Lecture 10 Flashcards
Genome-wide association studies
- seek correlations between SNP patterns and phenotype in large groups of individuals
- seek SNPs that are shared with much greater frequency among individuals with the same trait than among others
SNPs (single nucleotide polymorphisms)
- sites in a genome where the DNA base varies in at least 1% of the population
- SNPs span the genome, rather than define a single gene (can be anywhere among our roughly 3.3 billion base pairs)
Study designs
- cohort study
- case-control study
- “affected sibling pair” strategy
- homozygosity mapping
The “affected sibling pair” strategy
scans genomes of siblings for SNPs shared by those with the condition, but not by those who don’t have it
homozygosity mapping
performed on families that are consanguineous - the children in this case are more likely to inherit two copies of the mutation
limitations of genome-wide association studies
- they include many data points and so are prone to error (false positives)
- they reveal associations between two types of information, not causes
- bias can be introduced in the way the patient population is selected
- their accuracy is affected by complicating factors, such as phenocopy and epistasis
- they may miss extremely rare SNPs
gene pool
the collection of all alleles in the members of the population
population genetics
the study of the genetics of a population and how the alleles vary with time
gene flow
movement of alleles between populations when people migrate and mate
microevolution
the small genetic changes due to changing allelic frequencies in populations
five factors:
1) nonrandom mating
2) migration
3) genetic drift
4) mutation
5) natural selection
macroevolution
- refers to the formation of new species
- occurs when enough microevolutionary changes have occurred to prevent individuals from two different populations from interbreeding to successfully produce fertile offspring
Hardy-weinberg equation
explains how allele frequencies predict genotypic and phenotypic frequencies in a population of diploid, sexually–reproducing species
what did hardy-weibberg disprove
disproved the assumption that dominant traits would become more common, while recessive traits would become rarer
Hardy-weinberg equilibrium
allele and genotypic frequencies do not change from one generation to the next
What’s uncommon for hardy-weinberg equilibrium?
it is uncommon for mutation in protein-encoding genes that affect the phenotype
but it does apply to mutations in portions of the genome that do not have a large affect on phenotype
these include many repeated DNA segments - “neutral variants that are not subject to natural selection
What is DNA repeats and what are the two types of repeats
Short repeated segments that can be considered as alleles and used to classify individuals
1) Variable number of tandem repeats (VNTRs) - minisatellites
2) Short tandem repeats (STRs) - microsatellites
DNA profiling
-a technique that detects differences in repeat copy number
what does DNA profiling calculate?
the probability that certain combinations can occur in two sources of DNA by chance
-DNA evidence is more often valuable in excluding a suspect
Who is DNA profiling developed by?
by British geneticist Sir Alec Jeffreys in the 1980s
What is another name for DNA profiling?
DNA fingerprinting because it identifies individuals
Polymerase chain reaction
2 primers complementary to 3’ end of sense and antisense strands of DNA
heat tolerant Taq DNA polymerase
DNA sources
- DNA obtained from any cell with a nucleus
- STR (amplified via PCR) are useful when DNA is scarce
- if DNA is extremely damaged, mitochondrial DNA (mtDNA) is sometimes used
- for forensics, the FBI developed the Combined DNA Index System (CODIS) - uses 13 STRs
CODIS
The probability that any two individuals have same 13 markers is 1 in 250 trillion
How is DNA profiling expanded?
by tracking repeats in different chromosomes - the number of copies of a repeat are assigned probabilities based on their observed frequencies in a population
