The impact of inversions across 33,924 families with rare disease from a national genome sequencing project

Detection of structural variants (SVs) is currently biased toward those that alter copy number. The relative contribution of inversions toward genetic disease is unclear. In this study, we analyzed genome sequencing data for 33,924 families with rare disease from the 100,000 Genomes Project. From a database hosting >500 million SVs, we focused on 351 genes where haploinsufficiency is a confirmed disease mechanism and identified 47 ultra-rare rearrangements that included an inversion (24 bp to 36.4 Mb, 20/47 de novo). Validation utilized a number of orthogonal approaches, including retrospective exome analysis. RNA-seq data supported the respective diagnoses for six participants. Phenotypic blending was apparent in four probands. Diagnostic odysseys were a common theme (>50 years for one individual), and targeted analysis for the specific gene had already been performed for 30% of these individuals but with no findings. We provide formal confirmation of a European founder origin for an intragenic MSH2 inversion. For two individuals with complex SVs involving the MECP2 mutational hotspot, ambiguous SV structures were resolved using long-read sequencing, influencing clinical interpretation. A de novo inversion of HOXD11-13 was uncovered in a family with Kantaputra-type mesomelic dysplasia. Lastly, a complex translocation disrupting APC and involving nine rearranged segments confirmed a clinical diagnosis for three family members and resolved a conundrum for a sibling with a single polyp. Overall, inversions play a small but notable role in rare disease, likely explaining the etiology in around 1/750 families across heterogeneous clinical cohorts.

The clinical and genetic spectrum of inherited glycosylphosphatidylinositol deficiency disorders

Inherited glycosylphosphatidylinositol deficiency disorders (IGDs) are a group of rare multisystem disorders arising from pathogenic variants in glycosylphosphatidylinositol anchor pathway (GPI-AP) genes. Despite associating 24 of at least 31 GPI-AP genes with human neurogenetic disease, prior reports are limited to single genes without consideration of the GPI-AP as a whole and with limited natural history data. In this multinational retrospective observational study, we systematically analyse the molecular spectrum, phenotypic characteristics, and natural history of 83 individuals from 75 unique families with IGDs, including 70 newly reported individuals: the largest single cohort to date. Core clinical features were developmental delay or intellectual disability (DD/ID, 90%), seizures (83%), hypotonia (72%), and motor symptoms (64%). Prognostic and biologically significant neuroimaging features included cerebral atrophy (75%), cerebellar atrophy (60%), callosal anomalies (57%), and symmetric restricted diffusion of the central tegmental tracts (60%). Sixty-one individuals had multisystem involvement including gastrointestinal (66%), cardiac (19%), and renal (14%) anomalies. Though dysmorphic features were appreciated in 82%, no single dysmorphic feature had a prevalence >30%, indicating substantial phenotypic heterogeneity. Follow-up data were available for all individuals, 15 of whom were deceased at the time of writing. Median age at seizure onset was 6 months. Individuals with variants in synthesis stage genes of the GPI-AP exhibited a significantly shorter time to seizure onset than individuals with variants in transamidase and remodelling stage genes of the GPI-AP (P=0.046). Forty individuals had intractable epilepsy. The majority of individuals experienced delayed or absent speech (95%); motor delay with non-ambulance (64%); and severe-to-profound DD/ID (59%). Individuals with a developmental epileptic encephalopathy (51%) were at greater risk of intractable epilepsy (P=0.003), non-ambulance (P=0.035), ongoing enteral feeds (P<0.001), and cortical visual impairment (P=0.007). Serial neuroimaging showed progressive cerebral volume loss in 87.5% and progressive cerebellar atrophy in 70.8%, indicating a neurodegenerative process. Genetic analyses identified 93 unique variants (106 total), including 22 novel variants. Exploratory analyses of genotype-phenotype correlations using unsupervised hierarchical clustering identified novel genotypic predictors of clinical phenotype and long-term outcome with meaningful implications for management. In summary, we expand both the mild and severe phenotypic extremities of the IGDs; provide insights into their neurological basis; and, vitally, enable meaningful genetic counselling for affected individuals and their families.

Toward robust clinical genome interpretation: Developing a consistent terminology to characterize Mendelian disease-gene relationships-allelic requirement, inheritance modes, and disease mechanisms

PURPOSE

The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here, we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation and to support variant classification within the ACMG/AMP framework.

METHODS

Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated.

RESULTS

We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both Sequence Ontology (SO) and Human Phenotype Ontology (HPO) ontologies. Gene Curation Coalition member groups intend to use or map to these terms in their respective resources.

CONCLUSION

The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.

Epigenotype-genotype-phenotype correlations in SETD1A and SETD2 chromatin disorders

Germline pathogenic variants in two genes encoding the lysine-specific histone methyltransferase genes SETD1A and SETD2 are associated with neurodevelopmental disorders (NDDs) characterized by developmental delay and congenital anomalies. The SETD1A and SETD2 gene products play a critical role in chromatin-mediated regulation of gene expression. Specific methylation episignatures have been detected for a range of chromatin gene-related NDDs and have impacted clinical practice by improving the interpretation of variant pathogenicity. To investigate if SETD1A and/or SETD2-related NDDs are associated with a detectable episignature, we undertook targeted genome-wide methylation profiling of > 2 M CpGs using a next-generation sequencing-based assay. A comparison of methylation profiles in patients with SETD1A variants (n = 6) did not reveal evidence of a strong methylation episignature. A review of the clinical and genetic features of the SETD2 patient group revealed that, as reported previously, there were phenotypic differences between patients with truncating mutations (n = 4, Luscan-Lumish syndrome; MIM:616831) and those with missense codon 1740 variants [p.Arg1740Trp (n = 4) and p.Arg1740Gln (n = 2)]. Both SETD2 subgroups demonstrated a methylation episignature, which was characterized by hypomethylation and hypermethylation events, respectively. Within the codon 1740 subgroup, both the methylation changes and clinical phenotype were more severe in those with p.Arg1740Trp variants. We also noted that two of 10 cases with a SETD2-NDD had developed a neoplasm. These findings reveal novel epigenotype-genotype-phenotype correlations in SETD2-NDDs and predict a gain-of-function mechanism for SETD2 codon 1740 pathogenic variants.

