Clinical and MRI phenotypes of sarcoidosis-associated myelopathy

OBJECTIVE

To determine the characteristic clinical and spinal MRI phenotypes of sarcoidosis-associated myelopathy (SAM), we analyzed a large cohort of patients with this disorder.

METHODS

Patients diagnosed with SAM at a single center between 2000 and 2018 who met the established criteria for definite and probable neurosarcoidosis were included in a retrospective analysis to identify clinical profiles, CSF characteristics, and MRI lesion morphology.

RESULTS

Of 62 included patients, 33 (53%) were male, and 30 (48%) were African American. SAM was the first clinical presentation of sarcoidosis in 49 patients (79%). Temporal profile of symptom evolution was chronic in 81%, with sensory symptoms most frequently reported (87%). CSF studies showed pleocytosis in 79% and CSF-restricted oligoclonal bands in 23% of samples tested. Four discrete patterns of lesion morphology were identified on spine MRI: longitudinally extensive myelitis (n = 28, 45%), short tumefactive myelitis (n = 14, 23%), spinal meningitis/meningoradiculitis (n = 14, 23%), and anterior myelitis associated with areas of disc degeneration (n = 6, 10%). Postgadolinium enhancement was seen in all but 1 patient during the acute phase. The most frequent enhancement pattern was dorsal subpial enhancement (n = 40), followed by meningeal/radicular enhancement (n = 23) and ventral subpial enhancement (n = 12). In 26 cases (42%), enhancement occurred at locations with coexisting structural changes (e.g., spondylosis).

CONCLUSIONS

Recognition of the clinical features (chronically evolving myelopathy) and distinct MRI phenotypes (with enhancement in a subpial and/or meningeal pattern) seen in SAM can aid diagnosis of this disorder. Enhancement patterns suggest that SAM may have a predilection for areas of the spinal cord susceptible to mechanical stress.

Diagnosis and Detection of Sarcoidosis. An Official American Thoracic Society Clinical Practice Guideline

Background: The diagnosis of sarcoidosis is not standardized but is based on three major criteria: a compatible clinical presentation, finding nonnecrotizing granulomatous inflammation in one or more tissue samples, and the exclusion of alternative causes of granulomatous disease. There are no universally accepted measures to determine if each diagnostic criterion has been satisfied; therefore, the diagnosis of sarcoidosis is never fully secure.

Methods: Systematic reviews and, when appropriate, meta-analyses were performed to summarize the best available evidence. The evidence was appraised using the Grading of Recommendations, Assessment, Development, and Evaluation approach and then discussed by a multidisciplinary panel. Recommendations for or against various diagnostic tests were formulated and graded after the expert panel weighed desirable and undesirable consequences, certainty of estimates, feasibility, and acceptability.

Results: The clinical presentation, histopathology, and exclusion of alternative diagnoses were summarized. On the basis of the available evidence, the expert committee made 1 strong recommendation for baseline serum calcium testing, 13 conditional recommendations, and 1 best practice statement. All evidence was very low quality.

Conclusions: The panel used systematic reviews of the evidence to inform clinical recommendations in favor of or against various diagnostic tests in patients with suspected or known sarcoidosis. The evidence and recommendations should be revisited as new evidence becomes available.

Association of Medication Adherence and Clinical Outcomes in Sarcoidosis

BACKGROUND

Sarcoidosis, one of the most common interstitial lung diseases, has significant health disparities. Approximately 50% of individuals affected with sarcoidosis will undergo spontaneous remission, but those who do not undergo remission often require long-term or lifelong treatment to prevent disease progression. We sought to assess the association between medication adherence and clinical outcomes in sarcoidosis.

METHODS

Adult patients in the Johns Hopkins Sarcoidosis Clinic diagnosed with pulmonary sarcoidosis on treatment were eligible for enrollment. Questionnaires were administered to assess medication adherence, health-related quality of life (HRQoL), health-care utilization, and sociodemographic information. Clinical information was abstracted from medical charts including lung function, disease duration, comorbidities, and sarcoidosis organ involvement.

