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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

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Resp Virus – updated guidelines

Updated September 25, 2023

Respiratory Virus Testing

Cleveland Clinic Laboratories offers several respiratory testing services to healthcare organizations & providers.

SARS-CoV-2, influenza A/B, and respiratory syncytial virus (RSV) testing is available for the qualitative detection of these viruses in respiratory specimens from individuals with appropriate signs, symptoms, and risk factors.

All three viruses are expected to be in circulation during the 2023-2024 respiratory virus season. SARS-CoV-2 + influenza A/B and standalone SARS-CoV-2 testing are also available.

Test Overview

Test Name

COVID & Influenza A/B, Routine (COVFLU)

COVID NAAT, Upper Respiratory, Routine (COVID)

Routine Flu A/B & RSV (RTFRSV)

Order COVID + RTFRSV for combination testing on a single specimen.

Turnaround Time

24 hours from the time of receipt by the laboratory*
Testing is performed 24 hours a day, 7 days a week

Testing will be performed at Cleveland Clinic as possible based on operational capacity. Samples may be referred to another laboratory without prior notice if onsite capacity is exceeded. Capacity restrictions and/or external referrals may impact turnaround time.

Specimen Requirements

Type:
(1) Nasopharyngeal (NP) Swab – preferred 

Volume:
3 mL

Specimen Container:
Universal Transport Media (UTM)

Accepted Alternatives

Type:
(1) Nasopharyngeal (NP) Swab, or
(1) Nasal (anterior nares) swab

Volume:
Swab

Transport Media:
Universal Transport Media (UTM), or
eSwab, or
Saline (sterile), or
Viral Transport Media (VTM), including M4RT, M5, or M6

Transport Temperature

Refrigerated; transport to the laboratories on cold packs or wet ice.

Stability

Ambient:
Unacceptable

Refrigerated (2-8ºC):
72 hours

Frozen:
Up to 30 days

Rejection Criteria

Swabs used for Group A Strep testing are not acceptable.

Test Overview – Lower Respiratory Specimens

Test Name

COVID NAAT, Lower Respiratory, Routine (ITCOVD)

Turnaround Time

24 hours from the time of receipt by the laboratory*
Testing is performed 24 hours a day, 7 days a week

Testing will be performed at Cleveland Clinic as possible based on operational capacity. Samples may be referred to another laboratory without prior notice if onsite capacity is exceeded. Capacity restrictions and/or external referrals may impact turnaround time.

Specimen Requirements

Type:
Aspirate, tracheal, or
Bronchoalveolar Lavage (BAL), or
Sputum

Volume:
1 mL

Transport Container:
Sterile Container

Transport Temperature

Refrigerated; transport to the laboratories on cold packs or wet ice.

Stability

Ambient:
Unacceptable

Refrigerated (2-8ºC):
72 hours

Frozen:
Up to 30 days

Ready to Place an Order?

Download and complete a Respiratory Virus Testing Requisition (required).

Need to Set Up an Account?

Request support from a regional Account Manager or contact Client Services for general inquiries.

Specimen Collection Instructions

You will need:

Personal protective equipment (PPE)

(1) tube of transport medium

– Universal Transport Media (UTM)
– Viral Transport Media (VTM)
– Saline solution

(1) swab

Patient identification labels

Before you begin:

• Confirm the patient’s name and date of birth.

• Wash your hands, then put on personal protective equipment, including gloves.

If you are having difficulties obtaining appropriate COVID-19 specimen collection and transport supplies, please contact your CCL Account Manager.

Nasopharyngeal (NP) Swabs

Step 1:
Carefully remove the swab from the packaging without touching the tip.

Step 2a for nasopharyngeal (NP) swabs:

– Gently insert the NP swab along the nasal septum just above the floor of the passage to the nasopharynx until resistance is met.

– Rotate the swab gently against the nasopharyngeal mucosa for 10 – 15 seconds, then remove.

Step 3:
Remove the cap from the tube, then insert the swab all the way to the bottom of the vial.

Step 4:
While holding the tube away from your face, bend the swab in the vial at a 180-degree angle to break at the marked breakpoint.

Step 5:
Close the tube tightly. If possible, wrap the cap with Parafilm.

Any leaking specimens will be rejected.

Step 6:
Label specimen with the printed label or write the patient’s first & last name, date of birth, and the date, time, and site of collection (e.g., NP) on the tube.

