Genetic polymorphisms in lung disease: bandwagon or breakthrough?

The study of genetic polymorphisms has touched every aspect of pulmonary and critical care medicine. We review recent progress made using genetic polymorphisms to define pathophysiology, to identify persons at risk for pulmonary disease and to predict treatment response. Several pitfalls are commonly encountered in studying genetic polymorphisms, and this article points out criteria that should be applied to design high-quality genetic polymorphism studies

Antegrade common femoral artery closure device use is associated with decreased complications.

ObjectiveAntegrade femoral artery access is often used for ipsilateral infrainguinal peripheral vascular intervention. However, the use of closure devices (CD) for antegrade access (AA) is still considered outside the instructions for use for most devices. We hypothesized that CD use for antegrade femoral access would not be associated with an increased odds of access site complications.MethodsThe Vascular Quality Initiative was queried from 2010 to 2019 for infrainguinal peripheral vascular interventions performed via femoral AA. Patients who had a cutdown or multiple access sites were excluded. Cases were then stratified into whether a CD was used or not. Hierarchical multivariable logistic regressions controlling for hospital-level variation were used to examine the independent association between CD use and access site complications. A sensitivity analysis using coarsened exact matching was performed using factors different between treatment groups to reduce imbalance between the groups.ResultsOverall, 11,562 cases were identified and 5693 (49.2%) used a CD. Patients treated with a CD were less likely to be white (74.1% vs 75.2%), have coronary artery disease (29.7% vs 33.4%), use aspirin (68.7% vs 72.4%), and have heparin reversal with protamine (15.5% vs 25.6%; all P < .05). CD patients were more likely to be obese (31.6% vs 27.0%), have an elective operation (82.6% vs 80.1%), ultrasound-guided access (75.5% vs 60.6%), and a larger access sheath (6.0 ± 1.0 F vs 5.5 ± 1.0 F; P < .05 for all). CD cases were less likely to develop any access site hematoma (2.55% vs 3.53%; P < .01) or a hematoma requiring reintervention (0.63% vs 1.26%; P < .01) and had no difference in access site stenosis or occlusion (0.30% vs 0.22%; P = .47) compared with no CD. On multivariable analysis, CD cases had significantly decreased odds of developing any access site hematoma (odds ratio, 0.75; 95% confidence interval, 0.59-0.95) and a hematoma requiring intervention (odds ratio, 0.56; 95% confidence interval, 0.38-0.81). A sensitivity analysis after coarsened exact matching confirmed these findings.ConclusionsIn this nationally representative sample, CD use for AA was associated with a lower odds of hematoma in selected patients. Extending the instructions for use indications for CDs to include femoral AA may decrease the incidence of access site complications, patient exposure to reintervention, and costs to the health care system

Understanding X-ray absorption in liquid water using triple excitations in multilevel coupled cluster theory

X-ray absorption (XA) spectroscopy is an essential experimental tool to investigate the local structure of liquid water. Interpretation of the experiment poses a significant challenge and requires a quantitative theoretical description. High-quality theoretical XA spectra require reliable molecular dynamics simulations and accurate electronic structure calculations. Here, we present the first successful application of coupled cluster theory to model the XA spectrum of liquid water. We overcome the computational limitations on system size by employing a multilevel coupled cluster framework for large molecular systems. Excellent agreement with the experimental spectrum is achieved by including triple excitations in the wave function and using molecular structures from state-of-the-art path-integral molecular dynamics. We demonstrate that an accurate description of the electronic structure within the first solvation shell is sufficient to successfully model the XA spectrum of liquid water within the multilevel framework. Furthermore, we present a rigorous charge transfer analysis of the XA spectrum, which is reliable due to the accuracy and robustness of the electronic structure methodology. This analysis aligns with previous studies regarding the character of the prominent features of the XA spectrum of liquid water

Physical mapping of the cystic fibrosis region by pulsed-field gel electrophoresis

The gene for cystic fibrosis (CF) is known to be flanked by the closely linked DNA markers met and J3.11 on chromosome 7. Using the technique of pulsed-field gel electrophoresis, we have constructed a complete overlapping restriction map of approximately 3000 kb of DNA in this regions. The met and J3.11 probes are found to be between 1300 and 1800 kb apart, which compares well with their genetic distance of 1-2 cM. The CF gene must be located within this interval, and the availability of this physical map should be of considerable utility in mapping additional clones as the search for the gene proceeds.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27317/1/0000339.pd

Efficient Generalized Least Squares Method for Mixed Population and Family‐based Samples in Genome‐wide Association Studies

Genome‐wide association studies (GWAS) that draw samples from multiple studies with a mixture of relationship structures are becoming more common. Analytical methods exist for using mixed‐sample data, but few methods have been proposed for the analysis of genotype‐by‐environment (G×E) interactions. Using GWAS data from a study of sarcoidosis susceptibility genes in related and unrelated African Americans, we explored the current analytic options for genotype association testing in studies using both unrelated and family‐based designs. We propose a novel method—generalized least squares (GLX)—to estimate both SNP and G×E interaction effects for categorical environmental covariates and compared this method to generalized estimating equations (GEE), logistic regression, the Cochran–Armitage trend test, and the W QLS and M QLS methods. We used simulation to demonstrate that the GLX method reduces type I error under a variety of pedigree structures. We also demonstrate its superior power to detect SNP effects while offering computational advantages and comparable power to detect G×E interactions versus GEE. Using this method, we found two novel SNPs that demonstrate a significant genome‐wide interaction with insecticide exposure—rs10499003 and rs7745248, located in the intronic and 3' UTR regions of the FUT9 gene on chromosome 6q16.1.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/107571/1/gepi21811.pd

