PWS - Fluorescence in situ hybridization (FISH) Testing.pdf

Performance Work Statement (PWS)

General:

Services are required to perform off-site Fluorescence in situ hybridization (FISH) and other select testing for the Department of Veterans Affairs Medical Center, VA VISN 1 Laboratories (herein referred to as VAMC). The services shall be provided in a state-of-the-art civilian medical facility. The standard of services shall be of quality; meeting or exceeding those outlined in the licensing and accreditation section of this PWS. Contractor policies and procedures shall comply with Health Insurance Portability and Accountability Act (HIPAA).

Description of Services/Introduction: The contractor shall provide all personnel, equipment, supplies, facilities, tools, materials, supervision, and other items and services necessary as defined in this PWS except for those items specified as government furnished property and services. The contractor shall perform to the standards in this agreement.

Objectives:

• Fluorescence in situ hybridization (FISH) technical component only- on majority of cases

• Fluorescence in situ hybridization (FISH) technical component and professional interpretation on select cases

• Oncology reference laboratory testing on peripheral blood, bone marrow and embedded paraffin tissue

• Professional interpretation for select cases

• Other select testing

• VAMC Physician-related FISH interpretation –VAMC physician to interpret majority of

FISH testing performed at contractor facility in conjunction with contractor provided web-based software interface to generate interpretation and downloadable final patient report

Scope:

The contractor shall provide testing as outlined in this PWS (see test menu). For laboratory samples, the VAMC will provide either an electronic generated patient worklist or contractor provided requisition form containing at a minimum the patient’s full name, date of birth (second identifier), hospital identification number, tests to be performed, sample collection date/time, ordering provider, and sample type. For specialized testing, the VAMC will provide a brief clinical history only when necessary.

CPT codes 80000-90000 and U0001-U1000 shall be included as well as generic codes when new tests are implemented. New tests or products not identified in the contract may be added with the permission of the Contracting Officer (CO).

Locations:

The following VA Medical Centers may utilize these services:

• VA Connecticut, West Haven Campus, 950 Campbell Ave, West Haven, CT 06516

• VA Connecticut, Newington Campus, 555 Willard Ave, Newington, CT 06111

• VA Central Western Massachusetts HCS, 421 North Main Street, Leeds, MA 01053

• VA West Roxbury 1400 VFW Parkway, West Roxbury, MA 02132

• VA Providence, 830 Chalkstone Ave, Providence, RI 02908

• VA Manchester, 718 Smyth Road, Manchester, NH 03104

• VA White River Junction, 215 North Main Street, White River Junction, VT 05009

• VA Maine HCS, 1 VA Center, Augusta, ME 04330

• VA Boston HCS, Brockton Campus, 940 Belmont St, Brockton, MA 02301

• VA Boston HCS, Jamaica Plains Campus, 150 S. Huntington Ave, Boston, MA 02130

• VA Bedford HCS, 200 Springs Rd, Bedford, MA 01730

General Information:

The Contractor Laboratory shall:

1. Perform testing services entirely upon their premises.

2. Accept VA generated manifests as patient test requisitions.

3. Accept the unique facility National Provider Identifier (NPI) number and not require an NPI for each individual ordering practitioner.

4. Perform analytical testing for VAMC patients for the tests defined in the test menu included in this PWS. The Contractor shall bill only for the tests specified in the request sent by the VAMC Laboratory service.

5. Provide a reference test manual, and report of analytical test results and consultative services as required, assimilating the full scope of its laboratory operations.

6. Provide VAMC with appropriate laboratory supplies not customarily utilized by the VAMC. These supplies are to be used by the VAMC only in connection with specimens being sent for testing to the contractor.

7. Carry out its functions hereunder in full compliance with all local, state, and federal laws or regulations.

8. Provide all test result reports/consults in less than 7 days of receiving the sample. Reports shall be downloadable in pdf format. VA user specific contact information to be provided upon contract award. Provide remote access and ensure successful connection from the VAMC to the contractor portal for viewing of processed samples and input of interpretation.

