Positioning whole exome sequencing in the diagnostic pathway for rare disease to optimise utility: a protocol for an observational cohort study and an economic evaluation

INTRODUCTION

Despite the superior diagnostic performance of exome and genome sequencing compared with conventional genetic tests, evidence gaps related to clinical utility and cost effectiveness have limited their availability in routine clinical practice in many jurisdictions. To inform adoption and reimbursement policy, this protocol provides a chain of evidence approach to determining the diagnostic utility, clinical utility and cost-effectiveness of whole exome sequencing (WES) from seven medical genetic centres in two Canadian provinces.

METHODS AND ANALYSIS

Using a multicentre observational cohort design, we will extract data specific to the pre-WES diagnostic pathway and 1-year post-WES medical management from electronic medical records for 650 patients with rare disease of suspected genetic aetiology who receive WES. The date from the clinical record will be linked to provincial administrative health database to capture healthcare resource use and estimate costs. Our analysis will: (1) define and describe diagnostic testing pathways that occur prior to WES among patients with rare disease, (2) determine the diagnostic utility of WES, characterised as the proportion of patients for whom causative DNA variants are identified, (3) determine the clinical utility of WES, characterised as a change in medical management triggered by WES results, (4) determine the pattern and cost of health service utilisation prior and 1 year following WES among patients who receive a diagnosis, do not receive a diagnosis, or receive an uncertain diagnosis and (5) estimate the cost-effectiveness of WES compared with conventional diagnostic testing pathways, measured by the incremental cost per additional patient diagnosed by WES using simulation modelling.

ETHICS AND DISSEMINATION

This protocol was approved by Clinical Trials Ontario (CTO-1577) and research ethics boards at the University of Calgary (REB18-0744 and REB20-1449) and University of Alberta (Pro0009156). Findings will be disseminated through academic publications and policy reports.

Effect of Probiotic Bifidobacterium breve in Improving Cognitive Function and Preventing Brain Atrophy in Older Patients with Suspected Mild Cognitive Impairment: Results of a 24-Week Randomized, Double-Blind, Placebo-Controlled Trial

Background:

Probiotics have been reported to ameliorate cognitive impairment.

Objective:

We investigated the effect of the probiotic strain Bifidobacterium breve MCC1274 (A1) in enhancing cognition and preventing brain atrophy of older patients with mild cognitive impairment (MCI).

Methods:

In this RCT, 130 patients aged from 65 to 88 years old with suspected MCI received once daily either probiotic (B. breve MCC1274, 2×10¹⁰ CFU) or placebo for 24 weeks. Cognitive functions were assessed by ADAS-Jcog and MMSE tests. Participants underwent MRI to determine brain atrophy changes using Voxel-based Specific Regional Analysis System for Alzheimer’s disease (VSRAD). Fecal samples were collected for the analysis of gut microbiota composition.

Results:

Analysis was performed on 115 participants as the full analysis set (probiotic 55, placebo 60). ADAS-Jcog subscale “orientation” was significantly improved compared to placebo at 24 weeks. MMSE subscales “orientation in time” and “writing” were significantly improved compared to placebo in the lower baseline MMSE (< 25) subgroup at 24 weeks. VSRAD scores worsened in the placebo group; probiotic supplementation tended to suppress the progression, in particular among those subjects with progressed brain atrophy (VOI Z-score ≥1.0). There were no marked changes in the overall composition of the gut microbiota by the probiotic supplementation.

Conclusion:

Improvement of cognitive function was observed on some subscales scores only likely due to the lower sensitiveness of these tests for MCI subjects. Probiotics consumption for 24 weeks suppressed brain atrophy progression, suggesting that B. breve MCC1274 helps prevent cognitive impairment of MCI subjects.

Targeting Impaired Antimicrobial Immunity in the Brain for the Treatment of Alzheimer's Disease

Alzheimer's disease (AD) is the most common form of dementia and aging is the most common risk factor for developing the disease. The etiology of AD is not known but AD may be considered as a clinical syndrome with multiple causal pathways contributing to it. The amyloid cascade hypothesis, claiming that excess production or reduced clearance of amyloid-beta (Aβ) and its aggregation into amyloid plaques, was accepted for a long time as the main cause of AD. However, many studies showed that Aβ is a frequent consequence of many challenges/pathologic processes occurring in the brain for decades. A key factor, sustained by experimental data, is that low-grade infection leading to production and deposition of Aβ, which has antimicrobial activity, precedes the development of clinically apparent AD. This infection is chronic, low grade, largely clinically silent for decades because of a nearly efficient antimicrobial immune response in the brain. A chronic inflammatory state is induced that results in neurodegeneration. Interventions that appear to prevent, retard or mitigate the development of AD also appear to modify the disease. In this review, we conceptualize further that the changes in the brain antimicrobial immune response during aging and especially in AD sufferers serve as a foundation that could lead to improved treatment strategies for preventing or decreasing the progression of AD in a disease-modifying treatment.

Association of Plasma Hemoglobin A1c with Improvement of Cognitive Functions by Probiotic Bifidobacterium breve Supplementation in Healthy Adults with Mild Cognitive Impairment

We demonstrated the benefit of the probiotic strain, Bifidobacterium breve MCC1274 (synonym B. breve A1), at improving cognition in our previous double-blind, placebo-controlled clinical study. Analysis of the association of blood parameters changes with the improvement of cognitive function revealed an inverse correlation of HbA1c with total RBANS score amelioration after the study only in the probiotic group (ρ= -0.4218, p = 0.0067). A stratified analysis based on baseline HbA1c with a median value showed a more remarkable benefit by the probiotic supplementation in the higher median subgroup. These data support the mechanism of anti-inflammation in improving cognition by the probiotic strain.

Probiotic Bifidobacterium breve in Improving Cognitive Functions of Older Adults with Suspected Mild Cognitive Impairment: A Randomized, Double-Blind, Placebo-Controlled Trial

BACKGROUND

Probiotics use has been associated with modulation of inflammation and considered as a possible intervention for CNS diseases such as mild cognitive impairment (MCI) and dementia.

