Confirmation of non-small cell lung cancer (NSCLC) diagnosis using ALK testing and genetic profiling in patients presenting with carcinoma of unknown primary site (CUP).

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e19062-e19062
Author(s):  
William Charles Penley ◽  
David R. Spigel ◽  
F Anthony Greco ◽  
John D. Hainsworth
Keyword(s):  
Treatment Options ◽  
Specific Treatment ◽  
Primary Site ◽  
Gene Profiling ◽  
Unknown Primary ◽  
Rt Pcr ◽  
Genetic Profiling ◽  
Pathologic Evaluation ◽  
Alk Positive ◽  
Support Methods

e19062 Background: Emerging data suggest real-time reverse transcriptase-polymerase chain reaction (RT-PCR) tumor profiling can predict the primary site in CUP. We report on CUP patients (pts) predicted to have NSCLC by RT-PCR, in whom detection of ALK rearrangements provided further diagnostic support. Methods: 4 pts were diagnosed with CUP based on standard clinical, radiographic, pathologic evaluation with immunohistochemistry (IHC), and bronchoscopy/endoscopy where indicated. All pts had a RT-PCR assay (CancerTYPE ID, bioTheranostics, Inc.) performed on tumor specimens for the purpose of predicting a primary site. Tissue was also tested for ALK by FISH using a break-apart probe. Results: Pt characteristics are shown (Table). RT-PCR results prompted ALK testing in Pts 2 and 3. ALK testing and RT-PCR testing were performed concurrently in Pts 1 and 4. Each specimen was diagnosed as lung adenocarcinoma (AC) by RT-PCR gene profiling, and also tested positive for an EML4-ALKrearrangement. All pts are being followed for clinical outcome. Conclusions: Gene expression profiling in CUP diagnosed lung AC in 4 pts who also had ALK rearrangements supporting the diagnosis. Identifying ALK-positive NSCLC among pts who present with CUP improves the site-specific treatment options. [Table: see text]

Gene profiling of tumor tissue in the diagnosis of patients with carcinoma of unknown primary site (CUP): Evaluation of the Veridex 10-gene molecular assay

2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 21109-21109
Author(s):  
J. D. Hainsworth ◽  
D. Talantov ◽  
T. Jatkoe ◽  
C. Meng ◽  
J. Baden ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Retrospective Study ◽  
Specific Treatment ◽  
Primary Site ◽  
Ffpe Tissue ◽  
Response To Treatment ◽  
Unknown Primary ◽  
Molecular Assay ◽  
Gene Markers ◽  
Pathologic Features

21109 Background: Standard treatment for most patients with CUP involves empiric chemotherapy. Since specific treatment now exists for most types of advanced carcinoma, precise identification of the primary site could lead to improved therapy. Veridex developed an optimized set of 10 gene markers, for a qRTPCR assay to identify tissue of origin of metastatic carcinoma in formalin-fixed, paraffin-embedded (FFPE) tissue samples (J Mol Diagn 8:320, 2006). The assay includes markers for 6 primary sites: lung, pancreas, colon, breast, ovary, and prostate. In this retrospective study, we evaluated the Veridex assay in patients with CUP. Methods: We obtained FFPE tissue from diagnostic biopsies on 69 CUP patients previously enrolled in empiric chemotherapy studies. The Veridex assay was performed as previously described. Assay results were correlated with clinical features, pathologic features, and response to treatment. Results: The Veridex assay yielded provisional diagnoses in 42 of 69 patients (61%): lung (15), pancreas (11), colon (12 ), ovary (4), breast (0), and prostate, (0 ). Most patients with diagnoses of lung and pancreas cancer had clinical and pathologic features compatible with these diagnoses; response rates to empiric chemotherapy (usually taxane/platinum-based) in patients with these diagnoses were 29% and 9%, respectively. The 12 patients with colon cancer diagnoses had predominantly intra-abdominal metastases (liver, peritoneum); response rate to therapy (usually taxane/platinum- based) was low (8%). The 4 patients with ovarian cancer had atypical clinical and pathologic features, and only 1 of 4 had PR to first-line taxane/platinum therapy. Conclusions: In this retrospective study, the Veridex 10-gene molecular assay was feasible and provided provisional diagnoses in a majority of patients with CUP. The diagnoses made using this assay (except ovarian cancer) were compatible with clinicopathologic features. The efficacy of cancer-specific treatment in patients diagnosed by this assay will be evaluated in prospective studies. No significant financial relationships to disclose.

