Clinical validity assessment of genes frequently tested on intellectual disability/autism sequencing panels.

PURPOSE: Neurodevelopmental disorders (NDDs), such as intellectual disability (ID) and autism spectrum disorder (ASD), exhibit genetic and phenotypic heterogeneity, making them difficult to differentiate without a molecular diagnosis. The Clinical Genome Resource Intellectual Disability/Autism Gene Curation Expert Panel (GCEP) uses systematic curation to distinguish ID/ASD genes that are appropriate for clinical testing (ie, with substantial evidence supporting their relationship to disease) from those that are not. METHODS: Using the Clinical Genome Resource gene-disease validity curation framework, the ID/Autism GCEP classified genes frequently included on clinical ID/ASD testing panels as Definitive, Strong, Moderate, Limited, Disputed, Refuted, or No Known Disease Relationship. RESULTS: As of September 2021, 156 gene-disease pairs have been evaluated. Although most (75%) were determined to have definitive roles in NDDs, 22 (14%) genes evaluated had either Limited or Disputed evidence. Such genes are currently not recommended for use in clinical testing owing to the limited ability to assess the effect of identified variants. CONCLUSION: Our understanding of gene-disease relationships evolves over time; new relationships are discovered and previously-held conclusions may be questioned. Without periodic re-examination, inaccurate gene-disease claims may be perpetuated. The ID/Autism GCEP will continue to evaluate these claims to improve diagnosis and clinical care for NDDs.

Exploring the Kinh Vietnamese genomic database for the polymorphisms of the P450 genes towards precision public health.

BACKGROUND: Human cytochrome P450 (CYPs) genes are essential in metabolising drugs. Due to their high polymorphism, population-specific studies are of great interest. AIM: This research examined the six CYP genes, including CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A5, and CYP4F2 in the Kinh Vietnamese (KHV) for population-scale precision medicine. SUBJECTS AND METHODS: We processed data from a genomics database of 206 healthy and unrelated KHV individuals to calculate CYP allele frequencies. First, we compared the CYP genes of the KHV to six other populations retrieved from the 1000 Genomes Project. Second, we searched the PharmGBK database for drug-CYP interaction data to compile a drug dosage recommendation for the KHV. RESULTS: We observed the diverging trends in genetic variations of CYP2B6, CYP2D6, and CYP3A5 in the KHV. Regarding phenotypic drug responses in the KHV, CYP2C19 exhibited all metabolic phenotypes at a non-trivial frequency. In addition, CYP3A5 metabolised drugs at a lower rate compared to the other five CYPs. CONCLUSION: This is the first large-scale study to investigate multiple CYP genes in the KHV for precision medicine from a public health perspective. Differences found in the distributions of metabolizers for the KHV suggest careful prescriptions for CYP2C19 and CYP3A5-metabolised drugs.

Current state and perspectives in hydrogen production by Escherichia coli: roles of hydrogenases in glucose or glycerol metabolism.

Escherichia coli has been a robust host strain for much biological research, in particular, research in metabolic engineering, protein engineering, and heterologous gene expression. In this mini review, to understand bacterial hydrogen production by E. coli, the effect of glucose and glycerol metabolism on hydrogen production is compared, and the current approaches to enhance hydrogen production from glycerol as a substrate are reviewed. In addition, the argument from past to present on the functions of E. coli hydrogenases, hydrogenase 1, hydrogenase 2, hydrogenase 3, and hydrogenase 4 is summarized. Furthermore, based on the literature that the E. coli formate-hydrogen lyase is essential for bacterial hydrogen production via recombinant hydrogenases, research achievements from the past regarding heterologous production of hydrogenase are rethought.

Beneficial knockouts in Escherichia coli for producing hydrogen from glycerol.