9. Provide complete processed samples as defined in the test menu.

10. Return all embedded tissue within 5 days of completing sample processing and reporting.

11. Provide a consultation/professional interpretation when requested on select cases.

12. Results shall include all applicable information, not limited to:

• Patient’s full name

• Patient’s date of birth

• Patient’s full social security number or unique VAMC hospital identification number

• Ordering Physician’s name

• Date/time of specimen collection, when available

• Date/time test completed

• Test(s) ordered

• Test result(s)

• Flagged abnormal results - if applicable

• Type of specimen/source

• Any additional comments related to test provided by ordering physician, if applicable

• Unsatisfactory specimen shall be reported with regard to its unsuitability for testing

• VAMC Lab accession number, if supplied

• VAMC submitting facility name

• Patient location- if supplied

• Date/time specimen receipt

• Abnormal intervals/Toxic & therapeutic ranges - if applicable

• Any other information the laboratory has that may indicate a questionable validity of test results.

• VAMC facility account number

• Contractor accession number

• Contractor address

• Contractor Department of Health and Human Services Clinical Laboratory Improvement

Act of 1988 (CLIA) number

• Reference intervals- if applicable

• Testing laboratory name

13. Consult with VAMC on test results by telephone, as needed.

14. Provide an online portal that allows VAMC pathologist(s) to retrieve processed specimen technical data and create their professional interpretation on the contractor’s portal. Patient reports shall be downloaded from contractor portal.

15. Provide training, at no additional charge, for pathologist(s) to retrieve processed specimen data and create interpretation report on the contractors’ portal and lab staff to download completed reports.

16. Allow add on markers for FISH testing after initial results are received. This should include but is not limited to the ability to add RPNI, MECOM, ETV6, 17p-, +19 to the MDS Standard FISH panel.

17. Provide a printed or electronic Laboratory Manual containing the following information:

• Testing methodology for a test must be defined in the laboratory user’s manual

• Department hours of operation

• Accreditation

• Technical Staff

• Service Departments (Method of contacting, phone numbers, hours of availability)

• Quality Assurance Information

• Billing Procedures & fee schedules for services provided

• Procedures and criteria for phoning reports and other important information

• Report forms

18. Provide telephone number(s) and contact person(s) to be used by the VAMC to make specimen problem inquiries and problem solving on weekdays. *NOTE: Also include names and telephone number(s) of Technical Directors and Pathologists available for consultation.

19. Maintain the minimum acceptable service, reporting systems, and quality control as specified herein. Immediate (within 24 hours) notification shall be given to VA upon adverse action by a regulatory agency.

20. Assign a specific local account representative.

21. Advise VAMC facility of any planned changes in methodology, procedure, or reference ranges at least 14 days prior to changes. In the event that two-week notification is not possible due to emergency, contractor shall notify VAMC as soon as possible.

22. Not release patient’s records that include test results to any person other than the ordering healthcare provider or VA Pathology and Laboratory Medicine staff member. All member records shall be treated as confidential so as to comply with all state and federal laws regarding the confidentiality of patient’s records. This provision shall survive termination of the resulting contract award.

23. Certify and ensure that all employees, officers, or agents do not use Protected Health Information received from any VAMC site that would constitute a violation of any applicable provision in standards set forth in HIPAA.

24. Provide 4 quarterly (Oct- December, January- March, April-June, July- September) utilization/cost reports and an annual report (for contract performance period) to the sending VA site laboratory administration and to the VISN 1 Network Consolidated Laboratory office (NCL). The reports shall be in Microsoft excel format and include at a minimum the following column headers: patient name, date of service, CPT code, test name/procedure, volume, cost per test, total cost. The data shall be provided in rows. These reports shall be forwarded to the sending VA site and NCL within 30 days of the end of the quarter.

