Admixture Mapping of Sepsis in European Individuals With African Ancestries

Sepsis is a severe systemic inflammatory response to infections that is accompanied by organ dysfunction. Although the ancestral genetic background is a relevant factor for sepsis susceptibility, there is a lack of studies using the genetic singularities of a recently admixed population to identify loci involved in sepsis susceptibility. Here we aimed to discover new sepsis loci by completing the first admixture mapping study of sepsis in Canary Islanders, leveraging their distinctive genetic makeup as a mixture of Europeans and African ancestries. We used a case-control approach and inferred local ancestry blocks from genome-wide data from 113,414 polymorphisms genotyped in 343 patients with sepsis and 410 unrelated controls, all ascertained for grandparental origin in the Canary Islands (Spain). Deviations in local ancestries between cases and controls were tested using logistic regressions, followed by fine-mapping analyses based on imputed genotypes, in silico functional assessments, and gene expression analysis centered on the region of interest. The admixture mapping analysis detected that local European ancestry in a locus spanning 1.2 megabases of chromosome 8p23.1 was associated with sepsis (lowest p = 1.37 × 10⁻⁴; Odds Ratio [OR] = 0.51; 95%CI = 0.40–0.66). Fine-mapping studies prioritized the variant rs13249564 within intron 1 of MFHAS1 gene associated with sepsis (p = 9.94 × 10⁻⁴; OR = 0.65; 95%CI = 0.50–0.84). Functional and gene expression analyses focused on 8p23.1 allowed us to identify alternative genes with possible biological plausibility such as defensins, which are well-known effector molecules of innate immunity. By completing the first admixture mapping study of sepsis, our results revealed a new genetic locus (8p23.1) harboring a number of genes with plausible implications in sepsis susceptibility.

Targeted analysis of genomic regions enriched in African ancestry reveals novel classical HLA alleles associated with asthma in Southwestern Europeans

Despite asthma has a considerable genetic component, an important proportion of genetic risks remain unknown, especially for non-European populations. Canary Islanders have the largest African genetic ancestry observed among Southwestern Europeans and the highest asthma prevalence in Spain. Here we examined broad chromosomal regions previously associated with an excess of African genetic ancestry in Canary Islanders, with the aim of identifying novel risk variants associated with asthma susceptibility. In a two-stage cases-control study, we revealed a variant within HLA-DQB1 significantly associated with asthma risk (rs1049213, meta-analysis p = 1.30 × 10^–7, OR [95% CI] = 1.74 [1.41–2.13]) previously associated with asthma and broad allergic phenotype. Subsequent fine-mapping analyses of classical HLA alleles revealed a novel allele significantly associated with asthma protection (HLA-DQA1*01:02, meta-analysis p = 3.98 × 10^–4, OR [95% CI] = 0.64 [0.50–0.82]) that had been linked to infectious and autoimmune diseases, and peanut allergy. HLA haplotype analyses revealed a novel haplotype DQA1*01:02-DQB1*06:04 conferring asthma protection (meta-analysis p = 4.71 × 10^–4, OR [95% CI] = 0.47 [0.29– 0.73]).

Whole-Blood Mitochondrial DNA Copies Are Associated With the Prognosis of Acute Respiratory Distress Syndrome After Sepsis

Acute respiratory distress syndrome (ARDS) is an inflammatory process of the lungs that develops primarily in response to pulmonary or systemic sepsis, resulting in a disproportionate death toll in intensive care units (ICUs). Given its role as a critical activator of the inflammatory and innate immune responses, previous studies have reported that an increase of circulating cell-free mitochondrial DNA (mtDNA) is a biomarker for fatal outcome in the ICU. Here we analyzed the association of whole-blood mtDNA (wb-mtDNA) copies with 28-day survival from sepsis and sepsis-associated ARDS. We analyzed mtDNA data from 687 peripheral whole-blood samples within 24 h of sepsis diagnosis from unrelated Spanish patients with sepsis (264 with ARDS) included in the GEN-SEP study. The wb-mtDNA copies were obtained from the array intensities of selected probes, with 100% identity with mtDNA and with the largest number of mismatches with the nuclear sequences, and normalized across the individual-probe intensities. We used Cox regression models for testing the association with 28-day survival. We observed that wb-mtDNA copies were significantly associated with 28-day survival in ARDS patients (hazard ratio = 3.65, 95% confidence interval = 1.39–9.59, p = 0.009) but not in non-ARDS patients. Our findings support that wb-mtDNA copies at sepsis diagnosis could be considered an early prognostic biomarker in sepsis-associated ARDS patients. Future studies will be needed to evaluate the mechanistic links of this observation with the pathogenesis of ARDS.

