Molecular Diagnostics and Next-Gen Gene Sequencing for Community Hospital Labs: Picking the Winners and Avoiding the Losers

Transcription

1 Molecular Diagnostics and Next-Gen Gene Sequencing for Community Hospital Labs: Picking the Winners and Avoiding the Losers Frederick L. Kiechle, MD, PhD Medical Director, Clinical Pathology Memorial Healthcare System Pathology Consultants of South Broward, LLP

2 Outline I. Molecular Pathology: Microbiology A. Economics 1. Send out vs. in-house 2. Cost avoidance: Enterovirus and MRSA II. III. B. Respiratory Viral Panel Genomic Analysis A. NGS methods 1. Hotspot panels: Commercial / Custom (LDT) 2. Targeted therapy: General 3. STAT BRAF FLT3 PML-RARA Summary / Conclusions

3 Memorial Healthcare System (MHS) MHW MHP MRH/JoeD MHM MRHS

4 Molecular Diagnostics The use of DNA/RNA to test for specific states of disease or health Infectious Diseases Oncology Pharmacogenomics Genetic Disease Screening Personalized Medicine Coagulation 4

5 Three Basic Steps Extraction & Purification of nucleic acid Amplification (making copies) Detection of amplified product Real-Time PCR End-Product Detection Microarrays Luminex (similar to flow analysis) 5 Sequencing

6 Pharmacogenomic Tests Drug Test Indication Benefit Erlotinib (Tarceva ) EGFR Non-small cell lung Response to Rx cancer Trastuzumab HER2 Breast cancer Response to Rx (Herceptin ) Pegylated interferon and ribavirin HCV genotype 1 HCV infection Rx duration and dose Clopidogrel (Plavix ) Warfarin (Coumadin, Jantoven ) CYP2C19 CYP2C9 VKORC1 Acute coronary syndrome Anticoagulant Rx Predict response failure with antithrombotic Predict dose 6 Conestaro WJ, et al. Pers Med 2012; 9: >120 FDA-approved drugs with pharmacogenomics information in their labeling.

7 CAP Resource Guides Genomic Analysis Resource Guide, 2013 Molecular Pathology Resource Guide, 2013 On CAP member website or for sale at

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9 Economics Send-out cost: test value X unit charge In-house cost: test value X unit cost (incremental) Revenue estimate: test value X state average Medicare reimbursement

10 MRHS Molecular Testing: 12 Month Financial Review Test Name Volume WBH Cost/Test MRHS Cost/ Test ARUP Cost/Test Fl Average Medicare MRHS inhouse Total Costs ARUP Total Cost C. Trachomatis 4 $11.02 $10.99 $ $41.65 $ 44 $ 72 $ 167 Medicare Reimbursement Enterovirus ,480 17,183 5,998 CSF NG probe NG/CT 9, , , ,513 HSV- ½ ,306 16, ,956 Subtotal $119,741 $207,617 $918,259 Summary: ARUP MRHS in-house = $87,876 savings Medicare MRHS in-house = $798,518 net profit (incremental)

11 Molecular Strategy Test Menu Reimbursement Test Description Chlamydia/Gonorrhea Clostridium Difficile MRSA Screening Respiratory Virus Panel Herpes Simplex Virus-1/2 Enterovirus Quantitative Cytomegalovirus HIV-1, Quantitative HCV, Quantitative HBV, Quantitative Varicella Zoster Virus Factor II Prothrombin DNA Factor V Leiden DNA Epstein-Barr Virus, Quantitative PCR CMV PCR (Qualitative) HSV-1/2 PCR (Qualitative) HIV-1 Genotyping HCV PCR, Qualitative HCV Genotyping Tuberculosis Detection/Drug Resistance Norovirus Cystic Fibrosis Adenovirus Quantitative Herpes Virus 6 Quantitative Gastrogen Pathogen Panel Medicare Fee $81.92 $40.96 $40.96 $ $40.96 $40.96 $58.88 $96.87 $58.88 $58.88 $40.96 $78.44 $78.44 $58.88 $40.96 $40.96 $ $40.96 $ $38.85 $81.92 No Reimbursement Yet $58.88 $57.39 $409.60

12 Cost Avoidance Examples Enterovirus MRSA

13 Enterovirus EV NEG EV POS September 2008 through May, 2009 Analyzed 20 Enterovirus positive and 20 negative patients and looked at: Length of Stay (LOS) Patient work-up cost (literature based)* Total patients Total LOS days Avg LOS days/patients * Literature based cost is based on admission due to EV status $304,368 $116,376 Estimated Savings (Avoidance): $187,992 for 20 patients * Arch Pathol Lab Med 1999; 123: The cost range for a hospitalization related to EV testing/infection was $4,476-$4,921 with an average LOS of 3-4 days. $4,476 was used in the calculations.

