Unit 3 Exam lecture 19 Flashcards
What is the difference between a physical map and a genetic map
Genetic map = linkage map
Physical map = individual nucleotide sequence that makes up entire chromosome
What are areas of the human genome that we have not fully sequenced
centromere regions and telomere regions due to lots of repeats, dont know exactly how many repeats there are
Process of map based sequencing
- partial digestion of DNA
- large insert clones are anylized for markers or overlapping sites
- allows assembly into a contig
- subset of overlapping clones that cover entire chromosome are selected and fractured and their pieces are cloned
- each small insert clone is sequenced and then used to overlap and assemble final sequence
What is the take home of map based sequencing
that it is a laborious process
What accounts for most of the variation in human genomes
SNPs
what is the frequency if SNPs
1 SNP every 1000 bps
What is a haplotype
a combination of SNPs that are inherited together
More haplotypes indicate
more genetic diversity
less haplotypes indicate
less genetic diversity
As you get more people and start to see individuals sharing the same haplotype what do you look for
similarities in their phenotypes
Linkage disequilibrium is what
the nonrandom association between genetic variants within a haplotype
Low recombination indicates what about LD and the alleles
High LD and association between alleles is not random
High recombination indicates what about the LD and the alleles
Low LD and do not see association between alleles at different positions in the genome
Why do we care about LD
ability to pinpoint a specific allele that might be making someone sick is almost impossible with high LD
Lots of haplotypes indicate what about LD
that LD is low
few hapoltypes indicate what about LD
that LD is high
what is GWAS
approach to determine link between phenotype and genotype
What does a large green line indicate on a GWAS
that there is a high correlation between genotype and phenotype of SNP in that one region
Functional genomics looks at what
characterizing what sequences do, specifically looking at transcriptome
How are model organisms associated with functional genomics
model organisms can be used to see how genomes are different between different species
How can you use related models to infer homology
if you know what gene A does in species X, and you see Gene B in species Y is similar to gene A then you are able to infer what that Gene B does in related species
What do microarrays allows for
allow you to generate data on differences in gene expression
What do microarrays target
expression of mRNA using probes
The DNA probe in microarrays are specific to what
specific genes (like a long primer that is specific to gene)
