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We describe the trajectory of the human sex ratio from conception to birth by analyzing data from (i) 3- to 6-d-old embryos, (ii) induced abortions, (iii) chorionic villus sampling, (iv) amniocentesis, and (v) fetal deaths and live births. Our dataset is the most comprehensive and largest ever assembled to estimate the sex ratio at conception and the sex ratio trajectory and is the first, to our knowledge, to include all of these types of data. Our estimate of the sex ratio at conception is 0.5 (proportion male), which contradicts the common claim that the sex ratio at conception is male-biased. The sex ratio among abnormal embryos is male-biased, and the sex ratio among normal embryos is female-biased. These biases are associated with the abnormal/normal state of the sex chromosomes and of chromosomes 15 and 17. The sex ratio may decrease in the first week or so after conception (due to excess male mortality); it then increases for at least 10-15 wk (due to excess female mortality), levels off after â¼20 wk, and declines slowly from 28 to 35 wk (due to excess male mortality). Total female mortality during pregnancy exceeds total male mortality. The unbiased sex ratio at conception, the increase in the sex ratio during the first trimester, and total mortality during pregnancy being greater for females are fundamental insights into early human development.
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Fertilização , Parto , Razão de Masculinidade , Aborto Induzido , Fatores Etários , Amostra da Vilosidade Coriônica , Embrião de Mamíferos/fisiologia , Feminino , Humanos , Cariotipagem , Masculino , Gravidez , Primeiro Trimestre da Gravidez , Técnicas de Reprodução AssistidaRESUMO
BACKGROUND: Exosomes and other extracellular vesicles (EVs) have emerged as an important mechanism of cell-to-cell communication. However, previous studies either did not fully resolve what genetic materials were shuttled by exosomes or only focused on a specific set of miRNAs and mRNAs. A more systematic method is required to identify the genetic materials that are potentially transferred during cell-to-cell communication through EVs in an unbiased manner. RESULTS: In this work, we present a novel next generation of sequencing (NGS) based approach to identify EV mediated mRNA exchanges between co-cultured adipocyte and macrophage cells. We performed molecular and genomic profiling and jointly considered data from RNA sequencing (RNA-seq) and genotyping to track the "sequence varying mRNAs" transferred between cells. We identified 8 mRNAs being transferred from macrophages to adipocytes and 21 mRNAs being transferred in the opposite direction. These mRNAs represented biological functions including extracellular matrix, cell adhesion, glycoprotein, and signal peptides. CONCLUSIONS: Our study sheds new light on EV mediated RNA communications between adipocyte and macrophage cells, which may play a significant role in developing insulin resistance in diabetic patients. This work establishes a new method that is applicable to examining genetic material exchanges in many cellular systems and has the potential to be extended to in vivo studies as well.
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Comunicação Celular , Vesículas Extracelulares/metabolismo , RNA Mensageiro/metabolismo , Adipócitos/metabolismo , Linhagem Celular , Técnicas de Cocultura , Expressão Gênica , Técnicas de Genotipagem , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Macrófagos/metabolismo , Transporte de RNA , Análise de Sequência de RNARESUMO
INTRODUCTION: Clinical guidelines offer little guidance for treatment selection following inadequate response to conventional synthetic disease-modifying antirheumatic drug (csDMARD) in rheumatoid arthritis (RA). A molecular signature response classifier (MSRC) was validated to predict tumor necrosis factor inhibitor (TNFi) inadequate response. The decision impact of MSRC results on biologic and targeted synthetic disease-modifying antirheumatic drug (b/tsDMARD) selection was evaluated. METHODS: This is an analysis of AIMS, a longitudinal, prospective database of patients with RA tested using the MSRC. This study assessed selection of b/tsDMARDs class after MSRC testing by surveying physicians, the rate of b/tsDMARD prescriptions aligning with MSRC results, and the percentage of physicians utilizing MSRC results for decision-making. RESULTS: Of 1018 participants, 70.7% (720/1018) had treatment selected after receiving MSRC results. In this MSRC-informed cohort, 75.6% (544/720) of patients received a b/tsDMARD aligned with MSRC results, and 84.6% (609/720) of providers reported using MSRC results to guide treatment selection. The most prevalent reason reported (8.2%, 59/720) for not aligning treatment selection with MSRC results from the total cohort was health insurance coverage issues. CONCLUSION: This study showed that rheumatologists reported using the MSRC test to guide b/tsDMARD selection for patients with RA. In most cases, MSRC test results appeared to influence clinical decision-making according to physician self-report. Wider adoption of precision medicine tools like the MSRC could support rheumatologists and patients in working together to achieve optimal outcomes for RA.
