Commercial Assays an Overview. Molecular Workshop

Transcription

1 Commercial Assays an Overview Molecular Workshop

2 Commercial Assays By Discipline Infectious Disease Blood borne viruses Respiratory Viruses and Bacteria Enteropathogens STD s bacteria, viruses and parasites, HPV Tuberculosis/rapid growers Nosocomial including resistance mechanisms Transplants CSF Haem-Oncol Lymphomas Leukaemias Coagulation Anatomical Pathology Somatic Mutation/Cancer cfdna/ctcs Tissue of origin Clinical Chemistry Pharmacogenomics Lipid metabolism Folate metabolism Cytogenetics/Molecular Genetics Developmental Delay Array CGH / SNP Arrays FISH MLPA Inherited Disorders Parentage NIPT PGD

3 Blood Borne Viruses Hepatitis C qualitative Hepatitis C quantitative (viral load) Hepatitis C genotyping Hepatitis B quantitative (viral load) HIV quantitative (viral load) HIV resistance genotyping

4 Roche Ampliprep/Taqman

5 Roche Ampliprep/DockedTaqman

6 Abbott m2000

7 Siemens Versant k-pcr

8 Siemens Versant 440

9 Siemens Lipa 2.0 HCV Genotyping

10 ViroSeq HIV-1 Resistance Genotyping

11 Siemens Trugene HIV-1 Resistance Genotyping

12 Respiratory Viruses and Bacteria Generally two categories Smaller kits FluA/B +/- RSV ParaInfluenza kits hmpv kits Mutliplexes >5 up to Large Panels 12+ including bacterial targets

13 GenProbe Prodesse ProFlu+ FluA/B/RSV Quidel Influenza A+B

14 Alere i FluA/B

15 Focus FluA/B/RSV DAD Direct Amplification Disc DAD

16 Focus Diagnostics Pertussis

17 Cepheid GeneXpert Flu

18 Seegene ACE RV15

19 Seegene TOCE RV16

20 Luminex RVP Fast Bead Array

21 Genera RTIplex Panel

22 Idaho/BioFire/bioMerieux FilmArray

23 BioFire/bioMerieux FilmArray

24 BioFire/bioMerieux FilmArray

25 AusDiagnostics Resp 12

26 Illumigene B. pertussis LAMP

27 STD s Chlamydia trachomatis Neisseria gonorrhoeae Trichomonas vaginalis Herpes simplex 1/2 (plus VZV) Mycoplasma genitalium Syphilis HPV

28 Roche Cobas 4800 CT/NG HPV (PCR)

29 Hologic Panther/Tigris Aptima CT/NG Trich HPV

30 Abbott m2000 CT/NG HPV (PCR)

31 BD Viper XTR/LT CT/NG Trich HPV (SDA)

32 BDMax

33 Siemens k-pcr CT/NG

34 High Throughput Systems

35 Consolidated Molecular Automation Roche FLOW Primary Sample Handler Magnapure 96 Extractor Flow PCR Setup LC480 qpcr LIS query all test(s) requested for a sample Extraction, PCR assay setup, Amplification, Reporting Consolidates in-house and commercial assays Assay inventory on board PCR setup module

36 Consolidated Molecular Automation Roche FLOW

37 Consolidated Molecular Automation Vela

38 Enteropathogens Multiplex PCR tests for bacterial/parasitic and viral gastroenteritis emerged since 2012 Rapid uptake by GPs due to better TAT for common causes of enteric disease Issues remain recovery of bacterial isolates for epidemiology/protecting food supply?molecular screening and then reflex culture Multiplex PCR assays or bead array implementations cover >90% of typical enteropathogens recovered

39 Enteropathogens

40 Enteropathogens BioFire Flim Array

41 Enteropathogens Roche LightMix

42 Enteropathogens Genetic Signatures

43 Enteropathogens Others

44 HPV Testing/Systems Renewal program of Cervical screening As described by Jenny Ross on Friday HPV testing expected to have a x25 multiple per annum (test of cure use) to per annum (screening) Requires Pre-Analytic equipment High throughput HPV test systems