Towards robust clinical genome interpretation: developing a consistent terminology to characterize disease-gene relationships - allelic requirement, inheritance modes and disease mechanisms

PURPOSE

The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation, and to support variant classification within the ACMG/AMP framework.

METHODS

Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition (GenCC) members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated.

RESULTS

We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both sequence ontology (SO) and human phenotype ontology (HPO) ontologies. GenCC member groups intend to use or map to these terms in their respective resources.

CONCLUSION

The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.

Personalized recurrence risk assessment following the birth of a child with a pathogenic de novo mutation

Following the diagnosis of a paediatric disorder caused by an apparently de novo mutation, a recurrence risk of 1-2% is frequently quoted due to the possibility of parental germline mosaicism; but for any specific couple, this figure is usually incorrect. We present a systematic approach to providing individualized recurrence risk. By combining locus-specific sequencing of multiple tissues to detect occult mosaicism with long-read sequencing to determine the parent-of-origin of the mutation, we show that we can stratify the majority of couples into one of seven discrete categories associated with substantially different risks to future offspring. Among 58 families with a single affected offspring (representing 59 de novo mutations in 49 genes), the recurrence risk for 35 (59%) was decreased below 0.1%, but increased owing to parental mixed mosaicism for 5 (9%)-that could be quantified in semen for paternal cases (recurrence risks of 5.6-12.1%). Implementation of this strategy offers the prospect of driving a major transformation in the practice of genetic counselling.

The Phenotypic Continuum of ATP1A3-Related Disorders

BACKGROUND AND OBJECTIVES

ATP1A3 is associated with a broad spectrum of predominantly neurologic disorders, which continues to expand beyond the initially defined phenotypes of alternating hemiplegia of childhood, rapid-onset dystonia parkinsonism, and cerebellar ataxia, areflexia, pes cavus, optic atrophy, sensorineural hearing loss syndrome. This phenotypic variability makes it challenging to assess the pathogenicity of an ATP1A3 variant found in an undiagnosed patient. We describe the phenotypic features of individuals carrying a pathogenic/likely pathogenic ATP1A3 variant and perform a literature review of all ATP1A3 variants published thus far in association with human neurologic disease. Our aim is to demonstrate the heterogeneous clinical spectrum of the gene and look for phenotypic overlap between patients that will streamline the diagnostic process.

METHODS

Undiagnosed individuals with ATP1A3 variants were identified within the cohort of the Deciphering Developmental Disorders study with additional cases contributed by collaborators internationally. Detailed clinical data were collected with consent through a questionnaire completed by the referring clinicians. PubMed was searched for publications containing the term "ATP1A3" from 2004 to 2021.

RESULTS

Twenty-four individuals with a previously undiagnosed neurologic phenotype were found to carry 21 ATP1A3 variants. Eight variants have been previously published. Patients experienced on average 2-3 different types of paroxysmal events. Permanent neurologic features were common including microcephaly (7; 29%), ataxia (13; 54%), dystonia (10; 42%), and hypotonia (7; 29%). All patients had cognitive impairment. Neuropsychiatric diagnoses were reported in 16 (66.6%) individuals. Phenotypes were extremely varied, and most individuals did not fit clinical criteria for previously published phenotypes. On review of the literature, 1,108 individuals have been reported carrying 168 different ATP1A3 variants. The most common variants are associated with well-defined phenotypes, while more rare variants often result in very rare symptom correlations, such as are seen in our study. Combined Annotation-Dependent Depletion (CADD) scores of pathogenic and likely pathogenic variants were significantly higher and variants clustered within 6 regions of constraint.

DISCUSSION

Our study shows that looking for a combination of paroxysmal events, hyperkinesia, neuropsychiatric symptoms, and cognitive impairment and evaluating the CADD score and variant location can help identify an ATP1A3-related condition, rather than applying diagnostic criteria alone.

Genetic architecture of a composite beef cattle population

Composite breeds are widely used in the beef industry. Composites allow producers to combine desirable traits from the progenitor breeds and simplify herd management, without repeated crossbreeding and maintenance of purebreds. In this study, genomic information was used to evaluate the genetic composition and characteristics of a three-breed beef cattle composite. This composite population referred to as Composite Gene Combination (CGC) consisted of 50% Red Angus, 25% Charolais, 25% Tarentaise. A total of 248 animals were used in this study CGC (n=79), Red Angus (n=61), Charolais (n=79) and Tarentaise (n=29). All animals were genotyped with 777k HD panel. Principal component and ADMIXTURE analyses were carried out to evaluate the genetic structure of CGC animals. The ADMIXTURE revealed the proportion of Tarentaise increased to approximately 57% while Charolais decreased to approximately 5%, and Red Angus decreased to 38% across generations. To evaluate these changes in the genomic composition across different breeds and in CGC across generations runs of homozygosity (ROH) were conducted. This analysis showed Red Angus to have the highest total length of ROH segments per animal with a mean of 349.92 Mb and lowest in CGC with a mean of 141.10 Mb. Furthermore, it showed the formation of new haplotypes in CGC around the sixth generation. Selection signatures were evaluated through Fst and HapFlk analyses. Several selection sweeps in CGC were identified especially in chromosomes 5 and 14 which have previously been reported to be associated with coat color and growth traits. The study supports our previous findings that progenitor combinations are not stable over generations and that either direct or natural selection plays a role in modifying the progenitor proportions. Furthermore, the results showed that Tarentaise contributed useful attributes to the composite in a cool semi-arid environment and suggests a re-exploration of this breed's role may be warranted.

