Clinical Validation of Fragile X Syndrome Screening by DNA Methylation Array

Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability. It is most frequently caused by an abnormal expansion of the CGG trinucleotide repeat (\u3e200 repeats) located in the promoter of the fragile X mental retardation gene (FMR1), resulting in promoter DNA hypermethylation and gene silencing. Current clinical tests for FXS are technically challenging and labor intensive, and may involve use of hazardous chemicals or radioisotopes. We clinically validated the Illumina Infinium HumanMethylation450 DNA methylation array for FXS screening. We assessed genome-wide and FMR1-specific DNA methylation in 32 males previously diagnosed with FXS, including nine with mosaicism, as well as five females with full mutation, and premutation carrier males (n = 11) and females (n = 11), who were compared to 300 normal control DNA samples. Our findings demonstrate 100% sensitivity and specificity for detection of FXS in male patients, as well as the ability to differentiate patients with mosaic methylation defects. Full mutation and premutation carrier females did not show FMR1 methylation changes. We have clinically validated this genome-wide DNA methylation assay as a cost- and labor-effective alternative for sensitive and specific screening for FXS, while ruling out the most common differential diagnoses of FXS, Prader-Willi syndrome, and Sotos syndrome in the same assay

Detection of skewed X-chromosome inactivation in Fragile X syndrome and X chromosome aneuploidy using quantitative melt analysis.

Methylation of the fragile X mental retardation 1 (FMR1) exon 1/intron 1 boundary positioned fragile X related epigenetic element 2 (FREE2), reveals skewed X-chromosome inactivation (XCI) in fragile X syndrome full mutation (FM: CGG > 200) females. XCI skewing has been also linked to abnormal X-linked gene expression with the broader clinical impact for sex chromosome aneuploidies (SCAs). In this study, 10 FREE2 CpG sites were targeted using methylation specific quantitative melt analysis (MS-QMA), including 3 sites that could not be analysed with previously used EpiTYPER system. The method was applied for detection of skewed XCI in FM females and in different types of SCA. We tested venous blood and saliva DNA collected from 107 controls (CGG < 40), and 148 FM and 90 SCA individuals. MS-QMA identified: (i) most SCAs if combined with a Y chromosome test; (ii) locus-specific XCI skewing towards the hypomethylated state in FM females; and (iii) skewed XCI towards the hypermethylated state in SCA with 3 or more X chromosomes, and in 5% of the 47,XXY individuals. MS-QMA output also showed significant correlation with the EpiTYPER reference method in FM males and females (P < 0.0001) and SCAs (P < 0.05). In conclusion, we demonstrate use of MS-QMA to quantify skewed XCI in two applications with diagnostic utility

Game of Stones:feasibility randomised controlled trial of how to engage men with obesity in text message and incentive interventions for weight loss

Objectives To examine the acceptability and feasibility of narrative text messages with or without financial incentives to support weight loss for men. Design Individually randomised three-arm feasibility trial with 12 months’ follow-up. Setting Two sites in Scotland with high levels of disadvantage according to Scottish Index for Multiple Deprivation (SIMD). Participants Men with obesity (n=105) recruited through community outreach and general practitioner registers. Interventions Participants randomised to: (A) narrative text messages plus financial incentive for 12 months (short message service (SMS)+I), (B) narrative text messages for 12 months (SMS only), or (C) waiting list control. Outcomes Acceptability and feasibility of recruitment, retention, intervention components and trial procedures assessed by analysing quantitative and qualitative data at 3, 6 and 12 months. Results 105 men were recruited, 60% from more disadvantaged areas (SIMD quintiles 1 or 2). Retention at 12 months was 74%. Fewer SMS+I participants (64%) completed 12-month assessments compared with SMS only (79%) and control (83%). Narrative texts were acceptable to many men, but some reported negative reactions. No evidence emerged that level of disadvantage was related to acceptability of narrative texts. Eleven SMS+I participants (31%) successfully met or partially met weight loss targets. The cost of the incentive per participant was £81.94 (95% CI £34.59 to £129.30). Incentives were acceptable, but improving health was reported as the key motivator for weight loss. All groups lost weight (SMS+I: −2.51 kg (SD=4.94); SMS only: −1.29 kg (SD=5.03); control: −0.86 kg (SD=5.64) at 12 months). Conclusions This three-arm weight management feasibility trial recruited and retained men from across the socioeconomic spectrum, with the majority from areas of disadvantage, was broadly acceptable to most participants and feasible to deliver

Peripheral Blood Epi-Signature of Claes-Jensen Syndrome Enables Sensitive and Specific Identification of Patients and Healthy Carriers with Pathogenic Mutations in KDM5C.

Background: Claes-Jensen syndrome is an X-linked inherited intellectual disability caused by mutations in the KDM5C gene. Kdm5c is a histone lysine demethylase involved in histone modifications and chromatin remodeling. Males with hemizygous mutations in KDM5C present with intellectual disability and facial dysmorphism, while most heterozygous female carriers are asymptomatic. We hypothesized that loss of KDM5C function may influence other components of the epigenomic machinery including DNA methylation in affected patients. Results: Genome-wide DNA methylation analysis of 7 male patients affected with Claes-Jensen syndrome and 56 age- and sex-matched controls identified a specific DNA methylation defect (epi-signature) in the peripheral blood of these patients, including 1769 individual CpGs and 9 genomic regions. Six healthy female carriers showed less pronounced but distinctive changes in the same regions enabling their differentiation from both patients and controls. Highly specific computational model using the most significant methylation changes demonstrated 100% accuracy in differentiating patients, carriers, and controls in the training cohort, which was confirmed on a separate cohort of patients and carriers. The 100% specificity of this unique epi-signature was further confirmed on additional 500 unaffected controls and 600 patients with intellectual disability and developmental delay, including other patient cohorts with previously described epi-signatures. Conclusion: Peripheral blood epi-signature in Claes-Jensen syndrome can be used for molecular diagnosis and carrier identification and assist with interpretation of genetic variants of unknown clinical significance in the KDM5Cgene

