Assessment of SNP-SNP interactions by using square contingency table analysis

Özge KaradaĞ1, GÖkÇen Altun2, Serpil AktaŞ1

  • 1Hacettepe University, Department of Statistics, 06800, Beytepe, Ankara, Turkey.

Summary

Investigating single nucleotide polymorphism (SNP) interactions is crucial for understanding complex traits. This study applies symmetry models to analyze SNP-SNP interactions for blood pressure, moving beyond single-SNP associations.

Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

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,...
17.5K
Contingency Table01:29

Contingency Table

A contingency table provides a way of portraying data that can facilitate calculating probabilities. It is a method of displaying a frequency distribution as a table with rows and columns to show how two variables may be dependent (contingent) upon each other; The table helps determine conditional probabilities quite quickly and can help systematically organize, analyze and quantify data. The table displays sample values concerning two variables that may be dependent or contingent on one...
3.5K
Introduction to Test of Independence01:21

Introduction to Test of Independence

In statistics, the term independence means that one can directly obtain the probability of any event involving both variables by multiplying their individual probabilities. Tests of independence are chi-square tests involving the use of a contingency table of observed (data) values.
The test statistic for a test of independence is similar to that of a goodness-of-fit test:
2.8K
McNemar's Test01:23

McNemar's Test

McNemar's Test is a nonparametric statistical test used to determine if there is a significant difference in proportions between two related groups when the outcome is binary (e.g., yes/no, success/failure). It is beneficial when we have paired data, such as pre-test/post-test designs, where the same subjects are measured under two different conditions. The test is named after the statistician Quinn McNemar, who introduced it in 1947. It is commonly used in situations where subjects are...
632
Genome-wide Association Studies-GWAS01:11

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...
15.0K
Comparing Copy Number Variations and SNPs02:26

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%...
18.4K