Table 1.

Glossary, Acronyms, and Definitions for Sociogenomics Terms

Concept	Acronym	Definition
Allele		a version or alternative form of a DNA sequence (e.g., a version of a SNP) or a gene.
Allele Frequency		the proportion of all variants at a given position that are the specific allele in question; usually reported as the frequency of the second most common variant (i.e. ‘minor allele frequency’).
Copy Number Variant	CNV	a type of genetic variant in which the number of copies of a particular sequence varies between individuals.*
Gene		sequences of DNA interspersed at irregular intervals on our chromosomes that serve as templates for making an RNA product.
Genetic Risk Score	GRS	Alternative for PGS
Genome		the total DNA sequence in an organism or cell; the human genome consists of roughly 6 billion nucleotide bases of nuclear DNA separated into 46 chromosomes plus mitochondrial DNA.
Genome-wide association study	GWAS	A statistical analysis that estimates the partial correlation between each measured DNA variant (usually SNPs) and a particular phenotype, net of a few controls (usually age, sex, and ancestry PCs).
Haplotype		a sequence of alleles found at linked loci on a chromosome
Haplotype Block		blocks of variants that are in linkage with each other but not with variants in adjacent blocks (separated by recombination); the consequence of shared ancestry.
(Short) Insertion-Deletion	Indel	Narrowly, a change where one or more nucleotides are inserted (or deleted) in a sequence; broadly as used here, all types of DNA change that cause a size change at a specific position: insertions, duplications, deletions, and compound insertion/deletion up to 50bp (includes short CNVs).
Linkage Disequilibrium	LD	when particular alleles at separate loci are associated with each other at a significantly higher frequency than would be expected by chance.
Locus		designated region on a chromosome. Can refer to a gene or a single base position.
Non-coding RNA	ncRNA	RNA that does not code for a protein; ncRNA has many functions in the cell.
(Genetic) Principal Components	PCs	Orthogonal controls for ancestry created from a principal components analysis (a dimension reduction technique) of the genetic relatedness matrix.
Polygenic Index	PGI	Alternative for PGS
Polygenic Risk Score	PRS	Alternative for PGS
Polygenic Score	PGS	A genetic summary score representing the additive genetic association with a trait; composite measure created as the sum of the GWAS-weighted allele dosages for each individual; human equivalent to the breeding value.
Quantitative Trait Locus	QTL	a locus (that statistical analysis has) linked to a continuous (quantitative) trait, like height.
Single Nucleotide Polymorphism	SNP	a position on the genome where two (or occasionally 3) alternative nucleotides are common (>1%) in the population; common SNVs.
Single Nucleotide Variant	SNV	a position on the genome where alternative nucleotides exist.
Structural Variant	SV	Sequence changes (insertions, deletions, translocations) that involve a change in more than 50 bases. (In the past, structural variation was concerned with large sequence changes >1kb, but with next generation sequencing, SVs it has come to represent smaller changes).
Tag SNPs		Mostly non-functional SNPs in GWAS used to tag a region of common variation; common SNPs used to tag haplotypes.

^*“The term copy number variant used to be applied to all variants that had a variable number of tandem repeats, including short tandem repeats, such as the microsatellite in (D ) where there are 12 or 11 copies of the CA dinucleotide. In genome sequencing projects, the term is reserved for large size changes only, such as variable numbers of repeats exceeding 50 nucleotides in the case of the 1000 Genomes Project.” (Strachan & Reed 2018).