Bioinformatics Final

Populations

Group of one species living in the same geographical area

Subpopulations

Local populations defined by areas where most individuals find their mates

Gene Pool

All genetic variation within a population

Allele Frequency

Proportion of individuals in a population with a specific allele

Genotype Frequency

Proportion of individuals in a population with a specific genotype

Hardy Weinberg Equilibrium

Calculates the frequency of alleles using the following equation, p²:2pq:q², (where p is dominant allele)

Gregory Mendel

Created laws of inheritance based on his experiments with pea plants

Genetic Drift

Random fixation of an allele causing the reduction of genetic diversity. This is more prominent in smaller populations

Bottleneck

Genetic drift caused by a temporary and sudden reduction in population size

Migration

Movement of individuals between populations between populations followed by breeding

Admixture

Combining two populations with different allele frequencies into one group

Fixation Index (Fst)

Estimates the genetic divergence between two populations using the following equation, Fst=AP/AI+WI+AP (where AP=estimated allele variance among populations, AI=among individuals, WI=within individuals, high score indicates no migration)

Non-random Mating

Individuals pairing up as mates does not occur based on chance

Assortative Mating

Pair bonding is based on an observable phenotype

Inbreeding

Mating between relatives that results in the reduction of heterozygotes

Natural Selection

The driving force behind adaptative evolution selection

Adaptation

Progressive genetic improvement as a result of natural selection

Balancing Selection

Preserves genetic diversity by allowing multiple different alleles to be favored

Directional Selection

Reduces genetic diversity by favoring one allele over the others

Relative Fitness

Compares the fitness offered by each parental genotype to the pool of offspring genotypes

Selection Coefficient

The selective disadvantage of a disfavored genotype calculated using the following equation, S=1-W (where W=relative fitness)

Linkage Map

Alleles on all loci are highly correlated

cM

Centimorgan is a measure of frequency of alleles on a chromosome based on how close they are to each other

Linkage Disequilibrium

Nonrandom association of alleles at two or more loci

Haplotype Block

Unique set of alleles that are all inherited together

Coefficient of Linkage Disequilibrium (D)

Measure the association of two alleles on different loci relative to random chance

TAG SNP

Single nucleotide polymorphism that correlates with variants in a linkage block

Genotype-Phenotype Association

Explains how genetic changes influence the phenotype

Additive Inheritance Model

Disease risk increased y-fold for Aa and 2y-fold for aa

Recessive Inheritance Model

Disease risk increases by y fold for aa

Codominant Inheritance Model

One or two A alleles required for a y-fold increase in disease risk

GWAS

Goal is to map mutations to chromosomes

Quantitative Traits

Are a result of many genes and the environment

Bonferroni Correction

Adjusts the significance based on the number of tests performed

Power

A study can get this by genotyping many individuals

Odds Ratio

Measures the strength of association, calculated by dividing the experimental over the control group

Multi-stage Approach

Has increasingly larger populations groups with more stringent p-values for each group

Permutation

Tests for the statistical significance

False Positives

Indicates that a condition is present when it is really not

Population Stratification

Identifies the presence of genetic differences in individuals based on subpopulations

Repetitive Elements

Repeated sequences that make up 45% of the human genome

Alu Transposable Element

Short repetitive part of the human genome that is 300 base pairs long these make up 10% of the human genome

L1 Retrotransposon

Parts of the genome that are able to move to another region of the genome

Hemophilia A

Bleeding disorder that is caused by the gene being interrupted by a L1 retrotransposon

Microsatellite

Length differences in repetitive elements of DNA

Indel

Genetic variation caused by insertion or deletion mutations

SNP

Mutation replacing a single nucleotide

Insertion

A portion of nucleotide base pairs are added to a DNA sequence

Deletion

A portion of nucleotide base pairs are removed from a DNA sequence

Inversion

A part of a DNA sequence is removed, flipped around and reinserted to the DNA sequence

Translocation

A portion of the DNA sequence is removed and transferred to a different chromosome

Alternative Splicing

mRNA transcripts can have certain portions of the sequence removed to produce a variety of proteins

