deleterious protein-coding variation among individuals and populations.

Authors:  Wenqing Fu; Rachel M Gittelman; Michael J Bamshad; Joshua M Akey
Journal:  Am J Hum Genet       Date:  2014-10-02       Impact factor: 11.025

5.  The fate of mutations surfing on the wave of a range expansion.

Authors:  Seraina Klopfstein; Mathias Currat; Laurent Excoffier
Journal:  Mol Biol Evol       Date:  2005-11-09       Impact factor: 16.240

6.  Genome-wide inference of natural selection on human transcription factor binding sites.

Authors:  Leonardo Arbiza; Ilan Gronau; Bulent A Aksoy; Melissa J Hubisz; Brad Gulko; Alon Keinan; Adam Siepel
Journal:  Nat Genet       Date:  2013-06-09       Impact factor: 38.330

7.  Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing.

Authors:  Yali Xue; Yuan Chen; Qasim Ayub; Ni Huang; Edward V Ball; Matthew Mort; Andrew D Phillips; Katy Shaw; Peter D Stenson; David N Cooper; Chris Tyler-Smith
Journal:  Am J Hum Genet       Date:  2012-12-07       Impact factor: 11.025

8.  Inference of human population history from individual whole-genome sequences.

Authors:  Heng Li; Richard Durbin
Journal:  Nature       Date:  2011-07-13       Impact factor: 49.962

9.  Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans.

Authors:  Ferran Casals; Alan Hodgkinson; Julie Hussin; Youssef Idaghdour; Vanessa Bruat; Thibault de Maillard; Jean-Christophe Grenier; Jean-Cristophe Grenier; Elias Gbeha; Fadi F Hamdan; Simon Girard; Jean-François Spinella; Mathieu Larivière; Virginie Saillour; Jasmine Healy; Isabel Fernández; Daniel Sinnett; Jacques L Michaud; Guy A Rouleau; Elie Haddad; Françoise Le Deist; Philip Awadalla
Journal:  PLoS Genet       Date:  2013-09-26       Impact factor: 5.917

10.  The impact of population demography and selection on the genetic architecture of complex traits.

Authors:  Kirk E Lohmueller
Journal:  PLoS Genet       Date:  2014-05-29       Impact factor: 5.917

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  96 in total

1.  Heterogeneity of dN/dS Ratios at the Classical HLA Class I Genes over Divergence Time and Across the Allelic Phylogeny.

Authors:  Bárbara Domingues Bitarello; Rodrigo dos Santos Francisco; Diogo Meyer
Journal:  J Mol Evol       Date:  2015-11-14       Impact factor: 2.395

2.  Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs.

Authors:  Clare D Marsden; Diego Ortega-Del Vecchyo; Dennis P O'Brien; Jeremy F Taylor; Oscar Ramirez; Carles Vilà; Tomas Marques-Bonet; Robert D Schnabel; Robert K Wayne; Kirk E Lohmueller
Journal:  Proc Natl Acad Sci U S A       Date:  2015-12-22       Impact factor: 11.205

3.  Patterns of deleterious variation between human populations reveal an unbalanced load.

Authors:  Rajiv C McCoy; Joshua M Akey
Journal:  Proc Natl Acad Sci U S A       Date:  2016-01-19       Impact factor: 11.205

4.  Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina.

Authors:  Benjamin Laenen; Andrew Tedder; Michael D Nowak; Per Toräng; Jörg Wunder; Stefan Wötzel; Kim A Steige; Yiannis Kourmpetis; Thomas Odong; Andreas D Drouzas; Marco C A M Bink; Jon Ågren; George Coupland; Tanja Slotte
Journal:  Proc Natl Acad Sci U S A       Date:  2018-01-04       Impact factor: 11.205

Review 5.  From Peas to Disease: Modifier Genes, Network Resilience, and the Genetics of Health.

Authors:  Jesse D Riordan; Joseph H Nadeau
Journal:  Am J Hum Genet       Date:  2017-08-03       Impact factor: 11.025

6.  MtDNA genomes reveal a relaxation of selective constraints in low-BMI individuals in a Uyghur population.

Authors:  Hong-Xiang Zheng; Lei Li; Xiao-Yan Jiang; Shi Yan; Zhendong Qin; Xiaofeng Wang; Li Jin
Journal:  Hum Genet       Date:  2017-08-10       Impact factor: 4.132

7.  Fine-scale genetic structure due to adaptive divergence among microhabitats.

Authors:  D N Wagner; T Z Baris; D I Dayan; X Du; M F Oleksiak; D L Crawford
Journal:  Heredity (Edinb)       Date:  2017-03-15       Impact factor: 3.821

8.  The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit.

Authors:  Casper-Emil T Pedersen; Kirk E Lohmueller; Niels Grarup; Peter Bjerregaard; Torben Hansen; Hans R Siegismund; Ida Moltke; Anders Albrechtsen
Journal:  Genetics       Date:  2016-11-30       Impact factor: 4.562

9.  Semiparametric Allelic Tests for Mapping Multiple Phenotypes: Binomial Regression and Mahalanobis Distance.

Authors:  Arunabha Majumdar; John S Witte; Saurabh Ghosh
Journal:  Genet Epidemiol       Date:  2015-10-23       Impact factor: 2.135

Review 10.  Immunotherapy and stereotactic ablative radiotherapy (ISABR): a curative approach?

Authors:  Michael B Bernstein; Sunil Krishnan; James W Hodge; Joe Y Chang
Journal:  Nat Rev Clin Oncol       Date:  2016-03-08       Impact factor: 66.675

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