BSHI/BTS guidance on crossmatching before deceased donor kidney transplantation.

All UK H&I laboratories and transplant units operate under a single national kidney offering policy, but there have been variations in approach regarding when to undertake the pre-transplant crossmatch test. In order to minimize cold ischaemia times for deceased donor kidney transplantation we sought to find ways to be able to report a crossmatch result as early as possible in the donation process. A panel of experts in transplant surgery, nephrology, specialist nursing in organ donation and H&I (all relevant UK laboratories represented) assessed evidence and opinion concerning five factors that relate to the effectiveness of the crossmatch process, as follows: when the result should be ready for reporting; what level of donor HLA typing is needed; crossmatch sample type and availability; fairness and equity; risks and patient safety. Guidelines aimed at improving practice based on these issues are presented, and we expect that following these will allow H&I laboratories to contribute to reducing CIT in deceased donor kidney transplantation.

Investigating diagnostic sequencing techniques for CADASIL diagnosis.

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a cerebral small vessel disease caused by mutations in the NOTCH3 gene. Our laboratory has been undertaking genetic diagnostic testing for CADASIL since 1997. Work originally utilised Sanger sequencing methods targeting specific NOTCH3 exons. More recently, next-generation sequencing (NGS)-based technologies such as a targeted gene panel and whole exome sequencing (WES) have been used for improved genetic diagnostic testing. In this study, data from 680 patient samples was analysed for 764 tests utilising 3 different sequencing technologies. Sanger sequencing was performed for 407 tests, a targeted NGS gene panel which includes NOTCH3 exonic regions accounted for 354 tests, and WES with targeted analysis was performed for 3 tests. In total, 14.7% of patient samples (n = 100/680) were determined to have a mutation. Testing efficacy varied by method, with 10.8% (n = 44/407) of tests using Sanger sequencing able to identify mutations, with 15.8% (n = 56/354) of tests performed using the NGS custom panel successfully identifying mutations and a likely non-NOTCH3 pathogenic variant (n = 1/3) identified through WES. Further analysis was then performed through stratification of the number of mutations detected at our facility based on the number of exons, level of pathogenicity and the classification of mutations as known or novel. A systematic review of NOTCH3 mutation testing data from 1997 to 2017 determined the diagnostic rate of pathogenic findings and found the NGS-customised panel increases our ability to identify disease-causing mutations in NOTCH3.

Genetic variants associated with exercise performance in both moderately trained and highly trained individuals.

Adaptation to exercise training is a complex trait that may be influenced by genetic variants. We identified 36 single nucleotide polymorphisms (SNPs) that had been previously associated with endurance or strength performance, exercise-related phenotypes or exercise intolerant disorders. A MassARRAY multiplex genotyping assay was designed to identify associations with these SNPs against collected endurance fitness phenotype parameters obtained from two exercise cohorts (Gene SMART study; n = 58 and Hawaiian Ironman Triathlon 2008; n = 115). These parameters included peak power output (PP), a time trial (TT), lactate threshold (LT), maximal oxygen uptake (VO2 max) in recreationally active individuals and a triathlon time-to-completion (Hawaiian Ironman Triathlon cohort only). A nominal significance threshold of α < 0.05 was used to identify 17 variants (11 in the Gene SMART population and six in the Hawaiian Ironman Triathlon cohort) which were significantly associated with performance gains in highly trained individuals. The variant rs1474347 located in Interleukin 6 (IL6) was the only variant with a false discovery rate < 0.05 and was found to be associated with gains in VO2 max (additional 4.016 mL/(kg min) for each G allele inherited) after training in the Gene SMART cohort. In summary, this study found further evidence to suggest that genetic variance can influence training response in a moderately trained cohort and provides an example of the potential application of genomic research in the assessment of exercise trait response.

The aquatic animal pandemic crisis.