MAPT Gene

Codes for the Tau protein

NGS

Next generation sequencing is advanced sequencing methods that allow for DNA and RNA to be rapidly sequenced

Illumina

Can rapidly analyze thousands of DNA fragments at once. Collects fragments through complementary binding on a flow cell creating clusters

Barcode

Short section of DNA that is able to identify a species

Adapter

Ligation of an oligonucleotide to a portion of DNA for a variety of purposes in NGS

Flow Cell

Consist of a bunch of nanowells where clusters of DNA fragments are formed to be prepared for Illumina sequencing

Cluster

A collection of DNA fragments that can be used to create reads

Bridge Amplification

DNA fragments bound to a nanopore bend over to adjacent DNA fragments which creates clusters

Cycle Sequencing

Increase the sensitivity of a sequencing protocol so only a small amount of DNA is required

Paired Reads

Sequences a DNA fragment from both ends

Fastq

A txt file where line one is the sequence identifier, line two is the nucleotide sequence, line three is a “+”, and line four is the quality values

Phred Score

Measures the quality of DNA sequencing above 30 is considered good

Vector

A particle used to carry a foreign DNA sequence into another cell

De Novo Assembly

Program that assembles short nucleotide sequences into longer ones without using a reference genome

C (Coverage)

Shows how many gaps are present within the sequence

String Graph

Used in sequencing to determine the relationships between sequences of DNA or RNA

Consensus

A calculated sequence of the most frequent residues

N50

Lines up the contigs from shortest to longest in order to find the shortest contig that covers at least 50% of the total assembly length

Contigs

Continuous region of DNA

Scaffolds

A collection of both contigs and gaps in the sequence

Collapsed Contig

Part of a DNA sequence that has been lost or merged due to repetitive elements

Repeat Region

Sequences of DNA that are repeated multiple times throughout the genome

Mate Pair Reads

Allows for sequencing of two DNA fragments that are far apart in the genome and have opposite orientations

Assembly Programs

Tools for constructing genomes from fragmented DNA sequences

Velvet

A powerful de novo genome assembly program

Re-sequencing

Method to analyze an organism’s DNA sequence after a genetic map has been created

Genome Resequencing

Process of completing the entire genome sequence after a genetic map has been created

Low-coverage Sequencing

Method that sacrifices sequencing depth in order to have larger genome coverage and a bigger sample size

Reduced-representation Sequencing

Method that covers a small portion of the genome with a large amount of detail

Restriction Enzyme Digestion

Uses enzymes to cut the DNA genome into fragments so that it can be sequences

Plasmodium Falciparum

Bacteria with a 22.9 Mb genome the genome is small enough to be sequenced in one go

Amylase

Enzyme used to break down carbohydrates domesticated dogs have a higher expression of this

Targeted Enrichment

Sequencing method that focuses on specific genes to discover hard to detect components like variants

Multiplex

Allows for multiple samples to be run at the same time in a single sequencing run

RainStorm

Technology for targeted sequencing that allows for thousands of loci to be amplified with high specificity

Hybridization

The binding of two complementary single stranded DNA molecules

Oligo Probes

Used to detect certain DNA sequences

Biotin

Used to mark specific DNA sequences and make them bind to the binding partner streptavidin

Streptavidin

Binds with high affinity to biotin

Miller Syndrome

Caused by a recessive mutation and causes eye, craniofacial, and limb deformities

RadSeq

Restriction site-associated DNA sequencing is used to study genetic variation among individuals by using restriction enzymes and identifying SNPs

GBS

Genotyping by sequencing is used in genetic analysis to examine genetic variation across samples

RadTag

Analyzes a genome without complete sequencing

Sliding Window Analysis

Maintains a subset of data points as the remainer of the dataset is sorted through

Selective Sweep

A beneficial mutation increases in a population which decreases the genetic diversity of the population

GPR158

Gene causing reduced energy expenditure which affects diabetes

LECT2

Gene effecting abdominal fat storage and lipid metabolism

Functional Analysis

Preformed to understand the relationship between an organism’s genotype and its phenotype