Recessive variants in COL25A1 gene as novel cause of arthrogryposis multiplex congenita with ocular congenital cranial dysinnervation disorder

A proper interaction between muscle-derived collagen XXV and its motor neuron-derived receptors protein tyrosine phosphatases σ and δ (PTP σ/δ) is indispensable for intramuscular motor innervation. Despite this, thus far, pathogenic recessive variants in the COL25A1 gene had only been detected in a few patients with isolated ocular congenital cranial dysinnervation disorders. Here we describe five patients from three unrelated families with recessive missense and splice site COL25A1 variants presenting with a recognizable phenotype characterized by arthrogryposis multiplex congenita with or without an ocular congenital cranial dysinnervation disorder phenotype. The clinical features of the older patients remained stable over time, without central nervous system involvement. This study extends the phenotypic and genotypic spectrum of COL25A1 related conditions, and further adds to our knowledge of the complex process of intramuscular motor innervation. Our observations indicate a role for collagen XXV in regulating the appropriate innervation not only of extraocular muscles, but also of bulbar, axial, and limb muscles in the human.

A practical approach to the genomics of kidney disorders

Rapid technological advances in genomic testing continue to increase our understanding of the genetic basis of a wide range of kidney disorders. Establishing a molecular diagnosis benefits the individual by bringing an end to what is often a protracted diagnostic odyssey, facilitates accurate reproductive counselling for families and, in the future, is likely to lead to the delivery of more targeted management and surveillance regimens. The selection of the most appropriate testing modality requires an understanding both of the technologies available and of the genetic architecture and heterogeneity of kidney disease. Whilst we are witnessing a far greater diagnostic yield with broader genetic testing, such approaches invariably generate variants of uncertain significance and secondary incidental findings, which are not only difficult to interpret but present ethical challenges with reporting and feeding back to patients and their families. Here, we review the spectrum of nephrogenetic disorders, consider the optimal approach to genetic testing, explore the clinical utility of obtaining a molecular diagnosis, reflect on the challenges of variant interpretation and look to the future of this dynamic field.

Biallelic P4HTM variants associated with HIDEA syndrome and mitochondrial respiratory chain complex I deficiency

We report a patient with profound congenital hypotonia, central hypoventilation, poor visual behaviour with retinal hypopigmentation, and significantly decreased mitochondrial respiratory chain complex I activity in muscle, who died at 7 months of age having made minimal developmental progress. Biallelic predicted truncating P4HTM variants were identified following trio whole-genome sequencing, consistent with a diagnosis of hypotonia, hypoventilation, intellectual disability, dysautonomia, epilepsy and eye abnormalities (HIDEA) syndrome. Very few patients with HIDEA syndrome have been reported previously and mitochondrial abnormalities were observed in three of four previous cases who had a muscle biopsy, suggesting the possibility that HIDEA syndrome represents a primary mitochondrial disorder. P4HTM encodes a transmembrane prolyl 4-hydroxylase with putative targets including hypoxia inducible factors, RNA polymerase II and activating transcription factor 4, which has been implicated in the integrated stress response observed in cell and animal models of mitochondrial disease, and may explain the mitochondrial dysfunction observed in HIDEA syndrome.

Expanding the phenotypic spectrum consequent upon de novo WDR37 missense variants

Structural eye disorders are increasingly recognised as having a genetic basis, although current genetic testing is limited in its success. De novo missense variants in WDR37 are a recently described cause of a multisystemic syndromic disorder featuring ocular coloboma. This study characterises the phenotypic spectrum of this disorder and reports 2 de novo heterozygous variants (p.Thr115Ile, p.Ser119Tyr) in three unrelated Caucasian individuals. All had a clinical phenotype consisting of bilateral iris and retinal coloboma, developmental delay and additional, variable multisystem features. The variants fall within a highly conserved region upstream of the WD-repeat domains, within an apparent mutation cluster. Consistent with the literature, intellectual disability, structural eye disorders, epilepsy, congenital heart disease, genitorenal anomalies and dysmorphic facial features were observed. In addition, a broader developmental profile is reported with a more specific musculoskeletal phenotype described in association with the novel variant (p.Thr115Ile). We further expand the phenotypic spectrum of WDR37-related disorders to include those with milder developmental delay and strengthen the association of ocular coloboma and musculoskeletal features. We promote the inclusion of WDR37 on gene panels for intellectual disability, epilepsy and structural eye disorders.

The Matrilin-3 T298M mutation predisposes for post-traumatic osteoarthritis in a knock-in mouse model

OBJECTIVE

The human matrilin-3 T303M (in mouse T298M) mutation has been proposed to predispose for osteoarthritis, but due to the lack of an appropriate animal model this hypothesis could not be tested. This study was carried out to identify pathogenic mechanisms in a transgenic mouse line by which the mutation might contribute to disease development.

METHODS

A mouse line carrying the T298M point mutation in the Matn3 locus was generated and features of skeletal development in ageing animals were characterized by immunohistology, micro computed tomography, transmission electron microscopy and atomic force microscopy. The effect of transgenic matrilin-3 was also studied after surgically induced osteoarthritis.

RESULTS

The matrilin-3 T298M mutation influences endochondral ossification and leads to larger cartilage collagen fibril diameters. This in turn leads to an increased compressive stiffness of the articular cartilage, which, upon challenge, aggravates osteoarthritis development.

CONCLUSIONS

The mouse matrilin-3 T298M mutation causes a predisposition for post-traumatic osteoarthritis and the corresponding knock-in mouse line therefore represents a valid model for investigating the pathogenic mechanisms involved in osteoarthritis development.

OP0243 SERPINA3N LIMITS CARTILAGE DESTRUCTION IN OSTEOARTHRITIS BY INHIBITING MACROPHAGE-DERIVED LEUKOCYTE ELASTASE

Background:

Interleukin-6 (IL-6) plays an important role in osteoarthritis (OA). Transcriptomic analyses (RNAseq) revealed that SerpinA3N, a serine protease inhibitor, is a key target of IL-6 in chondrocyte.

