Development and validation of a custom panel including 183 Y-SNPs for Chinese Y-chromosomal haplogroups dissection using a MALDI-TOF MS system.
Asian People
/ genetics
China
Chromosomes, Human, Y
/ genetics
DNA
/ analysis
Forensic Genetics
/ methods
Genetics, Population
Haplotypes
/ genetics
Humans
Male
Polymerase Chain Reaction
Polymorphism, Single Nucleotide
/ genetics
Reproducibility of Results
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
/ methods
Forensic genetics
MALDI-TOF MS
Y haplogroup
Y-SNPs
Journal
Electrophoresis
ISSN: 1522-2683
Titre abrégé: Electrophoresis
Pays: Germany
ID NLM: 8204476
Informations de publication
Date de publication:
12 2020
12 2020
Historique:
received:
01
06
2020
revised:
21
08
2020
accepted:
25
08
2020
pubmed:
28
8
2020
medline:
2
4
2021
entrez:
28
8
2020
Statut:
ppublish
Résumé
Y-chromosome SNP haplogroups exhibit geographic structuring in many populations around the world. Therefore, Y-chromosome haplogroups have been widely used to infer paternal biogeographical ancestry and high-resolution paternal lineage classification. In the present study, we designed a customized panel containing 183 Y-SNPs based on previous studies and evaluated the genotyping performance and repeatability, concordance, sensitivity, and ability of analysing case-type samples using a MALDI-TOF MS platform. The average call rate for duplicate typing of any one SNP in the panel was 97.0%. In the concordance and accuracy study, the results of haplogroup designation obtained from MALDI-TOF MS platform were fully consistent with those obtained from the next-generation sequencing (NGS) platform. The optimal amount of template DNA in the PCR seemed to be 10 ng. However, if less DNA (≥156.25 pg) was available, it was still possible to obtain meaningful haplogroup information. For the application part, this panel could be applied for the detection of blood, semen, and buccal swabs samples. Particularly, blood stain on FTA card samples could be dissected by direct PCR amplification on the MALDI-TOF MS platform. Besides, 371 unrelated male individuals from four Chinese ethnic groups (Han, Hui, Mongolian, and Kazak) were detected using this panel. Total 78 terminal haplogroups were found and the haplogroup diversity was 0.933576. The results demonstrate that this panel could be an accurate, fast, and cost-effective method for database construction where the amount of sample material is less of a concern and when the cost of the assay is taken into consideration.
Identifiants
pubmed: 32854146
doi: 10.1002/elps.202000145
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2047-2054Subventions
Organisme : National Natural Science Foundation of Chin
Pays : International
Organisme : National Key R&D Program of China
ID : 2016YFC0800703
Pays : International
Organisme : Ministry of Finance of China
ID : GY2020D-2
Pays : International
Organisme : Shanghai Science and Technology Innovation Fund
ID : 17DZ2273200
Pays : International
Organisme : Shanghai Science and Technology Innovation Fund
ID : 19DZ2292700
Pays : International
Informations de copyright
© 2020 Wiley-VCH GmbH.
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