Daniel H. Farkas
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View article: EWSR1-SMAD3 fibroblastic tumour: emerging cutaneous soft tissue neoplasm
EWSR1-SMAD3 fibroblastic tumour: emerging cutaneous soft tissue neoplasm Open
View article: 1064. Intra-Host SARS-CoV-2 Evolution Dynamics
1064. Intra-Host SARS-CoV-2 Evolution Dynamics Open
Background Our understanding of SARS-CoV-2 evolution is limited. Most estimates arise from analysis of global databases populated with unrelated sequences and is currently estimated at ∼27.7 substitutions/genome/year. SARS-CoV-2 polymerase…
View article: Alpha to Omicron: Disease Severity and Clinical Outcomes of Major SARS-CoV-2 Variants
Alpha to Omicron: Disease Severity and Clinical Outcomes of Major SARS-CoV-2 Variants Open
Background Four severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants predominated in the United States since 2021. Understanding disease severity related to different SARS-CoV-2 variants remains limited. Method Viral genom…
View article: Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples Open
View article: Circulating Tumor DNA Testing Supports Rapid Therapeutic Decision-Making in Metastatic Melanoma: A Case Report
Circulating Tumor DNA Testing Supports Rapid Therapeutic Decision-Making in Metastatic Melanoma: A Case Report Open
Treatment of metastatic melanoma includes the option of targeted therapy in patients with driver BRAF mutations. BRAF-MEK inhibitor drugs improve survival in the approximately 50% of patients with melanoma that harbor BRAF mutations. As BR…
View article: Most Frequently Cited Accreditation Inspection Deficiencies for Clinical Molecular Oncology Testing Laboratories and Opportunities for Improvement
Most Frequently Cited Accreditation Inspection Deficiencies for Clinical Molecular Oncology Testing Laboratories and Opportunities for Improvement Open
Context.— The College of American Pathologists (CAP), a laboratory accreditation organization with deemed status under the Clinical Laboratories Improvement Amendments of 1988 administers accreditation checklists. Checklists are used by la…
View article: A Model for Design and Implementation of a Laboratory Information-Management System Specific for Molecular Pathology Laboratory Operations
A Model for Design and Implementation of a Laboratory Information-Management System Specific for Molecular Pathology Laboratory Operations Open
The Molecular Pathology Section, Cleveland Clinic (Cleveland, OH), has undergone enhancement of its testing portfolio and processes. An Excel 2013- and paper-based data-management system was replaced with a commercially available laborator…
View article: Additional file 2 of Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
Additional file 2 of Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples Open
Additional file 2. A multiple tab Microsoft Excel file of FFPE experiment information, extensive quality check data and analysis results for FFPE samples, and analysis results for free DNA samples.
View article: Additional file 3 of Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
Additional file 3 of Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples Open
Additional file 3. List of known variants for four participating oncology panels.
View article: Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity
Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity Open
Within weeks of SARS-CoV-2 circulation, a profound shift toward 23403A>G (D614G) specific genotypes occurred. Replaced clades were associated with worse clinical outcomes, including mortality. These findings help explain persistent hospita…
View article: Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samples
Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samples Open
Clinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE) tissue or cell block cytology samples in oncology panel sequencing to identify mutations that can predict patient response to targeted therapy. To understand the t…
View article: Supplementary Material for: Effects of Exercise Dose and Detraining Duration on Mobility at Late Midlife: A Randomized Clinical Trial
Supplementary Material for: Effects of Exercise Dose and Detraining Duration on Mobility at Late Midlife: A Randomized Clinical Trial Open
Background: Office workers near retirement tend to be sedentary and can be prone to mobility limitations and diseases. We examined the dose effects of exergaming volume and duration of detraining on motor and cognitive functi…
View article: Diagnostic Utility of a Custom 34-Gene Anchored Multiplex PCR-Based Next-Generation Sequencing Fusion Panel for the Diagnosis of Bone and Soft Tissue Neoplasms With Identification of Novel <i>USP6</i> Fusion Partners in Aneurysmal Bone Cysts
Diagnostic Utility of a Custom 34-Gene Anchored Multiplex PCR-Based Next-Generation Sequencing Fusion Panel for the Diagnosis of Bone and Soft Tissue Neoplasms With Identification of Novel <i>USP6</i> Fusion Partners in Aneurysmal Bone Cysts Open
Context.— Bone and soft tissue tumors are heterogeneous, diagnostically challenging, and often defined by gene fusions. Objective.— To present our experience using a custom 34-gene targeted sequencing fusion panel. Design.— Total nucleic a…
View article: Targeted next generation sequencing (<scp>NGS</scp>) to classify melanocytic neoplasms
Targeted next generation sequencing (<span>NGS</span>) to classify melanocytic neoplasms Open
This study piloted a pan‐solid‐tumor next generation sequence (NGS)‐based laboratory developed test as a diagnostic aid in melanocytic tumors. 31 cases (4 “epithelioid” nevi, 5 blue nevi variants, 7 Spitz tumors [3 benign and 4 malignant] …
View article: Superficial sarcomas with <scp><i>CIC</i></scp> rearrangement are aggressive neoplasms: A series of eight cases
Superficial sarcomas with <span><i>CIC</i></span> rearrangement are aggressive neoplasms: A series of eight cases Open
CIC rearranged sarcomas have significant overlap with Ewing sarcoma, are aggressive, and typically present in deep soft tissue. They most commonly have a t (4;19)(q35;q13) with CIC ‐ DUX4 fusion. Superficial presentation is rare. We report…
View article: Incidental Detection of Maternal Neoplasia in Noninvasive Prenatal Testing
Incidental Detection of Maternal Neoplasia in Noninvasive Prenatal Testing Open
BACKGROUND Noninvasive prenatal testing (NIPT) uses cell-free DNA (cfDNA) as an analyte to detect copy-number alterations in the fetal genome. Because maternal and fetal cfDNA contributions are comingled, changes in the maternal genome can…
View article: Clinical outcome of subchromosomal events detected by whole‐genome noninvasive prenatal testing
Clinical outcome of subchromosomal events detected by whole‐genome noninvasive prenatal testing Open
Objective A novel algorithm to identify fetal microdeletion events in maternal plasma has been developed and used in clinical laboratory‐based noninvasive prenatal testing. We used this approach to identify the subchromosomal events 5pdel,…
View article: The Evolving Role of the Laboratory Professional in the Age of Genome Sequencing
The Evolving Role of the Laboratory Professional in the Age of Genome Sequencing Open