chapter 5 part 2 Flashcards
what facilitated human genome mapping efforts
- methods to identify polymorphic DNA sequences
- improved gene-mapping software
genetic markers
polymorphic DNA sequences
the availability of large numbers of DNA markers on each chromosome led to the identification of __________ ___________
linkage groups
linkage groups
clusters of systemic genes that are linked to one another
what constitutes the genetic markers used to study locations of a gene
different variants of a DNA sequence
where are genetic markers typically found?
noncoding regions of the genome
3 types of genetic markers
- variable number tandem repeats
- single nucleotide polymorphisms
- restriction fragment length polymorphisms
how long are VNTRs
short DNA sequences - 3-20 bp
where do VNTRs repeat
end-to-end in a chromosomal region
how long are SNPs
1 bp
what are SNPs
variants where one base pair is substituted by another base pair
how many SNPs in human genome
3.3 million
RFLPs
changes in DNA sequence that are detected using DNA-cutting enzymes restriction endonucleases/enzymes
restriction fragments
pieces of DNA resulting from restriction enzyme cutting
haplotype
specific array of SNPs in a small region on a single chromosome
haplotype SNP behavior during meiosis
SNPs closely linked, will be passed on together during meiosis
allelic phase
arrangement of alleles of linked genes on parental chromosomes
what does LOD score analysis compare
likelihood of obtaining genotypes/phenotypes observed in linked genes versus unlinked
what does LOD stand for
logarithm of odds ratio
formula for LOD score
log(10) = likelihood of being linked/likelihood of not being linked
theta values
recombinant frequencies
theta =
map units
theta = 0.1
10 m.u.
theta = 0
complete linkage
theta = 0.5
not linked - independent assortment
what does a LOD score of 3 or higher mean
in favor of linkage at theta value
what does a LOD score of -2 or lower mean
against genetic linkage
LOD scores between -2 and 3
inconclusive
Zmax
indicates recombination frequency most likely to be correct
what does GWAS stand for
genome-wide association studes
GWAS
detects and locates genes that influence traits as a group of multiple genes
what does GWAS identify
where in genome the genes influencing a single trait are located
what does GWAS look for associations between
traits and groups of alleles in populations
what genetic markers are typically used for GWAS
SNPs
how are GWAS results represented
Manhattan plot
how to interpret Manhattan plot
- 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
linkage disequilibrium
when frequencies of haplotypes deviate from what is expected
does disequilibrium reflect random or non-random relationships between alleles of closely linked genes
non-random
what does disequilibrium indicate
that things are linked - only way you can separate is by crossovers
does nonrandom and disequilibrium mean that the gene we are studying is associated to the SNP haplotype?
yes - closely associated
what happens when linkage disequilibrium is found in a SNP haplotype
all genes located in that chromosome region must be identified
ex. of investigating GWAS results
- CARD15 gene suggested to be associated with Crohn’s disease (NOD2)
- allies associated with CD increased inflammatory response