The growth of aquaculture over the past 50 years has been accompanied by the emergence of aquatic animal diseases, many of which have spread to become pandemic in countries or continents. An analysis of 400 emerging disease events in aquatic animals that were logged by the Centre for Environment, Fisheries and Aquaculture Science between 2002 and 2017 revealed that more than half were caused by viruses. However, in molluscs, most events were parasitic. Categorising these events indicated that the key processes underpinning emergence were the movement of live animals and host switching. Profiles of key pathogens further illustrate the importance of wild aquatic animals as the source of new infections in farmed animals. It is also clear that the spread of new diseases through the largescale movement of aquatic animals for farming, for food and for the ornamental trade has allowed many to achieve pandemic status. Many viral pathogens of fish (e.g. infectious salmon anaemia, viral haemorrhagic septicaemia) and shrimp (e.g. white spot syndrome virus) affect a large proportion of the global production of key susceptible species. Wild aquatic animal populations have also been severely affected by pandemic diseases, best exemplified by Batrachochytrium dendrobatidis, a fungal infection of amphibians, whose emergence and spread were driven by the movement of animals for the ornamental trade. Batrachochytrium dendrobatidis is now widespread in the tropics and subtropics and has caused local extinctions of susceptible amphibian hosts. Given the rising demand for seafood, aquacultural production will continue to grow and diseases will continue to emerge. Some will inevitably achieve pandemic status, having significant impacts on production and trade, unless there are considerable changes in global monitoring and the response to aquatic animal diseases.

Au cours des 50 dernières années, la forte croissance qu'a connue l'aquaculture est allée de pair avec l'émergence de nombreuses maladies affectant les animaux aquatiques, dont certaines se sont propagées jusqu'à devenir pandémiques à l'échelle nationale ou continentale. L'analyse de 400 événements sanitaires survenus chez des animaux aquatiques et consignés entre 2002 et 2017 par le Centre for Environment, Fisheries and Aquaculture Science a déterminé l'origine virale de plus de la moitié d'entre eux. Toutefois, chez les mollusques la plupart des événements analysés étaient d'ordre parasitaire. Le classement des événements par catégories a montré que les principaux processus sous-jacents à cette émergence étaient liés aux transferts d'animaux vivants et à la colonisation de nouveaux hôtes par les agents pathogènes. Les profils des agents pathogènes majeurs illustrent le rôle des espèces aquatiques sauvages en tant que sources d'infections nouvelles chez les animaux aquatiques d'élevage. Il apparaît clairement que la propagation de nouvelles maladies à la faveur des transferts massifs d'animaux aquatiques à des fins d'élevage, de production alimentaire ou de commerce d'espèces d'ornement a conféré un statut pandémique à nombre de ces maladies. De nombreux virus affectant les poissons (par ex., le virus de l'anémie infectieuse du saumon, le virus de la septicémie hémorragique virale) et les crevettes (par ex., le virus du syndrome des points blancs) ont une incidence majeure sur de vastes segments de la production mondiale d'espèces sensibles cruciales. Les populations sauvages d'animaux aquatiques sont également touchées par des maladies pandémiques, dont l'exemple type est l'infection à Batrachochytrium dendrobatidis, une affection fongique des amphibiens dont l'émergence et la propagation sont le fruit des transferts d'animaux aquatiques destinés au commerce aquariophile. Batrachochytrium dendrobatidis est désormais largement présent dans les eaux tropicales et subtropicales où il est responsable d'extinctions locales parmi les espèces d'amphibiens sensibles. La croissance de la production aquacole se poursuivra afin de répondre à une demande toujours plus forte en poissons et fruits de mer, entraînant l'émergence continue de nouvelles maladies. Si des changements déterminants ne sont pas introduits dans la surveillance exercée au niveau mondial sur les maladies des animaux aquatiques et dans la réponse qui leur est apportée, certaines de ces maladies vont inéluctablement acquérir une dimension pandémique avec des conséquences importantes sur la production et le commerce.

