Mixtures and Incomplete DNA Profiles

Question 1

What are the repeating units within an STR marker called?

Answer 1

motif

Question 2

When is a profile described as mixed?

Answer 2

When it contains DNA from two or more individuals

Question 3

What are the major issues associated with aspects of complex interpretation?

Answer 3

1. incomplete information
2. scenarios where relatives are connected with the crime profile
3. mixtures

Question 4

Why has DNA mixtures and trace DNA become so prevalent?

Answer 4

• can generate a profile from just a few skin cells
• very little DNA is needed

Question 5

What is the problem with DNA mixtures?

Answer 5

• difficult to determine how and in what order the DNA was deposited
• may prevent statistical evaluation
• low level DNA transfer may lack information

Question 6

What is the issue with the high sensitivity of new multiplexes?

Answer 6

When sensitivity was lower they wouldnt have been able to detect small amounts of DNA that we just naturally shed but now we can
* might cause mixtures of unrelated people

Question 7

What type of probability is Pr(B | A)?

Answer 7

Conditional

Question 8

What is the | called in Pr(B | A) and what does it mean?

Answer 8

Conditioning bar
* given or if the events behind this bar (B) are true what is the probability of A occuring

Question 9

What is the odds equation?

Answer 9

odds = probability / (1 - probability)

Question 10

If in single source DNA profiles we use the random match probabiloty, what do we do with a mixed profile?

Answer 10

liklihood ratio

Question 11

What is the liklihood ratio?

Answer 11

probability of the evidence under prosecution hypothesis / probability of the evidence under defence hypothesis

Question 12

What are the three main factors that make mixtures complex?

Answer 12

• How many people contributed DNA to the mixture
• How much DNA did each person contribute
• How degraded is the DNA

Question 13

What do the different liklihood ratio results mean?

Answer 13

1 = neutral
1< = supports the prosecution
1> = supports the defence

Question 14

What is the issue with very small peaks on an EPG?

Answer 14

• they might disappear entirely (drop out of the profile)
• small blips could be mistaken as real peaks (drop in to the profile)

Question 15

What are the two thresholds that are set to know if a peak is real or just an artefact?

Answer 15

• AT: analytical threshold
• ST: stochastic threshold

Question 16

What is probabilisitic genotyping software?

Answer 16

• uses statistical and biological methods to calculate probabilities
• accounts for drop-in and drop-out and other effects by using mathematics to approximate what happens in a real mixture
• considers that some alleles are more common in the population than others

Question 17

What is continous probabilistic methods?

Answer 17

• uses all the data present, including allele and peak height, and incorporates biological parameters
• uses quantitative information from peak heights to calculate the probability of the observed peak heights given all possible genotype combinations

Question 18

What are the biological parameters that continous probabilistic methods incorporates?

Answer 18

• peak height ratios
• mixture ratios
• stutter percentages

Question 19

What is the semi-continous probabilistic method?

Answer 19

• uses height information and alleles present in a mixture without considering biological parameters
• accounts for the probability of allele drop-out and drop in
• fast but doesnt use all available data

Question 20

What is the analytical threshold?

Answer 20

allows the analyst to reliably distinguish a peak as being allelic vs an artifact
* lower threshold

Question 21

What is the stochastic threshold?

Answer 21

• any single allele above the ST is considered homozygous
• any allele below the ST is treated as having a missing sister allele
• higher threshold

Question 22

How do laboratories determine the AT and ST?

Answer 22

empirically from validation studies for their STR kits and CE combinations
* AT is usually set at some amount above the lower detection limit of an instrument, where an analyst can reliably assign a peak as allelic with a low or nil risk of the peak being a baseline artifact

Question 23

What is a stutter?

Answer 23

the most common artifact within a profile

Question 24

What is a pull-up artifact?

Answer 24

Where the RFU signal from one dye colour is so strong it ‘bleeds’ into another dye channel creating a peak that may fall in the region of an allele

Question 25

How does a stutter occur in a DNA profile?

Answer 25

due to a slippage of DNA polymerase when synthesising the new strand, this deletes or adds one or more repeat units in the amplified DNA fragment

Question 26

What are the Clayton Rules?

Answer 26

1. identify the presence of a mixture
2. allele or artifact
3. determine number of contributors
4. determine the approximate ratio of the contributors
5. determine the possible pairwise genotype combinations for the different contributors to the mixture
6. compare the resultant genotype profiles for the contributors with those from the reference samples
7. perform statstical analyses

Question 27

What is allele dropout?

Answer 27

when a sample is produced and one or more alleles are not present
* when an alleic peak falls below the analytical threshold of an instrument

Question 28

What causes allele dropout?

Answer 28

1. the initial input quantity of DNA is too low, resulting in a failure to amplify one or more alleles in the sample
2. a mutation in the primer binding site is present, which causes a failure in the amplification of the alle
3. an allele sizes outside of the normal calling range for a particular locus and goes undetected

Question 29

What are the seven steps used to analyse mixtures referred to as?

Answer 29

Clayton Rules