Molecular tumor profiling (MTP) of poorly differentiated neoplasms (PDN) of unknown primary site.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 11080-11080 ◽  
Author(s):  
F Anthony Greco ◽  
David R. Spigel ◽  
John D. Hainsworth
Keyword(s):  
Germ Cell ◽  
Clinical Features ◽  
Germ Cell Tumors ◽  
Unknown Primary ◽  
Genetic Profiling ◽  
Genetic Sequencing ◽  
Pathologic Evaluation ◽  
Appropriate Therapy ◽  
Chromosomal Changes ◽  
Specific Tissue

11080 Background: The inability to definitively determine the lineage of neoplasms is less common with modern immunohistochemistry (IHC) and genetic profiling. Nonetheless some PDN defy lineage classification by extensive standard pathologic evaluation. The advent of MTP may provide a new method of improving the diagnosis of these challenging cancers. Methods: A total of 30 of 751 (4%) patients (pts) seen from 2000 – 2012 with cancer of unknown primary (CUP) had PDN without a definitive lineage determined by IHC (median 18 IHC stains, range 9 – 51). From 2008 – 2012 the 30 biopsies had MTP (RT-PCR mRNA CancerTYPE ID, bioTheranostics, Inc.). Additional IHC, genetic sequencing, fluorescent in situ hybridization for specific chromosomal changes and repeat biopsies were performed when feasible to support the MTP diagnosis, and clinical features correlated. Results: MTP lineage diagnoses were made in 25 of 30 (83%), including 10 carcinomas (3 germ cell, 2 neuroendocrine, 5 others), 5 melanomas, 8 sarcomas (3 peritoneal mesothelioma, 1 PNET) and 2 hematopoietic neoplasms (1 lymphoma, 1 chloroma). Additional IHC, genetic testing [BRAF, i(12)p] or repeat biopsies confirmed the MTP diagnoses in 11 of 15 tumors, and the clinical features were consistent with the MTP diagnoses in the majority of patients. Conclusions: This MTP assay can frequently provide a diagnosis for CUP pts and PDN without a definitive lineage defined by extensive IHC. The earlier application of MTP will likely provide an expedited diagnosis, and for some neoplasms is the only test capable of defining lineage and a more specific diagnosis. Appropriate therapy, particularly for pts with germ cell tumors, melanoma, and lymphoma depends on a specific tissue of origin diagnosis.

NGSCUP: Phase II trial of site-specific treatment based on gene expression and mutation profiling by next generation sequencing (NGS) for patients (pts) with cancer of unknown primary site (CUP).

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15577-e15577
Author(s):  
Hidetoshi Hayashi ◽  
Yuichi Takiguchi ◽  
Hironobu Minami ◽  
Kohei Akiyoshi ◽  
Yoshihiko Segawa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Survival Rate ◽  
Specific Treatment ◽  
Diagnostic Technique ◽  
Gene Profiling ◽  
Unknown Primary ◽  
Phase 2 ◽  
Site Specific ◽  
One Year ◽  
Tumor Types

e15577 Background: Although gene profiling is a promising diagnostic technique to determine the tissue of origin for pts with CUP, we reported that site-specific treatment based on gene profiling using microarray did not result in an improvement the survival compared with empirical therapy in the previous randomized phase 2 trial (Hayashi, et. al, JCO 2019). Recently, we have established new integrative diagnostic system combined the gene expression from RNA-sequencing and mutation/copy number variation data from targeted genomic-sequencing using NGS. We have performed a single-arm phase 2 study to assess the efficacy of site-specific therapy determined by this system in previously untreated pts with CUP. Methods: Comprehensive gene profiling was performed by NGS, and an established algorithm was applied to predict tumor origin. Pts with CUP was received site-specific chemotherapy determined by the predicted site. The primary endpoint was one-year survival rate. Results: A total of 111 pts was enrolled and all had sufficient biopsy tissue for gene profiling. Efficacy analysis was performed for 97 pts who received site-specific treatment. Cancer types most commonly predicted were lung (21%), liver (15%), kidney (15%), and colorectal cancer (12%). The one-year survival rate, median overall survival (OS), and progression free survival (PFS) was 53.1% (95%CI, 42.6-62.5%), 13.7 months (95% CI, 9.3-19.7 months), and 5.2 months (95% CI, 3.3-7.1 months), respectively. Median OS (15.7 versus 11.0 months, P = .078) and PFS (5.5 versus 2.8 months, P = .019) were better for predicted tumor types categorized as more responsive types than for less responsive ones. Conclusions: Site-specific treatment based on NGS demonstrated promising efficacy. Pts with CUP predicted to have more responsive tumor types had longer survival compared with pts with less responsive tumor types, suggesting that molecular tumor profiling by both DNA and RNA testing contributes to the management of pts with CUP. Clinical trial information: UMIN051180009.

