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Analytic validation and clinical utilization of the comprehensive genomic profiling test, GEM ExTra^®.

ABSTRACT: We developed and analytically validated a comprehensive genomic profiling (CGP) assay, GEM ExTra, for patients with advanced solid tumors that uses Next Generation Sequencing (NGS) to characterize whole exomes employing a paired tumor-normal subtraction methodology. The assay detects single nucleotide variants (SNV), indels, focal copy number alterations (CNA), TERT promoter region, as well as tumor mutation burden (TMB) and microsatellite instability (MSI) status. Additionally, the assay incorporates whole transcriptome sequencing of the tumor sample that allows for the detection of gene fusions and select special transcripts, including AR-V7, EGFR vIII, EGFRvIV, and MET exon 14 skipping events. The assay has a mean target coverage of 180X for the normal (germline) and 400X for tumor DNA including enhanced probe design to facilitate the sequencing of difficult regions. Proprietary bioinformatics, paired with comprehensive clinical curation results in reporting that defines clinically actionable, FDA-approved, and clinical trial drug options for the management of the patient's cancer. GEM ExTra demonstrated analytic specificity (PPV) of > 99.9% and analytic sensitivity of 98.8%. Application of GEM ExTra to 1,435 patient samples revealed clinically actionable alterations in 83.9% of reports, including 31 (2.5%) where therapeutic recommendations were based on RNA fusion findings only.

SUBMITTER: White T

PROVIDER: S-EPMC8057276 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:FoundationOne®CDx (F1CDx) is a United States (US) Food and Drug Administration (FDA)-approved companion diagnostic test to identify patients who may benefit from treatment in accordance with the approved therapeutic product labeling for 28 drug therapies. F1CDx utilizes next-generation sequencing (NGS)-based comprehensive genomic profiling (CGP) technology to examine 324 cancer genes in solid tumors. F1CDx reports known and likely pathogenic short variants (SVs), copy number alterations (CNAs), and select rearrangements, as well as complex biomarkers including tumor mutational burden (TMB) and microsatellite instability (MSI), in addition to genomic loss of heterozygosity (gLOH) in ovarian cancer. CGP services can reduce the complexity of biomarker testing, enabling precision medicine to improve treatment decision-making and outcomes for cancer patients, but only if test results are reliable, accurate, and validated clinically and analytically to the highest standard available. The analyses presented herein demonstrate the extensive analytical and clinical validation supporting the F1CDx initial and subsequent FDA approvals to ensure high sensitivity, specificity, and reliability of the data reported. The analytical validation included several in-depth evaluations of F1CDx assay performance including limit of detection (LoD), limit of blank (LoB), precision, and orthogonal concordance for SVs (including base substitutions [SUBs] and insertions/deletions [INDELs]), CNAs (including amplifications and homozygous deletions), genomic rearrangements, and select complex biomarkers. The assay validation of >30,000 test results comprises a considerable and increasing body of evidence that supports the clinical utility of F1CDx to match patients with solid tumors to targeted therapies or immunotherapies based on their tumor's genomic alterations and biomarkers. F1CDx meets the clinical needs of providers and patients to receive guideline-based biomarker testing, helping them keep pace with a rapidly evolving field of medicine.

Project description:ObjectiveTo introduce a novel technology currently under final development before regulatory approvals for the furtherment of cataract surgery, using the FemtoMatrix® laser system, and to demonstrate its safety and efficacy as compared to standard ultrasound phacoemulsification.MethodsThirty-three patients with bilateral cataracts were operated on with one eye undergoing PhotoEmulsification® treatment on the FemtoMatrix® device and the contralateral eye receiving the control procedure, i.e., standard ultrasound phacoemulsification treatment. The number of "zero-phaco" procedures (denoting that I/A alone was sufficient to aspirate the lens fragments and that no ultrasound energy was needed) was recorded and Effective Phaco Time (EPT) values were compared. The patient follow-up was 3 months.ResultsThirty-three eyes from a population with a mean cataract grade of 2.6 were treated on the FemtoMatrix®, of which 29 were "zero-phaco" (88%). All patients were operated on by a single surgeon who was a relative novice to the technology (63 patients treated prior to this study). Conversely, of the 33 fellow eyes who underwent standard ultrasound phacoemulsification, none were zero-phaco (0%) - all required varying degrees of ultrasound energy to make lens aspiration possible. The mean EPT was significantly lower in the PhotoEmulsification® laser group (0.2 ± 0.8 s) than in the phaco group (1.3 ± 1.2 s) (p < 0.0001). The safety profiles of the two procedures were comparable, with no device-related adverse events noted.ConclusionFemtoMatrix® is a promising femtosecond laser platform that, when compared to phacoemulsification, significantly decreases or eliminates EPT altogether. The system is used to perform PhotoEmulsification®, making zero-phaco cataract procedures feasible including in high-grade cataracts (>3). It enables personalized treatment by automatically measuring and adapting the laser energy required to obtain the most efficient cutting of the crystalline lens. This new technology appears to be safe and effective in cataract surgery.

Project description:IntroductionThe CIMZIA® AutoClicks® pre-filled pen (CZP PFP) was developed to overcome barriers to self-injection, by improving self-injection confidence, reducing fear associated with needle use, and supporting patients with impaired dexterity. The purpose of this research was to gather feedback on injection experience and the usefulness of training materials.MethodsEligible patients with rheumatoid arthritis (RA), axial spondyloarthritis (axSpA) or psoriatic arthritis (PsA) were at least 18 years of age and initiated onto the CZP PFP. Routine self-injection training and support were provided by trained specialist nurses. Patient experience (pain and skin reactions, confidence, satisfaction, and ease of use) was evaluated at visits 1-3 using an amended version of the self-injection assessment questionnaire (SIAQ) v2.0. Nurse and patient feedback on the training materials, and nurse opinions on patient self-injection after self-injection at visit 1, were also collected.ResultsOf 355 patients invited to participate, 196 provided informed consent and 79 participated in all three visits. Patients generally found the CZP PFP easy to use, and self-confidence and satisfaction were high. From visit 1 to visit 3, there was a numerical trend towards improvement in all three aspects of patient experience, most notably in both confidence and satisfaction. After self-injection at visit 1, confidence around safe patient self-injection was higher among nurses than among patients. Meanwhile, "pain and skin reactions" remained low at all visits. Patients thought the training materials contained sufficient information and were easy to understand and useful.ConclusionAfter training, patients generally found the device easy to use and showed high confidence and satisfaction with self-injection. Some patients may have been competent (based on nurse opinion), but initially lacked self-confidence. Increasing self-injection experience, together with patient training and continued support, may have facilitated high patient confidence and satisfaction, thereby potentially overcoming some of the barriers to self-injection.

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Analytic validation and clinical utilization of the comprehensive genomic profiling test, GEM ExTra^®.

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OmicsDI is part of the ELIXIR infrastructure

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Dataset Information

Analytic validation and clinical utilization of the comprehensive genomic profiling test, GEM ExTra®.

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OmicsDI is part of the ELIXIR infrastructure

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Analytic validation and clinical utilization of the comprehensive genomic profiling test, GEM ExTra^®.