El crecimiento de la acuicultura en los últimos 50 años se ha acompañado de la aparición de enfermedades de los animales acuáticos, que en muchos casos se han propagado hasta llegar a ser pandémicas en ciertos países o continentes. Tras analizar 400 episodios de enfermedades emergentes de animales acuáticos registrados entre 2002 y 2017 por el Centre for the Environment, Fisheries and Aquaculture Science, los autores constataron que más de la mitad de esos episodios fueron causados por virus, si bien en el caso de los moluscos la mayoría de ellos eran parasitarios. De la clasificación de esos episodios se desprende que los procesos básicos que subyacen a su aparición son los desplazamientos de animales vivos y los cambios de anfitrión. El perfil de los principales patógenos revela además la importancia que revisten los animales acuáticos silvestres como fuente de nuevas infecciones de los animales de acuicultura. También está claro que la propagación de nuevas enfermedades por el movimiento a gran escala de animales acuáticos con fines de producción acuícola, consumo alimentario o comercio de animales ornamentales ha propiciado que muchas de ellas adquieran carácter pandémico. Muchos patógenos víricos de los peces (como el virus de la anemia infecciosa del salmón o el de la septicemia hemorrágica viral) y camarones (como el virus del síndrome de las manchas blancas) afectan a una gran parte de la producción mundial de las principales especies sensibles. Las poblaciones silvestres de animales acuáticos también se han visto afectadas de gravedad por enfermedades pandémicas, como ejemplifica perfectamente la infección por Batrachochytrium dendrobatidis, micosis de los anfibios cuya aparición y propagación fue alimentada por el comercio y el consiguiente movimiento de animales con fines ornamentales. Este hongo, muy extendido ahora en las regiones tropicales y subtropicales, ha causado la extinción en ciertas áreas de especies anfibias sensibles. Habida cuenta de la creciente demanda de alimentos de origen marino, la producción acuícola seguirá creciendo y también seguirán surgiendo enfermedades. Inevitablemente, algunas de ellas se harán pandémicas y resultarán muy dañinas para la producción y el comercio, a menos que haya cambios de calado en los sistemas mundiales de vigilancia y respuesta ante las enfermedades de los animales acuáticos.

Geisinger high-risk osteoporosis clinic (HiROC): 2013-2015 FLS performance analysis.

Geisinger Health System (GHS) high-risk osteoporosis clinic (HiROC), which treats patients with low-trauma, fragility fractures, reports their 2013-2015 performance measures in secondary fracture prevention. This fracture liaison service (FLS) pathway treats 75% of high-risk, drug eligible patients, compared to 13.8% in GHS primary care. This performance points to the need for more FLS programs throughout the world. INTRODUCTION: The purpose of this study is to analyze and report ongoing performance measures in outpatient and inpatient high-risk osteoporosis clinic (HiROC) program designed for patients with low-trauma, fragility fractures. METHODS: Retrospective chart review of outpatient HiROC (511 patients) and inpatient HiROC (1279 patients) performance from 2013 to 2015 is reported within Geisinger Health System (GHS). RESULTS: Similar to a prior report, we document that Geisinger's branded outpatient and inpatient HiROC pathways continue to function as an all-fracture FLS. Importantly, this analysis emphasizes the importance of FLS care that HiROC's treatment rate of 75% was markedly superior to GHS-PCP care of 13.8%. However, a large percentage of patients (37.8%) were lost to follow-up care. This led to the identification of multiple care gaps/barriers to ideal best practice. CONCLUSIONS: FLS programs use case finding strategies and address secondary fracture prevention. GHS HiROC's performance and initiation of drug therapy in this fracture patient population contrasts with GHS-PCP care's much lower rate of treatment, documenting the need for ongoing FLS care. Importantly, the results of this analysis have prompted the beginnings of GHS programmatic changes, designed to narrow the reported care gaps in this mature FLS.

Field trial to evaluate the effect of an intranasal respiratory vaccine protocol on calf health, ultrasonographic lung consolidation, and growth in Holstein dairy calves.

