Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases

PURPOSE

This study aims to assess the diagnostic utility and provide reporting recommendations for clinical DNA methylation episignature testing based on the cohort of patients tested through the EpiSign Clinical Testing Network.

METHODS

The EpiSign assay utilized unsupervised clustering techniques and a support vector machine-based classification algorithm to compare each patient's genome-wide DNA methylation profile with the EpiSign Knowledge Database, yielding the result that was reported. An international working group, representing distinct EpiSign Clinical Testing Network health jurisdictions, collaborated to establish recommendations for interpretation and reporting of episignature testing.

RESULTS

Among 2399 cases analyzed, 1667 cases underwent a comprehensive screen of validated episignatures, imprinting, and promoter regions, resulting in 18.7% (312/1667) positive reports. The remaining 732 referrals underwent targeted episignature analysis for assessment of sequence or copy-number variants (CNVs) of uncertain significance or for assessment of clinical diagnoses without confirmed molecular findings, and 32.4% (237/732) were positive. Cases with detailed clinical information were highlighted to describe various utility scenarios for episignature testing.

CONCLUSION

Clinical DNA methylation testing including episignatures, imprinting, and promoter analysis provided by an integrated network of clinical laboratories enables test standardization and demonstrates significant diagnostic yield and clinical utility beyond DNA sequence analysis in rare diseases.

Improving newborn screening test performance for metachromatic leukodystrophy: Recommendation from a pre-pilot study that identified a late-infantile case for treatment

Metachromatic leukodystrophy (MLD) is a devastating rare neurodegenerative disease. Typically, loss of motor and cognitive skills precedes early death. The disease is characterised by deficient lysosomal arylsulphatase A (ARSA) activity and an accumulation of undegraded sulphatide due to pathogenic variants in the ARSA gene. Atidarsagene autotemcel (arsa-cel), an ex vivo haematopoietic stem cell gene therapy was approved for use in the UK in 2021 to treat early-onset forms of pre- or early-symptomatic MLD. Optimal outcomes require early diagnosis, but in the absence of family history this is difficult to achieve without newborn screening (NBS). A pre-pilot MLD NBS study was conducted as a feasibility study in Manchester UK using a two-tiered screening test algorithm. Pre-established cutoff values (COV) for the first-tier C16:0 sulphatide (C16:0-S) and the second-tier ARSA tests were evaluated. Before the pre-pilot study, initial test validation using non‑neonatal diagnostic bloodspots demonstrated ARSA pseudodeficiency status was associated with normal C16:0-S results for age (n = 43) and hence not expected to cause false positive results in this first-tier test. Instability of ARSA in bloodspot required transfer of NBS bloodspots from ambient temperature to -20°C storage within 7-8 days after heel prick, the earliest possible in this UK pre-pilot study. Eleven of 3687 de-identified NBS samples in the pre-pilot were positive for C16:0-S based on the pre-established COV of ≥170 nmol/l or ≥ 1.8 multiples of median (MoM). All 11 samples were subsequently tested negative determined by the ARSA COV of <20% mean of negative controls. However, two of 20 NBS samples from MLD patients would be missed by this C16:0-S COV. A further suspected false negative case that displayed 4% mean ARSA activity by single ARSA analysis for the initial test validation was confirmed by genotyping of this NBS bloodspot, a severe late infantile MLD phenotype was predicted. This led to urgent assessment of this child by authority approval and timely commencement of arsa-cel gene therapy at 11 months old. Secondary C16:0-S analysis of this NBS bloodspot was 150 nmol/l or 1.67 MoM. This was the lowest result reported thus far, a new COV of 1.65 MoM is recommended for future pilot studies. Furthermore, preliminary data of this study showed C16:1-OH sulphatide is more specific for MLD than C16:0-S. In conclusion, this pre-pilot study adds to the international evidence that recommends newborn screening for MLD, making it possible for patients to benefit fully from treatment through early diagnosis.

Truncating and zinc-finger variants in GLI2 are associated with hypopituitarism

Variants in transcription factor GLI2 have been associated with hypopituitarism and structural brain abnormalities, occasionally including holoprosencephaly (HPE). Substantial phenotypic variability and nonpenetrance have been described, posing difficulties in the counseling of affected families. We present three individuals with novel likely pathogenic GLI2 variants, two with truncating and one with a de novo missense variant p.(Ser548Leu), and review the literature for comprehensive phenotypic descriptions of individuals with confirmed pathogenic (a) intragenic GLI2 variants and (b) chromosome 2q14.2 deletions encompassing only GLI2. We show that most of the 31 missense variants previously reported as pathogenic are likely benign or, at most, low-risk variants. Four Zn-finger variants: p.(Arg479Gly), p.(Arg516Pro), p.(Gly518Lys), and p.(Tyr575His) were classified as likely pathogenic, and three other variants as possibly pathogenic: p.(Pro253Ser), p.(Ala593Val), and p.(Pro1243Leu). We analyze the phenotypic descriptions of 60 individuals with pathogenic GLI2 variants and evidence a morbidity spectrum that includes hypopituitarism (58%), HPE (6%) or other brain structure abnormalities (15%), orofacial clefting (17%) and dysmorphic facial features (35%). We establish that truncating and Zn-finger variants in GLI2 are associated with a high risk of hypopituitarism, and that a solitary median maxillary central incisor is part of the GLI2-related phenotypic variability. The most prevalent phenotypic feature is post-axial polydactyly (65%) which is also the mildest phenotypic expression of the condition, reported in many parents of individuals with systemic findings. Our approach clarifies clinical risks and the important messages to discuss in counseling for a pathogenic GLI2 variant.

