Quant Analysis
Define the targets in QT:
-Small
-Large
-Male
-IPC
Small= amp targeting
Large= degredation
Male= YSTR targeting
IPC= checks for inhibitors/the rxn worked.
What is ILS? What would happen if ILS isn't added to a tray?
ILS is the internal lane standard that sizes the length of the unknown DNA fragment.
If ILS isn't added, then the data would not be able to size correctly, and may not show up.
What's the difference between random and systemic contamination?
Random= one single RB or sample
Systemic= Multiple samples/RBs affected
What are the conclusion requirements for a single source profile?
Under 3 alleles= INC
3 alleles= Inclusion
3+ Loci= Exclusion
Who is Bode Accredited by?
-ISO 17025
-ANAB
What does a high or low Ct mean?
High= reaction worked, DNA is not degraded
Low= degraded sample, or too much DNA template
What is the purpose of a ladder?
The ladder provides the allele calls for the unknown peaks. If ladder isn't added properly, the peak will not be called, or will be all OL.
What if an RB passes per SOP?
1. Attempt to Source
2. Determine if random or systemic
3. Random= RB passes, case note
4. Systemic= RB fails, reprocess all processed in parallel. No TL for new data, case note
What do we use RMP for and why?
Single Source inclusions, because it follows the product rule of independent assortment.
GF: 600, 125
PPF: 500, 100
6C: 600, 100
24plex: 600, 100
What does it mean when IPC flags? with a large DI? Large DI and no IPC flag?
That the sample is inhibited. The sample is inhibited and degraded. That the sample isn't inhibited but is degraded.
What is stutter? What is the N and the -X?
Stutter is caused by an amplification error where the template bulges out and a repeat is either added or not included.
N=true allele peak
-4= minus one repeat, -4bp behind the true peak
What if an RB fails per SOP?
Attempt to source and determine if random or systemic.
Systemic= RB and associated samples fail. Reprocess
Random= Check quant data
What is CPI and why do we use it?
CPI is used for mixture statistics that were not able to be deduced to single source. They are more conservative because they don't use product rule.
What is the purpose of Y Markers in STR kits? and Yindel?
-Can be used to determine a male profile if Y is null
-Yindel is a shorter polymorphism that men have either an insertion 1 or deletion 2
What if the IPC flags with a quant value?
There's too much template DNA
What do you check when deciding to reload/amp/inject?
-Check what went wrong
-amp target, reagent issue, instrument issue
What if the RB/Sample quant doesn't indicate contamination?
1. Reload
2. Reamp
3. Reextract
if contamination is gone, then can report data. If not, data fails and scrutinize data to determine if impacted.
Which locus are suitable for stats?
SS: all locus with a pair or 2p rule for one allele at a locus
Mix: 3+ all locus over ST, 2 if all alleles are accounted for
Define and identify Stochastic Effects
When other alleles/loci are preferably amplified over others resulting in drop out and alleles under ST
How to troubleshoot high female profile in SF
-ProK spike
-YSTRs
-try to deduce
What's required for a foreign mixture worksheet?
-2 person mix
-body swab
-need a reference sample
How to source Contamination
1. Check GMIDX
2. Check BodeMatch if it's a known contaminate
3. If sourced, check steps of coprocessing to determine when it occurred.
What are conclusion requirements for a mixture?
Inclusion: 3+ complete alleles
Exclusion: Represented at 3+ loci
INC: Under 3 loci
What are the RB passing guidelines
GF/PPF/6C: no more than 1 peak over AT, or up to 3 peaks under AT and one under 250rfu
24plex: no more than 3 peaks under AT