Comment on Kokshoorn, B, and Blankers, BJ 'Response to Grisedale, KS and van Daal, A: comparison of STR profiling from low template DNA extracts with and without the consensus profiling method'.

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by  Grisedale, Kelly

GrisedaleandDaalInvestigativeGenetics2013,4:2
http://www.investigativegenetics.com/content/4/1/2
LETTER TO THE EDITOR Open Access
Comment on Kokshoorn, B, and Blankers, BJ
‘
Response to Grisedale, KS and van Daal,
A: comparison of STR profiling from low template
DNA extracts with and without the consensus
’
profiling method
Kelly Grisedale* and Angela van Daal
Abstract
Kokshoorn and Blankers responded to our recent article bysayingthat replicate analysis and consensus profiling of
low template samples was best in terms ofreliability and objectivity.We agree thattheconsensus approach has
benefits, particularly ineliminating non-repeating spurious alleles from thefinal profile. However, with the
development of statistical models that can accommodate stochastic effects and allele drop in, it may be beneficial
to perform a single amplificationwith three times the amount of template, since much informationis lost from the
profile using the consensus approach.
Please see related article:http://www.investigativegenetics.com/content/4/1/1
Keywords: LowtemplateDNA, Stochastic effects, Consensus profiling
Background just how much information is lost from the profile when
In response to our recent article ‘Comparison of STR the consensusmethodisapplied.
profiling from low template DNA extracts with and Kokshoorn and Blankers are correct in their response
without the consensus profiling method’ [1], Kokshoorn that our paper did not discuss the use of a stochastic
and Blankers concluded that ‘one should distinguish threshold. Use of a stochastic threshold provides a means
between the quantity and the quality of information’, to confidently call alleles in mixture profiles. We believe
with quality being preferred when deciding on an ana- that stochastic thresholds have value. However, with the
lysis and interpretation strategy for low template DNA increased sensitivity of LTDNA analyses, one mustaccept
(LTDNA) profiles. Thiswas in fact the conclusion of our thatmost,ifnotall,resultsexperiencesubstantialstochas-
paper. We agree that the consensus profiling works to ticeffectsandfallbelowastochasticthreshold.Ourwork,
reduce allele drop in (ADI) from the interpretation of instead, was an exercise to simply observe how many
the final consensus profile. However, other measures of alleles were obtained or lost when a consensus approach
quality, such as peak heights, peak height ratios and was implemented for single source samples. For that pur-
allele and locus drop out (ADO and LDO) were all im- pose we used the 50 RFU detection threshold implemen-
proved when a single amplification with three times the tedbyothers[2].
amount of template was performed. We agree that con- In casework, a stochastic threshold is an important
sensus profiling has benefits, but it is important to note component of LTDNA profile interpretation and the
Netherland Forensic Institute’s use of a validated relative
fluorescence units (RFU) threshold is to be lauded. How-
*Correspondence:[email protected] ever, Kokshoorn and Blankers’ statement that ‘a single
FacultyofHealthSciencesandMedicine,BondUniversity,GoldCoastQLD
analysis of all available template material in LTDNA
4229,Australia
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GrisedaleandDaalInvestigativeGenetics2013,4:2 Page2of2
http://www.investigativegenetics.com/content/4/1/2
samples,asproposedbyGrisedaleandVanDaal,willgen- interpretations that accommodate the stochastic effects
erallynotyieldaDNAprofileofsufficientquality(thatis, andcontamination.
with all alleles of all donors above the stochastic thresh-
old)’and therefore any results from a single amplification Abbreviations
ADI:Alleledropin;ADO:Alleledropout;LDO:Locusdropout;LTDNA:Low
are less objective than a consensus profile, seems odd, templateDNA;RFU:Relativefluorescenceunit.STR,Shorttandemrepeats..
since there is no guarantee that a consensus profile will
Competinginterests
achieve this measure of validity either. Indeed, splitting a
Theauthorsdeclarethattheyhavenocompetinginterests.
sample reduces the chance that any alleles in each of the
aliquots can meet the stochastic threshold. Thus, under Received:4December2012Accepted:4December2012
Published:3January2013
theKokshoornandBlankersapproachmostLTDNAsam-
ples would yield little information. In addition, if only References
alleles above the threshold are called in a consensus pro- 1. GrisedaleKS,vanDaalA:ComparisonofSTRprofilingfromlowtemplate
DNAextractswithandwithouttheconsensusprofilingmethod.
file, then this approach can equally be applied to a profile
InvestigativeGenet2012,3:14.
