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  1. Article ; Online: Multicenter Evaluation of the DiaSorin Molecular Simplexa Congenital CMV Direct PCR Test on Neonatal Saliva and Urine Specimens.

    Dunn, James J / Selvarangan, Rangaraj / Maggert, Kevin / Young, Stephen / Leber, Amy L

    Journal of clinical microbiology

    2023  Volume 61, Issue 6, Page(s) e0028323

    Abstract: Cytomegalovirus (CMV) is the most common virus associated with congenital infection worldwide and is a major cause of sensorineural hearing loss (SNHL) and developmental delay. Up to 90% of infants with congenital CMV (cCMV) infection are asymptomatic at ...

    Abstract Cytomegalovirus (CMV) is the most common virus associated with congenital infection worldwide and is a major cause of sensorineural hearing loss (SNHL) and developmental delay. Up to 90% of infants with congenital CMV (cCMV) infection are asymptomatic at birth, making the diagnosis challenging. Postnatal diagnosis involves testing newborn saliva and/or urine collected before 21 days of life to confirm cCMV infection. This multicenter study evaluated the performance of the Simplexa Congenital CMV Direct real-time PCR assay for the qualitative detection of CMV in newborn saliva (
    MeSH term(s) Infant ; Infant, Newborn ; Humans ; Saliva ; Neonatal Screening/methods ; Cytomegalovirus Infections/diagnosis ; Cytomegalovirus/genetics ; Real-Time Polymerase Chain Reaction/methods
    Language English
    Publishing date 2023-05-15
    Publishing country United States
    Document type Multicenter Study ; Journal Article
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/jcm.00283-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Development and evaluation of ActSeq: A targeted next-generation sequencing panel for clinical oncology use.

    Shi, Zonggao / Lopez, Jacqueline / Kalliney, William / Sutton, Bobbie / Simpson, Joyce / Maggert, Kevin / Liu, Sheng / Wan, Jun / Stack, M Sharon

    PloS one

    2022  Volume 17, Issue 4, Page(s) e0266914

    Abstract: Purpose: The demand for high-throughput genetic profiling of somatic mutations in cancer tissues is growing. We sought to establish a targeted next generation sequencing (NGS) panel test for clinical oncology practice.: Methods: Customized probes ... ...

    Abstract Purpose: The demand for high-throughput genetic profiling of somatic mutations in cancer tissues is growing. We sought to establish a targeted next generation sequencing (NGS) panel test for clinical oncology practice.
    Methods: Customized probes were designed to capture exonic regions of 141 genes selected for the panel, which was aimed for the detection of clinically actionable genetic variations in cancer, including KRAS, NRAS, BRAF, ALK, ROS1, KIT and EGFR. The size of entire targeted regions is 0.8 Mb. Library preparation used NEBNext Ultra II FS kit coupled with target enrichment. Paired-end sequencing was run on Illumina NextSeq 500 at a read length of 150 nt. A bioinformatics workflow focusing on single nucleotide variant and short insertions and deletions (SNV/indel) discovery was established using open source, in-house and commercial software tools. Standard reference DNA samples were used in testing the sensitivity and precision and limit of detection in variant calling.
    Results: The general performance of the panel was observed in pilot runs. Average total reads per sample ranged from 30 million to 48 million, 73% ~82% unique reads. All runs had more than 99% average mapping rate. Mean target coverage ranged from 727x to 879x. Depth of coverage at 50x or more reached 87% of targeted region and 60% of targeted region received 500x or more coverage depth. Using OncoSpan HD827 DNA, which bears 144 variants (SNV/indel) from 80 genes that are within the targeted region on the panel, our somatic variant calling pipeline reached 97% sensitivity and 100% precision respectively, with near 48 million reads. High concordance with orthogonal approaches in variant detection was further verified with 7 cancer cell lines and 45 clinical specimens.
    Conclusion: We developed a NGS panel with a focus on clinically actionable gene mutations and validated the performance in library construction, sequencing and variant calling. High concordance with reference materials and orthogonal mutation detection was observed.
    MeSH term(s) Computational Biology ; High-Throughput Nucleotide Sequencing ; Humans ; Medical Oncology ; Mutation ; Neoplasms/genetics ; Protein-Tyrosine Kinases/genetics ; Proto-Oncogene Proteins/genetics
    Chemical Substances Proto-Oncogene Proteins ; Protein-Tyrosine Kinases (EC 2.7.10.1)
    Language English
    Publishing date 2022-04-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0266914
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Assessment of common somatic mutations of EGFR, KRAS, BRAF, NRAS in pulmonary non-small cell carcinoma using iPLEX® HS, a new highly sensitive assay for the MassARRAY® System.