Unknown primary cancer (UPC): Accuracy of tissue of origin prediction by molecular profiling

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. 11070-11070
Author(s):  
F. A. Greco ◽  
D. R. Spigel ◽  
D. A. Yardley ◽  
M. Erlander ◽  
X. Ma ◽  
...  
Keyword(s):  
Molecular Profiling ◽  
Primary Site ◽  
Unknown Primary ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Arch Pathol ◽  
Pcr Diagnosis ◽  
Formalin Fixed Paraffin ◽  
Diagnostic Biopsy ◽  
Formalin Fixed Paraffin Embedded

11070 Background: Molecular profiling may be useful to identify the primary site and direct therapy for patients (pts) with UPC. Since most UPC pts never have a primary site identified, the accuracy of molecular profiling diagnoses are difficult to verify. We identified a group of UPC pts who had a primary site subsequently identified during their clinical course, and performed a 92-gene real time polymerase chain reaction (RT-PCR) assay (Arch Pathol Lab Med 130:465, 2006) on tissue from the initial diagnostic biopsy. We then compared the RT-PCR diagnosis with the subsequent clinical diagnosis. Methods: 38 of 501 UPC pts (7%) seen between 2000 and 2008 had their primary tumor subsequently identified during life. 24 of the 38 pts had tissue biopsies (excluding FNA cytology) and are the subject of this study. The RT-PCR assay was performed on unstained slides from the formalin-fixed, paraffin-embedded (FFPE) initial diagnostic biopsy, and the assay predictions were compared to the actual primary sites (found later). No clinical or pathologic data (other than sex, biopsy site, and 1 H&E stained slide) were used in the prediction of the primary site. Results: 16 of 24 assays were successful (8 had no tumor or RNA in the material). 11 of 16 predictions of the site of origin (68%) were correct, corresponding to the actual primary sites found 3–58 months (median 8.5 months) after the initial diagnosis of UPC. Primary sites correctly identified included breast 2, ovary/peritoneal 4, NSCLC 1, colorectal 2, gastric 1, melanoma 1. 3 predictions were inaccurate (colorectal, testicular, sarcoma) in patients with gastroesophageal, pancreas and NSCLC, respectively. 2 assays were unclassifiable. Conclusions: RT-PCR performed on FFPE initial diagnostic tissue was accurate in predicting the primary site of origin in 11 of 16 pts with UPC who eventually had their primary site identified clinically. These data provide a direct validation of the reliability of this RT-PCR assay in predicting the primary site in pts with UPC. When used in concert with clinical features and IHC stains, molecular profiling may provide the basis for more successful site-directed therapy for many of these pts. Prospective studies of RT-PCR in UPC are ongoing. [Table: see text]

Differential expression of biomarkers in gastrointestinal versus pulmonary carcinoid tumors.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. e13571-e13571
Author(s):  
Erika Fong ◽  
Gilbert Peterson ◽  
Gargi D. Basu ◽  
Richard Blevins ◽  
Raheela Ashfaq
Keyword(s):  
Differentially Express ◽  
Treatment Options ◽  
Chemotherapeutic Agents ◽  
Primary Site ◽  
Carcinoid Tumors ◽  
Unknown Primary ◽  
Computer Search ◽  
Pulmonary Carcinoid ◽  
Pulmonary System ◽  
Pulmonary Carcinoids

e13571 Background: Carcinoid tumors are endocrine neoplasms that commonly arise in the GI and pulmonary system. About 12,000 cases of carcinoid tumor are diagnosed a year with a 5-year survival rate of 67.2% .The majority of the cases present with advance disease with limited treatment options,therefore evaluation of predictive markers for chemotherapeutic agents is highly desirable. We studied the biomarker expression in carcinoid tumors and evaluated any differences based on site of origin. Methods: By computer search we retrospectively identified all cases submitted to Caris Life Sciences with the diagnosis of “carcinoid”. The cases were classified by primary site into three groups: Pulmonary, GI tract (including esophagus, stomach, small bowel, colon, rectum, appendix and pancreas) and miscellaneous. Biomarker expression performed by IHC and scored semi quantitatively by a pathologist for SPARC mono, SPARC poly, Her2, TOPO2, TOPO1, PGP, MRP1, PTEN, TS, ERCC1, RRM1,MGMT, C-KIT, ER, PR and AR and SSTR2 and SSTR5 analysis by DNA Microarray were compared between the groups. Results: 146 carcinoid tumors were interrogated for biomarkers, 33 pulmonary, 97 GI and 16 miscellaneous (mediastinum, thymus, cervix, breast and unknown primary site). Due to small number of tumors in the miscellaneous category, analysis was restricted to pulmonary and GI carcinoid tumors only. Based on our analysis the pulmonary carcinoids differentially express Topo2, PGP, MGMT, CKIT and PR, while the GI carcinoids differentially express Topo1, RRM1 and ER and SSTR2 and SSTR5. There is equivalent expression of SPARC, MRP1, PTEN, TS, ERCC1 at both sites . All pulmonary and GI carcinoid tumors were negative for Her2. Conclusions: Based on this study it appears that there are differences in biomarker expression in GI and Pulmonary Carcinoid tumors. Treatment with irinotecan, gemcitabine, anti-estrogens and Octreotide may be more relevant in GI carcinoids based on molecular markers present while targets associated with response to anthracyclines, temozolomide, imatinib may be more commonly expressed in pulmonary carcinoid tumors. Further studies are needed to understand the underlying biology and molecular drivers in this group of tumors.

