Human Identification Solutions Conference, Mar , Madrid Quantifiler Trio kit and forensic samples management: a matter of degradation

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1 Human Identification Solutions Conference, Mar , Madrid Quantifiler Trio kit and forensic samples management: a matter of degradation Stefano Vernarecci Forensic Genetics Laboratory Scientific Police Service Department of Ministry of Interior 1

2 The ForensicGeneticLaboratoriesof the ItalianNational Police Scientific Police Service Central Direction for the Anticrime Police Turin Rome Naples ForensicGeneticLaboratoryof Rome Palermo 2

3 Degraded samples: an issue for forensic genetic analysis «ski slope pattern» From Advanced topic in Forensic DNA Typing: Methodology J.M. Butler Obtaining a partial DNA profile is analogous to only having a portion of a phone number. A full phone number might be If you only had 4049, this information would be of limited value since it could match to other phone numbers from different area codes. However, in some situations, a few digits may be enough information to narrow down the possibilities in an investigation. Likewise, while full DNA profiles are preferable, partial profiles may be helpful in some instances. J.M. Butler 3

4 Degraded samples: an issue for forensic genetic analysis Sample Collection DNA EXtraction Quantitation Amplification of STR markers C.E. Data Analysis Mini STR (< 200bp) Conbine Different STR- Kits IncreaseInput DNA amount Time consuming Money consuming Sample consuming 4

5 Quantifiler Trio DNA Quantification Kit provideinformation aboutbothconcentrationand qualityof a sample in termsof the presence of inhibitors and degradation Degradation Index = Small autosomal target DNA conc(ng/µl) Large autosomal target DNA conc(ng/µl) The DI represents a general indicator of the level of degradation in the sample where the higher the DI the greater the degradation. ADI=1shouldindicateabsenceofdegradation. 5

6 Quantifiler Trio DNA Quantification Kit Evaluatethe reliability of the Quantifiler Triokit in providinginformation on the levelof degradationin a sample. Studythe opportunityto use thisinformation in predictingthe qualityof the profile obtained after genotyping. Define operative implications, taking into account the DI, to apply to our routine analysisin orderto choosethe best PCR strategywhendealingwith degraded samples 6

7 Comparison between Quantifiler Trio and Quantifiler Duo quantitation data Totally 181 forensic samples from adjudicated casework (oral swab, blood, touch DNA, bones, sperm, hairs ), previously analyzed with Quantifiler Duo were selected on the basis of the obtained profile, including single source samples and mixture with distinguishable major contribuitor, showing different levels of degradation. Quantifiler Duo (probe -140bp) 13 3 Quantifiler Trio (small Probe Data 80bp) Undeterminated 0 - undetermined < 1 Pg/uL < 1 Pg/uL 62 1 Pg - 20 Pg/uL Pg/uL 1 Pg - 20 Pg/uL Pg/uL > 100 Pg/uL > 100 Pg/uL

8 Quantifiler Trio Large and Small probe values and the Degradation Index Overall we observed DI values ranging from a minimum of 0.47to a maximum of 158 Log (10) of Concentrations (Ng/ml) 100, , , , , , , ,00001 Small and Large autosomal amplicons( Degradation Index < 1,5) Samples at increasing concentration 10, , , , , , ,00001 Small and Large autosomal amplicons( Degradation Index > 4) Samples at increasing concentration 8

9 Analysis of degradation pattern and comparison with DI parameter Is the DI parameter obtained during the quantification reliable in providing information about the degradation in a sample? Coulditbe usedto predict the qualityof a profilein termof degradationafterpcr? sometimes appearances could be deceptive.. 9

10 STR analysis with the GlobalFiler PCR Amplification kit A subset of 95 samples were amplified with the GlobalFiler PCR Amplification kit using 0.5 ng of input DNA as established after our internal validation. 0.5 ngof input DNA (SA probe) 10

11 Analysis of degradation pattern and comparison with DI parameter MeanPeakHeight(80) Mean PeakHeight(214) = 3.8 peak heights from homozygous loci were divided by bp bp ph(80)/ph(214) y = 1,4602x + 1,2875 R² = 0,8201 Samples MeanPH (80) +/-SD Total of sample /- 664 Not-degraded samples Degraded samples 2041+/ / DI 11

12 Analysis of degradation pattern and comparison with DI parameter Drop-out probability and degradation level in a sample can be estimated based on a log-linear relationship between Bp and H(bp). Log H(bp) = log (c) + log (p) bp= α 0 + α 1 bp P =exp(α 1 ) 12 The levelof degradationisrepresented by the P value.it is calculated as the exponential function of the angular coefficient of the regression line obtained by plotting the logarithm of observed peak height against the fragment length. P is 1 for not-degraded sample, decreasing at an increase of degradation. In the author s experience P 0.98 represents a moderately degraded sample.

