Standard Methods for the Management of Immunogenetic Data

Abstract

In this chapter, we outline some basic principles for the consistent management of immunogenetic data. These include the preparation of a single master data file that can serve as the basis for all subsequent analyses, a focus on the quality and homogeneity of the data to be analyzed, the documentation of the coding systems used to represent the data, and the application of nomenclature standards specific for each immunogenetic system being evaluated. The data management principles discussed here are intended to provide a foundation for the data analysis methods detailed in Chaps. 13 and 14. The relationship between the data management and analysis methods covered in these three chapters is illustrated in Fig. 3.

The application of these data management principles is a first step toward consistent and reproducible data analyses. While it may take extra time and effort to apply them, we feel that it is better to take this approach than to assume that low data quality can be compensated for by large sample sizes.

In addition to their relevance for analytical reproducibility, it is important to consider these data management principles from an ethical perspective. The reliability of the data collected and generated as part of a research study should be as important a component of the ethical review of a research application as the security of those data. Finally, in addition to ensuring the integrity of the data from collection to publication, the application of these data management principles will provide a means to foster research integrity and to improve the potential for collaborative data sharing.

Glossary

Genetic data

1.Allele: Any of the alternative forms (sets of forms) of DNA sequence at locus. These variants may occur for genes and/or genetic markers.

Example: B, HLA-DRB1*01:01:01, HLA-A*01, D6S1666 (184).

2.Diplotype: The pair of haplotypes within a given genotype. The chromosomal phase between alleles is always known.

Example: HLA (A*01 B*08 DR*17, A*26 B*27 DR*17).

HLA (A*01 B*27 DR*17, A*26 B*08 DR*17).

When analyzing data for more than one locus, diplotypic data must be distinguished from genotypic data. Because the alleles at different loci in a given genotype can be combined to make many possible haplotype pairs, a genotype must be considered to correspond to multiple diplotypes. Unfortunately, the term “genotype” is sometimes used to refer to a given pair of haplotypes, especially when familial segregation has been studied.

3.Gene: The functional and physical unit of heredity. A gene consists of a DNA segment with a specific sequence. It includes information for the synthesis of mRNA molecules that direct the synthesis of proteins.

Example: ABO Glycosyltransferase gene, HLA-DRB1 gene, KIR-2DS3/S5 gene.

4.Genotype: The genetic makeup at one or more loci of an individual. It refers to a set of alleles carried by an individual (regardless of the expression of those alleles). The chromosomal phase (chromosomal identity of alleles at different loci) between alleles may not be known.

Example: HLA-A (1, 2); HLA-B (8, 44); HLA-DRB1 (03, 04).

KIR: KIR (A, A).

Microsatellites: D6S273 (134, 136) D6S273 (*(GT) ₁₉ , *(GT) ₂₀ ).

SNP: RS345336443 (G/G).

5.Haplotype: Set of alleles of contiguous loci. They are usually co-transmitted on a parental chromosome.

Example: HLA-A*01-B*08-DRB1*03.

6.Locus: Literally, “place” in Latin, it is the specific usual physical location of genes, an individual genetic marker, or set of genetic markers in a genome.

Example: ABO locus, HLA-DRB locus, KIR-2DS3/S5cen locus, D6S1666 microsatellite locus.

7.Phenotype: The observable expression of alleles as a physical or biochemical trait resulting from the interaction of the genome, the environment, and the experimental settings. In disease studies it may refer to the presence or a manifestation of the disease under study. Disease phenotypes may be reflected in a variety of ways as quantitative or qualitative variables.

This term may also refer to a set of alleles (expressed or not) detected by a technique. In codominant or heterozygous situations, phenotypes are noted as pairs of data; each pair is specific to a particular gene and locus.

Example: ABO system: [A].

HLA system: [HLA-A (1, 2); HLA-B (8,44); HLA-DR (3, 4)].

Phenotypic and demographic data

1.Admixture: The outcome of interbreeding between members of different populations. An admixed population is generally derived from populations in different geographic regions.

