afirma genomic sequencing classifier gsc  (Veracyte Inc)

Journal: Frontiers in Endocrinology

Article Title: Risk of malignancy in cytologically indeterminate thyroid nodules harboring thyroid stimulating hormone receptor mutations

doi: 10.3389/fendo.2022.1073592

Figure Lengend Snippet: Proportion of TSHR variants assigned as Afirma GSC-B or GSC-S as well as the breakdown of ITN Bethesda categories and Afirma result for each cytology type.

Article Snippet: To evaluate the frequency and risk of malignancy of TSHRpI568T mutations discovered in indeterminate thyroid nodules (ITN) within the Veracyte CLIA laboratory undergoing Afirma ® Genomic Sequencing Classifier (GSC) testing, and to evaluate a broader cohort of TSHR variants and their categorization as Afirma GSC benign (GSC-B) or suspicious (GSC-S).

Techniques:

Journal: Frontiers in Endocrinology

Article Title: Risk of malignancy in cytologically indeterminate thyroid nodules harboring thyroid stimulating hormone receptor mutations

doi: 10.3389/fendo.2022.1073592

Figure Lengend Snippet: Proportion of TSHR variant distribution by gender and age amongst Afirma GSC-B or GSC-S results.

Article Snippet: To evaluate the frequency and risk of malignancy of TSHRpI568T mutations discovered in indeterminate thyroid nodules (ITN) within the Veracyte CLIA laboratory undergoing Afirma ® Genomic Sequencing Classifier (GSC) testing, and to evaluate a broader cohort of TSHR variants and their categorization as Afirma GSC benign (GSC-B) or suspicious (GSC-S).

Techniques: Variant Assay

Journal: Frontiers in Endocrinology

Article Title: Risk of malignancy in cytologically indeterminate thyroid nodules harboring thyroid stimulating hormone receptor mutations

doi: 10.3389/fendo.2022.1073592

Figure Lengend Snippet: Proportion of TSHRpI568T mutated nodules by Bethesda category and Afirma GSC category as well as the malignancy rate of GSC-S nodules.

Article Snippet: To evaluate the frequency and risk of malignancy of TSHRpI568T mutations discovered in indeterminate thyroid nodules (ITN) within the Veracyte CLIA laboratory undergoing Afirma ® Genomic Sequencing Classifier (GSC) testing, and to evaluate a broader cohort of TSHR variants and their categorization as Afirma GSC benign (GSC-B) or suspicious (GSC-S).

Techniques:

Journal: Frontiers in Endocrinology

Article Title: Risk of malignancy in cytologically indeterminate thyroid nodules harboring thyroid stimulating hormone receptor mutations

doi: 10.3389/fendo.2022.1073592

Figure Lengend Snippet: Patient and tumor characteristics of malignancies discovered within Afirma GSC-S TSHR variants.

Article Snippet: To evaluate the frequency and risk of malignancy of TSHRpI568T mutations discovered in indeterminate thyroid nodules (ITN) within the Veracyte CLIA laboratory undergoing Afirma ® Genomic Sequencing Classifier (GSC) testing, and to evaluate a broader cohort of TSHR variants and their categorization as Afirma GSC benign (GSC-B) or suspicious (GSC-S).

Techniques:

Journal: Frontiers in Endocrinology

Article Title: Risk of malignancy in cytologically indeterminate thyroid nodules harboring thyroid stimulating hormone receptor mutations

doi: 10.3389/fendo.2022.1073592

Figure Lengend Snippet: TSHR codon variants associated with malignancies in Afirma GSC-S thyroid nodules.

Article Snippet: To evaluate the frequency and risk of malignancy of TSHRpI568T mutations discovered in indeterminate thyroid nodules (ITN) within the Veracyte CLIA laboratory undergoing Afirma ® Genomic Sequencing Classifier (GSC) testing, and to evaluate a broader cohort of TSHR variants and their categorization as Afirma GSC benign (GSC-B) or suspicious (GSC-S).

Techniques:

Journal: Journal of Personalized Medicine

Article Title: Maximizing Small Biopsy Patient Samples: Unified RNA-Seq Platform Assessment of over 120,000 Patient Biopsies

doi: 10.3390/jpm13010024

Figure Lengend Snippet: Unified Assay workflow. GA, genomic Atlas; GC, genomic classifier; GSC, Genomic Sequencing Classifier; ILD, interstitial lung disease; LOH, loss of heterozygosity; NS, nasal swab; SNV, single-nucleotide variant; UIP, usual interstitial pneumonia; XA, Expression Atlas.

