Understanding molecular mechanisms of response and resistance to anticancer therapies requires prospective patient follow-up and clinical and functional validation of both common and low-frequency ...mutations. We describe a whole-exome sequencing (WES) precision medicine trial focused on patients with advanced cancer.
To understand how WES data affect therapeutic decision making in patients with advanced cancer and to identify novel biomarkers of response.
Patients with metastatic and treatment-resistant cancer were prospectively enrolled at a single academic center for paired metastatic tumor and normal tissue WES during a 19-month period (February 2013 through September 2014). A comprehensive computational pipeline was used to detect point mutations, indels, and copy number alterations. Mutations were categorized as category 1, 2, or 3 on the basis of actionability; clinical reports were generated and discussed in precision tumor board. Patients were observed for 7 to 25 months for correlation of molecular information with clinical response.
Feasibility, use of WES for decision making, and identification of novel biomarkers.
A total of 154 tumor-normal pairs from 97 patients with a range of metastatic cancers were sequenced, with a mean coverage of 95X and 16 somatic alterations detected per patient. In total, 16 mutations were category 1 (targeted therapy available), 98 were category 2 (biologically relevant), and 1474 were category 3 (unknown significance). Overall, WES provided informative results in 91 cases (94%), including alterations for which there is an approved drug, there are therapies in clinical or preclinical development, or they are considered drivers and potentially actionable (category 1-2); however, treatment was guided in only 5 patients (5%) on the basis of these recommendations because of access to clinical trials and/or off-label use of drugs. Among unexpected findings, a patient with prostate cancer with exceptional response to treatment was identified who harbored a somatic hemizygous deletion of the DNA repair gene FANCA and putative partial loss of function of the second allele through germline missense variant. Follow-up experiments established that loss of FANCA function was associated with platinum hypersensitivity both in vitro and in patient-derived xenografts, thus providing biologic rationale and functional evidence for his extreme clinical response.
The majority of advanced, treatment-resistant tumors across tumor types harbor biologically informative alterations. The establishment of a clinical trial for WES of metastatic tumors with prospective follow-up of patients can help identify candidate predictive biomarkers of response.
Background
Characterization of circulating tumor DNA (ctDNA) has been integrated into clinical practice. Although labs have standardized validation procedures to develop single locus tests, the ...efficacy of on‐site plasma‐based next‐generation sequencing (NGS) assays still needs to be proved.
Materials and Methods
In this retrospective study, we profiled DNA from matched tissue and plasma samples from 75 patients with cancer. We applied an NGS test that detects clinically relevant alterations in 33 genes and microsatellite instability (MSI) to analyze plasma cell‐free DNA (cfDNA).
Results
The concordance between alterations detected in both tissue and plasma samples was higher in patients with metastatic disease. The NGS test detected 77% of sequence alterations, amplifications, and fusions that were found in metastatic samples compared with 45% of those alterations found in the primary tumor samples (p = .00005). There was 87% agreement on MSI status between the NGS test and tumor tissue results. In three patients, MSI‐high ctDNA correlated with response to immunotherapy. In addition, the NGS test revealed an FGFR2 amplification that was not detected in tumor tissue from a patient with metastatic gastric cancer, emphasizing the importance of profiling plasma samples in patients with advanced cancer.
Conclusion
Our validation experience of a plasma‐based NGS assay advances current knowledge about translating cfDNA testing into clinical practice and supports the application of plasma assays in the management of oncology patients with metastatic disease. With an in‐house method that minimizes the need for invasive procedures, on‐site cfDNA testing supplements tissue biopsy to guide precision therapy and is entitled to become a routine practice.