Evaluation of Whole-Exome Enrichment Solutions: Lessons from the High-End of the Short-Read Sequencing Scale

Whole-exome sequencing has become a popular technique in research and clinical settings, assisting in disease diagnosis and increasing the understanding of disease pathogenesis. In this study, we aimed to compare common enrichment capture solutions available in the market. Peripheral blood-purified DNA samples were enriched with SureSelect^QXT V6 (Agilent) and various Illumina solutions: TruSeq DNA Nano, TruSeq DNA Exome, Nextera DNA Exome, and Illumina DNA Prep with Enrichment, and sequenced on a HiSeq 4000. We found that their percentage of duplicate reads was as much as 2 times higher than previously reported values for the previous HiSeq series. SureSelect^QXT and Illumina DNA Prep with Enrichment showed the best average on-target coverage, which improved when off-target regions were included. At high coverage levels and in shared bases, these two solutions and TruSeq DNA Exome provided three of the best performances. With respect to the number of small variants detected, SureSelect^QXT presented the lowest number of detected variants in target regions. When off-target regions were considered, its ability equalized to other solutions. Our results show SureSelect^QXT and Illumina DNA Prep with Enrichment to be the best enrichment capture solutions.

Admixture mapping of asthma in southwestern Europeans with North African ancestry influences

The prevalence of asthma symptoms in Canary Islanders, a southwestern European population from Spain, is almost three times higher than the country average. Because the genetic risks identified so far explain <5% of asthma heritability, here we aimed to discover new asthma loci by completing the first admixture mapping study in Canary Islanders leveraging their distinctive genetic makeup, where significant northwest African influences coexist in the European genetic diversity landscape. A 2-stage study was conducted in 1,491 unrelated individuals self-declaring having a Canary Islands origin for the 4 grandparents. Local ancestry estimates were obtained for the shared positions with reference data from putative ancestral populations from Europe, North Africa, and sub-Saharan Africa. Case-control deviations in local ancestry were tested for each ancestry separately using logistic regressions adjusted for principal components, followed by fine-mapping analyses based on imputed genotypes and analyses of the likely deleterious exonic variants. The admixture mapping analysis of asthma detected that local North African ancestry in a locus spanning 365 kb of chromosome 16q23.3 was associated with asthma risk at study-wide significance [lowest P = 1.12 × 10^-4; odds ratio (OR) = 2.05; 95% confidence interval (CI) = 1.41-3.00]. Fine-mapping studies identified a variant associated with asthma, and results were replicated in independent samples (rs3852738, OR = 1.34; 95% CI = 1.13-1.59, P = 7.58 × 10^-4). Whole exome sequencing data from a subset of individuals revealed an enrichment of likely deleterious variants among asthma cases in 16q23.3, particularly in the phospholipase Cγ2 (PLCG2) gene (P = 3.67 × 10^-4). By completing the first mapping study of asthma in admixed populations from Europe, our results revealed a new plausible asthma locus.

Major amputations in type 2 diabetes between 2001 and 2015 in Spain: regional differences

Background

To analyze the trend of lower extremity major amputations (MA) among patients with type 2 diabetes mellitus (T2DM) in the Regions of Spain from year 2001 until 2015.

Methods

Descriptive study of 40,392 MA. Data were obtained from the national hospital discharge database in patients with T2DM. The incidence rate was calculated in each Region, in addition to the incidence ratios (IR) between annual incidence and incidence of the year 2001. The length of hospital stay and mortality risks were analyzed using regression models adjusted for sex, age and smoking.

Results

The major amputations incidence rate per 100,000 person-years was 0.48 in Spain; Canary Islands showed the highest incidence (0.81). The trend was a slight decrease or stability of the incidence in all Regions except in the Canary Islands (IR₂₀₁₅ = 2.0 [CI95% = 1.5, 2.6]) and in Madrid (IR₂₀₁₅ = 0.1 [CI95% = 0.1, 0.2]). Mortality after major amputations was 10% in Spain; Cantabria suffered the highest risk of death [1.7 (CI95% = 1.4; 2.1), p < 0.001] and La Rioja the lowest risk (0.5 [CI95% = 0.2; 0.9]; p = 0.026). The longest hospital stay was registered in the Canary Islands [(CI95% = 11.4;13.3], p < 0.001)], and the shortest in the Valencian Community [(CI95% = − 7.3; − 5.8), p < 0.001)].

