November 2023: Test Update – Chromogranin A, New Assay

Test Update – Chromogranin A (CHROMA), New Assay

Effective November 9, 2023.

Chromogranin A (CHROMA) will be updated to a new assay effective November 9, 2023.

The results of the current and new tests are not interchangeable. Due to a reagent shortage, the laboratory will not be able to undergo a rebaseline/parallel testing process.

Please contact Client Services for laboratory assistance with interpreting results in patients undergoing serial monitoring.

Test Change Overview

Chromogranin A (CHROMA)

Update?

Details

Methodology

Yes

New Assay:
Immunoassay, BRAHMS CGA II Kryptor Kit

Discontinued:
Cisbio CGA II, ELISA

The results in the new assay are, on average, 20% lower than the previous assay. The bias is more pronounced at concentrations below 200 ng/mL, where the observed bias is 30%.

Test Code

CHROMA

Specimen

Type
Serum

Container
Gold Serum Separator Tube, or
Red Plain (No Additive) Tube

Stability

Yes

Ambient:
48 hours

Refrigerated:
48 hours

Frozen:
3 months

Transport samples frozen.

Days Performed

Yes

Days Performed
Tuesday, Friday

Reported
1-4 days

Reporting

Yes

Reference Interval
<187 ng/mL

The results of the new and old assays will not trend together in the laboratory information system (e.g., Beaker/EPIC).

Special Communications

Immediate Test Changes

News & Updates

November 2023: Test Delay – Oxalate, Plasma and Oxalate, 24-hour Urine

Test Delay – Oxalate, Plasma (OXLATE) and Oxalate, 24-hour Urine (UOXALD)

Effective November 6, 2023.

Oxalate, Plasma (OXLATE) and Oxalate, 24-hour Urine (UOXALD) will be delayed effective November 6, 2023, due to a global reagent shortage.

Currently, there are no alternative testing options available.

The vendor expects the reagent to be available in late November/December 2023.

For Existing Orders/Specimens
Specimens will be stored frozen, pending the arrival of the reagent. However, if specimens exceed validated stability (4 weeks for plasma specimens, 7 days for urine specimens), testing will be canceled.

Questions?
Please contact Client Services for assistance.

Special Communications

Immediate Test Changes

News & Updates

2024 Cleveland Clinic Laboratories Soft Tissue Pathology Course – Registration Now Open

Clinical Updates

Comprehensive & Immersive Soft Tissue Pathology Course

May 16-19, 2024

InterContinental Hotel at Cleveland Clinic Main Campus | Cleveland, OH

Overview

Join us for an Interactive, Immersive, and Comprehensive Soft Tissue Pathology Course

This four-day course is a one-of-a-kind experience set in the heart of one of the country’s busiest soft tissue pathology consultation practices.

Participants will have the opportunity to digitally preview a wide variety of soft tissue cases spanning from benign lesions and reactive mimics to high grade sarcomas, followed by interactive case-based discussions with world-renown faculty. Interspersed lectures focusing on a practical approach to common diagnostic scenarios will complement these case sessions.

During this course, pathologists will develop skills and tools to work-up and triage mesenchymal lesions encountered in every-day practice.

Symposium Director

Karen Fritchie, MD
Director, Soft Tissue Pathology

Course Objectives

Comprehend the utility of immunohistochemical, molecular techniques, and radiology studies in the work-up of soft tissue tumors
Develop a work-up strategy for the diagnosis of mesenchymal neoplasms
Identify common and uncommon soft tissue tumors
Recognize pitfalls commonly encountered in soft tissue pathology

Course Includes:

• Access to over 100 digital soft tissue cases
• Opportunity to tour our CCF pathology department
• Designated time for questions and discussion with faculty
• After-hours reception with participants and staff

Who Should Attend?

Pathologists, Pathology Residents & Fellows

CME Credits

This live activity is approved for continuing medical education credits. Read more.

Faculty Presenters

John Goldblum, MD
Chair, Department of Pathology

John Reith, MD
Staff Pathologist, Orthopaedic Pathology

Steven D. Billings, MD
Staff Pathologist, Dermatopathology & Soft Tissue Pathology

Scott Kilpatrick, MD
Director, Orthopaedic Pathology
Medical Director, Cleveland Clinic Laboratories

Brian Rubin, MD, PhD
Chair, Pathology & Laboratory Medicine Institute

Josephine Dermawan, MD, PhD
Director, AP Molecular Pathology
Staff Pathologist, Soft Tissue & Orthopaedic Pathology

Jesse McKenney, MD
Staff Pathologist, Genitourinary & Gynecologic Pathology

Registration

Visit clevelandclinicmeded.com/live/courses/comprehensivesofttissue/ for complete registration information.