Implications for Practice
This study proposes a solution for decentralized liquid biopsy testing based on validation of a next‐generation sequencing (NGS) test that detects four classes of genomic alterations in blood: sequence mutations (single nucleotide substitutions or insertions and deletions), fusions, amplifications, and microsatellite instability (MSI). Although there are reference labs that perform single‐site comprehensive liquid biopsy testing, the targeted assay this study validated can be established locally in any lab with capacity to offer clinical molecular pathology assays. To the authors' knowledge, this is the first report that validates evaluating an on‐site plasma‐based NGS test that detects the MSI status along with common sequence alterations encountered in solid tumors.
This report describes the concordance between circulating tumor DNA and matched tumor tissue molecular profiles, discusses interpretation of observed discordant data, and illustrates applications through clinical cases. It is the first known report to evaluate the performance of an on‐site plasma‐based next‐generation sequencing test to detect microsatellite instability status along with common sequence alterations in the context of its clinical utility and therapeutic applications in precision oncology.
Background
Tumor sample quality and quantity determine the success of somatic mutation analysis. Thus, a rapid on‐site evaluation (ROSE) tumor cytology adequacy assessment was incorporated into the ...workflow of precision oncology at Weill Cornell Medicine in New York City. Optimal samples were obtained from 68 patients with metastatic cancer.
Methods
Cytopathologists performed ROSE on fine‐needle aspirate samples via telepathology, and subsequently core‐needle biopsies were obtained. In a retrospective manner, the concordance between adequacy assessment and the success rate of the procedure was evaluated to obtain sufficient tumor tissue for next‐generation sequencing (NGS).
Results
Out of the 68 procedures, 43 were documented as adequate and 25 were documented as inadequate. The diagnostic yield of adequate procedures was 100%. Adequacy evaluation predicted the success rate of molecular profiling in 40 of 43 procedures (93%; 95% CI, 80.9‐98.5 procedures). The success rate of molecular testing was significantly higher in the adequate group: 93% compared with 32% in the inadequate group (P < .0005). Seven procedures that failed to provide quality material for mutational analysis and pathological diagnosis were evaluated as inadequate. Cell block provided sufficient DNA for NGS in 6 cases. In 2 cases, a core biopsy could not be performed; hence, the fine‐needle aspirate material confirmed the diagnosis and was used for NGS testing.
Conclusion
These results support the incorporation of ROSE into the workflow of precision oncology to obtain high‐quality tissue samples from metastatic lesions. In addition, NGS testing of concurrent cytology specimens with adequate cellularity can be a surrogate for NGS testing of biopsy specimens.
Rapid on‐site evaluation (ROSE) of fine‐needle aspirate samples via telepathology predicted the success of molecular profiling of concurrent core‐needle biopsies. Thus, ROSE is an effective protocol that allows for a rapid assessment of the quality of tumor tissue submitted for diagnosis and precision oncology studies.
Sarcomatoid urothelial carcinoma (SUC) is a rare subtype of urothelial carcinoma (UC) that typically presents at an advanced stage compared to more common variants of UC. Locally advanced and ...metastatic UC have a poor long-term survival following progression on first-line platinum-based chemotherapy. Antibodies directed against the programmed cell death 1 protein (PD-1) or its ligand (PD-L1) are now approved to be used in these scenarios. The need for reliable biomarkers for treatment stratification is still under research. Here, we present a novel case report of the first Imaging Mass Cytometry (IMC) analysis done in SUC to investigate the immune cell repertoire and PD-L1 expression in a patient who presented with metastatic SUC and experienced a prolonged response to the anti-PD1 immune checkpoint inhibitor pembrolizumab after progression on first-line chemotherapy. This case report provides an important platform for translating these findings to a larger cohort of UC and UC variants.
