Terms commonly used in HLA immunogenetics and disease mapping
| Term . | Definition . |
|---|---|
| Association mapping | A method for linking clinical characteristics to genetic traits. |
| Block | The physical region of DNA encoding 2 or more SNPs or genes in strong positive LD with one another, such that any one polymorphism is a marker for all of the others in that region. |
| Candidate gene | A gene that has been identified through discovery methods, but not yet validated. |
| Deep sequencing | Sequencing approaches that incorporate multifold coverage of nucleotide positions. |
| Direct sequencing | PCR-based sequencing approaches that use the target DNA strand for amplification and sequencing. |
| Discovery-validation study design | The use of 2 independent cohorts, where one cohort is used to “discover” new trait-associated markers (“candidate” SNPs or genes), and the second cohort is used to “validate” the candidates. |
| Expression quantitative locus | A genetic locus that regulates the level of expression of mRNAs and proteins. |
| Fine mapping | Approaches that use dense SNPs or sequencing to narrow down the region(s) that most likely harbor the causative gene(s). |
| GWAS | The examination of variants across the human genome for association to specific traits or diseases. |
| Genotype | An individual’s DNA sequence (gene, allele, SNP) to be distinguished from phenotype, the trait of the expressed protein, or a clinical characteristic. |
| Haplotype | Markers that travel together on the same chromosome 6 strand (example: HLA-A1-B8-DR3). |
| Heterozygous | Two different HLA alleles/antigens at the HLA locus (example: HLA-A1,2). |
| HLA | HU-1 (human-1 antigen) and LA (leukocyte antigen), antigens that govern tissue type and histocompatibility. |
| HLA class I | The telomeric (further from the centromere) region of the MHC encoding HLA genes. The class I region contains HLA-A, HLA-B, and HLA-C (“classical class I genes”) and HLA-E, F, G; MICA, MICB (“non-classical class I”). |
| HLA class II | The centromeric (closer to the centromere) region of the MHC encoding HLA genes. The class II region contains HLA-DR, HLA-DQ, and HLA-DP. |
| HLA class III | The region of the MHC mapping between class I HLA-B and class II HLA-DR. The class III region contains TNF and the complement pathway genes. |
| Homozygous | Two copies of the same polymorphism or allele (example: SNP genotype AA, TT, CC, or GG; HLA genotype HLA-A*02:01,02:01) |
| Imputation (of SNPs) | Methods that use LD to infer SNPs that have not been directly genotyped. |
| LD | The nonrandom association of alleles or antigens (example: HLA-B8 with HLA-DR3). |
| MHC | A 7.6-Mb region of chromosome 6p21.3 that encodes the histocompatibility genes important in transplantation. |
| Phenotype | A trait. Phenotype can refer to the expressed protein (HLA-A2) or to a clinical characteristic. |
| Proxy | A genetic marker that can be used in lieu of another marker, usually in high LD |
| SNP | The simplest form of human genetic variation. An SNP is a biallelic nucleotide change (example: A vs C). |
| TaqMan | A real-time 5′ nuclease method for genotyping biallelic SNPs. |
| TagSNP | A SNP that is in 100% LD with another SNP(s) so that they serve as proxies for one another. |
| Term . | Definition . |
|---|---|
| Association mapping | A method for linking clinical characteristics to genetic traits. |
| Block | The physical region of DNA encoding 2 or more SNPs or genes in strong positive LD with one another, such that any one polymorphism is a marker for all of the others in that region. |
| Candidate gene | A gene that has been identified through discovery methods, but not yet validated. |
| Deep sequencing | Sequencing approaches that incorporate multifold coverage of nucleotide positions. |
| Direct sequencing | PCR-based sequencing approaches that use the target DNA strand for amplification and sequencing. |
| Discovery-validation study design | The use of 2 independent cohorts, where one cohort is used to “discover” new trait-associated markers (“candidate” SNPs or genes), and the second cohort is used to “validate” the candidates. |
| Expression quantitative locus | A genetic locus that regulates the level of expression of mRNAs and proteins. |
| Fine mapping | Approaches that use dense SNPs or sequencing to narrow down the region(s) that most likely harbor the causative gene(s). |
| GWAS | The examination of variants across the human genome for association to specific traits or diseases. |
| Genotype | An individual’s DNA sequence (gene, allele, SNP) to be distinguished from phenotype, the trait of the expressed protein, or a clinical characteristic. |
| Haplotype | Markers that travel together on the same chromosome 6 strand (example: HLA-A1-B8-DR3). |
| Heterozygous | Two different HLA alleles/antigens at the HLA locus (example: HLA-A1,2). |
| HLA | HU-1 (human-1 antigen) and LA (leukocyte antigen), antigens that govern tissue type and histocompatibility. |
| HLA class I | The telomeric (further from the centromere) region of the MHC encoding HLA genes. The class I region contains HLA-A, HLA-B, and HLA-C (“classical class I genes”) and HLA-E, F, G; MICA, MICB (“non-classical class I”). |
| HLA class II | The centromeric (closer to the centromere) region of the MHC encoding HLA genes. The class II region contains HLA-DR, HLA-DQ, and HLA-DP. |
| HLA class III | The region of the MHC mapping between class I HLA-B and class II HLA-DR. The class III region contains TNF and the complement pathway genes. |
| Homozygous | Two copies of the same polymorphism or allele (example: SNP genotype AA, TT, CC, or GG; HLA genotype HLA-A*02:01,02:01) |
| Imputation (of SNPs) | Methods that use LD to infer SNPs that have not been directly genotyped. |
| LD | The nonrandom association of alleles or antigens (example: HLA-B8 with HLA-DR3). |
| MHC | A 7.6-Mb region of chromosome 6p21.3 that encodes the histocompatibility genes important in transplantation. |
| Phenotype | A trait. Phenotype can refer to the expressed protein (HLA-A2) or to a clinical characteristic. |
| Proxy | A genetic marker that can be used in lieu of another marker, usually in high LD |
| SNP | The simplest form of human genetic variation. An SNP is a biallelic nucleotide change (example: A vs C). |
| TaqMan | A real-time 5′ nuclease method for genotyping biallelic SNPs. |
| TagSNP | A SNP that is in 100% LD with another SNP(s) so that they serve as proxies for one another. |