Ancestry, ethnicity, and race: explaining inequalities in cardiometabolic disease

Population differences in cardiometabolic disease remain unexplained. Misleading assumptions over genetic explanations are partly due to terminology used to distinguish populations, specifically ancestry, race, and ethnicity. These terms differentially implicate environmental and biological causal pathways, which should inform their use. Genetic variation alone accounts for a limited fraction of population differences in cardiometabolic disease. Research effort should focus on societally driven, lifelong environmental determinants of population differences in disease. Rather than pursuing population stratifiers to personalize medicine, we advocate removing socioeconomic barriers to receipt of and adherence to healthcare interventions, which will have markedly greater impact on improving cardiometabolic outcomes. This requires multidisciplinary collaboration and public and policymaker engagement to address inequalities driven by society rather than biology per se.

Radiographers' knowledge and attitudes toward dementia

INTRODUCTION

Dementia is a syndrome associated with a decline in brain function, impacting how we speak, think, feel, and behave. Misunderstanding of dementia and how it affects patients and their carers is common. There is limited research on how radiographers provide adequate care to those with dementia. Radiographers with knowledge and positive attitudes can reduce stigma and fear, improving the quality of care. This study aimed to assess radiographers' knowledge and attitudes towards dementia.

METHODS

A cohort of registered radiographers in Ireland participated in an online survey. Two pre-existing validated questionnaires: The Alzheimer's Disease Knowledge Scale (ADKS) and the Dementia Attitudes Scale (DAS), assessed radiographers' knowledge and attitudes towards dementia and people with dementia. Scores were compared across variables such as gender, age, grade, qualification, work setting, and the number of years qualified.

RESULTS

A total of 123 radiographers responded. Knowledge scores did not significantly differ across demographic groups (p > 0.05). Total knowledge scores ranged from 60% to 100%. Total attitude scores ranged from 50% to 100%. Participants with a BSc, MSc, and other post-graduate degrees scored higher on the attitude scale than those with a diploma qualification (p = 0.027). Those with less than 20 years' experience scored higher than those with more. Knowledge had little correlation with attitude (r = 0.0522; p = 0.5667).

CONCLUSION

Findings indicate variations in attitudes linked to age and experience, and some misconceptions can be observed across varying groups. Interventions to improve attitudes and raise awareness are needed.

IMPLICATIONS FOR PRACTICE

There is a need for further research and education on dementia care in the imaging department. We have identified areas requiring further education.

NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naïve pluripotent stem cells

Gene duplication events can drive evolution by providing genetic material for new gene functions, and they create opportunities for diverse developmental strategies to emerge between species. To study the contribution of duplicated genes to human early development, we examined the evolution and function of NANOGP1, a tandem duplicate of the transcription factor NANOG. We found that NANOGP1 and NANOG have overlapping but distinct expression profiles, with high NANOGP1 expression restricted to early epiblast cells and naïve-state pluripotent stem cells. Sequence analysis and epitope-tagging revealed that NANOGP1 is protein coding with an intact homeobox domain. The duplication that created NANOGP1 occurred earlier in primate evolution than previously thought and has been retained only in great apes, whereas Old World monkeys have disabled the gene in different ways, including homeodomain point mutations. NANOGP1 is a strong inducer of naïve pluripotency; however, unlike NANOG, it is not required to maintain the undifferentiated status of human naïve pluripotent cells. By retaining expression, sequence and partial functional conservation with its ancestral copy, NANOGP1 exemplifies how gene duplication and subfunctionalisation can contribute to transcription factor activity in human pluripotency and development.

Identifying barriers to Irish traveller women attending breast screening

INTRODUCTION

Breast cancer is one of the most prevalent cancers in women, however Irish Traveller women have lower breast screening rates than that of the general population. This work aims to address the gap in knowledge of Irish Traveller womens' perceptions of breast screening and the perceived barriers and enablers to attendance.