Objectives:

This study aimed to examine the role of SerpinA3N and Leukocyte Elastase (Elane), a serine protease targeted by SerpinA3N, in cartilage destruction during OA.

Methods:

The role of SerpinA3N was investigated in the destabilization of medial meniscus (DMM) model of murine OA with 1) mice with conditional inducible knockdown ofSerpina3nin cartilage (Col2CreER;Serpina3nfl/flmice [ΔSerpina3nCol2]) and 2) C57BL/6 wild type (WT) mice treated with intra-articular injection of SerpinA3N (1,5 or 15 nM/week). OA joint lesions were assessed by histology (OARSI and synovitis scores) and micro-CT analysis (osteophyte volume, subchondral bone remodeling).

Because serine proteases targeted by SerpinA3N are not produced by murine chondrocytes,Elaneexpression (qRT-PCR) was determined in murine macrophages (Raw) stimulated or not by IL-6 (100 ng/ml). Recombinant SerpinA3N (30 nM) and a specific Elane inhibitor, Sivelestat (100 µg/ml) were used on cartilage explants treated by conditioned medium of macrophages pre-treated or not by IL-6 (CM–IL-6). Cartilage catabolism was determined by histology and matrix metalloproteinase MMP-3 production was evaluated by Western Blot and immunohistochemistry (IHC). Weekly intra-articular injections of Sivelestat (1mM) were performed in the DMM to determine the role of Elane in OA.

Results:

ΔSerpina3nCol2mice had more severe OA lesions than control littermates 6 weeks after DMM, with greater cartilage damage (mean±SD OARSI score: 5.6±0.4 vs 3.4±0.5, p=0.01), increased synovitis scores (3.0±0.3 vs 1.9±0.3, p=0.03) and bigger osteophytes (7.2±0.8x107 vs 3.8±0.8x107 µ3, p=0.048). Conversely, WT mice treated with intra-articular injections of SerpinA3N 15nM exhibited less severe cartilage loss than mice treated with PBS after DMM (OARSI score: 2.1±0.4 vs 3.9±0.5, p=0.02). Elane mRNA expression was increased in macrophages upon IL-6 stimulation. In cartilage explants, CM–IL-6 activated cartilage catabolism and MMP-3 production, and effect that was blunted by SerpinA3N and Sivelestat. Finally, mice treated with intra-articular injections of Sivelestat had less severe cartilage damage than those treated with PBS after DMM (OARSI score: 3.3±0.47 vs 5.8±0.53, p=0.0046).

Conclusion:

SerpinA3N protects against experimental OA via the inhibition of Elane, a pro-catabolic serine protease produced by macrophages. This results highlight the crosstalk between cartilage and surrounding macrophages and open up new therapeutic perspectives.

Acknowledgments:

This work has been supported by French Society of Rheumatology and ART Viggo association.

Disclosure of Interests:

None declared

Genotype by environment interaction in response to cold stress in a composite beef cattle breed

Extreme weather conditions such as cold stress influence the productivity and survivability of beef cattle raised on pasture. The objective of this study was to identify and evaluate the extent of the impact of genotype by environment interaction due to cold stress on birth weight (BW) and weaning weight (WW) in a composite beef cattle population. The effect of cold stress was modelled as the accumulation of total cold load (TCL) calculated using the Comprehensive Climate Index units, considering three TCL classes defined based on temperature: less than -5°C (TCL5), -15°C (TCL15) and -25°C (TCL25). A total of 4221 and 4217 records for BW and WW, respectively, were used from a composite beef cattle population (50% Red Angus, 25% Charolais and 25% Tarentaise) between 2002 and 2015. For both BW and WW, a univariate model (ignoring cold stress) and a reaction norm model were implemented. As cold load increased, the direct heritability slightly increased in both BW and WW for TCL5 class; however, this heritability remained consistent across the cold load of TCL25 class. In contrast, the maternal heritability of BW was constant with cold load increase in all TCL classes, although a slight increase of maternal heritability was observed for TCL5 and TCL15. The direct and maternal genetic correlation for BW and maternal genetic correlation for WW across different cold loads between all TCL classes were high (r > 0.99), whereas the lowest direct genetic correlations observed for WW were 0.88 for TCL5 and 0.85 for TCL15. The Spearman rank correlation between the estimated breeding value of top bulls (n = 79) using univariate and reaction norm models across TCL classes showed some re-ranking in direct and maternal effects for both BW and WW particularly for TCL5 and TCL15. In general, cold stress did not have a big impact on direct and maternal genetic effects of BW and WW.

Stratified primary care versus non-stratified care for musculoskeletal pain: findings from the STarT MSK feasibility and pilot cluster randomized controlled trial

BACKGROUND

Musculoskeletal (MSK) pain from the five most common presentations to primary care (back, neck, shoulder, knee or multi-site pain), where the majority of patients are managed, is a costly global health challenge. At present, first-line decision-making is based on clinical reasoning and stratified models of care have only been tested in patients with low back pain. We therefore, examined the feasibility of; a) a future definitive cluster randomised controlled trial (RCT), and b) General Practitioners (GPs) providing stratified care at the point-of-consultation for these five most common MSK pain presentations.

METHODS

The design was a pragmatic pilot, two parallel-arm (stratified versus non-stratified care), cluster RCT and the setting was 8 UK GP practices (4 intervention, 4 control) with randomisation (stratified by practice size) and blinding of trial statistician and outcome data-collectors. Participants were adult consulters with MSK pain without indicators of serious pathologies, urgent medical needs, or vulnerabilities. Potential participant records were tagged and individuals sent postal invitations using a GP point-of-consultation electronic medical record (EMR) template. The intervention was supported by the EMR template housing the Keele STarT MSK Tool (to stratify into low, medium and high-risk prognostic subgroups of persistent pain and disability) and recommended matched treatment options. Feasibility outcomes included exploration of recruitment and follow-up rates, selection bias, and GP intervention fidelity. To capture recommended outcomes including pain and function, participants completed an initial questionnaire, brief monthly questionnaire (postal or SMS), and 6-month follow-up questionnaire. An anonymised EMR audit described GP decision-making.