Detection of a dna methylation signature for the intellectual developmental disorder, x-linked, syndromic, armfield type

A growing number of genetic neurodevelopmental disorders are known to be associated with unique genomic DNA methylation patterns, called episignatures, which are detectable in peripheral blood. The intellectual developmental disorder, X-linked, syndromic, Armfield type (MRXSA) is caused by missense variants in FAM50A. Functional studies revealed the pathogenesis to be a spliceosomopathy that is characterized by atypical mRNA processing during development. In this study, we assessed the peripheral blood specimens in a cohort of individuals with MRXSA and detected a unique and highly specific DNA methylation episignature associated with this disorder. We used this episignature to construct a support vector machine model capable of sensitive and specific identification of individuals with pathogenic variants in FAM50A. This study contributes to the expanding number of genetic neurodevelopmental disorders with defined DNA methylation episignatures, provides an additional understanding of the associated molecular mechanisms, and further enhances our ability to diagnose patients with rare disorders

Identification of Epigenetic Signature Associated With Alpha Thalassemia/Mental Retardation X-linked Syndrome

BACKGROUND: Alpha thalassemia/mental retardation X-linked syndrome (ATR-X) is caused by a mutation at the chromatin regulator gene RESULTS: We performed genome-wide DNA methylation assessment of the peripheral blood samples from 18 patients with ATR-X and compared it to 210 controls. We demonstrated the evidence of a unique and highly specific DNA methylation epi-signature in the peripheral blood of ATRX patients, which was corroborated by targeted bisulfite sequencing experiments. Although genomically represented, differentially methylated regions showed evidence of preferential clustering in pericentromeric and telometric chromosomal regions, areas where ATRX has multiple functions related to maintenance of heterochromatin and genomic integrity. CONCLUSION: Most significant methylation changes in the 14 genomic loci provide a unique epigenetic signature for this syndrome that may be used as a highly sensitive and specific diagnostic biomarker to support the diagnosis of ATR-X, particularly in patients with phenotypic complexity and in patients wit

A Programme for Women achieving Excellence in Research (PoWER): theoretically informed intervention design and evaluation

Academics in Higher Education are often expected both to teach and to research; this is a particular challenge for women both structurally and individually. Initiatives to address structural issues include AdvanceHE. Here, we focus on individual issues and report on the Programme for Women Achieving Excellence in Research, a theory-based intervention. Barriers to success were assessed and course content tailored accordingly. Evaluation demonstrated that barriers were reduced and that confidence increased. Although the barriers are both individual and contextual, our rigorous approach allows international application through intervention modification without loss of fidelity. This offers a new approach for academic developers to enable female researchers

Pulmonary Rehabilitation With Balance Training for Fall Reduction in Chronic Obstructive Pulmonary Disease: Protocol for a Randomized Controlled Trial

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality worldwide. A growing body of evidence shows that individuals with COPD have important deficits in balance control that may be associated with an increased risk of falls. Pulmonary rehabilitation (PR) is a key therapeutic intervention for individuals with COPD; however, current international guidelines do not include balance training and fall prevention strategies. OBJECTIVE: The primary aim of this trial is to determine the effects of PR with balance training compared to PR with no balance training on the 12-month rate of falls in individuals with COPD. Secondary aims are to determine the effects of the intervention on balance, balance confidence, and functional lower body strength, and to estimate the cost-effectiveness of the program. METHODS: A total of 400 individuals from nine PR centers across Canada, Europe, and Australia will be recruited to participate in a randomized controlled trial. Individuals with COPD who have a self-reported decline in balance, a fall in the last 2 years, or recent near fall will be randomly assigned to an intervention or control group. The intervention group will undergo tailored balance training in addition to PR and will receive a personalized home-based balance program. The control group will receive usual PR and a home program that does not include balance training. All participants will receive monthly phone calls to provide support and collect health care utilization and loss of productivity data. Both groups will receive home visits at 3, 6, and 9 months to ensure proper technique and progression of home exercise programs. The primary outcome will be incidence of falls at 12-month follow-up. Falls will be measured using a standardized definition and recorded using monthly self-report fall diary calendars. Participants will be asked to record falls and time spent performing their home exercise program on the fall diary calendars. Completed calendars will be returned to the research centers in prepaid envelopes each month. Secondary measures collected by a blinded assessor at baseline (pre-PR), post-PR, and 12-month follow-up will include clinical measures of balance, balance confidence, functional lower body strength, and health status. The cost-effectiveness of the intervention group compared with the control group will be evaluated using the incremental cost per number of falls averted and the incremental cost per quality-adjusted life years gained. RESULTS: Recruitment for the study began in January 2017 and is anticipated to be complete by December 2019. Results are expected to be available in 2020. CONCLUSIONS: Findings from this study will improve our understanding of the effectiveness and resource uses of tailored balance training for reducing falls in individuals with COPD. If effective, the intervention represents an opportunity to inform international guidelines and health policy for PR in individuals with COPD who are at risk of falling