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Precision medicine's potential to transform complex autoimmune disease treatment is often challenged by limited data availability and inadequate sample size when compared with the number of molecular features found in high-throughput multi-omics data sets. Addressing this issue, the novel framework PRoBeNet (Predictive Response Biomarkers using Network medicine) was developed. ProBeNet operates under the hypothesis that the therapeutic effect of a drug propagates through a protein-protein interaction network to reverse disease states. ProBeNet prioritizes biomarkers by considering the following: i) therapy-targeted proteins, ii) disease-specific molecular signatures, and iii) an underlying network of interactions among cellular components (the human interactome). With ProBeNet, biomarkers were discovered predicting patient responses to both an established autoimmune therapy (infliximab) and an investigational compound (a mitogen-activated protein kinase 3/1 inhibitor). The predictive power of ProBeNet biomarkers was validated with retrospective gene-expression data from patients with ulcerative colitis and rheumatoid arthritis and prospective data from patient-derived tissues from patients with ulcerative colitis and Crohn disease. Machine-learning models using ProBeNet biomarkers significantly outperformed models using either all genes or randomly selected genes, especially when data were limited (<20 samples). These results illustrate the value of ProBeNet for reducing features and for constructing robust machine-learning models when limited data are available. ProBeNet may be used to develop companion and complementary diagnostic assays for complex autoimmune disease therapies, which may help stratify suitable patient subgroups in clinical trials, approve new drugs, and improve patient outcomes.
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A 2021 study described the development and validation of a blood-based precision medicine test called the molecular signature response classifier (MSRC) that uses 23 features to identify rheumatoid arthritis (RA) patients who are likely nonresponders to tumor necrosis factor-α inhibitor (TNFi) therapy. Both the gene expression features and clinical components (sex, body mass index, patient global assessment, and anti-cyclic citrullinated protein) included in the MSRC were statistically significant contributors to MSRC results. In response to continued inquiries on this topic, we write this letter to provide additional insights into the contribution of clinical components to the MSRC on the Network-004 validation cohort.
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This cross-cohort study aimed to (1) determine a network-based molecular signature that predicts the likelihood of inadequate response to the tumor necrosis factor-É inhibitor (TNFi) therapy, infliximab, in ulcerative colitis (UC) patients, and (2) address biomarker irreproducibility across different cohort studies. Whole-transcriptome microarray data were derived from biopsies of affected colon tissue from 2 cohorts of infliximab-treated UC patients (training N = 24 and validation N = 22). Response was defined as endoscopic and histologic healing at 4-6 weeks and 8 weeks, respectively. From the training cohort, genes with RNA expression that significantly correlated with clinical response outcomes were mapped onto the Human Interactome network map of protein-protein interactions to identify a largest connected component (LCC) of proteins indicative of infliximab response status in UC. Expression levels of transcripts within the LCC were fed into a probabilistic neural network model to generate a classifier that predicts inadequate response to infliximab. A classifier predictive of inadequate response to infliximab was generated and tested in a cross-cohort, blinded fashion; the AUC was 0.83 and inadequate response was predicted with a 100% positive predictive value and 64% sensitivity. Genes separately identified from the 2 cohorts that correlated with response to infliximab appeared distinct but mapped onto the same network region of the Human Interactome, reflecting a common underlying biology of response among UC patients. Cross-cohort validation of a classifier predictive of infliximab response status in UC patients indicates that a molecular signature of non-response to TNFi therapies is present in patients' baseline gene expression data. The goal is to develop a diagnostic test that predicts which patients will have an inadequate response to targeted therapies and define new targets and pathways for therapeutic development.