RESULTS

A total of 117 participants were enrolled (57% women; 55% black; median age, 57 years). Within the cohort, 66% of individuals reported at least one nonadherent behavior. Higher medication adherence was associated with better HRQoL (P < .05). There was no association between medication adherence and the odds of health-care utilization, FVC % predicted, FEV₁ % predicted, or diffusion capacity of the lungs for carbon monoxide % predicted. Black participants reported lower medication adherence than white participants (P < .05).

CONCLUSIONS

This is the first observational study of medication adherence in sarcoidosis. We found that higher medication adherence was associated with better HRQoL, with blacks more likely to report nonadherence. Medication adherence may be an important target to improve patient-reported outcomes and health disparities in sarcoidosis.

Design tools for MPRA experiments

Motivation

Genetic reporter assays are a convenient, relatively inexpensive method for studying the regulation of gene expression. Massively Parallel Reporter Assays (MPRA) are high-throughput functionalization assays that interrogate the transcriptional activity of many genetic variants at once using a library of synthetic barcoded constructs. Despite growing interest in this area, there are few computational tools to design and execute MPRA studies.

Results

We designed an online web-tool and R package that allows for interactive MPRA experimental design encompassing both power analysis and design of constructs. Our tool is tuned using data from real MPRA studies. Users can adjust experimental parameters to examine the predicted effect on assay power as well as upload VCFs for automated construct sequence generation.

Availability and implementation

The MPRA Design Tools web application is available here: https://andrewghazi.shinyapps.io/designmpra/, https://github.com/andrewGhazi/designMPRA and https://github.com/andrewGhazi/mpradesigntools.

Supplementary information

Supplementary data are available at Bioinformatics online.

A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing

Background

Although mosaic variation has been known to cause disease for decades, high-throughput sequencing technologies with the analytical sensitivity to consistently detect variants at reduced allelic fractions have only recently emerged as routine clinical diagnostic tests. To date, few systematic analyses of mosaic variants detected by diagnostic exome sequencing for diverse clinical indications have been performed.

Methods

To investigate the frequency, type, allelic fraction, and phenotypic consequences of clinically relevant somatic mosaic single nucleotide variants (SNVs) and characteristics of the corresponding genes, we retrospectively queried reported mosaic variants from a cohort of ~ 12,000 samples submitted for clinical exome sequencing (ES) at Baylor Genetics.

Results

We found 120 mosaic variants involving 107 genes, including 80 mosaic SNVs in proband samples and 40 in parental/grandparental samples. Average mosaic alternate allele fraction (AAF) detected in autosomes and in X-linked disease genes in females was 18.2% compared with 34.8% in X-linked disease genes in males. Of these mosaic variants, 74 variants (61.7%) were classified as pathogenic or likely pathogenic and 46 (38.3%) as variants of uncertain significance. Mosaic variants occurred in disease genes associated with autosomal dominant (AD) or AD/autosomal recessive (AR) (67/120, 55.8%), X-linked (33/120, 27.5%), AD/somatic (10/120, 8.3%), and AR (8/120, 6.7%) inheritance. Of note, 1.7% (2/120) of variants were found in genes in which only somatic events have been described. Nine genes had recurrent mosaic events in unrelated individuals which accounted for 18.3% (22/120) of all detected mosaic variants in this study. The proband group was enriched for mosaicism affecting Ras signaling pathway genes.

Conclusions

In sum, an estimated 1.5% of all molecular diagnoses made in this cohort could be attributed to a mosaic variant detected in the proband, while parental mosaicism was identified in 0.3% of families analyzed. As ES design favors breadth over depth of coverage, this estimate of the prevalence of mosaic variants likely represents an underestimate of the total number of clinically relevant mosaic variants in our cohort.

Electronic supplementary material

The online version of this article (10.1186/s13073-019-0658-2) contains supplementary material, which is available to authorized users.

