hmmIBD: software to infer pairwise identity by descent between haploid genotypes

Malaria Journal
Stephen F SchaffnerDaniel E Neafsey

Abstract

A number of recent malaria studies have used identity by descent (IBD) to study epidemiological processes relevant to malaria control. In this paper, a software package, hmmIBD, is introduced for estimating pairwise IBD between haploid genomes, such as those of the malaria parasite, sampled from one or two populations. Source code is freely available. The performance of hmmIBD was verified using simulated data and benchmarked against an existing method for detecting IBD within populations. Code for all tests is freely available. The utility of hmmIBD for detecting IBD across populations was demonstrated using Plasmodium falciparum data from Cambodia and Ghana. Alongside an existing method, hmmIBD was highly accurate, sensitive and specific. It is fast, requiring only 70 s on average to analyse 50 whole genome sequences on a laptop computer, and scales linearly in the number of pairwise comparisons. Treatment of different populations under hmmIBD improves detection of IBD across populations. Fast and accurate software for detecting IBD in malaria parasite genetic data sampled from one or two populations is presented. The latter will likely be a useful feature for malaria elimination efforts, since it could facilitate identificat...Continue Reading

References

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Citations

Jan 23, 2019·The Journal of Infectious Diseases·Carol Hopkins Sibley
Sep 4, 2019·Malaria Journal·Sofonias K TessemaBryan Greenhouse
Dec 11, 2019·Tropical Medicine and Infectious Disease·Christian Nsanzabana
Jul 4, 2020·The American Journal of Tropical Medicine and Hygiene·Rachel F DanielsSarah K Volkman
Aug 5, 2020·Malaria Journal·Rachel F DanielsSarah K Volkman
Jun 19, 2019·Genetics·Aimee R TaylorCaroline O Buckee
Oct 20, 2018·BMC Medicine·Amy WesolowskiCaroline O Buckee
Oct 29, 2020·PLoS Neglected Tropical Diseases·Thaís Crippa de OliveiraMarcelo U Ferreira
Dec 15, 2020·PLoS Neglected Tropical Diseases·Lucas E BuyonNicanor Obaldia Iii
Jan 7, 2020·Cell Host & Microbe·Standwell C NkhomaIan H Cheeseman
Mar 23, 2021·Current Epidemiology Reports·Matthew M IppolitoJonathan J Juliano
Apr 10, 2021·Nature Reviews. Genetics·Daniel E NeafseyBronwyn L MacInnis
Jul 30, 2021·Wellcome Open Research·UNKNOWN MalariaGENHtut Ye
Apr 30, 2021·Science Advances·Josquin DaronVirginie Rougeron
May 28, 2021·Nature Communications·Ernest Diez BenaventeTaane G Clark
Aug 11, 2019·Microbiology Spectrum·Ananias A Escalante, M Andreína Pacheco
Apr 20, 2021·The Journal of Infectious Diseases·Thaís C de OliveiraMarcelo U Ferreira
Aug 2, 2021·International Journal for Parasitology. Drugs and Drug Resistance·Yaye Die NdiayeSarah K Volkman
Dec 21, 2021·PLoS Genetics·Tyler S BrownHsiao-Han Chang

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Methods Mentioned

BETA
genotyping

Software Mentioned

hmmIBD
isoRelate

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