13 Analysis of degradation pattern and comparison with DI parameter Log peak height 8 7,5 7 6,5 6 5,5 5 y = -0,0103x + 8,4308 R² = 0,8645 peak heights from homozygous loci were divided by 2 The loci DYS391, Y-Indeldue to their male specificity. The Loci TH01, FGA and D19S433 were excluded from the analysis because showing generally higher peak heights than the rest of the profile 4,5 4 GlobalFiler, 0.5 ng DNA CSF1PO,D16S539;D3S1358,TPOX,vWA,AMEL,D18S1179,D10S1248,D12S391,D1S1656,D2S1338,D13S317, D22S1045,D5S818,D7S820,SE33 D19S433, FGA, TH01 Size(bp) P= exp( )= 0.99 DI= Sample sdatafittingtothemodelwasverifiedbygraphicaldiagnosticandr 2 statisticforthelog-linearity as suggested by the model. Samples with R 2 value less than 0.7 were excluded from comparison with DI parameter.notablymostofanalyzed samplesachievedr 2 valuemorethan

14 DI comparison with P value calculated by logit-regression model P 0,995 0,99 y = -0,0008x + 0,9909 R² = 0,7006 0,985 0,98 0,975 0, DI Together these results suggest that the DI parameter, obtained after the Quantification, couldbereliablyusedtopredictthequalityoftheprofileintermofdegradation 14

15 Four arbitrary categories of degradation were proposed Degradation Index Degradation < 1.5 No degradation Mild Degradation 4 10 Degradation > 10 Severe degradation 15

16 Analysis of the locus drop-out for different degradation categories Percentage of markers called above AT * * * Markers in the plot are ordered at increasing of average alleles length No degradation (DI <1.5) Mild degradation (DI >1.5 and <4) Degradation (DI >4 and <10) Severe degradation (DI >10) non-normalized samples(input DNA <0.5 Ng and > 45 Pg 16

17 Comparing the performance of different PCR protocols GlobalFiler Kit (Input DNA 0,5 ng) Percentage of markers called NGM-SElect Kit (Input DNA 0.5 ng) GlobalFiler Kit (Input DNA 1 ng) No degradation (DI <1.5) Mild degradation (DI >1.5 and <4) Degradation (DI >4 and <10) Severe degradation (DI >10) 17

18 Comparing the performance of different protocols Number of Loci called GlobalFiler (Input DNA 0,5 ng) GlobalFiler (Input DNA 1 ng) NGM-Select (Input DNA 0,5 ng) ,4 0,8 1,6 3,2 6,4 12,8 25,6 51,2 Log (10) DI 18

19 Analysis of the power of discrimination Average Random Match Probabilities (RMPs) 1E-28 1E-26 1E-24 1E-22 1E-20 1E-18 1E-16 1E-14 1E-12 1E-10 1E ,0001 0,01 1 2,20247E-28 5,20187E-23 7,95E-16 1,67E-10 DI DI DI DI > 10 GF 1ng GF0.5 ng NSE 0.5 ng The Random Match Probability was calculated as recommended from ISFG, for each profile obtained from the samples that was possible to amplify with all the three protocols 19

20 some possibleoperative implicationsin managingforensicsamplestakingintoaccount the Degradation Index in order to maximize allele recovery No Degradation. DI: <4 Degradation. DI: >4 Concentration < 33,3 pg/µl and >3 Pg/µL FULL or PARTIALPROFILE Expected GlobalFiler or other STR-Kit with large volume of Input DNA PARTIAL or NO profile Expected Mini STR or other STR kits for exclusion purposes Concentration > 33,3 pg/µl FULL PROFILE Expected GlobalFiler (0.5ng), NGM-SE or other STR kits PARTIAL PROFILE Expected GlobalFiler (1 Ng of Input DNA if possible) or other STR kits In case of degraded samplesconcentratedlessthan3 Pg/µL No Profileor a maximum of 3 markers are expected to be typed 20

21 To Conclude. Sample Collection DNA EXtraction Quantitation Amplification of STR markers C.E. Data Analysis Profile Mini STR (< 200bp) Conbine Different STR- Kits IncreaseInput DNA amount SNPsand NGS technology 21

22 Daniela Stradiotto Director of Scientific Police Service Egidio Lumaca Director of III Division Paola Montagna Forensic Genetics Laboratory Chief Elisabetta Mei Responsible of Validation Alessandro Agostino Laura Sard Lisa Calandro Enrica Ottaviani Thank You! 22

23 Speaker was provided travel and hotel support by Thermo Fisher Scientific for this presentation, but no remuneration. Quantifiler Trio DNA Quantification Kit is For Research, Forensic and Paternity Use Only. Globalfiler PCR Amplification kit and NGM SElectPCR Amplification kit are For Forensic or Paternity Use Only.