A5034810093- Cancer Genomics and Diagnostics
- Lung Cancer Treatments and Mutations
- Genetic factors in colorectal cancer
- Genomics and Rare Diseases
- Molecular Biology Techniques and Applications
- Lung Cancer Diagnosis and Treatment
- Chronic Lymphocytic Leukemia Research
- SARS-CoV-2 detection and testing
- SARS-CoV-2 and COVID-19 Research
- Lung Cancer Research Studies
- Lymphoma Diagnosis and Treatment
- Viral gastroenteritis research and epidemiology
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Traumatic Brain Injury Research
- Colorectal Cancer Screening and Detection
- Biomedical and Engineering Education
- Full-Duplex Wireless Communications
- Clinical Laboratory Practices and Quality Control
- Brain Metastases and Treatment
- RNA modifications and cancer
- BRCA gene mutations in cancer
- MicroRNA in disease regulation
- CRISPR and Genetic Engineering
- Radiomics and Machine Learning in Medical Imaging
- Cancer Immunotherapy and Biomarkers
NewYork–Presbyterian Hospital
2015-2025
Columbia University Irving Medical Center
2018-2025
New York Hospital Queens
2015-2025
Columbia University
2020-2025
Rockefeller University
2021
Cornell University
2014-2020
Weill Cornell Medicine
2016-2020
Loyola University Medical Center
2017-2018
Huazhong University of Science and Technology
2018
Tongji Hospital
2018
This paper describes the Precision Medicine Knowledge Base (PMKB; https://pmkb.weill.cornell.edu ), an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations.PMKB was built using Ruby on Rails Web framework. Leveraging existing standards such as Human Genome Variation Society variant description format, we implemented a data model that links variants to tumor-specific tissue-specific interpretations. Key...
Introduction: MET Exon 14 skipping alterations are drivers of non-small cell lung carcinoma (NSCLC) with responses to tyrosine kinase inhibitors. Amplicon-based DNA NGS assays (DNA NGSs) for the detection METex14 can yield false-negative results. We examined efficacy a and reflex RNA-based (RNA NGS) strategy. Materials Methods: Clinical cases definitive or suspected adenocarcinoma (LungCa), lacking driver mutations targeted NGS, underwent RNA identify oncogenic drivers. Samples identified on...
We describe Exome Cancer Test v1.0 (EXaCT-1), the first New York State-Department of Health-approved whole-exome sequencing (WES)-based test for precision cancer care. EXaCT-1 uses HaloPlex (Agilent) target enrichment followed by next-generation (Illumina) tumour and matched constitutional control DNA. present a detailed clinical development validation pipeline suitable simultaneous detection somatic point/indel mutations copy-number alterations (CNAs). A computational framework data...
Distinguishing synchronous and metachronous primary lung adenocarcinomas from with intrapulmonary metastasis is essential for optimal patient management. In this study, multiple occurring in the same were evaluated using comprehensive histopathologic evaluation supplemented molecular analysis. The cohort included 18 patients a total of 52 adenocarcinomas. Eleven had new diagnosis lobe (n=5) or different (n=6). Seven history cancer developed tumors. final was made resection specimens (n=49),...
Gastric carcinoma with lymphoid stroma is an uncommon variant enriched for mutually exclusive Epstein-Barr virus (EBV) positivity and mismatch repair (MMR) deficiency. We performed this study to evaluate molecular alterations in morphologically homogeneous subtype compare them 295 conventional gastric cancers analyzed The Cancer Genome Atlas study. identified 31 cases subjected situ hybridization EBV-encoded RNAs assessment MMR status. Immunostains PD-L1, β-catenin, HER2 were performed;...
Minimally invasive diagnostic procedures such as needle-core biopsy and fine-needle aspiration provide adequate material for molecular analyses. Advances in precision oncology are trending toward the interrogation of limited amounts genomic to guide clinical therapeutic decisions. The aim this study was investigate minimum cellularity needed on cytologic smears identification clinically relevant variants with next-generation sequencing (NGS).Thirty cases cytologically diagnosed,...
The routine use of large next-generation sequencing (NGS) pan-cancer panels is required to identify the increasing number of, but often uncommon, actionable alterations guide therapy. Inconsistent coverage and variable payment hindering NGS adoption into clinical practice. A review test utilization, utility, coverage, reimbursement was conducted in a cohort patients diagnosed with high-risk cancer who received panel testing as part their care.The Columbia Combined Cancer Panel (CCCP),...
As doenças cardiovasculares (DCV) continuam a ser principal causa de morte em todo o mundo, representando uma preocupação saúde pública global significativa. A elevada prevalência fatores risco, como hipertensão, diabetes, dislipidemias e estilo vida sedentário, contribui para aumento do número casos alta morbimortalidade associada essas condições. Portanto, necessidade estratégias eficazes detecção precoce, diagnóstico preciso prevenção DCV se torna cada vez mais urgente. Nesse cenário,...
Background/Objectives: While the genomic landscape of primary lung carcinomas is well characterized, there a relative scarcity fusion data on corresponding central nervous system (CNS) metastases. This study aimed to elucidate molecular profiles CNS metastases (1) assess significance combined DNA-reflex RNA testing approach and (2) compare mutational between patients who present initially [early (≤2 months)] with those develop thereafter [late (>2 months)]. Methods: We performed...
