Category: Clinical Updates

Pathology Insights – Pathology of Vaping-Associated Lung Injury with Sanjay Mukhopadhyay, MD

Pathology Insights Video Series

Pathology of Vaping-Associated Lung Injury

Presented by Sanjay Mukhopadhyay, MD

Sanjay Mukhopadhyay, MD, discusses the findings of a study on the lung pathology of vaping.

Featured in an article co-authored by Dr. Mukhopadhyay and published in the American Journal of Clinical Pathology, the study focuses on the results of microscopic examination of biopsied lung tissue from individuals who developed severe lung illness associated with vaping.

This is one of the first case series in the world to examine lung biopsies from patients with vaping-associated lung illness and is the first-ever study on vaping published in a pathology journal. These findings have important public health implications and are detailed in the video.

As part of our educational mission for our clients and communities, Cleveland Clinic Laboratories presents the Pathology Insights video series.
These short videos break down information about interesting pathology cases to better inform doctors, laboratory staff, patients, or anyone interested in the field of pathology. Each episode features important cases, methods, and practices that are personally presented by our staff pathologists.

CC-SIGN® NTRK Plus Gene Fusion Next-Generation Sequencing Panel

CC-SIGN® NTRK Gene Fusion Next-Generation Sequencing Panel

This NGS-based laboratory-developed test is designed to detect fusion events in NTRK1, NTRK2, and NTRK3, regardless of fusion partner.

Clinical information obtained from the CC-SIGN® NTRK Gene Fusion NGS Panel can determine if a patient is a candidate for TRK tyrosine kinase inhibitor treatment.

The US Food and Drug Administration (FDA) has approved the use of first-generation TRK tyrosine kinase inhibitors—including larotrectinib (Vitrakvi®) and entrectinib (Rozlytrek®)—to treat patients whose tumors harbor NTRK1, NTRK2, or NTRK3 fusions.

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Molecular Pathology at Cleveland Clinic

NTRK Fusions are Clinically Actionable

TRK tyrosine kinase inhibitors, such as larotrectinib and entrectinib, are drugs utilized to treat solid tumors with a neurotrophic receptor tyrosine kinase (NTRK) gene fusion without a known acquired resistance mutation. These drugs provide a treatment option to patients with no satisfactory alternative therapies or whose cancer has progressed following treatment, specifically in cases that are either metastatic or where surgical resection is likely to result in severe morbidity.1,2 This treatment targets cancers with NTRK fusions and is not limited by tissue or tumor type.

1. U.S. Food & Drug Administration. FDA approves larotrectinib for solid tumors with NTRK gene fusions. Available at https://www.fda.gov/Drugs/InformationOnDrugs/ApprovedDrugs/ucm626720.htm. [Online]  Updated Dec 17, 2018.
2. U.S. Food & Drug Administration. FDA approves entrectinib for NTRK solid tumors and ROS-1 NSCLC. Available at https://www.fda.gov/drugs/resources-information-approved-drugs/fda-approves-entrectinibntrk-solid-tumors-and-ros-1-nsclc [Online] Updated Aug 16, 2019.

Test Overview

Test Name

NTRK Gene Fusion NGS Panel (NTRK)

CPT Codes

81445, 88381

Turnaround Time

14 days (upon specimen receipt)

Specimen Requirements

Please include the original pathology report with any submitted specimens.

Ten (10) unstained, 4 µM sections of formalin-fixed, paraffin-embedded (FFPE) on charged, unbaked slides

One H&E stained slide with best tumor area circled by a pathologist (minimum of 20% tumor content for best results)

Transport Temperature

Room (ambient) temperature

Specimen Mailing Address

Cleveland Clinic Laboratories
2119 E. 93rd Street, L15
Cleveland, OH 44106

Specimens must be sent via UPS, FedEx, or DHL – review our Shipping Information for more details.

Clinical Indications

This test is intended for determining NTRK gene fusion status to identify candidates for larotrectinib treatment.

Limitations

This test does not detect single nucleotide variants; some data show acquired kinase domain resistance mutations that are not interrogated by this test.

