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Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

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,...

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

Epistasis Analysis

Epistasis Analysis

Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...

Chi-square Analysis

Chi-square Analysis

The chi-square test is a statistical hypothesis test. It is used to check whether there is a significant difference between an expected value and an observed value. In the context of genetics, it enables us to either accept or reject a hypothesis, based on how much the observed values deviate from the expected values.
The chi-square test was developed by Pearson in 1990.
The first step of performing a Chi-square analysis is to establish a null hypothesis, which assumes that there is no real...

Polygenic Traits

Polygenic Traits

When more than one gene is responsible for a given phenotype, the trait is considered polygenic. Human height is a polygenic trait. Studies have uncovered hundreds of loci that influence height, and there are believed to be many more. Due to the high number of genes involved, as well as environmental and nutritional factors, height varies significantly within a given population. The distribution of height forms a bell-shaped curve, with relatively few individuals in the population at the...

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Updated: May 20, 2026

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

A confidence set inference method for identifying SNPs that regulate quantitative phenotypes.

Charalampos Papachristou¹, Shili Lin

¹Department of Mathematics, Physics, and Statistics, University of the Sciences, Philadelphia, PA 19104, USA. c.papach@usciences.edu

|July 11, 2012

Summary

This summary is machine-generated.

We developed a new family-based confidence set inference (CSI) method for genome-wide association studies. This method identifies single nucleotide polymorphisms (SNPs) contributing to quantitative trait genetic variance and outperforms existing methods.

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

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Published on: June 21, 2018

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Infinium Assay for Large-scale SNP Genotyping Applications

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Published on: November 19, 2013

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Area of Science:

Genetics
Statistical Genetics
Bioinformatics

Background:

Genome-wide association studies (GWAS) aim to identify genetic variants influencing complex traits.
Accurate identification of causal single nucleotide polymorphisms (SNPs) is crucial for understanding trait heritability.
Current methods may lack the precision needed for efficient preliminary GWAS analysis.

Purpose of the Study:

Introduce a novel family-based confidence set inference (CSI) method.
Enable the identification of SNPs contributing to the additive genetic variance of quantitative traits.
Provide a tool for preliminary GWAS to narrow down candidate SNPs.

Main Methods:

Developed a CSI method within the generalized linear mixed model framework.
Utilized data from outbred families of varying sizes and structures.
Compared CSI performance against the Chen and Abecasis family association method using simulations and real data.

Main Results:

Simulation studies confirmed that CSI provides confidence sets with correct coverage.
CSI demonstrated superior performance compared to the Chen and Abecasis method in simulations.
Analysis of Framingham Heart Study data identified five candidate SNPs for high-density lipoprotein levels.

Conclusions:

The CSI method offers a competitive alternative to existing family association methods for GWAS.
CSI effectively reduces the number of SNPs requiring further investigation in GWAS.
This approach enhances the efficiency of genetic studies for quantitative traits.