OBJECTIVE

We aimed to test the effect of the probiotic strain, Bifidobacterium breve A1 (MCC1274), to restore cognition in a physically healthy, suspected MCI population.

METHODS

In this randomized, double-blind, placebo-controlled trial, 80 healthy older adults suffering from MCI were divided into two even groups to receive once daily either probiotic (B. breve A1, 2×1010 CFU) or placebo for 16 weeks using a computer-generated algorithm. Cognitive functions were assessed by the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) and the Japanese version of the MCI Screen (JMCIS) tests before and after the study as primary and secondary endpoints, respectively.

RESULTS

79 participants completed the study, and no adverse events were observed. RBANS total score was significantly improved in probiotic group compared with placebo (mean between-group difference 11.3 [95% CI 6.7 to 15.8]; p < 0.0001) after 16 weeks of consumption, in particular with significant improvement in domain scores of immediate memory, visuospatial/constructional, and delayed memory (p < 0.0001), in both intention-to-treat (ITT) analysis and per-protocol (PP) analysis. JMCIS score was also improved versus placebo in ITT analysis (p = 0.052) and PP analysis (p = 0.036).

CONCLUSION

Study results indicate B. breve A1 is a safe and effective approach for improving memory functions of suspected MCI subjects.

Validation of Dried Blood Spots for Maternal Biomonitoring of Nonessential Elements in an Artisanal and Small-Scale Gold Mining Area of Tanzania

Biomonitoring studies of vulnerable populations in low- and middle-income countries are limited because traditional sampling methods are challenging to implement in low-resource settings. The present study examined the feasibility, precision, and accuracy of dried blood spots (DBS) for human biomonitoring of nonessential elements (cadmium [Cd], mercury [Hg], and lead [Pb]) in an area of northern Tanzania with artisanal and small-scale gold mining activities. Pregnant women (n = 44) were recruited in Geita during antenatal clinic visits, and DBS from capillary blood were collected on filter paper. As a gold-standard comparison, venous blood was sampled from the same participants and compared with the DBS. Venous blood, DBS, and quality control samples were analyzed for chemical elements by inductively coupled plasma mass spectrometry. Field blanks were very clean for most elements, generally only twice as high as corresponding laboratory filter blanks. No significant differences were found between duplicate DBS samples taken from the same participants, with near perfect intraclass correlation coefficients (0.99) for Cd, Hg, and Pb, indicating excellent reliability. Moreover, correlation was strong (r² > 0.9) and significant (p < 0.0001) between DBS and the quantitative venous blood, with regression line slopes close to 1.0 (0.847, 0.976, and 0.969 for Cd, Hg, and Pb, respectively), indicating high accuracy of the DBS method compared with the gold-standard approach. The DBS method is minimally invasive and was a feasible, precise, and accurate means of measuring exposure to Cd, Hg, and Pb in pregnant women in a low-resource setting. Environ Toxicol Chem 2019;38:1285-1293. © 2019 SETAC.

Whole-exome sequencing is a valuable diagnostic tool for inherited peripheral neuropathies: Outcomes from a cohort of 50 families

The inherited peripheral neuropathies (IPNs) are characterized by marked clinical and genetic heterogeneity and include relatively frequent presentations such as Charcot-Marie-Tooth disease and hereditary motor neuropathy, as well as more rare conditions where peripheral neuropathy is associated with additional features. There are over 250 genes known to cause IPN-related disorders but it is estimated that in approximately 50% of affected individuals a molecular diagnosis is not achieved. In this study, we examine the diagnostic utility of whole-exome sequencing (WES) in a cohort of 50 families with 1 or more affected individuals with a molecularly undiagnosed IPN with or without additional features. Pathogenic or likely pathogenic variants in genes known to cause IPN were identified in 24% (12/50) of the families. A further 22% (11/50) of families carried sequence variants in IPN genes in which the significance remains unclear. An additional 12% (6/50) of families had variants in novel IPN candidate genes, 3 of which have been published thus far as novel discoveries (KIF1A, TBCK, and MCM3AP). This study highlights the use of WES in the molecular diagnostic approach of highly heterogeneous disorders, such as IPNs, places it in context of other published neuropathy cohorts, while further highlighting associated benefits for discovery.

Advancing Concussion Assessment in Pediatrics (A-CAP): a prospective, concurrent cohort, longitudinal study of mild traumatic brain injury in children: protocol study

INTRODUCTION

Paediatric mild traumatic brain injury (mTBI) is a public health burden. Clinicians urgently need evidence-based guidance to manage mTBI, but gold standards for diagnosing and predicting the outcomes of mTBI are lacking. The objective of the Advancing Concussion Assessment in Pediatrics (A-CAP) study is to assess a broad pool of neurobiological and psychosocial markers to examine associations with postinjury outcomes in a large sample of children with either mTBI or orthopaedic injury (OI), with the goal of improving the diagnosis and prognostication of outcomes of paediatric mTBI.

METHODS AND ANALYSIS

A-CAP is a prospective, longitudinal cohort study of children aged 8.00-16.99 years with either mTBI or OI, recruited during acute emergency department (ED) visits at five sites from the Pediatric Emergency Research Canada network. Injury information is collected in the ED; follow-up assessments at 10 days and 3 and 6 months postinjury measure a variety of neurobiological and psychosocial markers, covariates/confounders and outcomes. Weekly postconcussive symptom ratings are obtained electronically. Recruitment began in September 2016 and will occur for approximately 24 months. Analyses will test the major hypotheses that neurobiological and psychosocial markers can: (1) differentiate mTBI from OI and (2) predict outcomes of mTBI. Models initially will focus within domains (eg, genes, imaging biomarkers, psychosocial markers), followed by multivariable modelling across domains. The planned sample size (700 mTBI, 300 OI) provides adequate statistical power and allows for internal cross-validation of some analyses.