Interrogated Genes

NTRK1
NM_002529
Exons 2, 4, 6, 8, 10-14

NTRK2
NM_006180
Exons 5, 7, 9, 11-18

NTRK3
NM_001007156
Exon 15

NTRK3
NM_002530
Exons 4, 7, 10, 12-16

CC-SIGN® Solid Tumor Gene Fusion Next-Generation Sequencing Panel

CC-SIGN® Solid Tumor Gene Fusion Next-Generation Sequencing Panel

This customized, 59-gene Next-Generation Sequencing (NGS)-based laboratory-developed test is intended for use in the diagnosis and management of benign and malignant mesenchymal tumors (sarcomas and their mimics) as well as other solid tumors.

The CC-SIGN® Solid Tumor Gene Fusion NGS Panel is available as part of a comprehensive, diagnostic consultation or as a stand-alone test. This laboratory-developed test interrogates gene targets associated with known translocations in mesenchymal and other solid tumors. Additionally, this panel identifies the corresponding fusion partner and predicted exon breakpoints, which can be of diagnostic and prognostic significance. Fluorescence in situ hybridization-based testing is available for specific fusion questions.

Results are delivered within 14 days of specimen receipt, allowing for a timely, definitive diagnosis in difficult sarcoma and solid tumor cases in a stand-alone fashion or with the support of our expert pathologists.

Request a Pathology Consult
Molecular Pathology at Cleveland Clinic

Test Overview

Test Name

Solid Tumor Gene Fusion NGS Panel (SRCNGS)

CPT Codes

81445
88381

Turnaround Time

14 days (upon specimen receipt)

Specimen Requirements

Formalin-fixed, paraffin-embedded (FFPE) tissue
• Ten (10) unstained, 4 μM sections of FFPE on charged, unbaked slides
• One (1) H&E stained slide with best tumor area* circled by a pathologist

*minimum of 20% tumor content for best results

Transport Temperature

Room (ambient) temperature

Specimen Shipping Address

Cleveland Clinic Laboratories
2119 E. 93rd Street, L15
Cleveland, OH 44106

Specimens must be sent via UPS, FedEx, or DHL – review our Shipping Information for more details.

Clinical Indications

This test is intended for the diagnosis of benign or malignant mesenchymal tumors (sarcomas & their mimics) as well as other solid tumors.

Targeted Gene Regions

Genes interrogated, including relevant transcripts and exons, are listed in alphabetical order.