The objective of this field trial was to evaluate the effect of a vaccine protocol using a commercially available trivalent vaccine designed for intranasal use. Experimental challenge studies have demonstrated varying efficacies of vaccines administered via the intranasal route. A total of 468 calves from 3 herds were enrolled and randomized into 3 treatment groups (positive control, PC, n = 211; intranasal vaccine, IN, n = 215; negative control, NC, n = 42) and followed for 8 to 12 wk. The PC consisted of one dose of commercially available multivalent injectable vaccine against bovine respiratory syncytial virus, infectious bovine rhinotracheitis, parainfluenza 3, and bovine viral diarrhea administered subcutaneously at 6 wk of age. The IN was administered at enrollment and 6 wk of age, and contained antigen against bovine respiratory syncytial virus, infectious bovine rhinotracheitis, and parainfluenza 3. The NC was sterile saline administered intranasally and subcutaneously at enrollment and 6 wk of age. Clinical illness was assessed using systematic respiratory scoring, and thoracic ultrasonography was used to identify the lung consolidation associated with pneumonia. Rib fractures were identified in 6% of calves, and an association was observed between rib fractures and calving ease. Overall, 54% of the calves had at least one episode of an abnormal respiratory score (ILL). Vaccination protocol did not affect the occurrence of ILL. Similarly, 54% of the calves had at least one episode of lung consolidation ≥3 cm (CON). Vaccine protocol affected the odds of CON. The odds of CON in PC were 1.63 (95% confidence interval: 1.04-2.56) times the odds of CON in IN, and 0.38 (95% confidence interval: 0.16-0.93) times the odds of CON in NC. The odds of CON in IN were 0.23 (95% confidence interval: 0.09-0.59) times the odds of CON in NC. The outcomes ILL and CON were associated; however, the measure of agreement was only fair (kappa = 0.38). Multivariable linear regression revealed an interaction between vaccine protocol and herd on average daily gain (ADG); therefore, these data were stratified. In herd 1, IN (0.53 ± 0.03 kg/d) decreased ADG compared with PC (0.63 ± 0.03 kg/d). In herd 2, IN increased ADG (0.41 ± 0.03 kg/d) compared with PC (0.38 ± 0.03 kg/d). In contrast, none of the protocols affected ADG at herd 3. In conclusion, this commercially available trivalent IN vaccine protocol did not alter the incidence of ILL, reduced the risk of lung lesions associated with pneumonia, and improved the ADG of the calves in one of the commercial study herds.

A de novo splice site mutation in CASK causes FG syndrome-4 and congenital nystagmus.

Mutations in CASK cause X-linked intellectual disability, microcephaly with pontine and cerebellar hypoplasia, optic atrophy, nystagmus, feeding difficulties, GI hypomotility, and seizures. Here we present a patient with a de novo carboxyl-terminus splice site mutation in CASK (c.2521-2A>G) and clinical features of the rare FG syndrome-4 (FGS4). We provide further characterization of genotype-phenotype correlations in CASK mutations and the presentation of nystagmus and the FGS4 phenotype. There is considerable variability in clinical phenotype among patients with a CASK mutation, even among variants predicted to have similar functionality. Our patient presented with developmental delay, nystagmus, and severe gastrointestinal and gastroesophageal complications. From a cognitive and neuropsychological perspective, language skills and IQ are within normal range, although visual-motor, motor development, behavior, and working memory were impaired. The c.2521-2A>G splice mutation leads to skipping of exon 26 and a 9 base-pair deletion associated with a cryptic splice site, leading to a 28-AA and a 3-AA in-frame deletion, respectively (p.Ala841_Lys843del and p.Ala841_Glu868del). The predominant mutant transcripts contain an aberrant guanylate kinase domain and thus are predicted to degrade CASK's ability to interact with important neuronal and ocular development proteins, including FRMD7. Upregulation of CASK as well as dysregulation among a number of interactors is also evident by RNA-seq. This is the second CASK mutation known to us as cause of FGS4. © 2017 Wiley Periodicals, Inc.

Contrasting evolutionary histories of MHC class I and class II loci in grouse--effects of selection and gene conversion.

Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens.

Identification of seven novel HLA class I alleles in New Zealand.

Seven new HLA class I alleles have been identified in the New Zealand population in the process of routine HLA typing and they are described here. Unusual bead positivity in Luminex typing identified potential new alleles in a bone marrow registry donor (B*40:285) and two HIV patients prior to abacavir prescription (B*14:02:09, B*41:29). In addition, four new class I alleles were identified through class I sequencing-based typing (SBT) outside of exons 2 and 3. One mutation was identified in exon 4 (new allele C*12:125) and three have been found in exon 5, an exon rarely sequenced. Two stem cell transplant recipients (B*07:02:45, C*03:279) had novel mutations in exon 5 and one was found in exon 5 of a potentially matched unrelated donor from DKMS, previously thought to be B*40:02:01 (B*40:303).

Contrasting patterns of selection on the size and coloration of a female plumage ornament in common yellowthroats.