Licensing and accreditation – Contractor Laboratory:

1. Shall have all licenses, permits, accreditation certificates required by Federal law and State law.

2. Shall be accredited by the Department of Health and Human Services Clinical Laboratory

Improvement Act of 1988 (CLIA), the College of American Pathologists (CAP), or the Joint Commission (TJC). Copies of all professional certifications, licensures and renewal certifications shall be provided and updated as needed to the Contracting Officer to include the contractor laboratory’s Laboratory Director(s) and/or Medical Director(s).

3. Medical Director(s) shall have suitable qualifications and experience to direct a laboratory providing consultation services under this contract according to CLIA, CAP, and TJC standards.

4. Personnel assigned to perform the services covered by this contract shall be eligible to provide the services of this contract and licensed in a State, Territory, or Commonwealth of the United States or the District of Columbia. All licenses held by Contractor personnel working on this contract shall be full and unrestricted licenses. Contractor personnel assigned by the Contractor to work under this contract shall be licensed by the governing or cognizant licensing board.

5. Shall comply with the regulatory requirements of Health and Human Services Health Care Financing Administration, Centers for Medicare and Medicaid (CMS).

6. Shall notify the Contracting Officer immediately, in writing, upon its loss (or any of its subcontractors) of any required certification, accreditation, or licensure.

7. Shall maintain safety and health standards consistent with the requirements set forth by the Occupational, Health, and Safety Administration (OSHA), and the Center for Disease Control (CDC) and Prevention.

Contract Performance Monitoring:

Quality Control: The contractor must operate a successful quality assurance program as required by CAP/CLIA/TJC. Services are to be performed in accordance with this PWS. The quality control program shall include procedures to identify, prevent, and ensure non-recurrence of defective services. The contractor’s quality control program is the means by which the contractor laboratory assures that work complies with the requirement of the contract.

• The VAMC will maintain an Internal Quality Control Program to monitor the quality of test results received from the contractor. The method used for monitoring is at the discretion of the VAMC and may include, but is not limited to, unidentified split specimens sent periodically to the contractor for testing, split specimen sent to another reference laboratory for comparison, or monitoring of turn-around-time.

• The contractor’s facilities, methodologies (defined as the principal of the method and the references), and quality control procedures may be examined by representatives of the VAMC during the life of the contract.

Quality Assurance: The Contractor shall comply with all applicable OSHA, Federal and State laws, the Joint commission, and regulations required for performing the type of services described herein. The government shall evaluate the contractor’s performance under this contract in accordance with the Quality Assurance Surveillance Plan (QASP). This plan is primarily focused on how the Government will monitor performance to ensure the contractor has performed in accordance with the performance standards. It defines how the performance standards will be applied, the frequency of surveillance, and the minimum acceptable defect rate(s).

Federal Holidays: (The contractor does not have to perform on these holidays)

New Year’s Day Labor Day Martin Luther King Jr.’s Birthday Columbus Day President’s Day Veteran’s Day Memorial Day Thanksgiving Day Juneteenth Independence Day Christmas Day Independence Day

Hours of Operation: The contractor is responsible for providing services 8:00 a.m. – 430 p.m. EST Monday – Friday. The Contractor shall at all times maintain an adequate workforce for the uninterrupted performance of all tasks defined within this PWS. When hiring personnel, the Contractor shall keep in mind that the stability and continuity of the workforce are essential. All certifications shall be kept current with any change of personnel assigned to this contract.

Physical Security:

The contractor shall be responsible for safeguarding all government equipment, information and property provided to the contractor laboratory.

Post Award Conference/Periodic Progress Meetings:

The Contractor agrees to attend a post award conference convened by the contracting activity in accordance with Federal Acquisition Regulation Subpart 42.5. The CO, COR, and other Government personnel, as appropriate, may meet periodically with the contractor to review the contractor's performance. At these meetings, the CO will apprise the contractor of how the government views the contractor's performance and the contractor will apprise the Government of problems, if any, being experienced. Appropriate action shall be taken to resolve outstanding issues. These meetings shall be at no additional cost to the government.

