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Related Concept Videos

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...
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,...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
What is Population Genetics?01:25

What 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.While some alleles of a given gene might be observed commonly, other variants...
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.
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Human Genetics01:28

Human Genetics

Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
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Related Experiment Video

Updated: Jun 25, 2026

Application of DNA Fingerprinting using the D1S80 Locus in Lab Classes
08:35

Application of DNA Fingerprinting using the D1S80 Locus in Lab Classes

Published on: July 17, 2021

Methods for human demographic inference using haplotype patterns from genomewide single-nucleotide polymorphism data.

Kirk E Lohmueller1, Carlos D Bustamante, Andrew G Clark

  • 1Department of Biostatistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA. kel38@cornell.edu

Genetics
|March 4, 2009
PubMed
Summary
This summary is machine-generated.

We developed a new method using haplotype counts and frequencies to analyze human genome data. This approach helps infer population history, revealing a significant European population size reduction.

Related Experiment Videos

Last Updated: Jun 25, 2026

Application of DNA Fingerprinting using the D1S80 Locus in Lab Classes
08:35

Application of DNA Fingerprinting using the D1S80 Locus in Lab Classes

Published on: July 17, 2021

Area of Science:

  • Population Genetics
  • Genomics
  • Statistical Genetics

Background:

  • Human demographic history is complex and challenging to infer from genomic data.
  • Existing methods often rely on single-nucleotide polymorphism (SNP) frequencies, which may not capture all relevant demographic signals.
  • Accurate demographic modeling is crucial for understanding human evolution and migration patterns.

Purpose of the Study:

  • To introduce a novel approximate-likelihood method for fitting demographic models to human genomewide SNP data.
  • To develop a new statistic, the Haplotype Count and frequency (HCN) statistic, for improved demographic inference.
  • To assess the robustness and applicability of the HCN statistic to real-world genomic datasets.

Main Methods:

  • Genome division into windows of constant genetic map width.
  • Tabulation of distinct haplotype counts and most frequent haplotype frequencies within windows.
  • Summarization of data via the genomewide joint distribution of these statistics (HCN statistic).
  • Utilizing coalescent simulations to generate expected HCN statistics for various demographic parameters.

Main Results:

  • The HCN statistic effectively disentangles complex demographic histories beyond single-SNP frequency-based statistics.
  • The method reliably infers parameters from simulated growth and bottleneck models, even with recombination hotspots.
  • Modifications enhance robustness against genetic map errors, haplotype phase uncertainty, and SNP ascertainment bias.

Conclusions:

  • The novel HCN statistic offers a powerful tool for inferring human demographic history from genomewide SNP data.
  • The method is robust to common practical issues encountered in genomic data analysis.
  • Application to Perlegen Sciences data suggests a severe population size reduction in northwestern Europe between 32,500-47,500 years ago.