Females often possess ornaments that appear smaller and duller than homologous traits in males. These ornaments may arise as nonfunctional by-products of sexual selection in males and cause negative viability or fecundity selection in females in proportion to the cost of their production and maintenance. Alternatively, female ornaments may function as signals of quality that are maintained by sexual or social selection. In a 4-year study of 83 female common yellowthroats (Geothlypis trichas) and their 222 young, we found strong viability and fecundity selection on the yellow bib, a carotenoid-based plumage ornament that is a target of sexual selection in males. Females with larger bibs were older, larger and more fecund than females with smaller bibs. However, bib size positively covaried with bib total brightness and carotenoid chroma, aspects of bib coloration that were under negative viability and fecundity selection. Females with more colourful bibs laid fewer eggs in their first clutch, were more likely to suffer total brood loss due to predation and were less likely to return to the study area. Selection against bib coloration limits the value of bib size as a quality indicator in females and may constrain the elaboration of bib attributes in males.

Epidemiology of Bonamia in the UK, 1982 to 2012.

Bonamiasis, caused by Bonamia ostreae, was confirmed in native flat oysters Ostrea edulis L. in England in 1982. Hudson & Hill (1991; Aquaculture 93:279-285) documented investigations into the initial spread of the disease in wild and cultivated stocks of native oysters in the UK. They also described the controls that were initially applied to prevent the further spread of the pathogen. This paper reports on subsequent controls and associated monitoring applied in the UK and reports on the epidemiology of the disease in the 30 yr from 1982 to 2012. Bonamiasis remained confined to the zones in England as documented by Hudson & Hill (1991) until 2005, when it was confirmed in Lough Foyle, Northern Ireland. In 2006 it was found in 2 new areas, one in Wales and one in Scotland. Subsequent further spread to additional areas in all parts of the UK has resulted in 9 zones being currently designated as infected with the disease. In addition, a single oyster from one area has tested positive for the closely related B. exitiosa. In general, analysis of the results of the monitoring programme in England and Wales shows no clear trend in infection levels over time, although there has been an apparent decrease in the level of infection in some fishery areas. In an autumn sampling programme the highest levels of infection were detected in October.

The effect of roasting on boron isotope ratio in coffee beans: Implications for provenance studies of roasted coffee.

We determined δ11B values of green and roasted coffee beans from 20 locations worldwide and conducted laboratory experiments with the aim to investigate boron isotope fractionation during roasting. Authentic single origin roasted coffees were found to be isotopically lighter than their green bean counterparts, with an average difference of 1.5‰. This isotope fractionation can be explained as arising from partial dissociation of boric acid in capillary water of green beans, where 11B isotopes are preferentially partitioned into molecules of undissociated boric acid and are then volatised during roasting. However, boron isotope fractionation induced by roasting was significantly smaller than between-origin variations in δ11B values of green coffee beans that had the range of ∼54‰. This implies that δ11B isotopic composition of roasted coffee retains the geographical origin information within δ11B values of green beans when regional differences in boron isotopic composition of coffee are considered.

Greater prairie chickens have a compact MHC-B with a single class IA locus.

The major histocompatibility complex (MHC) plays a central role in innate and adaptive immunity, but relatively little is known about the evolution of the number and arrangement of MHC genes in birds. Insights into the evolution of the MHC in birds can be gained by comparing the genetic architecture of the MHC between closely related species. We used a fosmid DNA library to sequence a 60.9-kb region of the MHC of the greater prairie chicken (Tympanuchus cupido), one of five species of Galliformes with a physically mapped MHC. Greater prairie chickens have the smallest core MHC yet observed in any bird species, and major changes are observed in the number and arrangement of MHC loci. In particular, the greater prairie chicken differs from other Galliformes in the deletion of an important class I antigen binding gene. Analysis of the remaining class IA gene in a population of greater prairie chickens in Wisconsin, USA revealed little evidence for selection at the region responsible for antigen binding.

Spatial distribution of nests constrains the strength of sexual selection in a warbler.