RESULTS

GPs screened 3063 patients (intervention = 1591, control = 1472), completed the EMR template with 1237 eligible patients (intervention = 513, control = 724) and 524 participants (42%) consented to data collection (intervention = 231, control = 293). Recruitment took 28 weeks (target 12 weeks) with > 90% follow-up retention (target > 75%). We detected no selection bias of concern and no harms identified. GP stratification tool fidelity failed to achieve a-priori success criteria, whilst fidelity to the matched treatments achieved "complete success".

CONCLUSIONS

A future definitive cluster RCT of stratified care for MSK pain is feasible and is underway, following key amendments including a clinician-completed version of the stratification tool and refinements to recommended matched treatments.

TRIAL REGISTRATION

Name of the registry: ISRCTN.

TRIAL REGISTRATION NUMBER

15366334. Date of registration: 06/04/2016.

Microcracks in subchondral bone plate is linked to less cartilage damage

OBJECTIVES

Osteoarthritis (OA) is a disease of the whole joint characterized by cartilage loss and subchondral bone remodeling. The role of microcracks in cartilage integrity and subchondral bone homeostasis is not fully understood. The main goal of this work was to evaluate microcrack density in both calcified cartilage and subchondral bone plate in relation to cartilage damage in humans and to better define the association of microcracks and osteocyte density in subchondral bone.

METHODS

We investigated 18 bone cores from cadaveric human knees that were stained with En-Bloc Basic Fuchsin. We quantified microcrack density, osteocyte density, cartilage surfaces and cartilage damage. The presence of microcracks was confirmed for each bone core by scanning electron microscopy. Finally, trabecular subchondral bone parameters were measured by micro-CT.

RESULTS

Microcracks were detected in both calcified cartilage and subchondral bone plate. The density of microcracks in both calcified cartilage (CC) and subchondral bone plate (SBP) was negatively correlated with cartilage damage (r = -0.45, p < 0.05). The presence of microcracks in SBP was associated with a lower histological OA score. Osteocytes formed a dendrite network that abruptly stopped at the border of calcified cartilage. Osteocyte density in subchondral bone plate was increased in the presence of microcracks in calcified cartilage.

CONCLUSIONS

Subchondral bone plate microcracks might be required for maintaining cartilage homeostasis. Microcracks in calcified cartilage may trigger osteocyte density in subchondral bone plate with subsequent regulation of subchondral bone remodeling to prevent cartilage damage.

Taxonomic and geographic bias in the genetic study of helminth parasites

The use of genetic information is now fundamental in parasite taxonomy and systematics, for resolving parasite phylogenies, discovering cryptic species, and elucidating patterns of gene flow among parasite populations. The accumulation of available gene sequences per geographical area or per parasite taxonomic group is likely proportional to species richness, but not without some biases. Certain areas and certain taxonomic groups receive more research effort than others, possibly causing a deficit in the relative number of parasite species being characterized genetically in some areas or taxonomic groups. Here, we use data on the number of parasite records per country or helminth family from the London Natural History Museum host-parasite database, and matching data on the number of gene sequences available from the National Center for Biotechnology Information (NCBI) GenBank database, to determine how available gene sequences scale with species richness across countries or parasitic helminth families. Our quantitative analysis identified countries/regions of the world and helminth families that have received the most effort in genetic research. More importantly, it allowed us to generate lists (based on residuals from the statistical model) of the 20 countries/regions and the 20 helminth families with the largest deficit in available gene sequences relative to their helminth species richness. We propose these lists as useful guides toward future allocation of effort to maximise advances in parasite biodiscovery, systematics and population structure.

Genomic prediction of continuous and binary fertility traits of females in a composite beef cattle breed

Reproduction efficiency is a major factor in the profitability of the beef cattle industry. Genomic selection (GS) is a promising tool that may improve the predictive accuracy and genetic gain of fertility traits. There is a wide range of traits used to measure fertility in dairy and beef cattle including continuous (days open), discrete (pregnancy status), and count (number of inseminations) responses. In this study, a joint analysis of age of puberty (AOP), age at first calving (AOC), and the heifer pregnancy status (HPS) was performed. Data used in this study consisted of records from 1,365 Composite Gene Combination (CGC; 50% Red Angus, 25% Charolais, 25% Tarentaise) first parity females born between 2002 and 2011. The pedigree file included 5,374 animals. A total of 3,902 animals were genotyped with different density SNP chips (3K to 50K SNP). Animals genotyped with low-density arrays were imputed to higher density (BovineSNP50 BeadChip) using FImpute. Data were analyzed using univariate and multivariate classical quantitative models (pedigree based) and univariate genomic approaches. For the latter, 3 different Bayesian methods (BayesA, BayesB, and BayesCπ) were implemented and compared. Estimates of heritabilities using univariate and multivariate analyses based on pedigree relationships ranged between 0.03 (for AOC) to 0.2 (AOP). Heritability of pregnancy status was 0.15 and 0.09 using the univariate and multivariate analyses, respectively. Genetic correlation between pregnancy status and the other 2 traits was low being 0.08 with age at puberty and -0.10 with age at first calving. Heritability estimates were slightly higher using genomic rather than average additive relationships. The accuracy of genomic prediction was similar across the 3 Bayesian methods with higher accuracies for age of puberty than the age at first calving likely due to the higher heritability of the former. The prediction of the binary pregnancy status measured using the area under the curve increased by 27% to 29% compared to a random classifier. Due to the small size of the data, all estimates have large posterior standard deviations and results should be interpreted with caution.

