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  • PCPs Can Manage Genomic Results but Clinical Utility Is Limited

    Abstract Full Text
    JAMA. 2017; 318(16):1532-1532. doi: 10.1001/jama.2017.15798
  • JAMA October 3, 2017

    Figure: Analysis of ctDNA and Clinical Applications

    A variety of tumor-derived genomic alterations may be detected in cfDNA (see text for description of methods for cfDNA analysis). Current clinical applications include treatment selection and identification of resistance mutations; future applications include monitoring of treatment response, detection of recurrence, and screening.
  • An International Human Cell Atlas Consortium Takes Shape

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    JAMA. 2017; 318(8):685-686. doi: 10.1001/jama.2017.5640

    This Medical News article discusses a project to map all cell types and states in the human body.

  • Pilot Programs Seek to Integrate Genomic Data Into Practice

    Abstract Full Text
    JAMA. 2017; 318(5):410-412. doi: 10.1001/jama.2017.7181

    This Medical News article discusses recent programs and initiatives aimed at better integrating genomic data into clinical practice.

  • Bench to Bedside and Back Again May Be Key to Clinical Breakthroughs

    Abstract Full Text
    JAMA. 2017; 318(1):16-17. doi: 10.1001/jama.2017.7276
  • Finding the Rare Pathogenic Variants in a Human Genome

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    JAMA. 2017; 317(18):1904-1905. doi: 10.1001/jama.2017.0432

    This Genomics and Precision Health essay discusses the risks and potential benefits of performing genome sequencing in healthy people.

  • JAMA November 1, 2016

    Figure: Water Bear Genome Uncovers Novel Stress-Tolerant Proteins

    Water bear genome provides novel insights on cellular stress-resistance.
  • Water Bear Genome Uncovers Novel Stress-Tolerant Proteins

    Abstract Full Text
    JAMA. 2016; 316(17):1755-1755. doi: 10.1001/jama.2016.15523
  • JAMA August 25, 2015

    Figure 1: Flowchart Outlining the Selection of Samples and Sequencing Approaches in the Study

    aAML-RMG is a capture reagent consisting of all of the exons of the genes that are currently known to be recurrently mutated in acute myeloid leukemia, based on The Cancer Genome Atlas AML study.bThe only samples with sufficient day 30 DNA for sequencing and assessment of disease clearance (refractory group, 6 patients; R6-12 group, 8 patients; LFR group, 11 patients).cEnhanced exome sequencing is exome capture-based sequencing supplemented with the AML-RMG panel of target genes, to improve coverage of critical regions of the exome. dTargeted Ampliseq is a polymerase chain reaction–based digital sequencing approach that allows for accurate determination of the frequency of specific mutations in acute myeloid leukemia samples.
  • JAMA July 14, 2015

    Figure 1: Whole-Genome View of Copy-Number Changes in 8 Cases of Maternal Cancer

    Whole-genome view of copy-number gains and losses in plasma samples from women with known cancer. Smoothed normalized coverage (in black) is plotted along the genomic coordinates (x-axis), sorted by chromosome number and genomic location within the chromosomes. The data for all samples are shown as normalized coverage on the same scale, on the left side of the y-axis (0.9-1.1). The scale chosen for this figure is less than 0.5-1.5 because of fractional representation of the tumor DNA in the mixed sample. For some samples, the amplitude of the copy-number variants exceeded the scale; the maximum deviation from expected diploid representation is shown as a percentage on the right side of the y-axis. Copy-number gains or losses relative to the diploid reference genome are shown as blue or red, respectively. If a trisomy was reported, the relevant chromosome is shown by a light blue bar. If a monosomy was reported, the relevant chromosome is shown by a light red bar. Cases 3 and 5 include replicates of the same blood sample, identified by an apostrophe (‘). Cases 1, 3, and 4 had longitudinal samples obtained (see text for details).
  • JAMA July 14, 2015

    Figure 2: Longitudinal Evolution of Chromosomal Profiles for Maternal Cancer Case 3

