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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...
Frequency-dependent Selection01:21

Frequency-dependent Selection

When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to as frequency-dependent selection. Frequency-dependent selection may occur between species or within a single species. This type of selection can either be positive—with more common phenotypes having higher fitness—or negative, with rarer phenotypes conferring increased fitness.
Incomplete Dominance01:43

Incomplete Dominance

Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.
Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Pedigree Analysis01:35

Pedigree Analysis

Overview
Hardy-Weinberg Principle01:49

Hardy-Weinberg Principle

Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.

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Related Experiment Video

Updated: May 20, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

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

Published on: June 21, 2018

Using identity by descent estimation with dense genotype data to detect positive selection.

Lide Han1, Mark Abney

  • 1Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

European Journal of Human Genetics : EJHG
|July 12, 2012
PubMed
Summary

We developed GIBDLD, a novel method to detect genetic selection by estimating identical by descent (IBD) sharing. This tool accurately identifies selection signals in populations like the Maasai, even with complex genetic factors.

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Last Updated: May 20, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

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

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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

Published on: August 21, 2016

Area of Science:

  • Population Genetics
  • Genomic Analysis
  • Statistical Genetics

Background:

  • Identical by descent (IBD) segments are crucial for understanding population genetics, including relatedness, disease mapping, and selection.
  • Existing methods for IBD detection often require data thinning due to linkage disequilibrium (LD) and may not fully account for inbreeding or multiple allele sharing.

Purpose of the Study:

  • To introduce and validate a novel statistical method, GIBDLD, for probabilistic estimation of IBD sharing.
  • To identify genomic regions under recent selection in the Maasai population from Kinyawa, Kenya (MKK) using the GIBDLD method.
  • To highlight the advantages of GIBDLD in handling complex genetic scenarios like inbreeding and LD without data thinning.

Main Methods:

  • Development of GIBDLD, a novel statistical method for estimating pairwise IBD sharing probabilities across all genotyped SNPs.
  • Application of GIBDLD to the Maasai from Kinyawa, Kenya (MKK) dataset to identify regions with excess IBD sharing in unrelated pairs.
  • Probabilistic estimation of all nine possible IBD sharing states between individuals, accounting for consanguinity and LD.

Main Results:

  • Identification of known selected loci (LCT, HLA) and numerous novel loci exhibiting excess IBD sharing in the MKK population.
  • Observation that highly selected loci (excluding HLA) show a significant proportion of unrelated pairs sharing all four alleles IBD.
  • Demonstration of GIBDLD's ability to accurately estimate IBD without SNP thinning and to model LD and inbreeding.

Conclusions:

  • GIBDLD offers a robust and accurate approach for estimating IBD sharing and detecting selection in diverse human populations.
  • The method's capacity to handle complex genetic factors like inbreeding and LD makes it a valuable tool for genetic studies.
  • This research advances the understanding of recent positive selection in the Maasai population and provides a powerful new method for genomic analysis.