Government Personnel:

The follow personnel are Program Managers for this effort:

Wendy Strollo, Program Director, VISN 1 Network Consolidated Laboratory Jaqueline Dang, Quality Manager/HHS, VISN 1 Network Consolidated Laboratory Jacqueline Hite, Program Support Medical Technologists, Network Consolidated Laboratory Lorna Orengo, Acting Laboratory Manager, VA Connecticut Healthcare System Dr. Gary Stack, Chief of Pathology and Laboratory Medicine Service, VA Connecticut Healthcare System

Contractor Program Manager:

The contractor shall provide a contract manager who shall be responsible for the performance of the work. The name of this person and an alternate who shall act for the contractor when the manager is absent shall be designated in writing to the CO. The contract manager or alternate shall have full authority to act for the contractor on all contract matters relating to daily operation of this contract.

The contract manager or alternate shall be available between 8:00 a.m. to 4:30p.m EST/EDT, Monday thru Friday, except Federal holidays or when the government facility is closed for administrative reasons.

Identification of Contractor Employees:

All contract personnel attending meetings and working in other situations, where their contractor status is not obvious to third parties, are required to identify themselves as such to avoid creating an impression in the minds of members of the public that they are Government officials. They must also ensure that all documents or reports produced by contractors are suitably marked as contractor products or that contractor participation is appropriately disclosed.

Continuing Education:

Contractor may provide either online educational sessions (webinar, webcast etc.) or in person at a central location designated by the Program Director of the VISN1 NCL at a mutually agreeable date/time. These educational sessions shall include educational/scientific updates related to Laboratory Medicine or other appropriate topics and shall be customized to meet the needs of the VA Pathology and Laboratory Medicine Service and Clinical Staff. Presentations shall be provided to the NCL Program Office at least two days prior to session commencement. No proprietary or promotional materials shall be included in the educational presentations.

Contractor Furnished Items and Responsibilities:

The Contractor shall furnish all supplies, equipment, facilities, and services required to perform work as outlined in this contract.

Test Menu:

Description

Description/Part Number* Est.

Qty.

Customized Panels

FISH, B-CELL CLL PANEL 88374 technical (CLL FISH Panel) 50 FISH, B-CELL CLL PANEL 88374 professional (CLL FISH Panel) 30 FISH MYELOMA PANEL 88374 technical (Multiple Myeloma-MGUS FISH Panel) ( 40 FISH MYELOMA PANEL 88374 professional (Multiple Myeloma-MGUS FISH Panel) 125 FISH, HES/LEUKEMIA 88367 technical (PDGFRA Rearrangement) 4 FISH, HES/LEUKEMIA 88367 professional (PDGFRA Rearrangement) 4 FISH,PDGFRB,5q33.1 88367 technical (PDGFRB Rearrangement) 1 FISH,PDGFRB,5q33.1 88367 professional (PDGFRB Rearrangement) 1 FISH MDS PANEL 88374 technical (MDS Standard FISH Panel) 100 FISH MDS PANEL 88374 professional (MDS Standard FISH Panel) 50 FISH MDS PANEL 88374 technical (MDS Standard FISH Panel) 1 FISH,MYELOMA,IGH PANEL 88374 professional (Mult. Myeloma IgH Complex Reflex FISH panel) 10