Glycerol is an inexpensive and abundant source for biofuel production on a large scale. Escherichia coli is a robust bacterium for producing hydrogen; however, its hydrogen productivity from glycerol is low. In this study, we conducted random transposon mutagenesis to identify uncharacterized genes whose inactivation is beneficial for hydrogen production from glycerol. Through screening, four mutant strains were found that are able to have from 1.3- to 1.6-fold higher hydrogen productivity (µmol H2/mg protein) than that of their parent strain (p < 0.05). These mutations were identified as aroM, gatZ, ycgR, and yfgI. The hydrogen yield (mol H2/mol glycerol consumed) of the aroM, gatZ, ycgR, and yfgI strains was 1.7-, 1.4-, 2.4-, and 2.1-fold higher than that of their parent strain, respectively. Moreover, a single disruption in these genes resulted in a faster cell growth and glycerol consumption under anaerobic conditions. In E. coli, AroM is predicted to be involved in the shikimate pathway, GatZ is tagatose-1,6-bisphosphate aldolase 2 which converts dihydroxyacetone phosphate to 1,6-biphosphate, and YcgR acts as a molecular brake limiting the swimming speed and ATP consumption. So far, the function of YfgI in general and in hydrogen production in particular remains unknown.

Metabolic engineering of Escherichia coli to enhance hydrogen production from glycerol.

Glycerol is an attractive carbon source for biofuel production since it is cheap and abundant due to the increasing demand for renewable and clean energy sources, which includes production of biodiesel. This research aims to enhance hydrogen production by Escherichia coli from glycerol by manipulating its metabolic pathways via targeted deletions. Since our past strain, which had been engineered for producing hydrogen from glucose, was not suitable for producing hydrogen from glycerol, we rescreened 14 genes related to hydrogen production and glycerol metabolism. We found that 10 single knockouts are beneficial for enhanced hydrogen production from glycerol, namely, frdC (encoding for furmarate reductase), ldhA (lactate dehydrogenase), fdnG (formate dehydrogenase), ppc (phosphoenolpyruvate carboxylase), narG (nitrate reductase), focA (formate transporter), hyaB (the large subunit of hydrogenase 1), aceE (pyruvate dehydrogenase), mgsA (methylglyoxal synthase), and hycA (a regulator of the transcriptional regulator FhlA). On that basis, we created multiple knockout strains via successive P1 transductions. Simultaneous knockouts of frdC, ldhA, fdnG, ppc, narG, mgsA, and hycA created the best strain that produced 5-fold higher hydrogen and had a 5-fold higher hydrogen yield than the parent strain. The engineered strain also reached the theoretical maximum yield of 1 mol H2/mol glycerol after 48 h. Under low partial pressure fermentation, the strain grew over 2-fold faster, indicating faster utilization of glycerol and production of hydrogen. By combining metabolic engineering and low partial pressure fermentation, hydrogen production from glycerol was enhanced significantly.

Role of seasonal importation and genetic drift on selection for drug-resistant genotypes of Plasmodium falciparum in high-transmission settings.

Historically Plasmodium falciparum has followed a pattern of drug resistance first appearing in low-transmission settings before spreading to high-transmission settings. Several features of low-transmission regions are hypothesized as explanations: higher chance of symptoms and treatment seeking, better treatment access, less within-host competition among clones and lower rates of recombination. Here, we test whether importation of drug-resistant parasites is more likely to lead to successful emergence and establishment in low-transmission or high-transmission periods of the same epidemiological setting, using a spatial, individual-based stochastic model of malaria and drug-resistance evolution calibrated for Burkina Faso. Upon controlling for the timing of importation of drug-resistant genotypes and examination of key model variables, we found that drug-resistant genotypes imported during the low-transmission season were (i) more susceptible to stochastic extinction due to the action of genetic drift, and (ii) more likely to lead to establishment of drug resistance when parasites are able to survive early stochastic loss due to drift. This implies that rare importation events are more likely to lead to establishment if they occur during a high-transmission season, but that constant importation (e.g. neighbouring countries with high levels of resistance) may produce a greater risk during low-transmission periods.

De novo copy number variations in candidate genomic regions in patients of severe autism spectrum disorder in Vietnam.