Genotype by environment interaction effects in genetic evaluation of preweaning gain for Line 1 Hereford cattle from Miles City, Montana

It has long been recognized that genotype × environment interaction potentially influences genetic evaluation of beef cattle. However, this recognition has largely been ignored in systems for national cattle evaluation. The objective of this investigation was to determine if direct and maternal genetic effects on preweaning gain would be reranked depending on an environmental gradient as determined by year effects. Data used were from the 76-yr selection experiment with the Line 1 Hereford cattle raised at Miles City, MT. The data comprised recorded phenotypes from 7,566 animals and an additional 1,862 ancestral records included in the pedigree. The presence of genotype × environment interaction was examined using reaction norms wherein year effects on preweaning gain were hypothesized to linearly influence the EBV. Estimates of heritability for direct and maternal effects, given the average environment, were 10 ± 2 and 26 ± 3%, respectively. In an environment that is characterized by the 5th (95th) percentile of the distribution of year effects, the corresponding estimates of heritability were 18 ± 3 (22 ± 3%) and 30 ± 3% (30 ± 3%), respectively. Rank correlations of direct and maternal EBV appropriate to the 5th and 95th percentiles of the year effects were 0.67 and 0.92, respectively. In the average environment, the genetic trends were 255 ± 1 g/yr for direct effects and 557 ± 3 g/yr for maternal effects. In the fifth percentile environment, the corresponding estimates of genetic trend were 271 ± 1 and 540 ± 3 g/yr, respectively, and in the 95th percentile environment, they were 236 ± 1 and 578 ± 3 g/yr, respectively. Linear genetic trends in environmental sensitivity were observed for both the direct (-8.06 × 10 ± 0.49 × 10) and maternal (8.72 × 10 ± 0.43 × 10) effects. Therefore, changing systems of national cattle evaluation to more fully account for potential genotype × environment interaction would improve the assessment of breeding stock, particularly for direct effects. Estimates of environmental sensitivity parameters could also facilitate identification of genetic limitations to production.

Animal models in OA: a means to explore bone

Cartilage damage which characterizes osteoarthritis is accompanied with bone lesions. Joint integrity results from the balance in the physiological interactions between bone and cartilage. Several local factors regulate physiological remodeling of cartilage, the disequilibrium of these leading to a higher cartilage catabolism. Several cytokines secreted by bone cells can induce chondrocyte differentiation which suggests their role in the dialogue between both cells. Several animal models of osteoarthritis have been developed in order to assess the mechanism of cartilage loss and chondrocyte functions that encompassed surgical, chemical, or genetic approaches. Indeed, the animal models are helpful to investigate the cartilage changes in relation to changes in bone remodeling. Accumulative in vivo evidence show that increased bone resorption occurs at early stage of the development of osteoarthritis. Inhibition of bone resorbing molecules prevents cartilage damage, confirming the role of bone factors in the cross talk between both tissues. Among these numerous molecules, some participate to the imbalance in cartilage homeostasis and in the pathophysiology of osteoarthritis. These local factors are potential candidates for new drug targets.

Radiographic hand osteoarthritis: patterns and associations with hand pain and function in a community-dwelling sample

OBJECTIVE

Patterns of radiographic osteoarthritis (ROA) of the hand are often examined by row, with the four joints of the thumb studied inconsistently. The objectives of this study were to determine relationships of ROA at different hand joints, use the findings to define radiographic sub-groups and investigate their associations with pain and function.

METHODS

Sixteen joints in each hand were scored for the presence of ROA in a community-dwelling cohort of adults, 50-years-and-over, with self-reported hand pain or problems. Principal components analysis (PCA) with varimax rotation was used to study patterns of ROA in the hand joints and identify distinct sub-groups. Differences in pain and function between these sub-groups were assessed using Australian/Canadian Osteoarthritis Index (AUSCAN), Grip Ability Test (GAT) and grip and pinch strength.

RESULTS

PCA was undertaken on data from 592 participants and identified four components: distal interphalangeal joints (DIPs), proximal interphalangeal joints (PIPs), metacarpophalangeal joints (MCPs), thumb joints. However, the left thumb interphalangeal (IP) joint cross-loaded with the PIP and thumb groups. On this basis, participants were categorised into four radiographic sub-groups: no osteoarthritis (OA), finger only OA, thumb only OA and combined thumb and finger OA. Statistically significant differences were found between the sub-groups for AUSCAN function, and in women alone for grip and pinch strength. Participants with combined thumb and finger OA had the worst scores.

CONCLUSION

Individual thumb joints can be clustered together as a joint group in ROA. Four radiographic sub-groups of hand OA can be distinguished. Pain and functional difficulties were highest in participants with both thumb and finger OA.

Does isolated patellofemoral osteoarthritis matter?

OBJECTIVES

To describe the structure-pain and structure-function associations in isolated patellofemoral osteoarthritis (PF OA).

DESIGN

Population-based study of 819 adults aged > or =50 years with knee pain. The severity of knee pain, stiffness and disability were measured using the Western Ontario and McMaster Osteoarthritis Index (WOMAC). Three radiographic views of the knee were obtained.

RESULTS

Isolated PF OA was mild in 142 participants and moderate/severe in 44. Mean WOMAC scores for pain, stiffness and function were associated with radiographic severity of PF OA (F(2,389)=4.7, P=0.01; F(2,392)=4.5, P=0.012 and F(2,392)=6.1, P=0.002, respectively, adjusted for age, gender, and body mass index (BMI)). Post-hoc tests demonstrated statistically significant differences for mean pain, stiffness and function score between those with mild PF OA and those with normal X-rays. In task-specific items there was evidence of a stepped response, the proportion of participants with moderate/severe/extreme pain or difficulty in performing everyday tasks increasing with the severity of PF OA. The strongest association was observed for pain going up and down stairs (age-gender-BMI adjusted odds ratio (OR) 3.0; 95% confidence interval (CI) 1.4,6.6. Functional tasks most strongly related to radiographic severity were: descending stairs (OR 3.2; (CI 1.5,6.5)), getting in/out of the bath (3.2; 1.5,6.6), getting in/out of a car (3.0; 1.4,6.1).