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Colite Ulcerativa , Anticorpos Monoclonais/uso terapêutico , Biomarcadores/metabolismo , Estudos de Coortes , Colite Ulcerativa/tratamento farmacológico , Colite Ulcerativa/genética , Humanos , Infliximab/genética , Infliximab/uso terapêutico , Transcriptoma , Resultado do TratamentoRESUMO
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the authors after consulting with the Editors. During a follow-up study, the authors regretfully discovered that the microarray probe-to-gene mapping was incorrect. Although the methodology and primary findings remain the same, the identity of the biomarker genes are incorrect as a result of this honest mistake. The extent of the changes to correct this information necessitated the publication of a corrected version of this article: https://doi.org/10.1016/j.trsl.2022.03.006.
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Colite Ulcerativa/tratamento farmacológico , Colite Ulcerativa/genética , Expressão Gênica/efeitos dos fármacos , Infliximab/uso terapêutico , Área Sob a Curva , Biomarcadores , Estudos de Casos e Controles , Colite Ulcerativa/metabolismo , Fármacos Gastrointestinais/uso terapêutico , Humanos , Mucosa Intestinal/efeitos dos fármacos , Mapas de Interação de Proteínas/genética , Reprodutibilidade dos Testes , Resultado do TratamentoRESUMO
Tumor necrosis factor-[Formula: see text] inhibitors (TNFi) have been a standard treatment in ulcerative colitis (UC) for nearly 20 years. However, insufficient response rate to TNFi therapies along with concerns around their immunogenicity and inconvenience of drug delivery through injections calls for development of UC drugs targeting alternative proteins. Here, we propose a multi-omic network biology method for prioritization of protein targets for UC treatment. Our method identifies network modules on the Human Interactome-a network of protein-protein interactions in human cells-consisting of genes contributing to the predisposition to UC (Genotype module), genes whose expression needs to be modulated to achieve low disease activity (Response module), and proteins whose perturbation alters expression of the Response module genes to a healthy state (Treatment module). Targets are prioritized based on their topological relevance to the Genotype module and functional similarity to the Treatment module. We demonstrate utility of our method in UC and other complex diseases by efficiently recovering the protein targets associated with compounds in clinical trials and on the market . The proposed method may help to reduce cost and time of drug development by offering a computational screening tool for identification of novel and repurposing therapeutic opportunities in UC and other complex diseases.
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Colite Ulcerativa , Humanos , Colite Ulcerativa/tratamento farmacológico , Colite Ulcerativa/genética , Multiômica , Biologia Computacional/métodosRESUMO
BACKGROUND: The molecular signature response classifier (MSRC) predicts tumor necrosis factor-É inhibitor (TNFi) non-response in rheumatoid arthritis. This study evaluates decision-making, validity, and utility of MSRC testing. METHODS: This comparative cohort study compared an MSRC-tested arm (N = 627) from the Study to Accelerate Information of Molecular Signatures (AIMS) with an external control arm (N = 2721) from US electronic health records. Propensity score matching was applied to balance baseline characteristics. Patients initiated a biologic/targeted synthetic disease-modifying antirheumatic drug, or continued TNFi therapy. Odds ratios (ORs) for six-month response were calculated based on clinical disease activity index (CDAI) scores for low disease activity/remission (CDAI-LDA/REM), remission (CDAI-REM), and minimally important differences (CDAI-MID) . RESULTS: In MSRC-tested patients, 59% had a non-response signature and 70% received MSRC-aligned therapy . In TNFi-treated patients, the MSRC had an 88% PPV and 54% sensitivity. MSRC-guided patients were significantly (p < 0.0001) more likely to respond to b/tsDMARDs than those treated according to standard care (CDAI-LDA/REM: 36.0% vs 21.9%, OR 2.01[1.55-2.60]; CDAI-REM: 10.4% vs 3.6%, OR 3.14 [1.94-5.08]; CDAI-MID: 49.5% vs 32.8%, OR 2.01[1.58-2.55]). CONCLUSION: MSRC clinical validity supports high clinical utility: guided treatment selection resulted in significantly superior outcomes relative to standard care; nearly three times more patients reached CDAI remission.
