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Polymorphism detection and sequence analysis of human T-cell receptor V alpha-chain-encoding gene segments
P Charmley1, D Nickerson, L Hood
1Virginia Mason Research Center, Seattle, WA 98101.
Immunogenetics
|January 1, 1994
Summary
Inherited variations in T-cell receptor variable (V) gene segments, specifically TCRAV, were identified. These genetic differences in antigen-binding regions may influence autoimmune susceptibility in human populations.
Area of Science:
- Immunogenetics
- Molecular immunology
- Human population genetics
Background:
- The T-cell receptor (TCR) mediates antigen recognition through its variable (V) regions, encoded by germline gene segments.
- Inherited variations (polymorphisms) in TCR V gene segments are hypothesized to impact immune responses, potentially contributing to autoimmunity.
- Investigating functional polymorphisms in germline TCR V alpha (TCRAV) gene segments is crucial for understanding immune variability.
Purpose of the Study:
- To identify potentially functional polymorphisms within the germline TCRAV gene segments.
- To analyze the impact of these polymorphisms on amino acid sequences within the TCR alpha chain's antigen-binding regions.
- To assess the frequency and distribution of these polymorphisms and their haplotypes in human populations.
Main Methods:
- Polymerase chain reaction (PCR) amplification of germline TCRAV gene segments using pooled DNA from multiple individuals.
- Denaturing gradient gel electrophoresis (DGGE) to detect polymorphisms in PCR products.
- Complete DNA sequencing of identified polymorphic PCR products.
- Genotype analysis to determine minor allele frequencies and haplotype combinations.
Main Results:
- Polymorphisms were identified in TCRAV2S1, AV4S1, AV7S1, and AV8S1 gene segments.
- Sequencing revealed polymorphisms affecting amino acids in predicted antigen-binding sites of the TCR alpha chain, as well as intronic variations.
- Minor allele frequencies ranged from 5% to 50% (average 35%), with frequent homozygous genotypes for alternate alleles.
- All combinations of amino acid-altering polymorphisms were observed, indicating extensive germline haplotype diversity.
Conclusions:
- Germline TCRAV coding region polymorphisms have been identified in human populations.
- These polymorphisms alter predicted antigen-binding regions and exhibit significant allele and haplotype frequencies.
- The identified TCRAV polymorphisms provide a basis for investigating their role in autoimmune susceptibility and differential immune responsiveness.