Implementation of a More Efficient Workflow to Meet New Demands

Transcription

1 Implementation of a More Efficient Workflow to Meet New Demands Cajsa Älgenäs, Head of Division, Division of Forensic Genetics, National Board of Forensic Medicin, Sweden

2 RMV Government agency, Ministry of Justice Forensic medicine, forensic psychiatry, forensic toxicology and forensic genetics, 6 sites in Sweden 480 employees Division of Forensic Genetics, Linköping (14 employees)

3 Fields of Areas Work Pharmacogenetics, Pyrosequencing Species analysis, Pyrosequencing Kinship, CE/NGS No. of cases 2016 Paternity (trios) 1229 Paternity/Maternity (duos) 1528 Kinship 236 Identification/Missing person 117 The principal task: routine kinship analysis Chimeras, CE SCD, MPS

4 No. of Samples Swedish Migration Agency (Duos)

5 Earlier Workflow FTA - Duos AmpF STR Identifiler Direct PCR Amplification Kit, Applied Biosystems + PowerPlex ESI 17 Fast System, Promega * 21 STRs FTA Duos with additional hypothesis (aunt/uncle/grandparents/sibling) AmpF STR Identifiler Direct PCR Amplification Kit, Applied Biosystems + PowerPlex ESI 17 Fast System, Promega + Investigator HDplex Kit, Qiagen * 29 STRs Bone or tissue Duos (and Duos with additional hypothesis (aunt/uncle/ grandparents/sibling)) Phenol-chloroform extraction**, AmpFlSTR Identifiler PCR Amplification Kit, Applied Biosystems + PowerPlex ESI 17 Fast System, Promega (+Investigator HDplex Kit, Qiagen) * 21 (+8) STRs Two parallel runs à Every sample was analyzed at least 4 times à costly and time consuming *Additional marker kits: Investigator Argus X-12, Qiagen and AmpFlSTR Yfiler PCR Amplification Kit, Applied Biosystems **Holmlund, G., Lodestad, I., Nilsson, H., Lindblom, B. (2006) Experiences from DNA analysis in Sweden for the identification of tsunami victims, International Congress Series 1288, pp

6 New workflow FTA - Duos GlobalFiler Express PCR Amplification Kit, Applied Biosystems * 21 STRs FTA Duos with additional hypothesis (aunt/uncle/grandparents/sibling) GlobalFiler Express PCR Amplification Kit, Applied Biosystems + Investigator HDplex Kit, Qiagen (+ QIAseq Investigator ID Panel) * 29 STRs (+131 s) Bone or tissue Duos (and Duos with additional hypothesis (aunt/uncle/ grandparents/sibling)) PrepFiler Express BTA Forensic DNA Extraction Kit, Applied Biosystems AutoMate Express DNA Extraction System, Applied Biosystems GlobalFiler PCR Amplification Kit, Applied Biosystems (+ Investigator HDplex Kit, Qiagen) * 21 (+8) STRs Two parallel runs à less costly and less time consuming * Additional marker kits: Investigator Argus X-12, Qiagen and AmpFlSTR Yfiler PCR Amplification Kit, Applied Biosystems

7 Parent vs unrelated 29 STRs 1521 STRs + STRs 131 s AmpF STR GlobalFiler GlobalFiler Identifiler Express Express Direct PCR PCR Amplification PCR Amplification Kit, Kit, Applied Kit, Applied Biosystems Biosystems + Investigator HDplex Kit, Qiagen + QIAseq Investigator ID Panel Requires additional testing

8 29 STRs s GlobalFiler Express PCR Amplification Kit, Applied Biosystems + Investigator HDplex Kit, Qiagen + QIAseq Investigator ID Panel Grandfather vs unrelated 29 STRs STRs 131 s GlobalFiler AmpF STR Express Identifiler PCR Amplification Direct PCR Kit, Amplification Applied Biosystems Kit, + Investigator HDplex Kit, Applied Qiagen Biosystems + QIAseq Investigator ID Panel

