Linkage Analysis Flashcards
describe genetic variation
differences in DNA sequence between individuals in a population
variation can be inherited or due to environmental factors
what effects can genetic variation have
alteration of amino acid sequence
changes in gene regulation
physical appearance
silent or no apparent effect
importance of genetic variation
underlies phenotypic differences among diff individuals
determines predisposition to complex diseases and responses to drugs and environmental factors
reveals clues of ancestral human migration history
mechanisms of genetic variation
- mutation/polymorphism = errors in DNA replication.
- homologous recombination = shuffling of chromosomal segments between partner chromosomes of a pair
- gene flow = movement of genes from one population to another is important source of genetic variation
describe 3 types of mutations
gremlin = passed on to descendants
somatic = not transmitted to descendants
de novo = new mutation not inherited from either parent
define mutation
rare change in DNA sequence that is diff to normal sequence. normal allele is prevalent in population and mutation changes to rare abnormal mutation
define polymorphism
a DNA sequence variant that is common by population. no single allele is regarded as normal. there are two or more equally acceptable alternatives
what’s the arbitrary cut-off between a mutation and polymorphism
a minor allele frequency of 1%
meiosis and recombination
creaction of haploid gametes
describe homologous recombination
crossing over = reciprocal breaking and re-joining of homologous chromosomes during meiosis
results in exchange of chromosome segments and new allele combinations
define these words
genotype = genetic makeup of an individual
phenotype = physical expression of genetic makeup
allele = genes in alternative versions
homozygous = same alleles heterozygous = diff alleles
haplotype = group of allele inherited from single parent
homozygosity and heterozygosity
chromosome pair = homologous chromosomes with genes at same loci
allele at that locus may be same or diff
define mendelian/monogenic disease
disease caused by a single gene, little or no impact from environment
non mendelian/polygenic disease
disease or traits caused by impact of many different genes, having small individual impact e.g. psoriasis
multifactorial disease
disease or trait resulting from interacting between multiple genes and multiple environmental factors e.g. heart disease
describe linkage analysis
method used to map location of disease gene in genome
linkage = assumption of two things being physically linked
linkage assumptions
genetic markers used to identify location of a disease gene based on their physical proximity
importance of maps
maps provide context to orientate yourself and calculate distance between landmarks
genetic maps
look at information in blocks or regions
principles of genetic linkage
genetic linkage = tendency for alleles at neighbouring loci to segregate together at meiosis
cross over more likely to occur between loci with distance
to be linked, two loci must be CLOSE together
describe micro satellite markers
less common now
highly polymorphic short tandem repeats of 2-6bp
differ in length between chromosomes
wide spaced apart
400 m markers 9cM spacing PCR based system fluroescently labelled primers manual assignment of genotypes labour intensive whole genome scan = 2-3 months
describe single nucleotide polymorphisms
- genetic marker of choice lower heterozygosity than micro satellites spaced closer together more informative spaced throughout the genome micro-array based system genotypes assigned automatically highly automated data returned within 1-2 months
what is mirosatellite genotyping used for?
- dna fingerprinting from small amounts of material
- standard test uses 13 core loci making likelihood of chance match 1 in three trillion
- paternity testing
- linkage analysis for disease gene identification
describe fluorescent genotyping
fluorescently tagged PCR primers
allows for multiplexing of PCR products with diff colours and fragment lengths
fragment sizes separated down to 1bp resolution
describe single nucleotide polymorphism
- single base change
- most common type of variation
- thought to occur approx 1 per 1000 bases
- human genome is 3 billion base pairs
describe SNP genotyping microarrays
- provides genome wide coverage of SNP markers
- SNPs are proxy markers, not casual disease variant
- amplify thousands of markers in single experiment
- alleles identified by relative fluorescence
homo for 1 allele = green
homo for 2 = red
heterozygous for 1/2 = yellow
uses of SNP genotyping microarrays
linkage analysis in families
GWAS in population - non mendelian and multifactorial diseases
linkage mapping using genetic markers
uses an observed locus to draw inferences about an unobserved locus
if marker linked to disease locus, same marker alleles inherited by 2 affected relatives
if marker and disease locus are unlinked, affected relatives in a family are less likely to inherit same marker alleles
statistical analysis of linkage
probability of linkage can be assessed using LOD score
LOD = logarithm of odds score
assesses probability of obtaining test data if two loci are linked to likelihood of observing same data by chance
what is recombination fraction
proportion of recombinant births
higher LOD score = higher likelihood of linkage
more about LODs
- can be calculated across whole genome using genotype data for many genetic markers in multiple members of family
- LODs are additive = diff families linked to same disease locus will increase overall score
- LOD score 3 is evidence for linkage
- LOD score 2 is considered evidence against linkage
describe parametric analysis
specifes analysis parameters el.g. inheritance pattern, disease, allele frequency,
describe non parametric analysis
no parameters specified
looks for allele sharing between affected individuals
describe Adam-oliver syndrome
neurological anomalies
cardiac malformations
vascular defects
describe ARHGAP31
disease causing variant identified through candidate gene analysis of genes in minimal linkage interval
