Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark

Highest frequencies of interleukin-22-producing T helper cells in alcoholic hepatitis patients with a favourable short-term course.

BACKGROUND: Alcoholic hepatitis (AH) has a severe prognosis due to hepatic inflammatory injury. The cytokine interleukin-22 (IL-22) is reported to exert anti-apoptotic and proliferative effects, but IL-22 has not been studied during the course of AH. IL-22 is mainly produced by CD4(+) (helper) T cells, including Th17 cells. In addition, Th17 cells produce the proinflammatory cytokine IL-17A, which has been implicated in AH. AIMS: We aimed to study the levels of circulating IL-22- and IL-17A-producing T helper cells and plasma cytokines in patients with AH and to examine the observations in relation to the short-term disease course. METHODS: We collected blood samples from 21 consecutive patients with severe AH on days 0, 14 and 30 after diagnosis, and included 10 stable alcoholic cirrhosis patients and 10 healthy subjects as controls. Analyses were performed using flow cytometry and ELISA. RESULTS: We found higher frequencies of IL-22-producing T helper cells in AH patients (median 1.7%) than in cirrhosis patients (1.0%, p = 0.03) and healthy controls (1.0%, p = 0.01), and a 1.5-fold increase in the plasma concentration of IL-17A in AH compared with healthy controls (p<0.01). Those patients who markedly improved their Glasgow Alcoholic Hepatitis Score demonstrated a 2-fold higher frequency of IL-22-producing T helper cells at baseline and during follow-up than patients whose condition deteriorated (p = 0.04). CONCLUSIONS: The frequency of IL-22-producing T helper cells was increased in AH patients and most so in those whose condition seemed to improve. T cell differentiation toward an IL-22-producing phenotype may thus be favourable in AH

Electrocardiographic precordial ST-segment deviations and the risk of cardiovascular death:results from the Copenhagen ECG study

BACKGROUND: We sought to perform a study assessing the association between electrocardiographic ST‐segment deviations and cardiovascular death (CVD), in relation to sex and age (≥ and <65 years), in a large primary care population without overt ischemic heart disease. METHODS AND RESULTS: Using computerized analysis of ECGs from 285 194 persons, we evaluated the association between precordial ST‐segment deviations and the risk of CVD. All data on medication, comorbidity, and outcomes were retrieved from Danish registries. After a median follow‐up period of 5.8 years, there were 6679 cardiovascular deaths. Increasing ST‐depression was associated with an increased risk of CVD in almost all of the precordial leads, with the most robust association seen in lead V5 to V6. ST‐elevations in lead V2 to V6 were associated with increased risk of CVD in young women, but not in men. However, ST‐elevations in V1 increased the risk for both genders and age groups, exemplified by a HR of 1.80 (95% CI [1.19 to 2.74], P=0.005) for men <65 years with ST‐elevations ≥150 μV versus a nondeviating ST‐segment (−50 μV to +50 μV). In contrast, for men <65 years, ST‐elevations in lead V2 to V3 conferred a decreased risk of CVD with a HR of 0.77 (95% CI [0.62 to 0.96], P<0.001) for ST‐elevations ≥150 μV in V2. CONCLUSION: We found that ST‐depressions were associated with a dose‐responsive increased risk of CVD in nearly all the precordial leads. ST‐elevations conferred an increased risk of CVD in women and with regard to lead V1 also in men. However, ST‐elevations in V2 to V3 were associated with a decreased risk of CVD in young men

Flow plot of cytokine production.

<p>Peripheral blood mononuclear cells were stimulated with phorbol-12-myristate-13-acetate, ionomycin and brefeldin A for 4 hours followed by intracellular staining for IL-17A and IL-22. The flow plots depict the population of CD4⁺CD45RO⁺ T cells from a representative AH patient. The values in the gate represent the percentage of IL-17A⁺, IL-22⁺ and double positive cells within the population of CD4⁺CD45RO⁺ T cells (right). The gate is set based on the control staining (left).</p

Patient baseline characteristics.

<p>Baseline characteristics are presented for healthy controls, stable alcoholic cirrhosis patients and alcoholic hepatitis patients. The alcoholic hepatitis patients are divided into two groups based on whether or not they experience a decline in GAHS≥2 during the 30 days of follow-up. Values are reported as median (IQR).</p><p>ALT = Alanine Amino Transferase.</p><p>MELD = Model of End Stage Liver Disease.</p><p>GAHS = Glasgow Alcoholic Hepatitis Score.</p>*<p>a vs. b.</p