ABSTRACT
Molecular features of gynecologic cancers have been investigated in comprehensive studies, but correlation of these molecular signatures with clinical significance for precision medicine is yet to be established. Towards this end, we evaluated 95 gynecologic cancer cases submitted for testing using The JAX ActionSeq™ NGS panel. Molecular profiles were studied and compared to TCGA datasets to identify similarities and distinguishing features among subtypes. We identified 146 unique clinically significant variants (Tier I and II) across 45 of the 212 genes (21%), in 87% (83/95) of cases. TP53, PTEN, ARID1A, PIK3CA and ATM were the most commonly mutated genes; CCNE1 and ERBB2 amplifications were the most frequently detected copy-number alterations. PARP inhibitors were among the most commonly reported drug class with clinical trials, consistent with the frequency of DNA damage-response pathway mutations in our cohort. Overall, our study provides additional insight into the molecular profiles of gynecologic cancers, highlighting regulatory pathways involved, raising the potential implications for targeted therapeutic options currently available.
Subject(s)
Genital Neoplasms, Female/genetics , Mutation , Practice Guidelines as Topic , Transcriptome , Adult , Aged , Aged, 80 and over , Antineoplastic Agents/therapeutic use , Cell Cycle/genetics , Cohort Studies , DNA Copy Number Variations , DNA Repair/genetics , DNA, Neoplasm/genetics , Datasets as Topic , Female , Gene Amplification , Gene Frequency , Genes, Neoplasm , Genital Neoplasms, Female/drug therapy , Genital Neoplasms, Female/pathology , Guideline Adherence , Humans , Middle Aged , Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use , Precision Medicine/methods , Retrospective StudiesABSTRACT
The World Health Organization (WHO) has defined more than 130 distinct central nervous system (CNS) tumor entities, of which glioblastoma is the most fatal primary brain tumor. However, the correlation of the molecular signatures of glioblastoma with clinical significance for precision medicine is not well-known. How, and to what extent these variants may affect clinical decision making remains uncertain. Here, we evaluate 48 glioblastomas submitted for testing using the JAX ActionSeq™ Next-generation sequencing (NGS) panel. We identified 131 clinically significant variants (Tier I and II) across 30 of the 212 genes (14%). TP53, EGFR, PTEN, IDH1 were the most commonly mutated genes; EGFR, CDK4 amplifications, and CDKN2A deletion were the most frequently detected copy-number alterations. CDK4/6 and PI3K inhibitors were among the most commonly reported drug class with FDA approved therapies and investigational therapies, which is consistent with the frequencies of these genes in our cohort. Overall, our study established the molecular profiles of glioblastoma based on the 2017 joint consensus guidelines by AMP/ASCO/CAP and provides the potential implications for targeted therapeutic options currently available.
Subject(s)
Central Nervous System Neoplasms/genetics , Glioblastoma/genetics , Precision Medicine/methods , Cohort Studies , Female , High-Throughput Nucleotide Sequencing , Humans , Mutation , Retrospective StudiesABSTRACT
OBJECTIVE: The study aimed to retrospectively evaluate the positive yield rate of a custom 212-gene next-generation sequencing (NGS) panel, the JAX ActionSeq™ assay, used in molecular profiling of solid tumors for precision medicine. METHODS: We evaluated 261 cases tested over a 24-month period including cancers across 24 primary tissue types and report on the mutation yield in these cases. RESULTS: Thirty-three of the 261 cases (13%) had no detectable clinically significant variants. In the remaining 228 cases (87%), we identified 550 clinically significant variants in 88 of the 212 genes, with four of fewer clinically significant variants being detected in 62 of 88 genes (70%). TP53 had the highest number of variants (125), followed by APC (47), KRAS (47), ARID1A (20), PIK3CA (20) and EGFR (18). There were 38 tier I and 512 tier II variants, with two genes having only a tier I variant, seven genes having both a tier I and tier II variant, and 79 genes having at least one tier II variant. Overall, the ActionSeq™ assay detected clinically significant variants in 42% of the genes included in the panel (88/212), 68% of which (60/88) were detected in more than one tumor type. CONCLUSIONS: This study demonstrates that of the genes with documented involvement in cancer, only a limited number are currently clinically significant from a therapeutic, diagnostic and/or prognostic perspective.
Subject(s)
Biomarkers, Tumor , High-Throughput Nucleotide Sequencing , Mutation , Neoplasms/diagnosis , Neoplasms/genetics , Precision Medicine , Gene Expression Profiling/methods , High-Throughput Nucleotide Sequencing/methods , Humans , Precision Medicine/methods , Prognosis , TranscriptomeABSTRACT
In August 2016, a local public health agency (LPHA) notified the Colorado Department of Public Health and Environment (CDPHE) of two culture-confirmed cases of Campylobacter infection among persons who consumed raw (unpasteurized) milk from the same herdshare dairy. In Colorado, the sale of raw milk is illegal; however, herdshare programs, in which a member can purchase a share of a herd of cows or goats, are legal and are not regulated by state or local authorities. In coordination with LPHAs, CDPHE conducted an outbreak investigation that identified 12 confirmed and five probable cases of Campylobacter jejuni infection. Pulsed-field gel electrophoresis (PFGE) patterns for the 10 cases with available isolates were identical using the enzyme Sma. In addition, two milk samples (one from the dairy and one obtained from an ill shareholder) also tested positive for the outbreak strain. Five C. jejuni isolates sent to CDC for antimicrobial susceptibility testing were resistant to ciprofloxacin, tetracycline, and nalidixic acid (1). Although shareholders were notified of the outbreak and cautioned against drinking the milk on multiple occasions, milk distribution was not discontinued. Although its distribution is legal through herdshare programs, drinking raw milk is inherently risky (2). The role of public health in implementing control measures associated with a product that is known to be unsafe remains undefined.
Subject(s)
Campylobacter Infections/epidemiology , Campylobacter jejuni/drug effects , Disease Outbreaks , Fluoroquinolones/pharmacology , Food Microbiology , Foodborne Diseases/epidemiology , Milk/microbiology , Adolescent , Adult , Aged , Animals , Campylobacter Infections/drug therapy , Child , Colorado/epidemiology , Drug Resistance, Bacterial , Female , Foodborne Diseases/drug therapy , Humans , Male , Middle Aged , Raw Foods , Young AdultABSTRACT
Since 2011, the New York City (NYC) Department of Health and Mental Hygiene (DOHMH) has typically been notified of three or fewer cases of hepatitis A virus (HAV) infection each year among men who have sex with men (MSM) who reported no travel to countries where HAV is endemic. This year, DOHMH noted an increase in HAV infections among MSM with onsets in January-March 2017, and notified other public health jurisdictions via Epi-X, CDC's communication exchange network. As a result, 51 patients with HAV infection involving MSM were linked to the increase in NYC.