FISH, AML M3, RARA TRANS 15,17 88374 technical (PML/RARA t(15;17) 2

FISH, MPN Panel, 88374 technical 45 FISH, MPN Panel, 88374 professional 25

Additional FISH Probes 88374 technical 10 NGS Myeloid Disorders Profile 1 NGS AML Prognostic Profile 1 NGS MDS/CMML Profile 6 NGS AITL/Peripheral T-Cell Lymphoma Profile 1 NGS DNA & RNA Brain 1 NGS CLL Prognostic Profile 50 Additional Tests Oncology Chromosome Analysis (Cytogenetics) 88264, 88291, 88237 80 ALL Adult 88374 technical 2 ALL Adult 88374 professional 5 AML Standard 88374 technical 2 AML Standard 88374 professional 10 AML Favorable Risk 88374 technical 1 AML Favorable Risk 88374 professional 1 AML Non-Favorable Risk 88374 technical 1 AML Non-Favorable Risk 88374 professional 4 Eosinophilia 88374 technical 3 Eosinophilia 88374 professional includes 8 High-Grade/Large B-Cell Lymphoma 88374 technical 3 High-Grade/Large B-Cell Lymphoma 88374 professional 3 Low-Grade/Small B-Cell Lymphoma 88374 technical 3 Low-Grade/Small B-Cell Lymphoma 88374 professional 3 MPN 88374 technical 4 MPN 88374 professional 4 NHL 88374 technical includes 1 NHL 88374 professional 1 X/Y for Engraftment 88374 technical 1 X/Y for Engraftment 88374 professional 1 Plasma Cell Myeloma Prognostic Panel 88374 technical 6 Plasma Cell Myeloma Prognostic Panel 88374 professional 6 B-Cell Gene Rearrangement 81261, 81264, MOLB 30 T-Cell Receptor Beta Gene Rearrangement 81340 30 T-Cell Receptor Gamma Gene Rearrangement 81342 15 BCR/ABL Translocation, t(9;22), Quant (RT-PCR) 3 BCR/ABL Major Breakpoint 81206 3 BCR/ABL Minor Breakpoint 81207 3 BCR/ABL, t(9;22) Major (p210) & Minor (p190) for CML 81479 3 BCR/ABL p230 81208 3 c-KIT Mutation Analysis (Bi-directional sequencing 1 B-Cell Gene Rearrangement (Fragment Length Analysis) 1 B-CELL IGK Gene Analysis 1

B-Cell IGH Gene Rearrangement 1 Cytogenetics no growth 5 B-Cell Gene Rearrangement (B-cell Clonality) (FFPE) 81261 5 B-Cell Gene Rearrangement (B-cell Clonality) 81261 5 T-Cell Gene Rearrangement (Fragment Length Analysis) 81342 1 TRG Gene Rearrangement (T-Cell Clonality) (FFPE) 81479 1 TRG Gene Rearrangement (T-Cell Clonality) 81479 1 TRG Gene Rearrangement (T-Cell Clonality) Beta 81340 1 TRG Gene Rearrangement (T-Cell Clonality) Beta (FFPE) 81340 1 TRG Gene Rearrangement (T-Cell Clonality) Gamma (FFPE) 81342 1 TRG Gene Rearrangement (T-Cell Clonality) Gamma (FFPE) 81342 1 B&T-Cell Gene Rearrangement (Fragment Length Analysis) 1 B&T-CELL IGK Gene Analysis 81261 1 B&T-Cell IGH Gene Rearrangement 81264 1 B&T-Cell TRG Gene Rearrangement 81342 1 BCL-1 Translocation t(11:14) 81401 1 BCL-2 Translocation t(14;18) 81402 1

SF3B1 81479 5

Cytogenetics Interpretation and Report 88291 60 Cytogenetics Study without interpretations 88237 or 88233 or 88264 or 88280 1

MYD88 5

Chromosome Analysis 88280 100 CXCR4 Mutation Analysis 81479 10

Panel Descriptions:

FISH, B-CELL CLL PANEL Probes: 6q- [SEC63 (6q21), MYB (6q23)] | ATM (11q22.3) | p53 (17p13.1) | Trisomy 12 (Cen 12) | 13q-/-13 (13q14, 13q34) | CCND1/IgH t(11;14) | Probes may be ordered separately (except 12 and 13 are tested together, and ATM is tested with p53).

FISH MYELOMA PANEL -

MGUS

Probes: 1p-, 1q+, iso(1q): CDKN2C (1p32), CKS1B (1q21) | +5, hyperdiploidy (5p15) | +9, hyperdiploidy (9q22) | +15, hyperdiploidy (15q22) | 13q- (13q14, 13q34) | IgH (14q32) | 17p- (TP53 17p13.1, NF1 17q11.2) Probes may be ordered separately except +5, +9 and +15 which are combined.