In-person fee includes:
Continental breakfasts, refreshment breaks, Saturday reception (in-person only), and online access to faculty PowerPoint presentations in PDF format pre and post-course.

Virtual option fee includes:
Access to view lectures and online access to faculty PowerPoint presentations.

Early Bird
on or before April 1, 2024

After
April 1, 2024

Physician (MD, Scientist, PhD)

$699

$749

Resident* / Fellow*

$349

$399

Non-Physician

$349

$399

*A letter from the program director is required to receive the discounted fee. If the letter is not received two weeks prior to the activity, the full physician fee will be charged.

Group Discount Available
Groups of three or more from the same office/institution will receive a $100 discount on the full registration fee. Registrants must call 216.444.9990 to receive a promotional code for special pricing.

Registration and Cancellation
Preregistrations are accepted until 11:59 p.m. ET on Monday, May 13, 2024. Register onsite after this date. Contactless registration on your own device will be required.
In case of cancellation, an email notification is required to process your refund. A full refund will be issued if canceled by May 2, 2024. After May 2, 2024, a $125 cancellation fee will be deducted from your refund. No refunds will be issued after May 6, 2024.

For questions about registration or cancellation, email [email protected] or call 216.448.8710.

Cleveland Clinic Center for Continuing Education reserves the right to cancel or postpone an activity at our sole discretion. In the unlikely event that this occurs, any registration fee(s) paid will be refunded. Be advised that Cleveland Clinic is not responsible for related costs including airline tickets, hotel costs, or any similar fee penalties incurred as a result of any meeting cancellations or changes.

General Information

Visit clevelandclinicmeded.com/live/courses/comprehensivesofttissue/ for complete registration information.

Location
InterContinental Cleveland
Cleveland Clinic Main Campus
9801 Carnegie Avenue
Cleveland, OH 44106
216.707.4100
iccleveland.com

Hotel Accommodations
A limited block of rooms has been reserved at the InterContinental Cleveland through April 16, 2024, at 5 p.m. EDT.

To make reservations, please call the Hotel Reservation Department at 855.765.8709 and reference the CCF Soft Tissue Pathology Program or reserve online at https://www.clevelandclinicmeded.com/live/courses/comprehensivesofttissue/ to receive the special rate of $209, plus tax.

Faculty Disclosure
The Cleveland Clinic Center for Continuing Education has implemented a policy to comply with the current Accreditation Council for Continuing Medical Education Standards for Integrity and Independence requiring mitigation of all faculty conflicts of interest. Faculty declaring a relevant financial relationship will be identified in the activity syllabus.

For further information about this activity, contact Karen Fritchie, MD, at [email protected].

Americans with Disabilities Act
Cleveland Clinic Center for Continuing Education fully intends to comply with the legal requirements of the Americans with Disabilities Act. If you need assistance, please notify us at least two weeks prior to the activity.

Accreditation
In support of improving patient care, Cleveland Clinic Center for Continuing Education is jointly accredited by the Accreditation Council for Continuing Medical Education (ACCME), the Accreditation Council for Pharmacy Education (ACPE), and the American Nurses Credentialing Center (ANCC) to provide continuing education for the healthcare team.

Credit Designation
American Medical Association (AMA)
Cleveland Clinic Center for Continuing Education designates this live activity for a maximum of 28.75 AMA PRA Category 1 Credits™. Physicians should claim only the credit commensurate with the extent of their participation in the activity.

Participants claiming CME credit from this activity may submit the credit hours to the American Osteopathic Association for Category 2 credit.

American Board of Pathology MOC (ABPath)
Successful completion of this CME activity, which includes participation in the evaluation component, earns 28.75 credits toward the Lifelong Learning requirement for the American Board of Pathology’s Continuing Certification program. It is the CME activity provider’s responsibility to submit learner completion information to ACCME for the purpose of granting credit. Credit will be reported within 30 days of claiming credit.

Certificate of Participation
A certificate of participation will be provided to other healthcare professionals for requesting credits in accordance with their professional boards and/or associations.

Study References
Faculty presentations will also be available online in PDF format pre and post-course. You will have access to download or print the slides.

Health and Safety
As participants are responsible for their own health choices, the use of masks by all participants at this event is optional. Additionally, attendees are not required to verify vaccination status nor to provide a negative COVID-19 test for entry. Please note this is subject to change based on the most recent status of CDC, local and/or state guidelines.

