Joshua Babiarz
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View article: Clinical Validation of a Prenatal Cell-Free DNA Screening Test for Fetal RHD in a Large U.S. Cohort
Clinical Validation of a Prenatal Cell-Free DNA Screening Test for Fetal RHD in a Large U.S. Cohort Open
OBJECTIVE: To present a large U.S. clinical validation of a next-generation sequencing–based, noninvasive prenatal cell-free DNA test for fetal RHD . METHODS: This clinical validation study assessed the performance of a commercially availa…
View article: Afirma Genomic Sequencing Classifier and Xpression Atlas Molecular Findings in Consecutive Bethesda III-VI Thyroid Nodules
Afirma Genomic Sequencing Classifier and Xpression Atlas Molecular Findings in Consecutive Bethesda III-VI Thyroid Nodules Open
Context Broad genomic analyses among thyroid histologies have been described from relatively small cohorts. Objective Investigate the molecular findings across a large, real-world cohort of thyroid fine-needle aspiration (FNA) samples. Des…
View article: Analytical validation of the Percepta genomic sequencing classifier; an RNA next generation sequencing assay for the assessment of Lung Cancer risk of suspicious pulmonary nodules
Analytical validation of the Percepta genomic sequencing classifier; an RNA next generation sequencing assay for the assessment of Lung Cancer risk of suspicious pulmonary nodules Open
Background Bronchoscopy is a common procedure used for evaluation of suspicious lung nodules, but the low diagnostic sensitivity of bronchoscopy often results in inconclusive results and delays in treatment. Percepta Genomic Sequencing Cla…
View article: Improving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts
Improving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts Open
Background Bronchoscopy for suspected lung cancer has low diagnostic sensitivity, rendering many inconclusive results. The Bronchial Genomic Classifier (BGC) was developed to help with patient management by identifying those with low risk …
View article: OR28-04 Identification of Novel and Rare Receptor Tyrosine Kinase Fusions in Thyroid Fine Needle Aspirates
OR28-04 Identification of Novel and Rare Receptor Tyrosine Kinase Fusions in Thyroid Fine Needle Aspirates Open
Introduction: Receptor tyrosine kinases (RTKs) initiate signaling cascades, including growth and differentiation. Activation can occur through chromosomal rearrangements that lead to gene fusions. RTK fusions are potential targets for smal…
View article: MON-LB88 Positive Predictive Value of TP53 Variants in Bethesda III/IV Thyroid Fine-Needle Aspirates
MON-LB88 Positive Predictive Value of TP53 Variants in Bethesda III/IV Thyroid Fine-Needle Aspirates Open
Introduction: Somatic DNA variants in the tumor suppressor gene TP53 have been reported in papillary thyroid carcinoma (PTC), Hürthle cell carcinoma (HCC), poorly differentiated thyroid cancer (PDTC), and anaplastic thyroid carcinoma. Howe…
View article: Additional file 3 of Improving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts
Additional file 3 of Improving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts Open
Additional file 3. Gene Ontology biological processes overrepresented in gene modules identified from the gene co-expression network.)
View article: Additional file 2 of Improving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts
Additional file 2 of Improving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts Open
Additional file 2. Cell type signature gene lists.
View article: Analytical and Clinical Validation of Expressed Variants and Fusions From the Whole Transcriptome of Thyroid FNA Samples
Analytical and Clinical Validation of Expressed Variants and Fusions From the Whole Transcriptome of Thyroid FNA Samples Open
Introduction: The Afirma® Xpression Atlas (XA) detects gene variants and fusions in thyroid nodule FNA samples from a curated panel of 511 genes using whole-transcriptome RNA-sequencing. Its intended use is among cytologically indeterminat…
View article: Molecular Variants and Their Risks for Malignancy in Cytologically Indeterminate Thyroid Nodules
Molecular Variants and Their Risks for Malignancy in Cytologically Indeterminate Thyroid Nodules Open
Background: Gene panels are routinely used to assess predisposition to hereditary cancers by simultaneously testing multiple susceptibility genes and/or variants. More recently, genetic panels have been implemented as part of solid tumor m…
View article: Analytical Verification Performance of Afirma Genomic Sequencing Classifier in the Diagnosis of Cytologically Indeterminate Thyroid Nodules
Analytical Verification Performance of Afirma Genomic Sequencing Classifier in the Diagnosis of Cytologically Indeterminate Thyroid Nodules Open
Background: Fine needle aspiration (FNA) cytology, a diagnostic test central to thyroid nodule management, may yield indeterminate results in up to 30% of cases. The Afirma® Genomic Sequencing Classifier (GSC) was developed and clinically …
View article: MON-LB097 The Genomic Landscape of Preoperative FNAs Positive for the Afirma GSC Medullary Thyroid Cancer Classifier
MON-LB097 The Genomic Landscape of Preoperative FNAs Positive for the Afirma GSC Medullary Thyroid Cancer Classifier Open
Background The Afirma Genomic Sequencing Classifier (GSC) uses RNA sequencing to assess FNA specimens from cytologically indeterminate thyroid nodules, which are also tested for specific molecular aberrations associated with thyroid cancer…
View article: Performance of a Genomic Sequencing Classifier for the Preoperative Diagnosis of Cytologically Indeterminate Thyroid Nodules
Performance of a Genomic Sequencing Classifier for the Preoperative Diagnosis of Cytologically Indeterminate Thyroid Nodules Open
The genomic sequencing classifier demonstrates high sensitivity and accuracy for identifying benign nodules. Its 36% increase in specificity compared with the gene expression classifier potentially increases the number of patients with ben…
View article: Short Call Abstracts
Short Call Abstracts Open
Hu ¨rthle cell (oncocytic) carcinoma is an uncommon form of thyroid cancer exhibiting follicular patterned growth, radioactive iodine resistance, and an accumulation of mitochondria.Focused DNA sequencing of small numbers of tumors has rev…
View article: Additional file 1 of Analytical performance of Envisia: a genomic classifier for usual interstitial pneumonia
Additional file 1 of Analytical performance of Envisia: a genomic classifier for usual interstitial pneumonia Open
RNA-seq raw counts of samples used in Envisia analytical verification studies. This file includes the raw expression counts of 190 classifier genes across all samples (n=292) used in the analytical verification studies described in this ma…
View article: Detection of Clonal and Subclonal Copy-Number Variants in Cell-Free DNA from Patients with Breast Cancer Using a Massively Multiplexed PCR Methodology
Detection of Clonal and Subclonal Copy-Number Variants in Cell-Free DNA from Patients with Breast Cancer Using a Massively Multiplexed PCR Methodology Open
We demonstrate proof-of-concept for the use of massively multiplexed PCR and next-generation sequencing (mmPCR-NGS) to identify both clonal and subclonal copy-number variants (CNVs) in circulating tumor DNA. This is the first report of a t…
View article: Clinical experience with single‐nucleotide polymorphism‐based non‐invasive prenatal screening for 22q11.2 deletion syndrome
Clinical experience with single‐nucleotide polymorphism‐based non‐invasive prenatal screening for 22q11.2 deletion syndrome Open
Objectives To evaluate the performance of a single‐nucleotide polymorphism ( SNP )‐based non‐invasive prenatal test ( NIPT ) for the detection of fetal 22q11.2 deletion syndrome in clinical practice, assess clinical follow‐up and review pa…