ETHICS AND DISSEMINATION

The ethics boards at all participating institutions have approved the study and all participants and their parents will provide informed consent or assent. Dissemination will follow an integrated knowledge translation plan, with study findings presented at scientific conferences and in multiple manuscripts in peer-reviewed journals.

Prenatal Array Comparative Genomic Hybridization in Fetuses With Structural Cardiac Anomalies

OBJECTIVES

To examine the diagnostic performance of array comparative genomic hybridization (CGH) for fetal cardiac anomalies in two medium-sized Canadian prenatal genetics clinics.

METHODS

We prospectively recruited 22 pregnant women with fetal structural cardiac anomalies, normal rapid aneuploidy detection, and FISH for 22q11.2 testing for array CGH analysis.

RESULTS

One case had an 8p deletion that was also visible on karyotype and included the GATA4 gene, which has been associated with congenital heart disease. Two cases had inherited pathogenic copy number variants (CNVs) of variable expressivity and penetrance: one was a duplication of 16p11.2 and the other a deletion of 15q11.2. One case had the incidental finding of being a carrier of a recessive disease unrelated to the cardiac anomaly.

CONCLUSIONS

Of these prospectively recruited cases of fetal cardiac anomalies, 14% had a pathogenic result on array CGH. Pathogenic CNVs of variable penetrance and expressivity were a significant proportion of the positive results identified. These CNVs are generally associated with neurodevelopmental issues and may or may not have been associated with the fetus' underlying congenital heart disease. Array CGH increases the diagnostic yield in this group of patients; however, certain CNVs remain a challenge for counselling in the prenatal setting.

Cerebro-costo-mandibular syndrome: Clinical, radiological, and genetic findings

Cerebro-Costo-Mandibular syndrome (CCMS) is a rare autosomal dominant condition comprising branchial arch-derivative malformations with striking rib-gaps. Affected patients often have respiratory difficulties, associated with upper airway obstruction, reduced thoracic capacity, and scoliosis. We describe a series of 12 sporadic and 4 familial patients including 13 infants/children and 3 adults. Severe micrognathia and reduced numbers of ribs with gaps are consistent findings. Cleft palate, feeding difficulties, respiratory distress, tracheostomy requirement, and scoliosis are common. Additional malformations such as horseshoe kidney, hypospadias, and septal heart defect may occur. Microcephaly and significant developmental delay are present in a small minority of patients. Key radiological findings are of a narrow thorax, multiple posterior rib gaps and abnormal costo-transverse articulation. A novel finding in 2 patients is bilateral accessory ossicles arising from the hyoid bone. Recently, specific mutations in SNRPB, which encodes components of the major spliceosome, have been found to cause CCMS. These mutations cluster in an alternatively spliced regulatory exon and result in altered SNRPB expression. DNA was available from 14 patients and SNRPB mutations were identified in 12 (4 previously reported). Eleven had recurrent mutations previously described in patients with CCMS and one had a novel mutation in the alternative exon. These results confirm the specificity of SNRPB mutations in CCMS and provide further evidence for the role of spliceosomal proteins in craniofacial and thoracic development.

The clinical application of genome-wide sequencing for monogenic diseases in Canada: Position Statement of the Canadian College of Medical Geneticists

Purpose and scope

The aim of this Position Statement is to provide recommendations for Canadian medical geneticists, clinical laboratory geneticists, genetic counsellors and other physicians regarding the use of genome-wide sequencing of germline DNA in the context of clinical genetic diagnosis. This statement has been developed to facilitate the clinical translation and development of best practices for clinical genome-wide sequencing for genetic diagnosis of monogenic diseases in Canada; it does not address the clinical application of this technology in other fields such as molecular investigation of cancer or for population screening of healthy individuals.

Methods of statement development

Two multidisciplinary groups consisting of medical geneticists, clinical laboratory geneticists, genetic counsellors, ethicists, lawyers and genetic researchers were assembled to review existing literature and guidelines on genome-wide sequencing for clinical genetic diagnosis in the context of monogenic diseases, and to make recommendations relevant to the Canadian context. The statement was circulated for comment to the Canadian College of Medical Geneticists (CCMG) membership-at-large and, following incorporation of feedback, approved by the CCMG Board of Directors. The CCMG is a Canadian organisation responsible for certifying medical geneticists and clinical laboratory geneticists, and for establishing professional and ethical standards for clinical genetics services in Canada.

Results and conclusions

Recommendations include (1) clinical genome-wide sequencing is an appropriate approach in the diagnostic assessment of a patient for whom there is suspicion of a significant monogenic disease that is associated with a high degree of genetic heterogeneity, or where specific genetic tests have failed to provide a diagnosis; (2) until the benefits of reporting incidental findings are established, we do not endorse the intentional clinical analysis of disease-associated genes other than those linked to the primary indication; and (3) clinicians should provide genetic counselling and obtain informed consent prior to undertaking clinical genome-wide sequencing. Counselling should include discussion of the limitations of testing, likelihood and implications of diagnosis and incidental findings, and the potential need for further analysis to facilitate clinical interpretation, including studies performed in a research setting. These recommendations will be routinely re-evaluated as knowledge of diagnostic and clinical utility of clinical genome-wide sequencing improves. While the document was developed to direct practice in Canada, the applicability of the statement is broader and will be of interest to clinicians and health jurisdictions internationally.

Reduced plasma desmosterol-to-cholesterol ratio and longitudinal cognitive decline in Alzheimer's disease

Background

We here examined whether plasma desmosterol-to-cholesterol ratio (DES/CHO) is decreased in patients with Alzheimer's disease (AD) and investigated the association between plasma DES/CHO and longitudinal cognitive decline.

Methods

Plasma DES/CHO of AD patients and age-matched controls in a Japanese cross-sectional cohort was determined. Plasma DES/CHO at baseline and follow-up visits was assessed in relation to cognitive decline in Japanese and Swedish longitudinal cohorts.

