Ethical aspects of genome diversity research: genome research into cultural diversity or cultural diversity in genome research?

The goal of the Human Genome Diversity Project (HGDP) was to reconstruct the history of human evolution and the historical and geographical distribution of populations with the help of scientific research. Through this kind of research, the entire spectrum of genetic diversity to be found in the human species was to be explored with the hope of generating a better understanding of the history of humankind. An important part of this genome diversity research consists in taking blood and tissue samples from indigenous populations. For various reasons, it has not been possible to execute this project in the planned scope and form to date. Nevertheless, genomic diversity research addresses complex issues which prove to be highly relevant from the perspective of research ethics, transcultural medical ethics, and cultural philosophy. In the article at hand, we discuss these ethical issues as illustrated by the HGDP. This investigation focuses on the confrontation of culturally diverse images of humans and their cosmologies within the framework of genome diversity research and the ethical questions it raises. We argue that in addition to complex questions pertaining to research ethics such as informed consent and autonomy of probands, genome diversity research also has a cultural–philosophical, meta-ethical, and phenomenological dimension which must be taken into account in ethical discourses. Acknowledging this fact, we attempt to show the limits of current guidelines used in international genome diversity studies, following this up by a formulation of theses designed to facilitate an appropriate inquiry and ethical evaluation of intercultural dimensions of genome research.     

Molecular epidemiology and diagnosis of Leishmania: what have we learnt from genome structure,dynamics and function?

This paper reviews our exploration of the dynamics of the Leishmania genome and its contribution to epidemiology and diagnosis. We used as a model Peruvian populations of L. (Viannia) braziliensis and L. (V.) peruviana, 2 species very close phylogenetically, but phenotypically very different in biotope and pathology. We initially focused on karyotype analysis. Our data showed that chromosomes were subject to a fast rate of evolution, and were sensitive indicators of genetic drift. Therefore, molecular karyotyping appeared an adequate tool for monitoring (i) emergence of close species, (ii) ecogeographical differentiation at the intraspecific level, and (iii) strain 'fingerprinting'. Chromosome size variation was mostly due to the number of tandemly repeated genes (rDNA, mini-exon, gp63, and cysteine proteinase genes), and could involve the deletion of unique genes (L. (V.) braziliensis-specific gp63 families). Considering the importance of these genes in parasitism, their rearrangement might have functional implications: adaptation to different environments and pleomorphic pathogenicity. Our knowledge of genome structure and dynamics was used to develop new polymerase chain reaction (PCR) techniques. Amplification of gp63 genes followed by cleavage with restriction enzymes and study of restriction fragment length polymorphism (gp63 PCR-RFLP) allowed the discrimination of all species tested, even directly in biopsies with 95% sensitivity (compared with PCR amplification of kinetoplast deoxyribonucleic acid). At the intra-specific level, RFLP was also observed and corresponded to mutations in major immunogen domains of gp63. These seem to be under strong selection pressure, and the technique should facilitate addressing how the host's immune pressure may modulate parasite population structure. Altogether, gp63 PCR-RFLP represents a significant operational improvement over the other techniques for molecular epidemiology and diagnosis: it combines sensitivity, discriminatory power and prognostic value.     

The genome and its metaphors. Detectives,heroes or prophets?

The new genetics, or the impetus given to this discipline by the Genome Project, aims to a change of paradigm of the Health Sciences. This change is postulated from a phenotypic approach to a genotypic one, thereby excluding the influence of the environment, which could seriously undermine the grounds for the development and exercise of Public Health.Since the beginning of the genome project, information on genetic discoveries has frequently been reported in the mass media. Metaphors are often used by geneticists and journalists to convey the complex concepts of genetic research for which there are no equivalents in the lay language. The media do not merely shape the social agenda but also provide the space in which health culture is constructed.We present the results of a preliminary study exploring the metaphors used in the three most widely-read national daily newspapers in Spain, namely ABC, El Pais and El Mundo, when reporting news of the new genetics. The possible consequences of the natural history of these metaphors, or the process through which figurative terms acquire a literal meaning, are discussed. A preliminary taxonomy for the metaphors identified was developed. Fifty-one out of 342 identified headings (14.8%) contained metaphors. Strategic metaphors such as program, control, code, map, and puzzle, were the most commonly used, followed by teleological ones such as mystery or God language and finally war-like metaphors such as attack, defeat, and capture. The three groups of metaphors are characterized by an attempt to giving intentionality to genes. Strategic metaphors predominated over teleological and war-like ones and thus a technocratic perspective could form the basis of the future construction of health culture.     

