Launching a Cancer Genetic Laboratory to Enhance Diagnosis and Treatment

Transcription

1 Launching a Cancer Genetic Laboratory to Enhance Diagnosis and Treatment Arthur L. Beaudet, M.D. Department of Molecular and Human Genetics Baylor College of Medicine

2 ORIGIN AND PRECEDENT Decades of experience operating Medical Genetics Lab (MGL) focused on pediatrics, prenatal diagnosis, and constitutional cancer mutations. Very positive effect on clinical care, training, research, and finances. Now offering 829 different tests and handling 73,26 samples last 12 months.

3 PRINCIPLES Hybrid academic/business model. Quality of work and clinical service are the highest priorities. Attract outstanding trainees and retain the best. Customer service is imperative; physician, counselor, family. Publish many papers; hundreds CMA. Strong financial performance.

4 PRINCIPLES Strong educational/marketing materials and modest sales team. Excellence in billing insurance. Focus on national market and on international especially Latin and South America, but also Europe and Asia. Create jobs by analyzing samples from around the country and around the world in Texas.

5 KEYS TO SUCCESS First to CAP and CLIA approved lab with novel and powerful new technologies; chromosomal microarray analysis. Work closely with companies developing new technologies. Linkage to very large academic Department of Molecular and Human Genetics and Human Genome Sequencing Center.

6 EMPLOYMENT (137 MGL +11 CGL)

7 FUTURE Continue as a shining star for translational medicine. Translate discoveries into the clinic. Major training center. Strong financial resource for BCM and for jobs in Texas. Goal is not to sell the lab. Probably most similar to Mayo Medical Labs.

8 PEDIATRIC DISABILITIES Chromosomal microarray analysis has revolutionized the evaluation of children with developmental disabilities. CMA may be the most significant advance in all of medicine secondary to the human genome project.

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10 Rank Top 1 Revenue-Generating Tests 12 Months (Nov 21 Oct 211) La b CYT Tes t Chromosomal Microarray Analysis (Blood) $ 1,183, % 6,351 MIT Whole Mitochondrial Genome $ 2,135, % 762 CYT Prenatal Chromosome Analysis $ 2,13,178 5.% 1,978 MIT Mitochondrial DNA Screening Panel $ 1,72, % 1,8 CYT Prenatal Chromosomal Microarray Analysis Charges % of MGL Volume $ 1,653, % 627 MIT POLG Related Disorders $ 1,46, % 797 CYT Aneuploidy FISH $ 762, % 1,231 CYT Chromosome Analysis (Blood) $ 653, % 1,66 DNA Cystic Fibrosis (Mutation) $ 67, % 5,575 DNA Rett Sequencing & Del/Dup $ 433, % 486 $ 21,551, % 2,673

11 NOW FOR CGL Started April 21; weekly 7:15 am meetings; many departments and centers. Many of the same approaches. Especially introduce new technologies and new tests. National and international focus. Engage oncologists and pathologists.

12 NOW FOR CGL Recruited two new lab directors; Marilyn Li and Federico Monzon; General Manager Condie Carmack. Hired two sales people. CPRIT and CTNeT provide a unique opportunity; grant from CPRIT. Total 123 tests offered; 39 new. Willingness to set up any analysis as a Laboratory Developed Test (LDT).

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15 Needs to triple in 12 months

16 CURRENT GOALS Launch the most important tests in routine use; tests currently sent to Mayo and other labs. Set up histology services and immunohistochemistry. Launch tests not currently widely available. Rapid growth.

17 NOVEL TESTS Copy number array with SNP screen. Rapid test for all actionable mutations. DNA methylation arrays. Novel translocation technology. Circulating tumor cells. Circulating tumor DNA. Whole exome/genome analysis. RNA and protein expression; Duke problem.

18 Oncotype DX The Oncotype DX test determines how 21 specific genes 16 genes linked to breast cancer and 5 control genes are expressed (that is, their level of activity) within a tumor sample. Quantitative RT-PCR. PMID:

19 Oncotype DX High False-Negative Rate of HER2 Quantitative Reverse Transcription Polymerase Chain Reaction of the Oncotype DX Test: An Independent Quality Assurance Study. Of the 36 positive cases, only 1 (28%; 95% CI, 14% to 45%) were reported as positive, 12 (33%) as equivocal, and 14 (39%) as negative. PMID:

20 CHALLENGES Enormous complexity. Data at many levels. DNA sequence RNA abundance Protein abundance Protein function and modification Cellular biology

