Pathology molecular reflex testing improves turn-around-time and overall molecular testing rates in NSCLC.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e13507-e13507
Author(s):  
David R. Braxton ◽  
Yancui Huang ◽  
Sourat Darabi ◽  
Frank Chavez ◽  
Partha Manas Das ◽  
...  
Keyword(s):  
Treatment Options ◽  
Community Setting ◽  
Third Party ◽  
Molecular Testing ◽  
Process Map ◽  
Biomarker Testing ◽  
Reflex Testing ◽  
Next Generation Sequencing Ngs ◽  
Traditional Approaches ◽  
Reflex System

e13507 Background: Dozens of genetic aberrations have become druggable targets or act as biomarkers of diseases for which pts may qualify for precision medicine treatment options. Biomarker informed treatments can lead to vast improvements in patient outcomes over traditional approaches like chemo. However, comprehensive molecular profiling (CMP) to identify eligible pts is not always accomplished, particularly in the community setting where molecular testing is often outsourced to third party laboratories. Here we report our experience with reflex testing protocols, where a pathology department has responsibility for initiating biomarker testing without the need for direct oncologist involvement. In this study we investigate and report how pathologist initiated reflex protocols influences access to molecular biomarker testing and assessed changes in testing rates, result tracking, and timeliness of results. Methods: We reviewed a reflex testing protocol at Hoag Hospital (Newport Beach, California), for NSCLC pts. A process map was generated to identify pts who qualified for reflex testing. After developing the process map, we used VIPER software that gathers data from electronic medical records and pathology systems to perform our analysis. We evaluated protocol adherence, failures, QNS rates, and TAT from test ordering to sample receipt and processing and ultimately all the way to results being received and compared patients that followed the reflex protocol as compared to those that did not to determine any differences. Data analysis was performed to understand how effective the reflex system was in ensuring the appropriate patients received CMP and any benefits in efficiency that resulted. Results: We evaluated 300 NSCLC pts over a 12-month timeframe for their reflex testing statuses. 78.5% of those pts tested received Next Generation Sequencing (NGS) tests, vs. 21.5% receiving non-NGS based tests. We also found over 75% of the pts that were qualified for reflex testing had complete tests, while 25% were not able to be completed. Of those who did not meet reflex criteria, only 28% went on to receive CMP. The primary reason for a patient who qualified for reflex testing but did not have testing initiated was due to insurance or reimbursement concerns (42%). The average time from a reflex test being ordered to results available was 25.9 days. Without reflex the TAT averaged 40.5 days (15.4 days difference). For reflexed cases, 78% of CMP results were available prior to treatment initiation. Conclusions: We demonstrate that implementation of a CMP reflex testing program is feasible and can ensure that a higher percentage of NSCLC pts receive molecular testing and that these results can be provided nearly two times sooner than without such programs. Our next steps are to automate this process to allow practices that do not have the personnel to manage such programs can still benefit via technology assistance.

scholarly journals The Impact of Foundation Medicine Testing on Cancer Patients: A Single Academic Centre Experience

2021 ◽  
Vol 11 ◽  
Author(s):  
Dalia Karol ◽  
Mathieu McKinnon ◽  
Lenah Mukhtar ◽  
Arif Awan ◽  
Bryan Lo ◽  
...  
Keyword(s):  
Treatment Options ◽  
Retrospective Chart Review ◽  
Molecular Testing ◽  
Test Results ◽  
Treatment Change ◽  
Microsoft Excel ◽  
Oncogenic Mutations ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Direct Change

BackgroundThe use of Next-Generation Sequencing (NGS) has recently allowed significant improvements in cancer treatment. Foundation Medicine® (FM) provides a genomic profiling test based on NGS for a variety of cancers. However, it is unclear if the Foundation Medicine test would result in a better outcome than the standard on-site molecular testing. In this retrospective chart review, we identified the FM cases from an academic Canadian hospital and determined whether these test results improved treatment options for those patients.Materials and MethodsA retrospective analysis was performed on patients with solid tumors who had FM testing between May 1, 2014 and May 1, 2018. Clinical factors and outcomes were measured using descriptive statistics using Microsoft Excel® Software.ResultsOut of 66 FM tests, eight patients (= 12%) had a direct change in therapy based on the FM tests. Identified were 285 oncogenic mutations (median 1, range 0–31); where TP53 (n = 31, 10.9%), CDKN2A (n = 19, 6.7%), KRAS (n = 16, 5.6%) and APC (n = 9, 3.2%) were the most common FM mutations identified.ConclusionA small proportion of FM reports identified actionable mutations and led to direct treatment change. FM testing is expensive and a few of the identified mutations are now part of routine on-site testing. NGS testing is likely to become more widespread, but this research suggests that its true clinical impact may be restricted to a minority of patients.