Functionalization of CD36 cardiovascular disease and expression associated variants by interdisciplinary high throughput analysis

CD36 is a platelet membrane glycoprotein whose engagement with oxidized low-density lipoprotein (oxLDL) results in platelet activation. The CD36 gene has been associated with platelet count, platelet volume, as well as lipid levels and CVD risk by genome-wide association studies. Platelet CD36 expression levels have been shown to be associated with both the platelet oxLDL response and an elevated risk of thrombo-embolism. Several genomic variants have been identified as associated with platelet CD36 levels, however none have been conclusively demonstrated to be causative. We screened 81 expression quantitative trait loci (eQTL) single nucleotide polymorphisms (SNPs) associated with platelet CD36 expression by a Massively Parallel Reporter Assay (MPRA) and analyzed the results with a novel Bayesian statistical method. Ten eQTLs located 13kb to 55kb upstream of the CD36 transcriptional start site of transcript ENST00000309881 and 49kb to 92kb upstream of transcript ENST00000447544, demonstrated significant transcription shifts between their minor and major allele in the MPRA assay. Of these, rs2366739 and rs1194196, separated by only 20bp, were confirmed by luciferase assay to alter transcriptional regulation. In addition, electromobility shift assays demonstrated differential DNA:protein complex formation between the two alleles of this locus. Furthermore, deletion of the genomic locus by CRISPR/Cas9 in K562 and Meg-01 cells results in upregulation of CD36 transcription. These data indicate that we have identified a variant that regulates expression of CD36, which in turn affects platelet function. To assess the clinical relevance of our findings we used the PhenoScanner tool, which aggregates large scale GWAS findings; the results reinforce the clinical relevance of our variants and the utility of the MPRA assay. The study demonstrates a generalizable paradigm for functional testing of genetic variants to inform mechanistic studies, support patient management and develop precision therapies.

Platelets are anucleate cells that are best known as regulators of vascular hemostasis and thrombosis but also play important roles in cancer, angiogenesis, and inflammation. CD36 is a platelet surface marker that can activate platelet in response to oxidized low density lipoprotein (oxLDL). CD36 has been associated with numerous cardiovascular traits in human including blood lipid levels, platelet count, and cardiovascular disease prevalence in human genetic studies. Human variability in platelet CD36 levels are associated with the platelet response to oxLDL. However, the genetic mechanisms responsible for the variability of CD36 levels are unknown. We examined 81 genetic variants associated with CD36 levels for functionality using a high-throughput assay. Of the ten variants that were identified in that assay, one doublet, rs2366739 and rs1194196, were confirmed using additional molecular and cellular assays. Deletion of the genomic region containing rs2366739 and rs1194196 resulted in overexpression of CD36 in a cell culture system. This finding indicates a control locus which can serve as a potential target in modulating CD36 expression and altering platelet function in cardiovascular disease.

Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2

DNA rearrangements resulting in human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. Evidence for an increased rate of clustered single-nucleotide variant (SNV) mutation in cis with non-recurrent rearrangements was found. Indel and SNV formation are associated with both copy-number gains and losses of 17p11.2, occur up to ∼1 Mb away from the breakpoint junctions, and favor C > G transversion substitutions; results suggest that single-stranded DNA is formed during the genesis of the SV and provide compelling support for a microhomology-mediated break-induced replication (MMBIR) mechanism for SV formation. Our data show an additional mutational burden of MMBIR consisting of hypermutation confined to the locus and manifesting as SNVs and indels predominantly within genes.

Electron affinities from gas chromatography electron capture detector and negative ion mass spectrometry responses and complementary methods

The use of the electron-capture detector, ECD, to measure molecular electron affinities and kinetic parameters for reactions of thermal electrons with molecules at atmospheric pressure separated by chromatography and the sensitive and selective quantitative analysis of certain classes molecules are reviewed. The evaluated ground state electron affinities of the main group elements and diatomic molecules from slightly positive, 0+, to 3.6 eV are summarized. The electron affinities of twenty-seven superoxide states determined from pulsed discharge ECD and other methods are used to calculate one dimensional potential energy curves in agreement with theory. Advances in literature searches have uncovered ECD data in dissertations and theses and in the Russian and Japanese literature. These data, unpublished radioactive and pulsed discharge ECD thermal data from the University of Houston laboratories are used to report and evaluate electron affinities. The accuracy and precision of ECD electron affinities of organic molecules are identified and tabulated so that they can be added to compilations. A procedure for calculating the temperature dependence of electron molecule reactions is presented using kinetic and thermodynamic data. These are used toselect the most appropriate equipment and conditions for ECD analyses and physical determinations.

