A deep learning approach to prediction of blood group antigens from genomic data.

BACKGROUND: Deep learning methods are revolutionizing natural science. In this study, we aim to apply such techniques to develop blood type prediction models based on cheap to analyze and easily scalable screening array genotyping platforms. METHODS: Combining existing blood types from blood banks and imputed screening array genotypes for ~111,000 Danish and 1168 Finnish blood donors, we used deep learning techniques to train and validate blood type prediction models for 36 antigens in 15 blood group systems. To account for missing genotypes a denoising autoencoder initial step was utilized, followed by a convolutional neural network blood type classifier. RESULTS: Two thirds of the trained blood type prediction models demonstrated an F1-accuracy above 99%. Models for antigens with low or high frequencies like, for example, Cw, low training cohorts like, for example, Cob, or very complicated genetic underpinning like, for example, RhD, proved to be more challenging for high accuracy (>99%) DL modeling. However, in the Danish cohort only 4 out of 36 models (Cob, Cw, D-weak, Kpa) failed to achieve a prediction F1-accuracy above 97%. This high predictive performance was replicated in the Finnish cohort. DISCUSSION: High accuracy in a variety of blood groups proves viability of deep learning-based blood type prediction using array chip genotypes, even in blood groups with nontrivial genetic underpinnings. These techniques are suitable for aiding in identifying blood donors with rare blood types by greatly narrowing down the potential pool of candidate donors before clinical grade confirmation.

Genetic prediction of 33 blood group phenotypes using an existing genotype dataset.

BACKGROUND: Accurate blood type data are essential for blood bank management, but due to costs, few of 43 blood group systems are routinely determined in Danish blood banks. However, a more comprehensive dataset of blood types is useful in scenarios such as rare blood type allocation. We aimed to investigate the viability and accuracy of predicting blood types by leveraging an existing dataset of imputed genotypes for two cohorts of approximately 90,000 each (Danish Blood Donor Study and Copenhagen Biobank) and present a more comprehensive overview of blood types for our Danish donor cohort. STUDY DESIGN AND METHODS: Blood types were predicted from genome array data using known variant determinants. Prediction accuracy was confirmed by comparing with preexisting serological blood types. The Vel blood group was used to test the viability of using genetic prediction to narrow down the list of candidate donors with rare blood types. RESULTS: Predicted phenotypes showed a high balanced accuracy >99.5% in most cases: A, B, C/c, Coa /Cob , Doa /Dob , E/e, Jka /Jkb , Kna /Knb , Kpa /Kpb , M/N, S/s, Sda , Se, and Yta /Ytb , while some performed slightly worse: Fya /Fyb , K/k, Lua /Lub , and Vel ~99%-98% and CW and P1 ~96%. Genetic prediction identified 70 potential Vel negatives in our cohort, 64 of whom were confirmed correct using polymerase chain reaction (negative predictive value: 91.5%). DISCUSSION: High genetic prediction accuracy in most blood groups demonstrated the viability of generating blood types using preexisting genotype data at no cost and successfully narrowed the pool of potential individuals with the rare Vel-negative phenotype from 180,000 to 70.

The health-related quality of life in hyperhidrosis and co-morbidities.

PURPOSE: Hyperhidrosis has been associated with a reduced health-related quality of life (HRQoL). The role of common confounding factors of this association such as stress and socioeconomic status, however, remain largely unexplored, and may affect the management strategy for hyperhidrosis. Therefore, the study objective was to compare the HRQoL in individuals with and without hyperhidrosis while adjusting for confounders. METHODS: In this retrospective cohort study, data on the HRQoL measured by the short-form-12 questionnaire and self-reported hyperhidrosis were collected from the Danish Blood Donor Study-cohort. Data on international classification of disease-10 codes and redeemed prescriptions were collected from nationwide registries. Linear regression investigated the association between hyperhidrosis and HRQoL. RESULTS: Total 2794 (9.1%) of 30,808 blood donors had self-reported hyperhidrosis and 284 (0.2%) of 122,225 had hospital diagnosed hyperhidrosis. Self-reported hyperhidrosis was associated with a reduced mental HRQoL (adjusted beta coefficient - 1.10; 95% confidence interval - 1.37, - 0.82; p < 0.001) and physical HRQoL (adjusted beta coefficient - 0.90; 95% confidence interval - 1.09, - 0.70; p < 0.001). Hospital diagnosed hyperhidrosis was associated with a reduced mental HRQoL (adjusted beta coefficient - 0.91; 95% confidence interval - 1.82, - 0.04; p = 0.049). CONCLUSION: Hyperhidrosis is associated with a reduced HRQoL, independently of confounders or mode of diagnosis. This supports an approach primarily targeting hyperhidrosis.

Exposure to air pollution and risk of respiratory tract infections in the adult Danish population-a nationwide study.