Gene profiling validation for cancer classification using known primary carcinoma samples

2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 21130-21130
Author(s):  
R. Lenzi ◽  
A. Rashid ◽  
N. Ordonez ◽  
N. M. Raber ◽  
G. R. Varadhachary ◽  
...  
Keyword(s):  
Gene Expression ◽  
Diagnostic Procedures ◽  
Primary Carcinoma ◽  
Primary Site ◽  
Gene Profiling ◽  
Unknown Primary ◽  
Malignant Neoplasms ◽  
Diagnostic Uncertainty ◽  
Primary Type ◽  
The Impact

21130 Background: Cancer of Unknown Primary Site (CUP) accounts for 3–5% of all malignant neoplasms. With current diagnostic procedures, approximately 20% of CUP patients have a primary identified. Since formulation of prognosis and treatment selection depends largely on the primary type, diagnostic uncertainty unfavorably affects CUP management. Gene expression profiling has permitted the development of diagnostic classifiers. A clinically usable methodology needs to differentiate a sufficiently large number of primary types. This study focuses on the estimate of the accuracy of gene expression for classification of metastatic tumors in formalin fixed (FF) FNA and core/surgical biopsies. Methods: CupPrint® is a 1900 gene microarray optimized for FF samples which uses a database of 643 cancer profiles to provide a robust method for the discrimination of 51 tumor (sub) types. Metastasis samples of six known primary carcinoma types were studied (lung, pancreas, colorectal, breast, liver, ovary/primary peritoneal carcinoma). To examine the impact of the metastatic site on diagnostic accuracy different biopsy sites were studied, including lung, brain, lymph nodes, liver, peritoneum. Samples were deemed evaluable that contained an estimated >33% tumor cells. mRNA samples from the metastatic lesions were provided in a blinded fashion to the microarray laboratory. Results: For 39 evaluable samples studied so far, the CupPrint® prediction was compared with the pathologic diagnosis. Of the 39, in 34 the primary site of origin was correctly predicted (87% accuracy). In two of the incorrectly predicted samples the site of biopsy (brain and liver respectively) was reported as the primary site. Correlations of molecular profiles to clinical parameters are being explored. Conclusions: CupPrint® appears to be sufficiently accurate to be of potential clinical utility in the diagnosis of CUP. No significant financial relationships to disclose.

Mutational burden of tumors with primary site unknown.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 3039-3039 ◽  
Author(s):  
Laurie M. Gay ◽  
David Fabrizio ◽  
Garrett Michael Frampton ◽  
Caitlin F. Connelly ◽  
James Sun ◽  
...  
Keyword(s):  
Clinical Care ◽  
Treatment Options ◽  
Additional Treatment ◽  
Primary Site ◽  
Unknown Primary ◽  
Tumor Type ◽  
Coding Region ◽  
Tissue Samples ◽  
Primary Tumor Site ◽  
Mutational Burden