Clinicians can offer rheumatoid arthritis patients many types of therapies but the response rate for each of these drugs is low. For example, within the first year of treatment, just about one-half of patients respond to the first-line drug, csDMARD. Only one-third of methotrexate-unresponsive patients will respond to the most common second-line agent, a tumor necrosis factor-α inhibitor. These low response rates present a critical challenge to treating patients. Clinicians try different cs- and b/tsDMARD and fail to quickly identify the most effective options. Then, disease will progress, irreversibly destroying patient joints, diminishing patient health-related quality of life, and increasing risks of cardiovascular disease, cancer, and death. To help clinicians quickly identify the best drugs for patients in a treat-to-target approach, a precision-medicine test was developed to identify patients unlikely to respond to tumor necrosis factor-α inhibitors. This molecular signature response classifier considers both molecular features (patient RNA-expression levels) and clinical features (e.g. body mass index, sex) to predict patient response. To evaluate the effectiveness of this test, the outcomes of patients treated with classifier-selected drugs (in a large, tested cohort) were compared with outcomes of patients treated with conventionally selected therapies (in an external cohort of electronic-health-record data). Patients treated with classifier-selected therapies were approximately three times as likely to achieve remission than were patients treated with conventionally selected drugs. These results suggest that this molecular signature response classifier is a valuable tool for more quickly identifying optimal therapies to treat rheumatoid arthritis.
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BACKGROUND: The incidence of cystic fibrosis (CF) and the frequency of specific disease-causing mutations vary among populations. Affected individuals experience a range of serious clinical consequences, notably lung and pancreatic disease, which are only partially dependent on genotype. METHODS: An allele-specific primer-extension reaction, liquid-phase hybridization to a bead array, and subsequent fluorescence detection were used in testing for carriers of 98 CFTR [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)] mutations among 364 890 referred individuals with no family history of CF. RESULTS: One in 38 individuals carried one of the 98 CFTR mutations included in this panel. Of the 87 different mutations detected, 18 were limited to a single ethnic group. African American, Hispanic, and Asian individuals accounted for 33% of the individuals tested. The mutation frequency distribution of Caucasians was significantly different from that of each of these ethnic groups (P < 1 × 10⻹°). CONCLUSIONS: Carrier testing using a broad mutation panel detects differences in the distribution of mutations among ethnic groups in the US.
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Regulador de Condutância Transmembrana em Fibrose Cística/genética , Fibrose Cística/genética , Testes Genéticos , Adolescente , Negro ou Afro-Americano , Ásia/etnologia , Povo Asiático , América Central/etnologia , Criança , Fibrose Cística/etnologia , Feminino , Genótipo , Heterozigoto , Hispânico ou Latino , Humanos , Judeus , Masculino , Mutação , América do Sul/etnologia , Estados Unidos/epidemiologia , População BrancaRESUMO
OBJECTIVES: This study reports analytical and clinical validation of a molecular signature response classifier (MSRC) that identifies rheumatoid arthritis (RA) patients who are non-responders to tumor necrosis factor-É inhibitors (TNFi). METHODS: The MSRC integrates patient-specific data from 19 gene expression features, anti-cyclic citrullinated protein serostatus, sex, body mass index, and patient global assessment into a single score. RESULTS: The MSRC results stratified samples (N = 174) according to non-response prediction with a positive predictive value of 87.7% (95% CI: 78-94%), sensitivity of 60.2% (95% CI: 50-69%), and specificity of 77.3% (95% CI: 65-87%). The 25-point scale was subdivided into three thresholds: signal not detected (<10.6), high (≥10.6), and very high (≥18.5). The MSRC relies on sequencing of RNA extracted from blood; this assay displays high gene expression concordance between inter- and intra-assay sample (R2 > 0.977) and minimal variation in cumulative gene assignment diversity, read mapping location, or gene-body coverage. The MSRC accuracy was 95.8% (46/48) for threshold concordance (no signal, high, very high). Intra- and inter-assay precision studies demonstrated high repeatability (92.6%, 25/27) and reproducibility (100%, 35/35). CONCLUSION: The MSRC is a robust assay that accurately and reproducibly detects an RA patient's molecular signature of non-response to TNFi therapies.
