Linkage Analysis

Question 1

Explain homologous recombination and genetic linkage

Answer 1

Homologous recombination
- caused by chromosome crossover during prophase 1 resulting in recombinant interior chromosome arms = introduce variation
- tracking location gives indication of close proximity using genetic markers to locate disease genes
Linkage: tendency of neighbouring alleles (in similar /close proximity of loci) are segregated together

Question 2

Describe how genetic disease can be classified by the number of genes required to cause the disease

Answer 2

Mendelian: single gene disorders - high penetrance but rare
Polygenic: multiple gene disorders, low penetrance, very common

Question 3

Describe the difference between genetic maps and physical maps of the genome

Answer 3

• provide framework to calculate distant between certain locus of genes
• know where genetic markers are located
  Genetic map: tube map (blocks/regions)
  Physical map: pinpoint distances between specific markers

Question 4

Describe the principles of linkage analysis and why it is useful

Answer 4

autosomal linkage, genes can be identified if their locusts are close together
if the markers which co-segregate together can be identified then the disease gene can be assumed to be proximal to a specific marker (if observed in all affected individuals of a family / across multiple families)

Question 5

Describe the differences between the two types of genetic marker routinely used in linkage studies

Answer 5

• Microsatellites: high polymorphic disease
  less common with short tandem repeats from 2-6 base pairs long.
  Varied in length between chromosomes (heterozygous) with markers relatively distal to each other.
  PCR based, with manual intensive procedure, long processing time
  uses fluorescent primers
• SNPs: single nucleotide polymorphisms
  proxy for disease genes
  ballelic (2 allele options)
  lower heterozygosity
  spaced closer together = greater linkage analysis across genome
  automated with automatic assignment of genotypes
  microarray based system

Question 6

Briefly describe the genotyping technologies used in linkage analysis

Answer 6

• SNP Genotyping Microarrays
   Provides genome-wide coverage of SNP markers
   SNPs are proxy markers; NOT the causal disease variants
   Can amplify thousands of markers in a single experiment
   Alleles are identified by relative fluorescence
   homozygous for allele 1 = green signal
   homozygous for allele 2 = red signal
   heterozygous (1/2) = yellow signal

Question 7

Describe what a haplotype is and how it is built

Answer 7

Halotype: group of alleles inherited together from one parent

Question 8

Briefly describe the statistical approaches used in linkage analysis, with specific emphasis on the logarithm of the odds (LOD) score

Answer 8

if the LOD is below -2 = no significance
if 1<n<3 = significant probability that causative gene is located

Question 9

Summarise how linkage analysis can be combined with whole exome sequencing to identify a disease-causing variant

Answer 9

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