Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data
© 2023 The Authors..
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:21 |
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| Enthalten in: |
Computational and structural biotechnology journal - 21(2023) vom: 09., Seite 4613-4618 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
García-Olivares, Víctor [VerfasserIn] |
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| Links: |
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| Themen: |
Comparative genomics |
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| Anmerkungen: |
Date Revised 12.10.2023 published: Electronic-eCollection Citation Status PubMed-not-MEDLINE |
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| doi: |
10.1016/j.csbj.2023.09.012 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
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| 520 | |a © 2023 The Authors. | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Comparative genomics | |
| 650 | 4 | |a NRY haplogroup classification | |
| 650 | 4 | |a Next-generation sequencing | |
| 650 | 4 | |a Population genetics | |
| 650 | 4 | |a Y chromosome | |
| 700 | 1 | |a Muñoz-Barrera, Adrián |e verfasserin |4 aut | |
| 700 | 1 | |a Rubio-Rodríguez, Luis A |e verfasserin |4 aut | |
| 700 | 1 | |a Jáspez, David |e verfasserin |4 aut | |
| 700 | 1 | |a Díaz-de Usera, Ana |e verfasserin |4 aut | |
| 700 | 1 | |a Iñigo-Campos, Antonio |e verfasserin |4 aut | |
| 700 | 1 | |a Veeramah, Krishna R |e verfasserin |4 aut | |
| 700 | 1 | |a Alonso, Santos |e verfasserin |4 aut | |
| 700 | 1 | |a Thomas, Mark G |e verfasserin |4 aut | |
| 700 | 1 | |a Lorenzo-Salazar, José M |e verfasserin |4 aut | |
| 700 | 1 | |a González-Montelongo, Rafaela |e verfasserin |4 aut | |
| 700 | 1 | |a Flores, Carlos |e verfasserin |4 aut | |
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