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Antirreumáticos , Artrite Reumatoide , Antirreumáticos/uso terapêutico , Artrite Reumatoide/diagnóstico , Artrite Reumatoide/tratamento farmacológico , Artrite Reumatoide/genética , Humanos , Valor Preditivo dos Testes , RNA , Reprodutibilidade dos Testes , Análise de Sequência de RNARESUMO
This study describes two complementary methods that use network-based and sequence similarity tools to identify drug repurposing opportunities predicted to modulate viral proteins. This approach could be rapidly adapted to new and emerging viruses. The first method built and studied a virus-host-physical interaction network; a three-layer multimodal network of drug target proteins, human protein-protein interactions, and viral-host protein-protein interactions. The second method evaluated sequence similarity between viral proteins and other proteins, visualized by constructing a virus-host-similarity interaction network. Methods were validated on the human immunodeficiency virus, hepatitis B, hepatitis C, and human papillomavirus, then deployed on SARS-CoV-2. Comparison of virus-host-physical interaction predictions to known antiviral drugs had AUCs of 0.69, 0.59, 0.78, and 0.67, respectively, reflecting that the scores are predictive of effective drugs. For SARS-CoV-2, 569 candidate drugs were predicted, of which 37 had been included in clinical trials for SARS-CoV-2 (AUC = 0.75, P-value 3.21 × 10-3). As further validation, top-ranked candidate antiviral drugs were analyzed for binding to protein targets in silico; binding scores generated by BindScope indicated a 70% success rate.
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Antivirais/uso terapêutico , Tratamento Farmacológico da COVID-19 , Reposicionamento de Medicamentos , SARS-CoV-2/fisiologia , Biologia de Sistemas , Antivirais/farmacologia , Ensaios Clínicos como Assunto , Simulação por Computador , Ontologia Genética , Interações Hospedeiro-Patógeno/efeitos dos fármacos , Humanos , Curva ROC , SARS-CoV-2/efeitos dos fármacos , Proteínas Virais/metabolismoRESUMO
INTRODUCTION: Timely matching of patients to beneficial targeted therapy is an unmet need in rheumatoid arthritis (RA). A molecular signature response classifier (MSRC) that predicts which patients with RA are unlikely to respond to tumor necrosis factor-α inhibitor (TNFi) therapy would have wide clinical utility. METHODS: The protein-protein interaction map specific to the rheumatoid arthritis pathophysiology and gene expression data in blood patient samples was used to discover a molecular signature of non-response to TNFi therapy. Inadequate response predictions were validated in blood samples from the CERTAIN cohort and a multicenter blinded prospective observational clinical study (NETWORK-004) among 391 targeted therapy-naïve and 113 TNFi-exposed patient samples. The primary endpoint evaluated the ability of the MSRC to identify patients who inadequately responded to TNFi therapy at 6 months according to ACR50. Additional endpoints evaluated the prediction of inadequate response at 3 and 6 months by ACR70, DAS28-CRP, and CDAI. RESULTS: The 23-feature molecular signature considers pathways upstream and downstream of TNFα involvement in RA pathophysiology. Predictive performance was consistent between the CERTAIN cohort and NETWORK-004 study. The NETWORK-004 study met primary and secondary endpoints. A molecular signature of non-response was detected in 45% of targeted therapy-naïve patients. The MSRC had an area under the curve (AUC) of 0.64 and patients were unlikely to adequately respond to TNFi therapy according to ACR50 at 6 months with an odds ratio of 4.1 (95% confidence interval 2.0-8.3, p value 0.0001). Odds ratios (3.4-8.8) were significant (p value < 0.01) for additional endpoints at 3 and 6 months, with AUC values up to 0.74. Among TNFi-exposed patients, the MSRC had an AUC of up to 0.83 and was associated with significant odds ratios of 3.3-26.6 by ACR, DAS28-CRP, and CDAI metrics. CONCLUSION: The MSRC stratifies patients according to likelihood of inadequate response to TNFi therapy and provides patient-specific data to guide therapy choice in RA for targeted therapy-naïve and TNFi-exposed patients.
