20.04.03 Linkage analysis

Question 1

What is linkage analysis

Answer 1

A statistical method for discovering the locations of loci underlying a trait of unknown position by testing for co-segregation with genetic polymorphisms of known position in the genome

Question 2

What does linkage analysis require

Answer 2

• Genetic marker to show a clear Mendelian pattern of inheritance.
• Informative markers (sufficient variation at locus)
• Results should be replicated to be credible.

Question 3

What is parametric linkage analysis

Answer 3

• When a series of parameters need to be specified before analysis can begin.
• e.g. Mode of inheritance, gene frequencies, penetrance

Question 4

When is parametric linkage analysis used

Answer 4

• Simple Mendelian disorders.
• not suitable for complex diseases such as diabetes or schizophrenia. i.e. conditions where we don’t know gene frequency, penetrance or mode of inheritance

Question 5

What is the recombination factor

Answer 5

• θ
• A genetic marker will segregate with disease more often the closer it is to the disease gene
• The further away the loci are the more likely recombination could occur, separating them.

Question 6

What does a θ score of 0.5 indicate

Answer 6

-That the two loci are on different chromosomes and that they segregate independently (not linked). Offspring have a 50% chance of inheriting either allele.

Question 7

What does a θ score of 0.1

Answer 7

Loci are linked, as 9/10 chance that offspring will inherit both loci

Question 8

What does 1 centiMorgan equal in terms of recombinant fraction

Answer 8

1 centimorgan= a recombinant fraction of 0.01 (1%)

Question 9

What is non-random and sex specific in terms of recombinants

Answer 9

Distribution of recombinants along a chromosome is non-random and sex-specific.

Question 10

What is an LOD score

Answer 10

• LOD= Log of the odds (Z)
• a statistical estimate of whether two genes, or a gene and a disease gene, are likely to be located near each other on a chromosome and are therefore likely to be inherited (i.e. linked).

Question 11

What LOD score is the threshold for significance for accepting linkage

Answer 11

• Z= 3

- i.e. 1000:1 odds. (log10(1000))= 3

Question 12

What LOD score is used to reject linkage

Answer 12

Z=

Question 13

Why are negative LOD scores useful

Answer 13

-They tell us where the disease gene is not. I.e. exclusion mapping

Question 14

What can make linkage analysis more efficient

Answer 14

• Multipoint mapping- data from two loci are analysed simultaneously.
• Also overcomes issues due to uninformative single markers.

Question 15

Problems with LOD score analysis

Answer 15

• Vulnerable to errors (switched samples, non-paternity, misassignment of disease)
• Computational limitations
• Locus heterogeneity
• Limits of resolution, depends on number of meioses
• Diseases with reduced penetrance, or presence of phenocopies in a family.

Question 16

What is autozygosity mapping

Answer 16

• Form of linkage analysis used in consanguineous families.

- Disease mapping blocks of homozygous markers that segregate with a disease of interest.

Question 17

What is autozygosity

Answer 17

When individuals are homozygous at a particular locus because the alleles are identical by descent- inherited from a common ancestor.

Question 18

What is non parametric linkage analysis

Answer 18

A method of mapping disease genes that does not require an inheritance model and makes no assumptions about other genes involved in disease risk.

Question 19

What is the principle behind non-parametric linkage analysis

Answer 19

The region of the genome within which the disease-causing gene is situated will be co-inherited from a common ancestor by affected members of the family more frequently that would be expected by chance.

Question 20

Which family members can be used in non-parametric linkage analysis

Answer 20

-Any set of affected relatives. Often affected sib pairs used

Question 21

What is the difference between identical by descent and identical by state

Answer 21

• Identical by descent (IBD): alleles shared by affected relatives are copies from the one specific allele present in a recent ancestor (must be demonstrable)
• Identical by state (IBS): alleles shared by affected relatives appear identical but common ancestry cannot be demonstrated. Allele frequency has to be taken into account (rare alleles suggest IBD)

Question 22

Which is considered to be more robust: parametric or non-parametric

Answer 22

Non-parametric methods are considered to be more robust

Question 23

Example of a successful non-parametric linkage analysis

Answer 23

• Crohn’s disease and NOD2 (chrom 16)
• Sibling-pairs used.
• NOD2 activated NF-kB making it responsive to bacterial lipopolysaccharides.

Question 24

Example of the limited success of non-parametric linkage analysis

Answer 24

• Genome wide scans in sib pairs to try and identify susceptibility factors in complex disease.
• often results can’t be reproduced

Question 25

What is affected sib pair analysis

Answer 25

• Model free method to identify alleles shared by affected siblings (regions identical by descent)
• If they inherit an allele more or less than would be expected by chance this indicates that the allele or its locus may be involved with disease.

Question 26

Uses of affected sib pair analysis

Answer 26

To identify genes that cause multifactorial disorders

Question 27

Steps in affected sib pair analysis

Answer 27

1. Genotype affected sib pairs (microsatellites or SNPs for whole genome). SNPs better as denser markers so more informative.
2. Markers will segregate according to Mendelian ratios unless segregation among affected people is distorted by linkage or association (i.e not 1:2:1).
3. Using combined data from all families, IBD/IBS frequencies at each locus can be determined and tested to see if it deviates from the null hypothesis of simple Mendelian segregation.
4. Regions of interest retested using more densely spaced markers in an independent data set.

Question 28

What can be inferred in affected sib pair analysis if parents are not available

Answer 28

That a variant is identical by state (not IBD). Unless a number of markers are used, as would be unlikely the parents are homozygous for a number of different markers

Question 29

Advantages and disadvantages of affected sib pair analysis

Answer 29

• Advantages= simple, robust

- Disadvantages= Large candidate regions identified. Sib pairs will share many segments by chance.

Question 30

Uses of linkage analysis in diagnostics

Answer 30

• DMD: identify high risk haplotype where no causative variant has been identified but dystophinopathy confirmed by muscle biopsy.
• SMA: identify high risk haplotype where homozygous SMN1 deletion in affected child but a parent carries 2 SMN1 on 1 allele. Linkage helps clarify carrier risk for other family members
• HD: prenatal testing where linking parent doesn’t want to know his or her HD status. If grandparent high risk haplotype is present in fetus then risk is increased to 50%. Work up must be done in advance to ensure enough informative markers.