CONCLUSIONS

Mild isolated PF OA is significantly associated with symptoms of pain, stiffness and functional limitation. Further research on its recognition in clinical practice and the development of targeted treatments to prevent or slow progression are warranted.

An economic evaluation of three physiotherapy treatments for non-specific neck disorders alongside a randomized trial

OBJECTIVES

Cost-effectiveness and cost-utility analyses were conducted to compare advice and exercise plus manual therapy (MT) and advice and exercise plus pulsed shortwave diathermy (PSWD) with advice and exercise alone (A&E) in the treatment of non-specific neck disorders by experienced physiotherapists.

METHODS

Between July 2000 and June 2002, 350 participants with neck disorders from 15 physiotherapy departments were randomized to: A&E (n = 115); MT (n = 114) and PSWD (n = 121). Outcome and resource-use data were collected using physiotherapist case report forms and participant self-complete questionnaires. Outcome measures were the Northwick Park Neck Pain Questionnaire (NPQ) and EuroQoL EQ-5D [used to derive quality-adjusted-life-year (QALY) utility scores]. Two economic viewpoints were considered (health care and societal). Cost-effectiveness acceptability curves were used to assess the probabilities of the interventions being cost-effective at different willingness-to-pay threshold values.

RESULTS

Mean improvement in NPQ at 6 months was 11.5 in the A&E group, 10.2 in the MT group and 10.3 in the PSWD group; mean QALY scores were 0.362, 0.342 and 0.360, respectively. Mean health care costs were pound sterling105, pound sterling119 and pound sterling123 in the A&E, MT and PSWD groups, respectively. Mean societal costs were pound sterling373, pound sterling303 and pound sterling 338 in each group, respectively. Depending on the viewpoint and the outcome measure, A&E or MT were most likely to be the cost-effective interventions. PSWD was consistently the least cost-effective intervention.

CONCLUSIONS

The cost-effective intervention is likely to be A&E or MT, depending on the economic perspective and preferred outcome, but not PSWD.

Symptoms and radiographic osteoarthritis: not as discordant as they are made out to be?

OBJECTIVES

Joint pain and radiographic osteoarthritis are often discordant.

AIM

To investigate this issue more closely by studying the detailed nature of pain and disability, and how this relates to radiographic osteoarthritis.

METHODS

Population-based study of 819 adults aged >or=50 years with knee pain. The severity of knee pain, stiffness and disability was measured using a validated scale (the Western Ontario and McMaster Universities (WOMAC) Score) and pain persistence was recorded. Global severity was measured by the graded chronic pain scale. Three radiographic views of the knees were obtained-weight-bearing posteroanterior metatarsophalangeal, supine skyline and supine lateral.

RESULTS

745 participants with knee pain in the past 6 months were eligible (mean age 65 years, 338 men). Radiographic osteoarthritis was more common in those with a longer history and more persistent symptoms. A strong trend was found of radiographic osteoarthritis being more strongly associated with higher WOMAC scores for pain severity, stiffness and disability (adjusted odds ratio (95% confidence interval (CI)) for highest v lowest WOMAC category: 3.7 (2.0 to 6.7), 3.0 (2.0 to 4.6) and 2.8 (1.6 to 5.0), respectively). Those individual WOMAC items for pain and disability pertaining to weight-bearing mobility were the most strongly associated with radiographic osteoarthritis. Combining pain persistence and global severity, persistent severe pain was associated with a significant increase in the occurrence of radiographic osteoarthritis (2.6 (95% CI 1.5 to 4.7)).

CONCLUSIONS

A consistent association was found between severity of pain, stiffness and physical function and the presence of radiographic osteoarthritis. This study highlights the potential contribution of underlying joint disease to the degree of pain and disability.

Clinical classification criteria for knee osteoarthritis: performance in the general population and primary care

BACKGROUND

Doubts have been expressed about the performance of the American College of Rheumatology (ACR) clinical classification criteria for osteoarthritis when applied in the general population.

OBJECTIVE

To investigate whether the distribution of population subgroups and underlying disease severity might explain the performance of these criteria in the population setting.

METHODS

Population-based cross-sectional study. 819 adults aged > or = 50 years reporting knee pain in the last 12 months were clinically assessed by research therapists using standardised protocols and blinded to radiographic status. All participants underwent plain radiography of the knees, scored by a single reader blinded to clinical status. The relationship between fulfilling the ACR clinical classification criteria for knee osteoarthritis and the presence of symptomatic radiographic knee osteoarthritis was summarised for the sample as a whole and within subgroups.

RESULTS

Radiographic osteoarthritis was present in 539 participants (68%) and symptomatic radiographic knee osteoarthritis in 259 (33%). 238 participants (30%) fulfilled the ACR clinical criteria for knee osteoarthritis. Agreement between the ACR clinical criteria and symptomatic radiographic knee osteoarthritis was low (sensitivity 41%; specificity 75%; positive predictive value 44%; negative predictive value 72%). Sensitivity and specificity did not vary markedly between population subgroups, although they were influenced by the underlying severity of radiographic osteoarthritis.

CONCLUSION

The ACR clinical criteria seem to reflect later signs in advanced disease. Other approaches may be needed to identify early, mild osteoarthritis in the general population and primary care.

KIWIN(TM): From prototype to product for use

2005 has seen the birth of the product KIWIN(TM)--an educational technology for nursing students in New Zealand involving web-based technology supported by Pocket PCs in the field. Nursing students use the technology to collect clinically relevant data at the point-of-care and transmit to a secure central server for storage using cradle synchronisation, WiFi or cellular wireless modalities. Later retrieval via the Internet enables collation of details, refinement of work, and construction with print-off of care reports to meet academic requirements. This demonstration will showcase the development to the international community. Critique and review will be welcomed.