OBJECTIVES: The association between air pollution and risk of respiratory tract infection (RTI) in adults needs to be clarified in settings with low to moderate levels of air pollution. We investigated this in the Danish population between 2004 and 2016. METHODS: We included 3 653 490 persons aged 18-64 years in a nested case-control study. Exposure was defined as the average daily concentration at the individual's residential address of CO, NOX, NO2, O3, SO2, NH3, PPM2.5, black carbon, organic carbon, mineral dust, sea salt, secondary inorganic aerosols, SO42-, NO3-, NH4+, secondary organic aerosols, PM2.5, and PM10 during a 3-month exposure window. RTIs were defined by hospitalization for RTIs. Incidence rate ratios (IRRs) and 95% CIs were estimated comparing highest with lowest decile of exposure using conditional logistic regression models. RESULTS: In total, 188 439 incident cases of RTI were identified. Exposure to most air pollutants was positively associated with risk of RTI. For example, NO2 showed an IRR of 1.52 (CI: 1.48-1.55), and PM2.5 showed an IRR of 1.45 (CI: 1.40-1.50). In contrast, exposure to sea salt, PM10, NH3, and O3 was negatively associated with a risk of RTIs. DISCUSSION: In this nationwide study comprising adults, exposure to air pollution was associated with risk of RTIs and subgroups hereof. Sea salt, PM10, NH3, and O3 may be proxies for rural areas, as the levels of these species in Denmark are higher near the western coastlines and/or in rural areas with fewer combustion sources.

Smoking is associated with infection risk in healthy blood donors.

OBJECTIVES: There is a gap in knowledge about the effects of smoking on overall infection risk in otherwise healthy populations, possibly leading to underestimation of the dangers of smoking. The present study aimed to examine the association of smoking with the risk of infections in a large cohort of healthy blood donors. METHODS: This cohort study used questionnaire and health register data from 127 831 Danish blood donors. Multivariable Cox proportional hazards analysis was applied to estimate the association of current smoking with the risk of all-cause infection defined as hospital-based treatment for infection or filled prescriptions of antimicrobials stratified for age and adjusted for relevant confounders. RESULTS: Among 18 272 current smokers, 12 272 filled an antimicrobial prescription and 2035 received hospital-based treatment for infections. Among 101 974 non-smokers, 65 117 filled a prescription and 8501 received hospital-based treatment for infections. Smokers had a higher risk of all-cause infection than non-smokers (hazard ratio estimates were 1.27 in males and 1.33 in females for hospital-based treatment and 1.11 in males and up to 1.20 in females for filled prescriptions). Smoking was most strongly associated with an increased incidence of respiratory tract infection, abscesses, skin infection, and prescriptions for these ailments (hazard ratio up to 2.29). Furthermore, smokers' risk of filled prescriptions of broad-spectrum penicillin was increased (hazard ratio up to 1.96). CONCLUSIONS: Current smoking was strongly associated with the risk of hospital-based treatment of infection and filled prescriptions of antimicrobials in a large cohort of healthy individuals. These findings warrant an increased focus on infectious disease risk among smokers.

Experience of loneliness during the COVID-19 pandemic: a cross-sectional study of 50 968 adult Danes.

OBJECTIVES: To examine the level of loneliness experienced during the COVID-19 pandemic in Denmark and to identify associated behavioural patterns and demographic factors. DESIGN: Cross-sectional cohort study. SETTING: Includes Danish active and former blood donors. PARTICIPANTS: A questionnaire was sent to 124 307 active and former blood donors, of these a total of 50 968 participants completed the study questionnaire (response rate=41%). PRIMARY AND SECONDARY OUTCOME MEASURES: Subjective experience of loneliness was measured using the 3-item University of California, Los Angeles Loneliness Scale (UCLA-3). Besides the UCLA-3, the respondents answered items on sociodemographic and economic characteristics, items on precautionary measures taken to avoid COVID-19 infection as well as on COVID-19 anxiety. RESULTS: The participants indicated their experienced level of loneliness both before and during the pandemic. Comparing the two reports yielded a mean increase in loneliness scores of 14.1% (p<0.001). Exploratory factor analysis identified the factor well-being, which comprised three questionnaire items related to emotional heath, physical health and happiness. A high score on the factor well-being was associated with reduced levels of loneliness (coefficient=-0.47, 95% CI -0.49 to -0.46)). Furthermore, women were more likely than men to have experienced increased levels of loneliness during the pandemic (coefficient=0.27, 95% CI 0.25 to 0.29). Furthermore, a negative correlation between higher age and change in loneliness score was observed. CONCLUSIONS: The findings document an increase in the level of experienced loneliness during the COVID-19 pandemic, particularly affecting individuals with low well-being, women and younger individuals.

Hyperhidrosis and the risk of being treated for skin infections.

