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Discovery of rare coding variants in OGDHL and BRCA2 in relation to breast cancer risk in Chinese women.
Guo X, Long J, Chen Z, Shu XO, Xiang YB, Wen W, Zeng C, Gao YT, Cai Q, Zheng W
(2020) Int J Cancer 146: 2175-2181
MeSH Terms: Adult, Aged, BRCA2 Protein, Breast Neoplasms, Case-Control Studies, China, Databases, Genetic, Female, Gene Frequency, Genetic Predisposition to Disease, Humans, Ketoglutarate Dehydrogenase Complex, Middle Aged, Mutation, Missense, Whole Exome Sequencing
Show Abstract · Added March 3, 2020
The missing heritability of breast cancer could be partially attributed to rare variants (MAF < 0.5%). To identify breast cancer-associated rare coding variants, we conducted whole-exome sequencing (~50×) in genomic DNA samples obtained from 831 breast cancer cases and 839 controls of Chinese females. Using burden tests for each gene that included rare missense or predicted deleterious variants, we identified 29 genes showing promising associations with breast cancer risk. We replicated the association for two genes, OGDHL and BRCA2, at a Bonferroni-corrected p < 0.05, by genotyping an independent set of samples from 1,628 breast cancer cases and 1,943 controls. The association for OGDHL was primarily driven by three predicted deleterious variants (p.Val827Met, p.Pro839Leu, p.Phe836Ser; p < 0.01 for all). For BRCA2, we characterized a total of 27 disruptive variants, including 18 nonsense, six frameshift and three splicing variants, whereas they were only detected in cases, but none of the controls. All of these variants were either very rare (AF < 0.1%) or not detected in >4,500 East Asian women from the genome Aggregation database (gnomAD), providing additional support to our findings. Our study revealed a potential novel gene and multiple disruptive variants of BRCA2 for breast cancer risk, which may identify high-risk women in Chinese populations.
© 2019 UICC.
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15 MeSH Terms
The Incidence of Laryngotracheal Stenosis in Neonates With a History of Ventilator-Associated Pneumonia.
Lowery AS, Gelbard A, Wootten C
(2020) Laryngoscope 130: 2252-2255
MeSH Terms: Bronchoalveolar Lavage, Bronchoalveolar Lavage Fluid, Case-Control Studies, Female, Humans, Incidence, Infant, Newborn, Intensive Care Units, Neonatal, Laryngostenosis, Male, Pneumonia, Ventilator-Associated, Retrospective Studies, Risk Factors, Tracheal Stenosis
Show Abstract · Added July 30, 2020
OBJECTIVES/HYPOTHESIS - Neonatal patients requiring prolonged intubation are susceptible to both infection and laryngotracheal stenosis (LTS). This study investigated the effect of ventilator-associated pneumonia (VAP) on the development of LTS in neonates.
STUDY DESIGN - Retrospective case-control study.
METHODS - The incidence of LTS in neonates with VAP was compared with the incidence of LTS in matched intubated controls without VAP. Patients were treated at a tertiary-care medical center from 2004 to 2014. Eligible patient records were assessed for the development of LTS. Demographics, medical comorbidities, infection characteristics, and treatment variables were compared using unpaired t test or χ test. Statistical significance was set a priori at P < .05.
RESULTS - When comparing the VAP patients with matched non-VAP controls, we found no significant differences in the incidence of LTS (VAP vs. non-VAP, 8.3% vs. 6.7%; P = .73). In subgroup analysis of the VAP cohort, LTS and non-LTS patients demonstrated similar VAP organisms on broncho-alveolar lavage (Klebsiella pneumoniae, Pseudomonas aeroginosa, Escherichia coli, methicillin-resistant Staphylococcus aureus, Streptococcus pneumoniae, and Enterobacter). Additionally, within the VAP cohort, LTS and non-LTS patients showed similar gestational age (LTS vs. non-LTS, 31.3 days vs. 28.1 days; P = .22), birth weight (LTS vs. non-LTS, 1.6 kg vs. 1.2 kg; P = .33), and similar intubation duration (LTS vs. non-LTS, 37.8 days vs. 27.5 days; P = .52).
CONCLUSIONS - In this neonatal cohort, VAP was not associated with an increased incidence of LTS. Given severity of the burden of LTS on the healthcare system, multi-institutional longitudinal investigation into contributing risk factors for neonatal LTS is warranted.