Autism spectrum disorder (ASD) is a developmental disorder with a prevalence of around 1% children worldwide and characterized by patient behaviour (communication, social interaction, and personal development). Data on the efficacy of diagnostic tests using copy number variations (CNVs) in candidate genes in ASD is currently around 10% but it is overrepresented by patients of Caucasian background. We report here that the diagnostic success of de novo candidate CNVs in Vietnamese ASD patients is around 6%. We recruited one hundred trios (both parents and a child) where the child was clinically diagnosed with ASD while the parents were not affected. We performed genetic screening to exclude RETT syndrome and Fragile X syndrome and performed genome-wide DNA microarray (aCGH) on all probands and their parents to analyse for de novo CNVs. We detected 1708 non-redundant CNVs in 100 patients and 118 (7%) of them were de novo. Using the filter for known CNVs from the Simons Foundation Autism Research Initiative (SFARI) database, we identified six CNVs (one gain and five loss CNVs) in six patients (3 males and 3 females). Notably, 3 of our patients had a deletion involving the SHANK3 gene-which is the highest compared to previous reports. This is the first report of candidate CNVs in ASD patients from Vietnam and provides the framework for building a CNV based test as the first tier screening for clinical management.

Role of Seasonal Importation and Random Genetic Drift on Selection for Drug-Resistant Genotypes of Plasmodium falciparum in High Transmission Settings.

Historically Plasmodium falciparum has followed a pattern of drug resistance first appearing in low transmission settings before spreading to high transmission settings. Several features of low-transmission regions are hypothesized as explanations: higher chance of symptoms and treatment seeking, better treatment access, less within-host competition among clones, and lower rates of recombination. Here, we test whether importation of drug-resistant parasites is more likely to lead to successful emergence and establishment in low-transmission or high-transmission periods of the same epidemiological setting, using a spatial, individual-based stochastic model of malaria and drug-resistance evolution calibrated for Burkina Faso. Upon controlling for the timing of importation of drug-resistant genotypes and examination of key model variables, we found that drug-resistant genotypes imported during the low transmission season were, (1) more susceptible to stochastic extinction due to the action of random genetic drift, and (2) more likely to lead to establishment of drug resistance when parasites are able to survive early stochastic loss due to drift. This implies that rare importation events are more likely to lead to establishment if they occur during a high-transmission season, but that constant importation (e.g., neighboring countries with high levels of resistance) may produce a greater risk during low-transmission periods.

Modeling policy interventions for slowing the spread of artemisinin-resistant pfkelch R561H mutations in Rwanda.

Artemisinin combination therapies (ACTs) are highly effective at treating uncomplicated Plasmodium falciparum malaria, but the emergence of the new pfkelch13 R561H mutation in Rwanda, associated with delayed parasite clearance, suggests that interventions are needed to slow its spread. Using a Rwanda-specific spatial calibration of an individual-based malaria model, we evaluate 26 strategies aimed at minimizing treatment failures and delaying the spread of R561H after 3, 5 and 10 years. Lengthening ACT courses and deploying multiple first-line therapies (MFTs) reduced treatment failures after 5 years when compared to the current approach of a 3-d course of artemether-lumefantrine. The best among these options (an MFT policy) resulted in median treatment failure counts that were 49% lower and a median R561H allele frequency that was 0.15 lower than under baseline. New approaches to resistance management, such as triple ACTs or sequential courses of two different ACTs, were projected to have a larger impact than longer ACT courses or MFT; these were associated with median treatment failure counts in 5 years that were 81-92% lower than the current approach. A policy response to currently circulating artemisinin-resistant genotypes in Africa is urgently needed to prevent a population-wide rise in treatment failures.

Side effects following first dose of COVID-19 vaccination in Ho Chi Minh City, Vietnam.

Vaccines are strongly recommended globally as an effective measure to prevent serious illness from and spread of COVID-19. Concerns about safety following vaccination continue to be the most common reason that people do not accept the vaccine. This retrospective study was carried out on 4341 people who received the first dose of ChAdOx1 nCoV-19, BBIBP-CorV, or mRNA-1273 vaccine at Jio Health Clinic in Ho Chi Minh City, Vietnam. Post-injection side effects were either reported by participants or actively collected by health care staff by means of telemedicine. Local side effects were reported by 35.5% of all individuals, with pain being the most common symptom (33.3%). Systemic side effects were reported by 44.2% of individuals, with fever (25.3%) and fatigue (21.4%) being the most common. Age ≤60 years, female gender, and ChAdOx1 nCoV-19 were significant independent risk factors for both local and systemic side effects, while a history of allergy was significant as a risk factor for local side effects. A total of 43 individuals (1.0%) reported concerning symptoms of rare severe complications, which were addressed and treated by physicians via Jio Health app.

