Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination

16S rRNA gene sequencing is widely used to characterize human and environmental microbiomes. Sequencing at scale facilitates better powered studies but is limited by cost and time. We identified two areas in our 16S rRNA gene library preparation protocol where modifications could provide efficiency gains, including (1) pooling of multiple PCR amplifications per sample to reduce PCR drift and (2) manual preparation of mastermix to reduce liquid handling. Using nasal samples from healthy human participants and a serially diluted mock microbial community, we compared alpha and beta diversity, and compositional abundance where the PCR amplification was conducted in triplicate, duplicate or as a single reaction, and where manually prepared or premixed mastermix was used. One hundred and fifty-eight 16S rRNA gene sequencing libraries were prepared, including a replicate experiment. Comparing PCR pooling strategies, we found no significant difference in high-quality read counts and alpha diversity, and beta diversity by Bray-Curtis index clustered by replicate on principal coordinate analysis (PCoA) and non-metric dimensional scaling (NMDS) analysis. Choice of mastermix had no significant impact on high-quality read and alpha diversity, and beta diversity by Bray-Curtis index clustered by replicate in PCoA and NMDS analysis. Importantly, we observed contamination and variability of rare species (<0.01 %) across replicate experiments; the majority of contaminants were accounted for by removal of species present at <0.1 %, or were linked to reagents (including a primer stock). We demonstrate no requirement for pooling of PCR amplifications or manual preparation of PCR mastermix, resulting in a more efficient 16S rRNA gene PCR protocol.

Bottlenecks to child health service delivery – how can Health System Performance Assessment help?

Health System Performance Assessment (HSPA) is an established tool that can help identify issues with the way health systems work to achieve their intended goals, improve transparency and account-ability, and provide stimulus for reform. However, HSPA frameworks tend to be adult-centric and therefore not generally sensitive to child health challenges. Using a new HSPA framework for Universal Health Coverage, we show how child health tracer conditions can be used to pinpoint system under-performance and flag major bottlenecks impeding service delivery overall. Based on the HSPA framework, health system bottlenecks can be traced backwards to explore possible origins (areas to be targeted for improvement) or forwards to understand potential implications for the achievement of health system goals. The following qualitative and quantitative data are used to highlight major bottlenecks to child health service delivery: eight health system-focused child health assessments which show that one of the main bottlenecks is weak primary care coverage of sexual, reproductive, maternal, newborn, child, and adolescent health services, leading to parents bypassing PHC in favour of hospitals; results from WHO missions (e.g. in Romania and Tajikistan) showing that paediatric patients were often admitted to hospitals for treatment, even for conditions that could be safely managed in the outpatient setting; quantitative data on responsiveness, user experience, client satisfaction and people-centredness from publicly available datasets and national datasets obtained in collaboration with WHO Country Offices for national level data, to contextualize the aforementioned findings.

Detecting cryptic clinically relevant structural variation in exome-sequencing data increases diagnostic yield for developmental disorders

Structural variation (SV) describes a broad class of genetic variation greater than 50 bp in size. SVs can cause a wide range of genetic diseases and are prevalent in rare developmental disorders (DDs). Individuals presenting with DDs are often referred for diagnostic testing with chromosomal microarrays (CMAs) to identify large copy-number variants (CNVs) and/or with single-gene, gene-panel, or exome sequencing (ES) to identify single-nucleotide variants, small insertions/deletions, and CNVs. However, individuals with pathogenic SVs undetectable by conventional analysis often remain undiagnosed. Consequently, we have developed the tool InDelible, which interrogates short-read sequencing data for split-read clusters characteristic of SV breakpoints. We applied InDelible to 13,438 probands with severe DDs recruited as part of the Deciphering Developmental Disorders (DDD) study and discovered 63 rare, damaging variants in genes previously associated with DDs missed by standard SNV, indel, or CNV discovery approaches. Clinical review of these 63 variants determined that about half (30/63) were plausibly pathogenic. InDelible was particularly effective at ascertaining variants between 21 and 500 bp in size and increased the total number of potentially pathogenic variants identified by DDD in this size range by 42.9%. Of particular interest were seven confirmed de novo variants in MECP2, which represent 35.0% of all de novo protein-truncating variants in MECP2 among DDD study participants. InDelible provides a framework for the discovery of pathogenic SVs that are most likely missed by standard analytical workflows and has the potential to improve the diagnostic yield of ES across a broad range of genetic diseases.