Agenda

Thursday

Thursday, May 16, 2024

7:30 am Continental Breakfast

8:00 am Course Introduction and Welcoming Remarks – Karen Fritchie, MD

8:15 am Slide Preview, Staff Q&A

11:00 am Lunch – On Your Own

12:00 pm When (and when not) to do MDM2 fluorescence in situ hybridization – Karen Fritchie, MD

1:00 pm Adipocytic tumors (slide review) – John Goldblum, MD

2:30 pm Break

3:00 pm Smooth muscle/pericytic tumors and their mimics (slide review) – John Goldblum, MD

4:00 pm Soft tissue tumors with skeletal muscle differentiation (slide review) – Scott Kilpatrick, MD

5:00 pm Matrix-forming mesenchymal neoplasms (slide review) – Karen Fritchie, MD

6:00 pm Adjourn

Friday

Friday, May 17, 2024

7:30 am Continental Breakfast

8:00 am Slide Preview, Staff Q&A

10:15 am Tour of Cleveland Clinic’s Department of Pathology – Optional (non-CME)

11:00 am Lunch – On your own

12:00 pm Common myofibroblastic lesions (slide review) – Karen Fritchie, MD

1:30 pm Practical approach to uterine mesenchymal neoplasms – Jesse McKenney, MD

2:30 pm Fibrohistiocytic tumors – Steven Billings, MD

3:00 pm Break

3:30 pm Practical approach to synovial biopsies – John Reith, MD

4:30 pm Tumors of uncertain histiogenesis – Steven Billings, MD

6:00 pm Adjourn

Saturday

Saturday, May 18, 2024

7:30 am Continental Breakfast

8:00 am Slide Preview, Staff Q&A

11:00 am Lunch – On your own

12:00 pm Vascular tumors – Steven Billings, MD

1:30 pm Diagnosing soft tissue tumors with “NextGen” immunohistochemistry – Scott Kilpatrick, MD

3:00 pm Break

3:30 pm The importance of morphologic correlation with molecular results – Josephine Dermawan, MD, PhD

6:00 pm Reception with Attendees & Cleveland Clinic Staff

Sunday

Sunday, May 19, 2024

7:30 am Continental Breakfast

8:00 am Slide Preview, Staff Q&A

10:00 am Peripheral nerve sheath tumors – Brian Rubin, MD, PhD

11:00 am How to work up a pleomorphic sarcoma – Karen Fritchie, MD

12:00 pm Course Conclusion & Adjourn

Special Communications

Immediate Test Changes

News & Updates

September 2023: Changes to Reference Ranges – Catecholamines, Fractionated, Plasma (PLCAT)

Special Communication

Changes to Reference Ranges – Catecholamines, Fractionated, Plasma (PLCAT)

Effective October 2, 2023.

Catecholamines, Fractionated, Plasma (PLCAT)

Epinephrine (18 years and older)
Seated (15 min): Less than or equal to 330 pmol/L
Supine (30 min): Less than or equal to 265 pmol/L

Norepinephrine (18 years and older)
Seated (15 min): 1050-4800 pmol/L
Supine (30 min): 680-3100 pmol/L

Dopamine (18 years and older)
Seated (15 min): Less than or equal to 240 pmol/L
Supine (30 min): Less than or equal to 240 pmol/L

Special Communications

Immediate Test Changes

News & Updates

August 2023: Test Discontinuation – HIV-1 Western Blot (HIV1CO)

Immediate Test Change

Test Discontinuation – HIV-1 Western Blot (HIV1CO)

Effective August 28, 2023.

HIV-1 Western Blot Antibody Confirmation (HIV1CO) has been discontinued by the performing reference laboratory.

As an alternative, Cleveland Clinic Laboratories recommends HIV-1 p24 Ag + HIV-1-2 Ab, with reflex to differentiation (HIV12C) testing.

This test, which is performed in-house, follows the CDC-recommended screening algorithm of reflex to differentiation.

HIV-1 p24 Ag +HIV-1-2 Ab, with reflex to differentiation (HIV12C)

CPT Code
87389

Performing Laboratory
Cleveland Clinic Laboratories

Methodology
Chemiluminescent microparticle immunoassay (CMIA)

Specimen Type
Serum: Gold Serum Separation Tube
Plasma: Sodium Heparin, Lithium Heparin (Green), or Lavender K₂EDTA Tube

Volume
1 mL

Stability (after separation from cells)
Ambient: 72 hours
Refrigerated: 7 days
Frozen ≤ -20°C: 14 days

Clinical Information
HIV screening and diagnosis

Reference Range
Negative

Additional Information
The screening assay is an antigen-antibody combination; when reactive, an HIV confirmatory assay is automatically added and performed.

The confirmatory assay is FDA-approved and can differentiate HIV-1 from HIV-2, making it an integral part of the testing algorithm.

If a client performs a fourth-generation screen, HIV-1/2 Ab Confirmatory (HIV12M) testing may be ordered following a repeatedly positive screen.

Special Communications

Immediate Test Changes

News & Updates

July 2023: Updates to COMAP, DRGTOF, MECDRG, TAPENU, and UASFR

Special Communication

July 2023: Changes to COMAP, DRGTOF, MECDRG, TAPENU, and UASFR Testing

All changes effective August 21, 2023.