METHODS

This phenomenological qualitative study involves interviews with Irish Traveller women and Health Care Professionals and discusses the incentives and barriers to attending breast screening mammography in Ireland. The work investigated attitudes and decision making amongst the Irish Traveller women across breast screening and breast health. The research investigated the participants knowledge, experience and opinions about the topic of Irish Traveller womens' attendance at BreastCheck and breast health RESULTS: Influences that create barriers to breast screening for Irish Traveller women include inequality and family/community support, fear, literacy and education, embarrassment and the health care professional, stress and appointment suitability. Findings also demonstrate inadequate data and information is available in Ireland regarding Irish Traveller women attending breast screening.

CONCLUSION

Irish Traveller women face several influences when it comes to attending breast screening. The existing Irish national breast screening programme provides a health promotion service however, it is impossible to assess poor attendance at screening without the presence of an ethnic identifier. It would be very beneficial for screening promotion to record the ethnicity of attendees for statistical progress. This would benefit Irish Traveller women by recording the progress of attendance in the breast screening programme and creating a need for awareness and education within the annual reports.

IMPLICATIONS FOR PRACTICE

Creating awareness and educating Irish Traveller women about the breast screening programme may remove barriers and lead to improved attendance rates.

Short-range template switching in great ape genomes explored using pair hidden Markov models

Many complex genomic rearrangements arise through template switch errors, which occur in DNA replication when there is a transient polymerase switch to an alternate template nearby in three-dimensional space. While typically investigated at kilobase-to-megabase scales, the genomic and evolutionary consequences of this mutational process are not well characterised at smaller scales, where they are often interpreted as clusters of independent substitutions, insertions and deletions. Here we present an improved statistical approach using pair hidden Markov models, and use it to detect and describe short-range template switches underlying clusters of mutations in the multi-way alignment of hominid genomes. Using robust statistics derived from evolutionary genomic simulations, we show that template switch events have been widespread in the evolution of the great apes’ genomes and provide a parsimonious explanation for the presence of many complex mutation clusters in their phylogenetic context. Larger-scale mechanisms of genome rearrangement are typically associated with structural features around breakpoints, and accordingly we show that atypical patterns of secondary structure formation and DNA bending are present at the initial template switch loci. Our methods improve on previous non-probabilistic approaches for computational detection of template switch mutations, allowing the statistical significance of events to be assessed. By specifying realistic evolutionary parameters based on the genomes and taxa involved, our methods can be readily adapted to other intra- or inter-species comparisons.

DNA replication is an imperfect process which causes the mutations that give rise to genetic diversity during the evolution of genomes. While many mutations are independent, single-nucleotide substitutions or small insertions and deletions, some mutations arise as nonindependent clusters of substitutions and larger scale chromosomal rearrangements. Large-scale rearrangements (also called structural variants) in particular can have a profound impact on genome evolution and contribute to both germline and somatic disease in humans. The replication-based mechanisms underlying structural variation typically involve a polymerase switch event in which a large segment of DNA is copied using a template from an alternate location in the genome. Methods for identifying these template switch mutations lack the power to detect smaller scale rearrangements which can arise through the same replication-based pathways. Here we outline a model which can detect and assess the statistical significance of such small-scale template switches within their evolutionary context. We show that these events are widespread in the evolution of great apes and that the genomic features associated with these small-scale rearrangements are similar to those of large-scale structural variants.

Insights into human genetic variation and population history from 929 diverse genomes

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.

Genomes reveal marked differences in the adaptive evolution between orangutan species

BACKGROUND

Integrating demography and adaptive evolution is pivotal to understanding the evolutionary history and conservation of great apes. However, little is known about the adaptive evolution of our closest relatives, in particular if and to what extent adaptions to environmental differences have occurred. Here, we used whole-genome sequencing data from critically endangered orangutans from North Sumatra (Pongo abelii) and Borneo (P. pygmaeus) to investigate adaptive responses of each species to environmental differences during the Pleistocene.

RESULTS

Taking into account the markedly disparate demographic histories of each species after their split ~ 1 Ma ago, we show that persistent environmental differences on each island had a strong impact on the adaptive evolution of the genus Pongo. Across a range of tests for positive selection, we find a consistent pattern of between-island and species differences. In the more productive Sumatran environment, the most notable signals of positive selection involve genes linked to brain and neuronal development, learning, and glucose metabolism. On Borneo, however, positive selection comprised genes involved in lipid metabolism, as well as cardiac and muscle activities.