Sex differences in sudden cardiac death: a nationwide study of 54,028 deaths in Denmark

Background

Sudden cardiac death (SCD) is a leading cause of death. SCD is more common among males. In women SCD is, however, still the leading cause of death. The SCD epidemiology among women is less studied.

Purpose

The aim of this study was to examine how incidence rates, clinical characteristics and causes of SCD vary between males and females.

Methods

All deaths in Denmark in the 2010 (54,028) were included in the study. Autopsy reports, death certificates, discharge summaries and nationwide health registries were reviewed to identify cases of SCD. Sex and age specific SCD incidence rates in the general population were calculated, and age-adjusted clinical characteristics were compared using logistic regression.

Results

A total of 6,867 SCD cases were identified, of which 3,859 (56%) were males and 3,008 (44%) were females. Incidence rates increased with age and was higher for males across all age groups in the adult population. Average age of SCD was 71.3±14.3 years among males compared to 79.4±13.3 among females (mean ± standard deviation, p&lt;0.0001). The greatest difference in incidence between males and females was found among the 35–50-year group with an incidence rate ratio of 3.7 (95% confidence interval: 2.8–4.8). Although the males were younger, males more often had cardiovascular diseases and diabetes mellitus prior to SCD. Among autopsied cases, coronary artery disease (CAD) was the leading cause of death among both sexes. Structural causes of SCD, other than CAD, were more common among women (p&lt;0.01).

Conclusion

In this nationwide study of sex differences in SCD across all age groups, the differences in incidence rates between males and females were greatest among young adults and the middle-aged. Incidence rates of SCD among older females approached that of the male population, despite significantly more cardiovascular disease and diabetes mellitus in the male population in the 10 years prior to SCD.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark

Usage and risk with phosphodiesterase type 5 inhibitors in male patients with chronic ischemic heart disease on oral organic nitrates

Background

Combining oral organic nitrates (OON) with phosphodiesterase type 5 (PDE5) inhibitors is contraindicated. Growing and liberal use of PDE5 inhibitors for erectile dysfunction among patients with ischemic heart disease (IHD) could pose serious health consequences especially among patients with IHD on OON.

Purpose

We hypothesize that concomitant prescription of OON and PDE5 inhibitors is prevalent and has increased in recent years, and further that possible co-exposure could be associated with an increased risk of ischemic stroke, myocardial infarction (MI) or acute coronary angiography (CAG).

Methods

During 2000–2018, we included all male patients with history of IHD between 18 and 85 years of age from nationwide Danish health registers. Patients with a history of pulmonary hypertension were excluded and not followed up afterwards if they developed the condition during follow-up. From this cohort, we identified an OON treated subgroup defined by two consecutively redeemed prescriptions of OON within 180 days from each other. Further, to become a case or control, patients had to redeem a prescription of OON within 180 days prior to the event or corresponding date among controls.

Temporal trends during 2001–2018 of PDE5 inhibitor use were calculated among all male patients with IHD and the subgroup on OON. Among OON treated patients, we examined associations between PDE5 inhibitor use and risk of ischemic stroke, MI or CAG using a case-crossover design where each individual serves as his/her own control thereby controlling for time-invariant confounding. The case-crossover design compares an individual's exposure in an index period just before the event occurred to a reference period prior to the index period. We investigated periods of varying length (7, 14, 21 and 28 days). To account for possible temporal trends in the use of PDE5 inhibitors, we also conducted a case-time-control analysis using a control group matched on age and calendar year.

Results

We identified 249,541 male patients with IHD (median age 65 years [IQR 56–73]), and a subgroup of 42,073 (17%) on OON treatment (median age 70 years [IQR 62–77]). From 2001 to 2018, the use of PDE5 inhibitors saw a 6-fold increase among all male IHD patients and a 10-fold rise in the subgroup on OON (Figure 1). The risk of ischemic stroke, MI or CAG following exposure to PDE5 inhibitors was not increased in the OON subgroup in neither the case-crossover nor the case-time-control analyses (Figure 2).

Conclusions

The use of PDE5 inhibitors has increased 6-fold since 2001 among male patients with IHD, and 10-fold among patients on OON–notwithstanding an established absolute contraindication. However, we did not find any evidence of an increased risk of ischemic stroke, MI or acute CAG following exposure to PDE5 inhibitors in the OON subgroup. This suggests that patients on OON are adequately informed and comply with the recommended pause in OON medication prior to PDE5 inhibitor use.