Comment on: Negative ions, molecular electron affinity and orbital structure of cata-condensed polycyclic aromatic hydrocarbons by Rustem V. Khatymov, Mars V. Muftakhov and Pavel V. Shchukin

RATIONALE

The anion mass spectral lifetimes for several aromatic hydrocarbons reported in the subject article were related to significantly different electron affinities. The different values are rationalized using negative ion mass spectral data.

METHODS

Electron affinities for polycyclic aromatic hydrocarbons are reported from the temperature dependence of unpublished electron capture detector data. These are compared with published values and the largest values are assigned to the ground state.

RESULTS

The ground state adiabatic electron affinities: (eV) pentacene, 1.41 (3); tetracene, 1.058 (5); benz(a)pyrene, 0.82 (4); benz(a) anthracene, 0.69 (2) anthracene, 0.68 (2); and pyrene, 0.59 (1) are used to assign excited state adiabatic electron affinities: (eV) tetracene: 0.88 (4); anthracene 0.53 (1); pyrene, 0.41 (1); benz(a)anthracene, 0.39 (10); chrysene, 0.32 (1); and phenanthrene, 0.12 (2) and ground state adiabatic electron affinities: (eV) dibenz(a,j)anthracene, 0.69 (3); dibenz(a,h)anthracene, 0.68 (3); benz(e)pyrene, 0.60 (3); and picene, 0.59 (3) from experimental data. The lifetime of benz(a)pyrene is predicted to be larger than 150 μs and for benzo(c)phenanthrene and picene about 40 μs, from ground state adiabatic electron affinities.

CONCLUSIONS

The assignments of adiabatic electron affinities of aromatic hydrocarbons determined from electron capture detector and mass spectrometric data to ground and excited states are supported by constant electronegativities. A set of consistent ground state adiabatic electron affinities for 15 polycyclic aromatic hydrocarbons is related to lifetimes from the subject article.

The effect of community socioeconomic status on sepsis-attributable mortality

PURPOSE

Community factors may play a role in determining individual risk for sepsis, as well as sepsis-related morbidity and mortality. We sought to define the relationship between community socioeconomic status and mortality due to sepsis in an urban locale.

METHODS

Using community statistical areas of Baltimore City, we dichotomized neighborhoods at median household income, and compared distribution of outcomes of interest within the two income categories. We performed multivariable regression analyses to determine the relationship between socioeconomic variables and sepsis-attributable mortality.

RESULTS

The collective median household income was $38,660 (IQR $32,530, 54,480), family poverty rate was 28.4% (IQR 13.5, 38.8%), and rate of death from sepsis was 3.1 per 10,000 persons (IQR 2.60, 4.10). Lower household income communities demonstrated higher rates of death from sepsis (3.65 (IQR 2.78, 4.40)) than higher household income communities (2.80 (IQR 2.05, 3.55)) (p = .02). In regression models, household income (β = -8.42, p = .006) and percentage of poverty in communities (β = 2.71, p = .01) demonstrated associations with sepsis-attributable mortality.

DISCUSSION

Our findings suggest that socioeconomic variables play significant role in sepsis-attributable mortality. Such confirmation of regional disparities in mortality due to sepsis warrants further consideration, as well as integration, for future national sepsis policies.