In socially monogamous species, extra-pair paternity may increase the strength of intersexual selection by allowing males with preferred phenotypes to monopolize matings. Several studies have found relationships between male signals and extra-pair mating, but many others fail to explain variation in extra-pair mating success. A greater appreciation for the role that ecological contingencies play in structuring behavioural processes may help to reconcile contradictory results. We studied extra-pair mating in a spatial context in the common yellowthroat (Geothlypis trichas), a territorial wood warbler. Over the course of 6 years, we observed 158 breeding attempts by 99 males, resulting in a total of 369 nests and 520 sampled nestlings. The spatial distribution of territories varied greatly, with males having between 0 and 10 close neighbours and between three and 39 neighbouring nestlings close enough to represent extra-pair siring opportunities. Both within-pair and extra-pair reproductive success increased with breeding density, but the opportunity for sexual selection and strength of selection varied with density. Total variance in reproductive success was highest at low density and was mostly explained by variation in within-pair success. In contrast, at high density, both within-pair and extra-pair successes contributed substantially to variance in reproductive success. The relationships between plumage and extra-pair mating also varied by density; plumage was under strong sexual selection via extra-pair mating success at high density, but no selection was detected at low density. Thus, ecological factors that structure social interactions can drive patterns of sexual selection by facilitating or constraining the expression of mating preferences.

Molecular approaches to transfusion medicine in Polynesians and Maori in New Zealand.

In recent years, with the application of genotyping technology, there has been a substantial increase in the number of reported blood group alleles. This survey was designed to evaluate new molecular blood group genotyping methods and compile reference blood group data sets for Polynesian and Maori subjects. Subsequent analyses of these results were used to calculate probability of random match, to trace Polynesian ancestry and migration patterns and to reveal past and present episodes of genetic admixture. Genomic DNA samples from Maori and Polynesian subjects were drawn from the Victoria University of Wellington DNA Bank and genotyped using combination of commercial PCR-SSP kits, hybridization SNP assay services or sequence-based typing. This survey also involves compilation of serological ABO and Rhesus blood group data from RakaiPaaka Iwi tribal members for comparison with those generated during our molecular blood group study. We observed perfect consistency between results obtained from all molecular methods for blood group genotyping. The A, O, DCcEe, DCCee, MNs, K-k+, Jk(a+b-), Jk(a+b+), Fy(a+b-), Fy(a+b+), Di(a+b-), Co(a+b-) and Do(a-b+) were predominant blood group phenotypes in both Polynesians and Maori. Overall, our survey data show only small differences in distributions of blood group phenotypes between Polynesian and Maori groups and their subgroups. These differences might be associated with selection, population history and gene flow from Europeans. In each case, we estimate that patients with certain blood groups have a very low probability of an exact phenotypic match, even if the patients were randomly transfused with blood from donors of their own ethnicity. The best way to avoid haemolytic transfusion reaction in such cases is to perform a pretransfusion cross-match and recruit increased numbers of donors with rare phenotype profiles. The conclusion of this study is that application of molecular method covering as many known variants as possible may help to improve the accuracy blood group genotyping and potentially conserve the routine requirements of transfusion centres.

16(th) IHIW: global distribution of extended HLA haplotypes.

This report describes the project to identify the global distribution of extended HLA haplotypes, a component of 16th International HLA and Immunogenetics Workshop (IHIW), and summarizes the initial analyses of data collected. The project aims to investigate extended HLA haplotypes, compare their distribution among different populations, assess their frequency in hematopoietic stem cell unrelated donor registries and initiate an international family studies database and DNA repository to be made publicly available. HLA haplotypes compiled in immunogenetics laboratories during the evaluation of transplant candidates and related potential donors were analysed. Haplotypes were determined using the pedigree analysis tool publicly available from the National Marrow Donor Program (NMDP) website. Nineteen laboratories from 10 countries (11 laboratories from North America, five from Asia, two from Latin America and one from Australia) contributed data on a total of 1719 families comprised of 7474 individuals. We identified 10393 HLA haplotypes, of which 1682 haplotypes included high-resolution typing at HLA-A, B, C, DRB1 and DQB1 loci. We also present haplotypes containing MICA and other HLA loci and haplotypes containing rare alleles seen in these families. The project will be extended through the 17th IHIW, and investigators interested in joining the project may communicate with the first author.

16(th) IHIW: analysis of HLA population data, with updated results for 1996 to 2012 workshop data (AHPD project report).