Funding Acknowledgement

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): Ib Mogens Kristiansens Almene FondandHelsefonden

Racial disparities in out-of-hospital cardiac arrest in Denmark

Introduction

American studies have pointed out racial disparities regarding sudden cardiac death occurrence and outcomes. Black individuals have higher sudden cardiac death rates and lower survival compared with white subjects (1). Although income and social status partly explain differences in outcomes (2), sudden cardiac death is 2-fold higher in black individuals after adjustment on these characteristics (3,4).

In Denmark, immigrants account for 9.1% of the population (5) but to date, no data exists regarding Out-of-Hospital Cardiac Arrest (OHCA) incidence.

Purpose

The main objective of this study was to compare the incidence of OHCA among native and immigrant individuals between 2001 and 2014 in Denmark.

Methods

This nationwide study included all patients identified from the Danish Cardiac Arrest Registry with OHCA of presumed cardiac cause between 18 and 80 years from 2001 to 2014 (6).

The primary outcome was OHCA occurrence defined as a clinical condition of cardiac arrest resulting in resuscitation efforts either by bystanders or by EMS personnel. The immigrant status was defined as native or immigrant according to the national database from Statistics Denmark. An immigrant was defined as a person born abroad whose both parents were either foreign citizens or born abroad.

The odds ratio of OHCA between immigrants and native Danes were adjusted according to age, sex, income, and education level.

Results

A total of 33,730 OHCA were recorded between 2001 and 2014. Among them, 1,684 occurred in immigrants and 32,046 in natives. Compared to natives, immigrant victims of OHCA were younger (62.0 [51.0, 71.0] vs. 66.0 [56.0, 74.0], p&lt;0.001), and more often had a history of diabetes (20.5% vs. 14.0; p&lt;0.001), myocardial infarction (11.9% vs. 8.7%; p&lt;0.001) and chronic heart failure (17.0% vs. 14.7%; p&lt;0.01). Female proportion was not statistically different between the two groups (30.2% vs. 31.3% of immigrants and natives respectively; p=0.32).

The incidence of OHCA was 61.0/100,000 person-years in natives and 35.0/100,000 person-years in immigrants (OR=0.57; 95% CI 0.54–0.60; p&lt;0.001). Between 2001 and 2014, the OHCA incidence decreased from 71.4 [67.9–75.0] to 70.9 [68.2–73.6]/100 000 person-years in natives (p=0.99) and from 40.2 [30.8–51.5] to 36.5 [31.1–42.6] /100,000 person-years in immigrants (p=0.91) (Figure).

After logistic regression, compared to natives, the immigrant status was associated with 0.61-fold odds of OHCA when adjusting on age and sex (OR=0.61; 95% CI 0.59–0.65; p&lt;0.001), and 0.65-fold odds of OHCA when adjusting on age, sex, income, and education level (OR=0.66; 95% CI 0.63–0.70; p&lt;0.001).

Conclusion

This is the first study assessing the incidence of OHCA in immigrants versus natives in a European country. Despite higher cardiovascular burden, the incidence of OHCA was lower in immigrants even when adjusted on sex, age, income, and education reflecting a selection of individuals migrating to Denmark.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): Fédération Française de Cardiologie

Gastrointestinal bleeding risk following concomitant treatment with oral glucocorticoids in patients with atrial fibrillation on direct-acting oral anticoagulants

Background

Oral glucocorticoids and direct-acting oral anticoagulants (DOAC) have both been associated with a risk of gastrointestinal (GI) bleeding. However, drug safety, especially regarding the risk of bleeding, in relation to concomitant treatment with oral glucocorticoids and DOACs is insufficiently explored.

Purpose

We aimed to investigate the short-term risk of GI bleeding in patients with atrial fibrillation (AF) following concomitant treatment with DOACs and oral glucocorticoids.

Methods

Register-based, retrospective and nationwide Danish study including patients with AF and on DOAC treatment during 2012–2018. Patients were defined as exposed to oral glucocorticoids from the date of a redeemed prescription and 60 days forward. We associated concomitant treatment with GI bleeding and reported hazard ratios (HR) via a nested case-control design and standardized 60-day absolute risk adjusted for comorbidities using a cohort design. In both analyses, exposed were compared to non-exposed controls matched on age, sex, calendar year, follow-up time and DOAC agent.

