Sudbury basics Flashcards
What are single-nucleotide variants?
What is a single nucleotide polymorphism
Single nucleotides in the genome that vary between individuals in a population.
Single-nucleotide polymorphism refers to a SNV that occurs at an appreciable frequency in a population (for example, >1%).
What is Heritability?
The proportion of phenotypic variation between individuals in a population that is due to genetic factors
What are rare variants?
Variations in the genome for
which the less prevalent form (minor allele) occurs at a frequency of 1% or less in the population.
What is Imputation?
Statistical inference of unobserved genotypes from a reference panel of known haplotypes in a population.
What are effect sizes?
The magnitudes of the effect of alleles on phenotypic values.
Explain linkage disequilibrium?
The nonrandom association of alleles at two or more loci due to limited recombination.
What is a haplotype?
A set of genetic markers that are present on a single chromosome and in linkage disequilibrium.
A haplotype refers to a set of DNA variants along a single chromosome that tend to be inherited together
What are Common variants?
Variation in the genome for which the less prevalent form (minor allele) occurs at a frequency of 5% or greater in the population.
What are minor allele frequencies?
The frequencies of the less common allele of a genetic variant in a population.
What are copy number variants (CNVs)?
Copy number variants (CNVs). A class of DNA sequence variants (including deletions and duplications) that lead to a departure from the expected diploid representation of DNA sequence.
What is clonal mosaicism?
The presence of clones of cells with different karyotypes within an individual derived from a single zygote.
What is fine-mapping?
The process of localizing association signals to causal variants using statistical, bioinformatic or functional methods.
What is Epistasis?
Statistical interaction between loci in their effect on a trait such that the effect of a genotype at one locus is dependent on the genotypes at the other locus (or loci)
What is population stratification?
Differences in allele frequencies between cases and controls resulting from systematic differences in ancestry rather than association of genes with disease.
What are the benefits of GWAS using SNP arrays?
Identifiction of novel SNP-trait associations
Discovery of novel biological mechnaisms
Diverse clinical applications
Insight to ethnic variation of complex traits
Relevant to low-frequency rare variants
Identification of novel monogenic and oligogenic disease genes
Relevant to the study of structural variation
Multiple applications beyond gene identification
Straighforward GWAS generation, mangement and analysis
Easy-to-share and publicly avaliable data.