Benign metastasizing leiomyoma (BML) is a rare benign smooth muscle neoplasm that originates in the uterus and metastasizes to distant sites-most commonly lungs. BMLs are often found incidentally patients with history of uterine leiomyoma(s) tend be indolent. Occasionally they may symptomatic rarely follow an aggressive clinical course. We report unusual case BML presenting 46-year-old woman as miliary nodular pattern bilaterally lungs progressive respiratory failure. Her past medical was...
Microsatellite instability (MSI), a hallmark of DNA mismatch repair deficiency, is key molecular biomarker with multiple clinical implications including the selection patients for immunotherapy, identifying who may have Lynch syndrome and predicting prognosis in colorectal tumours. Next-generation sequencing (NGS) provides opportunity to interrogate large numbers microsatellite loci concurrently genomic variants. We sought develop method detect MSI that would not require paired normal tissue...
Validation of RNA-based NGS assays for the detection therapeutically targetable gene fusions is challenging. Here, we report systematic validation and quality control monitoring our targeted fusion panel 17 clinically relevant transcripts across several tumor types. We implemented this RNA Fusion Panel as a reflex test tumors lacking DNA driver mutations.Forty-four formalin-fixed, paraffin-embedded (FFPE) or fresh-frozen lung, brain, soft tissue skin were used to determine accuracy assay....
9036 Background: Exon 14 skipping mutations in the mesenchymal-epithelial transition ( MET) gene are reported 2-5% of lung adenocarcinomas and mutually exclusive other driver mutations. Small-molecule MET tyrosine kinase inhibitors, capmatinib tepotinib, showed durable responses previously treated treatment-naïve patients harboring MET-exon-14 Studies suggest that for detection MET-ex14 mutations, DNA-based assays alone may be sub-optimal when compared to RNA-based NGS assays. We performance...
Context.— An increasing number of molecular laboratories are implementing next-generation sequencing platforms to identify clinically actionable and relevant genomic alterations for precision oncology. Objective.— To describe the validation studies as per New York State–Department Health (NYS-DOH) guidelines Oncomine Comprehensive Panel v2, which was originally tailored National Cancer Institute Molecular Analysis Therapy Choice (NCI-MATCH) trial. Design.— Accuracy, precision,...
To determine concordance/discordance between morphology and molecular testing (MT) among synchronous pulmonary carcinomas using targeted next generation sequencing (NGS), with without comprehensive review (CMR), vs analyses of multiple singe genes (non-NGS).Results morphologic MT assessment were classified as concordant, discordant, or indeterminate. For discordant cases, histologic (CHA) was performed.Forty-seven cases 108 tumors identified underwent (NGS, n = 23 non-NGS, 24). Histology...
Assessment of ALK gene rearrangements is strongly recommended by the Molecular Testing Guideline for Selection Lung Cancer Patients proposed IASLC, AMP, and CAP at time diagnosis patients with advanced stage disease. Non-small-cell lung cancer (NSCLC) or resulting fusion proteins have been, most part, successfully targeted tyrosine kinase inhibitors (TKIs). The frequent rearrangement, EML4-ALK oncogenic fusion, has more than 10 distinct variants, each a discrete breakpoint in EML4 . Recent...
Lymphangiomatosis (eg, generalized lymphatic anomaly) is an abnormal proliferation of endothelial cells. It often a childhood disease, but it may present in adulthood by infiltrating organs and cause obstruction, bleeding, or disruption flow. Pulmonary involvement be mild diffuse interstitial lung airway hemoptysis, chylothorax, chylopericardium, culminate respiratory failure. Treatment has been limited to surgical resection drainage procedures because there no accepted effective systemic...
Cell blocks are being used more frequently in cytology for ancillary testing, including molecular diagnostics. There several different methods of processing cell blocks, with plasma-thrombin one the most common. Plasma is a blood-derived product and may be source DNA. The aim this study was to determine whether plasma block method has amplifiable DNA that potentially interfere testing results.Expired bags fresh frozen were collected from blood bank. From each sample, extracted 1-mL aliquot...
Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) is a sensitive and specific tool in the risk stratification of pancreatic lesions, including cysts. The sensitivity specificity EUS-FNA has been shown to improve when cytology combined with next-generation sequencing (NGS). Ideally, fresh cyst fluid used for NGS. In this pilot study, we explore possibility DNA derived from residual alcohol-fixed aspirates.
Context Next-generation sequencing–based approaches using RNA have increasingly been used by clinical laboratories for the detection of fusion genes, intragenic rearrangements, and exon-skipping events. Correspondingly, College American Pathologists (CAP) has advanced sequencing proficiency testing (PT) to ensure optimal performance these assays. Objective To report on laboratory practices events CAP PT data from 8 mailings (2018-A through 2021-B). Design program results 153 across 24 test...
Lung cancer is the most common cause of deaths worldwide, accounting for 1.8 million each year. Only 20% lung cases are reported to occur in low- and middle-income countries. An estimated 1.5% all Ethiopian cancers involved lung; however, no nationwide registry exists Ethiopia. Thus, accurate data on clinical history, histopathology, molecular characteristics, risk factors not available. The aim this study was describe clinical, radiologic, pathologic including available profiles, at Tikur...