Genetic markers

Question 1

what is a genetic marker

Answer 1

some feature in the genome that allows us to differentiate between different alleles

Question 2

uses of genetic markers

Answer 2

forensics (crime scenes, paternity tests, conservation genetics)
GWAS and QTL analysis to evaluate whether markers are associated with phenotypic variation
measuring genetic variability

Question 3

reduced representation methods

Answer 3

measure variation at intervals rather than sequencing entire genome

Question 4

copy number variation

Answer 4

type of structural variation in the genome where sections of DNA are repeated, and the number of repeats varies between individuals
not detected in traditional sequencing methods
can create phenotypic variation

Question 5

copy number variation detection

Answer 5

measure level of sequence coverage

Question 6

coverage

Answer 6

how many sequence reads there are in the genome. if there is a deletion or duplication, there will be fewer or more sequences detected

Question 7

allozymes

Answer 7

different forms of an enzyme that are encoded by different alleles at the same locus
Differ in electric charge, which affects
migration through an electric field
Detected with enzyme-specific stain
noticed variation in the same protein across individuals

Question 8

RFLP

Answer 8

undegraded DNA cut into fragments using specific restriction enzymes
fragments differ in length because of differences in number of large DNA repeats (VNTRs) which changes the distance they migrate in the gel

Question 9

microsatellite loci

Answer 9

short tandem repeats
highly polymorphic
highly abundant
can distinguish many alleles at a locus as alleles differ in the number of repeats
more repeats=shorter distance on gel

Question 10

variation at microsatellite loci

Answer 10

huge variation due to high mutation rate
slippage-misalignment of strands

Question 11

backwards slippage of newly forming strand causes..

Answer 11

insertions of repeat

Question 12

forward slippage of template strand causes..

Answer 12

deletion of repeat copy

Question 13

haplotype in terms of SNPs

Answer 13

haplotype is the specific set of SNPs and other genetic variants observed on a single chromosome or part of one. SNPs within a haplotype are physically linked and tend to be inherited together. new haplotypes can arise through mutation or crossing over which breaks up the sets of SNPs. rate of crossing over is proportional to the physical distance between genes. the nonrandom association between genetic variants within a haplotype is called linkage disequilibrium.

Question 14

uses of SNPs

Answer 14

track haplotypes
infer variation
GWAS
Studies almost always based on comparing alternative alleles at
SNP loci across the genome

Question 15

infering haplotypes using SNPs

Answer 15

if you know the SNP at one allele, can infer the rest as they are close together
using a subset of SNPs to infer rest of genome
too far apart and recombination mixes them so cant infer one from the other

Question 16

studies of linkage disequilibrium with SNPs

Answer 16

recombination is not random
there are hotspots where it occurs more by chance

Question 17

SNPs and evolution

Answer 17

distribution of SNPs provides information about regions of the genome that have evolved quickly in the recent past-shows how humans respond to natural selection

Question 18

SNPs and disease

Answer 18

when an SNP is physically close to a disease-causing locus, it will tend to be inherited along with the disease-causing allele so people with the disease tend to have SNPs near the disease-causing gene that are different from those of healthy people. (the SNPs dont normally cause the disease but are linked to disease-causing alleles).

Question 19

genealogy

Answer 19

idea that if you take all individuals now and trace them back in time all lineages will eventually coalesce to a common ancestor

Question 20

SNPs in ancestry

Answer 20

SNPs reflect ancestry of haplotypes
can infer from a set of haplotypes the ancestry
different lineages show variation at linked SNPs

Question 21

low coverage sequencing

Answer 21

Sequence individuals at very low
coverage (coverage is the average
number of ‘reads’ per base of genomic
DNA)
missing sequences inferred from known
used to infer haplotypes

Question 22

mitochondrial markers features

Answer 22

no recombination
uniparental inheritance
haploid
highly polymorphic sequences
can capture different evolutionary histories
maternal lineages
used in genotyping arrays

Question 23

genotyping arrays

Answer 23

Set of SNP loci identified
K-mer probes developed that bind to DNA– hybridisation of DNA to spots on array identifies genotype

Question 24

pros of genotyping arrays

Answer 24

low error rate– low cost per sample (especially when using existing arrays)– reliable and comparable results from each individual

Question 25

cons of genotyping arrays

Answer 25

requires adequate information on SNP loci
costly to create a new array
fixed set of SNPs may not be representative of all variation in a population
biased to reference group used to identify the SNPs

Question 26

illumina infinium assay

Answer 26

identifies SNPs
silica bead in wells of etched array have probes attached
specific SNPs hybridise to probes
(Sequence stops one base-pair from the SNP location)
Single base extension adds a fluorescently labelled base to SNP position

Question 27

SNPs in infering ancestries

Answer 27

populations differ in SNP frequencies and pattern of SNPs that are linked together along the chromosome
can find pattern of migration of humans

Question 28

genetic diversity is ….. in more recently founded populations

Answer 28

lower, isolation by distance

Question 29

chromosome painting

Answer 29

used to assign different ancestries or genealogies to specific regions of the genome based on SNP (Single Nucleotide Polymorphism) information. This technique helps visualize how different chromosome regions have distinct evolutionary histories.