Changes to Specimen Requirements

Complement, Alternate Pathway (AH50), Functional (COMAP)

Specimen Type
Serum

Volume
1 mL

Minimum Volume
0.3 mL

Collection Container
Red Serum (Plain) Tube

Transport Temperature
Frozen, Critical (-70°C)

Specimen Instructions/Other Information
Locations without a -70°C freezer should not collect this test.

Do not use gel separator tubes.

Allow specimen to clot for 1 hour at room temperature. Centrifuge (at refrigerated temperature if possible) and separate serum from cells ASAP or within 2 hours of collection. Transfer into standard aliquot tube and freeze immediately in a -70°C freezer.

Separate specimens must be submitted when multiple tests are ordered.

Unacceptable conditions include specimen types other than serum, specimens left to clot at refrigerated temperature, specimens exposed to repeated freeze/thaw cycles, or specimens that are grossly hemolyzed, lipemic, or icteric.

Changes to Reference Ranges

Complement, Alternate Pathway (AH50), Functional (COMAP)

Reference Range
>= 31 % normal

Drug Detection Panel, TOF-MS, Umbilical Cord Tissue (DRGTOF)

Benzoylecgonine
Cutoff 1 ng/g

Cocaine
Cutoff 1 ng/g

Proinsulin, Intact (IPROIN)

18 Years to 99 Years:
<= 7.2 pmol/L

Changes to Test Build

Drug Detection Panel, Meconium, Qualitative (MECDRG)

New Component

Mitragynine (Kratom)
Cutoff 25 ng/g

Tapentadol Quant, Urine (TAPENU)

Remove Components

Tapentadol glucuronide, Urine
Tapentadol-O-sulfate, Urine
N-desmethyltapentadol, Urine

Arsenic, Fractionated Urine (UASFR)

New Component

Arsenic Fractionation Interpretation

Special Communications

Immediate Test Changes

News & Updates

July 2023: Updates to Genital & Sexual Health Specimen Collection

Clinical Updates

Updates to Genital & Sexual Health Specimen Collection

Follow these guidelines for specimen submission in accordance with changes outlined in the May 2023 Technical Update.

Effective July 17, 2023, the laboratory will reject incorrectly submitted specimens.

Aptima® Multitest Swab

Aptima® Multitest Swab Collection Kit

This kit is used for the following tests:

Gonorrhea & Chlamydia (GCCT)
Mycoplasma genitalium (MYGAMP)
Trichomonas vaginalis (TRVAMP)
Candida & Trichomonas (CVTV)
Bacterial Vaginosis (BVAMP)

Order Aptima® Multitest Swab Collection Kits

Sample Type

Gonorrhea & Chlamydia (GCCT)

Mycoplasma genitalium (MYGAMP)

Trichomonas vaginalis (TRVAMP)

Candida & Trichomonas (CVTV)

Bacterial Vaginosis (BVAMP)

Clinician-Collected Vaginal Swab

✓ ✓ ✓

Patient-Collected Vaginal Swab

✓ ✓ ✓

Patient-Collected Penile Meatal Swab

✓ ✓

Clinician-Collected Throat Swab

✓ ✓ ✓

Clinician-Collected Rectal Swab

✓ ✓ ✓

FDA-approved and preferred

✓ ✓

FDA-approved and acceptable

✓

FDA-approved but not recommended due to inferior
performance

Lab-Developed Test (not FDA-approved)

Aptima® Unisex Swab

Aptima® Unisex Swab Collection Kit

This kit is used for the following tests:

Gonorrhea & Chlamydia (GCCT)
Mycoplasma genitalium (MYGAMP)
Trichomonas vaginalis (TRVAMP)

Order Aptima® Unisex Swab Collection Kits

Sample Type

Gonorrhea & Chlamydia (GCCT)

Mycoplasma genitalium (MYGAMP)

Trichomonas vaginalis (TRVAMP)

Candida & Trichomonas (CVTV)

Bacterial Vaginosis (BVAMP)

Clinician-Collected Endocervical Swab

✓ ✓

✓

✓ ✓

Clinician-Collected Male Urethral Swab

✓ ✓

✓ ✓ ✓

FDA-approved and preferred

✓ ✓

FDA-approved and acceptable

✓

FDA-approved but not recommended due to inferior
performance

Lab-Developed Test (not FDA-approved)

Aptima® Urine Kit

Aptima® Urine Specimen Collection Kit

This kit is used for the following tests:

Gonorrhea & Chlamydia (GCCT)
Mycoplasma genitalium (MYGAMP)
Trichomonas vaginalis (TRVAMP)

