Gene Mapping and Disease gene identification

Question 1

What are some applications of gene mapping?

Answer 1

Indirect linkage methods can be developed for use in prenatal dx, pre symptomatic diagnosis and carrier testing.
Positional cloning of disease genes.
Characterization of the disorders-heterogeneity, penetrance, positive predictive value of mutations.
Further our understanding of disease pathogenesis.

Question 2

What is the approach to Linkage analysis-family based?

Answer 2

Family pedigrees are used to follow inheritance of a disease over a few generations, looking for a consistent inheritance of a particular region of the genome whenever the disease is transmitted.

Question 3

What is the approach to Association analysis-population based?

Answer 3

Looks for an increase or decrease in freq of a particular allele or a set of alleles in a sample of affected individuals taken from a population.

Question 4

How can you distinguish homologous chromosomes?

Answer 4

Use genetic markers-any characteristic located at the same position on a pair of homologous chromosomes that allows us to distinguish one homolog from another.

Question 5

Syntenic

Answer 5

genes that are located on the same chromosome.

Question 6

Non-recombinants?

Answer 6

No observable recombination b/w 2 genes. Chromosomes in the offspring match the 2 original parental chromosomes(DM&dm)

Question 7

Recombinant?

Answer 7

Observable recombination b/w 2 genes. Chromosomes in offspring have new combination of alleles that differs from the parental copies.(Dm & dM)

Question 8

What is independent assortment in meiosis?

Answer 8

alleles at loci on different chromosomes.

Alleles at loci on same chromosomes.

Question 9

What is recombination frequency and map distance?

Answer 9

Recombination freq is given by theta and varies b/w 0(no recombination) and 0.5(independent assortment)

Question 10

A parent must be Heterozygous informative at both loci in order to?

Answer 10

detect recombinant events. We know link b/w a polymorphic marker and the “disease”allele in heterozygotes->PHASE.
Alleles on same homolog-cis coupling
Alleles in diff homologs-trans coupling

Question 11

Co-inheritance of AD form of Retinitis Pigmentosa with marker at locus 2 and not with marker at locus 1 is an example of?

Answer 11

Heterozygosity and phase

Question 12

What is linkage?

Answer 12

Tendency for adjacent genes on the same chromosome to be transmitted together (as an intact unit) thru meiosis

Question 13

What information is needed to determine if 2 loci are linked?

Answer 13

Recombination fraction (theta), and whether theta is its truly significant->Likelihood Odds Ratio [LOD Score (z)]
Theta =0, tightly linked
Theta =.5, unlinked.

Question 14

What units is genetic distance measured in?

Answer 14

centiMorgans(cM), genetic distance on a chromosome over which, on average, one observes a recombination freq of 1%. I.e. a recomb freq of 20% b/w 2 genes is a genetic distance of 20cM.

Question 15

What are the limitations of measuring genetic distance?

Answer 15

Valid only if the number of offspring has been sufficient to confident. Ex: 4/5 children are non recombinant in a family vs. several families.

Question 16

How are linkage maps created?

Answer 16

by combining measurements of genetic distances b/w closely linked loci taken 2 at a time. Distances not strictly additive. . Sex differences in map distances due to diffs in recombs.

Question 17

What is linkage equilibrium?

Answer 17

the allelic freqs at 2 loci can be predicted by the product of the population freqs of the alleles at the individual loci-> 1:1 for recomb vs. non-recomb.

Question 18

What is Linkage disequilibrium?

Answer 18

disease producing mutation is found to be in coupling with a marker allele that is closely linked to the “disease” gene.
Alleles at diff loci are not associated at random!
Due to founder effect
Permits higher resolution map based on inferring recombs that occurred during millions of meiosis.

Question 19

What is the goal of a haplotype map? (HapMap)

Answer 19

to make LD measurements b/w a dense collection of millions of SNPs through out genome-> delineate genetic landscape of genome on a fine scale.

Question 20

What are the observations from the HapMap study? 1

Answer 20

1.Differences in allelic frequencies b/w populations are seen for a small fraction of SNPs->ancestry informative markers due to genetic drift/founder effect or selection in localized geographical regions

Question 21

What are the observations from the HapMap study? 2

Answer 21

2.Pairwise measurement of LD for neighboring SNPs allowed contiguous SNPs to be grouped together into clusters of various sizes.

Question 22

What are the observations from the HapMap study? 3

Answer 22

3.The rate of recomb showed great variation over the genome->presence of “Hotspots of recomb” separated by regions showing little or no recomb.

Question 23

What are the observations from the HapMap study? 4.

Answer 23

Boundaries b/w neighboring LD blocks and regions of markedly increased recombination are found to coincide

Question 24

Application of HapMap?

Answer 24

powerful new tool to find genetic variants that contribute to human disease.

Question 25

Why does Linkage analysis use FAMILY STUDIES?

Answer 25

to determine whether 2 genes show linkage when passed on from one generation to the next.
To determine whether 2 loci are linked; need recomb fraction (theta) and Likelihood of odds ratio (LOD)

Question 26

Theta is MAX when?

Answer 26

value of theta for which Z reaches a maximum positive value is best estimate of the distance b/w 2 loci.

Question 27

LOD scores can be generated for individual families and added together, what needs to be excluded?

Answer 27

Locus heterogeneity

Question 28

Phase known pedigree can be made possible by?

Answer 28

the availability of a 3rd generation, the strength of evidence supporting linkage is twice as great in phase-known situation as in phase-unknown.

Question 29

Linkage analysis summary?

Answer 29

Linkage at a particular theta max of a disease locus to a marker with known physical location implies disease gene locus must be nearer to marker.

Question 30

What are 2 methods used to identify genes that predispose to complex diseases or contribute to genetic variance of quantitative traits?

Answer 30

Affected pedigree member method-type of linkage analysis that relies on pairs of family members.
Association-looks for increased freq of particular alleles in affected compared with unaffected individuals in population.

Question 31

Mapping of complex traits using MODEL-FREE (NONPARAMETRIC) METHODS.

Answer 31

depend on the assumption that affected relatives are more likely to have disease predisposing alleles in common than is expected by chance alone.
Qualitative traits-affected sibpair method
Quantitative traits-highly discordant sib pair method.

Question 32

What is disease association?

Answer 32

presence of a particular allele at a locus at increased or decreased freq in affected individuals compared with controls.
Case-control study-odds ratio
Cross-sectional/cohort study-relative risk ratio
Significance is measure by x^2 test ot 95% conficence interval

Question 33

What are strengths of disease association?

Answer 33

powerful tools for pinpointing genes that contribute to genetic disease.
Relatively easy to perform.

Question 34

What are weaknesses of disease association?

Answer 34

Assoc. does not prove involvement in disease pathogenesis.
LD can lead to apparent assoc b/w an allele and disease, even when allele is functionally not involved in disease pathogenesis.

Question 35

A positive assoc b/w a disease and even one allele within an LD block does what?

Answer 35

pinpoints the location as the region containing the disease associated allele.
By using Tag SNPs-Most useful minimum set of SNPs that are capable of defining most of the haplotypes in a LD block.

Question 36

What is POSITIONAL CLONING?

Answer 36

map the location of a disease gene by linkage analysis or other means to identify the gene on the basis of map position.
Cystic fibrosis
Inflammatory bowel disease (Crohn’s)
Age-related macular Degeneration (AMD)