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16 MRSA Screening Progress Report Memorial Healthcare System Memorial Hospital Miramar (Oct 2008) Memorial Hospital Pembroke (Dec 2008) Memorial Regional Hospital South (Jan 2009) Memorial Hospital West (March 2009) Memorial Regional Hospital (May 2009) Testing performed on high-risk patients but is currently not being reimbursed High risk group includes: all ICU admissions and transfers, Patients with history of MRSA, all long term care patient admissions, all Ortho and Neuro implants and Open Heart cases.

17 MRSA Screening (Molecular) Molecular testing from the anterior nares to detect the presence of MRSA DNA Any patients that are positive are Decolonized with: Bactroban ointment in nares, 2x daily Chlorhexidine bath or wipedowns Total decolonization is for 7 days In a hospital, MRSA is primarily transmitted by the hands of healthcare workers (J Hosp Infect 2010; 74: )

18 MHS Hospitals MRSA Infection Rates

19 MHM MRSA Infection Rates Started MRSA Screening in Oct 2008

20 MHW MRSA Infection Rates Infection Rate per 1000 patient days Started MRSA Screening in Mar 2009

21 MRH MRSA Infection Rates # Infections/ Rate per 1000 days JAN '08 FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC JAN '09 FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC JAN '10 FEB MAR Started MRSA Screening in Jun 2009

22 Overall MHS MRSA Screening numbers PCR Screening positive rate: Oct 2008 Dec 2009: 16.95% Jan 2010 Dec 2010: 16.33% Jan 2011 Dec 2011: 16.22% Jan 2012 Nov 2012: 15.02% Relatively steady PCR positive rate is an indication of what is coming in from the community The declining MRSA infection rates support prevention strategies (PCR testing) that allow for rapid identification and IC interventions for patient safety.

23 MHS Expenses

24 $450,000 $400,000 $350,000 MHS Expenses PCR: $25/test Pharmacy (decolonization): $10.49 $362,664 $346,195 $412,645 $300,000 $272,324 $250,000 $200,000 $150,000 $100,000 $50,000 $0 2008/ (Through June) MHS Total: $1,393,828

25 Excess cost of MRSA HAI The following graph shows the excess cost of MRSA healthcare acquired infection. ($9,449 per MHS) An analysis of cases with and without MRSA HAI was done in order to determine an average cost of our MRSA infections. Literature based excess cost of MRSA healthcare acquired infection ($27,000-$35,000)* Year # of Infections at MHS Number of infections documented by ICPs. (Numbers for MHM were extrapolated based on Infection Rates) * Infect Cont Hosp Epid :365 Emerg Infect Dis 2007; 13:1840 Amer J Infect Cont 2006 E40 Infect Cont Hosp Epid :408

26 Excess Cost of MRSA HAI (using $27,000 per MRSA infection) $6,000,000 $5,000,000 $4,968,000 $4,000,000 $3,780,000 $3,000,000 $2,000,000 $2,295,000 $1,944,000 $1,000,000 $648,000 $ MHS Total Excess Cost: $13,635,000 (Through June)

27 Cost Avoidance of MRSA HAI (using $27,000 per MRSA infection) $6,000,000 $5,000,000 $1,188,000 $4,000,000 $2,673,000 $3,024,000 $3,000,000 $4,968,000 $4,320,000 $2,000,000 $3,780,000 $1,000,000 $2,295,000 $1,944,000 $648,000 $ MHS Total Cost Avoidance: $11,205,000 (Through June)

28 Conclusions MRSA Screening at MHS from Oct 2008 to Nov 2012 has demonstrated a similar annual positive rate from 16.95% to 15.02% This screening program has successfully reduced the MRSA infection rate over the same time period MHS total cost avoidance varies from $3,921,335 ($9,449 per MRSA infection) to $11,205,000 ($27,000 per MRSA infection)

29 Future Use of whole genome sequencing of MRSA strains to enhance detection of MRSA transmission between hospital and community settings. (Lancet Infect Dis, Nov 2012; NEJM 2012; 366: )