Step 7:
Double-bag the specimen, place on wet ice, then refrigerate.

Step 8:
Complete a Coronavirus 2019 (COVID) Test Requisition.

Step 9:
Place the completed requisition in the pocket of the specimen bag.

Do not place any paperwork in the part of the bag containing the specimen.

Step 10:
For the fastest turnaround time, deliver the specimen directly to the Main Campus LL Building Specimen Receiving Area:

Cleveland Clinic Laboratories
10300 Carnegie Avenue
Cleveland, OH 44106

Need a COVID-19 Test Requisition? 

Contact your CCL Account Manager or Client Services.

Nasal (Anterior Nares) Swabs

Specimen Collection:

Step 1:Carefully remove the swab from the packaging without touching the tip.

Step 2:

Position the patient’s head slightly back, then insert the swab into their LEFT nostril (less than one inch) and gently push until a slight resistance is met.

Step 3:

Rotate the swab against the inside of the patient’s nostril four times for 10-15 seconds.

Step 4:
Remove the swab, then repeat Steps 2 & 3 in the RIGHT nostril with the same swab.

Remove the swab from the patient’s nose when finished.

Preparing for Transport:

Step 5:

While holding the swab, open the tube and set the cap down with the threads facing up.

Insert the swab into the tube until the breakpoint is level with the tube opening.

Step 6:

While holding the tube away from your face, bend the swab until it snaps at the break point.

You may need to gently rotate the swab shaft to complete the breakage.

Step 7:

After discarding the remaining swab shaft into an approved disposal container, screw the cap back onto the tube.

Apply the test label or write the patient’s information onto the tube.

Step 8:

Place the specimen into a biohazard bag, then insert any lab paperwork into the outside pouch.

Refrigerate the specimen during storage and transport to the lab.

If you have any questions, please contact your CCL Account Manager or Client Services for assistance.

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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.

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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

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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 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)

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 Collection Kit

This kit is used for the following tests:

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

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 Specimen Collection Kit

This kit is used for the following tests:

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

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® 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)

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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-optimalCHRMDS
  • 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.

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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.

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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)
TOPPB (Peripheral Blood)

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

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 & 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

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

1. Li MM, et al. Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn. 2017 Jan;19(1):4-23. doi: 10.1016/j. jmoldx.2016.10.002. PMID: 27993330; PMCID: PMC5707196.

2. Kumar-Sinha C, Tomlins SA, Chinnaiyan AM. Recurrent gene fusions in prostate cancer. Nat Rev Cancer. 2008 Jul;8(7):497-511. doi: 10.1038/nrc2402. Epub 2008 Jun 19. PMID: 18563191; PMCID: PMC2711688.

3. Baca SC, Garraway LA. The genomic landscape of prostate cancer. Front Endocrinol (Lausanne). 2012 May 16;3:69. doi: 10.3389/fendo.2012.00069. PMID: 22649426; PMCID: PMC3355898.

4. Bennett C, et al. Breast Cancer Genomics: Primary and Most Common Metastases. Cancers (Basel). 2022 Jun 21;14(13):3046. doi: 10.3390/cancers14133046. PMID: 35804819; PMCID: PMC9265113.

5. Natrajan R, Tutt ANJ, Lord CJ. Driver Oncogenes but Not as We Know Them: Targetable Fusion Genes in Breast Cancer. Cancer Discov. 2018 Mar;8(3):272-275. doi: 10.1158/2159-8290.CD-18-0091. PMID: 29500329; PMCID: PMC6372062.

6. Singh A, Ham J, Po JW, Niles N, Roberts T, Lee CS. The Genomic Landscape of Thyroid Cancer Tumourigenesis and Implications for Immunotherapy. Cells. 2021 May 1;10(5):1082. doi: 10.3390/cells10051082. PMID: 34062862; PMCID: PMC8147376.

7. Sepulveda AR, et al. Molecular Biomarkers for the Evaluation of Colorectal Cancer: Guideline From the American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and the American Society of Clinical Oncology. J Clin Oncol. 2017 May 1;35(13):1453-1486. doi: 10.1200/JCO.2016.71.9807. Epub 2017 Feb 6. PMID: 28165299.

8. Lindeman NI, et al. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. Arch Pathol Lab Med. 2018 Mar;142(3):321-346. doi: 10.5858/arpa.2017-0388-CP. Epub 2018 Jan 22. PMID: 29355391.

9. Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Oct 23;455(7216):1061-8. doi: 10.1038/nature07385. Epub 2008 Sep 4. Erratum in: Nature. 2013 Feb 28;494(7438):506. PMID: 18772890; PMCID: PMC2671642.

10. Lombardi MY, Assem M. Glioblastoma Genomics: A Very Complicated Story. In: De Vleeschouwer S, editor. Glioblastoma [Internet]. Brisbane (AU): Codon Publications; 2017 Sep 27. Chapter 1. PMID: 29251861.

11 .Guhan S, Klebanov N, Tsao H. Melanoma genomics: a state-of-the-art review of practical clinical applications. Br J Dermatol. 2021 Aug;185(2):272-281. doi: 10.1111/bjd.20421. Epub 2021 Jun 6. PMID: 34096042.

12. Tornillo L, Terracciano LM. An update on molecular genetics of gastrointestinal stromal tumours. J Clin Pathol. 2006 Jun;59(6):557-63. doi: 10.1136/jcp.2005.031112. PMID: 16731599; PMCID: PMC1860404.

13. Malone ER, Oliva M, Sabatini PJB, Stockley TL, Siu LL. Molecular profiling for precision cancer therapies. Genome Med. 2020 Jan 14;12(1):8. doi: 10.1186/s13073-019-0703-1. PMID: 31937368; PMCID: PMC6961404.

14. Chakravarty D et al. Somatic Genomic Testing in Patients With Metastatic or Advanced Cancer: ASCO Provisional Clinical Opinion. J Clin Oncol. 2022 Apr 10;40(11):1231-1258. doi: 10.1200/JCO.21.02767. Epub 2022 Feb 17. Erratum in: J Clin Oncol. 2022 Jun 20;40(18):2068. PMID: 35175857.

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CC-SIGN® Targeted Oncology Panel (TOP) by Next-Generation Sequencing

Clinical Updates

New Test: CC-SIGN® Targeted Oncology Panel (TOP) by Next-Generation Sequencing

Available to order starting on June 20, 2023.

A new, enhanced 59-gene hotspot Next-Generation Sequencing (NGS) panel is available for tumor DNA and RNA evaluation.

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.

Targeted Oncology Panel by NGS

Order Codes
TOPTO (FFPE Tissue)
TOPCY (Cytology Alcohol or Formalin fixed cell block)
TOPBM (Bone Marrow Aspirate)
TOPPB (Peripheral Blood)

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

CPT Code
81445

Methodology
Next-Generation Sequencing

Specimen Type
FFPE Tissue
15 charged, unbaked, and unstained slides sectioned at 7 μm.
One pre and one post H&E slide with tumor area circled, and percent rumor indicated.

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

Bone Marrow Aspirate
2 mL, Lavender K2EDTA Tube

Peripheral Blood
4 mL, Lavender K2EDTA Tube

Days Performed
2–3 times per week

Turnaround Time
8 days

Overview

Single nucleotide variants (SNVs), small insertions and deletions (indels), copy number gains, select fusions, and aberrant transcripts 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. In particular, this panel can be utilized for small biopsies and cytology specimens that may not be amenable to more comprehensive genomic sequencing.

Targeted Genes & RNA Fusions

For a full list of targeted genes & RNA fusions, please refer to the Targeted Oncology Panel by Next-Generation Sequencing Technical Brief.

How to Order

Place an order through an electronic interface or complete a Molecular Oncology & Associated Biomarkers Requisition and submit it with the specimen(s).

Hot Spot Panel Discontinuation

The TOP NGS panel will replace solid tumor hotspot mini-panels (Lung, Colorectal, Melanoma, GIST, etc.), as all previously detected biomarkers are included in the new testing.

In situations where the mini-panels were previously used as part of an upfront diagnostic workup, pathologist diagnostic and reflex ordering will utilize TOP testing.

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May 2023: Discontinued – Natural Killer Cells, Functional (NKFUNC)

Immediate Test Change

Test Discontinuation – Natural Killer Cells, Functional (NKFUNC)

Effective May 22, 2023.

Natural Killer Cells, Functional (NKFUNC) testing has been discontinued.

Discontinuation is due to limited availability, logistical limitations, and short specimen stability (less than 23 hours).

Please do not order Natural Killer Cells, Functional (NKFUNC) testing. If you have an urgent need for testing, please get in touch with Client Services.