scholarly journals Liquid Biopsy Analysis in Clinical Practice: Focus on Lung Cancer

2021 ◽  
Vol 2 (3) ◽  
pp. 241-254
Author(s):  
Pasquale Pisapia ◽  
Francesco Pepe ◽  
Antonino Iaccarino ◽  
Roberta Sgariglia ◽  
Mariantonia Nacchio ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Liquid Biopsy ◽  
Treatment Options ◽  
Molecular Testing ◽  
Specific Information ◽  
Sample Collection ◽  
Timely Manner ◽  
Oncology Practice ◽  
Nsclc Patients ◽  
To Receive

Lung cancer is the leading cause of cancer death worldwide. Despite the emergence of highly effective targeted therapies, up to 30% of advanced stage non-small cell lung cancer (NSCLC) patients do not undergo tissue molecular testing because of scarce tissue availability. Liquid biopsy, on the other hand, offers these patients a valuable opportunity to receive the best treatment options in a timely manner. Indeed, besides being much faster and less invasive than conventional tissue-based analysis, it can also yield specific information about the genetic make-up and evolution of patients’ tumors. However, several issues, including lack of standardized protocols for sample collection, processing, and interpretation, still need to be addressed before liquid biopsy can be fully incorporated into routine oncology practice. Here, we reviewed the most important challenges hindering the implementation of liquid biopsy in oncology practice, as well as the great advantages of this approach for the treatment of NSCLC patients.

Biomarker testing patterns and actionability in advanced non-small cell lung cancer (aNSCLC) at OneOncology (OneOnc).

2021 ◽  
Vol 39 (28_suppl) ◽  
pp. 287-287
Author(s):  
Ari M. Vanderwalde ◽  
Esprit Ma ◽  
Elaine Yu ◽  
Tania Szado ◽  
Richard Price ◽  
...  
Keyword(s):  
Performance Status ◽  
Ecog Performance Status ◽  
Personalized Care ◽  
Specimen Collection ◽  
Targeted Treatments ◽  
Biomarker Testing ◽  
Next Generation Sequencing Ngs ◽  
To Receive ◽  
Testing Patterns ◽  
Test Result

287 Background: Recent approvals of targeted treatments (tx) have improved personalized care in aNSCLC. Biomarker testing is crucial for patients (pts) to receive optimal tx expeditiously. This study examined aNSCLC biomarker testing and tx patterns at OneOnc. Methods: Pts diagnosed with aNSCLC (stage ≥ IIIb) from 1/1/2015 to 5/31/2020, aged ≥ 18 years, and with ≥ 1 visit ≤ 90 days of advanced (Adv) diagnosis (Dx) were retrospectively evaluated using the nationwide Flatiron Health electronic health record derived de-identified database from selected OneOnc sites. Descriptive analyses were conducted to evaluate testing patterns for ALK, BRAF, EGFR, KRAS, PD-L1, and ROS-1 biomarkers and actionable mutation tx pattern. Results: Overall 3,860 aNSCLC pts were included, median age was 69 years, 47% females, 66% non-squamous, 29% squamous, 4% histology NOS, and 23% with ECOG performance status 0-1. Of the 3,152 (82%) pts tested for any biomarker, 64% received next-generation sequencing (NGS) vs. 36% received other biomarker tests only. Testing rates varied by biomarker: EGFR (74%), ALK (72%), ROS-1 (66%), PD-L1 (57%), BRAF (56%), KRAS (54%). Pts who received all 6 biomarker tests increased from 12% (2015), 23% (2016), 40% (2017), 41% (2018), 48% (2019) to 56% (2020). Among the tested pts, the median time from Adv Dx to the first test result was 20 days (d) and from specimen collection after Adv Dx to the first test result was 12 d. Pts tested and treated before test result available declined from 28% (2015) to 16% (2020). Of 1,207 pts with actionable mutations, 390 (32%) received tx before the test result: 35% chemotherapy (chemo) only, 28% chemo + cancer immunotherapy (CIT), and 15% CIT only. After the test result, 26% to 81% of pts received no or other tx not specific to actionable mutations [Table]. Conclusions: Findings from this study demonstrated an increase in aNSCLC biomarker testing at OneOnc over time, while 44% pts in 2020 did not receive testing on all 6 biomarkers. Some pts had tx prior to the test result, but this trend appeared to decline. Further studies are warranted to better understand the reasons for pts receiving tx that were not specific to their actionable mutations.[Table: see text]

scholarly journals Optimizing the Diagnosis and Biomarker Testing for Patients with Intrahepatic Cholangiocarcinoma: A Multidisciplinary Approach