A blood-based molecular signature response classifier (MSRC) integrating next-generation RNA sequencing data with clinical features predicts the likelihood that a patient with rheumatoid arthritis will have an inadequate response to TNFi therapy. Treatment selection guided by test results, with likely inadequate responders appropriately redirected to a different therapy, could improve response rates to TNFi therapies, generate healthcare cost savings, and increase rheumatologists' confidence in prescribing decisions and altered treatment choices. The MSRC described in this study predicts the likelihood of inadequate response to TNFi therapies among targeted therapy-naïve and TNFi-exposed patients in a multicenter, 24-week blinded prospective clinical study: NETWORK-004. Patients with a molecular signature of non-response are less likely to have an adequate response to TNFi therapies than those patients lacking the signature according to ACR50, ACR70, CDAI, and DAS28-CRP with significant odds ratios of 3.48.8 for targeted therapy-naïve patients and 3.326.6 for TNFi-exposed patients. This MSRC provides a solution to the long-standing need for precision medicine tools to predict drug response in rheumatoid arthritisa heterogeneous and progressive disease with an abundance of therapeutic options. These data validate the performance of the MSRC in a blinded prospective clinical study of targeted therapy-naïve and TNFi therapy-exposed patients.
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Prostate-specific antigen (PSA) screening for prostate cancer (PCa) is limited by the lack of specificity but is further complicated in the benign prostatic hyperplasia (BPH) population which also exhibit elevated PSA, representing a clear unmet need to distinguish BPH from PCa. Herein, we evaluated the utility of FLNA IP-MRM, age, and prostate volume to stratify men with BPH from those with PCa. Diagnostic performance of the biomarker panel was better than PSA alone in discriminating patients with negative biopsy from those with PCa, as well as those who have had multiple prior biopsies (AUC 0.75 and 0.87 compared to AUC of PSA alone 0.55 and 0.57 for patients who have had single compared to multiple negative biopsies, respectively). Of interest, in patients with PCa, the panel demonstrated improved performance than PSA alone in those with Gleason scores of 5-7 (AUC 0.76 vs. 0.56) and Gleason scores of 8-10 (AUC 0.74 vs. 0.47). With Gleason scores (8-10), the negative predictive value of the panel is 0.97, indicating potential to limit false negatives in aggressive cancers. Together, these data demonstrate the ability of the biomarker panel to perform better than PSA alone in men with BPH, thus preventing unnecessary biopsies.
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Biomarcadores Tumorais/sangue , Diagnóstico Diferencial , Hiperplasia Prostática/diagnóstico , Neoplasias da Próstata/diagnóstico , Idoso , Humanos , Masculino , Pessoa de Meia-Idade , Gradação de Tumores , Próstata/metabolismo , Antígeno Prostático Específico/sangue , Hiperplasia Prostática/sangue , Hiperplasia Prostática/patologia , Neoplasias da Próstata/sangue , Neoplasias da Próstata/patologiaRESUMO
Reactive oxygen species (ROS) are implicated in triggering cell signalling events and pathways to promote and maintain tumorigenicity. Chemotherapy and radiation can induce ROS to elicit cell death allows for targeting ROS pathways for effective anti-cancer therapeutics. Coenzyme Q10 is a critical cofactor in the electron transport chain with complex biological functions that extend beyond mitochondrial respiration. This study demonstrates that delivery of oxidized Coenzyme Q10 (ubidecarenone) to increase mitochondrial Q-pool is associated with an increase in ROS generation, effectuating anti-cancer effects in a pancreatic cancer model. Consequent activation of cell death was observed in vitro in pancreatic cancer cells, and both human patient-derived organoids and tumour xenografts. The study is a first to demonstrate the effectiveness of oxidized ubidecarenone in targeting mitochondrial function resulting in an anti-cancer effect. Furthermore, these findings support the clinical development of proprietary formulation, BPM31510, for treatment of cancers with high ROS burden with potential sensitivity to ubidecarenone.
