study guide: Mutations and Polymorphisms Flashcards

A set of comprehensive vocabulary flashcards covering basic genetics terminology, mutation types, genetic polymorphisms, and GWAS methodologies based on the lecture notes.

Locus

A DNA segment that occupies a specific position on a chromosome.

Alleles

Alternative versions of DNA sequence at a specific locus.

Wild-type Allele

The single prevailing or most common allele at a specific locus in a population.

Polymorphic Locus

A locus that has more than $2$ common alleles in a population.

Private Alleles

Rare genetic variants that are confined to specific families.

Zygosity

The degree of allele similarity at one locus in an organism.

Homozygous

Having $2$ copies of the exact same allele at a specific locus.

Heterozygous

Having $2$ different alleles at the same locus.

Genotype

The genetic information present at a specific locus.

Phenotype

The observable appearance of an organism based on its genotype.

Reference Sequence

The most common genomic sequence in a population, used as a baseline standard.

Euploidy

A chromosome mutation characterized by the multiplication of an entire chromosome set (e.g., tetraploidy).

Aneuploidy

A chromosome mutation involving additional or missing individual chromosomes (e.g., trisomy, monosomy).

Subchromosomal Mutations

Structural changes occurring in portions of chromosomes, such as copy number variations and structural rearrangements.

DNA Mutations

Sequence changes including base substitutions, deletions, and insertions of up to $100\,bp$.

Mutation Frequency

The number of mutations occurring per locus per cell division, determined by nucleotide change frequency, repair probability, and detection probability.

Synonymous Mutation

A nucleotide substitution in coding DNA that specifies the exact same amino acid.

Missense Mutation

A single nucleotide substitution that changes a codon to specify a new amino acid.

Transition Mutation

A nucleotide substitution involving a change from a purine to another purine ($A \rightarrow G$ or $G \rightarrow A$) or a pyrimidine to another pyrimidine ($T \rightarrow C$ or $C \rightarrow T$).

Transversion Mutation

A nucleotide substitution involving a change between a purine and a pyrimidine (such as $A \rightarrow C$, $A \rightarrow T$, $G \rightarrow C$, or $G \rightarrow T$).

Nonsense Mutation

A point mutation resulting in the replacement of a coding codon by a stop codon.

Dynamic Mutation

An amplification process involving repeated expansions of simple trinucleotide repeats within coding or untranslated genomic regions.

Frameshift Mutation

An insertion or deletion of a number of nucleotides that is not a multiple of $3$, shifting the reading frame and producing a functionally altered protein.

Gain-of-Function Mutation

A mutation resulting in the overproduction or inappropriate production of a novel or excess protein product.

Loss-of-Function Mutation

A mutation that reduces or completely eliminates protein product formation.

Haploinsufficiency

A state in which a $50\%$ level of normal protein product from a single wild-type allele is insufficient for standard cellular function.

Dominant Negative Mutation

A mutation where an abnormal protein product produced by a mutant allele directly interferes with or inhibits the product of the normal allele in heterozygosity.

Germline Mutations

Mutations inherited from parents or arising de novo in germ cells that are transmitted to offspring.

Somatic Mutations

Mutations occurring in non-germline body cells that are not passed to future generations.

Genetic Polymorphism

A genetic mutation or variant with a frequency exceeding $1\%$ of all alleles in a population.

Single Nucleotide Polymorphism (SNP)

A single base pair change occurring on average $1$ for every $1000\,bp$ across the genome.

Insertion-Deletion Polymorphisms (Indels)

Genetic variations involving the insertion or deletion of short DNA fragments up to $1000\,bp$ in length.

Simple Indel

An insertion-deletion polymorphism characterized by the simple presence or absence of a short DNA fragment, yielding $2$ alleles.

Microsatellite (Short Tandem Repeat / STR)

A polymorphism defined by a variable number of repeated short tandem nucleotide segments ($2$, $3$, or $4\,nt$), yielding multiple alleles useful for DNA fingerprinting.

Copy Number Variant (CNV)

A structural variation involving segment length differences up to hundreds of kilobases ($kb$) that can alter gene dosage across multiple genes.

Inversion Polymorphism

A balanced structural rearrangement ranging from a few base pairs to megabases where a DNA segment is inverted without loss or gain of DNA.

Genome-Wide Association Study (GWAS)

A molecular technique that simultaneously analyzes hundreds of thousands or millions of genomic DNA variations to determine association with a specific phenotype without prior hypothesis.

Linkage Disequilibrium

The non-random association of alleles at linked loci, reflecting the tendency of certain alleles to be inherited together as haplotypes.

Haplotype

A set of closely linked SNPs or genetic markers located on the same chromosome that tend to be inherited together.

SNP Imputation

A computational method that determines non-genotyped neighboring SNP variants in an individual by matching genotyped markers to a reference genome based on linkage disequilibrium.

Manhattan Plot

A scatter plot displaying statistical significance ($-\log_{10}(P\text{-value})$) on the y-axis against chromosome locations on the x-axis in GWAS analyses.

Risk Variants

Clinically functional genetic variants that increase susceptibility to disease.

Protective Variants

Clinically functional genetic variants that lower susceptibility to disease.