Performance of a 74-Microhaplotype Assay in Kinship Analyses
Microhaplotypes (MHs) consisting of multiple SNPs and indels on short stretches of DNA are new and interesting loci for forensic genetic investigations. In this study, we analysed 74 previously defined MHs in two of the populations that our laboratory provides with forensic genetic services, Danes a...
Published in: | Genes |
---|---|
Main Authors: | , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
MDPI AG
2024
|
Subjects: | |
Online Access: | https://doi.org/10.3390/genes15020224 https://doaj.org/article/8df42ee4fc804956a25e5ec8f085176a |
id |
ftdoajarticles:oai:doaj.org/article:8df42ee4fc804956a25e5ec8f085176a |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:8df42ee4fc804956a25e5ec8f085176a 2024-09-15T18:10:14+00:00 Performance of a 74-Microhaplotype Assay in Kinship Analyses Carmen Tomas Pedro Rodrigues Carina G. Jønck Zohal Barekzay Halimureti Simayijiang Vania Pereira Claus Børsting 2024-02-01T00:00:00Z https://doi.org/10.3390/genes15020224 https://doaj.org/article/8df42ee4fc804956a25e5ec8f085176a EN eng MDPI AG https://www.mdpi.com/2073-4425/15/2/224 https://doaj.org/toc/2073-4425 doi:10.3390/genes15020224 2073-4425 https://doaj.org/article/8df42ee4fc804956a25e5ec8f085176a Genes, Vol 15, Iss 2, p 224 (2024) microhaplotype STR SNP forensic genetics relationship testing massively parallel sequencing Genetics QH426-470 article 2024 ftdoajarticles https://doi.org/10.3390/genes15020224 2024-08-05T17:49:58Z Microhaplotypes (MHs) consisting of multiple SNPs and indels on short stretches of DNA are new and interesting loci for forensic genetic investigations. In this study, we analysed 74 previously defined MHs in two of the populations that our laboratory provides with forensic genetic services, Danes and Greenlanders. In addition to the 229 SNPs that originally made up the 74 MHs, 66 SNPs and 3 indels were identified in the two populations, and 45 of these variants were included in new definitions of the MHs, whereas 24 SNPs were considered rare and of little value for case work. The average effective number of alleles (A e ) was 3.2, 3.0, and 2.6 in Danes, West Greenlanders, and East Greenlanders, respectively. High levels of linkage disequilibrium were observed in East Greenlanders, which reflects the characteristics of this population that has a small size, and signs of admixture and substructure. Pairwise kinship simulations of full siblings, half-siblings, first cousins, and unrelated individuals were performed using allele frequencies from MHs, STRs and SNPs from Danish and Greenlandic populations. The MH panel outperformed the currently used STR and SNP marker sets and was able to differentiate siblings from unrelated individuals with a 0% false positive rate and a 1.1% false negative rate using an LR threshold of 10,000 in the Danish population. However, the panel was not able to differentiate half-siblings or first cousins from unrelated individuals. The results generated in this study will be used to implement MHs as investigative markers for relationship testing in our laboratory. Article in Journal/Newspaper greenlander* greenlandic Directory of Open Access Journals: DOAJ Articles Genes 15 2 224 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
microhaplotype STR SNP forensic genetics relationship testing massively parallel sequencing Genetics QH426-470 |
spellingShingle |
microhaplotype STR SNP forensic genetics relationship testing massively parallel sequencing Genetics QH426-470 Carmen Tomas Pedro Rodrigues Carina G. Jønck Zohal Barekzay Halimureti Simayijiang Vania Pereira Claus Børsting Performance of a 74-Microhaplotype Assay in Kinship Analyses |
topic_facet |
microhaplotype STR SNP forensic genetics relationship testing massively parallel sequencing Genetics QH426-470 |
description |
Microhaplotypes (MHs) consisting of multiple SNPs and indels on short stretches of DNA are new and interesting loci for forensic genetic investigations. In this study, we analysed 74 previously defined MHs in two of the populations that our laboratory provides with forensic genetic services, Danes and Greenlanders. In addition to the 229 SNPs that originally made up the 74 MHs, 66 SNPs and 3 indels were identified in the two populations, and 45 of these variants were included in new definitions of the MHs, whereas 24 SNPs were considered rare and of little value for case work. The average effective number of alleles (A e ) was 3.2, 3.0, and 2.6 in Danes, West Greenlanders, and East Greenlanders, respectively. High levels of linkage disequilibrium were observed in East Greenlanders, which reflects the characteristics of this population that has a small size, and signs of admixture and substructure. Pairwise kinship simulations of full siblings, half-siblings, first cousins, and unrelated individuals were performed using allele frequencies from MHs, STRs and SNPs from Danish and Greenlandic populations. The MH panel outperformed the currently used STR and SNP marker sets and was able to differentiate siblings from unrelated individuals with a 0% false positive rate and a 1.1% false negative rate using an LR threshold of 10,000 in the Danish population. However, the panel was not able to differentiate half-siblings or first cousins from unrelated individuals. The results generated in this study will be used to implement MHs as investigative markers for relationship testing in our laboratory. |
format |
Article in Journal/Newspaper |
author |
Carmen Tomas Pedro Rodrigues Carina G. Jønck Zohal Barekzay Halimureti Simayijiang Vania Pereira Claus Børsting |
author_facet |
Carmen Tomas Pedro Rodrigues Carina G. Jønck Zohal Barekzay Halimureti Simayijiang Vania Pereira Claus Børsting |
author_sort |
Carmen Tomas |
title |
Performance of a 74-Microhaplotype Assay in Kinship Analyses |
title_short |
Performance of a 74-Microhaplotype Assay in Kinship Analyses |
title_full |
Performance of a 74-Microhaplotype Assay in Kinship Analyses |
title_fullStr |
Performance of a 74-Microhaplotype Assay in Kinship Analyses |
title_full_unstemmed |
Performance of a 74-Microhaplotype Assay in Kinship Analyses |
title_sort |
performance of a 74-microhaplotype assay in kinship analyses |
publisher |
MDPI AG |
publishDate |
2024 |
url |
https://doi.org/10.3390/genes15020224 https://doaj.org/article/8df42ee4fc804956a25e5ec8f085176a |
genre |
greenlander* greenlandic |
genre_facet |
greenlander* greenlandic |
op_source |
Genes, Vol 15, Iss 2, p 224 (2024) |
op_relation |
https://www.mdpi.com/2073-4425/15/2/224 https://doaj.org/toc/2073-4425 doi:10.3390/genes15020224 2073-4425 https://doaj.org/article/8df42ee4fc804956a25e5ec8f085176a |
op_doi |
https://doi.org/10.3390/genes15020224 |
container_title |
Genes |
container_volume |
15 |
container_issue |
2 |
container_start_page |
224 |
_version_ |
1810447830981017600 |