STR interpretation- complex profile

Question 1

how can mixtures occur:

Answer 1

1. victim and suspect DNA on a single sample.
   - vaginal swab after sexual assault.
2. multiple suspect DNA on a single sample. - vaginal swab after gang rape.
3. suspect and background DNA on single sample.
   - sample from a robbery is likely to provide some victim DNA.
4. contamination of sample during handling. - CSI, police, lab analyst.

Question 2

steps to avoid mixture analysis:

Answer 2

differential extraction during DNA recovery.
laser microdissection.
use of quantification kit with mixture detection capabilities.
Y-STR profiling.
processing of additional non mixed stains.

Question 3

identified mixture:

Answer 3

once a mixture is identified it becomes necessary to assess the extent of the mixture. this is done by using the quantitative peak height information that is provided by the CE.

Question 4

major and minor component:

Answer 4

in a simple 2 person mixture the 2 contributors are described as either being the major component or the minor component. you can also have 2 equal major contributors.

Question 5

mixture ratio equation:

Answer 5

Mr=sum of peak heights of major/sum of peak of minor.

Question 6

mixture proportion equation:

Answer 6

Mx= sum heights of major/sum of all peak heights.

Question 7

1 allele observed:

Answer 7

if 1 allele is observed interpretation can be straightforward.
single homozygote (no mixture).
2 homozygote with overlapping alleles.
if balance between the loci is good it suggests a true homozygote.
if balance is poor it may suggest 2 homozygotes with an overlapping allele.

Question 8

2 alleles observed:

Answer 8

if 2 alleles are observed interpretation becomes more complicated.
single heterozygote (no mixture).
2 heterozygotes with overlapping alleles.
2 homozygotes with non overlapping alleles.
heterozygote and homozygote with 1 overlapping allele

Question 9

3 and 4 allele combinations:

Answer 9

3 allele and 4 allele combinations become very difficult to interpret. most current mixture analysis is done using software.

Question 10

2 main stochastic effects at low level:

Answer 10

allelic drop out- where an allele is not detected during testing.
allelic drop in- appearance of of an unexpected allele in a DNA profile that does not come from any of the known contributors.

Question 11

mechanism of drop out:

Answer 11

the mechanism for drop out is thought to be due to:
-the random collection of template material during pipetting.
-the random preferential amplification of an allele during STR.
the starting concentration should be (in theory) the same.

Question 12

mechanism for drop in:

Answer 12

the mechanism for drop in is thought to be due to:
-airborne material entering the mix before PCR.
-airborne PCR product entering the reaction before CE.
allelic drop in is unlikely to happen across all loci, but can complicate the interpretation of a single locus.

Question 13

best way to manage these uncontrollable events:

Answer 13

repeat runs of the same DNA sample and report consensus sequence.
set a stochastic threshold based on validation data.
there a variety of different approaches to use.

Question 14

null alleles:

Answer 14

a non functional gene variant that results in a complete lack of the associated gene product. while rare, null alleles do occur and are recorded.
usually designed out.
population genetic analysis.
have to look at whole profile to make a rational assessment.

Question 15

variant and off ladder alleles:

Answer 15

sometimes alleles occur that are off ladder. they are not a whole STR repeat unit different. this can be due to the presence of a recognised partial repeat.
can also occur due to mutations in the flanking region of the STR.

Question 16

tri allelic patterns:

Answer 16

occasionally you can observe 3 alleles at a single locus.
type 1: 1+2=3 common. 1 and 2 are half the height of 3
type 2: 1=2=3 rare.
tri allelic patterns are more associated with some loci than others.

Question 17

what do inheritance studies suggest:

Answer 17

• tri allelic patterns occur due to inheritance of 2 chromosomal regions from 1 parent.
  -can be observed from 1 parent.
  -sometimes the parent whos tri allelic can pass on any one of the 3 alleles.

Question 18

dye artefacts:

Answer 18

-easy to spot. noise breaks threshold.
-peaks may be observed that are not caused by PCR product. they usually display a different morphology to an allele- blob.
-such peaks are usually an artefact of instrumentation.
-they are not real amplification products. -usually CE software identifies and removes. -can also dilute PCR product.
-software has to detect fluorescence in a number of different wavelengths.