Article Snippet: Sequencing data were analyzed via the following advanced machine learning-based classifiers (all developed/licensed by Veracyte, Inc., South San Francisco, CA, USA) that are applied to the diagnosis of thyroid cancer, interstitial lung disease (ILD), and lung cancer, and may be applicable to other disease indications: the Afirma ® Genomic Sequencing Classifier (GSC), which uses RNA exome sequencing information derived from a fine-needle aspiration (FNA) biopsy to classify cytologically indeterminate thyroid nodules as Afirma GSC Benign or Suspicious [ , , , , ]; the Afirma Xpression Atlas (XA), which provides genomic alteration information from FNA samples with an Afirma GSC Suspicious result, or cytologically suspicious for malignancy or malignancy nodule [ ]; the Envisia ® Genomic Classifier (GC), a diagnostic test that uses a 190-gene expression signature to differentiate between usual interstitial pneumonia (UIP) and non-UIP subtypes in lung transbronchial biopsy (TBB) samples from patients with ILD [ ]; the Percepta GSC, which uses RNA exome sequencing information from bronchial brushing samples for classification of lung cancer risk among bronchoscopy nondiagnostic samples [ ]; the Percepta Nasal Swab (NS) classifier that uses RNA exome sequencing information from nasal (inferior turbinate) samples to classify the risk of lung cancer in patients with previously detected lung nodules [ ]; and the Percepta Genomic Atlas (GA) test, which was developed to detect lung cancer-associated fusions and MET exon-skipping events in diagnostic TBB specimens and transbronchial needle aspirates (TBNAs) [ ].

Techniques: Genomic Sequencing, Variant Assay, Expressing

Journal: Journal of Personalized Medicine

Article Title: Maximizing Small Biopsy Patient Samples: Unified RNA-Seq Platform Assessment of over 120,000 Patient Biopsies

doi: 10.3390/jpm13010024

Figure Lengend Snippet: Fusion discovery across Unified Assay samples. ( a ) Number of fusions identified per sample across thyroid (Afirma), ILD (Envisia), and lung (Percepta) samples; ( b , c ) canonical fusions identified in thyroid Afirma CLIA samples. The following fusion calls were filtered out: having <3 junction reads; involving HLA, hemoglobin, or mitochondrial genes as one or both fusion partners; being between two immunoglobulin genes; and being called in >10% of samples from any one product with CLIA samples. ONLY_REF_SPLICE = having both splice sites matching a known reference splice site. INCL_NON_REF_SPLICE = having one or both splice sites not matching a known reference splice site. CLIA, Clinical Laboratory Improvement Amendments; GA, Genomic Atlas; GSC, Genomic Sequencing Classifier; HLA, human leukocyte antigen; NS, Nasal Swab; UIP, usual interstitial pneumonia; XA, Expression Atlas.

Article Snippet: Sequencing data were analyzed via the following advanced machine learning-based classifiers (all developed/licensed by Veracyte, Inc., South San Francisco, CA, USA) that are applied to the diagnosis of thyroid cancer, interstitial lung disease (ILD), and lung cancer, and may be applicable to other disease indications: the Afirma ® Genomic Sequencing Classifier (GSC), which uses RNA exome sequencing information derived from a fine-needle aspiration (FNA) biopsy to classify cytologically indeterminate thyroid nodules as Afirma GSC Benign or Suspicious [ , , , , ]; the Afirma Xpression Atlas (XA), which provides genomic alteration information from FNA samples with an Afirma GSC Suspicious result, or cytologically suspicious for malignancy or malignancy nodule [ ]; the Envisia ® Genomic Classifier (GC), a diagnostic test that uses a 190-gene expression signature to differentiate between usual interstitial pneumonia (UIP) and non-UIP subtypes in lung transbronchial biopsy (TBB) samples from patients with ILD [ ]; the Percepta GSC, which uses RNA exome sequencing information from bronchial brushing samples for classification of lung cancer risk among bronchoscopy nondiagnostic samples [ ]; the Percepta Nasal Swab (NS) classifier that uses RNA exome sequencing information from nasal (inferior turbinate) samples to classify the risk of lung cancer in patients with previously detected lung nodules [ ]; and the Percepta Genomic Atlas (GA) test, which was developed to detect lung cancer-associated fusions and MET exon-skipping events in diagnostic TBB specimens and transbronchial needle aspirates (TBNAs) [ ].

Techniques: Genomic Sequencing, Expressing

Journal: Journal of Personalized Medicine

Article Title: Maximizing Small Biopsy Patient Samples: Unified RNA-Seq Platform Assessment of over 120,000 Patient Biopsies

doi: 10.3390/jpm13010024

Figure Lengend Snippet: Chromosome and genome-wide LOH across diseases and tissues. ( a ) Chromosome and genome-wide LOH across lung (Percepta), thyroid (Afirma), and ILD (Envisia) samples; ( b ) chromosome and genome-wide LOH across specific lung cancer specimens; ( c ) comparison of results using TSO500 and expression-based CNV identification in an NSCLC-adenocarcinoma sample. The center of the highlighted region on chromosome 11 is gene CCND1, for which a duplication was identified by both TSO500 and expression-based CNV identification; ( d ) chromosome and genome-wide LOH across specific thyroid cancer specimens. Numbers next to the color bar represent the color scale of LOH scores, whereby blue indicates low LOH scores, yellow indicates intermediate LOH scores, and red represents high LOH scores. Expression-based CNV calls were made by the JRB identification method , with increased expression JRBs identified as amplification events and decreased expression JRBs as deletion events. Chr, chromosome; CLIA, Clinical Laboratory Improvement Amendments; CNV, copy number variation; GA, Genomic Atlas; GSC, Genomic Sequencing Classifier; ILD, interstitial lung disease; JRB, Jointly Regulated Block; LOH, loss of heterozygosity; NA, not available; NSCLC, non-small cell lung cancer; NS, Nasal Swab; SNV, single-nucleotide variant; TBNA, transbronchial needle aspiration; TSO500, TruSight Oncology 500; UIP, usual interstitial pneumonia.

