Biological Artifacts (Exam 3) Flashcards
(25 cards)
What is the main cause of biological artifacts?
Too much PCR product
How much DNA can be used for PCR?
1-2 ng
Are artifacts considered real STR marker peaks?
No
What should you do if you get too much DNA from the amplification?
Dilute it as much as needed and try again
These are PCR products/artifacts that are 4 bases smaller than the original allele and are usually about 10% or below the original peak.
What are stutter products?
If a real peak/allele has 124 bases, how many bases does the stutter have?
120
How are stutter products caused?
Unavoidable strand slippage during PCR process
How do you calculate the stutter size percentage?
Divide stutter height by peak height and multiply by 100
Bruce Budowle refers to this locus as the “notorious” locus (HINT: Division 3 School, Racist Dog Whistle).
D3S1358
Why is locus D3S1358 called the “notorious” locus?
It is the only locus that sometimes has a stutter product that can go above 10%
This mutation is the addition of adenine (A) nucleotide at the end of the PCR product, occurring irrespective of whether thymine (T) is present (HINT: name the type of addition and the biochemical term).
Non-template nucleotide addition (adenylation).
With non-template nucleotide addition (adenylation), you could expect 120 bp per product, but you end up with { } bp instead.
121
This mutation is the deletion or addition of one or more bases in a repeat.
What are microvariants?
What does a microvariant amount of 9.3 mean?
-9 full repeats
-only 3 bases in one repeat
If there are 122 bp in 5 whole repeats, how many bp are in 4.3 repeats?
121
This mutation occurs when we expect two autosomal alleles, but only one shows up.
What is a null allele?
What are the 2 possibilities for why null alleles exist?
1) Mutation
2) Preferential amplification of one allele compared to the other
What does a null allele look like in Y STR analysis?
You expect one peak per locus, but it is absent
What happens to the STR peaks if there is a mutation at the 5’ end of the primer binding site in PCR?
No problem/mutation
What happens to the STR peaks if there is a mutation somewhere in the middle of the primer binding site?
One peak is smaller
What happens to the STR peaks if there is a mutation at the 3’ end of the primer binding site in PCR?
Allele drop i.e. one peak will be missing
This mutation denotes the presence of three peaks in a locus, not to be confused with mixed samples.
What is a tri-allelic pattern?
What are 3 causes of a tri-allelic pattern?
1) 2nd contributor
2) Contamination
3) Trisomy-21
In which locus do we see Trisomy-21?
D21S11