2.Collection site: The location where the sample was collected. This can be identified using latitude and longitude coordinates, or by specifying the country or nation, and city/town/village, or other locale where the collection took place.

3.Complexity: An ordinal variable that represents an estimate of the degree of admixture and population sub-structure in each population sample.

Example:

Complexity 1: a population sample collected from a single settlement or group of closely related settlements.

Complexity 2: a population sample collected from a group of separate but discrete settlements.

Complexity 3: a population sample collected in a metropolitan area or across an entire nation.

Complexity 4: an admixed population.

4.Data management methods: The approaches used in storing and processing the data in preparation for analysis. This can include the formats and programs used to store and edit the data (e.g., a specific spreadsheet program or database system), as well as any modifications that were made to the data between the generation of the data resulting from the typing assay and the inclusion of the data in the master data file. For example, if ambiguities were resolved, the approach used to resolve them should be documented in the data dictionary; if HLA allele data were truncated to a common level, or “binned” into a common sequence category (e.g., treating all alleles that encode the same peptide-binding region as the same allele) this should documented.

5. Ethnicity: A group of individuals (or populations) sharing a common language, culture, or religion, and who are assumed to share a common ancestry. Ethnicity should be distinguished from geography (e.g., “North American” is not an ethnicity), and though ethnicity is often associated with indigenous nationality (e.g., “Irish,” “Chinese”) qualifiers are often necessary to distinguish ethnicity from nationality (e.g., “Han Chinese”).

6. Family: If individuals in the study belong to discrete familial groups, a family ID is qualitative variable identifying membership in a particular pedigree, as well as the relationship to the index case (proband).

7. Geographic region: A specific continental or subcontinental area comprised by multiple nations in which the population is located, or from which the population was derived, if the population is a migrant population. For example, European Americans or European Australians would be assigned to the European region, or to a specific subregion of Europe. Conversely North America would only pertain to Native American/Amerindian/Aleut/Eskimo populations. Populations derived from more than one region (admixed populations) can be assigned to a specific class for the type of admixture (depending on the regions of origin) or included in a single class for all admixed populations. The definitions of each region and admixed class should be defined in the data dictionary.

8. Latitude and longitude: Geographic coordinates that specify specific locations on the surface of the Earth. Latitude and longitude values should be recorded in a decimal format, with minutes and seconds indicated as factions of each degree value. North latitudes and east longitudes should be recorded with positive values, and south latitudes and west longitudes should be recorded with negative values. For example, 35° 20 min south latitude would be recorded as −35.333, and 2° 30 min east longitude should be recorded as 2.5 or +2.5.

10. Population: A group of individuals living in a specific geographic area. More specifically, a population is defined such that all pairs of individual members have the opportunity to mate, and are more likely to mate with each other than with members of other populations. A population should be documented in the data dictionary in terms of the pertinent geographic area and the approximate number of included individuals.

Population sample: A unique descriptor for the individuals from a given population that were included in the study. If the study involves multiple sets of individuals (samples) from the same population, each set of individuals should be given a unique name; usually it is sufficient to append the number of individuals to the end of the population name (e.g., antarctica_87, antarctica_207, antarctica_597).

11. Population substructure: A barrier to the opportunity of mating between all pairs of individuals in a population.

12. Proband: The individual under study, primarily used in family-based disease association studies.

13. Status: The status of an individual as affected or unaffected with respect to a disease phenotype, or belonging to a case or a control group.

14. Typing assay: The laboratory method(s) and associated protocols used to generate the data included in the analysis. Many of them are described in this volume. Commonly used molecular methods for HLA and KIR genotyping include sequence-specific priming (SSP), sequence-specific oligo probe (SSO or SSOP), sequence/sequencing-based typing (SBT), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), and reference strand conformation analysis (RSCA). Serology has been used historically for HLA phenotype data generation. When possible, a description of the assay identifying the assay manufacturer and reagent version/lot employed should be included in the data dictionary. Literature citations or references to specific protocols should also be associated with the methods used, especially if multiple distinct methods have been employed in generating the data.