Microsatellites and Individual ID
No description yet. This curated deck is ready for daily study.
Card preview (24)
What is CODIS 20 Loci?
a loci with many varients which has lot of power to individualize.
how many loci do wildlife cases use?
at least 10
for muscox and bison how many loci are used? Why?
20-40, they have little variation (very inbred)
what are the applications of microsatelites?
• individual identification • relatedness • population assignment • much more variation than markers for species ID. • no “universal” primers • sometimes used to delineate b/w very closely related species and their hybrids or breeds.
How often are STR or VNTR scattered in a genome?
~1/10,000 base pairs
where do primers go on STR regions? Why?
flank them on either side, for subsequent amplification of locus and incorporating fluorescent tags during PCR
what is the name of ACATACATACAT?
tetranucleotide
T/F: CCACCC is an uninteruppted microsatellite.
false, this is interupted
what kind of repeats are most common?
di and tetra nucleotides
T/F: STRs have high discriminating power, at >0.8 per locus.
false, it is >0.9 per locus
STRs have a high percentage of what?
heterozygotes
how do you avoid linkages of loci?
separating chromosomal locations
T/F: STRs amplify well in degraded samples and in combination with other microsatellites.
true
What are the applications of STRs?
• low stutter characteristics • low mutation rate • allele range b/w 100 and 500 bp
how large are microsatellite profiles?
7 locus profile for each individual, 14 numbers = genotype
once a microsatellite profile is created what do you do with it?
evaluate rarity of genotype in frequency of alleles in population
what are challenges with genotype interpretations?
• stutter • non-template addition • microvariants • null alleles • mutation • allelic dropout
what are stutters?
peaks smaller than allele by one or more repeats
how do stutters occur?
from DNA pol slipping during PCR
which kind of nucleotide has more stutters?
dinucleotides, tetra have some not a lot.
when do stutters happen more frequently?
repeated sequences
what is backward slippage?
in the reverse strand which is an insertion causing the backwards slippage resulting in shorter STR
what is forward slippage?
Occurs when the DNA polymerase slips forward on the template strand, leading to an extra repeat unit being added to the amplified sequence. This results in a longer PCR product than expected.
What are the complications from stutter peaks?
its hard to discern stutter from alleles when numerous sources contribute to DNA profile because stutter has same size as potential alleles