Linkage and Recombination

Question 1

indirect testing with markers

Answer 1

• not possible to test for disease causing mutations because too many mutations or because gene isn’t known- use linkage to perform carrier testing or prenatal diagnosis
• when disease is on large gene its impractical to try and find disease causing mutation
• indirect test using linkage analysis

Question 2

disadvantages of indirect testing with linkage

Answer 2

• need correct disease diagnosis and no locus heterogeneity
• DNA from critical family members will be needed and their cooperation is required- paternity needs to be as stated!
• need to find marker that is informative- need to flag bad gene
• if using extragenic marker, error rate associated with recombination-intragenic better

Question 3

polymorphisms

Answer 3

• need to flag the chromosomes to follow them through meiosis
• SNPs or microsatellites (Tandem repeats)
• microsatellites likely more variable and thus more useful than SNPs, but higher mutation rate so need more than one marker

Question 4

mutation

Answer 4

• permanent heritable change in genomic DNA sequence

- often used incorrectly to indicate a bad change

Question 5

polumorphism

Answer 5

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

Question 6

-rare genetic variant

Answer 6

-mutation with a frequency of less than 1%

Question 7

informative markers

Answer 7

• ex- parents are heterozygote carriers and affected child is homozygous- can id gene that travels with disease causing gene
• if parents were homozygote and child hetero- can’t tell because all progeny will be hetero
• if parents hetero but child is too- can’t tell (parents don’t have it) two 1/2 combos- one diseased one not (risk-50%)

**disease is linked to different alleles in different families

Question 8

recombination

Answer 8

• formation of new combinations of linked genes by crossing over between loci
• on average three crossovers per chromosome per generation

Question 9

linkage/haplotype

Answer 9

• genes close enough together on the same chromosome have a tendency to be transmitted together through meiosis more often than expected by chance
• linked genes form haplotypes

Question 10

haplotype

Answer 10

• a group of alleles from closely linked loci, usually inherited as a unit
• a set of restriction fragment lenth polymorphisms closely linked to one another and to a gene of interest

Question 11

crossing over

Answer 11

• reciprocal exchange of segments between chromatids of homologous chromosomes
• mechanism of recombination
• happens at prophase I
• misalignment can lead to deletions or duplications

Question 12

double corssovers

Answer 12

-the reason why map distance and recombination fraction don’t follow same path

Question 13

centimorgan (cM)

Answer 13

-1 cM is a 1% chance of recombination between loci as the chromosome is passed from parent to child

Question 14

recombination distance

Answer 14

• 3,300 cM in human genome

- 1 cM per 10^6 bp, average chromosome is 150 cM, but that can vary

Question 15

linkage disequilibrium

Answer 15

• tendency of specific combinations of alleles at two or more linked loci to occur together (in coupling) on the same chromosome more frequently than one would expect by chance
• deviation from Mendel’s second law of Independent Assortment
• is the difference between genotypic frequencies and the product of the allele frequencies
• decays with recombination distance and time
• can indicate loci are close and can be used to indicate that gene mapping is closing in on target gene

Question 16

linkage disequilibrium and CF

Answer 16

• deltaF508 arose on chromosome 7 with markers 60 kb from CFTR
• few crossover events, CFTR still found with the same alleles
• mutation arose once in human history 52,000 years ago
• same conserved region of mutation

Question 17

three classes of mutations

Answer 17

• linked extragenic markers-label attached to suitcase by string (the longer the string the more likely crossing over will happen)
• intragenic-label on suitcase
• disease causing mutations-see inside suitcase

**DMD intragenic still have high rates of recombination because gene is so big

**flanking markers more useful- double cross over to cause error

Question 18

coupling

Answer 18

• alleles at different loci are in coupling when on the same chromosome
• cis
• likely to travel together onto next generation-depends on recombination distance
• same parent inheritence

Question 19

repulsion

Answer 19

• alleles at different loci are in repulsion when on opposite chromosome
• trans
• different parent inheritence

Question 20

phase

Answer 20

• mutations are known to be on the same or different homologous chromosomes (2- one from mom, one from dad), in coupling or repulsion, phase is known
• unknown when it is not known which mutation is on which homologous crhomosome
• can tell down pedigree but not up

Question 21

theta

Answer 21

• recombination distance

- see pedigrees

Question 22

Lod Score

Answer 22

• statistical method that tests genetic marker data in families to determine whether two loci are linked
• lod score is the log base 10 of the odds in favor of linkage
• lod of 3 in autosome or 2 in x-linked is taken as proof of linkage and -2 is unlinked
• threshold for a genome wide level allowing for multiple markers is 3.3, for non-mendelian characters any score below 5 is provisional
• series of likelihood ratios at various possible recombination distances and plotted in a table or graph
• theta varies from 0 (linked) -0.5 (unlinked)
• value of theta that gives highest value of Z is best estimate of distance between marker and disease causing gene (7 in family)

Question 23

likelihood of odds

Answer 23

= [likelihood (data/given theta)]/ [likelihood (data/given theta=0.5)]

Question 24

Meiotic Recombination Hot Spots

Answer 24

• 30,000 + spaced om average every 50-100 kb
• avoid coding regions
• 1-2kb long
• 13 bp motif is over represented in ~40% of hotspots
• variation within motif associated with variation in hotspot activity
• PRDM9, several tandem zinc fingers of 28 aa, recognizes this motif and trimethylates H3K4 on nucleosomes
• PRDM9 and hotspots are rapidly evolving