Results

Plasma DES/CHO was significantly reduced in Japanese AD patients and significantly correlated with Mini-Mental State Examination (MMSE) score. The longitudinal analysis revealed that plasma DES/CHO in AD patients shows a significant decrease at follow-up intervals. The decline in plasma DES/CHO is larger in the AD group with rapid progression than in that with slow progression. The changes in plasma DES/CHO significantly correlated with changes in the MMSE score.

Conclusion

Plasma DES/CHO is decreased in AD patients and may serve as a longitudinal surrogate marker associated with cognitive decline.

Validation of an obstetric comorbidity index in an external population

Objectives

An obstetric comorbidity index has been developed recently with superior performance characteristics relative to general comorbidity measures in an obstetric population. This study aimed to externally validate this index and to examine the impact of including hospitalisation/delivery records only when estimating comorbidity prevalence and discriminative performance of the obstetric comorbidity index.

Design

Validation study.

Setting

Alberta, Canada.

Population

Pregnant women who delivered a live or stillborn infant in hospital (n = 5995).

Methods

Administrative databases were linked to create a population‐based cohort. Comorbid conditions were identified from diagnoses for the delivery hospitalisation, all hospitalisations and all healthcare contacts (i.e. hospitalisations, emergency room visits and physician visits) that occurred during pregnancy and 3 months pre‐conception. Logistic regression was used to test the discriminative performance of the comorbidity index.

Main outcome measures

Maternal end‐organ damage and extended length of stay for delivery.

Results

Although prevalence estimates for comorbid conditions were consistently lower in delivery records and hospitalisation data than in data for all healthcare contacts, the discriminative performance of the comorbidity index was constant for maternal end‐organ damage [all healthcare contacts area under the receiver operating characteristic curve (AUC) = 0.70; hospitalisation data AUC = 0.67; delivery data AUC = 0.65] and extended length of stay for delivery (all healthcare contacts AUC = 0.60; hospitalisation data AUC = 0.58; delivery data AUC = 0.58).

Conclusions

The obstetric comorbidity index shows similar performance characteristics in an external population and is a valid measure of comorbidity in an obstetric population. Furthermore, the discriminative performance of the comorbidity index was similar for comorbidities ascertained at the time of delivery, in hospitalisation data or through all healthcare contacts.

Improving completeness of ascertainment and quality of information for pregnancies through linkage of administrative and clinical data records

PURPOSE

Birth cohorts are a common tool used in epidemiological studies about pregnancy; yet these datasets systematically miss pregnancies that are spontaneously lost or terminated. This study examined the feasibility of linking administrative and clinical datasets from Alberta Canada to identify a pregnancy cohort that includes spontaneous and medical pregnancy losses.

METHODS

Deterministic linkage was used to link data from twelve clinical and administrative datasets for women who conceived between November 2007 and February 2008. Descriptive statistics were used to characterize the relative contribution of each dataset to the overall dataset.

RESULTS

Overall, 6,477 unique pregnancies were eligible for inclusion, resulting in a live birth rate of 94.1%, a stillbirth rate of 0.5%, a fetal death rate of 4.1%, and an estimated 1.3% of the cohort moving out of the study area. No single dataset could identify all pregnancies. Individual databases identified 2.0-99.1% of the cohort. Fetal deaths were most frequently identified in outpatient physician claims, emergency room visits, ultrasound data, or from the cytogenetic laboratory.

CONCLUSIONS

Linkage of clinical and administrative databases to identify pregnancy is feasible and can overcome many limitations associated with the use of a single dataset; however, fetal deaths continue to be under-ascertained.

Circulating miRNA biomarkers for Alzheimer's disease

A minimally invasive diagnostic assay for early detection of Alzheimer's disease (AD) is required to select optimal patient groups in clinical trials, monitor disease progression and response to treatment, and to better plan patient clinical care. Blood is an attractive source for biomarkers due to minimal discomfort to the patient, encouraging greater compliance in clinical trials and frequent testing. MiRNAs belong to the class of non-coding regulatory RNA molecules of ∼22 nt length and are now recognized to regulate ∼60% of all known genes through post-transcriptional gene silencing (RNAi). They have potential as useful biomarkers for clinical use because of their stability and ease of detection in many tissues, especially blood. Circulating profiles of miRNAs have been shown to discriminate different tumor types, indicate staging and progression of the disease and to be useful as prognostic markers. Recently their role in neurodegenerative diseases, both as diagnostic biomarkers as well as explaining basic disease etiology has come into focus. Here we report the discovery and validation of a unique circulating 7-miRNA signature (hsa-let-7d-5p, hsa-let-7g-5p, hsa-miR-15b-5p, hsa-miR-142-3p, hsa-miR-191-5p, hsa-miR-301a-3p and hsa-miR-545-3p) in plasma, which could distinguish AD patients from normal controls (NC) with >95% accuracy (AUC of 0.953). There was a >2 fold difference for all signature miRNAs between the AD and NC samples, with p-values<0.05. Pathway analysis, taking into account enriched target mRNAs for these signature miRNAs was also carried out, suggesting that the disturbance of multiple enzymatic pathways including lipid metabolism could play a role in AD etiology.

Comparative lipidomics of mouse brain exposed to enriched environment

Several studies have shown that housing conditions and environmental exposure to a series of stimuli lead to behavior improvement in several species. While more works have been focused on illustrating changes of the proteome and transcriptome following enriched environment exposure in mice, little has been done to understand changes in the brain metabolome in this paradigm due to the complexity of this type of analysis. In this paper, lipidomics focused on phospholipids and gangliosides were conducted for brain tissues of mice exposed to enriched or impoverished conditions. We optimized previously reported method and established a reliable relative comparison method for phospholipids and gangliosides in brain tissue using prefractionation with weak anion exchange cartridge. We used liquid chromatography mass spectrometry to explore metabolic signatures of the cerebral cortex and hippocampus after confirming the animals had significant memory differences using the fear conditioning paradigm and brain immunohistochemistry. Although both cerebral cortex and hippocampus regions did not show major alterations in ganglioside composition, we found significant differences in a series of phospholipids containing 22:6 fatty acid in the prefrontal cortex, indicating that environmental enrichment and impoverished housing conditions might be a relevant paradigm to study aberrant lipid metabolism of docosahexaenoic acid consumption. Our study highlights the hypothesis-generating potential of lipidomics and identifies novel region-specific lipid changes possibly linked not only to change of memory function in these models, but also to help us better understand how lipid changes may contribute to memory disorders.