45 HPV Testing/Systems Available Platforms Now Roche Cobas 4800 Hologic Panther Hologic Tigris QIAGEN QIASymphony/RCS BD Onclarity (Viper LT) Abbott m2000 Available Platforms 2016 Roche Cobas 6800/8800 Abbott MQ Hologic Panther Hologic Tigris QIAGEN QIASymphony/RCS BD Onclarity (Viper LT)

46 HPV PreAnalytics

47 HPV Test Platforms Roche Cobas 4800

48 HPV Test Platforms Roche Cobas 6800/ /8hr /8hr

49 HPV Test Platforms Hologic Panther

50 HPV Test Platforms Hologic Tigris

51 HPV Test Platforms Abbott m2000

52 HPV Test Platforms BD Viper LT (PCR mode)

53 HPV Test Platforms Qiagen RCS

54 Transplant/CSF CMV Viral Load BK EBV HSV1/2 Enteroviruses

55 Roche Ampliprep/Taqman CAP/CTM CMV Monitor

56 Focus Diagnostics CMV/ BK/ EBV/ HSV

57 Qiagen Symphony/AS Rotorgene and Artus Assay Kits

58 Seegene CMV Quantitative

59 Diasorin Iam QLAMP

60 Haem-Oncol - Lymphomas T-cell receptor rearrangements/clonality B-cell IgH/K rearrangements/clonality

61 Invivoscribe B-cell

62 Invivoscribe T-cell

63 Invivoscribe Translocations

64 Haem-Oncol - Leukaemias CML: BCR-abl Jak-2, CALR, MPL AML: NPM1, FLT3

65 Ipsogen/Qiagen

66 Cepheid BCR-ABL Monitor

67 Coagulation Factor V Leiden FactorII/Prothrombin G20210A MTHFR Pharmacogenomics / Warfarin metabolism

68 Focus Diagnostics

69 Drug Metabolism

70 Warfarin Pharmacogenomics

71 Autogenomics Infiniti Warfarin Assay

72 Sequenome MassArray

73 Anatomical Pathology Somatic Mutation/Cancer cfdna/ctcs Tissue of origin

74 Cell Pathways Targeted Therapies

75 Companion Diagnostics

76 Automated Paraffin Extraction Siemens Tissue Preparation System

77 COBAS 4800 EGFR,KRAS,BRAF

78 Qiagen Rotorgene Therascreen

79 Qiagen PyroMark/Pyrosequencing

80 Seegene BRAF ACE

81 Autogenomics Infiniti

82 NGS PCR Targeted Panels PCR based targeted sequencing enrichment panels Using NGS can detect to the 1%-5% sensitivity range Known Hot spots or full pathways Price dropping, question will be 2-3 genes by current methods or all for same price via NGS panel

83 NGS PCR Targeted Panels PCR based targeted sequencing enrichment panel TrueSeq Amplicon Cancer Panel TSACP

84 NGS PCR Targeted Panels

85 NGS PCR Targeted Panels

86 NGS PCR Targeted Panels

87 Cell Free DNA cfdna / ctdna Circulating Tumour Cells cfdna cell free DNA CTC circulating tumour cells Circulating tumour DNA (ctdna) cell-free DNA released from a solid tumour as tumour cells turn over small DNA fragments <120 bp

88 Liquid Biopsy Concept Tumor Load Surgery Therapy New threshold of detection

89

90 NIPT - Reducing Amniocentesis Analyses cell-free DNA (cfdna) derived from the foetus that can be found in the mother's plasma Used to detect trisomy 21 (T21) pregnancies (and T18, T13 +) Sits between the current maternal age/nuchal/papp risk score and CVS/Amniocentesis Several tests and technologies

91 Non Invasive Prenatal Genetic Testing - NIPT