Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations

Bioinformatics
Marc PybusJohannes Engelken

Abstract

Detecting positive selection in genomic regions is a recurrent topic in natural population genetic studies. However, there is little consistency among the regions detected in several genome-wide scans using different tests and/or populations. Furthermore, few methods address the challenge of classifying selective events according to specific features such as age, intensity or state (completeness). We have developed a machine-learning classification framework that exploits the combined ability of some selection tests to uncover different polymorphism features expected under the hard sweep model, while controlling for population-specific demography. As a result, we achieve high sensitivity toward hard selective sweeps while adding insights about their completeness (whether a selected variant is fixed or not) and age of onset. Our method also determines the relevance of the individual methods implemented so far to detect positive selection under specific selective scenarios. We calibrated and applied the method to three reference human populations from The 1000 Genome Project to generate a genome-wide classification map of hard selective sweeps. This study improves detection of selective sweep by overcoming the classical selection...Continue Reading

References

Feb 1, 1974·Genetical Research·J M Smith, J Haigh
Apr 14, 2000·American Journal of Human Genetics·M T Hamblin, A Di Rienzo
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Jul 26, 2002·Genes and Immunity·P SabetiD Kwiatkowski
Mar 12, 2004·Molecular Ecology·Mark A Beaumont, David J Balding
Sep 11, 2004·Human Molecular Genetics·Eric J Vallender, Bruce T Lahn
Oct 28, 2005·Genome Research·Rasmus NielsenCarlos Bustamante
Oct 28, 2005·Genome Research·Stephen F SchaffnerDavid Altshuler
Feb 3, 2006·Genetics·Wolfgang StephanCharles H Langley
Feb 24, 2006·PLoS Biology·Benjamin F VoightJonathan K Pritchard
May 12, 2006·Genome Research·Kosuke M TeshimaMolly Przeworski
Jun 17, 2006·Science·P C SabetiE S Lander
Jul 1, 2006·Trends in Genetics : TIG·Shameek Biswas, Joshua M Akey
Jul 11, 2006·Genome Research·Joanna L KelleyJoshua M Akey
Dec 13, 2006·Nature Genetics·Sarah A TishkoffPanos Deloukas
Jun 15, 2007·Molecular Biology and Evolution·Kai ZengChung-I Wu
Mar 25, 2009·Genome Research·Joseph K PickrellJonathan K Pritchard
Jun 9, 2009·PLoS Genetics·Graham CoopJonathan K Pritchard
Jan 21, 2010·Genome Research·Hua ChenDavid Reich
Sep 11, 2012·Genetics·Julie M GrankaMarcus W Feldman
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
Feb 19, 2013·Cell·Sharon R GrossmanPardis C Sabeti
Jun 19, 2013·Genetics·Roy RonenVineet Bafna
Oct 1, 2013·Trends in Ecology & Evolution·Philipp W Messer, Dmitri A Petrov
Nov 28, 2013·Annual Review of Genetics·Joseph J VittiPardis C Sabeti
Jan 1, 2014·Nucleic Acids Research·William DynanBarry Stoddard
Apr 4, 2014·Molecular Biology and Evolution·Maud FagnyGuillaume Laval
Jul 26, 2014·Genetics·Benjamin A WilsonPhilipp W Messer

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Citations

Nov 20, 2015·Molecular Biology and Evolution·Johannes EngelkenElena Bosch
Nov 1, 2016·Molecular Biology and Evolution·Alexander CaganAida M Andrés
Apr 8, 2018·G3 : Genes - Genomes - Genetics·Andrew D Kern, Daniel R Schrider
May 23, 2019·FEBS Letters·Michał SzpakChris Tyler-Smith
Sep 5, 2019·Biology Direct·Begoña DobonHafid Laayouni
Aug 24, 2017·Computational and Mathematical Methods in Medicine·Andreas MayrOlaf Gefeller
Mar 16, 2016·PLoS Genetics·Daniel R Schrider, Andrew D Kern
Oct 24, 2020·BMC Genetics·Sandra WalshJaume Bertranpetit

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