FISH, HES/LEUKEMIA -

PDGFRA Rearrangement

Probes: PDGFRA | CHIC2 | FIP1L1 (4q12)

FISH,PDGFRB,5q33.1 - PDGFRB Rearrangement

Probes: PDGFRB | (5q33.1)

FISH MDS PANEL -

Standard

Probes: 5q-, -5 (5p15, 5q31, 5q33) | 7q-, -7 (Cen 7, 7q22, 7q31) | Trisomy 8 (Cen 8) | MLL (11q23) | 20q- (20q12, 20qter)

FISH MDS PANEL -

Extended

Probes: RPN1, MECOM (3q21, 3q26.2) | 5q-, -5 (5p15, 5q31, 5q33) | 7q-, -7 (Cen 7, 7q22, 7q31) | Trisomy 8 (Cen 8) | MLL (11q23) | ETV6 (12p13) | 17p- (TP53 17p13.1, NF1 17q11.2) | +19 (19p13.2, 19q13) | 20q- (20q12, 20qter)Probes may be ordered separately except +8 and 20q- which are combined.

FISH,MYELOMA,IGH

PANEL

Probes: FGFR3/IgH t(4;14) | CCND1/IgH t(11;14) | IgH/MAF t(14;16)

FISH, AML M3, RARA

TRANS 15,17

Probes: PML/RARA t(15;17)

Oncology Chromosome Analysis (Cytogenetics)

Cytogenetics, karyotyping

ALL Adult Probes: TCF3/PBX1 (E2A/PBX1) t(1;19) | Trisomy or Tetrasomy 4, 6, 10, 17 (Cen 4, Cen 6, Cen 10, Cen 17) | MYC (8q24) | BCR/ABL1/ASS1 t(9;22) | MLL (11q23) | IgH (14q32)

AML Standard 5q-, -5 (5p15, 5q31, 5q33) | 7q-, -7 (Cen 7, 7q22, 7q31) | Trisomy 8 (Cen 8) | MLL (11q23) | 20q- (20q12, 20qter) | RUNX1/RUNX1T1 (ETO/AML1) t(8;21) | PML/RARA t(15;17) | CBFB inv(16), t(16;16) Probes may be ordered separately except +8 and 20q- which are combined.

AML Favorable Risk Probes: RUNX1/RUNX1T1 (ETO/AML1) t(8;21) | PML/RARA t(15;17) | CBFB inv(16), t(16;16)

AML Non-Favorable Risk Probes: RPN1, MECOM (3q21, 3q26.2) | 5q-, -5 (5p15, 5q31, 5q33 | 7q-, -7 (Cen 7, 7q22, 7q31) | Trisomy 8 (Cen 8) | DEK/NUP214 (CAN) t(6;9) | MLL (11q23) | ETV6 (12p13) | 17p- (TP53 17p13.1, NF1 17q11.2)

Eosinophilia Probes: PDGFRa, CHIC2, FIP1L1 (4q12) | PDGFRb (5q33) | FGFR1 (8p11) | CBFB inv(16), t(16;16) | Probes may be ordered separately.

High-Grade/Large B-Cell Lymphoma

Probes: BCL6 (3q27) | MYC (8q24) | IgH/BCL2 t(14;18) | Optional probes: MYC/IgH/CEN8 t(8;14)

Low-Grade/Small B-Cell Lymphoma

Probes: BCL6 (3q27) | CCND1/IgH t(11;14) IgH/BCL2 t(14;18) | MALT1 (18q21) Probes may be ordered separately.

NGS AITL/Peripheral T-Cell Lymphoma Profile

Sequencing of all exons in the genes IDH1, IDH2, DNMT3A, TET2, and RHOA.