Environmental agents in Lake Łuknajno (Poland) affecting the genome of Chironomus melanotus Keyl, 1961 (Diptera, Chironomidae) — a new species of Polish fauna

Chironomus melanotus Keyl, a new species of Polish fauna, is described on the basis of cytogenetic characteristics. It belongs to the cytocomplex thummi with the chromosome set 2n = 8, chromosome arm combinations AB CD EF G and species-specific karyotype markers. Two types (somatic and inherited) of structural chromosome rearrangements in salivary gland chromosomes were identified in the species and somatic rearrangements (heterozygous inversions, deficiencies, deletions — Somatic index — 0.54) were observed for the first time in this species. In addition to those in the mosaic state, some genome alterations — trisomy and “B” chromosome, as well as larval malformations (10.27%) were detected for a first time. The malformations and somatic structural and genome aberrations may have been caused by different stress agents in the environment. Thus, we suggest that the high spectrum of somatic rearrangements observed in C. melanotus may indicate the existence of pollution (elevated Cd and Pb concentrations) in Lake ?uknajno (the study area) and perhaps trace metals and different chemicals produced by the Chara species.     

The human genome and translational research: how much evidence is enough?

Multiple new genomic diagnostic tests are currently under development. Given the lack of an efficient translational infrastructure, it is not clear how, or whether, robust evidence for their clinical value will be generated.     

The eMERGE genotype set of 83,717 subjects imputed to ~40 million variants genome wide and association with the herpes zoster medical record phenotype

The Electronic Medical Records and Genomics (eMERGE) network is a network of medical centers with electronic medical records linked to existing biorepository samples for genomic discovery and genomic medicine research. The network sought to unify the genetic results from 78 Illumina and Affymetrix genotype array batches from 12 contributing medical centers for joint association analysis of 83,717 human participants. In this report, we describe the imputation of eMERGE results and methods to create the unified imputed merged set of genome-wide variant genotype data. We imputed the data using the Michigan Imputation Server, which provides a missing single-nucleotide variant genotype imputation service using the minimac3 imputation algorithm with the Haplotype Reference Consortium genotype reference set. We describe the quality control and filtering steps used in the generation of this data set and suggest generalizable quality thresholds for imputation and phenotype association studies. To test the merged imputed genotype set, we replicated a previously reported chromosome 6 HLA-B herpes zoster (shingles) association and discovered a novel zoster-associated loci in an epigenetic binding site near the terminus of chromosome 3 (3p29).     

Identification of circulating porcine–human reassortant G4P[6] rotavirus from children with acute diarrhea in China by whole genome analyses

P[6] group A rotavirus (RVA) strains identified in four stool specimens collected from children with acute diarrhea in Guangxi Province, southern China in 2010, with unknown G type were further analyzed by full genomic analysis. It was revealed by whole genome sequencing that 11 genomic cognate gene segments of these P[6] RVA strains shared almost 100% nucleotide identities and all exhibited an identical G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1 genotype constellation. Phylogenetic analyses of VP7, VP1-VP4, NSP1, NSP2, NSP4 and NSP5 genes revealed that these Guangxi G4P[6] RVA strains were closely related to porcine and porcine-like human RVAs, while VP6 and NSP3 were closely related to those of common human RVAs. Interestingly, the four infants from whom these specimens were collected had come from different villages and/or towns. They had not contacted with each other and had had acute diarrhea before admitted into the same hospital. The genomic analyses and the clinical data revealed that these four Guangxi G4P[6] RVA strains from China were reassortants possessing VP6 and NSP3 gene segments of human origin yet all other nine gene segments of porcine origin. It is the first report on porcine–human reassortant G4P[6] RVA with identical genome configuration circulating in children.     

Total genome polymorphism and low frequency of intra-genomic variation in the uspA1 and uspA2 genes of Moraxella catarrhalis in otitis prone and non-prone children up to 2 years of age. Consequences for vaccine design?

