chapter 5 part 2

Question 1

what facilitated human genome mapping efforts

Answer 1

• methods to identify polymorphic DNA sequences
• improved gene-mapping software

Question 2

genetic markers

Answer 2

polymorphic DNA sequences

Question 3

the availability of large numbers of DNA markers on each chromosome led to the identification of __________ ___________

Answer 3

linkage groups

Question 4

linkage groups

Answer 4

clusters of systemic genes that are linked to one another

Question 5

what constitutes the genetic markers used to study locations of a gene

Answer 5

different variants of a DNA sequence

Question 6

where are genetic markers typically found?

Answer 6

noncoding regions of the genome

Question 7

3 types of genetic markers

Answer 7

1. variable number tandem repeats
2. single nucleotide polymorphisms
3. restriction fragment length polymorphisms

Question 8

how long are VNTRs

Answer 8

short DNA sequences - 3-20 bp

Question 9

where do VNTRs repeat

Answer 9

end-to-end in a chromosomal region

Question 10

how long are SNPs

Answer 10

1 bp

Question 11

what are SNPs

Answer 11

variants where one base pair is substituted by another base pair

Question 12

how many SNPs in human genome

Answer 12

3.3 million

Question 13

RFLPs

Answer 13

changes in DNA sequence that are detected using DNA-cutting enzymes restriction endonucleases/enzymes

Question 14

restriction fragments

Answer 14

pieces of DNA resulting from restriction enzyme cutting

Question 15

haplotype

Answer 15

specific array of SNPs in a small region on a single chromosome

Question 16

haplotype SNP behavior during meiosis

Answer 16

SNPs closely linked, will be passed on together during meiosis

Question 17

allelic phase

Answer 17

arrangement of alleles of linked genes on parental chromosomes

Question 18

what does LOD score analysis compare

Answer 18

likelihood of obtaining genotypes/phenotypes observed in linked genes versus unlinked

Question 19

what does LOD stand for

Answer 19

logarithm of odds ratio

Question 20

formula for LOD score

Answer 20

log(10) = likelihood of being linked/likelihood of not being linked

Question 21

theta values

Answer 21

recombinant frequencies

Question 22

theta =

Answer 22

map units

Question 23

theta = 0.1

Answer 23

10 m.u.

Question 24

theta = 0

Answer 24

complete linkage

Question 25

theta = 0.5

Answer 25

not linked - independent assortment

Question 26

what does a LOD score of 3 or higher mean

Answer 26

in favor of linkage at theta value

Question 27

what does a LOD score of -2 or lower mean

Answer 27

against genetic linkage

Question 28

LOD scores between -2 and 3

Answer 28

inconclusive

Question 29

Zmax

Answer 29

indicates recombination frequency most likely to be correct

Question 30

what does GWAS stand for

Answer 30

genome-wide association studes

Question 31

GWAS

Answer 31

detects and locates genes that influence traits as a group of multiple genes

Question 32

what does GWAS identify

Answer 32

where in genome the genes influencing a single trait are located

Question 33

what does GWAS look for associations between

Answer 33

traits and groups of alleles in populations

Question 34

what genetic markers are typically used for GWAS

Answer 34

SNPs

Question 35

how are GWAS results represented

Answer 35

Manhattan plot

Question 36

how to interpret Manhattan plot

Answer 36

- bars show locations of genes contributing to traits - higher the green bar, the stronger the association between a potential contributing gene and a chromosomal location

Question 37

linkage disequilibrium

Answer 37

when frequencies of haplotypes deviate from what is expected

Question 38

does disequilibrium reflect random or non-random relationships between alleles of closely linked genes

Answer 38

non-random

Question 39

what does disequilibrium indicate

Answer 39

that things are linked - only way you can separate is by crossovers

Question 40

does nonrandom and disequilibrium mean that the gene we are studying is associated to the SNP haplotype?

Answer 40

yes - closely associated

Question 41

what happens when linkage disequilibrium is found in a SNP haplotype

Answer 41

all genes located in that chromosome region must be identified

Question 42

ex. of investigating GWAS results

Answer 42

- CARD15 gene suggested to be associated with Crohn's disease (NOD2) - allies associated with CD increased inflammatory response