Cancers ◽  
2022 ◽  
Vol 14 (2) ◽  
pp. 392
Author(s):  
May T. Cho ◽  
Sepideh Gholami ◽  
Dorina Gui ◽  
Sooraj L. Tejaswi ◽  
Ghaneh Fananapazir ◽  
...  
Keyword(s):  
Treatment Options ◽  
Biliary Tree ◽  
Physician Education ◽  
Community Healthcare ◽  
Heterogenous Group ◽  
Treatment Paradigm ◽  
Tissue Acquisition ◽  
Biomarker Testing ◽  
Standard Practices ◽  
The University

Cholangiocarcinoma (CCA) is a heterogenous group of malignancies originating in the biliary tree, and associated with poor prognosis. Until recently, treatment options have been limited to surgical resection, liver-directed therapies, and chemotherapy. Identification of actionable genomic alterations with biomarker testing has revolutionized the treatment paradigm for these patients. However, several challenges exist to the seamless adoption of precision medicine in patients with CCA, relating to a lack of awareness of the importance of biomarker testing, hurdles in tissue acquisition, and ineffective collaboration among the multidisciplinary team (MDT). To identify gaps in standard practices and define best practices, multidisciplinary hepatobiliary teams from the University of California (UC) Davis and UC Irvine were convened; discussions of the meeting, including optimal approaches to tissue acquisition for diagnosis and biomarker testing, communication among academic and community healthcare teams, and physician education regarding biomarker testing, are summarized in this review.

scholarly journals Frequent Mutations in Natural Killer/T Cell Lymphoma

2018 ◽  
Vol 49 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Yanjie Zhang ◽  
Chaoping Li ◽  
Weili Xue ◽  
Mingzhi Zhang ◽  
Zhaoming Li
Keyword(s):  
T Cell ◽  
Natural Killer ◽  
Cell Lymphoma ◽  
Treatment Options ◽  
Gene Mutations ◽  
T Cell Lymphoma ◽  
Somatic Gene ◽  
Frequent Mutations ◽  
New Biomarkers ◽  
Next Generation Sequencing Ngs

Extranodal natural killer (NK)/T cell lymphoma (ENKTL-NT or NKTCL), with its aggressive nature and poor prognosis, has been widely studied to discover more effective treatment options. Various somatic gene alterations have been identified by traditional Sanger sequencing. However, recently, novel gene mutations in NKTCL have been revealed by next-generation sequencing (NGS) technology, suggesting the potential for novel targeted therapies. This review discusses recurrent aberrations in NKTCL detected by NGS, which can be categorized into three main groups, specifically, tumor suppressors (TP53, DDX3X, and MGA), the JAK/STAT cascade, and epigenetic modifiers (KMT2D, BCOR, ARID1A, and EP300). Some epigenetic dysregulation and DDX3X mutation, which have been rarely identified by traditional sequencing technology, were recently uncovered with high frequencies by NGS. In this review, we summarize the mutational frequencies of various genes in NKTCL. In general, based on our analysis, BCOR is the most frequently mutated gene (16.9%), followed by TP53 (14.7%), and DDX3X (13.6%). The characterization of such genes provides new insight into the pathogenesis of this disease and indicates new biomarkers or therapeutic targets.

PLAG1 Immunohistochemical Staining Is a Surrogate Marker for PLAG1 Fusions in Lipoblastomas

2021 ◽  
pp. 109352662110433
Author(s):  
Mikako Warren ◽  
Nishant Tiwari ◽  
Sabrina Sy ◽  
Gordana Raca ◽  
Ryan J Schmidt ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gold Standard ◽  
Immunohistochemical Staining ◽  
Surrogate Marker ◽  
Molecular Testing ◽  
Protein Overexpression ◽  
Conventional Cytogenetics ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Lipomatous Tumors

Background The hallmark of lipoblastoma is a PLAG1 fusion. PLAG1 protein overexpression has been reported in sporadic PLAG1-rearranged lipoblastomas. Methods We evaluated the utility of PLAG1 immunohistochemical staining (IHC) in 34 pediatric lipomatous tumors, correlating the results with histology and conventional cytogenetics, FISH and/or next generation sequencing (NGS) results. Results The study included 24 lipoblastomas, divided into 2 groups designated as “Lipoblastoma 1” with both lipoblastoma histology and PLAG1 rearrangement (n = 16) and “Lipoblastoma 2” with lipoblastoma histology but without PLAG1 cytogenetic rearrangement (n = 8), and 10 lipomas with neither lipoblastoma histology nor a PLAG1 rearrangement. Using the presence of a fusion as the “gold standard” for diagnosing lipoblastoma (Lipoblastoma 1), the sensitivity of PLAG1 IHC was 94%. Using histologic features alone (Lipoblastoma 1 + 2), the sensitivity was 96%. Specificity, as defined by the ability to distinguish lipoma from lipoblastoma, was 100%, as there were no false positives in the lipoma group. Conclusions Cytogenetics/molecular testing is expensive and may not be ideal for detecting PLAG1 fusions because PLAG1 fusions are often cytogenetically cryptic and NGS panels may not include all partner genes. PLAG1 IHC is an inexpensive surrogate marker of PLAG1 fusions and may be useful in distinguishing lipoblastomas from lipomas.