Long-term effects of increased adoption of artemisinin combination therapies in Burkina Faso.

Artemisinin combination therapies (ACTs) are the WHO-recommended first-line therapies for uncomplicated Plasmodium falciparum malaria. The emergence and spread of artemisinin-resistant genotypes is a major global public health concern due to the increased rate of treatment failures that result. This is particularly germane for WHO designated 'high burden to high impact' (HBHI) countries, such as Burkina Faso, where there is increased emphasis on improving guidance, strategy, and coordination of local malaria response in an effort to reduce the prevalence of P. falciparum malaria. To explore how the increased adoption of ACTs may affect the HBHI malaria setting of Burkina Faso, we added spatial structure to a validated individual-based stochastic model of P. falciparum transmission and evaluated the long-term effects of increased ACT use. We explored how de novo emergence of artemisinin-resistant genotypes, such as pfkelch13 580Y, may occur under scenarios in which private-market drugs are eliminated or multiple first-line therapies (MFT) are deployed. We found that elimination of private market drugs would result in lower treatment failures rates (between 11.98% and 12.90%) when compared to the status quo (13.11%). However, scenarios incorporating MFT with equal deployment of artemether-lumefantrine (AL) and dihydroartemisinin-piperaquine (DHA-PPQ) may accelerate near-term drug resistance (580Y frequency ranging between 0.62 to 0.84 in model year 2038) and treatment failure rates (26.69% to 34.00% in 2038), due to early failure and substantially reduced treatment efficacy resulting from piperaquine-resistant genotypes. A rebalanced MFT approach (90% AL, 10% DHA-PPQ) results in approximately equal long-term outcomes to using AL alone but may be difficult to implement in practice.

Novel findings from family-based exome sequencing for children with biliary atresia.

Biliary atresia (BA) is a progressive inflammation and fibrosis of the biliary tree characterized by the obstruction of bile flow, which results in liver failure, scarring and cirrhosis. This study aimed to explore the elusive aetiology of BA by conducting whole exome sequencing for 41 children with BA and their parents (35 trios, including 1 family with 2 BA-diagnosed children and 5 child-mother cases). We exclusively identified and validated a total of 28 variants (17 X-linked, 6 de novo and 5 homozygous) in 25 candidate genes from our BA cohort. These variants were among the 10% most deleterious and had a low minor allele frequency against the employed databases: Kinh Vietnamese (KHV), GnomAD and 1000 Genome Project. Interestingly, AMER1, INVS and OCRL variants were found in unrelated probands and were first reported in a BA cohort. Liver specimens and blood samples showed identical variants, suggesting that somatic variants were unlikely to occur during morphogenesis. Consistent with earlier attempts, this study implicated genetic heterogeneity and non-Mendelian inheritance of BA.

Outcomes of bone marrow mononuclear cell transplantation combined with interventional education for autism spectrum disorder.

The aim of this study was to evaluate the safety and efficacy of autologous bone marrow mononuclear cell transplantation combined with educational intervention for children with autism spectrum disorder. An open-label clinical trial was performed from July 2017 to August 2019 at Vinmec International Hospital, Hanoi, Vietnam. Thirty children who fulfilled the autism criteria of the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition, and had Childhood Autism Rating Scale (CARS) scores >37 were selected. Bone marrow was harvested by anterior iliac crest puncture under general anesthesia. The volume collected was as follows: 8 mL/kg for patients under 10 kg (80 mL + [body weight in kg - 10] × 7 mL) for patients above 10 kg. Mononuclear cells were isolated with a Ficoll gradient and then infused intrathecally. The same procedure was repeated 6 months later. After the first transplantation, all patients underwent 8 weeks of educational intervention based on the Early Start Denver Model. There were no severe adverse events associated with transplantation. The severity of autism spectrum disorder (ASD) was significantly reduced, with the median CARS score decreasing from 50 (range 40-55.5) to 46.5 (range 33.5-53.5) (P < .05). Adaptive capacity increased, with the median Vineland Adaptive Behavior Scales score rising from 53.5 to 60.5. Social communication, language, and daily skills improved markedly within 18 months after transplantation. Conversely, repetitive behaviors and hyperactivity decreased remarkably. Autologous bone marrow mononuclear cell transplantation in combination with behavioral intervention was safe and well tolerated in children with ASD (Trial registration: ClinicalTrials.gov identifier: NCT03225651).

