STR Analysis

Question 1

for heterozygous loci (equation)

Answer 1

P = 2pq

Question 2

P

Answer 2

probability

Question 3

p & q

Answer 3

frequencies of alleles in a given population

Question 4

find the probability: for the locus D3S1358 & individual is 15,18 with frequencies of 0.2825 & 0.1450 respectively

Answer 4

P = 2(0.2825)(0.1450) = 0.0819

Question 5

3 steps in data interpretation

Answer 5

• asses the internal size standards (ISS), allelic ladders & controls
• assess each sample for the presence of extraneous peaks & determine if they may interfere with the interpretation process
• assess the data from each sample

Question 6

Internal Size Standards (ISS)

Answer 6

• contains DNA fragments of known sizes that provide reference points determining the length of a samples DNA fragments
• in general, the peaks or bands from as ISS are uniformity or miscalled peaks cans indicate problems with the sample, injection &/or run

Question 7

allelic ladder

Answer 7

contain the more common alleles in general population for specific chromosomal locations

Question 8

positive control

Answer 8

• positive controls are included in most commercial DNA analysis kits
• amplified with each batch of samples
• show the expected alleles
• if no peaks are seen, this may indicate problem with amplification or injection

Question 9

ISS negative control

Answer 9

see nothing

Question 10

ISS data evaluation

Answer 10

peak height percentage

Question 11

Peak Height Percentage

Answer 11

• heterozygous peaks within a locus should be similar in height to each other
• heterozygous alleles have peak heights that are within 70% of each other

Question 12

peak height percentage: degraded DNA

Answer 12

may have peak height percentages much lower than 70%

Question 13

how to calculate Peak Height Percentage

Answer 13

(small/big) * 100

Question 14

sex identification with Amelogenin

Answer 14

6 bp deletion on the X chromosome

Question 15

the following may indicate a mixture:

Answer 15

• the presence of more than 2 alleles at any one locus
• imbalanced &/or unexpected peak height percentage

Question 16

what to do after indication its a mixture

Answer 16

it may be helpful to use the case info &/or sample type to aid in the interpretation

Question 17

minor/major contributors

Answer 17

determining genotype of major contributor is easier than determining the minor contributor

Question 18

with known contributors

Answer 18

• subtract the contribution of the known donor from the mixed profile
• common aproach for intimate samples

Question 19

unknown contributors

Answer 19

• 2 or more people
• commonly use the approach of estimating percent contribution or percent peak height ratio

Question 20

calculating percent contribution

Answer 20

• assuming there are 2 donors, the mixture proportions are estimated by summing the peak heights of the 2 major or minor alleles & dividing by the peak heights of all four alleles
• this is multiplied by 100 to provide a percentage contribution

Question 21

reporting guidelines

Answer 21

• inclusion/match
• exclusion/nonmatch
• inconclusive/uninterpretable
• no results

Question 22

reporting guidelines: inclusion/match

Answer 22

all loci match between a questioned & known sample

Question 23

reporting guidelines: exclusion/nonmatch

Answer 23

one locus does not match

Question 24

reporting guidelines: inconclusive/uninterpretable

Answer 24

a potential determination with complex mixtures or degraded samples

Question 25

reporting guidelines: no results

Answer 25

no discernable allelic activity observed at a locus

Question 26

common interpretation problems

Answer 26

• thresholds
• spurious peaks
• stutter
• degradation
• allelic drop out

Question 27

common interpretation problems: thresholds

Answer 27

• established peak-height levels for scoring alleles
• only if fluorescence exceeds this value
• each laboratory must set its own as part of its validation procedure

Question 28

common interpretation problems: spurious peaks

Answer 28

• dye blobs, noise, spikes
• not reproducible - run the sample again

Question 29

common interpretation problems: stutter

Answer 29

• by-product of the amplification of STR loci - a minor product, typically one repeat smaller than the primary allele is generated
• due to slipped strand mispairing during the amplification process

Question 30

common interpretation problems: degradation

Answer 30

can result in a partial profile or null allele

Question 31

common interpretation problems: allelic dropout

Answer 31

• the initial input quantity of DNA is too low, resulting in the failure to amplify one or more alleles in the sample
• a mutation in the primer binding site is present, which causes a failure in the amplification of the allele

Question 32

allelic dropout

Answer 32

a sample is typed & one or more alleles are not present