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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Published on: June 23, 2012

SNP uniqueness problem: a proof-of-principle in HapMap SNPs.

Shany Doron¹, Dorit Shweiki

¹Bioinformatics Program, School of Computer Science, The Academic College of Tel Aviv-Yaffo, Tel Aviv, Israel.

|March 18, 2011

Summary

Nonunique single nucleotide polymorphisms (SNPs) in the HapMap dataset can lead to inaccurate clinical conclusions. This study reveals significant rates of nonunique SNPs, questioning the validity of some genetic association analyses.

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Area of Science:

Genomics
Bioinformatics
Medical Genetics

Background:

Single nucleotide polymorphisms (SNPs) are crucial for biomedical and clinical research.
The presence of nonunique or false-positive SNPs in datasets can bias research findings and lead to inaccurate conclusions.
The HapMap dataset is a widely used resource for SNP information.

Purpose of the Study:

To computationally assess the extent of nonunique and false-positive SNPs within the HapMap dataset.
To evaluate the impact of nonunique SNPs on clinical association studies and genotyping arrays.

Main Methods:

Utilized BLAT analysis with two sets of SNP flanking sequences against the human genome.
Assessed the representation of identified nonunique SNPs in commercial genotyping arrays and clinical association databases.

Main Results:

4.2% and 11.9% of HapMap SNPs showed nonunique alignment to the human genome (long and short sequences, respectively).
An average of 7.9% of nonunique SNPs were found in common commercial genotyping arrays.
Identified nonunique SNPs are present in clinical association databases, indicating potential inaccuracies.

Conclusions:

A significant proportion of SNPs in the HapMap dataset are nonunique, potentially compromising the accuracy of genetic research.
The findings raise concerns about the validity of certain disease-related genotyping analyses due to SNP annotation errors.