Biosimilar medicines.

Biological medicines have become indispensable in the treatment of patients with serious diseases such as cancer and inflammatory diseases. Biosimilars are medicines which are developed to be similar to existing biological medicines (the 'reference product'). For the European market, they are approved by the European Medicines Agency. Owing to the rising importance of biosimilar medicines, the European Association of Hospital Pharmacists (EAHP) decided to set out its position on key issues concerning biosimilar medicines in a position paper. The topics included the role of hospital pharmacists in the uptake of biosimilar medicines in healthcare with regard to selection, procurement, logistics, information, education and collecting real-life experience (eg, in monitoring and pharmacovigilance). In addition, the paper touches on the views of the association for the naming of biosimilar medicines, extrapolation of indications, interchangeability, switching and substitution of biosimilar medicines and the provision of information about biosimilar medicines.

Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity.

Denmark has played a substantial role in the history of Northern Europe. Through a nationwide scientific outreach initiative, we collected genetic and anthropometrical data from ∼800 high school students and used them to elucidate the genetic makeup of the Danish population, as well as to assess polygenic predictions of phenotypic traits in adolescents. We observed remarkable homogeneity across different geographic regions, although we could still detect weak signals of genetic structure reflecting the history of the country. Denmark presented genomic affinity with primarily neighboring countries with overall resemblance of decreasing weight from Britain, Sweden, Norway, Germany, and France. A Polish admixture signal was detected in Zealand and Funen, and our date estimates coincided with historical evidence of Wend settlements in the south of Denmark. We also observed considerably diverse demographic histories among Scandinavian countries, with Denmark having the smallest current effective population size compared to Norway and Sweden. Finally, we found that polygenic prediction of self-reported adolescent height in the population was remarkably accurate (R2 = 0.639 ± 0.015). The high homogeneity of the Danish population could render population structure a lesser concern for the upcoming large-scale gene-mapping studies in the country.

Spitting for Science: Danish High School Students Commit to a Large-Scale Self-Reported Genetic Study.

Scientific outreach delivers science to the people. But it can also deliver people to the science. In this work, we report our experience from a large-scale public engagement project promoting genomic literacy among Danish high school students with the additional benefit of collecting data for studying the genetic makeup of the Danish population. Not only did we confirm that students have a great interest in their genetic past, but we were also gratified to see that, with the right motivation, adolescents can provide high-quality data for genetic studies.

[The first case of cap polyposis in Denmark].

Cap polyposis (CP) is characterized by the presence of inflammatory polyps mainly involving the rectosigmoid. It primarily causes mucous to bloody diarrhoea and is often misdiagnosed initially. We report the first case in Denmark with multiple polyps in the rectosigmoid causing constipation in between periods of mucous and bloody diarrhoea. He was initially misdiagnosed as having ulcerative colitis with pseudopolyps. Due to insufficient effect of medical treatment biopsies from the polyps were obtained. They showed typical histological signs of CP. He was successfully treated by rectosigmoid resection.

Evolution and regulation of the Lotus japonicus LysM receptor gene family.

LysM receptor kinases were identified as receptors of acylated chitin (Nod factors) or chitin produced by plant-interacting microbes. Here, we present the identification and characterization of the LysM receptor kinase gene (Lys) family (17 members) in Lotus japonicus. Comprehensive phylogenetic analysis revealed a correlation between Lys gene structure and phylogeny. Further mapping coupled with sequence-based anchoring on the genome showed that the family has probably expanded by a combination of tandem and segmental duplication events. Using a sliding-window approach, we identified distinct regions in the LysM and kinase domains of recently diverged Lys genes where positive selection may have shaped ligand interaction. Interestingly, in the case of NFR5 and its closest paralog, LYS11, one of these regions coincides with the predicted Nod-factor binding groove and the suggested specificity determining area of the second LysM domain. One hypothesis for the evolutionary diversification of this receptor family in legumes is their unique capacity to decipher various structures of chitin-derived molecules produced by an extended spectrum of interacting organisms: symbiotic, associative, endophytic, and parasitic. In a detailed expression analysis, we found several Lotus Lys genes regulated not only during the symbiotic association with Mesorhizobium loti but also in response to chitin treatment.

Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola.