A rare case of cardiac rhabdomyomas in a dizygotic twin pair

Cardiac rhabdomyoma (CR) is the cardiac tumour most commonly diagnosed in utero. Eighty percent of CRs are associated with tuberous sclerosis (TS). TS is a rare multi-system disease, with autosomal dominant genetic transmission. If the parents of an affected child do not have features of TS, then either one parent is mosaic for the TS gene mutation or the affected child is the result of a de novo germline mutation. We present a case of a dizygotic twin pregnancy complicated by CRs in both fetuses at 24 weeks. Twin A died in utero at 28 weeks. Preterm labour and delivery of twin B occurred at 33 weeks. Twin B had multiple small CRs and a large apical CR. At six weeks after delivery, the CRs had disappeared or reduced in size. Regression in the third trimester or postnatally is the natural course of CRs. Molecular testing for TS identified two variants in the TSC2 gene. The parents were clinically unaffected; however, the father was subsequently found on an MRI of the head to have cortical tubers, and he was found to carry the pathogenic TSC2 mutation. Since dizygotic twin pregnancy is akin to two consecutive pregnancies, the etiology in our case is due to one parent having subclinical TS. To the best of our knowledge, this is the first such case to be reported.

Identification of a new plasma biomarker of Alzheimer's disease using metabolomics technology

We performed unbiased analysis of steroid-related compounds to identify novel Alzheimer's disease (AD) plasma biomarkers using liquid chromatography-atmospheric pressure chemical ionization-mass spectroscopy. The analysis revealed that desmosterol was found to be decreased in AD plasma versus controls. To precisely quantify variations in desmosterol, we established an analytical method to measure desmosterol and cholesterol. Using this LC-based method, we discovered that desmosterol and the desmosterol/cholesterol ratio are significantly decreased in AD. Finally, the validation of this assay using 109 clinical samples confirmed the decrease of desmosterol in AD as well as a change in the desmosterol/cholesterol ratio in AD. Interestingly, we could also observe a difference between mild cognitive impairment and control. In addition, the decrease of desmosterol was somewhat more significant in females. Receiver operating characteristic (ROC) analysis between controls and AD, using plasma desmosterol shows a score of 0.80, indicating a good discrimination power for this marker in the two reference populations and confirms the potential usefulness of measuring plasma desmosterol levels for diagnosing AD. Further analysis showed a significant correlation of plasma desmosterol with Mini-Mental State Examination scores. Although larger sample populations will be needed to confirm this diagnostic marker sensitivity, our studies demonstrate a sensitive and accurate method of detecting plasma desmosterol concentration and suggest that plasma desmosterol could become a powerful new specific biomarker for early and easy AD diagnosis.

Application of microarray-based comparative genomic hybridization in prenatal and postnatal settings: three case reports

Microarray-based comparative genomic hybridization (array CGH) is a newly emerged molecular cytogenetic technique for rapid evaluation of the entire genome with sub-megabase resolution. It allows for the comprehensive investigation of thousands and millions of genomic loci at once and therefore enables the efficient detection of DNA copy number variations (a.k.a, cryptic genomic imbalances). The development and the clinical application of array CGH have revolutionized the diagnostic process in patients and has provided a clue to many unidentified or unexplained diseases which are suspected to have a genetic cause. In this paper, we present three clinical cases in both prenatal and postnatal settings. Among all, array CGH played a major discovery role to reveal the cryptic and/or complex nature of chromosome arrangements. By identifying the genetic causes responsible for the clinical observation in patients, array CGH has provided accurate diagnosis and appropriate clinical management in a timely and efficient manner.

Exome sequencing identifies SMAD3 mutations as a cause of familial thoracic aortic aneurysm and dissection with intracranial and other arterial aneurysms

RATIONALE

Thoracic aortic aneurysms leading to acute aortic dissections (TAAD) can be inherited in families in an autosomal dominant manner. As part of the spectrum of clinical heterogeneity of familial TAAD, we recently described families with multiple members that had TAAD and intracranial aneurysms or TAAD and intracranial and abdominal aortic aneurysms inherited in an autosomal dominant manner.

OBJECTIVE

To identify the causative mutation in a large family with autosomal dominant inheritance of TAAD with intracranial and abdominal aortic aneurysms by performing exome sequencing of 2 distantly related individuals with TAAD and identifying shared rare variants.

METHODS AND RESULTS

A novel frame shift mutation, p. N218fs (c.652delA), was identified in the SMAD3 gene and segregated with the vascular diseases in this family with a logarithm of odds score of 2.52. Sequencing of 181 probands with familial TAAD identified 3 additional SMAD3 mutations in 4 families, p.R279K (c.836G>A), p.E239K (c.715G>A), and p.A112V (c.235C>T), resulting in a combined logarithm of odds score of 5.21. These 4 mutations were notably absent in 2300 control exomes. SMAD3 mutations were recently described in patients with aneurysms osteoarthritis syndrome and some of the features of this syndrome were identified in individuals in our cohort, but these features were notably absent in many SMAD3 mutation carriers.

CONCLUSIONS

SMAD3 mutations are responsible for 2% of familial TAAD. Mutations are found in families with TAAD alone, along with families with TAAD, intracranial aneurysms, abdominal aortic and bilateral iliac aneurysms segregating in an autosomal dominant manner.

