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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
Published on: May 6, 2010
Inter-chromosomal variation in the pattern of human population genetic structure
1Cincinnati Children's Hospital Medical Center, Division of Asthma Research, Department of Pediatrics, University of Cincinnati, OH 45229, USA. tesfaye.mersha@cchmc.org
Human Genomics
|June 30, 2011
Summary
This study identifies 126 stratified genomic regions in human populations using millions of genetic markers. These regions contain genes linked to pigmentation and immune responses, offering insights into human adaptation.
Area of Science:
- Human genetics
- Population genetics
- Genomics
Background:
- Advancements in genotyping technology enable large-scale analysis of human genetic variation.
- Understanding genetic variation at finer scales is crucial for genomic and geographic insights.
Purpose of the Study:
- To identify and characterize stratified genomic regions across global human populations.
- To link these regions to functional gene annotations and biological networks.
Main Methods:
- Utilized 3.7 million single nucleotide polymorphisms (SNPs) across HapMap populations.
- Employed five complementary methods: principal component (PC), cluster, discriminant, fixation index (FST), and network/pathway analyses.
- Conducted global and chromosomal level analyses to detect population structure.
Main Results:
- Identified 126 stratified genomic regions, with subtle population structures detected at the chromosomal level.
- Found genes associated with melanin production (OCA2, HERC2, EDAR, SLC45A2) and immune responses (IFNG, DAPK1) within these regions.
- Demonstrated the utility of complementary statistical and network analyses for dissecting human genetic variation.
Conclusions:
- The identified genomic regions and associated genes provide insights into human adaptation and phenotypic variations.
- The study presents a robust strategy for analyzing chromosome-based population structure and differentiation.
- Highlights the importance of integrating statistical and functional network analyses in human genetic studies.
Related Concept Videos
01:25What is Population Genetics?
A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, they pass down their genes to their offspring. Many of these genes are polymorphic, meaning that they occur in multiple variants. Such variations of a gene are referred to as alleles. The collective set of all the alleles within a population is known as the gene pool.
01:09Mutation, Gene Flow, and Genetic Drift
In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
01:25Genetic Variation
Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles, which...
Genes exist in different versions called alleles, which...
02:26Comparing 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%...
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%...
01:05Single 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,...
02:32Position-effect Variegation
In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.