CONCLUSIONS

We find strikingly different sets of genes appearing to have evolved under strong positive selection in each species. In Sumatran orangutans, selection patterns were congruent with well-documented cognitive and behavioral differences between the species, such as a larger and more complex cultural repertoire and higher degrees of sociality. However, in Bornean orangutans, selective responses to fluctuating environmental conditions appear to have produced physiological adaptations to generally lower and temporally more unpredictable food supplies.

Detecting archaic introgression using an unadmixed outgroup

Human populations outside of Africa have experienced at least two bouts of introgression from archaic humans, from Neanderthals and Denisovans. In Papuans there is prior evidence of both these introgressions. Here we present a new approach to detect segments of individual genomes of archaic origin without using an archaic reference genome. The approach is based on a hidden Markov model that identifies genomic regions with a high density of single nucleotide variants (SNVs) not seen in unadmixed populations. We show using simulations that this provides a powerful approach to identifying segments of archaic introgression with a low rate of false detection, given data from a suitable outgroup population is available, without the archaic introgression but containing a majority of the variation that arose since initial separation from the archaic lineage. Furthermore our approach is able to infer admixture proportions and the times both of admixture and of initial divergence between the human and archaic populations. We apply the model to detect archaic introgression in 89 Papuans and show how the identified segments can be assigned to likely Neanderthal or Denisovan origin. We report more Denisovan admixture than previous studies and find a shift in size distribution of fragments of Neanderthal and Denisovan origin that is compatible with a difference in admixture time. Furthermore, we identify small amounts of Denisova ancestry in South East Asians and South Asians.

The genetic history of present-day individuals includes episodes of mating between divergent groups, which have led to 'introgressed' genetic material persisting in modern genome sequences. Perhaps the most notable examples of such events in humans are the introgressions from Neanderthals into non-Africans 50,000 or so years ago, and from a related archaic group known as Denisovans into the ancestors of indigenous people from Papua-New Guinea and Australia. Methods to identify introgressions and the genomic regions that derive from them generally involve the use of reference genome sequences for the source populations. However, there are advantages in having methods independent of reference sequences, both to reduce bias and to detect possible introgression from groups for which we currently lack a reference genome. In this paper we describe such an approach, in a statistical framework which exploits the fact that introgressed regions will contain a high density of genetic variants that are private to the group receiving the divergent material. We apply this method to 89 Papuan genome sequences, estimating times of introgression and initial divergence between archaic and modern humans, and compare it to other related methods.

Ancient human parallel lineages within North America contributed to a coastal expansion

Little is known regarding the first people to enter the Americas and their genetic legacy. Genomic analysis of the oldest human remains from the Americas showed a direct relationship between a Clovis-related ancestral population and all modern Central and South Americans as well as a deep split separating them from North Americans in Canada. We present 91 ancient human genomes from California and Southwestern Ontario and demonstrate the existence of two distinct ancestries in North America, which possibly split south of the ice sheets. A contribution from both of these ancestral populations is found in all modern Central and South Americans. The proportions of these two ancestries in ancient and modern populations are consistent with a coastal dispersal and multiple admixture events.

Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species

Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive. VIDEO ABSTRACT.

Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes

Heterozygous mutations within homozygous sequences descended from a recent common ancestor offer a way to ascertain de novo mutations across multiple generations. Using exome sequences from 3222 British-Pakistani individuals with high parental relatedness, we estimate a mutation rate of 1.45 ± 0.05 × 10-8 per base pair per generation in autosomal coding sequence, with a corresponding non-crossover gene conversion rate of 8.75 ± 0.05 × 10-6 per base pair per generation. This is at the lower end of exome mutation rates previously estimated in parent-offspring trios, suggesting that post-zygotic mutations contribute little to the human germ-line mutation rate. We find frequent recurrence of mutations at polymorphic CpG sites, and an increase in C to T mutations in a 5' CCG 3' to 5' CTG 3' context in the Pakistani population compared to Europeans, suggesting that mutational processes have evolved rapidly between human populations.Estimates of human mutation rates differ substantially based on the approach. Here, the authors present a multi-generational estimate from the autozygous segment in a non-European population that gives insight into the contribution of post-zygotic mutations and population-specific mutational processes.

