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Showing papers in "The Journal of Molecular Diagnostics in 2016"


Journal ArticleDOI
TL;DR: A targeted next-generation sequencing assay that uses 266 single-nucleotide polymorphisms to accurately quantify dd-cfDNA in transplant recipients without separate genotyping is developed, providing the practical turnaround time preferred for transplanted organ surveillance.

172 citations


Journal ArticleDOI
TL;DR: This study provides evidence in favor of preemptive PGx testing by identifying the risk of a variant being present in the population the authors studied and identifying the fraction of subjects carrying actionable PGx variant(s) in individual genes.

145 citations


Journal ArticleDOI
TL;DR: The results from 20,000 hereditary-cancer NGS panels spanning 47 genes illustrate the importance of setting quality thresholds for panel testing only after thousands of samples have been processed and the necessity of Sanger confirmation of NGS variants to maintain the highest possible sensitivity.

139 citations


Journal ArticleDOI
TL;DR: The design, validation, and implementation of a comprehensive 95-gene next-generation sequencing panel targeted for hematologic malignancies that is amplicon based and covers hotspot regions of oncogenes and most of the coding regions of tumor suppressor genes are reported.

131 citations


Journal ArticleDOI
TL;DR: In this paper, the Coriell cell lines were selected based on ethnic diversity and partial genotype characterization from earlier testing, and DNA samples were coded and distributed to volunteer testing laboratories for targeted genotyping using a number of commercially available and laboratory developed tests.

104 citations


Journal ArticleDOI
TL;DR: The validation of a 23-gene panel covering 41 hotspot regions using single-molecule tagging of DNA molecules by single- molecule molecular inversion probes (smMIPs), allowing assessment of library complexity, outperforms Sanger and Ampliseq-Personal Genome Machine-based sequencing in clinical diagnostic setting.

94 citations


Journal ArticleDOI
TL;DR: A new SEPT9 assay and combined testing as an aid in cancer detection, providing a new approach for opportunistic CRC screening is validated, suggesting that the combined tests may be an effective option for future opportunistic screening.

84 citations


Journal ArticleDOI
TL;DR: The Association for Molecular Pathology invested in a cost and value analysis of specific genomic sequencing procedures newly coded by the American Medical Association Current Procedural Terminology Editorial Panel, with demonstrated value by either reducing health care costs or identifying appropriate care pathways.

83 citations


Journal ArticleDOI
TL;DR: The impact of the context of genetic and epigenetic alterations and tumor type on the classification is investigated and technical aspects, such as robustness of cutoff definition and preprocessing of the data are reported on.

79 citations


Journal ArticleDOI
TL;DR: The results suggest that ancillary NGS testing offers advantages over FISH, although studies with larger cohorts are needed to verify these findings.

74 citations


Journal ArticleDOI
TL;DR: A next-generation sequencing approach that uses a multiplex PCR-based amplicon panel to interrogate fusion transcripts that involve 19 driver genes and 94 partners implicated in solid tumors and shows good concordance between the solid tumor fusion gene panel and other methods.

Journal ArticleDOI
TL;DR: The spectrum of CFTR variants and their frequencies in CF patients in the United States with African, Native American, Asian, East Indian, or Middle Eastern backgrounds is established and equity in mutation detection between white and nonwhite or mixed-ethnicity CF patients is facilitated.

Journal ArticleDOI
TL;DR: The results show that the UltraSEEK chemistry is a particularly powerful approach for the detection of somatic variants, with the potential to be an invaluable resource to investigators in saving time and material without compromising analytical sensitivity and accuracy.

Journal ArticleDOI
TL;DR: Deep NGS analysis not only provides insights into the spectrum of mosaic mutations but also underlines the importance of the detection of mosaicism as an integral part of clinical molecular diagnosis and genetic counseling.

Journal ArticleDOI
TL;DR: It is shown that targeted SNP analysis by NGS allows reliable detection of 1p and/or 19q deletion in a background of 70% of normal cells according to calculated outcomes, is more sensitive than microsatellite-based LOH analysis, and requires much less DNA.

Journal ArticleDOI
TL;DR: The molecular testing approaches and laboratory guidelines for carrier screening, prenatal testing, newborn screening, and clinical diagnostic testing are reviewed, as well as recent developments in CF treatment, and reasons for the lack of a molecular diagnosis in some patients are reviewed.

Journal ArticleDOI
TL;DR: TruSight HLA assay enables high-throughput HLA typing with an accuracy, precision, ambiguity rate, and cost savings that should facilitate adoption of NGS technology in clinical HLA laboratories.


Journal ArticleDOI
TL;DR: The high concordance of tumor-associated gene expression changes between BX and RP samples provides evidence for the adequate performance of the assay platform with samples from prostate needle biopsy specimens with limited tumor volume.

Journal ArticleDOI
TL;DR: A standardized NGS pipeline designed to replace Sanger sequencing and multiplex ligation-dependent probe amplification analysis and to facilitate detection of sequence and copy number alterations in a single test focusing on a BRCA1/BRCA2 gene analysis panel is clinically validated.

Journal ArticleDOI
TL;DR: In this paper, the authors address the challenges in defining the clinical utility of molecular diagnostics for inherited diseases or cancer and provide assessment recommendations, and recommend promotion of patient-centered definitions of clinical utility that appropriately recognize the valuable contribution of molecular diagnostic testing.

Journal ArticleDOI
TL;DR: Current concepts in molecular testing for glial tumors are summarized, including recent findings by large-scale discovery efforts and technologic advances that are affecting routine diagnostic work.

Journal ArticleDOI
TL;DR: The emergence of advanced matrix-assisted laser desorption ionization time-of-flight MS applications, including the identification of filamentous fungi and mycobacteria and the current and future state of antimicrobial resistance testing are discussed.

Journal ArticleDOI
TL;DR: The NCI-MPACT assay is well suited for its intended investigational use and can serve as a template for developing next-generation sequencing assays for other cancer clinical trial applications.

Journal ArticleDOI
TL;DR: In this paper, the authors used the NanoVelcro/laser capture microdissection CTC platform, combined with whole genome amplification and Sanger sequencing, to identify the ubiquitous KRAS mutation in single CTCs from pancreatic cancer (PC) patients.

Journal ArticleDOI
TL;DR: The data suggest that hotspot mutations screening such as SNaPshot could be an effective preliminary screening alternative adopted in a standard clinical laboratory without NGS setup, and the detection sensitivity of NGS is comparable with Sanger sequencing.

Journal ArticleDOI
TL;DR: A protocol for measuring TL on the LightCycler platform that provides a robust high-throughput method applicable to clinical diagnostics or large-scale studies of archived specimens and sources of variability and quality control relevant to the MMqPCR TL assay on any instrument are described.

Journal ArticleDOI
TL;DR: It is found that all tumor types and subtypes are hypermethylated at this locus compared with normal tissue, suggesting that hypermethylation of the ZNF154 CpG island is a relevant biomarker for identifying solid tumor DNA and may have utility as a generalizable biomarkers for circulating tumor DNA.

Journal ArticleDOI
TL;DR: This study provides a protocol for robust, sensitive detection of circulating tumor DNA for future clinical applications by improving on the robustness of dPCR for mutation detection and using this protocol on clinical samples to detect known, tumor-specific mutations in patient sera.

Journal ArticleDOI
TL;DR: A custom next-generation sequencing panel that enables the affordable and simultaneous screening of 24 PCD genes was developed and the molecular diagnosis of PCD was achieved in 43% of the patients, and 5 homozygous and 27 compound heterozygous mutations, 21 of which were never reported before, were identified in 11PCD genes.