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MCB1 Block 4 > Recombination, Linkage & Gene mapping > Flashcards

Recombination, Linkage & Gene mapping Flashcards

(75 cards)

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1
Q

What are the two approaches to identifying genes?

A

Functional cloning & positional cloning

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2
Q

how does functional cloning identify genes

A

identify a gene by it’s product

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3
Q

what do you have to know in order to successfully do functional cloning

A

have some knowledge of its function

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4
Q

how does positional cloning identify a gene

A

by its location

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5
Q

Positional cloning uses markers to do what

A

to look for association of marker with phenotype which will show the genotype

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6
Q

if you see linkage b/w marker and disease you know what

A

disease must be in that area

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7
Q

is positional cloning family specific?

A

yes

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8
Q

when is positional cloning easier to use

A

mendelian disorders with predictable inheritance patterns

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9
Q

mapping the disease allele to specific marker position is what

A

positional cloning

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10
Q

what is used to find gene for achondorplasia

A

positional cloning

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11
Q

when does crossing over occur

A

prophase 1

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12
Q

there is at least how many recombinations per homologous chromosome pair

A

one

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13
Q

what is mendel’s second law

A

genes segregate independently of each other

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14
Q

for each gene, there’s two alleles, each one from where?

A

a different parent

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15
Q

what is linkage

A

the tendency for two different oci to be transmitted together as an intact unit through meiosis

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16
Q

linkage is opposing what?

A

mendel’s second law

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17
Q

mendel’s law is only true if what

A

linkage doesn’t occur

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18
Q

when is linkage analysis used

A

mapping genes

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19
Q

if there are parental types did recombination happen

A

no

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20
Q

if there are nonparental types did recombinatino happen

A

yes

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21
Q

what is used to determine how often recombination happens b/w the marker and gene

A

estimate of distance

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22
Q

how much recombination frequency is the theoretical maximum

A

50%

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23
Q

what is chance offspring will have parental type

A

50%

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24
Q

what is chance offspring will have nonparental type

A

50%

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25
genes far apart on the same chromosome will exhibit how much recombination
50%
26
if there is 50% recombination is there linkage
no
27
if two markers are close together what happens to probability that there will be recombination
less chance of recombination
28
if two markers are close together what happens to probability that there will be recombination
less chance of recombination
29
what is genetic distance
estimate of physical distance measured by frequency of recombination b/w two loci
30
what is physical distance
the actual distance b/w two loci measured in basepairs
31
what happens to loci that are tightly linked
they will most likely stay together through multiple generations
32
there is an average of how many recombinations on homologous chromosmes in humans
2
33
1cM = how many base pair?
1.1 million basepair
34
is recombination random?
no it is non-random, different chromosomes have recombination at different frequencies
35
describe the diffrence b/w female and male recombination rate
females have higher recombinatino rate and so have larger genetic maps
36
males and females have different genetic maps, why?
females have higher recombination rate
37
are genetic maps in line with physical map?
no, just rough estimate of each other
38
why is there more recomination in females?
b/c females oocytes arrest in prophase 1 (which is where recombination happens) for years
39
what is minimum number of samples needed for dominant disease
10
40
what is minimum number of samples needed for recessive disease
20
41
are larger or smaller families more informative
larger
42
In the positional cloning workflow, what steps are taken care of b/c of genome project
second and third steps: obtaining clones of all DNA in region & identifying all the genes in the region
43
what do we still have to do in positional cloning workflow
still have to define candidate region, prioritize them for mutation screening, test candidate genes for mutations n affected people
44
What does DSH stand for?
Dyschromatosis Symmetrica Hereditaria
45
What is MOI of DSH
AD
46
how do we assess how reliable our linkage calculations are
use lod score
47
what does lod stand for
log of the odds
48
what does a lod score compare
the probabliity of obtaining our data if the 2 loci are linked at theta value versus the probablitiy that they are not linked
49
theta value tells you waht
distance
50
lod value tells you what
how reliable the distance is from theta value
51
if Z > 0 (positive) what does that mean
evidence for linkage
52
If Z < 0 (negative number) what does that mean
evidence against lnkage
53
What does it mean if Z > (or equal to) 3
statistically reliable evidence for linkage
54
what p value does Z>3 mean
p value = .05
55
If Z < -2 what does that mean
statistically reliable evidence against linkage
56
what p value does Z < -2 mean
p value = .05
57
if Z is b/w -2 and 3 what does that mean
evidence is inconvlusive
58
what is the actual theta value when looking at a graph
pick the peak of the curve
59
.1 theta is how many cM
10
60
when analyzig statistically reliable Z scores, which one is closest to disease gene
the one with smallest theta value
61
what is used to narrow down linkage analysis
haplotype analysis
62
In the DSH disease where was the mutation they found (what gene?)
DSRAD gene
63
function of protein can be looked at by doing what
sequencing among evolution - so seeing if sequence of gene that makes protein is conserved throughout different species
64
what types of mutations are causing DSH
null - loss of function
65
If DSH has loss of function leading to disease what is causing it
haploinsufficiency
66
if a chromosomal translcoation disrupts a gene it results in what
same phenotype as point mutation
67
can you see breakpoint karyotype
yes you can see but can't identify where it is
68
what method woudl you use to identify where breakpoint is
FISH
69
when you see homozygosity coming from same ancestral origin what is it
autozygosity
70
In autozygosity mapping if it is black what does it mean
homozygosity for the snps
71
what is exome sequecing
method for specifcially the coding regions of all genes
72
what allows identification of disease genes when linkage isn't present
exome sequencing
73
symptoms: distinctive faces, cardiac & skeeltal abonomalities, immunological problems, mental retardation, is what disease
kabuki syndrome
74
what disease was found using exome sequencing
kabuki syndrome
75
they think that kabuki syndrome is AD, what would cause it to be dominant
haploinsufficiency

MCB1 Block 4 (17 decks)

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