fromasingleamplification. 2. TuckerVC,HopwoodAJ,SprecherCJ,McLarenRS,RabbachDR,
Kokshoorn and Blankers are stating well accepted prin- EnsenbergerMG,ThompsonJM,StortsDR:Developmentalvalidationof
thePowerPlexWESI16andPowerPlexWESI17systems:STRmultiplexes
ciples in their comments that mixture profiles involve forthenewEuropeanstandard.ForensicSciIntGenet2011,5:436–448.
morecomplexinterpretations.Thisistruewhetherornot 3. GillP,CurranJ,NeumannC,KirkhamA,ClaytonT,WhitakerJ,LambertJ:
aconsensusapproachisapplied.Allelesfromaminorcon- InterpretationofcomplexDNAprofilesusingempiricalmodelsanda
methodtomeasuretheirrobustness.ForensicSciIntGenet2008,2:91–103.
tributor shouldalwaysbeinterpretedwithcarebecauseof
4. GillP,WhitakerJ,FlaxmanC,BrownN,BuckletonJ:Aninvestigationofthe
the potential for stochastic effects and the possibility of rigorofinterpretationrulesforSTRsderivedfromlessthan100pgof
allele-sharing with a major contributor. Their points fur- DNA.ForensicSciInt2000,112:17–40.
5. GillP,KirkhamA,CurranJ:LoComatioN:asoftwaretoolfortheanalysisof
ther support our position; allele-sharing and stochastic lowcopynumberDNAprofiles.ForensicSciInt2006,166:128–138.
effectsincrease withdecreasing amounts of total template 6. CurranJ,GillP,BillMR:InterpretationofrepeatmeasurementDNA
DNAperamplification.However,statisticaltoolsarebeing evidenceallowingformultiplecontributorsandpopulationsubstructure.
ForensicSciInt2005,148:47–53.
developed that may accommodate these issues and have 7. MitchellAA,TamarizJ,O’ConnellK,DucasseN,BudimlijaZ,PrinzM,
beenimplementedinsomelaboratories. CaragineT:ValidationofaDNAmixturestatisticstoolincorporating
In 2008, Gill et al. [3] stated, ‘There is currently no allelicdrop-outanddrop-in.ForensicSciIntGenet2012,6:749–761.
8. HanedH:Forensim:Anopen-sourceinitiativefortheevaluationof
statistical model that incorporates all these parameters
statisticalmethodsinforensicgenetics.ForensicSciIntGenet2011,
simultaneously. In this respect, all existing models must 5:265–268.
be considered incomplete (indeed we must consider that 9. PerlinMW,LeglerMM,SpencerCE,SmithJL,AllanWP,BelroseJL,DucemanBW:
a complete model is unattainable)’. However, the state- 5V6a:l1id4a3t0in–g14T4r7u.eAlleleWDNAMixtureInterpretation.JForensicSci2011,
ment following the aforementioned quote was, ‘Howe 10. BaldingDJ,BuckletonJ:InterpretinglowtemplateDNAprofiles.
ver, the theory is well established, and the parameters of ForensicSciIntGenet2009,4:1–10.
probability of dropout and probability of contamination
doi:10.1186/2041-2223-4-2
can be universally applied to all DNA profiles using the Citethisarticleas:GrisedaleandDaal:CommentonKokshoorn,B,and
framework originally described by Gill et al. [4], and Blankers,BJ‘ResponsetoGrisedale,KSandvanDaal,A:comparisonof
programmed into an expert system [5,6]’. In the four ScoTRnspernosfuilsinpgrofrfoilminglomwettehmodp’l.aItneveDstNigAateivxetrGaecntsetwicisth20a1n3d4w:2i.thoutthe
years since this paper by Gill et al. [3] was published,
further statistics software programs for the interpre-
tation of mixture profiles have been developed which
may accommodate ADO and ADI [7-10]. The consensus
profiling method was initially developed to overcome
the stochastic effects, particularly ADI [4]. If the statis-
tical programs can incorporate these stochastic issues Submit your next manuscript to BioMed Central
into the model, the evidence would be maximized by and take full advantage of:
applying these tools to the DNA profile that contains the
most information with the proper uncertainty/confidence • Convenient online submission
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Overall, our conclusions remain the same: the consen- • No space constraints or color figure charges
sus approach will certainly be beneficial for dealing with • Immediate publication on acceptance
ADI. However, when the template amount is limited, the • Inclusion in PubMed, CAS, Scopus and Google Scholar
most informative profile will likely be gained by a single • Research which is freely available for redistribution
amplification which can be analyzed using statistical
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