BACKGROUND: A few studies have described an increased prevalence of skin infections in individuals with hyperhidrosis compared to others. However, it remains uncertain whether hyperhidrosis is an independent risk factor for skin infections. OBJECTIVE: To compare the risk of skin infections in individuals with and without hyperhidrosis. METHODS: In this retrospective cohort study, data on hyperhidrosis were collected from the Danish Blood Donor Study. Blood donors included in 2010-2019 were followed from inclusion until December 2019. Data on redeemed prescriptions against skin infections were collected from the National Prescription Register. The intensity of prescription-use by hyperhidrosis status was assessed in Andersen-Gill models. RESULTS: Overall, 4,176 (9.6%) of 43,477 blood donors had self-reported hyperhidrosis and 437 (0.34%) of 127,823 blood donors had hospital diagnosed hyperhidrosis. Self-reported hyperhidrosis was associated with the use of antibiotic prescriptions (adjusted hazard ratio = 1.21; 95% confidence interval 1.00-1.45, p = 0.047). Hospital diagnosed hyperhidrosis was associated with the use of antibiotic (adjusted hazard ratio = 1.33; 95% confidence interval 1.03-1.68, p = 0.028) and topical antifungal prescriptions (adjusted hazard ratio = 1.43; 95% confidence interval 1.04-1.97, p = 0.027). CONCLUSIONS: Hyperhidrosis is associated with the use of prescriptions for antibiotics and topical antifungals. This suggests a clinically relevant association between hyperhidrosis and skin infections.

The association between water hardness and xerosis-Results from the Danish Blood Donor Study.

BACKGROUND: The pathophysiology of xerosis depends on extrinsic and intrinsic exposures. Residential hard water may constitute such an exposure. OBJECTIVES: To estimate the prevalence of xerosis and to compare water hardness exposure in blood donors with and without xerosis. METHODS: In this retrospective cohort study in 2018-2019, blood donors with self-reported moderately or severely dry skin were compared to blood donors without dry skin. Blood donors with ichthyosis, lichen planus and psoriasis were excluded. Water hardness data was collected from the Geology Survey of Denmark and Greenland. RESULTS: Overall, 4,748 of 30,721 (15.5%; 95% confidence interval 15.1-15.9%) blood donors had xerosis. After excluding blood donors with ichthyosis, lichen planus and psoriasis, 4,416 blood donors (2,559 females; median age 38.4 years [interquartile range 28.0-49.8]; 700 smokers) remained in this study. Water softer than 12-24 degrees Deutsche härte was associated with decreased probability of xerosis (odds ratio 0.83; 95% confidence interval 0.74-0.94) and water harder than 12-24 degrees Deutsche härte was associated with increased probability of xerosis (odds ratio 1.22; 95% confidence interval 1.03-1.45). The association between water hardness and xerosis remained significant after excluding blood donors with dermatitis. CONCLUSIONS: Water hardness is associated with xerosis independent of other dermatoses.

A genome-wide meta-analysis yields 46 new loci associating with biomarkers of iron homeostasis.

Iron is essential for many biological functions and iron deficiency and overload have major health implications. We performed a meta-analysis of three genome-wide association studies from Iceland, the UK and Denmark of blood levels of ferritin (N = 246,139), total iron binding capacity (N = 135,430), iron (N = 163,511) and transferrin saturation (N = 131,471). We found 62 independent sequence variants associating with iron homeostasis parameters at 56 loci, including 46 novel loci. Variants at DUOX2, F5, SLC11A2 and TMPRSS6 associate with iron deficiency anemia, while variants at TF, HFE, TFR2 and TMPRSS6 associate with iron overload. A HBS1L-MYB intergenic region variant associates both with increased risk of iron overload and reduced risk of iron deficiency anemia. The DUOX2 missense variant is present in 14% of the population, associates with all iron homeostasis biomarkers, and increases the risk of iron deficiency anemia by 29%. The associations implicate proteins contributing to the main physiological processes involved in iron homeostasis: iron sensing and storage, inflammation, absorption of iron from the gut, iron recycling, erythropoiesis and bleeding/menstruation.

The impact of CCR5-Δ32 deletion on C-reactive protein levels and cardiovascular disease: Results from the Danish Blood Donor Study.

BACKGROUND AND PURPOSE: The C-C chemokine receptor 5-Δ32 deletion (CCR5-Δ32) has been associated with lower levels of C-reactive protein (CRP), but the effect on cardiovascular diseases is uncertain. This study addresses the impact of CCR5-Δ32 on the risk of low-grade inflammation and hospitalization with cardiovascular diseases in a large cohort of blood donors. METHODS: Genotyping of 15,206 healthy participants from The Danish Blood Donor Study for CCR5-Δ32 was performed and combined with CRP measurements and questionnaire data. Cardiovascular disease diagnoses were identified by ICD-10 codes in the Danish National Patient Registry. RESULTS: CCR5-Δ32-carriers had a higher risk of hospitalization for cardiovascular diseases when compared with wild-type homozygotes (hazard ratio = 1.35, 95%-confidence interval: 1.00-1.87). CRP levels were unaffected by the CCR5-Δ32 deletion. CONCLUSION: In this cohort, carriers of the CCR5-Δ32 deletion had normal CRP levels but a borderline significant increased risk of cardiovascular diseases.