Intra-genomic variation in the uspA1 and uspA2 genes of Moraxella catarrhalis was studied using pulsed field gel electrophoresis (PFGE) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. From a set of 91 M. catarrhalis isolates, 19 pairs of PFGE identical isolates were found. Five pairs originated from otitis non-prone children, 11 pairs from otitis prone children and for 3 pairs, one of the pair originated from an otitis prone and the other from an otitis non-prone child. No particular M. catarrhalis isolate was associated with either the otitis prone or non-prone children. One of these 19 pairs of isolates was found to exhibit both uspA1 and uspA2 intra-genomic variation, whilst another pair exhibited uspA2 intra-genomic variation only. Sequence data obtained from these variants showed that PCR-RFLP pattern differences reflected actual changes in predicted amino acid composition and that minor amino acid changes in a 23 base pair "NINNIY" repeat region (a conserved UspA1 and UspA2 binding site for the neutralising antibody mAb17C7) occurred. Variation in the uspA2 5' non-coding "AGAT" repeat region was also observed. These results may have implications for future M. catarrhalis vaccines comprising UspA1 or UspA2 components.     

Modification of the multiplex plasmid PCR assay for Borrelia miyamotoi strain LB-2001 based on the complete genome sequence reflecting genomic rearrangements differing from strain CT13–2396

The genome of Borrelia spp. consists of an approximate 1 megabase chromosome and multiple linear and circular plasmids. We previously described a multiplex PCR assay to detect plasmids in the North American Borrelia miyamotoi strains LB-2001 and CT13–2396. The primer pair sets specific for each plasmid were derived from the genome sequence for B. miyamotoi strain CT13–2396, because the LB-2001 complete sequence had not been generated. The recent completion of the LB-2001 genome sequence revealed a distinct number of plasmids (n = 12) that differed from CT13–2396 (n = 14). Notable was a 97-kilobase plasmid in LB-2001, not present in CT13–2396, that appeared to be a rearrangement of the circular plasmids of strain CT13–2396. Strain LB-2001 contained two plasmids, cp30–2 and cp24, that were not annotated for strain CT13–2396. Therefore, we re-evaluated the original CT13–2396-derived multiplex PCR primer pairs and determined their location in the LB-2001 plasmids. We modified the original multiplex plasmid PCR assay for strain LB-2001 to include cp30–2 and cp24. We also determined which LB-2001 plasmids corresponded to the amplicons generated from the original CT13–2396 primer sets. These observations provide a more precise plasmid profile based on the multiplex PCR assay and reflect the complexity of gene rearrangements that occur in B. miyamotoi strains isolated from the same geographic region.     

Evolutionary rates and timescale comparison of Chikungunya viruses inferred from the whole genome/E1 gene with special reference to the 2005–07 outbreak in the Indian subcontinent

Chikungunya (CHIK) virus reemerged during 2005–07 as an important pathogen causing massive disease outbreaks affecting India and several countries of the Indian Ocean. Knowledge of the evolutionary rates and divergence times of the CHIK virus may help to better understand the disease epidemiology. Considering the limited availability of such information, we estimated the substitution rates and the ancestral times for all the CHIK genotypes and also the time to the most recent common ancestor (tMRCA) of the 2005–07 isolates. Using whole genomes and partial E1 gene datasets, we applied the Bayesian Markov Chain Monte Carlo (MCMC) framework that explicitly accounts for lineage-specific evolutionary rates through the use of ‘relaxed’ molecular clock models. Under a constant population relaxed clock model, the evolutionary timescale of CHIK viruses in this study was estimated to be in the last 300 years. The progenitor of the 2005–07 viruses was found to have existed around 9 years ago, and to have originated from Central Africa. The presence of a strain in India in 2000 that bears 99% identity with a Ugandan strain of 1982, which correlates with the tMRCA of the Indian and Indian Ocean isolates, confirms our earlier report that the progenitor of the 2005–07 isolates originates from Uganda's neighbourhood. The ‘A226V’ mutation that existed in the Indian Ocean isolates since late 2005 was found to occur only in the 2007 isolate from India. The study confirms the epidemiological data, specifically with regard to the re-emergence of CHIKV and throws light on the evolutionary dynamics of CHIK viruses.     

The accuracy of parents' perceptions of children of divorceThe accuracy of parents' perceptions of children of divorce†

The present study investigated the relationship between the self‐reported attitudes and adjustment of young children of divorce (N = 48) and their parents' (N = 48) perception of this adjustment. When compared to a nuclear family control group (N = 49), the divorced parents were able to accurately assess their children's current attitudes about the family situation with the following three exceptions: child's self‐rating of feeling upset, sad or worried; current behavior problems at school; and estimates of father's emotional state. Analysis of errors made by the divorced parents revealed their tendency to over‐estimate the children's level of concern in these and other areas.