A

Gene, Transcript, Exons

ABL1
NM_004304
2, 4, 6, 10, 16-23, 25, 26

B

Gene, Transcript, Exons

BCOR
NM_001123385
Exons 3-8, 12, 14, 15

BCOR
NM_017745
Exon 8

BRAF
NM_004333
Exons 1-5, 7-16, 18

C

Gene, Transcript, Exons

CAMTA1
NM_015215
Exons 3, 8-10

CCNB3
NM_033031
Exons 2-6

CIC
NM_015125
Exons 12, 17-20

CRTC1
NM_015321
Exons 1-4

CSF1
NM_000757
Exons 5-8

CSF1
NM_172212
Exon 9

E

Gene, Transcript, Exons

EPC1
NM_025209
Exons 9-11

ETV6
NM_001987
Exons 1-7

EWSR1
NM_005243
Exons 4-14

F

Gene, Transcript, Exons

FOS
NM_005252
Exon 4

FOSB
NM_006732
Exons 1, 2

FOXO1
NM_002015
Exons 1-3

FUS
NM_004960
Exons 3-11, 13, 14

G

Gene, Transcript, Exons

GLI1
NM_005269
Exons 4-7

H

Gene, Transcript, Exons

HMGA2
NM_003483
Exons 1-5

J

Gene, Transcript, Exons

JAZF1
NM_175061
Exons 2-4

M

Gene, Transcript, Exons

MAML2
NM_032427
Exons 2, 3

MEAF6
NM_001270875
Exons 4, 5

MKL2
NM_014048
Exons 11-13

MYB
NM_001130173
Exons 7-9, 11-16

N

Gene, Transcript, Exons

NCOA1
NM_147223
Exons 12-15

NCOA2
NM_006540
Exons 11-16

NCOA3
NM_006534
Exons 2, 13-16

NCOA3
NM_181659
Exon 20

NOTCH1
NM_017617
Exons 2, 4, 24-31

NOTCH2
NM_024408
Exons 5-7, 24-29

NOTCH3
NM_000435
Exons 25-30

NR4A3
NM_006981
Exon 2

NR4A3
NM_173200
Exons 3, 4

NTRK1*
NM_002529
Exons 2, 4, 6, 8, 10-14

NTRK2*
NM_006180
Exons 5, 7, 9, 11-18

NTRK3*
NM_001007156
Exon 15

NTRK3*
NM_002530
Exons 4, 7, 10, 12-16

NUTM1
NM_175741
Exons 2-4, 6

*A specimen positive for a fusion in one of these genes makes the patient a candidate for larotrectinib treatment.
Standalone NTRK testing is also available via the CC-SIGN® NTRK Gene Fusion NGS Panel.

P

Gene, Transcript, Exons

PAX3
NM_181459
Exons 6-8

PAX7
NM_002584
Exons 6-8

PDGFB
NM_002608
Exons 2, 3

PDGFD
NM_025208
Exons 5-7

PGR
NM_000926
Exons 1-3

PHF1
NM_024165
Exons 1, 2, 10-12

PLAG1
NM_002655
Exons 1-4

PRDM10
NM_199437
Exons 12, 13

PRKD1
NM_002742
Exons 10-13

R

Gene, Transcript, Exons

RAF1
NM_002880
Exons 4-12

RELA
NM_021975
Exons 3 , 4, 11

RET
NM_020630
Exons 2, 4, 6, 11, 15, 16

RET
NM_020975
Exons 8-14

ROS1
NM_002944
2, 4, 7, 31-38

S

Gene, Transcript, Exons

SRF
NM_003131
Exons 2-4

SS18
NM_001007559
Exons 2-6, 8-11

SS18
NM_005637
Exons 2, 3

STAT6
NM_001178078
Exons 1-7, 15-20

T

Gene, Transcript, Exons

TAF15
NM_139215
Exons 5-7

TCF12
NM_207036
Exons 4-6

TFE3
NM_006521
Exons 2-8

TFEB
NM_007162
Exons 1-4, 9

TFG
NM_006070
Exons 3-7

TRIM11
NM_145214
Exons 2, 3

U

Gene, Transcript, Exons

USP6
NM_004505
Exons 1-3

W

Gene, Transcript, Exons

WWTR1
NM_015472
Exons 3, 4

Y

Gene, Transcript, Exons

YAP1
NM_001130145
Exons 1-9

YWHAE
NM_006761
Exon 5

Pathology Insights – Pleural Fluid: Cyto-Histo Correlation by Sanjay Mukhopadhyay, MD and Charles Sturgis, MD

Pathology Insights Video Series

Pleural Fluid: Cyto-Histo Correlation

Presented by Sanjay Mukhopadhyay, MD and Charles Sturgis, MD

A cytopathologist (Charles Sturgis, MD) and a thoracic pathologist (Sanjay Mukhopadhyay, MD) discuss their diagnostic approach on a case involving pleural fluid cytology and a concurrent pleural biopsy.

As part of our educational mission for our clients and communities, Cleveland Clinic Laboratories presents the Pathology Insights video series.
These short videos break down information about interesting pathology cases to better inform doctors, laboratory staff, patients, or anyone interested in the field of pathology. Each episode features important cases, methods, and practices that are personally presented by our staff pathologists.

Pathology Insights – Lung Granulomas Caused by Fungal Infection with Sanjay Mukhopadhyay, MD

Pathology Insights Video Series

Lung Granulomas Caused by Fungal Infection

Presented by Sanjay Mukhopadhyay, MD

Not all lung nodules are malignant.

In this video, Dr. Mukhopadhyay compares and contrasts two cases of lung granulomas caused by fungal infection. These types of fungal infection cause granulomas in the lung, which can be mistaken for each other.

As part of our educational mission for our clients and communities, Cleveland Clinic Laboratories presents the Pathology Insights video series.
These short videos break down information about interesting pathology cases to better inform doctors, laboratory staff, patients, or anyone interested in the field of pathology. Each episode features important cases, methods, and practices that are personally presented by our staff pathologists.