LEVEL OF EVIDENCE - NA Laryngoscope, 130:2252-2255, 2020.
© 2019 The American Laryngological, Rhinological and Otological Society, Inc.
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14 MeSH Terms
Hyperactivity and Reduced Activation of Anterior Hippocampus in Early Psychosis.
McHugo M, Talati P, Armstrong K, Vandekar SN, Blackford JU, Woodward ND, Heckers S
(2019) Am J Psychiatry 176: 1030-1038
MeSH Terms: Case-Control Studies, Female, Hippocampus, Humans, Magnetic Resonance Imaging, Male, Photic Stimulation, Schizophrenia, Time Factors, Young Adult
Show Abstract · Added January 31, 2020
OBJECTIVE - In schizophrenia, the anterior hippocampus is hyperactive and shows reduced task-related recruitment, but the relationship between these two findings is unclear. The authors tested the hypothesis that hyperactivity impairs recruitment of the anterior hippocampus during scene processing.
METHODS - Functional MRI data from 45 early-psychosis patients and 35 demographically matched healthy control subjects were analyzed using a block-design 1-back scene-processing task. Hippocampal activation in response to scenes and faces compared with scrambled images was measured. In a subset of 20 early-psychosis patients and 31 healthy control subjects, baseline hippocampal activity using cerebral blood volume (CBV) mapping was measured. Correlation analyses were used to examine the association between baseline hippocampal activity and task-related hippocampal activation.
RESULTS - Activation of the anterior hippocampus was significantly reduced and CBV in the anterior hippocampus was significantly increased in the early stages of psychosis. Increased CBV in early-psychosis patients was inversely correlated with task-related activation during scene processing in the anterior hippocampus.
CONCLUSIONS - Anterior hippocampal hyperactivity in early-psychosis patients appears to limit effective recruitment of this region during task performance. These findings provide novel support for the anterior hippocampus as a therapeutic target in the treatment of cognitive deficits in psychosis.
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10 MeSH Terms
Genome-Wide Association Study of Apparent Treatment-Resistant Hypertension in the CHARGE Consortium: The CHARGE Pharmacogenetics Working Group.
Irvin MR, Sitlani CM, Floyd JS, Psaty BM, Bis JC, Wiggins KL, Whitsel EA, Sturmer T, Stewart J, Raffield L, Sun F, Liu CT, Xu H, Cupples AL, Tanner RM, Rossing P, Smith A, Zilhão NR, Launer LJ, Noordam R, Rotter JI, Yao J, Li X, Guo X, Limdi N, Sundaresan A, Lange L, Correa A, Stott DJ, Ford I, Jukema JW, Gudnason V, Mook-Kanamori DO, Trompet S, Palmas W, Warren HR, Hellwege JN, Giri A, O'donnell C, Hung AM, Edwards TL, Ahluwalia TS, Arnett DK, Avery CL
(2019) Am J Hypertens 32: 1146-1153
MeSH Terms: African Americans, Aged, Antihypertensive Agents, Blood Pressure, Case-Control Studies, DNA (Cytosine-5-)-Methyltransferases, DNA-Binding Proteins, Drug Resistance, Dystrophin-Associated Proteins, Europe, European Continental Ancestry Group, Female, Genetic Loci, Genome-Wide Association Study, Humans, Hypertension, Male, Middle Aged, Myosin Heavy Chains, Myosin Type V, Neuropeptides, Pharmacogenetics, Pharmacogenomic Variants, Polymorphism, Single Nucleotide, Risk Assessment, Risk Factors, Transcription Factors, United States
Show Abstract · Added March 3, 2020
BACKGROUND - Only a handful of genetic discovery efforts in apparent treatment-resistant hypertension (aTRH) have been described.
METHODS - We conducted a case-control genome-wide association study of aTRH among persons treated for hypertension, using data from 10 cohorts of European ancestry (EA) and 5 cohorts of African ancestry (AA). Cases were treated with 3 different antihypertensive medication classes and had blood pressure (BP) above goal (systolic BP ≥ 140 mm Hg and/or diastolic BP ≥ 90 mm Hg) or 4 or more medication classes regardless of BP control (nEA = 931, nAA = 228). Both a normotensive control group and a treatment-responsive control group were considered in separate analyses. Normotensive controls were untreated (nEA = 14,210, nAA = 2,480) and had systolic BP/diastolic BP < 140/90 mm Hg. Treatment-responsive controls (nEA = 5,266, nAA = 1,817) had BP at goal (<140/90 mm Hg), while treated with one antihypertensive medication class. Individual cohorts used logistic regression with adjustment for age, sex, study site, and principal components for ancestry to examine the association of single-nucleotide polymorphisms with case-control status. Inverse variance-weighted fixed-effects meta-analyses were carried out using METAL.