     

Validity of self-reports of psychopathology from children of 4–11 years of age

Abstract

Self-reports from children below primary age are rarely used in assessments of psychopathology. This study uses a version of the Strengths and Difficulties Questionnaire (SDQ), previously validated for children 11–15 years, to assess the internal validity of self-reports of psychopathology from primary aged children. The SDQ was completed by primary aged children (N?=?1118). The sample consisted of children who had been referred to a school counselling service. The internal validity and the factor analytical structure of the child self-reports was examined. Self-reports given by infant school-aged children (4–7 years) did not fit well with predicted factor structures, indicating that they may not have been able to report consistently or accurately on their own emotions and behaviour. However, results indicated that junior school-aged (7–11 years) children may be able to report accurately on their own symptomology. These children's reports appeared to distinguish well between internalising and externalising symptoms and fitted the hypothesized structure. However, there was some question of whether children are able to distinguish hyperactivity from other types of psychopathology. This study indicated that junior school-aged children may be able to report reliably on some aspects of their emotional and behaviour difficulties.     

Whole genome characterization of Streptococcus pneumoniae from respiratory and blood cultures collected from Canadian hospitals before and after PCV-13 implementation in Canada: Focus on serotypes 22F and 33F from CANWARD 2007–2018

The population of pneumococci circulating in Canada is constantly shifting under the pressures of antimicrobial and conjugate vaccine use. A new 15-valent pneumococcal conjugate vaccine (PCV), containing PCV-13 serotypes plus additional serotypes 22F and 33F, is currently undergoing clinical trials. The purpose of this study was to utilize whole genome sequencing to characterize invasive and respiratory Streptococcus pneumoniae isolates collected from Canadian hospitals pre- (2007–2011) and post-PCV-13 implementation (2012–2018) in Canada, particularly serotypes 22F and 33F. Isolates were obtained from the CANWARD 2007 to 2018 study. Overall, 597 S. pneumoniae isolates were sequenced using the Illumina MiSeq platform: 180 (101 respiratory, 79 blood) isolates of serotype 22F, 74 (41 respiratory, 33 blood) isolates of serotype 33F and 343 isolates randomly selected to broadly encompass pneumococci in Canada. Genomes were clustered using PopPUNK v2.0.2 and assigned to a Global Pneumococcal Sequencing Cluster (GPSC) and MLST sequence type (ST), and visualized using Cytoscape v3.8.0. Acquired resistance genes were identified using ResFinder 2.1, and genes with chromosomal mutations conferring resistance were extracted and compared to standard reference genome R6. PopPUNK clustering suggests that a clone of S. pneumoniae serotype 22F/ST433/GPSC19 demonstrating mefA-mediated macrolide resistance is emerging in Canada post-PCV-13 introduction, collected from both invasive and respiratory sources. Similarly, there is evidence to support a post-PCV-13 shift towards macrolide- and trimethoprim/sulfamethoxazole-resistant serotype 33F/ST100/GPSC3, including a cluster associated with invasive isolates. While some lineages containing vaccine serotypes were predominantly identified pre-PCV-13 implementation (serotype 5/GPSC8, serotype 7F/GPSC15), others (serotype 19A/GPSC1 and 4, serotype 3/GPSC12) continue to maintain a significant presence over time despite inclusion in PCV-13. Further genomic surveillance is necessary to determine additional trends over time in these upcoming vaccine serotypes, as well as the overall pneumococcal population in Canada.     

Socio-political aspects of the implantation of the Transplant Center of Piauí

A qualitative study aiming at understanding the socio-political aspects that mediate the implantation of the Transplant Center of Piauí, identify the social topics involved in this implantation and analyze the participation of the organized civil society. Ten people directly related to the implantation of the transplant center were involved in the study, selected through the "snowball" technique. A loosely structured interview, taped, transcribed and submitted for thematic analysis was used. It was concluded that the implantation of the transplant center in Piauí was the fruit of a complex series of negotiations and interests among the State and organized civil society, as there was no political project for action in the area of transplants. This distancing from the responsibility of the public sector characterizes the importance that was given to this implantation.