Results

We included 98,376 patients (age [interquartile range]: 75 [68– 82], 44% females) with AF on DOAC treatment. The use of oral glucocorticoids among included patients was widespread with 16% redeeming at least one prescription within three years, 4% redeeming at least five (Figure 1A). Lung disease was the most frequent indication (Figure 1B). Concomitant treatment with DOACs and oral glucocorticoids was associated with an increased incidence of GI bleeding (total n=4,946) compared with only DOAC treatment, including a dose-response trend (&lt;20mg daily dose, HR [95% confidence interval (CI)]: 1.64 [1.38–1.95]; ≥20mg daily dose, HR [95% CI]: 2.29 [1.90–2.77]). Likewise, the standardized 60-day absolute risk of GI bleeding from first oral glucocorticoid exposure was increased compared with non-exposed (Figure 2).

Conclusion

Caution should be exercised when prescribing even short-term oral glucocorticoid treatment for DOAC treated patients, most notably in high doses and for patients with elevated bleeding risk.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): Ib Mogens Kristiansens Almene FondandHelsefonden

Effect of beta blocker therapy following myocardial infarction in optimally treated patients in the reperfusion era – a Danish, nationwide, and registry-based cohort study

Background and purpose

European and American cardiovascular treatment guidelines advocate for two and three years of beta-blocker (BB) treatment, respectively, following myocardial infarction (MI). Contemporary continued efficacy of longer-term use of BB in stable coronary artery disease has been debated in the era of reperfusion. We aim to investigate the cardio-protective effect associated with BB treatment in patients following MI.

Methods

Using nationwide databases, we included optimally treated patients with first-time MI undergoing coronary angiography (CAG) or percutaneous coronary intervention (PCI) during admission and treated with both acetyl-salicylic acid and statins post-discharge between 2003 and 2017. Patients with prior history of MI, BB use or any other possible indication or contraindication for BB treatment (heart failure, cardiac arrhythmias or procedures, asthma, chronic obstructive pulmonary disease) were excluded. Continued BB exposure was defined as two redeemed prescriptions within the first 180 days following discharge, one of them within 90 days. Follow-up began 180 days following discharge in patients alive and with no further cardiovascular events or procedures prior. Patients were followed for a maximum of three years. Primary outcomes were cardiovascular death and recurrent MI in patients stratified by BB treatment using adjusted Cox regression models.

Results

A total of 27,068 patients optimally treated for MI were included (57% acute PCI, 26% sub-acute PCI, 17% CAG without intervention). At study start 180 days following MI, 79% of the patients were on BB treatment (median age 61 years, 75% male) and 21% were not (median age 62 years, 69% male). Cumulative incidence of cardiovascular death and recurrent MI did not differ significantly comparing patients on BB treatment with patients not on BB treatment (Figure). In multivariable analyses, BB treatment was associated with a similar risk of cardiovascular death and recurrent MI compared to the patients not receiving BB treatment (hazard ratios with [95% confidence intervals] correspondingly; 0.89 [0.68–1.17] and 1.02 [0.89–1.18]) (Figure 1). When stratifying the cohort according to calendar year and type of procedure during admission, we found similar results as the main analysis. No interaction for sex was found.

Conclusions

In this nationwide cohort study of optimally treated patients following MI at 180 days in the reperfusion era, we found a very good prognosis with only 1.2% suffering cardiovascular death and 4.7% suffering a recurrent MI within three years. In total 79% of patients were receiving BB treatment, but we found no difference suggesting BB to be associated with an improved cardiovascular prognosis. These findings challenge current clinical practice and guideline recommendation, suggesting that the role of long-term BB use may be obsolete among optimally treated MI patients. Further investigations, preferably a randomized trial, are warranted.

Figure 1

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): Ib Mogens Kristiansens Almene Fond, Snedkermester Sophus Jacobsen og Hustru Astrid Jacobsens Fond

Assessing health system functions

Health system functions are the core components of the HSPA Framework for UHC. In line with the existing work, we have distinguished four health system functions: governance, financing, resource generation and service delivery. For each of those functions we have identified a number of sub-functions through a systematic process. We then linked the sub-functions and functions to specific assessment areas and identified indicative measures from routinely collected data and/or existing health system assessment tools that can be used to operationalize the framework.