RESULTS - The known hypertension locus, CASZ1, was a top finding among EAs (P = 1.1 × 10-8) and in the race-combined analysis (P = 1.5 × 10-9) using the normotensive control group (rs12046278, odds ratio = 0.71 (95% confidence interval: 0.6-0.8)). Single-nucleotide polymorphisms in this locus were robustly replicated in the Million Veterans Program (MVP) study in consideration of a treatment-responsive control group. There were no statistically significant findings for the discovery analyses including treatment-responsive controls.
CONCLUSION - This genomic discovery effort for aTRH identified CASZ1 as an aTRH risk locus.
© American Journal of Hypertension, Ltd 2019. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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28 MeSH Terms
Addressing Limitations in Case-Control Study of Patients Undergoing Resuscitative Endovascular Balloon Occlusion of the Aorta.
Guidry CA, Peetz AB, Patel MB
(2019) JAMA Surg 154: 1165-1166
MeSH Terms: Aorta, Balloon Occlusion, Case-Control Studies, Humans, Resuscitation
Added September 2, 2019
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5 MeSH Terms
High prevalence of antibiotic allergies in cladribine-treated patients with hairy cell leukemia - lessons for immunopathogenesis and prescribing.
Meher-Homji Z, Tam CS, Siderov J, Seymour JF, Holmes NE, Chua KYL, Phillips EJ, Slavin MA, Trubiano JA
(2019) Leuk Lymphoma 60: 3455-3460
MeSH Terms: Adult, Aged, Anti-Bacterial Agents, Antineoplastic Combined Chemotherapy Protocols, Australia, Case-Control Studies, Cladribine, Drug Hypersensitivity, Female, Follow-Up Studies, Humans, Leukemia, Hairy Cell, Male, Middle Aged, Prevalence, Prognosis, Retrospective Studies, Survival Rate, Vidarabine
Show Abstract · Added March 30, 2020
The relationship between hematological malignancy and chemotherapy on the prevalence of antibiotic allergy label (AAL) is ill-defined. We performed a multicenter retrospective case-control study comparing AAL rates among cladribine-treated hairy cell leukemia (C-HCL) cases, non-HCL cladribine-treated controls (control-1), and fludarabine-treated controls (control-2). The prevalence of AALs in C-HCL patients was 60%, compared with control-1 (14%,  < .01) and control-2 patients (25%,  < .01). The predominant phenotype was maculopapular exanthem (92%). The drugs implicated in AAL causality in C-HCL patients included beta-lactams (81%), trimethoprim-sulfamethoxazole (58%), and allopurinol (69%). C-HCL patients demonstrate high rates of AAL, potentially due to immune dysregulation, impacting beta-lactam utilization.
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19 MeSH Terms
Geospatial analyses identify regional hot spots of diffuse gastric cancer in rural Central America.
Dominguez RL, Cherry CB, Estevez-Ordonez D, Mera R, Escamilla V, Pawlita M, Waterboer T, Wilson KT, Peek RM, Tavera G, Williams SM, Gulley ML, Emch M, Morgan DR
(2019) BMC Cancer 19: 545
MeSH Terms: Aged, Case-Control Studies, Central America, Disease Susceptibility, Female, Geography, Helicobacter Infections, Helicobacter pylori, Humans, Male, Middle Aged, Risk Assessment, Risk Factors, Rural Health, Spatial Analysis, Stomach Neoplasms
Show Abstract · Added June 10, 2019
BACKGROUND - Geospatial technology has facilitated the discovery of disease distributions and etiology and helped target prevention programs. Globally, gastric cancer is the leading infection-associated cancer, and third leading cause of cancer mortality worldwide, with marked geographic variation. Central and South America have a significant burden, particularly in the mountainous regions. In the context of an ongoing population-based case-control study in Central America, our aim was to examine the spatial epidemiology of gastric cancer subtypes and H. pylori virulence factors.