Order Aptima® Urine Specimen Collection Kits

Sample Type

Gonorrhea & Chlamydia (GCCT)

Mycoplasma genitalium (MYGAMP)

Trichomonas vaginalis (TRVAMP)

Candida & Trichomonas (CVTV)

Bacterial Vaginosis (BVAMP)

Female Urine

✓

Male Urine

✓ ✓ ✓

✓ ✓ ✓

✓ ✓ ✓

FDA-approved and preferred

✓ ✓

FDA-approved and acceptable

✓

FDA-approved but not recommended due to inferior
performance

Lab-Developed Test (not FDA-approved)

Aptima® Transfer Kit

Aptima® Specimen Transfer Kit

Note: This can only be ordered as an add-on test by contacting Client Services.

This kit is used for the following tests:

Gonorrhea & Chlamydia (GCCT)
Trichomonas vaginalis (TRVAMP)

Sample Type

Gonorrhea & Chlamydia (GCCT)

Mycoplasma genitalium (MYGAMP)

Trichomonas vaginalis (TRVAMP)

Candida & Trichomonas (CVTV)

Bacterial Vaginosis (BVAMP)

ThinPrep® PreservCyt®

✓

✓ ✓ ✓

FDA-approved and preferred

✓ ✓

FDA-approved and acceptable

✓

FDA-approved but not recommended due to inferior
performance

Lab-Developed Test (not FDA-approved)

Special Communications

Immediate Test Changes

News & Updates

July 2023: Updates to Recommended Myelodysplastic Syndrome Testing

Clinical Updates

Updates to Recommended Myelodysplastic Syndrome (MDS) Testing

Effective August 17, 2023.

Cleveland Clinic Laboratories’ Molecular Pathology & Cytogenomics section offers several testing options for individuals suspected to have Myelodysplastic Syndrome (MDS):

Chromosome Analysis Only CHRBMH
Chromosome Analysis with reflex to FISH with MDS Panel* (if there are no chromosome results or the chromosome analysis was sub-optimal) CHRMDS
Chromosome Analysis with reflex to Microarray (CMA) BMCHF

FISH Only with MDS Panel*, blood FSHMDS
FISH Only with MDS Panel*, bone marrow FSMDSM

*MDS Panel contains FISH probes specific to chromosomes 5, 7, 8, and 20.

Testing Guidelines

Per the National Comprehensive Cancer Network (NCCN) Myelodysplastic Syndromes Guidelines [version 1.2023 (09/12/22)]:

If standard cytogenetics (with ≥20 metaphases) cannot be obtained, a chromosome microarray [(CMA), also known as chromosome genomic array testing (CGAT)] or MDS-related fluorescence in situ hybridization (FISH) panel should be performed. If karyotype is normal, consider CMA. Note that CMA will detect not only somatic but constitutional (germline) changes.

Recommended Testing

In keeping with the NCCN guidelines, Chromosome Analysis with Reflex to FISH (CHRMDS) is Cleveland Clinic Laboratories’ recommended test for individuals suspected to have MDS.

Discontinued Testing

Beginning August 17, 2023, the FISH Only with MDS Panel (FSHMDS & FSMDSM) for blood and bone marrow will be discontinued.
Note: Chromosome Analysis Only (CHRBMH) and Chromosome Analysis with reflex to Microarray (BMCHF) may still be ordered.

Questions?

Please contact your CCL Sales Manager or Client Services at 800.628.6816.

Special Communications

Immediate Test Changes

News & Updates

Cleveland Clinic and LabConnect Announce Strategic Alliance

Clinical Update

Cleveland Clinic and LabConnect Announce Strategic Alliance

Collaboration on lab services will accelerate clinical trials to better impact patient care.

Cleveland Clinic Laboratories and LabConnect have announced a strategic alliance to accelerate clinical trials and connect patients to new medicines for improved patient care.

Through this alliance, LabConnect will utilize Cleveland Clinic Laboratories, the reference laboratory within Cleveland Clinic. LabConnect will leverage the health system’s extensive array of testing and assay validation services to support laboratory testing for an increasing number of clinical trials.

CC-SIGN Targeted Oncology Panel by Next-Generation Sequencing

Technical Brief:

Targeted Oncology Panel by Next-Generation Sequencing

Test Name

Targeted Oncology Panel by NGS

TOPTO (FFPE Tissue)
TOPCY (Cytology Alcohol or Formalin fixed cell block)
TOPBM (Bone Marrow Aspirate)

This test requires 5-10% tumor purity and does not evaluate circulating tumor DNA.

CPT Code

81445

Methodology

Next-Generation Sequencing (NGS)

Turnaround Time

8 days

Specimen Requirements

Type:
FFPE Tissue

Volume:
– 15 charged, unbaked, and unstained slides sectioned at 7 μm.
– One pre and one post H&E slide with tumor area circled, and percent tumor indicated.