MPN Probes: PDGFRa, CHIC2, FIP1L1 (4q12) | PDGFRb (5q33) | FGFR1 (8p11) | BCR/ABL1 t(9;22) including ASS1 (9q34) Probes may be ordered separately.

NHL Probes: ALK (2p23) | BCL6 (3q27) | MYC (8q24) | CCND1/IgH t(11;14) | IgH (14q32) | IgH/BCL2 t(14;18) | MALT1 (18q21)

X/Y for Engraftment Probes: Centromere X | DYZ1

Plasma Cell Myeloma Prognostic Panel

Probes: 1p-, 1q+, iso(1q): CDKN2C (1p32), CKS1B (1q21) | FGFR3/IgH t(4;14) | CCND1/IgH t(11;14) | 13q- (13q14, 13q34) | IgH/MAF t(14;16) | IgH/MAFB t(14;20) |17p- (TP53 17p13.1, NF1 17q11.2) | Probes may be ordered separately.

NGS Myeloid Disorders Profile

Sequencing the entire coding regions of the genes listed.ABL1, ASXL1, ATRX, BCOR, BCORL1, BRAF, CALR, CBL, CBLB, CBLC, CDKN2A, CEBPA, CSF3R, CUX1, DDX41, DNMT3A, ETNK1, ETV6, EZH2, FBXW7, FLT3, GATA1, GATA2, GNAS, GNB1, HRAS, IDH1, IDH2, IKZF1, JAK2 including V617F and Exons 12+14, JAK3, KDM6A, KIT, KRAS, MLL, MPL, MYD88, NF1, NOTCH1, NPM1, NRAS, PDGFRA, PHF6, PML, PPM1D, PTEN, PTPN11, RAD21, RUNX1, SETBP1, SF3B1, SH2B3, SMC1A, SMC3, SRSF2, STAG2, STAT3, STAT5B, TET2, TP53, U2AF1, WT1, ZRSR2.

NGS AML Prognostic Profile Sequencing the entire coding regions of the genes listed.

ASXL1, BCOR, BRAF, CEBPA, CSF3R, DNMT3A, ETV6,

EZH2, FLT3, HRAS, IDH1, IDH2, JAK2 including V617F and Exons 12+14, KIT, KMT2A (MLL), KRAS, NPM1, NRAS, PDGFRA, PHF6, PML, PTPN11, RUNX1, SETBP1, STAG2, TET2, TP53 and WT1.

NGS MDS/CMML Profile Sequencing the entire coding regions of the genes listed unless another method is noted. ASXL1, BCOR, BCORL1, BRAF, CALR, CBL, CEBPA, CUX1, DDX41, DNMT3A, ETV6, EZH2, FLT3, GATA2, HRAS, IDH1, IDH2, JAK2 including V617F and Exons 12+14, KIT, KRAS, MPL, NF1, NPM1, NRAS, PDGFRA, PHF6, PPM1D, PTEN, PTPN11, RUNX1, SETBP1, SF3B1, SRSF2, STAG2, STAT3, TET2, TP53, U2AF1, WT1, and ZRSR2.

NGS Brain DNA & RNA SNVs/Indels (62 genes): AKT1, APC, ATRX, BAP1, BCOR, BCORL1, BRAF, CDK6, CDKN2A, CDKN2B, CIC, CTNNB1, DICER1, EED, EGFR, EPCAM, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, FUBP1, GNA11, GNAQ, H3F3A (H3-3A), HIST1H3C (H3C3), HRAS, IDH1, IDH2, KDM6A, KRAS, MAP2K1, MET, MLH1, MSH2, MSH6, MYC, MYCN, NOTCH1, NF1, NF2, NRAS, PDGFRA, PIK3CA, PMS2, PTCH1, PTEN, RB1, SETD2, SF3B1, SMAD4, SMARCA4, SMARCB1, SMO, SRC, SUFU, SUZ12, TERT Promoter, TP53, TSC1, TSC2, and VHL RNA Fusions (28 genes): ALK, BRAF, CIC, EGFR including EGFRvIII, EML4, ETV6, EWSR1, FGFR1, FGFR2, FGFR3, FUS, KIAA1549, MAML2, MET, MN1, MYB, MYBL1, NTRK1, NTRK2, NTRK3, PRKCA, RAF1, ROS1, STAT6, TACC3, TFG, YAP1, and ZFTA (C11orf9) CNVs by FISH (9 CNVs): 1p/19q co-deletion, +7/-10 (trisomy 7, monosomy 10), CDKN2A (p16) deletion, EGFR amplification, MET amplification, MYCN amplification, PDGFRa amplification, and PTEN deletion IHC: PD-L1 LDT Other Biomarkers: Microsatellite Instability (MSI) and Tumor Mutation Burden (TMB) included. MGMT Promoter Methylation Analysis may be added.