Usage of nutritional supplements and its side effects among gym goers in Pune

Nutritional supplements have always been a point of attractionfor physically active people. These have improved exercise performance,increased muscular strength, weight gain or weight loss,etc. The irrational use of supplements has led to various side effectsassociated with them. There is a shortage of evidence suggestingthe usage and knowledge regarding the consumption ofdietary supplements. A cross-sectional study was conducted witha 121 sample size randomly chosen from 5 different zones of thecity. A structured questionnaire was designed to collect informationwherein participants reported their demographics, physical activity,supplement usage patterns, source of information, and side effects.Descriptive statistics, chi-square test, was used with p<0.05 as significant.Samples used different dosages, forms, brands, and accessto supplements. The participants coming to the gym for moreextended periods were likely to consume supplements in higherdosages (p = 0.020). Protein powder was consumed by 97.5% ofthe samples. There was a significant association between differenttypes of supplements across gender, age group, and period of exercisingin the gym. Side effects such as cramps (p = 0.015) andnausea were significantly associated with high dosages of supplementconsumption. The majority of them (51.2%) took advice fromtrainers. Only 9.9% consulted dieticians. Individuals consumed supplementswithout the guidance of any health professionals, whichwas predisposing them to various side effects. This reflects a lackof knowledge and awareness of supplement usage and highlightseducating various stakeholders and gym-goers.

Hedonic hunger: eating for desire and not calories

Hedonic hunger can be described as a state where an individualexperiences recurrent feelings, thoughts, and desires about foodin the absence of energy deprivation. Living in an obesogenicenvironment where cheap, tasty foods are available in plentifulamounts is one of the major causes of hedonic hunger development.Hedonic hunger can be analyzed using a power of foodscale (PFS) which estimates appetite and not palatable food consumption.The current epidemic of obesity globally (termed as“globesity” by WHO) is seen to be majorly driven by the hedoniceating system and an imbalance in the energy homeostasis system.Previous studies indicate that hedonic hunger and obesityare associated, and a weak but no significant correlation existsbetween BMI and PFS score. It can lead to the development ofvarious lifestyle disorders in the longer run. High levels of pleasure-driven hunger can even lead to detrimental health outcomeslike poor glycaemic control, unhealthy dietary behavior,and increased lipid profile levels which are aggravated explicitlyin cardiovascular diseases. With the adaptation to western dietarylifestyle, people are keener to opt for food options that canbe damaging and harmful when low levels of self-control, dietarymotivation, and healthy dietary habits are absent. Apart from thereward regulation system, which has a direct effect on hedonichunger, certain external factors like emotional eating, meals andmeal preparation, food cravings, sleep, physical activity, stress,social media, portion size, peer influence, an atmosphere of arestaurant can also promote more than required intake of food.This review article summarizes the above findings taking into accountthe plethora of research studies conducted so far.

Personalised virtual gene panels reduce interpretation workload and maintain diagnostic rates of proband-only clinical exome sequencing for rare disorders

Purpose

The increased adoption of genomic strategies in the clinic makes it imperative for diagnostic laboratories to improve the efficiency of variant interpretation. Clinical exome sequencing (CES) is becoming a valuable diagnostic tool, capable of meeting the diagnostic demand imposed by the vast array of different rare monogenic disorders. We have assessed a clinician-led and phenotype-based approach for virtual gene panel generation for analysis of targeted CES in patients with rare disease in a single institution.

Methods

Retrospective survey of 400 consecutive cases presumed by clinicians to have rare monogenic disorders, referred on singleton basis for targeted CES. We evaluated diagnostic yield and variant workload to characterise the usefulness of a clinician-led approach for generation of virtual gene panels that can incorporate up to three different phenotype-driven gene selection methods.

Results

Abnormalities of the nervous system (54.5%), including intellectual disability, head and neck (19%), skeletal system (16%), ear (15%) and eye (15%) were the most common clinical features reported in referrals. Combined phenotype-driven strategies for virtual gene panel generation were used in 57% of cases. On average, 7.3 variants (median=5) per case were retained for clinical interpretation. The overall diagnostic rate of proband-only CES using personalised phenotype-driven virtual gene panels was 24%.