Congenital megalourethra: prenatal diagnosis and postnatal/autopsy findings in 10 cases

OBJECTIVE

Congenital megalourethra is a rare urogenital malformation characterized by dilation and elongation of the penile urethra associated with absence or hypoplasia of the corpora spongiosa and cavernosa. Postnatal complications include voiding and erectile dysfunction as well as renal insufficiency and pulmonary hypoplasia. To date, only a few prenatally diagnosed cases have been reported. We report on 10 cases diagnosed prenatally and their postnatal/autopsy findings.

METHODS

The study involved retrospective chart review of all cases diagnosed antenatally in three tertiary care centers over 5 years. Antenatal ultrasound images and medical records from obstetrics, genetics, urology and nephrology were reviewed.

RESULTS

Ten fetuses with megalourethra were identified at a median gestational age of 19 (range, 13-24) weeks and all were confirmed postnatally or at autopsy. Three pregnancies were terminated and seven continued. All cases presented with a distended bladder and megalourethra and all cases had normal karyotype. Of seven liveborn babies, one died neonatally of pulmonary hypoplasia. All six infants alive at the time of writing had a dysfunctional urethra and three suffered from impaired or end-stage renal disease. Associated anomalies were found in half of the cases.

CONCLUSION

Congenital megalourethra is caused by abnormal development or hypoplasia of the penile erectile tissue, secondary to distal urethral obstruction. When the amniotic fluid volume is normal, survival is possible. However, all liveborn infants have voiding and renal dysfunction and sexual dysfunction is expected. Megalourethra should be considered in all male fetuses presenting prenatally with megacystis and detailed fetal ultrasonography should look for an elongated and/or distended phallic structure as well as any associated anomalies.

Cardiac features of a novel autosomal recessive dilated cardiomyopathic syndrome due to defective importation of mitochondrial protein

Dilated cardiomyopathy as seen in children is clinically and genetically heterogeneous, with an increasing proportion of cases known to be caused by disorders of single genes. An autosomal recessive syndrome with a high incidence of dilated cardiomyopathy was recently described in the Canadian Dariusleut Hutterite population. It is caused by homozygous mutations in a novel gene, DNAJC19, presumed to play a role in importation of mitochondrial proteins. We discuss the cardiac features of this syndrome, and its relationship to cardiac mitochondrial function.

Découverte et structure cristallographique d’une apolipoprotéine humaine

We report the serendipitous discovery of a human plasma phosphate binding protein (HPBP). This 38 kDa protein is co-purified with paraoxonase (PON1). The association between HPON1 and HPBP is modulated by phosphate and calcium concentrations. The HPBP X-ray structure solved at 1.9 A resolution is similar to the prokaryotic phosphate solute-binding proteins (SBPs) associated with ATP binding cassette transmembrane transporters, though phosphate-SBPs have never been characterized or predicted from nucleic acid databases in eukaryotes. However, HPBP belongs to the family of ubiquitous eukaryotic proteins named DING, meaning that phosphate-SBPs are also widespread in eukaryotes. The absence of complete genes for eukaryotic phosphate-SBP from databases is intriguing, but the astonishing 90% sequence conservation of genes between evolutionary distant species suggests that the corresponding proteins play an important function. HPBP is the first identified transporter capable of binding phosphate ions in human plasma. Thus it is thought to become a new predictor and a potential therapeutic agent for phosphate-related diseases such as atherosclerosis.

Heart Rate Responses During a Breath-Holding Competition in Well-Trained Divers

The diving response elicited by breath-holding (BH) and immersion mainly consists of bradycardia, decreased cardiac output, and peripheral vasoconstriction. These responses reduce oxygen consumption and thereby prolong the duration of the dive. They may also lead to cardiac arrhythmias or hypoxia, however, which in turn may play a role in the occurrence of syncope during BH. The aim of the present study was to analyze the cardiac responses to prolonged breath-holding in elite divers during a competition. Heart rate behaviour and the incidence of arrhythmia were recorded in 16 well-trained breath-hold divers (BHD) using a cardio-frequency meter (for 15 divers) and a Holter (for one diver) during maximal static breath-holding. Anthropometric, spirometric, and training characteristics such as percentage of body fat, pulmonary volumes and years of BH training were also determined. Forced vital capacity (FVC) and forced expiratory volume in one second (FEV (1)) were higher than the predicted values (+7.7%, p<0.05 and+6.6%, p<0.05, respectively). During the static BH, divers presented apneic bradycardia (-44%) correlated with static BH times (p<0.05); this was associated with cardiac arrhythmias (supraventricular extrasystoles and ventricular extrasystoles) in the Holter-equipped subject. These results are in agreement with those obtained in laboratory conditions and confirm the existence of cardiac arrhythmias in well-trained BHD.

Microduplication and triplication of 22q11.2: a highly variable syndrome

22q11.2 microduplications of a 3-Mb region surrounded by low-copy repeats should be, theoretically, as frequent as the deletions of this region; however, few microduplications have been reported. We show that the phenotype of these patients with microduplications is extremely diverse, ranging from normal to behavioral abnormalities to multiple defects, only some of which are reminiscent of the 22q11.2 deletion syndrome. This diversity will make ascertainment difficult and will necessitate a rapid-screening method. We demonstrate the utility of four different screening methods. Although all the screening techniques give unique information, the efficiency of real-time polymerase chain reaction allowed the discovery of two 22q11.2 microduplications in a series of 275 females who tested negative for fragile X syndrome, thus widening the phenotypic diversity. Ascertainment of the fragile X-negative cohort was twice that of the cohort screened for the 22q11.2 deletion. We also report the first patient with a 22q11.2 triplication and show that this patient's mother carries a 22q11.2 microduplication. We strongly recommend that other family members of patients with 22q11.2 microduplications also be tested, since we found several phenotypically normal parents who were carriers of the chromosomal abnormality.

Sexually transmitted infections in male clients of female sex workers in Benin: risk factors and reassessment of the leucocyte esterase dipstick for screening of urethral infections

OBJECTIVES

(1) To assess risk factors for urethral infections with Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis among male clients of female sex workers (FSWs) in Benin; (2) to study the validity of LED testing of male urine samples compared to a highly sensitive gold standard (PCR) for the diagnosis of urethral infections with the organisms cited above.

