Unit 2: 10

Question 0

Name some disadvantages of indirect testing with markers

Answer 0

• need correct diagnosis and no locus heterogeneity (or use links to est which is involved)
• DNA from critical family members will be needed and their cooperation is required - paternity must be correct
• need to find marker that is informative -need to “flag” bad gene to answer the clinical question
• if using extrageneic markers there maybe an error rate associated with recombination -thus intragenic markers are better than extragenic because recombination is usually not an issue

Question 1

When do we use indirect genetic testing with markers ?

Answer 1

• Whenever it is not possible to test for disease causing mutations either because there are too many mutations or because the disease causing gene although mapped is not known, it may still be possible to use linked markers to perform carrier testing and or prenatal diagnosis
• when a genetic disease has a large gene and many mutations, it is often impractical and or to costly to find the disease causing mutation
• an alternative is to perform an indirect test using a linkage analysis with linked markers

Question 2

Define mutation

Answer 2

a permanant heritable change in a genomic DNA sequence, often incorrectly used to indicate “bad” change

Question 3

Define polymorphism

Answer 3

is a sequence variant found at a frequency of at least 1% ( at least 2% of people are heterozygotes)
-often incorrectly used to mean benign

Question 4

Define “rare genetic event”

Answer 4

a mutation with a frequency of less than 1%

Question 5

Define Haplotype

Answer 5

a group of alleles from closely linked loci, usually inherited as a unit

Question 6

Define crossing-over

Answer 6

• the reciprocal exchange of segments between chromatids of homologous chromosomes
• mechanism of recombination
• happens at prophase of first meiotic division

Question 7

define recombination distance

Answer 7

1 centiMorgan (cM) is a 1% chance of recombination between loci as the chromosome is passed from parent to child (per generation) 
- on average 1 cM = 10^6 bp

Question 8

Define linkage disequilibrium

Answer 8

• the tendency of specific combinations of alleles at two or more linked loci to occur together (in coupling) on the same chromosome more frequently than would be expected by chance
• the deviation from Mendel’s second law of independent assortment
• IS THE DIFFERENCE BTWN THE GENOTYPE FREQUENCIES AND THE PRODUCT OF THE ALLEL FREQUENCIES
• decays with recombination distance and time
• can indicate that loci are close and can be used to indicate that a gene mapping is closing in on target gene (ie km19 for CTFR)

Question 9

Describe linkage disequilibrium in CF gene

Answer 9

• the delta F508 CF mutation arose once, it arose on chromosome 7 with the 2.1 kb Taq allele at xv-2cand 6.6 kb Pst I allele at km19 which are marker loci bout 60 kb from CTFR
• over the succeeding generations there have been few cross-over events between these marker loci and he CTFR gene such that the DElta F508 mutation is still usually found (>90%) with these alleles at theses loci

Question 10

Name the three classes of mutations

Answer 10

• linked extragenic markers (label attached to suitcase by a length of string)
• intragenic markers (label on suitcase)
• disease-causing mutations (see inside suitcase)

Question 11

duchenne muscular dystrophy gene is the exception to what

Answer 11

usually intragenic markers have insignificant recombination with disease causing mutation, but this gene is so large that it may still have a significant recombination rate with disease causing mutation

Question 12

Ways to get best results for indirect testing

Answer 12

• using flanking markers rather than two on one side

- use first degree relatives

Question 13

Define coupling

Answer 13

alleles at two different loci are said to be in coupling when on the same chromosome (in cis)

Question 14

Define repulsion

Answer 14

alleles at different loci are said to be in repulsion when on opposite chromosomes (trans)

Question 15

Define phase

Answer 15

• when mutations are known to be on the same of different homologous chromosomes -known to be in coupling or repulsion then phase is said to be known
• when it is not known which mutation is on which homologous chromosome -ie whether the alleles at different loci are in coupling or repulsion, then phase is unknown.

Question 16

Lod score

Answer 16

• statistical method that tests genetic marker data in families to determine whether two loci are linked
• the lod score is the logarithm to base 10 of the odds in favor of linkage
• by convention a lod of 3 in an autosome or 2 in an X-linked is taken as proof of linkage, and a lod score of -2 as proof that loci are unlinked
• threshold for a genome wide level allowing for multiple markers is 3.3 while for non-medelian characters any score below 5 should be regarded as provisional

Question 17

Math behind lod score

Answer 17

theta = recombination distance

likelihood of odds = likelihood data/given theta / likelihood (data/ theta = .5)

for a lod score to be meaningful it needs to be associated with a specific recombination distance

• a series of likelihood ratios (relative odds) are calculated at various possible recombination distances and plotted in a table or graph. Typically theta varies from 0 (complete linkage) to .50 (when unlinked)
• the value of theta that gives the highest value of Z is the best estimate of the distance btwn markers