NGS CLL Prognostic Profile NGS (12 genes): ATM, BCL2, BIRC3, BTK, CARD11, CD79B, CXCR4, MYD88, NOTCH1, PLCG2, SF3B1, TP53 FISH probes: 6q- [SEC63 (6q21), MYB (6q23)] | ATM (11q22.3) | p53 (17p13.1) | Trisomy 12 (Cen 12) | 13q-/-13 (13q14, 13q34) | CCND1/IgH t(11;14) Optional Add-on: IgVH Mutation Analysis

NGS MDS/CMML Profile Sequencing the entire coding regions of the genes listed unless another method is noted. ASXL1, BCOR, BCORL1, BRAF, CALR, CBL, CEBPA, CUX1, DDX41, DNMT3A, ETV6, EZH2, FLT3, GATA2, HRAS, IDH1, IDH2, JAK2 including V617F and Exons 12+14, KIT, KRAS, MPL, NF1, NPM1, NRAS, PDGFRA, PHF6, PPM1D, PTEN, PTPN11, RUNX1, SETBP1, SF3B1, SRSF2, STAG2, STAT3, TET2, TP53, U2AF1, WT1, and ZRSR2.

NGS AITL/Peripheral T-Cell Lymphoma Profile

Sequencing of all exons in the genes IDH1, IDH2, DNMT3A, TET2, and RHOA.

NGS Brain DNA & RNA SNVs/Indels (62 genes): AKT1, APC, ATRX, BAP1, BCOR, BCORL1, BRAF, CDK6, CDKN2A, CDKN2B, CIC, CTNNB1, DICER1, EED, EGFR, EPCAM, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, FUBP1, GNA11, GNAQ, H3F3A (H3-3A), HIST1H3C (H3C3), HRAS, IDH1, IDH2, KDM6A, KRAS, MAP2K1, MET, MLH1, MSH2, MSH6, MYC, MYCN, NOTCH1, NF1, NF2, NRAS, PDGFRA, PIK3CA, PMS2, PTCH1, PTEN, RB1, SETD2, SF3B1, SMAD4, SMARCA4, SMARCB1, SMO, SRC, SUFU, SUZ12, TERT Promoter, TP53, TSC1, TSC2, and VHL RNA Fusions (28 genes): ALK, BRAF, CIC, EGFR including EGFRvIII, EML4, ETV6, EWSR1, FGFR1, FGFR2, FGFR3, FUS, KIAA1549, MAML2, MET, MN1, MYB, MYBL1, NTRK1, NTRK2, NTRK3, PRKCA, RAF1, ROS1, STAT6, TACC3, TFG, YAP1, and ZFTA (C11orf9) CNVs by FISH (9 CNVs): 1p/19q co-deletion, +7/-10 (trisomy 7, monosomy 10), CDKN2A (p16) deletion, EGFR amplification, MET amplification, MYCN amplification, PDGFRa amplification, and PTEN deletion IHC: PD-L1 LDT Other Biomarkers: Microsatellite Instability (MSI) and Tumor Mutation Burden (TMB) included. MGMT Promoter Methylation Analysis may be added.