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A faster implementation of association mapping from k-mers

Mehrab, Zakaria and Mobin, Jaiaid and Tahmid, Ibrahim Asadullah and Pachter, Lior and Rahman, Atif (2020) A faster implementation of association mapping from k-mers. Bio-protocol, 10 (21). Art. No. e3815. ISSN 2331-8325. https://resolver.caltech.edu/CaltechAUTHORS:20210309-074448590

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Abstract

Association mapping is the process of linking phenotypes with genotypes. In genome wide association studies (GWAS), individuals are first genotyped using microarrays or by aligning sequenced reads to reference genomes. However, both these approaches rely on reference genomes which limits their application to organisms with no or incomplete reference genomes. To address this, reference free association mapping methods have been developed. Here we present the protocol of an alignment free method for association studies which is based on counting k-mers in sequenced reads, testing for associations between k-mers and the phenotype of interest, and local assembly of the k-mers of statistical significance. The method can map associations of categorical phenotypes to sequence and structural variations without requiring prior sequencing of reference genomes.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.21769/bioprotoc.3815DOIArticle
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Rahman, Atif0000-0003-1805-3971
Additional Information:© 2020 Copyright Mehrab et al. This article is distributed under the terms of the Creative Commons Attribution License (CC BY 4.0). Lior Pachter, and Atif Rahman were funded in part by NIH R21 HG006583. This paper describes protocol of a method originally presented in the paper “Association mapping from sequencing reads using k-mers” by Atif Rahman, Ingileif Hallgrímsdóttir, Michael Eisen and Lior Pachter, and extended in “A faster implementation of association mapping from k-mers” by Zakaria Mehrab, Jaiaid Mobin, Ibrahim Asadullah Tahmid and Atif Rahman. The authors declare no competing interests.
Funders:
Funding AgencyGrant Number
NIHR21 HG006583
Subject Keywords:Association mapping, Genome wide association studies (GWAS), Reference free, k-mer
Issue or Number:21
Record Number:CaltechAUTHORS:20210309-074448590
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210309-074448590
Official Citation:Mehrab, ., Mobin, J., Tahmid, I. A., Pachter, L. and Rahman, A. (2020). Reference-free Association Mapping from Sequencing Reads Using k-mers. Bio-protocol 10(21): e3815. DOI: 10.21769/BioProtoc.3815
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:108356
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:10 Mar 2021 20:13
Last Modified:10 Mar 2021 20:13

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