Pharmacy Data for Tuberculosis Surveillance and Assessment of Patient Management

Pharmacy data help locate tuberculosis cases and assess their management

Climate forcing for dynamics of dissolved inorganic nutrients at Palmer Station, Antarctica: An interdecadal (1993-2013) analysis

We analyzed 20 years (1993–2013) of observations of dissolved inorganic macronutrients (nitrate, N; phosphate, P; and silicate, Si) and chlorophyll a (Chl) at Palmer Station, Antarctica (64.8°S, 64.1°W) to elucidate how large-scale climate and local physical forcing affect the interannual variability in the seasonal phytoplankton bloom and associated drawdown of nutrients. The leading modes of nutrients (N, P, and Si empirical orthogonal functions 1, EOF1) represent overall negative anomalies throughout growing seasons, showing a mixed signal of variability in the initial levels and drawdown thereafter (low-frequency dynamics). The second most common seasonal patterns of nitrate and phosphate (N and P EOF2) capture prolonged drawdown events during December–March, which are correlated to Chl EOF1. Si EOF2 captures a drawdown event during November–December, which is correlated to Chl EOF2. These different drawdown patterns are shaped by different sets of physical and climate forcing mechanisms. N and P drawdown events during December–March are influenced by the winter and spring Southern Annular Mode (SAM) phase, where nutrient utilization is enhanced in a stabilized upper water column as a consequence of SAM-driven winter sea ice and spring wind dynamics. Si drawdown during November–December is influenced by early sea ice retreat, where ice breakup may induce abrupt water column stratification and a subsequent diatom bloom or release of diatom cells from within the sea ice. Our findings underscore that seasonal nutrient dynamics in the coastal WAP are coupled to large-scale climate forcing and related physics, understanding of which may enable improved projections of biogeochemical responses to climate change

Performance of HLA allele prediction methods in African Americans for class II genes HLA-DRB1, -DQB1, and -DPB1

BACKGROUND: The expense of human leukocyte antigen (HLA) allele genotyping has motivated the development of imputation methods that use dense single nucleotide polymorphism (SNP) genotype data and the region’s haplotype structure, but the performance of these methods in admixed populations (such as African Americans) has not been adequately evaluated. We compared genotype-based—derived from both genome-wide genotyping and targeted sequencing—imputation results to existing allele data for HLA–DRB1, −DQB1, and –DPB1. RESULTS: In European Americans, the newly-developed HLA Genotype Imputation with Attribute Bagging (HIBAG) method outperformed HLA*IMP:02. In African Americans, HLA*IMP:02 performed marginally better than HIBAG pre-built models, but HIBAG models constructed using a portion of our African American sample with both SNP genotyping and four-digit HLA class II allele typing had consistently higher accuracy than HLA*IMP:02. However, HIBAG was significantly less accurate in individuals heterozygous for local ancestry (p ≤0.04). Accuracy improved in models with equal numbers of African and European chromosomes. Variants added by targeted sequencing and SNP imputation further improved both imputation accuracy and the proportion of high quality calls. CONCLUSION: Combining the HIBAG approach with local ancestry and dense variant data can produce highly-accurate HLA class II allele imputation in African Americans

Polygenic Risk Assessment Reveals Pleiotropy between Sarcoidosis and Inflammatory Disorders in the Context of Genetic Ancestry

Sarcoidosis is a complex disease of unknown etiology characterized by the presence of granulomatous inflammation. Though various immune system pathways have been implicated in disease, the relationship between the genetic determinants of sarcoidosis and other inflammatory disorders has not been characterized. Herein, we examined the degree of genetic pleiotropy common to sarcoidosis and other inflammatory disorders to identify shared pathways and disease systems pertinent to sarcoidosis onset. To achieve this, we quantify the association of common variant polygenic risk scores from nine complex inflammatory disorders with sarcoidosis risk. Enrichment analyses of genes implicated in pleiotropic associations were further used to elucidate candidate pathways. In European-Americans, we identify significant pleiotropy between risk of sarcoidosis and risk of asthma (R2=2.03%; p=8.89×10−9), celiac disease (R2=2.03%; p=8.21×10−9), primary biliary cirrhosis (R2=2.43%; p=2.01×10−10), and rheumatoid arthritis (R2=4.32%; p=2.50×10−17). These associations validate in African Americans only after accounting for the proportion of genome-wide European ancestry, where we demonstrate similar effects of polygenic risk for African-Americans with the highest levels of European ancestry. Variants and genes implicated in European-American pleiotropic associations were enriched for pathways involving interleukin-12, interleukin-27, and cell adhesion molecules, corroborating the hypothesized immunopathogenesis of disease