Genetic, Immunologic, and Environmental Basis of Sarcoidosis

Sarcoidosis is a multisystem disease with tremendous heterogeneity in disease manifestations, severity, and clinical course that varies among different ethnic and racial groups. To better understand this disease and to improve the outcomes of patients, a National Heart, Lung, and Blood Institute workshop was convened to assess the current state of knowledge, gaps, and research needs across the clinical, genetic, environmental, and immunologic arenas. We also explored to what extent the interplay of the genetic, environmental, and immunologic factors could explain the different phenotypes and outcomes of patients with sarcoidosis, including the chronic phenotypes that have the greatest healthcare burden. The potential use of current genetic, epigenetic, and immunologic tools along with study approaches that integrate environmental exposures and precise clinical phenotyping were also explored. Finally, we made expert panel-based consensus recommendations for research approaches and priorities to improve our understanding of the effect of these factors on the health outcomes in sarcoidosis.

HER2 Reactivation through Acquisition of the HER2 L755S Mutation as a Mechanism of Acquired Resistance to HER2-targeted Therapy in HER2+ Breast Cancer

Purpose: Resistance to anti-HER2 therapies in HER2+ breast cancer can occur through activation of alternative survival pathways or reactivation of the HER signaling network. Here we employed BT474 parental and treatment-resistant cell line models to investigate a mechanism by which HER2+ breast cancer can reactivate the HER network under potent HER2-targeted therapies.Experimental Design: Resistant derivatives to lapatinib (L), trastuzumab (T), or the combination (LR/TR/LTR) were developed independently from two independent estrogen receptor ER+/HER2+ BT474 cell lines (AZ/ATCC). Two derivatives resistant to the lapatinib-containing regimens (BT474/AZ-LR and BT474/ATCC-LTR lines) that showed HER2 reactivation at the time of resistance were subjected to massive parallel sequencing and compared with parental lines. Ectopic expression and mutant-specific siRNA interference were applied to analyze the mutation functionally. In vitro and in vivo experiments were performed to test alternative therapies for mutant HER2 inhibition.Results: Genomic analyses revealed that the HER2L755S mutation was the only common somatic mutation gained in the BT474/AZ-LR and BT474/ATCC-LTR lines. Ectopic expression of HER2L755S induced acquired lapatinib resistance in the BT474/AZ, SK-BR-3, and AU565 parental cell lines. HER2L755S-specific siRNA knockdown reversed the resistance in BT474/AZ-LR and BT474/ATCC-LTR lines. The HER1/2-irreversible inhibitors afatinib and neratinib substantially inhibited both resistant cell growth and the HER2 and downstream AKT/MAPK signaling driven by HER2L755S in vitro and in vivoConclusions: HER2 reactivation through acquisition of the HER2L755S mutation was identified as a mechanism of acquired resistance to lapatinib-containing HER2-targeted therapy in preclinical HER2-amplified breast cancer models, which can be overcome by irreversible HER1/2 inhibitors. Clin Cancer Res; 23(17); 5123-34. ©2017 AACR.

Development and implementation of an alcohol withdrawal protocol using a 5-item scale, the Brief Alcohol Withdrawal Scale (BAWS)

BACKGROUND

The standard of care for management of alcohol withdrawal is symptom-triggered treatment using the Clinical Institute Withdrawal Assessment for Alcohol (CIWA-Ar). Many items of this 10-question scale rely on subjective assessments of withdrawal symptoms, making it time-consuming and cumbersome to use. Therefore, there is interest in shorter and more objective methods to assess alcohol withdrawal symptoms.

METHODS

A 6-item withdrawal scale developed at another institution was piloted. Based on comparison with the CIWA-Ar, this was adapted into a 5-item scale named the Brief Alcohol Withdrawal Scale (BAWS). The BAWS was compared with the CIWA-Ar and a withdrawal protocol utilizing the BAWS was developed. The new protocol was implemented on an inpatient unit dedicated to treating substance withdrawal. Data was collected on the first 3 months of implementation and compared with the 3 months prior to that.

