Linkage Analysis

Question 1

describe genetic variation

Answer 1

differences in DNA sequence between individuals in a population

variation can be inherited or due to environmental factors

Question 2

what effects can genetic variation have

Answer 2

alteration of amino acid sequence
changes in gene regulation
physical appearance
silent or no apparent effect

Question 3

importance of genetic variation

Answer 3

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

Question 4

mechanisms of genetic variation

Answer 4

• 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

Question 5

describe 3 types of mutations

Answer 5

gremlin = passed on to descendants

somatic = not transmitted to descendants

de novo = new mutation not inherited from either parent

Question 6

define mutation

Answer 6

rare change in DNA sequence that is diff to normal sequence. normal allele is prevalent in population and mutation changes to rare abnormal mutation

Question 7

define polymorphism

Answer 7

a DNA sequence variant that is common by population. no single allele is regarded as normal. there are two or more equally acceptable alternatives

Question 8

what’s the arbitrary cut-off between a mutation and polymorphism

Answer 8

a minor allele frequency of 1%

Question 9

meiosis and recombination

Answer 9

creaction of haploid gametes

Question 10

describe homologous recombination

Answer 10

crossing over = reciprocal breaking and re-joining of homologous chromosomes during meiosis

results in exchange of chromosome segments and new allele combinations

Question 11

define these words

Answer 11

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

Question 12

homozygosity and heterozygosity

Answer 12

chromosome pair = homologous chromosomes with genes at same loci

allele at that locus may be same or diff

Question 13

define mendelian/monogenic disease

Answer 13

disease caused by a single gene, little or no impact from environment

Question 14

non mendelian/polygenic disease

Answer 14

disease or traits caused by impact of many different genes, having small individual impact e.g. psoriasis

Question 15

multifactorial disease

Answer 15

disease or trait resulting from interacting between multiple genes and multiple environmental factors e.g. heart disease

Question 16

describe linkage analysis

Answer 16

method used to map location of disease gene in genome

linkage = assumption of two things being physically linked

Question 17

linkage assumptions

Answer 17

genetic markers used to identify location of a disease gene based on their physical proximity

Question 18

importance of maps

Answer 18

maps provide context to orientate yourself and calculate distance between landmarks

Question 19

genetic maps

Answer 19

look at information in blocks or regions

Question 20

principles of genetic linkage

Answer 20

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

Question 21

describe micro satellite markers

Answer 21

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

Question 22

describe single nucleotide polymorphisms

Answer 22

- 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

Question 23

what is mirosatellite genotyping used for?

Answer 23

• 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

Question 24

describe fluorescent genotyping

Answer 24

fluorescently tagged PCR primers
allows for multiplexing of PCR products with diff colours and fragment lengths
fragment sizes separated down to 1bp resolution

Question 25

describe single nucleotide polymorphism

Answer 25

• single base change
• most common type of variation
• thought to occur approx 1 per 1000 bases
• human genome is 3 billion base pairs

Question 26

describe SNP genotyping microarrays

Answer 26

• 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

Question 27

uses of SNP genotyping microarrays

Answer 27

linkage analysis in families

GWAS in population - non mendelian and multifactorial diseases

Question 28

linkage mapping using genetic markers

Answer 28

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

Question 29

statistical analysis of linkage

Answer 29

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

Question 30

what is recombination fraction

Answer 30

proportion of recombinant births

higher LOD score = higher likelihood of linkage

Question 31

more about LODs

Answer 31

• 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

Question 32

describe parametric analysis

Answer 32

specifes analysis parameters el.g. inheritance pattern, disease, allele frequency,

Question 33

describe non parametric analysis

Answer 33

no parameters specified

looks for allele sharing between affected individuals

Question 34

describe Adam-oliver syndrome

Answer 34

neurological anomalies
cardiac malformations
vascular defects

Question 35

describe ARHGAP31

Answer 35

disease causing variant identified through candidate gene analysis of genes in minimal linkage interval