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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,...
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...
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%...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scaleĀ  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
Multiple Allele Traits01:49

Multiple Allele Traits

The Concept of Multiple Allelism

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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

Defining multiple common "completely" conserved major histocompatibility complex SNP haplotypes.

Erin E Baschal1, Theresa A Aly, Jean M Jasinski

  • 1Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Building M20, Aurora, CO 80045-6511, USA.

Clinical Immunology (Orlando, Fla.)
|May 12, 2009
PubMed
Summary
This summary is machine-generated.

Researchers analyzed human leukocyte antigen (HLA) data and single nucleotide polymorphism (SNP) genotypes in families. They found conserved chromosome regions within the major histocompatibility complex (MHC), impacting type 1 diabetes and transplantation.

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

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Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Area of Science:

  • Genetics
  • Immunogenetics
  • Population Genetics

Background:

  • The Major Histocompatibility Complex (MHC) is crucial for immune response and is highly polymorphic.
  • Understanding chromosomal conservation within the MHC is vital for studying diseases like type 1 diabetes and for transplantation compatibility.
  • Previous studies have focused on specific alleles, but the extent of conserved megabase regions across unrelated individuals within the MHC is less understood.

Purpose of the Study:

  • To analyze the occurrence and extent of megabase contiguous identity for founder chromosomes from unrelated individuals within the MHC.
  • To investigate whether this conserved identity is specific to the MHC or a more general phenomenon facilitated by HLA allele binning.

Main Methods:

  • Utilized HLA data and genotypes for thousands of single nucleotide polymorphisms (SNPs) from 1240 complete families of the Type 1 Diabetes Genetics Consortium.
  • Analyzed conserved megabase regions of SNP identity within HLA-defined haplotype groups.
  • Compared the frequency of conserved regions within the MHC to potential general phenomena.

Main Results:

  • Identified 82 HLA-defined haplotype groups within the MHC.
  • Observed readily apparent megabase regions of SNP identity within these haplotype groups.
  • Found that conserved chromosomes within these 82 haplotype groups comprise approximately one third of the founder chromosomes.

Conclusions:

  • Frequent conservation of megabase contiguous regions exists within the MHC among unrelated individuals, defined by HLA alleles.
  • This conserved identity within the MHC has implications for type 1 diabetes susceptibility.
  • The findings may also impact transplantation outcomes between unrelated individuals.