First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA

@article{Bouakaze2007FirstSA,
  title={First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA},
  author={C. Bouakaze and C. Keyser and S. Amory and E. Crub{\'e}zy and B. Ludes},
  journal={International Journal of Legal Medicine},
  year={2007},
  volume={121},
  pages={493-499}
}
In the present study, a set of 13 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) selected for the identification of the most frequent Asian Y-haplogroups was included in an allele-specific primer extension assay. [...] Key Method Single nucleotide polymorphism (SNP) genotyping was accomplished by co-amplification of these 13 DNA fragments within 2 multiplex PCRs followed by detection with 1 minisequencing reaction using the SNaPshot™ Multiplex kit and analysis of extension products by capillary…Expand
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TLDR
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TLDR
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References

SHOWING 1-10 OF 44 REFERENCES
Multiplex PCR development of Y-chromosomal biallelic polymorphisms for forensic application.
TLDR
A first multiplex with 7 SNPs (M35, M89, M9, M170, M172, M45, M173), which occur in the basal branches of the phylogenetic tree and are able to assign a subject to known most frequent European haplogroups, was designed. Expand
Typing of Y chromosome SNPs with multiplex PCR methods.
We describe a method for the simultaneous typing of Y-chromosome single nucleotide polymorphism (SNP) markers by means of multiplex polymerase chain reaction (PCR) strategies that allow the detectionExpand
Multiplex PCR and minisequencing of SNPs--a model with 35 Y chromosome SNPs.
TLDR
A robust single nucleotide polymorphism (SNPs) typing assay with co-amplification of 25 DNA-fragments and the detection of 35 human Y chromosome SNPs is developed and female DNA did not influence the results of Y chromosome SNP typing when added in concentrations more than 300 times the concentrations of male DNA. Expand
Hierarchical analysis of 30 Y-chromosome SNPs in European populations
TLDR
The selected method for allele discrimination was a single base extension reaction using the SNaPshot multiplex kit and no significant differences were detected among the different districts, except for the population from Mariña Lucense, which showed a distant haplogroup frequency but not higher Φst values. Expand
A multiplex assay with 52 single nucleotide polymorphisms for human identification
TLDR
A highly sensitive and reproducible SNP‐typing method is established with amplification of all 52 DNA fragments in one PCR reaction followed by detection of the SNPs with two single base extension reactions analysed using CE. Expand
Y-SNP typing of U.S. African American and Caucasian samples using allele-specific hybridization and primer extension.
TLDR
This paper examined 50 different SNPs on the Y-chromosome using three primer extension multiplexes and five hybridization multiplex assays and found that for certain loci, the allele-specific hybridization method exhibited sizable background signal from the absent alternate allele. Expand
Introduction of an single nucleodite polymorphism‐based “Major Y‐chromosome haplogroup typing kit” suitable for predicting the geographical origin of male lineages
TLDR
The approach takes advantage of the specific geographic distribution of the Y‐chromosome haplogroups and demonstrates the utility of binary polymorphisms to infer the origin of a male lineage. Expand
Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups
TLDR
This work presents a selection of 16 SNPs from the coding region of the human mitochondrial DNA, used for the assignment of individuals to one of the nine major European Caucasian mitochondrial haplogroups. Expand
Development of multiplex PCRs for evolutionary and forensic applications of 37 human Y chromosome SNPs.
TLDR
The sequential application of these multiplexes is a robust and effective resource for typing the most frequent European Y-SNP haplogroups, and appears to be suitable for forensic purposes and evolutionary studies. Expand
A new method for ABO genotyping using a multiplex single-base primer extension reaction and its application to forensic casework samples.
TLDR
A new method using a multiplex single-base primer extension reaction that enables the sensitive, simultaneous detection of six SNP sites in the ABO gene by two specific reactions holds promise as an effective method of ABO genotyping particularly for forensic samples. Expand
...
1
2
3
4
5
...