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  • Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing

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    JAMA. 2017; 318(9):825-835. doi: 10.1001/jama.2017.11137

    This case series of patients with advanced cancer evaluates the proportion and potential clinical implications of inherited variants detected using DNA sequencing of tumor and normal tissue compared with genetic test results based on current guidelines.

  • From JAMA ’s Daily News Site

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    JAMA. 2013; 309(18):1884-1884. doi: 10.1001/jama.2013.4959
  • Next-Generation DNA Sequencing, Regulation, and the Limits of Paternalism: The Next Challenge

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    JAMA. 2011; 306(21):2376-2377. doi: 10.1001/jama.2011.1788
  • Conversion Analysis for Mutation Detection in MLH1 and MSH2 in Patients With Colorectal Cancer

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    JAMA. 2005; 293(7):799-809. doi: 10.1001/jama.293.7.799
  • JAMA January 26, 2005

    Figure 2: Identification of SCN5A Mutations and Localization of Cardiac Sodium Channel Defects

    A, Heteroduplex mutation scans of exons comprising the entire coding region of SCN5A were performed by denaturing high-performance liquid chromatography (DHPLC). Heterozygous variation in DNA sequence was detected in exons 6, 16, 17, 21, and 27 for the 5 family probands in Figure 1 and Figure 3. In contrast to normal exons generating single peaks on chromatographic profiles, exons harboring mutations had anomalous profiles characterized by 2 peaks. B, To determine if detected variations were benign or pathogenic, genomic DNA sequencing was performed. In 4 of the exons (exons 6, 16, 21, and 27), mutations were discovered in 1 copy of the gene, resulting in amino acid substitutions. In the remaining exon (exon 17), insertion of 2 bases disrupts the coding sequence (only the mutant gene is shown). C, Regions in the cardiac sodium channel protein altered by mutations were aligned with protein sequences of other human and nonhuman sodium channels. The 4 missense mutations alter highly conserved amino acids as indicated by vertical boxes wherein identical amino acids are designated by dots. The frameshift mutation creates a series of 18 anomalous amino acids, shown by the horizontal box in the fs851 panel, and an early stop codon, designated by an asterisk. D, Two-dimensional schematic of SCN5A, demonstrating the predicted transmembrane topology. SCN5A is a monomeric channel composed of 4 repeat domains (DI-DIV), each with 5 homologous hydrophobic transmembrane segments (S1-S3, S5, and S6) and 1 positively charged voltage-sensing segment (S4). Mutations map to all 4 domains, altering residues within membrane-spanning segments; 2 mutations occur within S4 voltage-sensing segments. The insertion or frameshift mutation severely truncates the protein by removing 13 of 24 transmembrane segments.
  • Doggy DNA Has Its Day

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    JAMA. 2003; 289(23):3080-3080. doi: 10.1001/jama.289.23.3080-a
  • Absence of HIV Transmission From an Infected Dentist to His Patients: An Epidemiologic and DNA Sequence Analysis

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    JAMA. 1993; 269(14):1802-1806. doi: 10.1001/jama.1993.03500140054035
  • Noninvasive Fetal Sex Determination Using Cell-Free Fetal DNA: A Systematic Review and Meta-analysis

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    JAMA. 2011; 306(6):627-636. doi: 10.1001/jama.2011.1114
  • Molecular Diagnostic Yield of Chromosomal Microarray Analysis and Whole-Exome Sequencing in Children With Autism Spectrum Disorder

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    JAMA. 2015; 314(9):895-903. doi: 10.1001/jama.2015.10078

    This case series of children with autism spectrum disorder compares the diagnostic yield of chromosomal microarray analysis vs whole-exome sequencing.

  • DNA Diagnosis of Neurofibromatosis 2: Altered Coding Sequence of the merlin Tumor Suppressor in an Extended Pedigree

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    JAMA. 1993; 270(19):2316-2320. doi: 10.1001/jama.1993.03510190072029
  • Integrative Clinical Sequencing in the Management of Refractory or Relapsed Cancer in Youth

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    JAMA. 2015; 314(9):913-925. doi: 10.1001/jama.2015.10080

    This case series involving children and young adults with cancer whose genomic sequencing results were the basis for clinical case recommendations charaterizes the number of clinically actionable findings and resulting patient outcomes.

  • A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

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    JAMA. 2013; 309(14):1502-1510. doi: 10.1001/jama.2013.3231
    Loman and coauthors report on a culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. In an accompanying Editorial, Relman discusses metagenomics, infectious disease diagnostics, and outbreak investigations.
  • Identification of a Novel TP53 Cancer Susceptibility Mutation Through Whole-Genome Sequencing of a Patient With Therapy-Related AML

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    JAMA. 2011; 305(15):1568-1576. doi: 10.1001/jama.2011.473
  • Use of Whole-Exome Sequencing to Determine the Genetic Basis of Multiple Mitochondrial Respiratory Chain Complex Deficiencies

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    JAMA. 2014; 312(1):68-77. doi: 10.1001/jama.2014.7184

    To determine the molecular basis of multiple respiratory chain complex deficiencies, Taylor and coauthors used a whole-exome sequencing approach in 53 patients with biochemical evidence of multiple respiratory chain complex defects but no primary pathogenic mitochondrial DNA mutation.

  • Noninvasive Prenatal Testing and Incidental Detection of Occult Maternal Malignancies

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    JAMA. 2015; 314(2):162-169. doi: 10.1001/jama.2015.7120

    This study describes the clinical and genetic characteristics of pregnant women with maternal-fetal karyotype discordance on noninvasive prenatal testing attributable to subsequently diagnosed malignancy.

  • New Approaches to Molecular Diagnosis

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    JAMA. 2013; 309(14):1511-1521. doi: 10.1001/jama.2013.3239
    Substantial advances in genetic and genomic testing mean that a greater variety of rare genetic and chromosomal disorders can be diagnosed, risk of common disorders can be estimated, and drug treatment can be tailored to individual needs. Korf and Rehm describe how physicians can recognize where new approaches to genetic and genomic testing may be applied clinically.
  • Cadaver Exome Sequencing for Teaching First-Year Medical Students—Reply

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    JAMA. 2016; 316(1):103-103. doi: 10.1001/jama.2016.4760
  • Cancer DNA in the Circulation: The Liquid Biopsy

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    JAMA. 2017; 318(13):1272-1274. doi: 10.1001/jama.2017.12131

    This JAMA Insights article explains cell-free circulating tumor DNA and its utility in noninvasive cancer detection and characterization, prediction of treatment response, monitoring of disease relapse, and identification of mechanisms of resistance to targeted therapies.

  • Exome Sequencing Comes to the Clinic

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    JAMA. 2015; 313(13):1301-1303. doi: 10.1001/jama.2015.1389