    Sutton, Bobbie C / Birse, Ryan T / Maggert, Kevin / Ray, Tammy / Hobbs, Jessica / Ezenekwe, Amobi / Kazmierczak, Jason / Mosko, Michael / Kish, Joan / Bullock, Andrew / Shi, Zonggao / Stack, M Sharon / Irwin, Darryl

    PloS one

    2017  Volume 12, Issue 9, Page(s) e0183715

    Abstract: Increased early detection and personalized therapy for lung cancer have coincided with greater use of minimally invasive sampling techniques such as endobronchial ultrasound-guided biopsy (EBUS), endoscopic ultrasound-guided biopsy (EUS), and ... ...

    Abstract Increased early detection and personalized therapy for lung cancer have coincided with greater use of minimally invasive sampling techniques such as endobronchial ultrasound-guided biopsy (EBUS), endoscopic ultrasound-guided biopsy (EUS), and navigational biopsy, as well as thin needle core biopsies. As many lung cancer patients have late stage disease and other comorbidities that make open surgical procedures hazardous, the least invasive biopsy technique with the highest potential specimen yield is now the preferred first diagnostic study. However, use of these less invasive procedures generates significant analytical challenges for the laboratory, such as a requirement for robust detection of low level somatic mutations, particularly when the starting sample is very small or demonstrates few intact tumor cells. In this study, we assessed 179 clinical cases of non-small cell lung carcinoma (NSCLC) that had been previously tested for EGFR, KRAS, NRAS, and BRAF mutations using a novel multiplexed analytic approach that reduces wild-type signal and allows for detection of low mutation load approaching 1%, iPLEX® HS panel for the MassARRAY® System (Agena Bioscience, San Diego, CA). This highly sensitive system identified approximately 10% more KRAS, NRAS, EGFR and BRAF mutations than were detected by the original test platform, which had a sensitivity range of 5-10% variant allele frequency (VAF).
    MeSH term(s) Carcinoma, Non-Small-Cell Lung/genetics ; Carcinoma, Non-Small-Cell Lung/metabolism ; Carcinoma, Non-Small-Cell Lung/pathology ; DNA/chemistry ; DNA/metabolism ; ErbB Receptors/genetics ; ErbB Receptors/metabolism ; GTP Phosphohydrolases/genetics ; GTP Phosphohydrolases/metabolism ; Genotype ; Humans ; Lung Neoplasms/genetics ; Lung Neoplasms/metabolism ; Lung Neoplasms/pathology ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Oligonucleotide Array Sequence Analysis ; Phosphatidylinositol 3-Kinases/genetics ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Proto-Oncogene Proteins B-raf/genetics ; Proto-Oncogene Proteins B-raf/metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; ras Proteins/genetics ; ras Proteins/metabolism
    Chemical Substances Membrane Proteins ; DNA (9007-49-2) ; Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; ErbB Receptors (EC 2.7.10.1) ; Proto-Oncogene Proteins B-raf (EC 2.7.11.1) ; GTP Phosphohydrolases (EC 3.6.1.-) ; NRAS protein, human (EC 3.6.1.-) ; ras Proteins (EC 3.6.5.2)
    Language English
    Publishing date 2017-09-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0183715
    Database MEDical Literature Analysis and Retrieval System OnLINE

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