Targeted therapies in cholangiocarcinoma: Assessment of US oncologist practice patterns.

2021 ◽  
Vol 39 (3_suppl) ◽  
pp. 347-347
Author(s):  
Kinjal Parikh ◽  
Davecia Ragoonath Cameron ◽  
Tristin Abair ◽  
Patrick Kugel ◽  
Arndt Vogel
Keyword(s):  
Clinical Practice ◽  
Targeted Therapies ◽  
Progressive Disease ◽  
Community Setting ◽  
Molecular Testing ◽  
Learning Needs ◽  
Self Awareness ◽  
Multiple Choice Questions ◽  
Molecular Alterations ◽  
Practice Assessment

347 Background: Chemotherapy is a mainstay treatment modality for patients with advanced cholangiocarcinoma (CCA). Recent developments and new approvals have led to changing paradigms, incorporating the use of targeted therapies for patients with progressive disease. Given the need for a greater understanding of the molecular alterations, varying targets, and available and emerging therapies, education is needed to assess knowledge regarding these recent advances in unresectable CCA. The goal of this activity was to increase the knowledge of self-assess the learning needs of oncologists in treating patients with unresectable CCA. Methods: The education included 25 multiple choice questions in a continuing medical education (CME)-certified clinical practice assessment to assess practice gaps. The questions were designed to measure knowledge, competence, confidence, and attitudes of oncologists regarding clinical evidence, role of molecular testing, and place in the treatment paradigm for targeted therapies in unresectable CCA. The self-assessment was made available online to physicians as a learning tool to gain foundational knowledge, as well as receive feedback about their performance as compared to other test-takers, to improve self-awareness of their own personal educational gaps. The activity launched 6/24/20, and data are reported through 8/31/20. Results: A total of 1,009 learners, including 758 physicians, participated in the activity. Of the 104 oncologists that participated, a majority practiced in the community setting, saw patients with a range of cancers, and were not confident about using targeted therapies or recognizing targets for biomarker testing. Oncologists demonstrated the following gaps related to: NGS sequencing and biomarkers: 21% do not use; 32% use upon progressive disease; 35% did not realize that not all panels detect FGFR2 fusions; 20% do not test for biomarkers; 29% and 56% test for IDH or FGFR, respectively; 60% recognize the incidence of IDH1 mutations; Clinical trial (FIGHT202 and ClarIDHy): 45% were able to identify biomarker eligibility for pemigatinib; 9% were able to identify pemigatinib OS outcomes; 30% were able to recognize most common grade 3 AE of pemigatinib; 51% recognized the PFS endpoint with ivosidenib; 34% were able to identify eligibility for ivosidenib; 55% recognized most common AEs of ivosidenib. Conclusions: This CME-certified clinical practice assessment identified gaps in knowledge, competence, and confidence regarding testing and use of targeted therapies and emerging data in patients with unresectable CCA. As new data emerges and the number of targets and targeted therapies expand, continued education remains important to continue to optimize patient care.

scholarly journals The Role of Single-Cell Technology in the Study and Control of Infectious Diseases

Cells ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 1440 ◽  
Author(s):  
Weikang Nicholas Lin ◽  
Matthew Zirui Tay ◽  
Ri Lu ◽  
Yi Liu ◽  
Chia-Hung Chen ◽  
...  
Keyword(s):  
Infectious Diseases ◽  
Single Cell ◽  
Single Cell Analysis ◽  
Treatment Options ◽  
Recent Decade ◽  
Cellular Heterogeneity ◽  
Biological Studies ◽  
Infection Mechanisms ◽  
Next Generation Sequencing Ngs ◽  
And Control

The advent of single-cell research in the recent decade has allowed biological studies at an unprecedented resolution and scale. In particular, single-cell analysis techniques such as Next-Generation Sequencing (NGS) and Fluorescence-Activated Cell Sorting (FACS) have helped show substantial links between cellular heterogeneity and infectious disease progression. The extensive characterization of genomic and phenotypic biomarkers, in addition to host–pathogen interactions at the single-cell level, has resulted in the discovery of previously unknown infection mechanisms as well as potential treatment options. In this article, we review the various single-cell technologies and their applications in the ongoing fight against infectious diseases, as well as discuss the potential opportunities for future development.

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