RESULTS

A BAWS score of 3 or more predicted CIWA-Ar score ≥8 with a sensitivity of 85.3% and specificity of 65.8%. The demographics of the patients in the 2 time periods were similar: the mean age was 45.9; 70.6% were male; 30.9% received concurrent treatment for opioid withdrawal; and 14.2% were receiving methadone maintenance. During the BAWS phase, patients received significantly less diazepam (mean dose 81.4 vs. 60.3 mg, P < .001). There was no significant difference in length of stay. No patients experienced a seizure, delirium, or required transfer to a higher level of care during any of the 664 admissions in either phase.

CONCLUSIONS

This simple protocol utilizing a 5-item withdrawal scale performed well in this setting. Its use in other settings, particularly with patients with concurrent medical illnesses or more severe withdrawal, needs to be explored further.

Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics

Background

Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors.

Methods

We investigated a cohort of 15 individuals with a clinical suspicion of SMS who showed neither deletion in the SMS critical region nor damaging variants in RAI1 using whole exome sequencing. A combination of network analysis (co-expression and biomedical text mining), transcriptomics, and circularized chromatin conformation capture (4C-seq) was applied to verify whether modified genes are part of the same disease network as known SMS-causing genes.

Results

Potentially deleterious variants were identified in nine of these individuals using whole-exome sequencing. Eight of these changes affect KMT2D, ZEB2, MAP2K2, GLDC, CASK, MECP2, KDM5C, and POGZ, known to be associated with Kabuki syndrome 1, Mowat-Wilson syndrome, cardiofaciocutaneous syndrome, glycine encephalopathy, mental retardation and microcephaly with pontine and cerebellar hypoplasia, X-linked mental retardation 13, X-linked mental retardation Claes-Jensen type, and White-Sutton syndrome, respectively. The ninth individual carries a de novo variant in JAKMIP1, a regulator of neuronal translation that was recently found deleted in a patient with autism spectrum disorder. Analyses of co-expression and biomedical text mining suggest that these pathologies and SMS are part of the same disease network. Further support for this hypothesis was obtained from transcriptome profiling that showed that the expression levels of both Zeb2 and Map2k2 are perturbed in Rai1^–/– mice. As an orthogonal approach to potentially contributory disease gene variants, we used chromatin conformation capture to reveal chromatin contacts between RAI1 and the loci flanking ZEB2 and GLDC, as well as between RAI1 and human orthologs of the genes that show perturbed expression in our Rai1^–/– mouse model.

Conclusions

These holistic studies of RAI1 and its interactions allow insights into SMS and other disorders associated with intellectual disability and behavioral abnormalities. Our findings support a pan-genomic approach to the molecular diagnosis of a distinctive disorder.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-016-0359-z) contains supplementary material, which is available to authorized users.

Mass spectrometric determination of Morse parameters for the fifty-four superoxide states dissociating to the lowest limit

RATIONALE

Superoxide is the most significant homonuclear diatomic anion in biochemistry. Theory predicts 12 doublet (X, A-K) and 12 quartet (a-l) electronic states split by spin orbital coupling into 54 states dissociating to the (3) P(O) + (2) P(O(-) ) limit. Dissociation energies for the 27 bonding states with positive electron affinities have been determined from mass spectrometric data. However, the 27 antibonding states with negative electron affinities have not been experimentally characterized.

METHODS

The electron affinity of the hydrogen atom per electron, the Hylleraas, is the fundamental measure of electron correlation. It has been used to assign and evaluate experimental electron affinities of atoms and diatomic molecules. The 27 negative electron affinities of oxygen are estimated from the 27 positive values and the Hylleraas. These values are used to determine frequencies and internuclear separations by fitting theoretical electron impact distributions to the gas-phase mass spectrometric atomic oxygen anion distribution peaking at about 6.5 eV.

RESULTS

The dissociation energies, internuclear distances and frequencies giving the first complete set of Morse potential energy curves for the 54 superoxide states dissociating to the lowest limit are reported from mass spectrometric data. The potentials are compared to theoretical and empirical literature curves.

