glossary.yml

Biallelic:
  definition: Affecting both alleles at a given a location. One allele is taken as a reference allowing for the other allele to be considered the variant allele.
CHG array:
  definition: A molecular method for analyzing copy number variations. You can compare quickly DNA from two sources to detect either gains or losses. This is often used in tumor identification and rapid identification of genetic anomalies.
ChipSeq:
  definition: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is extensively used to determine transcription factor binding sites (TFBSs). DNA binding proteins can be cross-linked to the DNA that they are binding and by using an antibody against said proteins, the entire DNA/protein complex can be precipitated out of solution.
  link: https://academic.oup.com/bioinformatics/article/29/21/2705/195767
DAF:
  definition: Derived allele frequency which represents the distribution of alleles at a given loci.
  link: https://en.wikipedia.org/wiki/Allele_frequency_spectrum
ENHCR:
  definition: Enhancers regulate the transcription of genes by increasing the levels than without them.
  link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445073/
GERP:
  definition: The Genomic Evolutionary Rate Profiling is a statistical approach to quantify the deficit of substitutions in base pairs based on neutral the neutral rate of substitution. The neutral rate of substitution is an estimate of the number of new mutations per each generation multiplied by the probability that the substitution reaches fixations. In cases where neutral mutations exist, the rate of substitution will be equal to the rate of mutations. The GERP Score thus indicates the deviation from the neutral rate of subsitution indicating that positive scores will indicate that fewer observed substitutions have taken place than would be expected under neutral substitution while negative scores indicate that more observed substitutions have taken place than would be expected under the neutral model.
  link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1172034/
GWAS:
  definition: Genome-wide association study. These studies examine the association between certain phenotypic outcomes and the genomic variations (generally just SNPs) to understand how the mutations are associated with particular outcomes.
IBD:
  definition: Any pair of alleles present in a single inbred individual, we call these alleles inbreeding by descent, if they both derived by the DNA replication of a single allele present in some ancestral population. If the ancestral population has no inbreeding then F = 0.
Immunoprecipitation:
  definition: Use of an antibody to precipitate out a particular protein antigen.
  link: https://en.wikipedia.org/wiki/Immunoprecipitation
LD:
  definition: Linkage disequilibrium is a measure of nonrandom association between loci. When D=0 the gametic frequencies equal the products of the relevant allele frequencies and are said to be in linkage equilibrium.
Nonsyn:
  definition: A non-synonymous mutation is a change in the DNA sequence which results in a change in the encoded amino acid.
  link: https://bmccancer.biomedcentral.com/articles/10.1186/s12885-019-5572-x
PSEUG:
  definition: Pseudogenes are nonfunctional segments of DNA which resemble genes. These could be artifacts from mutations of prior functioning genes.
  link: https://en.wikipedia.org/wiki/Pseudogene
SNP:
  definition: Single nucleotide polymorphism, i.e., a single nucleotide substitution at a specific position. Generally associated with a sufficiently large proportion of the population (over 1%). Multiple SNPs at the same location are alleles.
  link: https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism
SmallRNA:
  definition: Small RNA sequences are short, normally non-coding regions with a nucleotide length less than 200 bases. RNA silencing has been associated with these sequences.
  link: https://en.wikipedia.org/wiki/Small_RNA
Splice:
  definition: Often associated with post-translational changes in either the N-terminal region or a change in the availability of glycosylationsites through a change in the signal peptide. This can lead to secondary changes due to changes in the structure and is associated with a loss of function.
  link: https://onlinelibrary.wiley.com/doi/10.1002/prot.10568
Stop:
  definition: A nucleotide substitution leading to the addition of a stop codon (UAA, UAG, UGA) and leads to premature truncation of a protein during transcription. These are associated with a loss of function.
  link: https://illustrated-glossary.nejm.org/term/stop-gain_variant
Syn:
  definition: A synonymous mutation is a change in the DNA sequence which does not result in a change in the encoded amino acid. Also can be called a silent polymorphism--however, it can have an impact due to codon selection bias.