Pathology Insights – Lung Cancer or Metastasis to Lung? with Sanjay Mukhopadhyay, MD

Pathology Insights Video Series

Lung Cancer or Metastasis to Lung?

Presented by Sanjay Mukhopadhyay, MD

Can metastases to the lung occur from cancers that were treated several years ago?  Dr. Mukhopadhyay discusses.

As part of our educational mission for our clients and communities, Cleveland Clinic Laboratories presents the Pathology Insights video series.
These short videos break down information about interesting pathology cases to better inform doctors, laboratory staff, patients, or anyone interested in the field of pathology. Each episode features important cases, methods, and practices that are personally presented by our staff pathologists.

Pathology Insights – Basics of Thymic Pathology with Sanjay Mukhopadhyay, MD

Pathology Insights Video Series

Basics of Thymic Pathology

Presented by Sanjay Mukhopadhyay, MD

What are the differences between normal thymic tissue and thymoma?

Learn the basics in this brief introduction to pathology of the thymus by thoracic pathologist, Sanjay Mukhopadhyay, MD.

As part of our educational mission for our clients and communities, Cleveland Clinic Laboratories presents the Pathology Insights video series.
These short videos break down information about interesting pathology cases to better inform doctors, laboratory staff, patients, or anyone interested in the field of pathology. Each episode features important cases, methods, and practices that are personally presented by our staff pathologists.

Pathology Insights – Challenging Cutaneous Spindle Cell Tumors with Steven Billings, MD

Pathology Insights Video Series

Challenging Cutaneous Spindle Cell Tumors

Presented by Steven Billings, MD

In this episode of Pathology Insights, Steven Billings, MD, staff pathologist for the Dermatopathology and Soft Tissue & Bone services, covers a set of challenging cutaneous spindle cell tumors, emphasizing a practical approach and key histologic features that allow accurate diagnosis.

As part of our educational mission for our clients and communities, Cleveland Clinic Laboratories presents the Pathology Insights video series.
These short videos break down information about interesting pathology cases to better inform doctors, laboratory staff, patients, or anyone interested in the field of pathology. Each episode features important cases, methods, and practices that are personally presented by our staff pathologists.

Pathology Insights – Atypical Epithelial Cells with Sanjay Mukhopadhyay, MD

Pathology Insights Video Series

Atypical Epithelial Cells

Presented by Sanjay Mukhopadhyay, MD

Sanjay Mukhopadhyay, MD, staff pathologist for Cleveland Clinic’s Pulmonary Pathology service, presents and discusses another unusual case of interstitial lung disease involving atypical epithelial cells.

Dr. Mukhopadhyay explains that the focus on the patient’s tumor changed completely once a full pathology interpretation was performed, and what factors led to the patient’s revised diagnosis.

As part of our educational mission for our clients and communities, Cleveland Clinic Laboratories presents the Pathology Insights video series.
These short videos break down information about interesting pathology cases to better inform doctors, laboratory staff, patients, or anyone interested in the field of pathology. Each episode features important cases, methods, and practices that are personally presented by our staff pathologists.

Pathology Insights – Nonspecific Interstitial Pneumonia (NSIP) with Sanjay Mukhopadhyay, MD

Pathology Insights Video Series

Nonspecific Interstitial Pneumonia (NSIP)

Sanjay Mukhopadhyay, MD, staff pathologist for Cleveland Clinic’s Pulmonary Pathology service, reviews an interesting case of Nonspecific Interstitial Pneumonia.

Dr. Mukhopadhyay highlights the differences between Usual Interstitial Pneumonia (UIP) and Nonspecific Interstitial Pneumonia (NSIP) and explains what a pathologist should look for when determining the patient’s diagnosis.

As part of our educational mission for our clients and communities, Cleveland Clinic Laboratories presents the Pathology Insights video series.
These short videos break down information about interesting pathology cases to better inform doctors, laboratory staff, patients, or anyone interested in the field of pathology. Each episode features important cases, methods, and practices that are personally presented by our staff pathologists.