Article Snippet: Sequencing data were analyzed via the following advanced machine learning-based classifiers (all developed/licensed by Veracyte, Inc., South San Francisco, CA, USA) that are applied to the diagnosis of thyroid cancer, interstitial lung disease (ILD), and lung cancer, and may be applicable to other disease indications: the Afirma ® Genomic Sequencing Classifier (GSC), which uses RNA exome sequencing information derived from a fine-needle aspiration (FNA) biopsy to classify cytologically indeterminate thyroid nodules as Afirma GSC Benign or Suspicious [ , , , , ]; the Afirma Xpression Atlas (XA), which provides genomic alteration information from FNA samples with an Afirma GSC Suspicious result, or cytologically suspicious for malignancy or malignancy nodule [ ]; the Envisia ® Genomic Classifier (GC), a diagnostic test that uses a 190-gene expression signature to differentiate between usual interstitial pneumonia (UIP) and non-UIP subtypes in lung transbronchial biopsy (TBB) samples from patients with ILD [ ]; the Percepta GSC, which uses RNA exome sequencing information from bronchial brushing samples for classification of lung cancer risk among bronchoscopy nondiagnostic samples [ ]; the Percepta Nasal Swab (NS) classifier that uses RNA exome sequencing information from nasal (inferior turbinate) samples to classify the risk of lung cancer in patients with previously detected lung nodules [ ]; and the Percepta Genomic Atlas (GA) test, which was developed to detect lung cancer-associated fusions and MET exon-skipping events in diagnostic TBB specimens and transbronchial needle aspirates (TBNAs) [ ].

Techniques: Genome Wide, Comparison, Expressing, Amplification, Genomic Sequencing, Blocking Assay, Variant Assay

Journal: Journal of Personalized Medicine

Article Title: Maximizing Small Biopsy Patient Samples: Unified RNA-Seq Platform Assessment of over 120,000 Patient Biopsies

doi: 10.3390/jpm13010024

Figure Lengend Snippet: RNA and gene expression across samples used in the development of each test. ( a ) RNA expression of CD274 (PD-L1); ( b ) gene expression of potential drug targets (focusing on B7 ligands and receptors), whereby blue indicates low expression values, yellow indicated intermediately expressed genes, and red represents highly expressed genes; ( c ) RNA expression of HHLA2. CLIA, Clinical Laboratory Improvement Amendments; GA, Genomic Atlas; GSC, Genomic Sequencing Classifier; HHLA2, HERV–H LTR-associating protein 2; NA, not applicable; NS, Nasal Swab; UIP, usual interstitial pneumonia; PD-L1, programmed death-ligand 1.

Article Snippet: Sequencing data were analyzed via the following advanced machine learning-based classifiers (all developed/licensed by Veracyte, Inc., South San Francisco, CA, USA) that are applied to the diagnosis of thyroid cancer, interstitial lung disease (ILD), and lung cancer, and may be applicable to other disease indications: the Afirma ® Genomic Sequencing Classifier (GSC), which uses RNA exome sequencing information derived from a fine-needle aspiration (FNA) biopsy to classify cytologically indeterminate thyroid nodules as Afirma GSC Benign or Suspicious [ , , , , ]; the Afirma Xpression Atlas (XA), which provides genomic alteration information from FNA samples with an Afirma GSC Suspicious result, or cytologically suspicious for malignancy or malignancy nodule [ ]; the Envisia ® Genomic Classifier (GC), a diagnostic test that uses a 190-gene expression signature to differentiate between usual interstitial pneumonia (UIP) and non-UIP subtypes in lung transbronchial biopsy (TBB) samples from patients with ILD [ ]; the Percepta GSC, which uses RNA exome sequencing information from bronchial brushing samples for classification of lung cancer risk among bronchoscopy nondiagnostic samples [ ]; the Percepta Nasal Swab (NS) classifier that uses RNA exome sequencing information from nasal (inferior turbinate) samples to classify the risk of lung cancer in patients with previously detected lung nodules [ ]; and the Percepta Genomic Atlas (GA) test, which was developed to detect lung cancer-associated fusions and MET exon-skipping events in diagnostic TBB specimens and transbronchial needle aspirates (TBNAs) [ ].

Techniques: Gene Expression, RNA Expression, Expressing, Genomic Sequencing