Lecture 4 - Gene mapping

Question 1

genetic linkage applies to genes that are physically linked aka _____. these (do or do not) usually undergo recombination

Answer 1

syntenic;

do not

Question 2

1% recombination = 1 map unit = 1 _____

Answer 2

cM (centimorgan)

Question 3

for detection of genetic linkage, you need to have individuals who are ____ ____

Answer 3

doubly heterozygous

Question 4

the farther apart the two genes, the ____ the likelihoood of crossover

Answer 4

greater

Question 5

____ is the determination of whether alternative alleles for 2 loci are on the same or different chromosomes

Answer 5

phase

Question 6

when alleles are on the same chromosome, they are said to be in ____. when they are on different chromosomes, they are said to be in _____

Answer 6

coupling,

repulsion

Question 7

____ = a group of alleles in coupling at closely linked loci ie genes that are usually transmitted as a unit

Answer 7

haplotype

Question 8

linkage vs association methods:
which follows inheritance of a disease in family pedigrees?

which looks at frequency of alleles/haplotypes with controls in a population?

Answer 8

linkage, association

Question 9

linkage v association:

which relies on finding a set of alleles that stay together due to lack of recombination?

which relies on recombination events occuring only in a few generations?

Answer 9

association,

linkage

Question 10

linkage v association:

which is used with disease that require a strong mendelian inheritance pattern?

which can be used for more complex traits?

Answer 10

linkage;

association

Question 11

____ looks at whether a marker and a disease tend to be inherited together

Answer 11

genetic linkage (Family study)

Question 12

LOD score equation

Answer 12

(likelihood of pedigree if 2 loci are linked) / (likelihood of pedigree if 2 foci are not linked)

Question 13

if LOD is negative, ____ linkage.
if LOD is positive, _____ linkage.

LOD of ____ considered good evidence of linkage

Answer 13

against,
for;

+3 or greater

Question 14

____ mapping is v useful for AR traits in populations in which consanquinity is common

Answer 14

homozygous

Question 15

with homozygosity mapping, you test multiple markers around a genome. you expect homozygosity for ____ linked markers

Answer 15

closely

Question 16

____ is when a particular maker allele is found significantly more or less frequently in a group of affected individuals than would be expected from the population frequency of the allele.

example =

Answer 16

association;

HLAB27 and ankylosing spondylitis

Question 17

2 loci are said to be in ____ _____ if specific combinations of alleles occurr more or less frequently than would be expected by change

Answer 17

linkage disequilibrium

Question 18

whole ____ sequencing focuses on coding regions only;

whole _____ sequencing looks at the entire genomic sequence

Answer 18

exome;

genomic

Question 19

whole exome vs whole genome:

which requires washing uncaptured DNA?

which mostly captures mutations resulting in changes in protein structure

which is associated with technical bias?

Answer 19

whole exome;
whole exome;
whole exome

Question 20

the goal of whole exome sequencing filtering is to retain ___ ____ with a predicted harmful effect on biological function

Answer 20

rare SNPs

Question 21

the simplest case of using Whole exome sequencing is in a ____ ____ disease

Answer 21

autosomal recessive