Dataset Information

Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes.

ABSTRACT:

Background

The analysis of human Y-chromosome variation in the context of population genetics and forensics requires the genotyping of dozens to hundreds of selected single-nucleotide polymorphisms (SNPs). In the present study, we developed a 121-plex (121 SNPs in a single array) TaqMan array capable of distinguishing most haplogroups and subhaplogroups on the Y-chromosome human phylogeny in Europe.

Results

We present data from 264 samples from several European areas and ethnic groups. The array developed in this study shows >99% accuracy of assignation to the Y human phylogeny (with an average call rate of genotypes >96%).

Conclusions

We have created and evaluated a robust and accurate Y-chromosome multiplex which minimises the possible errors due to mixup when typing the same sample in several independent reactions.

SUBMITTER: Martinez-Cruz B

PROVIDER: S-EPMC3130649 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature

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Publications

Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes.

Martínez-Cruz Begoña B Ziegle Janet J Sanz Paula P Sotelo Graciela G Anglada Roger R Plaza Stéphanie S Comas David D

Investigative genetics 20110531

<h4>Background</h4>The analysis of human Y-chromosome variation in the context of population genetics and forensics requires the genotyping of dozens to hundreds of selected single-nucleotide polymorphisms (SNPs). In the present study, we developed a 121-plex (121 SNPs in a single array) TaqMan array capable of distinguishing most haplogroups and subhaplogroups on the Y-chromosome human phylogeny in Europe.<h4>Results</h4>We present data from 264 samples from several European areas and ethnic gr ...[more]

PMID: 21627798

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Project description:Summary In this work, we developed a simple and robust assay to rapidly detect SNPs in nucleic acid samples. Our approach combines loop-mediated isothermal amplification (LAMP)-based target amplification with fluorescent probes to detect SNPs with high specificity. A competitive “sink” strand preferentially binds to non-SNP amplicons and shifts the free energy landscape to favor specific activation by SNP products. We demonstrated the broad utility and reliability of our SNP-LAMP method by detecting three distinct SNPs across the human genome. We also designed an assay to rapidly detect highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants from crude biological samples. This work demonstrates that competitive SNP-LAMP is a powerful and universal method that could be applied in point-of-care settings to detect any target SNP with high specificity and sensitivity. We additionally developed a publicly available web application for researchers to design SNP-LAMP probes for any target sequence of interest. Graphical abstract Highlights • A simple and rapid assay to detect specific SNPs in complex nucleic acid samples• Approach leverages competitive probes to specifically detect SNP over non-SNP sequences• Demonstrated utility across diverse targets and sample types• Web application for researchers to design SNP-LAMP probes for any target of interest Motivation Single-nucleotide polymorphisms (SNPs) are the most common source of genetic variation between individuals and have implications in human disease, pathogen drug resistance, and agriculture. SNPs are often detected using DNA sequencing or PCR, both of which can be difficult to deploy for on-site testing or in low-resource settings. There is a need for new SNP detection methods that can be performed rapidly without advanced laboratory equipment or a cold supply chain. Detecting single-nucleotide polymorphisms (SNPs) is important for understanding human disease, the emergence of pathogen variants, and the application of genetic agricultural breeding programs. Hyman et al. develop a simple and rapid assay to detect SNPs in complex nucleic acid samples. A web-based tool allows researchers to design custom SNP probes.

Project description:BACKGROUND: Efficient screening of bacterial artificial chromosome (BAC) libraries with polymerase chain reaction (PCR)-based markers is feasible provided that a multidimensional pooling strategy is implemented. Single nucleotide polymorphisms (SNPs) can be screened in multiplexed format, therefore this marker type lends itself particularly well for medium- to high-throughput applications. Combining the power of multiplex-PCR assays with a multidimensional pooling system may prove to be especially challenging in a polyploid genome. In polyploid genomes two classes of SNPs need to be distinguished, polymorphisms between accessions (intragenomic SNPs) and those differentiating between homoeologous genomes (intergenomic SNPs). We have assessed whether the highly parallel Illumina GoldenGate Genotyping Assay is suitable for the screening of a BAC library of the polyploid Brassica napus genome. RESULTS: A multidimensional screening platform was developed for a Brassica napus BAC library which is composed of almost 83,000 clones. Intragenomic and intergenomic SNPs were included in Illumina's GoldenGate Genotyping Assay and both SNP classes were used successfully for screening of the multidimensional BAC pools of the Brassica napus library. An optimized scoring method is proposed which is especially valuable for SNP calling of intergenomic SNPs. Validation of the genotyping results by independent methods revealed a success of approximately 80% for the multiplex PCR-based screening regardless of whether intra- or intergenomic SNPs were evaluated. CONCLUSIONS: Illumina's GoldenGate Genotyping Assay can be efficiently used for screening of multidimensional Brassica napus BAC pools. SNP calling was specifically tailored for the evaluation of BAC pool screening data. The developed scoring method can be implemented independently of plant reference samples. It is demonstrated that intergenomic SNPs represent a powerful tool for BAC library screening of a polyploid genome.

Dataset Information

Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes.

Background

Results

Conclusions

Publications

Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes.

Similar Datasets

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