This presentation will introduce the four functions in terms of: 1) where they fit in the framework; 2) how they are conceptualised through sub-functions and 3) how they can be assessed using the framework. It will elaborate on how each of these functions makes contribution towards health system performance and will highlight the linkages between performance of the functions and health system goals.

Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia

The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Ca_v2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca²⁺ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Ca_v2.2 in normal human neurodevelopment.

Beta-ketothiolase deficiency in a Malaysian infant

Methylacetoacetyl-coenzyme A thiolase (MAT) deficiency is an autosomal recessive disease caused by a defect of mitochondrial acetoacetyl-CoA thiolase (T2). There is an error of isoleucine catabolism and ketone body utilization due to mutations in the acetyl-Coenzyme A acetyltransferase 1 (ACAT1) gene. We report a case of a 14 months old Sabahan boy with beta deficiency who presented with severe sepsis and ketoacidosis who subsequently recovered.

Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing

Congenital heart defects (CHDs) have a neonatal incidence of 0.8-1% (refs. 1,2). Despite abundant examples of monogenic CHD in humans and mice, CHD has a low absolute sibling recurrence risk (∼2.7%), suggesting a considerable role for de novo mutations (DNMs) and/or incomplete penetrance. De novo protein-truncating variants (PTVs) have been shown to be enriched among the 10% of 'syndromic' patients with extra-cardiac manifestations. We exome sequenced 1,891 probands, including both syndromic CHD (S-CHD, n = 610) and nonsyndromic CHD (NS-CHD, n = 1,281). In S-CHD, we confirmed a significant enrichment of de novo PTVs but not inherited PTVs in known CHD-associated genes, consistent with recent findings. Conversely, in NS-CHD we observed significant enrichment of PTVs inherited from unaffected parents in CHD-associated genes. We identified three genome-wide significant S-CHD disorders caused by DNMs in CHD4, CDK13 and PRKD1. Our study finds evidence for distinct genetic architectures underlying the low sibling recurrence risk in S-CHD and NS-CHD.

Recurrent duplications of 17q12 associated with variable phenotypes

The ability to identify the clinical nature of the recurrent duplication of chromosome 17q12 has been limited by its rarity and the diverse range of phenotypes associated with this genomic change. In order to further define the clinical features of affected patients, detailed clinical information was collected in the largest series to date (30 patients and 2 of their siblings) through a multi-institutional collaborative effort. The majority of patients presented with developmental delays varying from mild to severe. Though dysmorphic features were commonly reported, patients do not have consistent and recognizable features. Cardiac, ophthalmologic, growth, behavioral, and other abnormalities were each present in a subset of patients. The newly associated features potentially resulting from 17q12 duplication include height and weight above the 95th percentile, cataracts, microphthalmia, coloboma, astigmatism, tracheomalacia, cutaneous mosaicism, pectus excavatum, scoliosis, hypermobility, hypospadias, diverticulum of Kommerell, pyloric stenosis, and pseudohypoparathryoidism. The majority of duplications were inherited with some carrier parents reporting learning disabilities or microcephaly. We identified additional, potentially contributory copy number changes in a subset of patients, including one patient each with 16p11.2 deletion and 15q13.3 deletion. Our data further define and expand the clinical spectrum associated with duplications of 17q12 and provide support for the role of genomic modifiers contributing to phenotypic variability.

Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data

BACKGROUND

Human genome sequencing has transformed our understanding of genomic variation and its relevance to health and disease, and is now starting to enter clinical practice for the diagnosis of rare diseases. The question of whether and how some categories of genomic findings should be shared with individual research participants is currently a topic of international debate, and development of robust analytical workflows to identify and communicate clinically relevant variants is paramount.

METHODS

The Deciphering Developmental Disorders (DDD) study has developed a UK-wide patient recruitment network involving over 180 clinicians across all 24 regional genetics services, and has performed genome-wide microarray and whole exome sequencing on children with undiagnosed developmental disorders and their parents. After data analysis, pertinent genomic variants were returned to individual research participants via their local clinical genetics team.

FINDINGS

Around 80,000 genomic variants were identified from exome sequencing and microarray analysis in each individual, of which on average 400 were rare and predicted to be protein altering. By focusing only on de novo and segregating variants in known developmental disorder genes, we achieved a diagnostic yield of 27% among 1133 previously investigated yet undiagnosed children with developmental disorders, whilst minimising incidental findings. In families with developmentally normal parents, whole exome sequencing of the child and both parents resulted in a 10-fold reduction in the number of potential causal variants that needed clinical evaluation compared to sequencing only the child. Most diagnostic variants identified in known genes were novel and not present in current databases of known disease variation.