9 Validation Validation GlobalFiler Express PCR Amplification Kit, Applied Biosystems Sample types: FTA/buccal cells, FTA/EDTA-blood, FTA/PM- blood, FTA/internal organ Sensitivity: 0,125 ng Validation PrepFiler Express BTA Forensic DNA Extraction Kit Applied Biosystems AutoMate Express DNA Extraction System, Applied Biosystems GlobalFiler PCR Amplification Kit, Applied Biosystems Sample types: Bone, Soft tissues, FTA/buccal swab, EDTA-blood, PM-blood, Chorionic villi Sensitivity: 0,125 ng Validation - GlobalFiler PCR Amplification Kit, Applied Biosystems (Phenolchloroform extraction**) Sample types: Tooth brush, Urine, Razor, Semen, Amniotic Fluid Sensitivity: 0,125 ng

10 Summary: new workflow Costs(kit)/sample reduced by ~ 48% Labour /sample reduced by ~50% Turnover time no change Performance same/better

11 D2S133 8 D3S135 8 D16S53 9 TH01 TPOX CSF1PO D7S820 D8S117 9 D21S11 D13S31 7 D19S43 3 vwa D18S51 D5S818 FGA GlobalFiler 21 STRs D1S165 6 D10S1248 D12S39 1 D2S441 SE33 D22S104 5 DXS10148 DXS10135 DXS8378 DXS7132 DXS10079 DXS10074 DXS10103 HPRTB DXS10101 DXS10146 DXS10134 DXS7423 Argus X12 12 STRs D3S174 4 HDplex 8 STRs D2S1360 D5S2500 D4S2366 D6S474 D7S1517 D8S1132 D10S2325 DYS437 DYS19 DYS385a DYS385b DYS389I DYS456 DYS438 DYS439 DYS389II DYS448 DYS390 DYS391 YFiler 17 STRs DYS458 DYS635 DYS392 YGATAH4 DYS393

12 D2S133 8 D3S135 8 D16S53 9 TH01 TPOX CSF1PO D7S820 D8S117 9 D21S11 D13S31 7 D19S43 3 vwa D18S51 D5S818 FGA GlobalFiler 21 STRs D1S165 6 D10S1248 D12S39 1 D2S441 SE33 D22S104 5 DXS10148 DXS10135 DXS8378 DXS7132 DXS10079 DXS10074 DXS10103 HPRTB DXS10101 DXS10146 DXS10134 DXS7423 Argus X12 12 STRs D3S174 4 HDplex 8 STRs D2S1360 D5S2500 D4S2366 D6S474 D7S1517 D8S1132 D10S2325 DYS437 DYS19 DYS385a DYS385b DYS389I DYS456 DYS438 DYS439 DYS389II DYS448 DYS390 DYS391 YFiler 17 STRs DYS458 DYS635 DYS392 YGATAH4 DYS393 - panel 134 s

13 Biostaistical Workflow Two parallel runs Familias Famlink FamlinkX

14 Disaster Victim Identification April 7th, 2017, Stockholm Case: Terror attack, 5 victims Sample types (no, minor or moderate decomposition): FTA - post mortem blood FTA - internal organs Kit: GlobalFiler Express PCR Amplification Kit, Applied Biosystems Conclusion: Efficient workflow

15 Disaster Victim Identification April 7th, 2017, Stockholm Case: Terror attack, 5 victims Sample types (no, minor or moderate decomposition): FTA - post mortem blood FTA - internal organs (muscle) Kit: GlobalFiler Express PCR Amplification Kit, Applied Biosystems Conclusion: Efficient workflow

16 Disaster Victim Identification April 7th, 2017, Stockholm Case: Terror attack, 5 victims Sample types (no, minor or moderate decomposition): FTA - post mortem blood FTA - internal organs (muscle) Kit: GlobalFiler Express PCR Amplification Kit, Applied Biosystems Conclusion: Efficient workflow

17 Thank you for your attention! Acknowledgements Division of Forensic Genetics, Linköping Andreas Tillmar Barbara Dell Amico

18 Speaker was provided travel and hotel support by Thermo Fisher Scientific for this presentation, but no remuneration When used for purposes other than Human Identification or Paternity Testing the instruments and software modules cited are for Research Use Only. Not for use in diagnostic procedures. Thermo Fisher Scientific and its affiliates are not endorsing, recommending, or promoting any use or application of Thermo Fisher Scientific products presented by third parties during this seminar. Information and materials presented or provided by third parties are provided as-is and without warranty of any kind, including regarding intellectual property rights and reported results. Parties presenting images, text and material represent they have the rights to do so.