Global clues to the nature of genomic mutations in humans

An analysis of worldwide human genetic variation reveals the footprints of ancient changes in genomic mutation processes.

Inference of Candidate Germline Mutator Loci in Humans from Genome-Wide Haplotype Data

The rate of germline mutation varies widely between species but little is known about the extent of variation in the germline mutation rate between individuals of the same species. Here we demonstrate that an allele that increases the rate of germline mutation can result in a distinctive signature in the genomic region linked to the affected locus, characterized by a number of haplotypes with a locally high proportion of derived alleles, against a background of haplotypes carrying a typical proportion of derived alleles. We searched for this signature in human haplotype data from phase 3 of the 1000 Genomes Project and report a number of candidate mutator loci, several of which are located close to or within genes involved in DNA repair or the DNA damage response. To investigate whether mutator alleles remained active at any of these loci, we used de novo mutation counts from human parent-offspring trios in the 1000 Genomes and Genome of the Netherlands cohorts, looking for an elevated number of de novo mutations in the offspring of parents carrying a candidate mutator haplotype at each of these loci. We found some support for two of the candidate loci, including one locus just upstream of the BRSK2 gene, which is expressed in the testis and has been reported to be involved in the response to DNA damage.

Chimpanzee genomic diversity reveals ancient admixture with bonobos

Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales. Multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another, possibly more recent contact (after 200,000 years ago), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.

The mutation rate in human evolution and demographic inference

The germline mutation rate has long been a major source of uncertainty in human evolutionary and demographic analyses based on genetic data, but estimates have improved substantially in recent years. I discuss our current knowledge of the mutation rate in humans and the underlying biological factors affecting it, which include generation time, parental age and other developmental and reproductive timescales. There is good evidence for a slowdown in mean mutation rate during great ape evolution, but not for a more recent change within the timescale of human genetic diversity. Hence, pending evidence to the contrary, it is reasonable to use a present-day rate of approximately 0.5×10^-9bp^-1year^-1 in all human or hominin demographic analyses.

Mutation rates and the evolution of germline structure

Genome sequencing studies of de novo mutations in humans have revealed surprising incongruities in our understanding of human germline mutation. In particular, the mutation rate observed in modern humans is substantially lower than that estimated from calibration against the fossil record, and the paternal age effect in mutations transmitted to offspring is much weaker than expected from our long-standing model of spermatogenesis. I consider possible explanations for these discrepancies, including evolutionary changes in life-history parameters such as generation time and the age of puberty, a possible contribution from undetected post-zygotic mutations early in embryo development, and changes in cellular mutation processes at different stages of the germline. I suggest a revised model of stem-cell state transitions during spermatogenesis, in which 'dark' gonial stem cells play a more active role than hitherto envisaged, with a long cycle time undetected in experimental observations. More generally, I argue that the mutation rate and its evolution depend intimately on the structure of the germline in humans and other primates.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

Rethinking the dispersal of Homo sapiens out of Africa

Current fossil, genetic, and archeological data indicate that Homo sapiens originated in Africa in the late Middle Pleistocene. By the end of the Late Pleistocene, our species was distributed across every continent except Antarctica, setting the foundations for the subsequent demographic and cultural changes of the Holocene. The intervening processes remain intensely debated and a key theme in hominin evolutionary studies. We review archeological, fossil, environmental, and genetic data to evaluate the current state of knowledge on the dispersal of Homo sapiens out of Africa. The emerging picture of the dispersal process suggests dynamic behavioral variability, complex interactions between populations, and an intricate genetic and cultural legacy. This evolutionary and historical complexity challenges simple narratives and suggests that hybrid models and the testing of explicit hypotheses are required to understand the expansion of Homo sapiens into Eurasia.

BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data

Summary: Runs of homozygosity (RoHs) are genomic stretches of a diploid genome that show identical alleles on both chromosomes. Longer RoHs are unlikely to have arisen by chance but are likely to denote autozygosity, whereby both copies of the genome descend from the same recent ancestor. Early tools to detect RoH used genotype array data, but substantially more information is available from sequencing data. Here, we present and evaluate BCFtools/RoH, an extension to the BCFtools software package, that detects regions of autozygosity in sequencing data, in particular exome data, using a hidden Markov model. By applying it to simulated data and real data from the 1000 Genomes Project we estimate its accuracy and show that it has higher sensitivity and specificity than existing methods under a range of sequencing error rates and levels of autozygosity.

Availability and implementation: BCFtools/RoH and its associated binary/source files are freely available from https://github.com/samtools/BCFtools.

Contact:vn2@sanger.ac.uk or pd3@sanger.ac.uk

Supplementary information:Supplementary data are available at Bioinformatics online.

Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians

The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt.

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

Mountain gorillas are an endangered great ape subspecies and a prominent focus for conservation, yet we know little about their genomic diversity and evolutionary past. We sequenced whole genomes from multiple wild individuals and compared the genomes of all four Gorilla subspecies. We found that the two eastern subspecies have experienced a prolonged population decline over the past 100,000 years, resulting in very low genetic diversity and an increased overall burden of deleterious variation. A further recent decline in the mountain gorilla population has led to extensive inbreeding, such that individuals are typically homozygous at 34% of their sequence, leading to the purging of severely deleterious recessive mutations from the population. We discuss the causes of their decline and the consequences for their future survival.

The impact of immediate reporting on interpretive discrepancies and patient referral pathways within the emergency department: a randomised controlled trial

OBJECTIVE

To determine whether an immediate reporting service for musculoskeletal trauma reduces interpretation errors and positively impacts on patient referral pathways.

METHODS

A pragmatic multicentre randomised controlled trial was undertaken. 1502 patients were recruited and randomly assigned to an immediate or delayed reporting arm and treated according to group assignment. Assessment was made of concordance in image interpretation between emergency department (ED) clinicians and radiology; discharge and referral pathways; and patient journey times.

RESULTS

1688 radiographic examinations were performed (1502 patients). 91 discordant interpretations were identified (n=91/1688; 5.4%) with a greater number of discordant interpretations noted in the delayed reporting arm (n=67/849, 7.9%). In the immediate reporting arm, the availability of a report reduced, but did not eliminate, discordance in interpretation (n=24/839, 2.9%). No significant difference in number of patients discharged, referred to hospital clinics or admitted was identified. However, patient ED recalls were significantly reduced (z=2.66; p=0.008) in the immediate reporting arm, as were the number of short-term inpatient bed days (5 days or less) (z=3.636; p<0.001). Patient journey time from ED arrival to discharge or admission was equivalent (z=0.79, p=0.432).

CONCLUSION

Immediate reporting significantly reduced ED interpretive errors and prevented errors that would require patient recall. However, immediate reporting did not eliminate ED interpretative errors or change the number of patients discharged, referred to hospital clinics or admitted overall.

ADVANCES IN KNOWLEDGE

This is the first study to consider the wider impact of immediate reporting on the ED patient pathway as a whole and hospital resource usage.

A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species

We present a hidden Markov model (HMM) for inferring gradual isolation between two populations during speciation, modelled as a time interval with restricted gene flow. The HMM describes the history of adjacent nucleotides in two genomic sequences, such that the nucleotides can be separated by recombination, can migrate between populations, or can coalesce at variable time points, all dependent on the parameters of the model, which are the effective population sizes, splitting times, recombination rate, and migration rate. We show by extensive simulations that the HMM can accurately infer all parameters except the recombination rate, which is biased downwards. Inference is robust to variation in the mutation rate and the recombination rate over the sequence and also robust to unknown phase of genomes unless they are very closely related. We provide a test for whether divergence is gradual or instantaneous, and we apply the model to three key divergence processes in great apes: (a) the bonobo and common chimpanzee, (b) the eastern and western gorilla, and (c) the Sumatran and Bornean orang-utan. We find that the bonobo and chimpanzee appear to have undergone a clear split, whereas the divergence processes of the gorilla and orang-utan species occurred over several hundred thousands years with gene flow stopping quite recently. We also apply the model to the Homo/Pan speciation event and find that the most likely scenario involves an extended period of gene flow during speciation.