INTERPRETATION

Implementation of a robust translational genomics workflow is achievable within a large-scale rare disease research study to allow feedback of potentially diagnostic findings to clinicians and research participants. Systematic recording of relevant clinical data, curation of a gene-phenotype knowledge base, and development of clinical decision support software are needed in addition to automated exclusion of almost all variants, which is crucial for scalable prioritisation and review of possible diagnostic variants. However, the resource requirements of development and maintenance of a clinical reporting system within a research setting are substantial.

FUNDING

Health Innovation Challenge Fund, a parallel funding partnership between the Wellcome Trust and the UK Department of Health.

Large-scale discovery of novel genetic causes of developmental disorders

Despite three decades of successful, predominantly phenotype-driven discovery of the genetic causes of monogenic disorders, up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. Particularly challenging are those disorders rare enough to have eluded recognition as a discrete clinical entity, those with highly variable clinical manifestations, and those that are difficult to distinguish from other, very similar, disorders. Here we demonstrate the power of using an unbiased genotype-driven approach to identify subsets of patients with similar disorders. By studying 1,133 children with severe, undiagnosed developmental disorders, and their parents, using a combination of exome sequencing and array-based detection of chromosomal rearrangements, we discovered 12 novel genes associated with developmental disorders. These newly implicated genes increase by 10% (from 28% to 31%) the proportion of children that could be diagnosed. Clustering of missense mutations in six of these newly implicated genes suggests that normal development is being perturbed by an activating or dominant-negative mechanism. Our findings demonstrate the value of adopting a comprehensive strategy, both genome-wide and nationwide, to elucidate the underlying causes of rare genetic disorders.

aCGH.Spline--an R package for aCGH dye bias normalization

MOTIVATION

The careful normalization of array-based comparative genomic hybridization (aCGH) data is of critical importance for the accurate detection of copy number changes. The difference in labelling affinity between the two fluorophores used in aCGH-usually Cy5 and Cy3-can be observed as a bias within the intensity distributions. If left unchecked, this bias is likely to skew data interpretation during downstream analysis and lead to an increased number of false discoveries.

RESULTS

In this study, we have developed aCGH.Spline, a natural cubic spline interpolation method followed by linear interpolation of outlier values, which is able to remove a large portion of the dye bias from large aCGH datasets in a quick and efficient manner.

CONCLUSIONS

We have shown that removing this bias and reducing the experimental noise has a strong positive impact on the ability to detect accurately both copy number variation (CNV) and copy number alterations (CNA).

FoSTeS, MMBIR and NAHR at the human proximal Xp region and the mechanisms of human Xq isochromosome formation

The recently described DNA replication-based mechanisms of fork stalling and template switching (FoSTeS) and microhomology-mediated break-induced replication (MMBIR) were previously shown to catalyze complex exonic, genic and genomic rearrangements. By analyzing a large number of isochromosomes of the long arm of chromosome X (i(Xq)), using whole-genome tiling path array comparative genomic hybridization (aCGH), ultra-high resolution targeted aCGH and sequencing, we provide evidence that the FoSTeS and MMBIR mechanisms can generate large-scale gross chromosomal rearrangements leading to the deletion and duplication of entire chromosome arms, thus suggesting an important role for DNA replication-based mechanisms in both the development of genomic disorders and cancer. Furthermore, we elucidate the mechanisms of dicentric i(Xq) (idic(Xq)) formation and show that most idic(Xq) chromosomes result from non-allelic homologous recombination between palindromic low copy repeats and highly homologous palindromic LINE elements. We also show that non-recurrent-breakpoint idic(Xq) chromosomes have microhomology-associated breakpoint junctions and are likely catalyzed by microhomology-mediated replication-dependent recombination mechanisms such as FoSTeS and MMBIR. Finally, we stress the role of the proximal Xp region as a chromosomal rearrangement hotspot.