Transport Temperature:
Ambient

Type:
Cytology

Volume:
– 15 charged, unbaked and unstained slides sectioned at 7 μm.
– One H&E slide with tumor percent indicated.

Transport Temperature:
Ambient

Type:
Bone Marrow Aspirate

Volume:
2 mL

Type:
Peripheral blood

Volume:
4 mL

Tube/Container:
Lavender BD Hemogard™ K₂EDTA Tubes

Transport Temperature:
Ambient

Stability

FFPE Tissue

Ambient:
Indefinitely

Refrigerated:
Indefinitely

Frozen:
Unacceptable

Cytology Alcohol or Formalin-Fixed Cell Block

Ambient:
Indefinitely

Refrigerated:
Indefinitely

Frozen:
Unacceptable

Bone Marrow or Peripheral Blood

Ambient:
48 hours

Refrigerated:
3 days

Frozen:
Unacceptable

Additional Information

Download this Technical Brief (PDF)

Overview

Recurrent somatic alterations are found in a variety of solid tumors. Identifying such alterations provides pathologists and clinicians with valuable data that may assist in the diagnosis, classification, prognostic evaluation, and therapeutic management of these malignancies.

The Targeted Oncology Panel (TOP) is a custom 59-gene Next-Generation Sequencing (NGS) panel developed for the identification of single nucleotide variants (SNVs), small insertions and deletions (indels), and copy number gains (CNVs) from DNA specimens, and fusion transcripts and aberrant transcripts from RNA specimens. The workflow allows for the concurrent testing of DNA and RNA to analyze over 1,000 biomarkers.

This panel is optimized to evaluate scant specimens, such as cytology specimens and limited biopsies; as such, TOP may be used for advanced tumor profiling and clinical trial evaluation when material is too limited to send for comprehensive sequencing. For example, TOP can detect resistance mutations in EGFR, KRAS, NRAS, and PDGFRA, as well as evolving biomarkers in AKT1, BRAF non-V600, CDK4, ERBB2, HRAS, MAP2K1/2, and MTOR, amongst others.

Besides providing useful information for cancer evaluation and diagnosis, this test can identify pan-cancer therapeutic markers, including:

TOP Biomarker

FDA-Approved Treatment Examples*

ALK fusions

Alectinib, Brigatinib, Ceritinib, Crizotinib for NSCLC

ALK oncogenic mutations

Lorlatinib for NSCLC

BRAF V600E

Vemurafenib, Dabrafenib and others for Melanoma
Dabrafenib + Trametinib for all solid tumors

EGFR exon 19 in-frame deletions

Gefitinib, Osimertinib for NSCLC

EGFR exon 20 in-frame insertions

Amivantamab, Mobocertinib for NSCLC

ERBB2 (HER2) amplification

Multiple therapy options for Breast Cancer
Tucatinib + Trastuzumab for CRC
Trastuzumab options for Esophagogastric Cancer

FGFR2 fusions

Erdafitinib for Bladder Cancer
Futibatinib, Pemigatinib for Cholangiocarcinoma

FGFR3 fusions or activating mutations

Erdafitinib for Bladder Cancer

IDH1 R132

Ivosidenib for Cholangiocarcinoma

KIT oncogenic mutations

Imatinib, Regorafenib, Ripretinib, Sunitinib for GIST

KRAS G12C

Adagrasib, Sotorasib for NSCLC

MET exon 14 skipping alterations or amplification

Capmatinib, Tepotinib for NSCLC

NTRK1/2/3 fusions

Entrectinib, Larotrectinib for all solid tumors

PDGFRA exon 18 alterations

Avapritinib for GIST

PIK3CA oncogenic mutations

Alpelisib + Fulvestrant in Breast Cancer

RET fusions

Selpercatinib for all tumors

RET mutations

Pralsetinib, Selpercatinib for Medullary Thyroid Cancer

ROS1 fusions

Crizotinib, Entrectinib for NSCLC

*For illustration purposes only; this table is not comprehensive, nor should it be used as a recommendation for treatment. The TOP report does not provide therapy recommendations. Clinical and histopathological correlation is required.

Clinical Indications

Hotspots, copy number variants, and selected fusions evaluated by this assay can aid in the diagnostic and therapeutic assessment of a variety of tumor types, including non-small cell lung cancer, melanoma, colorectal cancer, prostate cancer, breast cancer, glioblastoma, thyroid cancer, and others.

This panel can also provide focused tumor profiling for patients with locally advanced/metastatic disease, who are candidates for anti-cancer therapy, to identify uncommon but targetable alterations.

Interpretation

Variants are classified according to established guidelines, and an interpretation is provided. Reported variants include those of strong or potential clinical significance and variants of unclear clinical significance.

