Related Experiment Video
Updated: Sep 23, 2025
22:27
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
Published on: May 6, 2010
409.8K
Characterizing Fractal Genetic Variation in the Human Genome from the Hapmap Project
Alessandro Borri1,2, Antonio Cerasa3,4,5, Paolo Tonin4
1CNR-IASI Biomathematics Laboratory, (BioMatLab), Rome, Italy.
International Journal of Neural Systems
|May 17, 2022
Summary
Higuchi's fractal dimension (HFD) effectively characterizes human genome variations and population differences. This method surpasses box-counting dimension (BCD) in accurately classifying global populations based on genetic data.
Area of Science:
- Genomics
- Computational Biology
- Bioinformatics
Background:
- Next-generation sequencing has revolutionized gene discovery and human genome mapping.
- Single nucleotide polymorphisms (SNPs) reveal individual genetic heterogeneity.
- Fractal dimension (FD) quantifies the complexity of self-similar natural phenomena.
Purpose of the Study:
- To compare two FD algorithms, Higuchi's fractal dimension (HFD) and box-counting dimension (BCD).
- To characterize genome-wide SNP patterns and assess their utility in population genetics.
- To evaluate the correlation between genetic and geographical distances among global populations.
Main Methods:
- Utilized HapMap data from 1184 individuals across eleven populations.
- Applied HFD and BCD algorithms to analyze genome-wide SNP data.
- Employed cluster and classification analyses to compare population groupings based on FD.
Main Results:
- HFD demonstrated superior performance over BCD in clustering and classification analyses.
- HFD achieved higher accuracy (79.0%) compared to BCD (69.1%) in population classification.
- HFD showed a high cophenetic correlation coefficient (0.981), indicating accurate clustering.
Conclusions:
- HFD is a reliable and effective measure for representing individual genetic variations across chromosomes.
- HFD analysis aids in categorizing individuals and global populations based on genomic patterns.
- The findings support the application of HFD in population genetics and understanding human diversity.
Related Concept Videos
01:25Genetic Variation
410
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,...
Genes exist in different versions called alleles,...
410
02:54Evolutionary Relationships through Genome Comparisons
6.2K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.2K
01:09Mutation, Gene Flow, and Genetic Drift
59.6K
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).
59.6K
01:11Genome-wide Association Studies-GWAS
14.5K
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...
GWAS does not require the identification of the target gene involved in...
14.5K
02:26Comparing Copy Number Variations and SNPs
18.0K
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%...
18.0K
01:05Single Nucleotide Polymorphisms-SNPs
16.1K
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,...
16.1K