Additive manufacturing has the potential to revolutionize the production of metallic components as it yields near net shape parts with complex geometries and minimizes waste. At the present day, ...additively manufactured components face qualification and certification challenges due to the difficulty in controlling defects. This has driven a significant research effort aimed at better understanding and improving processing controls – yielding a plethora of in-situ measurements aimed at correlating defects with material quality metrics of interest. In this work, we develop machine-learning methods to learn correlations between thermal history and subsurface porosity for a variety of print conditions in laser powder bed fusion. Un-normalized surface temperatures (in the form of black-body radiances) are obtained using high-speed infrared imaging and porosity formation is observed in the sample cross-section through synchrotron x-ray imaging. To demonstrate the predictive power of these features, we present four statistical machine-learning models that correlate temperature histories to subsurface porosity formation in laser fused Ti-6Al-4V powder.
Agmination and/or satellitosis in pigmented blue lesions is a phenomenon rarely mentioned in the literature and not well known. This phenomenon can be expressed by several benign and malignant ...pigmented blue lesions, such as blue nevi, Spitz nevi, melanocytoma and melanoma. On this spectrum, dermoscopy, reflectance confocal microscopy (RCM) and dynamic Optical coherence tomography (D-OCT) represent non-invasive imaging technologies, which may help clinicians in the diagnosis of melanoma and non-melanoma skin cancers in daily clinical practice.
Currently, in the literature there is a lack of new data about agminated blue lesions and blues lesions with satellitosis, as well as the lack of a recent and updated review of the literature about this topic. Therefore, considering that clinicians must be confident with the diagnosis of these rare skin lesions, we decided to carry out this work.
In this paper, four new cases of agminated pigmented cutaneous lesions were described. Moreover, a review of the current literature on this topic was performed.
A clinical-pathological correlation is often needed to reach a correct diagnosis; currently, dermoscopy and non-invasive diagnostic techniques, such as reflectance confocal microscopy and optical coherence tomography, due to the depth of these skin lesions in the dermis, can only make a partial and limited contribution.
Vibrio natriegens
is a naturally occurring marine bacterium that is emerging as a microbiological model system. Here, we describe Aquatic Killer 99 (AQKL99), a novel phage that infects
Vibrio ...natriegens
14048. The genome of the phage is 58,464 bp long, has a GC content of 45.9%, and contains 51 protein-coding genes.
ABSTRACT
Vibrio natriegens
is a naturally occurring marine bacterium that is emerging as a microbiological model system. Here, we describe Aquatic Killer 99 (AQKL99), a novel phage that infects
Vibrio natriegens
14048. The genome of the phage is 58,464 bp long, has a GC content of 45.9%, and contains 51 protein-coding genes.
Spiders produce nature's toughest fiber using renewable components at ambient temperatures and with water as solvent, making it highly interesting to replicate for the materials industry. Despite ...this, much remains to be understood about the bioprocessing and composition of spider silk fibers. Here, we identify 18 proteins that make up the spiders' strongest silk type, the major ampullate fiber. Single-cell RNA sequencing and spatial transcriptomics revealed that the secretory epithelium of the gland harbors six cell types. These cell types are confined to three distinct glandular zones that produce specific combinations of silk proteins. Image analysis of histological sections showed that the secretions from the three zones do not mix, and proteomics analysis revealed that these secretions form layers in the final fiber. Using a multi-omics approach, we provide substantial advancements in the understanding of the structure and function of the major ampullate silk gland as well as of the architecture and composition of the fiber it produces.Spiders produce nature's toughest fiber using renewable components at ambient temperatures and with water as solvent, making it highly interesting to replicate for the materials industry. Despite this, much remains to be understood about the bioprocessing and composition of spider silk fibers. Here, we identify 18 proteins that make up the spiders' strongest silk type, the major ampullate fiber. Single-cell RNA sequencing and spatial transcriptomics revealed that the secretory epithelium of the gland harbors six cell types. These cell types are confined to three distinct glandular zones that produce specific combinations of silk proteins. Image analysis of histological sections showed that the secretions from the three zones do not mix, and proteomics analysis revealed that these secretions form layers in the final fiber. Using a multi-omics approach, we provide substantial advancements in the understanding of the structure and function of the major ampullate silk gland as well as of the architecture and composition of the fiber it produces.
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