A novel de novo variant of LAMA2 contributes to merosin deficient congenital muscular dystrophy type 1A: Case report.

Merosin deficient congenital muscular dystrophy type 1A (MDC1A) is caused by defects in the LAMA2 gene. Patients with MDC1A exhibit severe symptoms, including congenital hypotonia, delayed motor development and contractures. The present case report describes a Vietnamese male child with clinical manifestations of delayed motor development, limb-girdle muscular dystrophy, severe scoliosis and white matter abnormality in the brain. Whole exome sequencing (WES) was performed with subsequent validation using Sanger sequencing, and a de novo missense variant (NM_000426.3:c.1964T>C, p.Leu655Pro) and a splice site variant (NG_008678.1:c.3556-13T>A) in the LAMA2 gene of the proband was detected. The missense variant located in exon 14 and has not been reported previously, to the best of our knowledge; whereas the splice site variant has been previously reported to cause premature termination of transcription in patients with MDC1A. In silico tools predicted that the missense variant was damaging. Phenotype-genotype analysis suggested that this proband was associated with classical early onset MDC1A. The co-existence of a de novo and a heterozygous variant in the LAMA2 gene suggested that the de novo variant contributed to the autosomal recessive manner of the disease. Careful consideration of this event by clinical confirmation of parental carrier status may help to accurately determine the risk of occurrence of this disease in future offspring. Additionally, WES is recommended as a powerful tool to assist in identifying potentially causative variants for heterogeneous diseases such as MDC1A.

Genetic landscape of autism spectrum disorder in Vietnamese children.

Autism spectrum disorder (ASD) is a complex disorder with an unclear aetiology and an estimated global prevalence of 1%. However, studies of ASD in the Vietnamese population are limited. Here, we first conducted whole exome sequencing (WES) of 100 children with ASD and their unaffected parents. Our stringent analysis pipeline was able to detect 18 unique variants (8 de novo and 10 ×-linked, all validated), including 12 newly discovered variants. Interestingly, a notable number of X-linked variants were detected (56%), and all of them were found in affected males but not in affected females. We uncovered 17 genes from our ASD cohort in which CHD8, DYRK1A, GRIN2B, SCN2A, OFD1 and MDB5 have been previously identified as ASD risk genes, suggesting the universal aetiology of ASD for these genes. In addition, we identified six genes that have not been previously reported in any autism database: CHM, ENPP1, IGF1, LAS1L, SYP and TBX22. Gene ontology and phenotype-genotype analysis suggested that variants in IGF1, SYP and LAS1L could plausibly confer risk for ASD. Taken together, this study adds to the genetic heterogeneity of ASD and is the first report elucidating the genetic landscape of ASD in Vietnamese children.

Nitrogen Fixation Genes and Nitrogenase Activity of the Non-Heterocystous Cyanobacterium Thermoleptolyngbya sp. O-77.

Cyanobacteria are widely distributed in marine, aquatic, and terrestrial ecosystems, and play an important role in the global nitrogen cycle. In the present study, we examined the genome sequence of the thermophilic non-heterocystous N2-fixing cyanobacterium, Thermoleptolyngbya sp. O-77 (formerly known as Leptolyngbya sp. O-77) and characterized its nitrogenase activity. The genome of this cyanobacterial strain O-77 consists of a single chromosome containing a nitrogen fixation gene cluster. A phylogenetic analysis indicated that the NifH amino acid sequence from strain O-77 was clustered with those from a group of mesophilic species: the highest identity was found in Leptolyngbya sp. KIOST-1 (97.9% sequence identity). The nitrogenase activity of O-77 cells was dependent on illumination, whereas a high intensity of light of 40 µmol m-2 s-1 suppressed the effects of illumination.