Conclusion

MA in T2DM followed a growing trend in the Canary Islands, which diverged from the downward trend in Spain. The variability of mortality and hospital stay, suggest to review the clinical management in some Regions. Sudden incidence decrease in Madrid suggests checking the record procedures of hospital discharges.

Genomic Analyses of Human European Diversity at the Southwestern Edge: Isolation, African Influence and Disease Associations in the Canary Islands

Despite the genetic resemblance of Canary Islanders to other southern European populations, their geographical isolation and the historical admixture of aborigines (from North Africa) with sub-Saharan Africans and Europeans have shaped a distinctive genetic makeup that likely affects disease susceptibility and health disparities. Based on single nucleotide polymorphism array data and whole genome sequencing (30×), we inferred that the last African admixture took place ∼14 generations ago and estimated that up to 34% of the Canary Islander genome is of recent African descent. The length of regions in homozygosis and the ancestry-related mosaic organization of the Canary Islander genome support the view that isolation has been strongest on the two smallest islands. Furthermore, several genomic regions showed significant and large deviations in African or European ancestry and were significantly enriched in genes involved in prevalent diseases in this community, such as diabetes, asthma, and allergy. The most prominent of these regions were located near LCT and the HLA, two well-known targets of selection, at which 40‒50% of the Canarian genome is of recent African descent according to our estimates. Putative selective signals were also identified in these regions near the SLC6A11-SLC6A1, KCNMB2, and PCDH20-PCDH9 genes. Taken together, our findings provide solid evidence of a significant recent African admixture, population isolation, and adaptation in this part of Europe, with the favoring of African alleles in some chromosome regions. These findings may have medical implications for populations of recent African ancestry.

Domain and intensity of physical activity are associated with metabolic syndrome: A population-based study

Introduction

Little is known on how the domain and intensity of physical activity (PA) associates with metabolic syndrome (MetS). The aim of this study was to examine associations between PA domains (leisure-time, domestic, active transport, total walking and total PA), PA intensities (light, moderate and vigorous) and PA levels with MetS in the general adult population.

Methods

Cross-sectional study. Anthropometry, blood biochemistry, 79-item PA-questionnaire, lifestyle and medical history were evaluated in a representative sample of Canary Island adults (n = 6,729). MetS was diagnosed using the harmonized IDF-NHLBI-AHA criteria. T-test and multivariable logistic regression was used to analyse associations between PA domains and intensities with MetS vs. no MetS, controlling for socio-demographic, lifestyle, family antecedents and body mass index (BMI).

Results

For each MET-h/day spent in moderate-vigorous PA intensities, as well as in recreational domain, active transport, total walking and total PA, the odds of MetS decreased between 3–10%. Energy expenditure exclusively in light and domestic PAs was not associated with MetS, however it was important to achieve a total PA level of 3 MET-h/day, which reduced the odds of MetS by 23%. This reduction was blunted in those with more than 2 h/d of TV watching time. A PA level of 3 MET-h/d also nullified the risk of MetS in those with low PA and high TV consumption.

Conclusions

Some types of leisure time PAs may contribute more than others to reducing MetS. Light and domestic PA play a complementary role in enhancing energy expenditure in the general population. TV watching time above 2 h/d counteracted the MetS risk reduction associated with PA level, but PA level also reduced the risk of METs presented by those with a low level of PA and an excess TV watching time. Physical activity explains a greater amount of the variance of MetS than any other factors of lifestyle, education, sex and family history, and substantially mitigates the strong association of age and BMI with MetS.

[Application of the Smoking Scale for Primary Care (ETAP) in clinical practice]

Objetivo

Averiguar si la escala de tabaquismo ETAP, que mide la exposición acumulada al tabaco tanto activa como pasivamente, es aplicable y efectiva en la práctica clínica de la atención primaria para la prevención del infarto agudo de miocardio (IAM).

Emplazamiento Centro de salud de Barranco Grande, en Tenerife.

Diseño

Estudio de 61 casos (IAM) y 144 controles. Muestreo con arranque aleatorio, sin apareamiento. Se realizó análisis de curvas COR-II y se estimó la efectividad mediante sensibilidad y valor predictivo negativo (VPN). Se administró una encuesta a los médicos de familia participantes sobre la aplicabilidad de la ETAP en la consulta.