21 ARUP BREAST CANCER TESTS Surgical pathology. Estrogen receptor IHC. HER-2/neu Quantitative by ELISA, IHC, FISH, CISH. ERBB2 (HercepTest ) Tissue Assay, FDA app. IHC for p53, Ki-67, keratin 93, E- cadherin, cytokeratin 8,18. Flow for cell cycle analysis Circulating Tumor Cell Count

22 ARUP BREAST CANCER TESTS Cytology, Breast Ductal Lavage or nipple secretion. Cytochrome P45 2D6 (CYP2D6) 14 Mutations & Gene. Cytochrome P45 2C19 (CYP2C19) 9 Mutations. PIK3CA Mutation Detection. Plus 1 more tests.

23 Marilyn M. Li, M.D. and CGL

24 B a y l o r C o l l e g e o f M e d i c i n e Genetic Counseling CGL provides cancer diagnostic and counseling services for pediatric and adult, inherited and sporadic cancers

25 B a y l o r C o l l e g e o f M e d i c i n e

26 B a y l o r C o l l e g e o f M e d i c i n e

27 B a y l o r C o l l e g e o f M e d i c i n e * FDA Approved

28 B a y l o r C o l l e g e o f M e d i c i n e

29 B a y l o r C o l l e g e o f M e d i c i n e M NEG H2O PT1 PT2 PT1 PT2 Cyto: t(9;22) plus a marker chromosome FISH and CMA : Double Ph1 chr. w. del. at BPTs.

30 Baylor College of Medicine

31 4K MLL DDX6 Backbone Backbone 2,3 cancer genes or cancer-related genes 235 cancer associated-mirnas Average of 6 probes per exon. Average resolutions <1 kb (large exons) to <1 kb (cancer genomic regions) in targeted regions, and ~12 kb in backbone regions 6, SNP probes

32 A large deletion of 3p and part of 3q Copy neutral LOH of part of 3q Genotype A, B Genotype AA, BB

33 High-level focal amplification on Chr1q32.1; Copy number 4, 5, 6

34 Case19: FF and FFPE

35 Baylor College of Medicine Cancer Genetics Laboratory Signature Test II

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37 Sanger Sequencing PIK3C A RT-PCR PML RARa bcr1 MLPA for exonic del M PT NB4 NEG H2O PT NB4 NEG Pyrosequenci ng BRA F FLT3 ITD Normal Capillary Electrophoresis FLT3 ITD mutation

38 46 genes, 739 mutations KRAS BRAF EGFR TP53 PIK3CA CSF1R JAK2 NRAS PTPN11 ERBB2 SRC FGFR3 NPM1 CDKN2A RET HNF1A SMAD4 GNAS PDGFRA MPL ABL1 PTEN FLT3 STK11 SMARCB1 KIT MET NOTCH1 FGFR2 RB1 JAK3 VHL KDR SMO HRAS AKT1 ALK MLH1 FBXW7 ERBB4 ATM CDH1 IDH1 CTNNB1 APC FGFR1

39 Mutation Location Top Five Tissue Distribution In 5 6% of advanced melanomas FDA approved Zelboraf (Vemurafenib)

40 BRAF V6E Mutation AmpliSeq C.1799T>A(p.V6 E) T T T T T 14.9% mutation T T T Pyrosequencing C.1799T>A(p.V6 E) 16% mutation

41 1 tube multiplex PCR generates 19 amplicons to cover 739 known mutations Mutation panel can be customized Short Turn Around Time (3-4 days w. manual; 2 days w. One Touch) Deep coverage - high sensitivity (5% mutation with 95% confidence at 5K coverage) Sample type independent: works on any types of samples: FFPE, FNB, FF, PB, BM, etc. Cost effective: $99/chip; ~ $4/case reagent cost

42 Illumina Human Methylation 45 BeadChip Arrays CpG sites outside of CpG islands Non-CpG methylated sites identified in human stem cells Differentially methylated sites identified in tumor versus normal (multiple forms of cancer) and across several tissue types CpG islands outside of coding regions mirna promoter regions

43 Illumina Human Methylation 45 BeadChip Arrays

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45 Prader-Willi Normal Angelman

46 PARTICIPANTS Dan L. Duncan Cancer Center Human Genome Sequencing Center Departments Pathology and Immunology Medicine Pediatrics Molecular and Human Genetics Molecular and Cellular Biology

47 CANCER GENETICS LAB CG L