METHODS

Male clients of FSWs (n=404) were recruited on site at prostitution venues in Cotonou, Benin, between 28 May and 18 August 1998. A urine sample was obtained from each participant just before he visited the FSW, and tested immediately using a leucocyte esterase dipstick (LED) test. It was then tested for HIV using the Calypte EIA with western blot confirmation, and for C. trachomatis, N. gonorrhoeae, and T. vaginalis by PCR. After leaving the FSW's room, participants were interviewed about demographics, sexual behaviour, STI history and current symptoms and signs, and were examined for urethral discharge, genital ulcers, and inguinal lymphadenopathies.

RESULTS

STI prevalences were: C. trachomatis, 2.7%; N. gonorrhoeae, 5.4%; either chlamydia or gonorrhoea 7.7%; T. vaginalis 2.7%; HIV, 8.4%. Lack of condom use with FSWs and a history of STI were independently associated with C. trachomatis and/or N. gonorrhoeae infection. Over 80% of these infections were in asymptomatic subjects. The overall sensitivity, specificity, positive and negative predictive values of the LED test for detection of either C. trachomatis or N. gonorrhoeae were 48.4%, 94.9%, 44.1%, and 95.7%, respectively. In symptomatic participants (n=22), all these parameters were 100% while they were 47.4%, 94.7%, 37.5%, and 96.4% in asymptomatic men (n=304).

CONCLUSIONS

Since most STIs are asymptomatic in this population, case finding programmes for gonorrhoea and chlamydia could be useful. The performance characteristics of the LED test in this study suggest that it could be useful to detect asymptomatic infection by either C. trachomatis or N. gonorrhoeae in high risk men.

Estrogen induces a rapid increase of calcium-calmodulin-dependent protein kinase II activity in the hippocampus

Molecular genetics experiments using gene targeting and transgenic technology demonstrated the importance of alpha-calcium-calmodulin-dependent protein kinase II (alphaCaMKII) in long-term potentiation (LTP) and memory. Little information is available though on how CaMKII activity may be regulated in vivo. We show that estradiol benzoate activates CaMKII in a dose and time-dependent manner in mouse hippocampus after 30 min stimulation. The effect of estrogen is via a very rapid nongenomic mechanism that is blocked in vitro in hippocampal primary neurons by the pure estrogen receptor antagonist, ICI 182,780. These results suggest that estrogen action in the hippocampus is linked to CaMKII activation.

Allergologic exploration of germins and germin-like proteins, a new class of plant allergens

BACKGROUND

Germins and the related germin-like proteins (GLPs) are glycoproteins expressed in many plants in response to biotic and abiotic stress. To test the potential impact of germins and GLPs, recombinant germin from Triticum aestivum (tGermin) and GLPs from Arabidopsis thaliana (tGLP), both produced in transformed tobacco plants, were used.

METHODS

Sera from 82 patients with type I allergy to birch, grass or mugwort pollen and/or wheat were tested in immunoblot for IgE binding to tGermin and tGLP, and the IgE reactivity after chemical and enzymatic deglycosylation was analysed. The biological activity of tGermin and tGLP was determined in a histamine release assay and in skin prick testing (SPT).

RESULTS

In an immunoblotting assay, 24 out of 82 tested sera (29.26%) from allergic patients showed IgE-binding to tGermin, and 18 of these sera (21.95%) displayed also IgE-binding to tGLP. The deglycosylation experiments indicated that glycan moieties contribute significantly to the IgE-binding of tGermin and tGLP. Both tGermins and tGLP induced specifically histamine release in an in vitro assay as well as in SPT.

CONCLUSION

Our in vitro and in vivo findings demonstrate that germin and GLPs are capable to bind IgE most likely via carbohydrate determinants, and represent allergenic molecules.

The value of mass screening for chlamydia control in high prevalence communities

The social context and epidemiology of STIs in remote communities in Northern Canada was examined. These communities have a persistently high reported incidence of gonorrhoea and chlamydial infection. They remain in the hyperendemic phase of the N. gonorrhoeae and C. trachomatis epidemics. They are ethnically and culturally homogeneous and contain no readily identifiable core groups, making it impossible to distinguish between spread and maintenance networks. Mass screening of the adult population can reduce the reservoir of C. trachomatis infection under these circumstances. It is particularly important to target men in settings such as this where women are routinely screened in antenatal and family planning clinics.

Prevalence of Chlamydia trachomatis and Neisseria gonorrhoeae among at-risk women, young sex workers, and street youth attending community organizations in Quebec City, Canada

BACKGROUND

Despite a relatively recent decline in the global incidence of Chlamydia trachomatis and Neisseria gonorrhoeae it seems that some segments of the population such as street youth, sex workers, and individuals with social problems or delinquent behavior could be part of a core group for STDs. These persons may be reluctant to undergo STD diagnosis in traditional medical settings.

GOALS

To determine the prevalence of C trachomatis and N gonorrhoeae infection using polymerase chain reaction on urine samples among subjects attending an anonymous HIV testing clinic and four community organizations in Quebec City, and to identify associated risk factors.

STUDY DESIGN

A cross-sectional study of 626 street youth, sex workers, and women with social problems or delinquent behavior was conducted.

RESULTS

The prevalences of N gonorrhoeae and C trachomatis were, respectively, 1.1% (95% CI, 0.5%--2.3%) and 5.8% (95% CI, 4.1%--7.9%). No significant difference was found between men and women, but the sexually transmitted disease (STD) prevalence was much higher in subjects younger than 20 years: 11.4% versus 3.6% (P < 0.01). In a logistic regression model, factors independently associated with STD infection were age younger than 20 years (OR, 2.6; P = 0.007), occasional sex partners (OR, 2.9; P = 0.007), and injection of drugs (OR, 2.8; P = 0.002) in the preceding 6 months.