We present here the results of the Analysis of HLA Population Data (AHPD) project of the 16th International HLA and Immunogenetics Workshop (16IHIW) held in Liverpool in May-June 2012. Thanks to the collaboration of 25 laboratories from 18 different countries, HLA genotypic data for 59 new population samples (either well-defined populations or donor registry samples) were gathered and 55 were analysed statistically following HLA-NET recommendations. The new data included, among others, large sets of well-defined populations from north-east Europe and West Asia, as well as many donor registry data from European countries. The Gene[rate] computer tools were combined to create a Gene[rate] computer pipeline to automatically (i) estimate allele frequencies by an expectation-maximization algorithm accommodating ambiguities, (ii) estimate heterozygosity, (iii) test for Hardy-Weinberg equilibrium (HWE), (iv) test for selective neutrality, (v) generate frequency graphs and summary statistics for each sample at each locus and (vi) plot multidimensional scaling (MDS) analyses comparing the new samples with previous IHIW data. Intrapopulation analyses show that HWE is rarely rejected, while neutrality tests often indicate a significant excess of heterozygotes compared with neutral expectations. The comparison of the 16IHIW AHPD data with data collected during previous workshops (12th-15th) shows that geography is an excellent predictor of HLA genetic differentiations for HLA-A, -B and -DRB1 loci but not for HLA-DQ, whose patterns are probably more influenced by natural selection. In Europe, HLA genetic variation clearly follows a north to south-east axis despite a low level of differentiation between European, North African and West Asian populations. Pacific populations are genetically close to Austronesian-speaking South-East Asian and Taiwanese populations, in agreement with current theories on the peopling of Oceania. Thanks to this project, HLA genetic variation is more clearly defined worldwide and better interpreted in relation to human peopling history and HLA molecular evolution.

Human platelet antigens frequencies in Maori and Polynesian populations.

BACKGROUND: Allele frequencies of human platelet antigens (HPA) reflect population history and possibility of platelet-specific alloimmunization. Here, we report on screening of variants at HPA loci for Polynesian and Maori subjects. OBJECTIVES: Our aims are to evaluate new HPA genotyping methods, compile and analyse new HPA datasets for these subjects, use HPA data for tracing ancestry, migration patterns, genetic admixture and its potential influence on health. MATERIALS AND METHODS: A total of 75 Maori and 25 Polynesian DNA samples were genotyped using commercial BAGene HPA-TYPE DNA-SSP kits, BLOODchip hybridization SNP assays and DNA sequence based typing. RESULTS: Genotyping was successful and cross validation of PCR-SSP and BLOODchip gave 100% agreement. Among the HPA loci tested, only six are dimorphic (HPA-1 to -3, -5, -6 and -15) and all others are monomorphic. The Polynesians and Maori have the 'a' allele form as the most common for all loci except HPA-15. CONCLUSIONS: The newly observed HPA data as well as principal coordinate analysis clearly indicate genetic contributions from both, Asia and Australasia in Maori and Polynesian populations together with recent admixture with Europeans. In addition, different prevalences of HPA alleles among Polynesian, Maori and European populations contribute towards different risk profiles for platelet-specific alloimmunization. This is the first report for these populations and our findings are of direct practical relevance for blood transfusion centres, the management of pregnancies, assessment of neonatal alloimmune thrombocytopenia and management of multi-transfused patients.

A complete BAC-based physical map of the Arabidopsis thaliana genome.

Arabidopsis thaliana is a small flowering plant that serves as the major model system in plant molecular genetics. The efforts of many scientists have produced genetic maps that provide extensive coverage of the genome (http://genome-www. stanford.edu/Arabidopsis/maps.html). Recently, detailed YAC, BAC, P1 and cosmid-based physical maps (that is, representations of genomic regions as sets of overlapping clones of corresponding libraries) have been established that extend over wide genomic areas ranging from several hundreds of kilobases to entire chromosomes. These maps provide an entry to gain deeper insight into the A. thaliana genome structure. A. thaliana has been chosen as the subject of the first large-scale project intended to determine the full genome sequence of a plant. This sequencing project, together with the increasing interest in map-based gene cloning, has highlighted the requirement for a complete and accurate physical map of this plant species. To supply the scientific community with a high-quality resource, we present here a complete physical map of A. thaliana using essentially the IGF BAC library. The map consists of 27 contigs that cover the entire genome, except for the presumptive centromeric regions, nucleolar organization regions (NOR) and telomeric areas. This is the first reported map of a complex organism based entirely on BAC clones and it represents the most homogeneous and complete physical map established to date for any plant genome. Furthermore, the analysis performed here serves as a model for an efficient physical mapping procedure using BAC clones that can be applied to other complex genomes.