Biological Artifacts (Exam 3)

Question 1

What is the main cause of biological artifacts?

Answer 1

Too much PCR product

Question 2

How much DNA can be used for PCR?

Answer 2

1-2 ng

Question 3

Are artifacts considered real STR marker peaks?

Answer 3

No

Question 4

What should you do if you get too much DNA from the amplification?

Answer 4

Dilute it as much as needed and try again

Question 5

These are PCR products/artifacts that are 4 bases smaller than the original allele and are usually about 10% or below the original peak.

Answer 5

What are stutter products?

Question 6

If a real peak/allele has 124 bases, how many bases does the stutter have?

Answer 6

120

Question 7

How are stutter products caused?

Answer 7

Unavoidable strand slippage during PCR process

Question 8

How do you calculate the stutter size percentage?

Answer 8

Divide stutter height by peak height and multiply by 100

Question 9

Bruce Budowle refers to this locus as the “notorious” locus (HINT: Division 3 School, Racist Dog Whistle).

Answer 9

D3S1358

Question 10

Why is locus D3S1358 called the “notorious” locus?

Answer 10

It is the only locus that sometimes has a stutter product that can go above 10%

Question 11

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).

Answer 11

Non-template nucleotide addition (adenylation).

Question 12

With non-template nucleotide addition (adenylation), you could expect 120 bp per product, but you end up with { } bp instead.

Answer 12

121

Question 13

This mutation is the deletion or addition of one or more bases in a repeat.

Answer 13

What are microvariants?

Question 14

What does a microvariant amount of 9.3 mean?

Answer 14

-9 full repeats
-only 3 bases in one repeat

Question 15

If there are 122 bp in 5 whole repeats, how many bp are in 4.3 repeats?

Answer 15

121

Question 16

This mutation occurs when we expect two autosomal alleles, but only one shows up.

Answer 16

What is a null allele?

Question 17

What are the 2 possibilities for why null alleles exist?

Answer 17

1) Mutation
2) Preferential amplification of one allele compared to the other

Question 18

What does a null allele look like in Y STR analysis?

Answer 18

You expect one peak per locus, but it is absent

Question 19

What happens to the STR peaks if there is a mutation at the 5’ end of the primer binding site in PCR?

Answer 19

No problem/mutation

Question 20

What happens to the STR peaks if there is a mutation somewhere in the middle of the primer binding site?

Answer 20

One peak is smaller

Question 21

What happens to the STR peaks if there is a mutation at the 3’ end of the primer binding site in PCR?

Answer 21

Allele drop i.e. one peak will be missing

Question 22

This mutation denotes the presence of three peaks in a locus, not to be confused with mixed samples.

Answer 22

What is a tri-allelic pattern?

Question 23

What are 3 causes of a tri-allelic pattern?

Answer 23

1) 2nd contributor
2) Contamination
3) Trisomy-21

Question 24

In which locus do we see Trisomy-21?

Answer 24

D21S11

Question 25

When setting parameters during the analysis of raw STR data, what is the initial peak that is excluded?

Answer 25

The primer peak