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  • JAMA July 5, 2016

    Figure 1: Clopidogrel-Aspirin vs Aspirin on Clinical Outcome Stratified by Metabolizer Phenotype

    NE indicates not estimable. Patients with two *2 or *3 alleles (ie, *2/*2, *2/*3, or *3/*3) were classified as having the poor metabolizer phenotype, those with one *2 or *3 allele (ie, *1/*2 or *1/*3) were classified as having the intermediate metabolizer phenotype, those without a *2, *3, or *17 allele (ie, *1/*1) were classified as having the extensive metabolizer phenotype, those with a single *17 allele (ie, *1/*17) and *17 homozygotes were classified as having the ultra metabolizer phenotype. Composite event was defined as a new clinical vascular event, including ischemic stroke, hemorrhagic stroke, myocardial infarction, or vascular death. The size of the data markers indicate the sample size of the subgroup.
  • JAMA September 1, 2015

    Figure: Prevalence of De Novo Mutations Affecting Coding Sequence From Whole-Exome Sequencing (WES)

    Prevalence estimates were calculated from de novo variants identified through WES and confirmed in blood-derived DNA from 89 children and parents (6 children had only cell line–derived DNA available). Differences in the prevalence between the different phenotypic groups (equivocal excluded) and sexes were performed using a 2-sided Poisson test. A significant increase was observed in the complex vs the essential group (P = .02), and the highest prevalance, detected in the girls in the complex group, was significantly higher than that in girls from the essential group (P = .01). The total morphology score was the sum of minor physical anomaly and major congenital abnormality score. Error bars indicate 95% confidence intervals for the mean prevalence. All putative de novo variants and pathogenic variants were confirmed using Sanger sequencing.
  • Cognitive Phenotypes and Genomic Copy Number Variations

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    JAMA. 2015; 313(20):2029-2030. doi: 10.1001/jama.2015.4846
  • 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).
  • Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing

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    JAMA. 2014; 312(18):1870-1879. doi: 10.1001/jama.2014.14601

    This observation trial reports that whole-exome sequencing provides a potential molecular diagnosis for patients referred for evaluation of suspected genetic conditions, including detection of rare genetic events and new mutations, contributing to disease.

  • Clinical Exome Sequencing for Genetic Identification of Rare Mendelian Disorders

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    JAMA. 2014; 312(18):1880-1887. doi: 10.1001/jama.2014.14604

    Lee and coauthors report on initial clinical indications for clinical exome sequencing referrals and molecular diagnostic rates for different indications and for different test types.

  • Nonmyeloablative HLA-Matched Sibling Allogeneic Hematopoietic Stem Cell Transplantation for Severe Sickle Cell Phenotype

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    JAMA. 2014; 312(1):48-56. doi: 10.1001/jama.2014.7192

    In a trial involving 30 adult patients with sickle cell phenotype with or without thalassemia, Hsieh and coauthors report that after undergoing nonmyeloablative allogeneic hematopoietic stem cell transplantation from human leukocyte antigen–matched siblings, 26 patients achieved long-term engraftment.

  • 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.

  • Database on Elder Health Broadens

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    JAMA. 2014; 311(16):1603-1603. doi: 10.1001/jama.2014.4501
  • JAMA November 20, 2013

    Figure: Patient-Specific iPSC-CMs Represent a Potential Platform for Phenotypic Drug Discovery Assays Because of Their Capacity to Recapitulate Cardiac Phenotypes

    Coupled with current advances in high-throughput screening technologies, patient-specific iPSC-CMs could help accelerate the ability to investigate the molecular mechanisms of cardiovascular disorders resistant to current pharmaceutical treatments and could potentially identify novel therapeutic targets for these diseases.
  • JAMA May 8, 2013

    Figure 1: Genome-wide Association Studies Meta-analysis: Statistical Significance of Association for All Single-Nucleotide Polymorphisms (SNPs) With Minor Allele Frequency Greater Than 1%

    Manhattan plot showing significance of association for all single-nucleotide polymorphisms (SNPs) with a minor allele frequency greater than 1% in the meta-analysis with the anti–Helicobacter pylori IgG phenotype defined as a dichotomous variable comparing samples with the highest 25% IgG titers vs those with the lowest 75% IgG titers. SNPs available in all 3 cohorts are plotted on the x-axis according to their chromosomal position against the association with the phenotype (shown as − log10P value) on the y-axis. The dotted line indicates the threshold for genome-wide statistical significance (P = 5 × 10−8).
  • JAMA May 8, 2013

    Figure 2: Genome-wide Association Studies Meta-analysis: Loci Associated With Anti–Helicobacter pylori IgG Titers on a Genome-Wide Level of Significance

    Regional plots of the 2 loci associated with anti–H pylori IgG titers on a genome-wide level of significance. The y-axis on the left indicates the − log10P value for the association with the anti–H pylori IgG phenotype. Single-nucleotide polymorphisms (SNPs) available in all 3 cohorts are plotted on the x-axis according to their chromosomal position against the association with the phenotype on the y-axis. Shown are the TLR (left) and FCGR2A (right) regions: purple diamonds indicate the top-ranked SNPs of the respective regions exhibiting the lowest P value for association with the phenotype. The blue y-axes on the right of each plot indicate the estimated recombination rates (based on HapMap phase II); the bottom of each panel shows the respective annotated genes at the locus and their transcriptional direction. cM indicates centimorgans; Mb, megabases.
  • 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.
  • JAMA December 12, 2012