    Individual chromosome views of data shown in Figure 1. Chromosomal coverage profiles in samples from case 3 taken at different intervals of time. The gray dots show the normalized coverage, and the solid colored lines show smoothed profiles (obtained from the median values across 31 genomic 100-kilobase bins). The upper panel is from the sample taken during pregnancy at 13 weeks of gestation. The middle panel is after delivery, immediately before surgical resection of an obstructing colorectal tumor. The lower panel is after delivery, following completion of chemotherapy and radiation. The x-axis shows the physical location of the increased counts as mapped against an ideogram for chromosomes 13 or 8 (SNPchip package, R version 3.1.2; resolution = 1 megabase pair). Chromosome 8 is included because it served as one of the reference chromosomes and contributed to the monosomy 18 classification in the postdelivery sample (see Table 1). The y-axis shows the percentage of signal above or below baseline corresponding to a diploid genome (y = 1.0). As an example, in the middle-right panel (chromosome 8 after delivery), the data at the highest peak (indicated by the arrow) show that there is approximately 12% excess representation of this part of the genome compared with the reference. NIPT indicates noninvasive prenatal testing.
  • Copy Number Variations and Cognitive Phenotypes in Unselected Populations

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    JAMA. 2015; 313(20):2044-2054. doi: 10.1001/jama.2015.4845

    This population-based study investigated the association of copy number variance and cognitive phenotypes and educational attainment and intellectual disability among individuals whose genetic samples are recorded in the Estonian Genome Center, the University of Tartu, 5% of the population, with the general Estonian population.

  • JAMA May 26, 2015

    Figure: Rare Intermediate-Size Copy Number Variations Associated With Lower Education Metrics

    Comparison of educational achievement of participants in the Estonian Genome Center, University of Tartu (EGCUT) with carriers of Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources (DECIPHER)–listed rearrangements or with carriers of deletions, female carriers of deletions, and duplications segregated by size (CNV frequencies ≤0.05%). The educational attainment decreases with copy number variation (CNV) size. See Table 2 for statistically significant differences between groups. Educational levels are coded according to the Estonian education curriculum (eMethods in the Supplement).
  • JAMA February 24, 2015

    Figure: Genomic Engineering Mediated by CRISPR-Cas9 Technology

    The natural dual-tracrRNA:crRNA complex was engineered as a single-guide RNA (sgRNA) that retains 2 critical features: the 20-nucleotide guide sequence that specifies DNA binding by Watson-Crick base pairing and the hairpin structure that recruits Cas9. Changes to the 20-nucleotide guide sequence serve to program CRISPR-Cas9 to target a DNA sequence adjacent to an NGG sequence motif (the protospacer-adjacent motif, PAM). Cas9-induced double-stranded DNA breaks are repaired either by nonhomologous end joining (NHEJ) or homology-directed repair (HDR). The NHEJ typically generates a small insertion or deletion at the site of the original break, which can be used for gene disruption. HDR can introduce new genetic information at the site of the break.
  • Genomic Engineering and the Future of Medicine

    Abstract Full Text
    JAMA. 2015; 313(8):791-792. doi: 10.1001/jama.2015.287
  • African Genome Variation Project Will Facilitate Genetic Studies in Africa

    Abstract Full Text
    JAMA. 2015; 313(7):659-659. doi: 10.1001/jama.2015.170
  • Grants Focus on Leveraging Biomedical Big Data

    Abstract Full Text
    JAMA. 2014; 312(20):2082-2082. doi: 10.1001/jama.2014.15837
  • Genome-Scale Sequencing in Clinical Care: Establishing Molecular Diagnoses and Measuring Value

    Abstract Full Text
    JAMA. 2014; 312(18):1865-1867. doi: 10.1001/jama.2014.14665

    This Editorial discusses possible contributions of genomic sequencing to progress in clinical care, from molecular diagnosis to improved outcomes.

  • Non–Small Cell Lung Cancer and Precision Medicine: A Model for the Incorporation of Genomic Features Into Clinical Trial Design

    Abstract Full Text
    JAMA. 2014; 311(19):1975-1976. doi: 10.1001/jama.2014.3742
  • Using Multiplexed Assays of Oncogenic Drivers in Lung Cancers to Select Targeted Drugs

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    JAMA. 2014; 311(19):1998-2006. doi: 10.1001/jama.2014.3741

    Kris and coauthors determine the frequency of oncogenic drivers in patients with lung adenocarcinomas and use the data to select treatments targeting the identified driver(s) and measure survival among 1007 US patients with metastatic lung adenocarcinomas.