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Apoptose , Mitocôndrias/metabolismo , Neoplasias Pancreáticas/patologia , Espécies Reativas de Oxigênio/metabolismo , Ubiquinona/análogos & derivados , Animais , Linhagem Celular Tumoral , Proliferação de Células , Respiração Celular , Sobrevivência Celular , Complexo II de Transporte de Elétrons/metabolismo , Glicerol-3-Fosfato Desidrogenase (NAD+) , Humanos , Potencial da Membrana Mitocondrial , Camundongos Nus , Organoides/patologia , Estresse Oxidativo , Consumo de Oxigênio , Neoplasias Pancreáticas/metabolismo , Especificidade por Substrato , Ubiquinona/metabolismoRESUMO
Pompe disease is an autosomal recessive lysosomal storage disorder (LSD) caused by deficiency of lysosomal acid alpha-glucosidase (GAA) activity. This is the first LSD in which newborn screening has been shown to improve clinical outcomes. Newborn screening also identified multiple rare gene variants in this population. Among 132,538 newborns screened, 107 babies (1 in 1239) who had low dried blood spot GAA activity were genotyped. Sixty-nine (64.5%) babies had a total of 54 mutations and 35 novel predictably pathogenic mutations; 36 babies (33.6%) who had no mutation were homozygous for the c.[1726A; 2065A] pseudodeficiency allele. Because 81% of the chromosomes (14% in the controls) were in haplotype *03, we found a link between the pseudodeficiency allele and other mutated alleles. The newborns with Pompe disease detected by screening had lymphocyte GAA activities 0.45 to 1.65 nmol/mg/h (normal 66.7+/-33.8), while only 2 of the 100 false-positive cases had GAA activity less than 2.00 nmol/mg/h (or 3% of the normal mean). Therefore, newborn screening for Pompe disease could be successfully conducted by including genotyping and lymphocyte GAA assay, even in a population with mutation heterozygosity and pseudodeficiency.
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Doença de Depósito de Glicogênio Tipo II/diagnóstico , Doença de Depósito de Glicogênio Tipo II/genética , Triagem Neonatal , alfa-Glucosidases/análise , alfa-Glucosidases/genética , Reações Falso-Positivas , Estudos de Viabilidade , Genótipo , Doença de Depósito de Glicogênio Tipo II/sangue , Haplótipos , Humanos , Recém-Nascido , Mutação , Projetos PilotoRESUMO
Structural learning of Bayesian networks (BNs) from observational data has gained increasing applied use and attention from various scientific and industrial areas. The mathematical theory of BNs and their optimization is well developed. Although there are several open-source BN learners in the public domain, none of them are able to handle both small and large feature space data and recover network structures with acceptable accuracy. bAIcis® is a novel BN learning and simulation software from BERG. It was developed with the goal of learning BNs from "Big Data" in health care, often exceeding hundreds of thousands features when research is conducted in genomics or multi-omics. This article provides a comprehensive performance evaluation of bAIcis and its comparison with the open-source BN learners. The study investigated synthetic datasets of discrete, continuous, and mixed data in small and large feature space, respectively. The results demonstrated that bAIcis outperformed the publicly available algorithms in structure recovery precision in almost all of the evaluated settings, achieving the true positive rates of 0.9 and precision of 0.8. In addition, bAIcis supports all data types, including continuous, discrete, and mixed variables. It is effectively parallelized on a distributed system and can work with datasets of thousands of features that are infeasible for any of the publicly available tools with a desired level of recovery accuracy.