    Figure 3: Computed Tomography (CT) Parameters Change From Baseline

    MSCs indicates mesenchymal stem cells; EED, early enhancement effect. Mean changes from baseline to 13 months are noted by triangles and depict change in cardiac phenotype assessed by cardiac CT scan. Error bars indicate 95% CIs. Individual patient changes from baseline are shown as circles. Shown are changes in cardiac structural and functional parameters from baseline to 13-month follow-up in allogeneic, autologous, and combined patient groups. Within-group P values are noted as aP <.05, bP <.01, and cP <.001.
  • Prevalence and Phenotypes of APC and MUTYH Mutations in Patients With Multiple Colorectal Adenomas

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    JAMA. 2012; 308(5):485-492. doi: 10.1001/jama.2012.8780
    To determine prevalence of pathogenic APC and MUTYH mutations in patients with multiple colorectal adenomas and compare characteristics of carriers of these mutations, Grover and coauthors conducted a cross-sectional study among 8676 unrelated individuals. Roy provides comments in the related Editorial.
  • JAMA December 21, 2011

    Figure 2: Expression of Cell Surface Receptors on Splenic CD4 and CD8 T Cells

    See Figure 3 legend for explanation of geo-mean fluorescence intensity units, laboratory methods and statistical analysis. Compared with nonsepsis controls (n = 24-26), sepsis patients (n = 28-31) had activated T cells (increased CD69 in CD4 and CD8 T cells as well as increased CD25 [interleukin {IL} 2 receptor α] in CD4 T cells). Despite an activation phenotype, sepsis induced down-regulation of positive costimulatory receptors (CD28 in CD4 and CD8 T cells) as well as increased inhibitory receptors (programmed cell death 1 [PD-1] for CD4 T cells and cytotoxic T-lymphocyte antigen 4 [CTLA-4] for CD8 T cells). The IL-7 receptor α chain (CD127) was decreased in CD4 and CD8 T cells in sepsis.
  • JAMA December 21, 2011

    Figure 3: Expression of Cell Surface Receptors on Splenic Antigen-Presenting Cells and Tissue Macrophages

    Splenocytes (2 × 106) were stained with fluorescently conjugated antibodies or isotype-matched control antibodies and analyzed by flow cytometry (eAppendix). A positive gate was established based on isotype control staining. The percentage positive for each marker was defined by subtracting the percentage within the positive gate in the isotype control from the percentage within the positive gate in the specific stain. The geo-mean fluorescence intensity was determined by subtraction of the nonspecific fluorescence of the isotype control antibody from the fluorescence of the specific conjugated antibody and is expressed in units, which are an average of fluorescence intensity of the data collected within the selected gate after subtracting fluorescence intensity of isotope control. Antigen-presenting cells, ie, dendritic cells and macrophages/monocytes, as well as tissue-specific macrophages, showed an immunosuppressive phenotype in sepsis as evidenced by decreased expression of CD86 and HLA-DR. In addition, antigen-presenting cells from sepsis patients had increased expression of PD-L1, the ligand for the inhibitory receptor programmed cell death 1 PD-1 on T cells. Each data marker represents an individual patient. Statistical analysis was performed by 2-tailed nonparametric t test (Mann-Whitney U test). Horizontal lines represent mean values.
  • Association of BRCA1 and BRCA2 Mutations With Survival, Chemotherapy Sensitivity, and Gene Mutator Phenotype in Patients With Ovarian Cancer

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    JAMA. 2011; 306(14):1557-1565. doi: 10.1001/jama.2011.1456
  • JAMA January 12, 2011

    Figure 2: Characteristic Findings Associated With Clinical and Autoantibody Phenotypes in Myositis

    A, Interstitial lung disease, defined by high-resolution computed tomographic (CT) scanning, is seen frequently in patients with polymyositis, as well as with the antisynthetase autoantibody phenotype. More recently, rapidly progressive interstitial lung disease has been associated with the anti–CADM-140 autoantibody. The chest CT scan depicted is from a 55-year-old female patient with anti–Jo-1 autoantibodies and interstitial lung disease. B, Dystrophic calcification around the elbow and forearm of a 10.5-year-old girl with juvenile dermatomyositis and anti-MJ autoantibodies. Anti-MJ autoantibodies are seen in up to 25% of patients with juvenile-onset dermatomyositis and less frequently in patients with adult-onset disease. Calcinosis is present in more than 60% of patients with the anti–MJ autoantibody phenotype. C, Lipodystrophy (loss of subcutaneous fat with frequent insulin resistance, diabetes, and hypertriglyceridemia) is associated with juvenile-onset dermatomyositis. Generalized lipodystrophy (a widespread loss of fat from the trunk and extremities), has been associated with anti-p155 autoantibodies. A loss of fat from the arm is seen in this 20-year-old woman with juvenile-onset dermatomyositis since age 8 years, who has anti-p155 autoantibodies and lipodystrophy.