Revising the human mutation rate: implications for understanding human evolution

It is now possible to make direct measurements of the mutation rate in modern humans using next-generation sequencing. These measurements reveal a value that is approximately half of that previously derived from fossil calibration, and this has implications for our understanding of demographic events in human evolution and other aspects of population genetics. Here, we discuss the implications of a lower-than-expected mutation rate in relation to the timescale of human evolution.

Insights into hominid evolution from the gorilla genome sequence

Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

A large genome center's improvements to the Illumina sequencing system

The Wellcome Trust Sanger Institute is one of the world's largest genome centers, and a substantial amount of our sequencing is performed with 'next-generation' massively parallel sequencing technologies: in June 2008 the quantity of purity-filtered sequence data generated by our Genome Analyzer (Illumina) platforms reached 1 terabase, and our average weekly Illumina production output is currently 64 gigabases. Here we describe a set of improvements we have made to the standard Illumina protocols to make the library preparation more reliable in a high-throughput environment, to reduce bias, tighten insert size distribution and reliably obtain high yields of data.

Self-expandable metal stent placement for the palliation of malignant gastroduodenal obstruction: experience in a large, single, UK centre

AIM

To assess the technical success rate, and evaluate the clinical outcome, length of hospital stay, and cost of palliative gastro-duodenal stenting in a single-centre.

MATERIALS AND METHODS

Eight-seven patients referred for insertion of a gastroduodenal stent between April 1999 and April 2004 were recruited to a non-randomized, before and after intervention study performed in a single centre. Demographic data, diagnosis and symptoms along with clinical and technical outcomes were recorded.

RESULTS

The technical success rate was 84/87 (96.6%), with inability to traverse the stricture in three patients. No immediate complications were demonstrated. There was marked improvement after stent placement with resolution of symptoms and commencement of dietary intake in 76 patients (87%). Stenting resulted in improved quality of life as reflected by an increase in Karnofsky score from 44/100, to 63/100 post-procedure. Late complications included perforation (n=1), migration (n=1) and stent occlusions due to tumour ingrowth/overgrowth (n=7; mean 165 days). Mean survival was 107 days (range 0-411 days). Median hospital stay post-stent placement was 5.5 days, (range 1-55 days) with a majority of patients (75%) discharged home. The mean cost of each treatment episode was 4146 pounds ($7132 $US, 6,028 EUROS).

CONCLUSION

The present series confirms that combined endoscopic and radiological gastroduodenal stenting is a highly favourable treatment for patients with inoperable malignant gastric outlet obstruction. The results suggest that this minimally invasive procedure has a very high technical success rate, whilst at the same time providing excellent palliation of symptoms with improved quality of life in the majority of patients.

Quality of care in diabetic patients attending routine primary care clinics compared with those attending GP specialist clinics

AIM

To determine the impact on clinical outcomes of specialist diabetes clinics compared with routine primary care clinics.

METHODS

Observational study measuring clinical performance (process/outcome measures) in the primary care sector. A cohort of patients attending specialist diabetes clinics was compared with a control cohort of patients attending routine primary care clinics.