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Teorema de Bayes , Genômica/métodos , Software , Algoritmos , Simulação por Computador , Perfilação da Expressão Gênica/métodos , HumanosRESUMO
Early diagnosis of sepsis and septic shock has been unambiguously linked to lower mortality and better patient outcomes. Despite this, there is a strong unmet need for a reliable clinical tool that can be used for large-scale automated screening to identify high-risk patients. We addressed the following questions: Can a novel algorithm to identify patients at high risk of septic shock 24 hours before diagnosis be discovered using available clinical data? What are performance characteristics of this predictive algorithm? Can current metrics for evaluation of sepsis be improved using novel algorithm? Publicly available data from the intensive care unit setting was used to build septic shock and control patient cohorts. Using Bayesian networks, causal relationships between diagnosis groups, procedure groups, laboratory results, and demographic data were inferred. Predictive model for septic shock 24 hours prior to digital diagnosis was built based on inferred causal networks. Sepsis risk scores were augmented by de novo inferred model and performance was evaluated. A novel predictive model to identify high-risk patients 24 hours ahead of time, with area under curve of 0.81, negative predictive value of 0.87, and a positive predictive value as high as 0.65 was built. The specificity of quick sequential organ failure assessment, systemic inflammatory response syndrome, and modified early warning score was improved when augmented with the novel model, whereas no improvements were made to the sequential organ failure assessment score. We used a data-driven, expert knowledge agnostic method to build a screening algorithm for early detection of septic shock. The model demonstrates strong performance in the data set used and provides a basis for expanding this work toward building an algorithm that is used to screen patients based on electronic medical record data in real time.
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Serial analysis of gene expression (SAGE) is a powerful technique for measuring global gene expression through sampling of transcript tags. SAGE tag collections or libraries serve as a rich data source for differential gene expression analysis, transcriptome mapping, and gene discovery. Transcriptome mapping and gene discovery are facilitated by extensions of SAGE, e.g., Long SAGE, where the transcript tags are elongated by utilization of a different tagging enzyme. SAGE, as a sequencing-based technique, is prone to errors resulting in artifact SAGE tag sequences and erroneous tag numbers. A methodology to pinpoint and correct tag artifacts is necessary to fully exploit the value of large SAGE libraries. SAGEScreen is a tag sequence correction algorithm. The algorithm is a multistep procedure that addresses error rates and performs ditag and tag processing. The error rate estimates are based on a stochastic model of PCR and sequencing related mutations. The ditag processing step is essential for calculation of unbiased tag numbers, and the tag processing step allows for filtration of tag sequence artifacts and adjustment of tag numbers.
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Perfilação da Expressão Gênica/estatística & dados numéricos , Algoritmos , Etiquetas de Sequências Expressas , Biblioteca Gênica , Reação em Cadeia da Polimerase , Análise de Sequência de DNA , Design de SoftwareRESUMO
Coiled-Coil Domain Containing 47 (CCDC47) is an endoplasmic reticulum (ER) transmembrane protein involved in calcium signaling through utilization of its calcium binding-acidic luminal domain. CCDC47 also interacts with ERAD (endoplasmic reticulum-associated degradation) complex and is involved in ER stress relief. In this report, we developed human CCDC47 monoclonal antibodies and a sandwich immunoassay for CCDC47 measurement in biological matrices. Specificity of developed antibodies were confirmed by immunoblot and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of immunoprecipitated cell lysates. To achieve high analytical sensitivity, traditional colorimetric enzyme-linked immunosorbent assay (ELISA) and electrochemiluminescence (ECL) technology were compared, and 3 logs of increased sensitivity was observed with the use of ECL. A CCDC47 sandwich ECL assay was subsequently developed and performances evaluated for calibration curves, precision and accuracy, as well as selectivity and interferences for sample measurement. Sample stability was also characterized for freeze/thaw cycles and short/long term storage conditions.