30 Respiratory Viral Infections Respiratory infections account for ~4 million deaths per year, about half of which are due to viruses Common viruses can cause serious respiratory infections New viruses are also being identified Metapneumovirus (MPV) Severe acute respiratory syndrome coronavirus (SARS-CoV) Avian influenza viruses H5N1, H7N9 Coronaviruses NL63 and HKU1 Human bocavirus Middle East respiratory syndrome coronavirus (MERS-CoV)

31 Why Identify the Virus? Many viruses have similar initial symptoms Some patients will quickly deteriorate, while others could be sent home to recuperate with reassurance Different viruses may require different isolation practices; allows hospital to utilize infection control practices where patients are separated into wards by virus type Important to distinguish viral from bacterial causes Avoid unnecessary antibiotics Select specific antiviral agents, if available By utilizing epidemiologic data from lab, can prescribe appropriate prophylactic treatments (influenza and RSV) when necessary for at risk patients

32 When should a viral panel be used vs. a single virus test? Single Virus Test During epidemic when there is one (or few) major virus(es) circulating When a new/prevalent pathogen suspected is not on a panel, but has a specific test When demand for test is too high for throughput available with panel Viral Panel When there isn t a single prevalent virus Follow CDC data In hospital setting when infection control measures must be implemented To rule out many viruses at once when a new virus is suspected

33 Significance of Positive Test Sensitive Assay: carriership vs. symptomatic infection 2% and 6% of healthy adults positive for RHNV or Influenza A RHNV detectable by PCR for 2 weeks after symptoms Immunocompromised may shed RSV in absence of symptoms Large panel (15 or greater agents) offers additional diagnosing value Negative result more valid if many agents targeted Clinical effects generated by one virus may be amplified by co-infection with another virus Olofson S, et al. Expert Rev Anti Infec Ther 2011;9:

34 RVP Time Summary Assay A: Instrument Time Hands-On Time Extraction Time (1.25 hrs) = 8.7 hrs Assay B: Extraction Time (1.25 hrs) = 7.43 hrs A = 10 steps B = 5 steps Decreased hands-on time Overall shorter assay (1.27 hrs shorter) Decreased manipulation of PCR products which means reduced risk for contamination

35 Annual RVP Volumes from

36 RVP Volume by Month for 2013

37 RVP: 20 Viral Targets Influenza A Influenza A H3 Subtype Influenza A H1 Subtype Influenza A 2009 H1N1 Influenza B RSV A RSV B Parainfluenza-1 Parainfluenza-2 Parainfluenza-4 Adenovirus B/E Adenovirus C Human Metapneumovirus Rhinovirus Coronavirus 229E Coronavirus NL63 Coronavirus HKU1 CoronavirusOC43 Parainfluenza-3

38 Patients With >1 Virus Detected Peds Adults Jul'13 Aug'13 Sep'13 Oct'13

39 Lower Respiratory Tract Infections Hospitalized Children (Norway) % co-infection/total Infections by Species Virus Norway Korea Florida RSV 40.3% - 32% CoV OC43 73% 48% 13% CoV NL63 40% NT 17% CoV 229E % 22% CoV HKU1 0 NT 0 Norway: CoV = shorter fever period and shorter LOS compared to RSV NT = not tested a Kristoffersen, AW, et al. Pediatr Inf Dis J. 2011;30: b Kim JK, et al. J Microbiol Biotechnol 2013;23:

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43 Next Generation Sequencing Platforms Ion Torrent PGM TESTS AmpliSeq Cancer Panel V.2 50 genes (ST) Ion Proton TESTS AmpliSeq Comprehensive: 409 genes (ST3 HEM) MiSeq HiSeq 2500 Cystic Fibrosis System: FDA-cleared; 139 variants of CFTR and sequences all protein coding regions and intron / exons of CFTR gene TESTS:TruSeq Cancer Panel 48 genes (HEM)

44 Massive Sequencing Techniques (Genetic Variants) Whole genome sequencing: includes coding and regulatory regions Exome sequencing: includes protein coding regions Selected DNA sequencing (hotspot): set of predetermined genes

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47 Validated Markers Cancer Lung (non-small cell) Colon Melanoma GI stromal tumor Acute Myeloid Leukemia Molecular Tests EGFR, KRAS, ALK, ROS1 KRAS, BRAF, MSI BRAF, KIT, NRAS KIT, PDGFRA FLT3, NPMI, CEBPA