METHODS - Patients diagnosed with gastric cancer from 2002 to 2013 in western Honduras were identified in the prospective gastric cancer registry at the principal district hospital. Diagnosis was based on endoscopy and confirmatory histopathology. Geospatial methods were applied using the ArcGIS v10.3.1 and SaTScan v9.4.2 platforms to examine regional distributions of the gastric cancer histologic subtypes (Lauren classification), and the H. pylori CagA virulence factor. Getis-Ord-Gi hot spot and Discrete Poisson SaTScan statistics, respectively, were used to explore spatial clustering at the village level (30-50 rural households), with standardization by each village's population. H. pylori and CagA serologic status was determined using the novel H. pylori multiplex assay (DKFZ, Germany).
RESULTS - Three hundred seventy-eight incident cases met the inclusion criteria (mean age 63.7, male 66.3%). Areas of higher gastric cancer incidence were identified. Significant spatial clustering of diffuse histology adenocarcinoma was revealed both by the Getis-Ord-GI* hot spot analysis (P-value < 0.0015; range 0.00003-0.0014; 99%CI), and by the SaTScan statistic (P-value < 0.006; range 0.0026-0.0054). The intestinal subtype was randomly distributed. H. pylori CagA had significant spatial clustering only in association with the diffuse histology cancer hot spot (Getis-Ord-Gi* P value ≤0.001; range 0.0001-0.0010; SaTScan statistic P value 0.0085). In the diffuse gastric cancer hot spot, the lowest age quartile range was 21-46 years, significantly lower than the intestinal cancers (P = 0.024).
CONCLUSIONS - Geospatial methods have identified a significant cluster of incident diffuse type adenocarcinoma cases in rural Central America, suggest of a germline genetic association. Further genomic and geospatial analyses to identify potential spatial patterns of genetic, bacterial, and environmental risk factors may be informative.
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16 MeSH Terms
DNA methylation profiles are associated with complex regional pain syndrome after traumatic injury.
Bruehl S, Gamazon ER, Van de Ven T, Buchheit T, Walsh CG, Mishra P, Ramanujan K, Shaw A
(2019) Pain 160: 2328-2337
MeSH Terms: Adult, Case-Control Studies, Combat Disorders, Complex Regional Pain Syndromes, DNA Methylation, Epigenesis, Genetic, Female, Genetic Profile, Hospitals, Veterans, Humans, Male, Veterans
Show Abstract · Added July 17, 2019
Factors contributing to development of complex regional pain syndrome (CRPS) are not fully understood. This study examined possible epigenetic mechanisms that may contribute to CRPS after traumatic injury. DNA methylation profiles were compared between individuals developing CRPS (n = 9) and those developing non-CRPS neuropathic pain (n = 38) after undergoing amputation following military trauma. Linear Models for Microarray (LIMMA) analyses revealed 48 differentially methylated cytosine-phosphate-guanine dinucleotide (CpG) sites between groups (unadjusted P's < 0.005), with the top gene COL11A1 meeting Bonferroni-adjusted P < 0.05. The second largest differential methylation was observed for the HLA-DRB6 gene, an immune-related gene linked previously to CRPS in a small gene expression study. For all but 7 of the significant CpG sites, the CRPS group was hypomethylated. Numerous functional Gene Ontology-Biological Process categories were significantly enriched (false discovery rate-adjusted q value <0.15), including multiple immune-related categories (eg, activation of immune response, immune system development, regulation of immune system processes, and antigen processing and presentation). Differentially methylated genes were more highly connected in human protein-protein networks than expected by chance (P < 0.05), supporting the biological relevance of the findings. Results were validated in an independent sample linking a DNA biobank with electronic health records (n = 126 CRPS phenotype, n = 19,768 non-CRPS chronic pain phenotype). Analyses using PrediXcan methodology indicated differences in the genetically determined component of gene expression in 7 of 48 genes identified in methylation analyses (P's < 0.02). Results suggest that immune- and inflammatory-related factors might confer risk of developing CRPS after traumatic injury. Validation findings demonstrate the potential of using electronic health records linked to DNA for genomic studies of CRPS.
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12 MeSH Terms
Thalamic arousal network disturbances in temporal lobe epilepsy and improvement after surgery.
