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Article
Open AccessComparing modalities for risk assessment in patients with pulmonary lesions and nondiagnostic bronchoscopy for suspected lung cancer
Bronchoscopy is commonly utilized for non-surgical sampling of indeterminant pulmonary lesions, but nondiagnostic procedures are common. Accurate assessment of the risk of malignancy is essential for decision ...
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Article
Open AccessPercepta Genomic Sequencing Classifier and decision-making in patients with high-risk lung nodules: a decision impact study
Incidental and screening-identified lung nodules are common, and a bronchoscopic evaluation is frequently nondiagnostic. The Percepta Genomic Sequencing Classifier (GSC) is a genomic classifier developed in cu...
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Article
Open AccessAnalytical validation of the Percepta genomic sequencing classifier; an RNA next generation sequencing assay for the assessment of Lung Cancer risk of suspicious pulmonary nodules
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 Gen...
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Article
Open AccessImproving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts
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 t...
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Article
Open AccessIdentification of Hürthle cell cancers: solving a clinical challenge with genomic sequencing and a trio of machine learning algorithms
Identification of Hürthle cell cancers by non-operative fine-needle aspiration biopsy (FNAB) of thyroid nodules is challenging. Resultingly, non-cancerous Hürthle lesions were conventionally distinguished from...
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Article
Open AccessIdentification of usual interstitial pneumonia pattern using RNA-Seq and machine learning: challenges and solutions
We developed a classifier using RNA sequencing data that identifies the usual interstitial pneumonia (UIP) pattern for the diagnosis of idiopathic pulmonary fibrosis. We addressed significant challenges, inclu...
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Article
Open AccessAnalytical performance of Envisia: a genomic classifier for usual interstitial pneumonia
Clinical guidelines specify that diagnosis of interstitial pulmonary fibrosis (IPF) requires identification of usual interstitial pneumonia (UIP) pattern. While UIP can be identified by high resolution CT of t...
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Article
Open AccessAnalytical performance of a bronchial genomic classifier
The current standard practice of lung lesion diagnosis often leads to inconclusive results, requiring additional diagnostic follow up procedures that are invasive and often unnecessary due to the high benign r...
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Article
Open AccessThe diagnostic application of RNA sequencing in patients with thyroid cancer: an analysis of 851 variants and 133 fusions in 524 genes
Thyroid carcinomas are known to harbor oncogenic driver mutations and advances in sequencing technology now allow the detection of these in fine needle aspiration biopsies (FNA). Recent work by The Cancer Geno...
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Article
Open AccessUse of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm
A resequencing microarray called PathogenID v2.0 has been developed and used to explore various strategies of sequence selection for its design. The part dedicated to influenza viruses was based on consensus s...
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Article
Open AccessPhi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR
Phi29 polymerase based amplification methods provides amplified DNA with minimal changes in sequence and relative abundance for many biomedical applications. RNA virus detection using microarrays, however, can...
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Article
Open AccessA genome-wide linkage analysis of alcoholism on microsatellite and single-nucleotide polymorphism data, using alcohol dependence phenotypes and electroencephalogram measures
The Collaborative Study on the Genetics of Alcoholism (COGA) is a large-scale family study designed to identify genes that affect the risk for alcoholism and alcohol-related phenotypes. We performed genome-wid...
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Article
Open AccessDescription of the data from the Collaborative Study on the Genetics of Alcoholism (COGA) and single-nucleotide polymorphism genoty** for Genetic Analysis Workshop 14
The data provided to the Genetic Analysis Workshop 14 (GAW 14) was the result of a collaboration among several different groups, catalyzed by Elizabeth Pugh from The Center for Inherited Disease Research (CIDR...
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Article
Genoty** over 100,000 SNPs on a pair of oligonucleotide arrays
We present a genoty** method for simultaneously scoring 116,204 SNPs using oligonucleotide arrays. At call rates >99%, reproducibility is >99.97% and accuracy, as measured by inheritance in trios and concord...
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Article
The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs
Understanding the nature of evolutionary relationships among persons and populations is important for the efficient application of genome science to biomedical research. We have analysed 8,525 autosomal single...
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Article
Large-scale genoty** of complex DNA
Genetic studies aimed at understanding the molecular basis of complex human phenotypes require the genoty** of many thousands of single-nucleotide polymorphisms (SNPs) across large numbers of individuals1. Publ...
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Estradiol Inhibition of Expression of the Human Glycoprotein Hormone α-Subunit Gene Through an ERE-Independent Mechanism
The α-subunit comprises one-half of all glycoprotein hormones. Expression of the α-subunit gene occurs in a variety of cell types (gonadotrophs, thyrotrophs, and syncytiotrophoblasts) and is regulated by a mul...