Common population variants are not included in the report.

Methodology

Methodology & Limitations

Extracted nucleic acid from the specimen, both DNA and RNA, were subjected to separate targeted amplification reactions using AmpliSeq custom primers designed by Thermo Fisher Scientific (Thermo Fisher Scientific, Waltham, MA). Hotspots and selected fusions in gene regions listed below were sequenced using Illumina (San Diego, CA) 2×150 paired-end cycle chemistry. A customized bioinformatics analytical platform was used for read alignment (Genome Build GRCh37/hg19), variant identification, and annotation. Single nucleotide variants (SNVs), insertion, deletion (indels), and copy number gain variants are detected by DNA sequencing. Select fusions and aberrant transcripts (EGFR vIII and MET exon 14 skipping transcripts) are detected by RNA sequencing. Variants are classified according to established guidelines. Reported results include variants of strong or potential clinical significance and variants of unclear clinical significance. Benign population polymorphisms are not included in the report.

Based on validation, the DNA testing delivered an average of >500x coverage, and >99% of targeted regions showed over 100x coverage. A minimum coverage depth of 100 reads is required across the entire region of interest; a list of low-coverage areas is included in the report as applicable. The test demonstrated 100% sensitivity and 100% specificity in identifying SNVs, indels, and copy number gains. The lower limit of detection of this assay is approximately 5% variant allele fraction (VAF) for SNV/indels and 6 copies or greater for copy number gains. Variants below these thresholds may be reported at the discretion of the molecular pathology professional staff if the technical quality of the sequencing is sufficient at that location and the call is unequivocal.

Based on validation, the RNA fusion testing averaged >150,000 total reads. The test demonstrated 93%sensitivity and 100% specificity in gene fusion identification compared to NGS sequencing and 69% sensitivity and 100% specificity compared to fluorescence in situ hybridization (FISH) of fusion drivers (unknown fusion partner). Overall sensitivity is 78%, and accuracy is 99%. The lower limit of detection is approximately 1% of total sequencing reads.

Sequence changes outside the analyzed alterations hotspots, including intronic and noncoding regions, will not be identified by this test. Insertions and deletions larger than 20 and 40 bp, respectively, may not be identified by this test. Negative results from specimens for which the percentage of tumor cells is 10% or less should be interpreted with caution. Although variant allele fraction is provided as a percentage, this is not a quantitative test. RNA fusions involving alternative partners or breakpoints outside of the targeted regions cannot be detected by this test. This test does not distinguish between somatic and inherited variants. Tumor heterogeneity, tumor burden, specimen degradation or other limitations of the technology may affect the sensitivity and limit of detection, either broadly across the regions of interest or for specific regions, and may lead to false negative results. This test is not intended to be used for circulating tumor evaluation.

Genes & Hotspot Regions

Genes & Hotspot Regions Covered for SNV/Indels:

*Only hotspots within designated exons are covered; full exons are not sequenced.

wdt_ID	Gene	Transcript	Exon(s)*
1	AKT1	NM_005163	3
2	ALK	NM_004304	21-25
3	AR	NM_000044	6, 8
4	BRAF	NM_004333	11, 15
5	CDK4	NM_000075	2
6	CTNNB1	NM_001904	3, 7-8
7	DDR2	NM_006182	5
8	EGFR	NM_005228	3 ,7, 12, 15, 18-21
9	ERBB2	NM_004448	8, 17-22
10	ERBB3	NM_001982	2-3, 6, 8-9
11	ERBB4	NM_005235	18
12	ESR1	NM_000125	8
13	FGFR1	NM_023110	12-14, 16-17
14	FGFR2	NM_000141	7-9, 12, 14
15	FGFR3	NM_000142	7, 9, 14, 16
16	GNA11	NM_002067	4, 5
17	GNAQ	NM_002072	4, 5
18	GNAS	NM_080425	8
19	H3-3A	NM_002107	2
20	H3-3B	NM_005324	2
21	HRAS	NM_005343	2, 3
22	IDH1	NM_005896	4
23	IDH2	NM_002168	4
24	JAK1	NM_002227	14-16
25	JAK2	NM_004972	14
26	JAK3	NM_000215	11-12, 15
27	KIT	NM_000222	8-11, 13, 17
28	KRAS	NM_033360	2-4
29	MAP2K1	NM_002755	2-3, 6
30	MAP2K2	NM_030662	2
31	MET	NM_000245	14, 16, 19
32	MTOR	NM_004958	30, 39-40, 43, 47, 53
33	NRAS	NM_002524	2-4
34	PDGFRA	NM_006206	12, 14, 18
35	PIK3CA	NM_006218	2, 5-6, 8, 10, 14, 19, 21
36	RAF1	NM_002880	7, 12
37	RET	NM_020975	11, 13, 15-16
38	ROS1	NM_002944	36, 38
39	SMO	NM_005631	4, 6, 8-9
40	TERT	NM_198253	Promoter
41	TP53	NM_000546	5, 7, 8

