Commercial Assays an Overview Molecular Workshop
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
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
Roche Ampliprep/Taqman
Roche Ampliprep/DockedTaqman
Abbott m2000
Siemens Versant k-pcr
Siemens Versant 440
Siemens Lipa 2.0 HCV Genotyping
ViroSeq HIV-1 Resistance Genotyping
Siemens Trugene HIV-1 Resistance Genotyping
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
GenProbe Prodesse ProFlu+ FluA/B/RSV Quidel Influenza A+B
Alere i FluA/B
Focus FluA/B/RSV DAD Direct Amplification Disc DAD
Focus Diagnostics Pertussis
Cepheid GeneXpert Flu
Seegene ACE RV15
Seegene TOCE RV16
Luminex RVP Fast Bead Array
Genera RTIplex Panel
Idaho/BioFire/bioMerieux FilmArray
BioFire/bioMerieux FilmArray
BioFire/bioMerieux FilmArray
AusDiagnostics Resp 12
Illumigene B. pertussis LAMP
STD s Chlamydia trachomatis Neisseria gonorrhoeae Trichomonas vaginalis Herpes simplex 1/2 (plus VZV) Mycoplasma genitalium Syphilis HPV
Roche Cobas 4800 CT/NG HPV (PCR)
Hologic Panther/Tigris Aptima CT/NG Trich HPV
Abbott m2000 CT/NG HPV (PCR)
BD Viper XTR/LT CT/NG Trich HPV (SDA)
BDMax
Siemens k-pcr CT/NG
High Throughput Systems
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
Consolidated Molecular Automation Roche FLOW
Consolidated Molecular Automation Vela
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
Enteropathogens
Enteropathogens BioFire Flim Array
Enteropathogens Roche LightMix
Enteropathogens Genetic Signatures
Enteropathogens Others
HPV Testing/Systems Renewal program of Cervical screening As described by Jenny Ross on Friday HPV testing expected to have a x25 multiple 10000 per annum (test of cure use) to 250000 per annum (screening) Requires Pre-Analytic equipment High throughput HPV test systems
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)
HPV PreAnalytics
HPV Test Platforms Roche Cobas 4800
HPV Test Platforms Roche Cobas 6800/8800 6800 300/8hr 8800 1000/8hr
HPV Test Platforms Hologic Panther
HPV Test Platforms Hologic Tigris
HPV Test Platforms Abbott m2000
HPV Test Platforms BD Viper LT (PCR mode)
HPV Test Platforms Qiagen RCS
Transplant/CSF CMV Viral Load BK EBV HSV1/2 Enteroviruses
Roche Ampliprep/Taqman CAP/CTM CMV Monitor
Focus Diagnostics CMV/ BK/ EBV/ HSV
Qiagen Symphony/AS Rotorgene and Artus Assay Kits
Seegene CMV Quantitative
Diasorin Iam QLAMP
Haem-Oncol - Lymphomas T-cell receptor rearrangements/clonality B-cell IgH/K rearrangements/clonality
Invivoscribe B-cell
Invivoscribe T-cell
Invivoscribe Translocations
Haem-Oncol - Leukaemias CML: BCR-abl Jak-2, CALR, MPL AML: NPM1, FLT3
Ipsogen/Qiagen
Cepheid BCR-ABL Monitor
Coagulation Factor V Leiden FactorII/Prothrombin G20210A MTHFR Pharmacogenomics / Warfarin metabolism
Focus Diagnostics
Drug Metabolism
Warfarin Pharmacogenomics
Autogenomics Infiniti Warfarin Assay
Sequenome MassArray
Anatomical Pathology Somatic Mutation/Cancer cfdna/ctcs Tissue of origin
Cell Pathways Targeted Therapies
Companion Diagnostics
Automated Paraffin Extraction Siemens Tissue Preparation System
COBAS 4800 EGFR,KRAS,BRAF
Qiagen Rotorgene Therascreen
Qiagen PyroMark/Pyrosequencing
Seegene BRAF ACE
Autogenomics Infiniti
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
NGS PCR Targeted Panels PCR based targeted sequencing enrichment panel TrueSeq Amplicon Cancer Panel TSACP
NGS PCR Targeted Panels
NGS PCR Targeted Panels
NGS PCR Targeted Panels
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
Liquid Biopsy Concept Tumor Load Surgery Therapy New threshold of detection
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
Non Invasive Prenatal Genetic Testing - NIPT