CONCLUSIONS

A moderate STD prevalence was found in the study population. The prevalence, however, can be considered high (>10%) among street youth and young sex workers. Providing community-based STD screening and treatment services appear to be an efficient method for reaching these high-risk groups.

Characterization of an interstitial deletion del(13)(q22q32) using microdissection and sequential FISH and G-banding

The objective of this study was to delineate a chromosome 13 abnormality and establish its clinical correlation by using molecular cytogenetics procedures. A newborn boy presented with clinical findings, including mild symmetric intrauterine growth retardation (IUGR), small ears with thickened helices, a scalp lesion, short fifth fingers, missing toes, and talipes equinovarus. Routine G-banding of cultured peripheral blood cells revealed that the patient had one abnormal and shortened chromosome 13, but uncertainty remained as to whether the abnormality was the result of an interstitial deletion or a translocation. Thirteen copies of G-banded abnormal chromosomes 13 were isolated with microdissection and amplified with PCR using degenerate oligonucleotide primers. Fluorescence in situ hybridization (FISH) of the PCR product to normal metaphases showed one pair of acrocentrics hybridized, more or less uniformly, along the length of the long arm with an unhybridized gap in the distal region, indicative of an interstitial deletion. Sequential FISH and G-banding of the same chromosome preparations conclusively demonstrated that the deleted segment was 13q22-q32. Four cases of del(13)(q22q32) have been previously reported. The common findings in all five cases, including the present one, are psychomotor and growth retardation, as well as hand and foot anomalies.

Management of sexually transmitted diseases and HIV prevention in men at high risk: targeting clients and non-paying sexual partners of female sex workers in Benin

OBJECTIVES

Male clients of female sex workers have rarely been specific targets for HIV/sexually transmitted diseases (STD) interventions in sub-Saharan Africa. We assessed the effectiveness of outreach methodology for contacting sexual partners of female sex workers for purposes of HIV/STD prevention in Cotonou, Benin.

DESIGN AND METHODS

In collaboration with owners/managers, outreach personnel and female sex workers, 404 clients were recruited on-site at prostitution venues, and provided urine samples for leukocyte esterase dipstick (LED), STD and HIV testing before having sex with female sex workers. After having sex they underwent an interview and physical examination. No payment was made for study participation. Prostitution site personnel (n = 41) and boyfriends of female sex workers (n = 56) were also recruited.

RESULTS

In all 68% of the clients approached agreed to participate. On-site LED testing and free STD treatment were important factors in participation. HIV-1 prevalence was several-fold higher than in the general population in Cotonou, at 8.4, 12.2 and 16.1% in clients, personnel and boyfriends respectively, and was associated with increasing age and lack of condom use with female sex workers. Condom use rates by clients with female sex workers were non-negligible but sub-optimal, and low with regular partners. Approximately one-third of clients with regular partners also had other non-female sex worker sex partners. Boyfriends of female sex workers are of particular concern due to high numbers of partners, very low condom use rates and high HIV prevalence.

CONCLUSIONS

Study findings indicate that male sex partners of female sex workers form a 'bridging population' for HIV/STD transmission both to female sex workers, as well as from female sex workers to the general population of women, particularly regular female partners.

Diagnostic performance of the Roche AMPLICOR PCR in detecting Neisseria gonorrhoeae in genitourinary specimens from female sex workers in Cotonou, Benin

The objective of this study was to evaluate the diagnostic performance of the Roche multiplex AMPLICOR Chlamydia trachomatis/Neisseria gonorrhoeae PCR test for the detection of Neisseria gonorrhoeae infection in female urine specimens and wet and dry endocervical swabs. Endocervical swabs and urine specimens were collected from 342 female sex workers from Cotonou, Benin, and were tested using the AMPLICOR C. trachomatis/N. gonorrhoeae test (Roche Diagnostic Systems, Inc., Branchburg, N.J.) with internal control detection. Endocervical swabs were also cultured on Thayer-Martin medium. A series of alternate standards that included a combination of all the tests but not the test being evaluated was used to assess the performance of the test with each type of specimen. The sensitivity, specificity, and positive and negative predictive values for the urine were 53.8, 98.9, 93.5, and 87.5%, respectively. Corresponding figures for the wet swab were 91.5, 100, 100, and 97.4%, respectively. Those for the dry swab were 96.3, 96.2, 88.5, and 98.8%, respectively. Based on this study, the AMPLICOR PCR assay showed a low sensitivity for detection of N. gonorrhoeae infection in urine specimens, whereas the test was found to be highly sensitive and specific with endocervical specimens.

Arabidopsis thaliana germin-like proteins: common and specific features point to a variety of functions

Germin-like proteins (GLPs) are ubiquitous plant proteins encoded by diverse multigene families. It is not known whether they share germin's unusual biochemical properties and oxalate oxidase activity. Using specific antibodies, we have studied three GLPs (AtGER1. AtGER2 and AtGER3) in Arabidopsis thaliana (L.) Heynh. as well as in transgenic tobacco (Nicotiana tabacum L.) plants overexpressing these proteins. Like wheat ( Triticum aestivum L.) germin, these Arabidopsis GLPs are associated with the extracellular matrix (ECM) and they also seem to exist as two glycosylated isoforms. However, none of them is an oxalate oxidase. Although GLPs display several conserved features, each has its specific characteristics. Both AtGER2 and AtGER3 are oligomeric proteins that share germin's resistance to pepsin and to dissociation by heat and SDS. In contrast, AtGER1 seems to exist as a monomer. The GLPs may interact with the ECM in a variety of ways, since each is efficiently extracted by different conditions. In addition, germins and GLPs all bind Cibacron Blue, a dye often but not exclusively used for the purification of enzymes having nucleotide cofactors. In the case of AtGER2, binding to the dye is so tight that it almost allows a one-step purification of this protein. The variety of sequences, expression patterns and biochemical features indicates that GLPs could be a class of receptors localized in the ECM and involved in physiological and developmental processes as well as stress response.