  link: https://bmccancer.biomedcentral.com/articles/10.1186/s12885-019-5572-x
TFmotif:
  definition: Transcription factor motif is the sequence associated with the proteins which are involved in the transcription of DNA to mRNA.
  link: https://en.wikipedia.org/wiki/Transcription_factor
TFpeak:
  definition: Transcription factor motif
  link: https://en.wikipedia.org/wiki/Transcription_factor
UTR:
  definition: The untranslated region. These appear on either side of the coding region with the 5' untranslated region called the leader sequence and the 3' untranslated region called the trailer sequence. The role of the untranslated region is not well described and may have a role in transcription regulation and mutations in this region may be associated with increased risk of certain cancers.
  link: https://en.wikipedia.org/wiki/Untranslated_region
admixture:
  definition: when two distinct, isolated, or previously isolated genetic lineages mix. This results in the introduction of a new genetic lineage to a population.
allele:
  definition: A variation in the same sequence of nucleotides at the same place on a long DNA molecule.
  link: https://en.wikipedia.org/wiki/Allele
codominance:
  definition: the condition in which multiple alleles are dominant; the heterozygote expresses phenotypes associated with both alleles.
  link: https://pubmed.ncbi.nlm.nih.gov/24274750/
codon usage bias:
  definition: Particular codons have higher speed and accuracy of translation as well as have impacts on protein folding and subsequent mRNA stability. This is important to consider that synonymous mutations may have selective advantages and are subject to background selection. This is more important for non-eukaryotes who have a much lower energy budget.
exon:
  definition: The regions between the introns that remain in the fully process RNA.
frequency dependent selection:
  definition: A trend in which the fitness of a given genotype is correlated with its prevalence in the population (e.g., if an allele is advantageous when it is rare)
  link: https://pubmed.ncbi.nlm.nih.gov/24274750/
gamete:
  definition: a reproductive cell. an a diploid organism it is the germ cell which unites with the opposite sex germ cell to create a zygote.
  link: https://www.genome.gov/genetics-glossary/Gamete
haplotype:
  definition: alleles which present together in the same region on a chromosome
heterozygote advantage:
  definition: A trend in which the fitness of a heterozygote is greater than that of either homozygote. Also referred to as overdominance.
  link: https://pubmed.ncbi.nlm.nih.gov/24274750/
indel:
  definition: an insertion/ deletion polymorphism. In most cases it is unclear if there was an insertion or a deletion in the ancestral sequence hence the terminology.
intron:
  definition: The segments which are eliminated in the RNA transcript.
lincRNA:
  definition: Large intergenic non-coding RNA are associated with remodelling of chromatin, genome architecture, RNA stabilisation, and transcription regulation.
  link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889127/
linked genes:
  definition: When two genes are sufficiently close on the same chromosome and this spatial relationship results in frequencies of these different types of gametes depends on the distance between the genes.
motif:
  definition: A motif is a nucleotide or amino acid sequence associated with a specific structure and are associated with functionally important sites.
  link: https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/download/lectures/PCB_Lect08_Bind_Motifs.pdf
negative selection:
  definition: in which an allele is disfavored (also called purifying selection). Random mutations are more likely to be deleterious and immediately removed from the gene pool before they reach appreciable levels. This can also be referred to as background selection.
  link: https://pubmed.ncbi.nlm.nih.gov/24274750/
polymorphism:
  definition: genetic differences that are common among organisms in the same species
positive selection:
  definition: in which an allele is favoured and is propagated. Positive selection is understood to be the primary mechanism of adaptation (and is often more conspicuous).
  link: https://pubmed.ncbi.nlm.nih.gov/24274750/
transcription:
  definition: the process by which a sequence of nucleotides present in one DNA strand of a gene is copied into the nucleotides of an RNA molecule.