Artifacts of STRs

Question 1

Types of STR mutations

Answer 1

affect length

affect sequence

Question 2

Causes for mutations that affect length

Answer 2

replication slippage

huge variation mutation rate among loci

Question 3

Causes for mutations that affect sequence

Answer 3

insertions and deletions create microvariants
nucleotide changes (not common or detectable)

Question 4

Stutter products

Answer 4

caused by replication slippage with no repair

quantify to help with interpretation of mixed samples

Question 5

Stutter products reduced by

Answer 5

longer repeat units
STR with imperfect repeat
polymerase with faster processivity

Question 6

Complete adenylation

Answer 6

polymerase often add extra A at 3’ end making the product 1 base pair longer than the template amplicon

Question 7

Incomplete adenylation

Answer 7

the polymerase didn’t add on the extra A which causes problems with differentiating microvariants

Question 8

Condition to favor complete adenylation

Answer 8

long final extension
5’ G on primers
correct starting quantity of DNA

Question 9

Causes for 3 peak patterns

Answer 9

gene duplication

extra chromosome

Question 10

Null alleles

Answer 10

template present, but not amplified

likely due to a mutation in the primer binding site

Question 11

Solutions for null alleles

Answer 11

new primers, degenerate primers (bind to mutation and non-mutation)
drop locus
reduce annealing temperature

Question 12

Peak imbalance

Answer 12

mutation in primer binding site reduces amplification efficiency