Distinct effects of allelic NFIX mutations on nonsense-mediated mRNA decay engender either a Sotos-like or a Marshall-Smith syndrome

By using a combination of array comparative genomic hybridization and a candidate gene approach, we identified nuclear factor I/X (NFIX) deletions or nonsense mutation in three sporadic cases of a Sotos-like overgrowth syndrome with advanced bone age, macrocephaly, developmental delay, scoliosis, and unusual facies. Unlike the aforementioned human syndrome, Nfix-deficient mice are unable to gain weight and die in the first 3 postnatal weeks, while they also present with a spinal deformation and decreased bone mineralization. These features prompted us to consider NFIX as a candidate gene for Marshall-Smith syndrome (MSS), a severe malformation syndrome characterized by failure to thrive, respiratory insufficiency, accelerated osseous maturation, kyphoscoliosis, osteopenia, and unusual facies. Distinct frameshift and splice NFIX mutations that escaped nonsense-mediated mRNA decay (NMD) were identified in nine MSS subjects. NFIX belongs to the Nuclear factor one (NFI) family of transcription factors, but its specific function is presently unknown. We demonstrate that NFIX is normally expressed prenatally during human brain development and skeletogenesis. These findings demonstrate that allelic NFIX mutations trigger distinct phenotypes, depending specifically on their impact on NMD.

Constitutional haploinsufficiency of tumor suppressor genes in mentally retarded patients with microdeletions in 17p13.1

Chromosome microdeletions or duplications are detected in 10-20% of patients with mental impairment and normal karyotypes. A few cases have been reported of mental impairment with microdeletions comprising tumor suppressor genes. By array-CGH we detected 4 mentally impaired individuals carrying de novo microdeletions sharing an overlapping segment of approximately 180 kb in 17p13.1. This segment encompasses 18 genes, including 3 involved in cancer, namely KCTD11/REN, DLG4/PSD95, and GPS2. Furthermore, in 2 of the patients, the deletions also included TP53, the most frequently inactivated gene in human cancers. The 3 tumor suppressor genes KCTD11, DLG4, and GPS2, in addition to the GABARAP gene, have a known or suspected function in neuronal development and are candidates for causing mental impairment in our patients. Among our 4 patients with deletions in 17p13.1, 3 were part of a Brazilian cohort of 300 mentally retarded individuals, suggesting that this segment may be particularly prone to rearrangements and appears to be an important cause (approximately 1%) of mental retardation. Further, the constitutive deletion of tumor suppressor genes in these patients, particularly TP53, probably confers a significantly increased lifetime risk for cancer and warrants careful oncological surveillance of these patients. Constitutional chromosome deletions containing tumor suppressor genes in patients with mental impairment or congenital abnormalities may represent an important mechanism linking abnormal phenotypes with increased risks of cancer.

Germline rates of de novo meiotic deletions and duplications causing several genomic disorders

Meiotic recombination between highly similar duplicated sequences (nonallelic homologous recombination, NAHR) generates deletions, duplications, inversions and translocations, and it is responsible for genetic diseases known as 'genomic disorders', most of which are caused by altered copy number of dosage-sensitive genes. NAHR hot spots have been identified within some duplicated sequences. We have developed sperm-based assays to measure the de novo rate of reciprocal deletions and duplications at four NAHR hot spots. We used these assays to dissect the relative rates of NAHR between different pairs of duplicated sequences. We show that (i) these NAHR hot spots are specific to meiosis, (ii) deletions are generated at a higher rate than their reciprocal duplications in the male germline and (iii) some of these genomic disorders are likely to have been underascertained clinically, most notably that resulting from the duplication of 7q11, the reciprocal of the deletion causing Williams-Beuren syndrome.

Arthroplasties (with and without bone cement) for proximal femoral fractures in adults

BACKGROUND

Numerous types of arthroplasties may be used in the surgical treatment of a hip fracture (proximal femoral fracture). The main differences between the implants are the design of the stems, whether the stem is fixed in place with or without cement, whether a second articulating joint is included within the prosthesis (bipolar prosthesis) or whether the whole hip joint is replaced.

OBJECTIVES

To review all randomised trials that have compared different arthroplasties for the treatment of hip fractures in adults.

SEARCH STRATEGY

We searched the Cochrane Musculoskeletal Injuries Group specialised register. Additional trials were identified by searching reference lists of relevant articles, conference proceedings, and contact with trialists. Date of most recent search: January 2001.

SELECTION CRITERIA

All randomised and quasi-randomised trials comparing different arthroplasties (and or cement), for the treatment of hip fractures.

DATA COLLECTION AND ANALYSIS

Two reviewers independently assessed trial quality, by use of a ten-item checklist and extracted data.

