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Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data
In anthropological, medical, and forensic studies, the nonrecombinant region of the human Y chromosome (NRY) enables accurate reconstruction of pedigree relationships and retrieval of ancestral information. Using high-throughput sequencing (HTS) data, we present a benchmarking analysis of command-li...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Research Network of Computational and Structural Biotechnology
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10560978/ https://www.ncbi.nlm.nih.gov/pubmed/37817776 http://dx.doi.org/10.1016/j.csbj.2023.09.012 |
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author | García-Olivares, Víctor Muñoz-Barrera, Adrián Rubio-Rodríguez, Luis A. Jáspez, David Díaz-de Usera, Ana Iñigo-Campos, Antonio Veeramah, Krishna R. Alonso, Santos Thomas, Mark G. Lorenzo-Salazar, José M. González-Montelongo, Rafaela Flores, Carlos |
author_facet | García-Olivares, Víctor Muñoz-Barrera, Adrián Rubio-Rodríguez, Luis A. Jáspez, David Díaz-de Usera, Ana Iñigo-Campos, Antonio Veeramah, Krishna R. Alonso, Santos Thomas, Mark G. Lorenzo-Salazar, José M. González-Montelongo, Rafaela Flores, Carlos |
author_sort | García-Olivares, Víctor |
collection | PubMed |
description | In anthropological, medical, and forensic studies, the nonrecombinant region of the human Y chromosome (NRY) enables accurate reconstruction of pedigree relationships and retrieval of ancestral information. Using high-throughput sequencing (HTS) data, we present a benchmarking analysis of command-line tools for NRY haplogroup classification. The evaluation was performed using paired Illumina data from whole-genome sequencing (WGS) and whole-exome sequencing (WES) experiments from 50 unrelated donors. Additionally, as a validation, we also used paired WGS/WES datasets of 54 individuals from the 1000 Genomes Project. Finally, we evaluated the tools on data from third-generation HTS obtained from a subset of donors and one reference sample. Our results show that WES, despite typically offering less genealogical resolution than WGS, is an effective method for determining the NRY haplogroup. Y-LineageTracker and Yleaf showed the highest accuracy for WGS data, classifying precisely 98% and 96% of the samples, respectively. Yleaf outperforms all benchmarked tools in the WES data, classifying approximately 90% of the samples. Yleaf, Y-LineageTracker, and pathPhynder can correctly classify most samples (88%) sequenced with third-generation HTS. As a result, Yleaf provides the best performance for applications that use WGS and WES. Overall, our study offers researchers with a guide that allows them to select the most appropriate tool to analyze the NRY region using both second- and third-generation HTS data. |
format | Online Article Text |
id | pubmed-10560978 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Research Network of Computational and Structural Biotechnology |
record_format | MEDLINE/PubMed |
spelling | pubmed-105609782023-10-10 Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data García-Olivares, Víctor Muñoz-Barrera, Adrián Rubio-Rodríguez, Luis A. Jáspez, David Díaz-de Usera, Ana Iñigo-Campos, Antonio Veeramah, Krishna R. Alonso, Santos Thomas, Mark G. Lorenzo-Salazar, José M. González-Montelongo, Rafaela Flores, Carlos Comput Struct Biotechnol J Research Article In anthropological, medical, and forensic studies, the nonrecombinant region of the human Y chromosome (NRY) enables accurate reconstruction of pedigree relationships and retrieval of ancestral information. Using high-throughput sequencing (HTS) data, we present a benchmarking analysis of command-line tools for NRY haplogroup classification. The evaluation was performed using paired Illumina data from whole-genome sequencing (WGS) and whole-exome sequencing (WES) experiments from 50 unrelated donors. Additionally, as a validation, we also used paired WGS/WES datasets of 54 individuals from the 1000 Genomes Project. Finally, we evaluated the tools on data from third-generation HTS obtained from a subset of donors and one reference sample. Our results show that WES, despite typically offering less genealogical resolution than WGS, is an effective method for determining the NRY haplogroup. Y-LineageTracker and Yleaf showed the highest accuracy for WGS data, classifying precisely 98% and 96% of the samples, respectively. Yleaf outperforms all benchmarked tools in the WES data, classifying approximately 90% of the samples. Yleaf, Y-LineageTracker, and pathPhynder can correctly classify most samples (88%) sequenced with third-generation HTS. As a result, Yleaf provides the best performance for applications that use WGS and WES. Overall, our study offers researchers with a guide that allows them to select the most appropriate tool to analyze the NRY region using both second- and third-generation HTS data. Research Network of Computational and Structural Biotechnology 2023-09-15 /pmc/articles/PMC10560978/ /pubmed/37817776 http://dx.doi.org/10.1016/j.csbj.2023.09.012 Text en © 2023 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Research Article García-Olivares, Víctor Muñoz-Barrera, Adrián Rubio-Rodríguez, Luis A. Jáspez, David Díaz-de Usera, Ana Iñigo-Campos, Antonio Veeramah, Krishna R. Alonso, Santos Thomas, Mark G. Lorenzo-Salazar, José M. González-Montelongo, Rafaela Flores, Carlos Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data |
title | Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data |
title_full | Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data |
title_fullStr | Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data |
title_full_unstemmed | Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data |
title_short | Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data |
title_sort | benchmarking of human y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10560978/ https://www.ncbi.nlm.nih.gov/pubmed/37817776 http://dx.doi.org/10.1016/j.csbj.2023.09.012 |
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