Conclusions

Our results show that personalised virtual gene panels are a cost-effective approach for variant analysis of CES, maintaining diagnostic yield and optimising the use of resources for clinical genomic sequencing in the clinic.

Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission

Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and healthcare workers (HCWs) across multiple geographically distinct UK hospitals, obtaining 173 high-quality SARS-CoV-2 genomes. We integrated patient movement and staff location data into the analysis of viral genome data to understand spatial and temporal dynamics of SARS-CoV-2 transmission. We identified eight patient contact clusters (PCC) with significantly increased similarity in genomic variants compared to non-clustered samples. Incorporation of HCW location further increased the number of individuals within PCCs and identified additional links in SARS-CoV-2 transmission pathways. Patients within PCCs carried viruses more genetically identical to HCWs in the same ward location. SARS-CoV-2 genome sequencing integrated with patient and HCW movement data increases identification of outbreak clusters. This dynamic approach can support infection control management strategies within the healthcare setting.

Prenatal diagnosis in a family with X-linked hydrocephalus

The neural cell adhesion molecule L1 is a transmembrane glycoprotein belonging to the immunoglobulin superfamily of cell adhesion molecules (CAMs). Its expression is essential during embryonic development of the nervous system and it is involved in cognitive function and memory. Mutations in the L1CAM gene are responsible for four related L1 disorders; X-linked hydrocephalus/HSAS (Hydrocephalus as a result of Stenosis of the Aqueduct of Sylvius), MASA (Mental retardation, Aphasia, Shuffling gait, and Adducted thumbs) syndrome, X-linked complicated spastic paraplegia type I (SPG1) and X-linked Agenesis of the Corpus Callosum (ACC). These four disorders represent a clinical spectrum that varies both between and within families. The main clinical features of this spectrum are Corpus callosum hypoplasia, mental Retardation, Adducted thumbs, Spastic paraplegia and Hydrocephalus (CRASH syndrome). Since there is no biochemically assayed disease marker, molecular analysis of the L1CAM gene is the only means of confirming a clinical diagnosis. Most L1CAM mutations reported to date are point mutations (missense, nonsense, splice site) and only a few patients with larger rearrangements have been documented. We have characterised a rare intragenic deletion of the L1CAM gene in a sample of DNA extracted from a chorionic villus biopsy (CVB) performed at 12 weeks' gestation. =

High detection rate for BRCA2 mutations in male breast cancer families from North West England

33 families with a history of male breast cancer aged 60 or less or with a family history of male and female breast cancer were screened for the presence of BRCA2 mutations. 12 pathogenic BRCA2 mutations were identified (36%) in samples from an affected family member. All mutations segregated with disease where it was possible to check. Of the 14 families fulfilling BCLC criteria, 9 (64%) had mutations whilst only 3/16 (19%) of male breast cancer patients with less significant female breast cancer family history having a mutation. All 3 families with ovarian cancer and 3 families with multiple male breast cancer cases had BRCA2 mutations. These data are a further guide to how to prioritise samples for BRCA2 mutation analysis.

Construction and use of recombinant Escherichia coli strains for the synthesis of toluene cis-glycol

The toluene dioxygenase genes derived from Pseudomonas putida NCIMB 11767 were subcloned from a previously constructed recombinant plasmid, pIG, using pUC18 as the cloning vector and E. coli TG2 as the host strain. The resulting strain, E. coli TG2 (p1/1), produced toluene cis-glycol when grown in LB broth or minimal medium in the presence of toluene. Restriction mapping and partial DNA sequencing provided evidence for the presence of ORFs with extensive homology to parts of the tod operon from P. putida F1. The clones exhibited some residual toluene cis-glycol dehydrogenase activity which resulted in the formation of small amounts of 3-methylcatechol. Expression of the dioxygenase was induced by toluene, but was not directed by the lac promoter within the cloning vector. The clones were assessed for toluene cis-glycol production in pH-controlled batch cultures, and the maximum product concentration obtained was 1.02 g l-1. Product formation was dependent upon the presence of glucose in the culture medium. Although the substrate was toxic, the biotransformation was apparently limited by the supply of toluene. The results suggest that it should be possible to improve toluene cis-glycol production by recombinants substantially by improving both the strain and fermentation process.

Isolation of intergeneric hybrids between Bacillus subtilis and Zymomonas mobilis and the production of thermostable amylase by hybrids

Stable hybrids were obtained by protoplast fusion between Bacillus subtilis and Zymomonas mobilis. All the hybrids were able to hydrolyse starch and possessed ampicillin- and tetracycline-resistant phenotypes. Two of the hybrids, BZ-1 and BZ-2, were hyperproducers of alpha-amylase. The enzyme produced by these hybrids exhibited increased thermostability. The results show that stable intergeneric gene transfer can be achieved through poly(ethylene glycol)-mediated protoplast fusion between two industrially important genera of bacteria.