3039 Background: Higher levels of tumor mutational burden (TMB) can predict sensitivity to immunotherapies (IO), which are FDA approved to treat NSCLC, melanoma, and urothelial carcinoma (Ca). TMB may be a biomarker for sensitivity to IO, irrespective of tumor type. TMB has not been explored widely for tumors of unknown primary site, but may reveal additional treatment options. Methods: Comprehensive genomic profiling of DNA from FFPE tissue samples was performed using hybrid-capture, next-generation sequencing. TMB was calculated by counting all coding short variant alterations (base substitutions and indels), including synonymous alterations, and subtracting from this functionally oncogenic or germline alterations (per ExAC, dbSNPT, or internal algorithmic analysis). To calculate the TMB per Mb, the total number of relevant mutations is divided by the coding region of the bait set (0.8 Mb, 1.1 Mb, or 1.2 Mb). High, intermediate, and low TMB were defined as ≥20 mut/Mb, ≥6 and <20 mut/Mb, or <6 mut/Mb, respectively. Tumor types with >100 samples were analyzed. Results: From a database of 102,878 samples sequenced during routine clinical care, 6116 samples for which the primary tumor site was unclear at sequencing were identified. Table shows TMB metrics (mut/Mb) and median patient age for these cohorts. Conclusions: Significant numbers of patients with each tumor type have high TMB that may indicate benefit from IO, excepting GIST. As expected, urothelial tumors have higher than average TMB and more patients have high TMB. SCC tumors are commonly TMB high (23%), as are tumors difficult to define histologically (15%). For ACUP or CUP, the most common tumors, 8-11% have high TMB. Analysis of responses to treatment with IO are ongoing. [Table: see text]

The 30 ROC trial: Precision intra-treatment imaging guiding major radiation reduction in human papillomavirus related oropharyngeal cancer.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 6019-6019
Author(s):  
Nancy Y. Lee ◽  
Eric Jeffrey Sherman ◽  
Heiko Schöder ◽  
Sean Matthew McBride ◽  
Yao Yu ◽  
...  
Keyword(s):  
Weight Loss ◽  
Human Papillomavirus ◽  
Specific Treatment ◽  
Concurrent Chemotherapy ◽  
Primary Site ◽  
Locoregional Control ◽  
Patient Specific ◽  
Unknown Primary ◽  
Oropharyngeal Carcinoma ◽  
Nodal Disease

6019 Background: Our previously published proof-of-concept trial using functional imaging to select patient with human papillomavirus (HPV) oropharyngeal carcinoma (OPC) for radiation de-escalation showed promising results. Here we report the outcome of a larger validation trial using the same paradigm where select HPV+ OPC patients received a definitive dose of 30Gy concurrently with chemotherapy and were subsequently observed. Methods: The trial enrolled patients who had p16+, T0-2, N1-N2c, M0 OPC by AJCC 7th TNM. Patients were required to have resection of the primary site (negative margin not required) or core biopsy of lymph node if unknown primary. In addition to standard positron emission tomography (PET), a pre-radiation dynamic 18F-FMISO (fluoromisonidazole) PET was performed to identify hypoxia in gross nodal disease. Patients with evidence of hypoxia ( > 1.2 tumor to muscle standard uptake value on 18F-FMISO) underwent repeat18F-FMISO PET around 2 weeks into radiation. Patients without pre-radiation hypoxia or with resolution of hypoxia on 18F-FMISO PET received 30Gy with 2 cycles of concurrent chemotherapy (cisplatin 100mg/m2 or carboplatin AUC 1.25 x 4 with 5-fluorouracil 2400 mg/m2). Results: From 11/2/17-1/4/21, 158 HPV+ OPC patients consented and were enrolled on trial. Patient characteristics were as follows: male (90%); ages 36-80 years; T-stage T0(26), T1(77), T2(55); N stage N1(19), N2a(15), N2b(95), N2c(29). Of the 114 patients with pre-treatment hypoxia, 24 had persistent hypoxia and received 70Gy. 128 patients were de-escalated to 30Gy and chemotherapy (86% cisplatin). 6 patients withdrew from trial [3 decided to receive standard of care; 3 refused 18F-FMISO PET]. Acute mucositis rates were 11% grade 0, 59% grade 1, and 30% grade 2, respectively. Acute xerostomia rates were 92% grade 1 and 8% grade 2, respectively. Weight loss was infrequent and only 19% complained of grade 1 and 5% complained of grade 2 weight loss. Six patients experienced grade 3 adverse events (diarrhea (2), syncope (2), vasovagal (1), dysphagia (1)). No patients required PEG tubes. With a median follow-up is 12 months (range: 2 months to 40 months), the 1-year locoregional control, distant metastasis-free overall survival rates were 94%, 100%, and 100%, respectively. Among the 30Gy de-escalated patients, none failed in the primary site. 8 patients had recurrent nodal disease underwent successful salvage surgery of which no additional therapy was given to 4 patients. Conclusions: Major de-escalation to 30Gy using patient specific treatment response based on hypoxia resolution resulted in excellent locoregional control with significant toxicity reduction. Updated results along with detailed correlative analysis will be presented. Clinical trial information: NCT03323463.

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