González HFJ, Chakravorti S, Goodale SE, Gupta K, Claassen DO, Dawant B, Morgan VL, Englot DJ
(2019) J Neurol Neurosurg Psychiatry 90: 1109-1116
MeSH Terms: Adult, Arousal, Brain Stem, Case-Control Studies, Epilepsy, Temporal Lobe, Female, Functional Neuroimaging, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Neocortex, Neural Pathways, Neurosurgical Procedures, Thalamic Nuclei, Thalamus
Show Abstract · Added June 22, 2019
OBJECTIVE - The effects of temporal lobe epilepsy (TLE) on subcortical arousal structures remain incompletely understood. Here, we evaluate thalamic arousal network functional connectivity in TLE and examine changes after epilepsy surgery.
METHODS - We examined 26 adult patients with TLE and 26 matched control participants and used resting-state functional MRI (fMRI) to measure functional connectivity between the thalamus (entire thalamus and 19 bilateral thalamic nuclei) and both neocortex and brainstem ascending reticular activating system (ARAS) nuclei. Postoperative imaging was completed for 19 patients >1 year after surgery and compared with preoperative baseline.
RESULTS - Before surgery, patients with TLE demonstrated abnormal thalamo-occipital functional connectivity, losing the normal negative fMRI correlation between the intralaminar central lateral (CL) nucleus and medial occipital lobe seen in controls (p < 0.001, paired t-test). Patients also had abnormal connectivity between ARAS and CL, lower ipsilateral intrathalamic connectivity, and smaller ipsilateral thalamic volume compared with controls (p < 0.05 for each, paired t-tests). Abnormal brainstem-thalamic connectivity was associated with impaired visuospatial attention (ρ = -0.50, p = 0.02, Spearman's rho) while lower intrathalamic connectivity and volume were related to higher frequency of consciousness-sparing seizures (p < 0.02, Spearman's rho). After epilepsy surgery, patients with improved seizures showed partial recovery of thalamo-occipital and brainstem-thalamic connectivity, with values more closely resembling controls (p < 0.01 for each, analysis of variance).
CONCLUSIONS - Overall, patients with TLE demonstrate impaired connectivity in thalamic arousal networks that may be involved in visuospatial attention, but these disturbances may partially recover after successful epilepsy surgery. Thalamic arousal network dysfunction may contribute to morbidity in TLE.
© Author(s) (or their employer(s)) 2019. No commercial re-use. See rights and permissions. Published by BMJ.
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16 MeSH Terms
Classifying intracranial stenosis disease severity from functional MRI data using machine learning.
Waddle SL, Juttukonda MR, Lants SK, Davis LT, Chitale R, Fusco MR, Jordan LC, Donahue MJ
(2020) J Cereb Blood Flow Metab 40: 705-719
MeSH Terms: Brain, Case-Control Studies, Cerebral Angiography, Cerebrovascular Circulation, Female, Humans, Image Processing, Computer-Assisted, Machine Learning, Magnetic Resonance Angiography, Middle Aged, Moyamoya Disease, Sensitivity and Specificity, Severity of Illness Index, Young Adult
Show Abstract · Added March 24, 2020
Translation of many non-invasive hemodynamic MRI methods to cerebrovascular disease patients has been hampered by well-known artifacts associated with delayed blood arrival times and reduced microvascular compliance. Using machine learning and support vector machine (SVM) algorithms, we investigated whether arrival time-related artifacts in these methods could be exploited as novel contrast sources to discriminate angiographically confirmed stenotic flow territories. Intracranial steno-occlusive moyamoya patients ( = 53; age = 45 ± 14.2 years; sex = 43 F) underwent (i) catheter angiography, (ii) anatomical MRI, (iii) cerebral blood flow (CBF)-weighted arterial spin labeling, and (iv) cerebrovascular reactivity (CVR)-weighted hypercapnic blood-oxygenation-level-dependent MRI. Mean, standard deviation (std), and 99th percentile of CBF, CVR, CVR, and CVR were calculated in major anterior and posterior flow territories perfused by vessels with vs. without stenosis (≥70%) confirmed by catheter angiography. These and demographic variables were input into SVMs to evaluate discriminatory capacity for stenotic flow territories using k-fold cross-validation and receiver-operating-characteristic-area-under-the-curve to quantify variable combination relevance. Anterior circulation CBF-std, attributable to heterogeneous endovascular signal and prolonged arterial transit times, was the best performing single variable and CVR-mean and CBF-std, both reflective of delayed vascular compliance, were a high-performing two-variable combination (specificity = 0.67; sensitivity = 0.75). Findings highlight the relevance of hemodynamic imaging and machine learning for identifying cerebrovascular impairment.
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14 MeSH Terms