Resultados

La opinión de los médicos participantes fue unánimemente favorable: la ETAP fue de fácil uso en la consulta, necesitó menos de 3 min por paciente y resultó útil para reforzar la intervención preventiva. La curva COR-II de la ETAP mostró que 20 años de exposición era el mejor punto de corte, con un área bajo la curva de 0,70 (IC 95%: 0,62-0,78) y una combinación de sensibilidad (98%) y VPN (96%) para el IAM. Al estratificar edad y sexo, en todos los grupos se alcanzaron sensibilidades y VPN cercanos al 100%, salvo en los hombres de edad ≥ 55 años, en quienes el VPN cayó hasta el 75%.

Conclusiones

Los resultados apuntan a que ETAP es una herramienta válida que puede ser aplicable y efectiva en la práctica clínica de la atención primaria para la prevención del IAM relacionado con el consumo de tabaco.

Clinical applicability and cost-effectiveness of DIABSCORE in screening for type 2 diabetes in primary care

AIMS

To evaluate the applicability and cost-effectiveness of a clinical risk score (DIABSCORE) to screen for type 2 diabetes in primary care patients.

METHODS

Multicenter cross-sectional study of 10,508 adult no previously diagnosed with diabetes, in 2 Spanish regions (Canary Islands and Valencian Community). The variables comprising DIABSCORE were age, waist to height ratio, family history of diabetes and gestational diabetes. ROC curves were obtained; the diabetes prevalences odds ratios (HbA1c ≥6.5%) between patients exposed and not exposed to DIABSCORE ≥100, and to fasting blood glucose ≥126mg/dL were calculated. The opinions of both the professionals and the patients concerning DIABSCORE were collected, and a cost-effectiveness analysis was performed.

RESULTS

In both regions, the valid cut-off point for diabetes (DIABSCORE=100), showed an area under the curve >0.80. The prevalences odds ratio of diabetes for DIABSCORE ≥100 was 9.5 (3.7-31.5) in Canarian and 18.3 (8.0-51.1) in Valencian; and for glucose ≥126mg/dL it was, respectively, 123.0 (58.8-259.2) and 303.1 (162.5-583.8). However, glucose ≥126mg/dL showed a low sensitivity (below 48% in both communities) as opposed to DIABSCORE ≥100 (above 90% in both regions). Professionals (100%) and patients (75%) satisfaction was greater when using DIABSCORE rather than glucose measurement for diabetes screening. The cost of each case of diabetes identified was lower with DIABSCORE ≥100 (7.6 € in Canarian and 8.3 € in Valencian) than glucose ≥126mg/dL (10.8 € and 10.5 €, respectively).

CONCLUSIONS

DIABSCORE is an applicable and cost-effective screening method for type 2 diabetes in primary care.

On the problem of type 2 diabetes-related mortality in the Canary Islands, Spain. The DARIOS Study

AIMS

To compare diabetes-related mortality rates and factors associated with this disease in the Canary Islands compared with other 10 Spanish regions.

METHODS

In a cross-sectional study of 28,887 participants aged 35-74 years in Spain, data were obtained for diabetes, hypertension, dyslipidemia, obesity, insulin resistance (IR), and metabolic syndrome. Healthcare was measured as awareness, treatment and control of diabetes, dyslipidemia, and hypertension. Standardized mortality rate ratios (SRR) were calculated for the years 1981 to 2011 in the same regions.

RESULTS

Diabetes, obesity, and hypertension were more prevalent in people under the age of 64 in the Canary Islands than in Spain. For all ages, metabolic syndrome and insulin resistance (IR) were also more prevalent in those from the Canary Islands. Healthcare parameters were similar in those from the Canary Islands and the rest of Spain. Diabetes-related mortality in the Canary Islands was the highest in Spain since 1981; the maximum SRR was reached in 2011 in men (6.3 versus the region of Madrid; p<0.001) and women (9.5 versus Madrid; p<0.001). Excess mortality was prevalent from the age of 45 years and above.

CONCLUSIONS

Diabetes-related mortality is higher in the Canary Islands population than in any other Spanish region. The high mortality and prevalence of IR warrants investigation of the genetic background associated with a higher incidence and poor prognosis for diabetes in this population. The rise in SRR calls for a rapid public health policy response.