The fungus Mycosphaerella graminicola has been a pathogen of wheat since host domestication 10,000-12,000 years ago in the Fertile Crescent. The wheat-infecting lineage emerged from closely related Mycosphaerella pathogens infecting wild grasses. We use a comparative genomics approach to assess how the process of host specialization affected the genome structure of M. graminicola since divergence from the closest known progenitor species named M. graminicola S1. The genome of S1 was obtained by Illumina sequencing resulting in a 35 Mb draft genome sequence of 32X. Assembled contigs were aligned to the previously sequenced M. graminicola genome. The alignment covered >90% of the non-repetitive portion of the M. graminicola genome with an average divergence of 7%. The sequenced M. graminicola strain is known to harbor thirteen essential chromosomes plus eight dispensable chromosomes. We found evidence that structural rearrangements significantly affected the dispensable chromosomes while the essential chromosomes were syntenic. At the nucleotide level, the essential and dispensable chromosomes have evolved differently. The average synonymous substitution rate in dispensable chromosomes is considerably lower than in essential chromosomes, whereas the average non-synonymous substitution rate is three times higher. Differences in molecular evolution can be related to different transmission and recombination patterns, as well as to differences in effective population sizes of essential and dispensable chromosomes. In order to identify genes potentially involved in host specialization or speciation, we calculated ratios of synonymous and non-synonymous substitution rates in the >9,500 aligned protein coding genes. The genes are generally under strong purifying selection. We identified 43 candidate genes showing evidence of positive selection, one encoding a potential pathogen effector protein. We conclude that divergence of these pathogens was accompanied by structural rearrangements in the small dispensable chromosomes, while footprints of positive selection were present in only a small number of protein coding genes.

Increased rate of human mutations where DNA and RNA polymerases collide.

Gene density and orientation of genes in eukaryotes seem to be correlated with the replication origin and the mutation rate is greater in late replicating regions; however, the reason for these patterns is unknown. Here, we investigate predicted replication origins in the human genome and find that levels of polymorphism as well as divergence from the chimpanzee genome are greater in genes transcribed on the lagging strand than those on the leading strand. This might be caused by interference between RNA and DNA polymerases, and avoidance of collisions between these enzymes might be an evolutionary force shaping gene orientation and density surrounding replication start sites. Physical constraints might have a larger influence on genome evolution than previously thought.

Heterogeneity in regional GC content and differential usage of codons and amino acids in GC-poor and GC-rich regions of the genome of Apis mellifera.

The honeybee (Apis mellifera) has a genome with a wide variation in GC content showing 2 clear modal GC values, in some ways reminiscent of an isochore-like structure. To gain insight into causes and consequences of this pattern, we used a comparative approach to study the genome-wide alignment of primarily coding sequence of A. mellifera with Drosophila melanogaster and Anopheles gambiae. The latter 2 species show a higher average GC content than A. mellifera and no indications of bimodality, suggesting that the GC-poor mode is a derived condition in honeybee. In A. mellifera, synonymous sites of genes generally adopt the GC content of the region in which they reside. A large proportion of genes in GC-poor regions have not been assigned to the honeybee assembly because of the low sequence complexity of their genome neighborhood. The synonymous substitution rate between A. mellifera and the other species is very close to saturation, but analyses of nonsynonymous substitutions as well as amino acid substitutions indicate that the GC-poor regions are not evolving faster than the GC-rich regions. We describe the codon usage and amino acid usage and show that they are remarkably heterogeneous within the honeybee genome between the 2 different GC regions. Specifically, the genes located in GC-poor regions show a much larger deviation in both codon usage bias and amino acid usage from the Dipterans than the genes located in the GC-rich regions.

Skip inflammation of the appendiceal orifice: a prospective endoscopic study.

OBJECTIVE: The purpose of the study was to evaluate the incidence of discontinuous inflammation of the appendiceal orifice in patients undergoing colonoscopy for diagnosis or surveillance of colonic disease. MATERIAL AND METHODS: Consecutive and unselected patients subjected to colonoscopy over a 3-year period were included in a prospective study. Biopsies were taken within 2 cm of the orifice of the appendix, from the caecum and from predefined colonic segments. Discontinuous inflammation of the appendiceal orifice was defined as an area of macroscopic inflammatory changes distinct from a normal caecum of ascending colon. The biopsies were graded histologically for the presence and severity of inflammation by a pathologist without knowledge of the endoscopic findings. RESULTS: A total of 271 patients were included. The final diagnoses were: ulcerative colitis (UC) (83 patients), Crohn's disease (CD) (54), indeterminate colitis (12), irritable bowel syndrome (IBS) (54), microscopic colitis (15) and other disease (53). Endoscopic discontinuous inflammation of the appendiceal orifice was found in 27% (95% CI: 17-38%) of patients with UC, 24% (95% CI: 13-39%) with CD, 40% (95% CI: 12-74%) with indeterminate colitis, 8% (95% CI: 0-36%) with microscopic colitis, 10% (95% CI: 3-24%) of patients with IBS and in 9% (95% CI: 2-021%) of other diseases (p<0.05). A correlation was found for endoscopic and histological discrimination between normal and inflamed mucosa (p<0.001). However, in 24% of patients, endoscopic inflammation was without histological signs of inflammation, primarily in an otherwise normal colon. CONCLUSIONS: Discontinuous inflammation of the appendiceal orifice is common in patients with IBD irrespective of clinical activity. However, patients with otherwise normal colon may also show congestion of this area without or with minimal microscopic inflammation.

Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

BACKGROUND: Comparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its evolutionary position in the artiodactyls. RESULTS: We have generated approximately 3.84 million shotgun sequences (0.66X coverage) from the pig genome. The data are hereby released (NCBI Trace repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project") together with an initial evolutionary analysis. The non-repetitive fraction of the sequences was aligned to the UCSC human-mouse alignment and the resulting three-species alignments were annotated using the human genome annotation. Ultra-conserved elements and miRNAs were identified. The results show that for each of these types of orthologous data, pig is much closer to human than mouse is. Purifying selection has been more efficient in pig compared to human, but not as efficient as in mouse, and pig seems to have an isochore structure most similar to the structure in human. CONCLUSION: The addition of the pig to the set of species sequenced at low coverage adds to the understanding of selective pressures that have acted on the human genome by bisecting the evolutionary branch between human and mouse with the mouse branch being approximately 3 times as long as the human branch. Additionally, the joint alignment of the shot-gun sequences to the human-mouse alignment offers the investigator a rapid way to defining specific regions for analysis and resequencing.

Comparative analysis of protein coding sequences from human, mouse and the domesticated pig.

BACKGROUND: The availability of abundant sequence data from key model organisms has made large scale studies of molecular evolution an exciting possibility. Here we use full length cDNA alignments comprising more than 700,000 nucleotides from human, mouse, pig and the Japanese pufferfish Fugu rubrices in order to investigate 1) the relationships between three major lineages of mammals: rodents, artiodactyls and primates, and 2) the rate of evolution and the occurrence of positive Darwinian selection using codon based models of sequence evolution. RESULTS: We provide evidence that the evolutionary splits among primates, rodents and artiodactyls happened shortly after each other, with most gene trees favouring a topology with rodents as outgroup to primates and artiodactyls. Using an unrooted topology of the three mammalian species we show that since their diversification, the pig and mouse lineages have on average experienced 1.44 and 2.86 times as many synonymous substitutions as humans, respectively, whereas the rates of non-synonymous substitutions are more similar. The analysis shows the highest average dN/dS ratio in the human lineage, followed by the pig and then the mouse lineages. Using codon based models we detect signals of positive Darwinian selection in approximately 5.3%, 4.9% and 6.0% of the genes on the human, pig and mouse lineages respectively. Approximately 16.8% of all the genes studied here are not currently annotated as functional genes in humans. Our analyses indicate that a large fraction of these genes may have lost their function quite recently or may still be functional genes in some or all of the three mammalian species. CONCLUSIONS: We present a comparative analysis of protein coding genes from three major mammalian lineages. Our study demonstrates the usefulness of codon-based likelihood models in detecting selection and it illustrates the value of sequencing organisms at different phylogenetic distances for comparative studies.

Comparison of drug-related problems in different patient groups.

BACKGROUND: There is a lack of knowledge concerning how drug-related problems (DRPs) vary in different patient groups. Possible dissimilarities need to be taken into consideration when guidelines for detecting and preventing DRPs are compiled. OBJECTIVE: To characterize and compare the frequency and categories of DRPs in different groups of hospitalized patients. METHODS: Patients admitted to 4 different types of departments at 5 hospitals in Norway were included consecutively. Medical records and information acquired at multidisciplinary morning meetings were sources for assessing the patients' DRPs. RESULTS: A total of 827 patients were included. Mean age was 70.8 years, 58.6% were female, and 81% had at least one DRP. An average of 1.9, 2.0, 2.1, and 2.3 DRPs per patient were found in the departments of cardiology, geriatrics, respiratory medicine, and rheumatology, respectively. Significant differences in the type of DRPs between the patient groups were found. The most frequent DRPs and the patient group in which they most often occurred were nonoptimal dose (cardiology, respiratory, geriatric) and need for additional drug (rheumatology). CONCLUSIONS: DRPs occurred in the majority of the patients in all departments. The type of DRP differed markedly between the patient groups. Knowledge of these differences is clinically valuable by enabling us to guide efforts toward prevention of DRPs. Antithrombotic agents, loop diuretics, angiotensin-converting enzyme inhibitors, penicillins, antiinflammatory drugs, and opioid analgesics commonly caused DRPs, even in departments where knowledge of these drugs is assumed to be extensive.