Studied by 15 people
Class 15
DNA polymorphisms
sequence differences
anonymous: don’t affect nature or amounts of any proteins (or ncRNA) in the body
most don’t influence phenotype
can serve as a DNA marker
Single nucleotide polymorphism (SNPs)
particular base positions in the genome where alternative letters of the DNA alphabet distinguish some people from others
most common type of genetic variant
inherited co-dominantly (bi-allelic)
two alleles for each SNP locus
can be heterozygous or homozygous
on average, occurs every 1000 (1kb) base pairs in any pairwise comparison
don’t influence phenotype (are uncoded)
Simple sequence repeats (SSR or micro-satellites)
loci that sequences of one or more bases that are repeated in tandem
different alleles have different numbers of repeat units
most common repeating units are one, two, or three-base sequences
meaning, either have one, two, or three types of nucleotide involved
3% of total DNA in genome, found once every 30kb
in non-coding regions, have no effect
in coding regions, remember trinucleotide repeat diseases (slipped mispairing)?
highly polymorphic, often with over 10 alleles at a single locus
but since they have a low mutation rate (relatively stable), can serve as DNA markers
Copy number variants (CNVs)
DNA length polymorphisms involving more than just a few nucleotides (like SSRs and DIPs)
variable number of copies of large blocks of genetic material up to 1mb in length
highly polymorphic, but stable
99% of alleles are inherited (not derived from a new mutation)
Pairwise comparison
comparing two genomes side by side
DNA fingerprint/profile
genotype of 13 unlinked, polymorphic SSR loci
unique to any one person (except identical twins)
any one person only has two alleles for any given locus
main point: it’s highly unlikely (statistically) that someone has the exact same alleleic combination for multiple loci by chance (would have to be related somehow)
Polymerase chain reaction (PCR)
amplifies a target region of DNA
requires only the smallest amounts of DNA
uses two 16-30 base long oligonucleotides as primers
primers are the beginning and end of the target region
one oligonucleotide is complementary to one strand at one end while the other is complementary at the other end
primers are dyed to fluoresce different colors with the 13 SSRs
put into gel electrophoresis
can identify allelic variants for each locus based on the colors and sizes of the products
Haplotype blocks
segments of DNA with particular sets of link SNP alleles that tend to travel together from one generation to another, because they are flanked by recombination hotspots
DNA within blocks contain NO hotspots for crossing over
Genetic genealogy
the basis of genetic analysis, that relatives share haplotype blocks
more closely related = more haplotype blocks shared and the longer their uninterrupted shared DNA segments
Genetic relatedness
estimated by the fraction of autosomal DNA shared
each parent has two alleles of each SNP; each child inherits a random one of those two SNPs (from each parent)
means that the child will share half of their DNA with each parent, and with each sibling (on average)
Nucleic acid hybridization
the ability of complementary single strands of DNA or RNA to come together to form double-stranded molecules
need a perfect match between all nucleotides in primers and template
if there’s a mismatch, it’s less stable (so in experimentation, researchers can weed out the imperfect ones but taking advantage of the fact that only perfect matches can withstand a particular temperature)
Anonymous loci
polymorphisms that don’t affect phenotype
serve as molecular markers for specific regions of the genome