RESULTS

Patients seen in specialist diabetes clinics had a significantly higher HbA1c than patients in routine primary care clinics (mean difference 0.58%; P < 0.001) but there was no significant difference in rate of improvement with visits compared with primary care clinics. In contrast, patients seen in the routine primary care clinics had significantly higher cholesterol levels (mean difference 0.24 mmol/l; P < 0.001) compared with patients in specialist diabetes clinics and their improvement was significantly greater over time (mean difference 0.14 mmol/l per visit compared with 0.10 mmol/l; P < 0.006). Patients in routine primary care clinics also had significantly higher diastolic blood pressure (mean difference 1.6 mmHg; P < 0.007) but there was no difference in improvement with time compared with specialist diabetes clinics. Uptake of podiatry and retinal screening was significantly lower in patients attending routine primary care clinics, but this difference disappeared with time, with significant increases in uptake in the primary care clinic group. Weight increased in both groups significantly with time, but more so in the specialist clinic patients (mean increase 0.18 kg per visit more compared with routine clinic primary care patients; P < 0.001).

CONCLUSIONS

This study provides evidence that the provision of primary care services for patients with diabetes, whether traditional general practitioner clinics or diabetes clinics run by general practitioners with special interests, is effective in reducing HbA1c, cholesterol and blood pressure. However, the same provision of care was unable to prevent increasing weight or creatinine over time. No evidence was found that patients in specialist clinics do better than patients in routine primary care clinics.

Accuracy of radiographers red dot or triage of accident and emergency radiographs in clinical practice: a systematic review

AIM

To determine the accuracy of radiographers red dot or triage of accident and emergency (A&E) radiographs in clinical practice.

MATERIALS AND METHODS

Eligible studies assessed radiographers red dot or triage of A&E radiographs in clinical practice compared with a reference standard and provided accuracy data to construct 2 x 2 tables. Data were extracted on study eligibility and characteristics, quality, and accuracy. Pooled sensitivities and specificities and chi-square tests of heterogeneity were calculated.

RESULT

Three red dot and five triage studies were eligible for inclusion. Radiographers' red dot of A&E radiographs in clinical practice compared with a reference standard is 0.87 [95% confidence interval (CI) 0.85-0.89] and 0.92 (0.91-0.93) sensitivity and specificity, respectively. Radiographers' triage of A&E radiographs of the skeleton is 0.90 (0.89-0.92) and 0.94 (0.93-0.94) sensitivity and specificity, respectively; and for chest and abdomen is 0.78 (0.74-0.82) and 0.91 (0.88-0.93). Radiographers' red dot of skeletal A&E radiographs without training is 0.71 (0.62-0.79) and 0.96 (0.93-0.97) sensitivity and specificity, respectively; and with training is 0.81 (0.72-0.87) and 0.95 (0.93-0.97). Pooled sensitivity and specificity for radiographers without training for the triage of skeletal A&E radiographs is 0.89 (0.88-0.91) and 0.93 (0.92-0.94); and with training is 0.91 (0.88-0.94) and 0.95 (0.93-0.96).

CONCLUSION

Radiographers red dot or triage of A&E radiographs in clinical practice is affected by body area, but not by training.

Accuracy of radiographer plain radiograph reporting in clinical practice: a meta-analysis

AIM

To determine the accuracy of radiographer plain radiograph reporting in clinical practice.

MATERIALS AND METHODS

Studies were identified from electronic sources and by hand searching journals, personal communication and checking reference lists. Eligible studies assessed radiographers' plain radiograph reporting in clinical practice compared with a reference standard, and provided accuracy data to construct 2 x 2 contingency tables. Data were extracted on study eligibility and characteristics, quality and accuracy. Summary estimates of sensitivity and specificity and receiver operating characteristic curves were used to pool the accuracy data.

RESULTS

Radiographers compared with a reference standard, report plain radiographs in clinical practice at 92.6% (95% CI: 92.0-93.2) and 97.7% (95% CI: 97.5-97.9) sensitivity and specificity, respectively. Studies that compared selectively trained radiographers and radiologists of varying seniority against a reference standard showed no evidence of a difference between radiographer and radiologist reporting accuracy of accident and emergency plain radiographs. Selectively trained radiographers were also found to report such radiographs as accurately as those not solely from accident and emergency, although some variation in reporting accuracy was found for different body areas. Training radiographers improved their accuracy when reporting normal radiographs.

CONCLUSION

This study systematically synthesizes the literature to provide an evidence-base showing that radiographers can accurately report plain radiographs in clinical practice.