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HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph

Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations to this reference. This approach biases haplogroup assignments towards the reference and prohibits accurate calculations of the uncertainty i...

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Autores principales: Rubin, Joshua Daniel, Vogel, Nicola Alexandra, Gopalakrishnan, Shyam, Sackett, Peter Wad, Renaud, Gabriel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10281577/
https://www.ncbi.nlm.nih.gov/pubmed/37285390
http://dx.doi.org/10.1371/journal.pcbi.1011148
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author Rubin, Joshua Daniel
Vogel, Nicola Alexandra
Gopalakrishnan, Shyam
Sackett, Peter Wad
Renaud, Gabriel
author_facet Rubin, Joshua Daniel
Vogel, Nicola Alexandra
Gopalakrishnan, Shyam
Sackett, Peter Wad
Renaud, Gabriel
author_sort Rubin, Joshua Daniel
collection PubMed
description Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations to this reference. This approach biases haplogroup assignments towards the reference and prohibits accurate calculations of the uncertainty in assignment. We present HaploCart, a probabilistic mtDNA haplogroup classifier which uses a pangenomic reference graph framework together with principles of Bayesian inference. We demonstrate that our approach significantly outperforms available tools by being more robust to lower coverage or incomplete consensus sequences and producing phylogenetically-aware confidence scores that are unbiased towards any haplogroup. HaploCart is available both as a command-line tool and through a user-friendly web interface. The C++ program accepts as input consensus FASTA, FASTQ, or GAM files, and outputs a text file with the haplogroup assignments of the samples along with the level of confidence in the assignments. Our work considerably reduces the amount of data required to obtain a confident mitochondrial haplogroup assignment.
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spelling pubmed-102815772023-06-21 HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph Rubin, Joshua Daniel Vogel, Nicola Alexandra Gopalakrishnan, Shyam Sackett, Peter Wad Renaud, Gabriel PLoS Comput Biol Research Article Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations to this reference. This approach biases haplogroup assignments towards the reference and prohibits accurate calculations of the uncertainty in assignment. We present HaploCart, a probabilistic mtDNA haplogroup classifier which uses a pangenomic reference graph framework together with principles of Bayesian inference. We demonstrate that our approach significantly outperforms available tools by being more robust to lower coverage or incomplete consensus sequences and producing phylogenetically-aware confidence scores that are unbiased towards any haplogroup. HaploCart is available both as a command-line tool and through a user-friendly web interface. The C++ program accepts as input consensus FASTA, FASTQ, or GAM files, and outputs a text file with the haplogroup assignments of the samples along with the level of confidence in the assignments. Our work considerably reduces the amount of data required to obtain a confident mitochondrial haplogroup assignment. Public Library of Science 2023-06-07 /pmc/articles/PMC10281577/ /pubmed/37285390 http://dx.doi.org/10.1371/journal.pcbi.1011148 Text en © 2023 Rubin et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Rubin, Joshua Daniel
Vogel, Nicola Alexandra
Gopalakrishnan, Shyam
Sackett, Peter Wad
Renaud, Gabriel
HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph
title HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph
title_full HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph
title_fullStr HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph
title_full_unstemmed HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph
title_short HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph
title_sort haplocart: human mtdna haplogroup classification using a pangenomic reference graph
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10281577/
https://www.ncbi.nlm.nih.gov/pubmed/37285390
http://dx.doi.org/10.1371/journal.pcbi.1011148
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