48 Tumor Molecular Profiling Using Next Gen Sequencing (2014) ABL1 EGFR GNAS MLH1 RET AKT1 ERBB2 HNF1A MPL SMAD4 ALK ERBB4 HRAS NOTCH1 SMARCB1 APC FBXW7 IDH1 NPM1 SMO ATM FGFR1 JAK2 NRAS SRC BRAF FGFR2 JAK3 PDGFRA STK11 CDH1 FGFR3 KDR PIK3CA TP53 CDKN2A FLT3 KIT PTEN VHL CSF1R GNA11 KRAS PTPN11 CTNNB1 GNAQ MET RB1 Neogenomics Laboratories: 48 genes

49 Foundation Medicine - Commercial Foundation One: Solid cancers 236 cancer related genes (3,769 exons) plus 47 introns from 19 genes after rearranged Foundation One Heme: Heme, sarcomas and pediatric cancers Entire coding sequence of 405 genes Selected introns of 31 genes involved in rearrangements RNA sequencing of 265 genes known to be somatically altered

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51 Annotation Databases, e.g. dbsnp: reported / clinical significance broad / less specific HGMD: association with inherited diseases COSMIC: association with Cancer (somatic) BIC: breast cancer genes My Cancer Genome: therapeutic significance

52 Interpretation Issues Greater number of base pairs sequenced the greater the number of incidental findings Limited evidence on the clinical utility of a specific mutation Clinical significance of well-studied mutations in a different tumor type; BRAF in breast cancer? Clinical significance of novel mutations in targetable genes EGFR-unreported mutation? Susceptibility to Geflifinib / Erlotinib?

53 Turnaround Time Driver for nearby Molecular Diagnostic Testing Molecular Dx: STAT: <12 hours: Enterovirus, MRSA, RVP, C. diff, TB Oncology: BRAF (V600E) in stage IV Melanoma Benefit from prompt initiation of BRAF inhibitors when there is a detectable activating mutation BRAF 50%; NRAS 15-25%; KIT 16-23% Grossman & Grossman CAP Today 2014; 28(3): 77-78

54 FMS-like Tyrosine Kinase 3 (FLT3) Internal tandem duplications (FLT3 ITD) 33% AML patients; 24.3% Cosmic Higher relapse rate Patent; #6,291,661 B1; 9/18/01 Invivoscribe Tech Inc Good clinical trial response with quizartinib or sorafenib FLT3 ITD combined with t(8;21), inv 16, or t(16;16)- favorable AML prognosis Also D835 mutations in TKD2 (tyrosine kinase domain 2)- prognostic impact = unknown

55 FL3 Mutation

56 Reciprocal Translocation of Retinoic Acid Receptor-Alpha (RARA). Chromosome 17 with promyelocytic leukemia gene (PML) on Chromosome 15 95% of cases of APL Rx: All-trans retinoic acid (ATRA;tretinoin) and arsenic trioxide (2013) or anthracycline (before 2013). TAT range 2-9 days for send out

57 PML rara Mutation

58 Summary Turnaround time (<12 hrs) drives need for STAT molecular diagnostic tests, e.g. enterovirus, MRSA, RVP, C. diff, TB, norovirus TAT (<48 hrs) drives need for STAT molecular oncology assays, e.g. BRAF(V600E) in Stage IV Melanoma, FLT3 ITD in AML, PML-RARA translocation t(15;17) in APL Cancer center status: TAT < 10 working days plus 1 working day for block in-house testing / 3 working days/block for send out

59 Conclusions 1. Reimbursement for molecular diagnostic tests will vary by third party payer and is more likely if used for hotspot oncology NGS is done compared to WGA or Exome Sequencing 2. Private pathology groups are more likely to be performing molecular diagnostic assays and are evaluating their strategy for solid tumors or hematologic oncology

60 Success / Future 1. Comprehensive analysis of the genome sequence of individual tumors has helped Uncover specific mutations that contribute to malignant phenotype Identify new targets for therapy Increase opportunities for choosing optimal Rx for each patient. Francis S. Collins, Margaret A. Hamburg. N Engl J Med 2013;369: Future: Molecular Tumor Board

61 Acknowledgements Molecular Lab Rodney Arcenas, PhD M. Liliana Bedoya,MT(ASCP) Maryanna Healy, MT(ASCP) PCSB Paul Allen Malek, MD CEO M. Ali Ansari-Lari, MD, PhD Hematopathologist Neil A. Abrahams, MD Solid Tumor