RNA Fusions

Fusions Detected in RNA

Genes reported for copy number gains: ALK, AR, BRAF, CCND1, CDK4, CDK6, EGFR, ERBB2, FGFR1, FGFR2, FGFR3, FGFR4, KIT, KRAS, MET, MYC, MYCN, PDGFRA, PIK3CA

TOP RNA Fusions

wdt_ID	Gene	Detected Fusions
1	ABL1	EML1::ABL1
2	AKT3	MAGI3::AKT3
3	ALK	A2M::ALK, ACTG2::ALK, ALK::PTPN3, ATIC::ALK, C2orf44::ALK, CARS::ALK, CLIP4::ALK, CLTC::ALK, DCTN1::ALK, EML4::ALK, GTF2IRD1::ALK, HIP1::ALK, KIF5B::ALK, KLC1::ALK, MEMO1::ALK, NCOA1::ALK, PRKAR1A::ALK, RANBP2::ALK, SEC31L1_SEC31A::ALK, SMEK2::ALK, STRN::
4	AXL	AXL::MBIP
5	BRAF	AGTRAP::BRAF, AKAP9::BRAF, CDC27::BRAF, FAM131B::BRAF, FCHSD1::BRAF, KIAA1549::BRAF, PAPSS1::BRAF, SLC45A3::BRAF, SND1::BRAF, TAX1BP1::BRAF, TRIM24::BRAF
6	EGFR	EGFR vIII transcript
7	ERBB2	WIPF2::ERBB2
8	ERG	SLC45A3::ERG, TMPRSS2::ERG
9	FGFR1	BAG4::FGFR1, ERLIN2::FGFR1, FGFR1::TACC1
10	FGFR2	FGFR2::AFF3, FGFR2::BICC1, FGFR2::CASP7, FGFR2::CIT, FGFR2::KIAA1967_CCAR2, FGFR2::MGEA5, FGFR2::OFD1, FGFR2::TACC1, SLC45A3::FGFR2
11	FGFR3	FGFR3::AES, FGFR3::BAIAP2L1, FGFR3::ELAVL3, FGFR3::TACC3
12	MET	MET Exon 14 Skipping, BAIAP2L1::MET, C8orf34::MET, CAPZA2::MET, OXR1::MET, TFG::MET, TPR::MET, PTPRZ1::MET
13	NTRK1	BCAN::NTRK1, CD74::NTRK1, CEL::NTRK1, IRF2BP2::NTRK1, LMNA::NTRK1, MPRIP::NTRK1, NFASC::NTRK1, NTRK1::DYNC2H1, RNF213::NTRK1, SQSTM1::NTRK1, SSBP2::NTRK1, TFG::NTRK1, TPM3::NTRK1, TPR::NTRK1
14	NTRK2	AFAP1::NTRK2, AGBL4::NTRK2, NACC2::NTRK2, QKI::NTRK2, SQSTM1::NTRK2, TRIM24::NTRK2, VCL::NTRK2
15	NTRK3	BTBD1::NTRK3, COX5A::NTRK3, ETV6::NTRK3
16	PDGFRA	SCAF11::PDGFRA
17	PPARG	PAX8::PPARG
18	RAF1	B4GALT1::RAF1, ESRP1::RAF1
19	RELA	C11orf95::RELA
20	RET	ACBD5::RET, AFAP1::RET, AKAP13::RET, CCDC6::RET, CUX1::RET, ERC1::RET, FKBP15::RET, GOLGA5::RET, HOOK3::RET, KIAA1468::RET, KIF5B::RET, KTN1::RET, NCOA4::RET, PCM1::RET, PRKAR1A::RET, RUFY2::RET, SPECC1L::RET, TBL1XR1::RET, TRIM24::RET, TRIM27::RET, TRIM3
21	ROS1	CCDC6::ROS1, CD74::ROS1, CEP85L::ROS1, CLIP1::ROS1, CLTC::ROS1, ERC1::ROS1, EZR::ROS1, GOPC::ROS1, HLA_A::ROS1, KDELR2::ROS1, KIAA1598::ROS1, LRIG3::ROS1, MSN::ROS1, MYO5A::ROS1, PPFIBP1::ROS1, PWWP2A::ROS1, SDC4::ROS1, SLC34A2::ROS1, TFG::ROS1, TPM3::ROS
22	TMPRSS2	TMPRSS2::ERG, TMPRSS2::ETV1, TMPRSS2::ETV4, TMPRSS2::ETV5

References

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