CONCLUSIONS

The existence of the 27 bonding and 27 antibonding spin orbital coupling superoxide states dissociating to (3) P(O) + (2) P(O(-) ) is established from mass analyzed thermal, photon, and electron ionization data. There are electron affinities from 0 to 0.15 eV, and onsets and peaks for dissociative electron attachment that cannot be explained by the 54 states. These support the existence of the 36 superoxide spin states dissociating to [(1) D(O) + (2) P(O(-) )] and [(1) S(O) + (2) P(O(-) )] predicted by quantum mechanics. Copyright © 2016 John Wiley & Sons, Ltd.

Etiologies of Sarcoidosis

Since sarcoidosis was first described more than a century ago, the etiologic determinants causing this disease remain uncertain. Studies suggest that genetic, host immunologic, and environmental factors interact together to cause sarcoidosis. Immunologic characteristics of sarcoidosis include non-caseating granulomas, enhanced local expression of T helper-1 (and often Th17) cytokines and chemokines, dysfunctional regulatory T-cell responses, dysregulated Toll-like receptor signaling, and oligoclonal expansion of CD4+ T cells consistent with chronic antigenic stimulation. Multiple environmental agents have been suggested to cause sarcoidosis. Studies from several groups implicate mycobacterial or propionibacterial organisms in the etiology of sarcoidosis based on tissue analyses and immunologic responses in sarcoidosis patients. Despite these studies, there is no consensus on the nature of a microbial pathogenesis of sarcoidosis. Some groups postulate sarcoidosis is caused by an active viable replicating infection while other groups contend there is no clinical, pathologic, or microbiologic evidence for such a pathogenic mechanism. The authors posit a novel hypothesis that proposes that sarcoidosis is triggered by a hyperimmune Th1 response to pathogenic microbial and tissue antigens associated with the aberrant aggregation of serum amyloid A within granulomas, which promotes progressive chronic granulomatous inflammation in the absence of ongoing infection.

A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics

Background

Genome-wide data are increasingly important in the clinical evaluation of human disease. However, the large number of variants observed in individual patients challenges the efficiency and accuracy of diagnostic review. Recent work has shown that systematic integration of clinical phenotype data with genotype information can improve diagnostic workflows and prioritization of filtered rare variants. We have developed visually interactive, analytically transparent analysis software that leverages existing disease catalogs, such as the Online Mendelian Inheritance in Man database (OMIM) and the Human Phenotype Ontology (HPO), to integrate patient phenotype and variant data into ranked diagnostic alternatives.

Methods

Our tool, “OMIM Explorer” (http://www.omimexplorer.com), extends the biomedical application of semantic similarity methods beyond those reported in previous studies. The tool also provides a simple interface for translating free-text clinical notes into HPO terms, enabling clinical providers and geneticists to contribute phenotypes to the diagnostic process. The visual approach uses semantic similarity with multidimensional scaling to collapse high-dimensional phenotype and genotype data from an individual into a graphical format that contextualizes the patient within a low-dimensional disease map. The map proposes a differential diagnosis and algorithmically suggests potential alternatives for phenotype queries—in essence, generating a computationally assisted differential diagnosis informed by the individual’s personal genome. Visual interactivity allows the user to filter and update variant rankings by interacting with intermediate results. The tool also implements an adaptive approach for disease gene discovery based on patient phenotypes.

Results

We retrospectively analyzed pilot cohort data from the Baylor Miraca Genetics Laboratory, demonstrating performance of the tool and workflow in the re-analysis of clinical exomes. Our tool assigned to clinically reported variants a median rank of 2, placing causal variants in the top 1 % of filtered candidates across the 47 cohort cases with reported molecular diagnoses of exome variants in OMIM Morbidmap genes. Our tool outperformed Phen-Gen, eXtasy, PhenIX, PHIVE, and hiPHIVE in the prioritization of these clinically reported variants.

Conclusions

Our integrative paradigm can improve efficiency and, potentially, the quality of genomic medicine by more effectively utilizing available phenotype information, catalog data, and genomic knowledge.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-016-0261-8) contains supplementary material, which is available to authorized users.