End tidal carbon dioxide as a predictor of the arterial PCO2 in the emergency department setting

OBJECTIVES

Patients arriving in the emergency department (ED) need rapid and reliable evaluation of their respiratory status. Mainstream end tidal carbon dioxide (ETCO(2)) is one of the methods used for this purpose during general anaesthesia of intubated patients in the operating theatre. Sidestream ETCO(2) (SSETCO(2)) might be a non-invasive, rapid, and reliable predictor of arterial Pco(2) in non-intubated patients in respiratory distress. The aim of this study was to verify whether SSETCO(2) can accurately predict the arterial Pco(2) and to detect variables that may affect this correlation.

METHODS

A prospective semi-blind study. The participants were 73 patients (47 men, 26 women) referred to the ED for respiratory distress. Arterial blood gas pressures and SSETCO(2) measurements were performed and recorded for all patients. Other parameters recorded were: age; body temperature; respiratory rate; blood pressure; pulse rate; and medical diagnosis.

RESULTS

A significant correlation was found between SSETCO(2) and arterial Pco(2) (r = 0.792). Compared with the correlation curve of the whole group, age under 50 years deflected the correlation curve to the left, while temperature above 37.6 degrees C deflected it to the right. The rest of the parameters had no clear influence on the SSETCO(2)/Pco(2) correlation curve.

CONCLUSIONS

There is a good correlation between SSETCO(2) and arterial Pco(2) in the ED setting. Young age may increase the arterial Pco(2)/SSETCO(2) gradient while raised temperature may decrease this gradient. Further studies are needed to confirm these findings in the normal healthy population.

Evidence-based recommendations for the role of exercise in the management of osteoarthritis of the hip or knee--the MOVE consensus

OBJECTIVES

Exercise is an effective and commonly prescribed intervention for lower limb osteoarthritis (OA). Many unanswered questions remain, however, concerning the practical delivery of exercise therapy. We have produced evidence-based recommendations to guide health-care practitioners.

METHODS

A multidisciplinary guideline development group was formed from representatives of professional bodies to which OA is of relevance and other interested parties. Each participant contributed up to 10 propositions describing key clinical points regarding exercise therapy for OA of the hip or knee. Ten final recommendations were agreed by the Delphi technique. The research evidence for each was determined. A literature search was undertaken in the Medline, PubMed, EMBASE, PEDro, CINAHL and Cochrane databases. The methodological quality of each retrieved publication was assessed. Outcome data were abstracted and effect sizes calculated. The evidence for each recommendation was assessed and expert consensus highlighted by the allocation of two categories: (1) strength of evidence and (2) strength of recommendation.

RESULTS

The first round of the Delphi process produced 123 propositions. This was reduced to 10 after four rounds. These related to aerobic and strengthening exercise, group versus home exercise, adherence, contraindications and predictors of response. The literature search identified 910 articles; 57 intervention trials relating to knee OA, 9 to hip OA and 73 to adherence. The evidence to support each proposition is presented.

CONCLUSION

These are the first recommendations for exercise in hip and knee OA to clearly differentiate research evidence and expert opinion. Gaps in the literature are identified and issues requiring further study highlighted.

Development of the Knee Standardized Clinical Interview: a research tool for studying the primary care clinical epidemiology of knee problems in older adults

OBJECTIVE

To develop a standardized clinical interview, incorporating the perspectives of general practitioners (GPs) and rheumatologists, for primary care clinical epidemiological studies of adults aged 50 yr and over with knee problems.

METHODS

Two parallel, consensus development studies using a modified nominal group technique involving GPs (n=5) and consultant rheumatologists (n=4) from North Staffordshire with reference panels of GPs (n=28) and rheumatologists (n=11) from selected centres in Great Britain, respectively. A single standardized clinical interview was formed using the clinical history questions identified in the consensus development studies and its feasibility was tested in a small sample of patients.

RESULTS

In the GP consensus development study, 115 clinical history questions were identified, of which 71 were of agreed importance following postal rating, face-to-face discussion and re-rating. In the rheumatologist study, 158 questions were identified, of which 47 were of agreed importance. There was considerable overlap in the clinical history questions independently developed by the two studies. A single standardized clinical interview containing 74 questions was formed. It contained questions on the history, onset and recent course of the complaint; nature, location and severity of current knee symptoms; impact of knee problem; past history of knee problems; family history; comorbidity; previous/current investigations and treatment; ideas, concerns and expectations. In preliminary testing it took 20-45 min to conduct and was comprehensible to patients.

CONCLUSIONS

A research tool-the Knee Standardized Clinical Interview (KNE-SCI)-has been formed from consensus development studies involving GPs and rheumatologists. In preliminary testing, it is comprehensible to patients, and forms a coherent clinical interview for research data collection. However, further evaluation is required to determine its accuracy and reliability and its usefulness for clinical epidemiological research.

Clinical assessment of the osteoarthritis patient

It is becoming apparent that the disease process of osteoarthritis should be regarded separately from the clinical syndrome of joint pain, use-related stiffness and disability. The latter may best be approached as a chronic regional pain disorder that requires attention to physical, psychological and social factors as well as those related to the disease process. This chapter sets out to look at some of the practical implications of taking this view for the clinical assessment. Starting with the syndrome of hip, knee or hand pain in older adults in the community, we consider what leads people to consult, what the important features to assess might be, the role of imaging in the clinical assessment of osteoarthritis, and finally how a management plan could be formulated. The usefulness of assessing clinical osteoarthritis as a regional pain disorder is uncertain. Even if this were demonstrated, the concept of osteoarthritis as a structural disease should be retained as an integral part.