MAIN RESULTS

Thirteen trials involving 1464 patients were included. One trial investigated two comparisons. Cemented prostheses, when compared with uncemented (four trials, 391 participants) were associated with a lower risk of failure to regain mobility (relative risk (RR) 0.60, 95% confidence interval (CI) 0.44, 0.82) and of post-operation pain at a year or later (RR 0.51, 95% CI 0.31, 0.81). For this comparison, there were no significant differences in any other outcome. Comparison of unipolar hemiarthroplasty with bipolar hemiarthroplasty (six trials, 742 participants) showed no significant differences between the two types of implant. Two trials of 269 patients compared different types of hemiarthroplasty with a total hip replacement and two trials of 151 patients compared either different types of prosthesis head or different bipolar prostheses. Because of the limited number of cases and the use of different prostheses, no definite conclusions could be made from these four studies.

REVIEWER'S CONCLUSIONS

Cementing prostheses in place seems to reduce pain post-operatively and results in better mobility, but because of the under-reporting of outcomes and the small number of patients involved, no definite conclusions can be made. The role of bipolar prostheses and total hip replacement is uncertain. Further well-conducted randomised trials are required.

Bacterial flora of the jejunum: a comparison of luminal aspirate and mucosal biopsy

The aerobic and anaerobic bacterial flora grown from 40 human jejunal aspirates were compared with the flora grown from an intestinal mucosal biopsy obtained simultaneously from the same level. In four paired samples the flora was identical; in nine the flora differed by only one organism. In six pairs the flora differed by two organisms, and in 11 pairs by three or more organisms. In nine pairs the jejunal aspirate grew only one organism or was sterile, but the biopsy showed considerable numbers of organisms. In one pair the jejunal aspirate grew organisms, but there was no growth from the biopsy. It is apparent that for adequate bacteriological study of the intestine, the flora at both sites should be investigated.

Jejunal microbial flora of southern indian infants in health and with acute gastroenteritis

The microbial flora of the jejunal lumen of 28 infants with acute gastroenteritis was compared with that of a group of 10 normal infants. The jejunum of control subjects harboured an "oral" type of flora and in a few instances enterobacteria in small numbers. The concentrations of all but one of the groups of organism were higher in the patients than in controls, and the differences were of statistical significance for enterobacteria and lactobacilli. In eight subjects, the same pathogen was identified in the jejunum and the stool. In six subjects with rotavirus infection, there were almost no Gram-negative aerobic rods in the jejunum. The possible role of other Gram-negative aerobic rods in producing gastroenteritis is discussed. It is suggested that studies of jejunal flora are of considerable importance in assigning an aetiological role to bacteria in the causation of acute gastroenteritis.

Faecal flora of South Indian infants and young children in health and with acute gastroenteritis

The faecal flora of 29 healthy infants and young children was compared with that of 49 children of similar age and socio-ecomonic status with acute gastroenteritis. In the healthy children the most common organisms in the faeces were bifidobacteria, veillonellae, enterobacteria and enterodocci with anaerobes outnumbering aerobes. Most members of the noraml faecal flora were present in the diarrhoeal stools, but anaerobes were signigicantly reduced in number and enterobacteria were significantly increased, thereby altering the ratio of anaerobes to aerobes. The alterations in the flora were not related to the nature of the aetiological agent or to the severity of the diarrhoea. The changes appeared to be a direct result of the altered colonic environment produced by the diarrhoeal state. In 13 of the 28 patients from whom bacterial pathogens were isolated, the pathogens were the predominant faecal organsims.

Comparative evaluation of desoxycholate citrate medium and xylose lysine desoxycholate medium in the isolation of shigellae

Studies of the relative efficacies of different modes of transport of fecal specimens intended for culture for the isolation of Shigellae have been carried out. When the delay between collection and culture was long, transportation in liquid nitrogen was slightly but not significantly better than transportation on ice. When the delay was short (10 hours or less) transportation at ambient temperature was as satisfactory as that on ice. A comparative study of the efficacies of three media for the isolation of Shigellae was also carried out. A total of 75 stool specimens containing Shigellae was studied. Isolation rates were highest with xylose lysine desoxycholate medium (XLD) and desoxycholate citrate medium (DCA). XLD was superior to DCA in that the Shigella colonies were clearly visible after overnight incubation, whereas use of DCA necessitated 48 hours of incubation. Also, colonial morphology on XLD was more specific. It is recommended that both XLD and DCA be employed, but if only one medium is to be used, XLD is the medium of choice.