WilsonGenAI a deep learning approach to classify pathogenic variants in Wilson Disease.

BACKGROUND: Advances in Next Generation Sequencing have made rapid variant discovery and detection widely accessible. To facilitate a better understanding of the nature of these variants, American College of Medical Genetics and Genomics and the Association of Molecular Pathologists (ACMG-AMP) have issued a set of guidelines for variant classification. However, given the vast number of variants associated with any disorder, it is impossible to manually apply these guidelines to all known variants. Machine learning methodologies offer a rapid way to classify large numbers of variants, as well as variants of uncertain significance as either pathogenic or benign. Here we classify ATP7B genetic variants by employing ML and AI algorithms trained on our well-annotated WilsonGen dataset. METHODS: We have trained and validated two algorithms: TabNet and XGBoost on a high-confidence dataset of manually annotated, ACMG & AMP classified variants of the ATP7B gene associated with Wilson's Disease. RESULTS: Using an independent validation dataset of ACMG & AMP classified variants, as well as a patient set of functionally validated variants, we showed how both algorithms perform and can be used to classify large numbers of variants in clinical as well as research settings. CONCLUSION: We have created a ready to deploy tool, that can classify variants linked with Wilson's disease as pathogenic or benign, which can be utilized by both clinicians and researchers to better understand the disease through the nature of genetic variants associated with it.

ICU Admissions and Outcomes of Childhood Cancer Patients in Single Tertiary Hospital in the Private Sector in India.

Ramandeep Singh AroraBackground Modern-day treatment of childhood cancer is punctuated by the necessary need for intensive care. This study was performed to understand the intensive care unit (ICU) admission rates and factors associated with ICU admission in a cohort of newly diagnosed childhood cancer patients in India. Materials and Methods All childhood (age <18 years) patients in the hospital-based cancer registry who had registered between March 1, 2013, and May 31, 2018, formed the cohort. ICU admissions were recorded and demographic and clinical factors associated with ICU admission were investigated. ICU admission rates were the primary outcome of interest and secondary outcomes were ICU admission rates for sick/supportive reasons, ICU admission rates for surgical/procedural reasons and mortality during ICU admission. Results In a cohort of 258 children (66% males, 61% from India, and median age 7 years), 149 (58%) patients needed one or more ICU admission (median one with range of one to five) with total 204 ICU admission episodes. While age group, gender, and nationality were not significantly associated with ICU admission, cancer type was (highest in neuroblastoma (82%) and central nervous system (CNS) tumors (71%)). Sick/supportive care ICU admissions were significantly higher in patients of younger age, Indian origin, and certain cancers (leukemias, lymphomas). Surgical/procedural ICU admissions were significantly higher in international patients and certain cancers (CNS tumors, neuroblastomas, and soft tissue sarcomas). There were 17 ICU deaths (11% of patients admitted to ICU) and all but one were from sick/supportive care ICU admissions. Conclusion Our study highlights higher than reported ICU admission rates and lower than reported mortality in children with cancer in low- and middle-income countries. We next plan to develop more specific ICU admission criteria, prospectively evaluating severity metrics in these patients, and explore the development of a high dependency unit.

Understanding the roles and regulation of mitochondrial microRNAs (MitomiRs) in neurodegenerative diseases: Current status and advances.

MicroRNAs (miRNA) are a class of small non-coding RNA, roughly 21-22 nucleotides in length, which are master gene regulators. These miRNAs bind to the mRNA's 3' - untranslated region and regulate post-transcriptional gene regulation, thereby influencing various physiological and cellular processes. Another class of miRNAs known as mitochondrial miRNA (MitomiRs) has been found to either originate from the mitochondrial genome or be translocated directly into the mitochondria. Although the role of nuclear DNA encoded miRNA in the progression of various neurological diseases such as Parkinson's disease, Alzheimer's disease, Huntington's disease, etc. is well known, accumulating evidence suggests the possible role of deregulated mitomiRs in the progression of various neurodegenerative diseases with unknown mechanism. We have attempted to outline the current state of mitomiRs role in controlling mitochondrial gene expression and function through this review, paying particular attention to their contribution to neurological processes, their etiology, and their potential therapeutic use.

Paroxysmal Cold Hemoglobinuria in a 4-year-old Child.

Paroxysmal Cold Hemoglobinuria is a rare cause of intravascular hemolysis presenting in children following an acute viral illness. It is usually self-limiting in nature. We present the details of a 4-year-old boy who presented with rapid onset intravascular hemolysis. Donath Landsteiner antibody test was positive and hemolysis resolved within two weeks of onset.

Guillain-Barre syndrome masquerading as acute respiratory failure in an infant.

Guillain-Barré syndrome (GBS) is a rare entity in infants. We report a case of GBS in a 5-month-old girl. The child presented with cough, loose stools, breathing difficulty, and listlessness. The child was treated as pneumonia with respiratory failure. Due to difficulty in weaning from ventilation with areflexia, marked hypotonia, and reduced power in all four limbs; possibilities of spinal muscular atrophy, poliomyelitis, and myopathies were kept. Nerve conduction velocity study was suggestive of mixed sensory-motor, severe axonal, and demyelinating polyradiculoneuropathy. Cerebrospinal fluid study revealed albuminocytological dissociation. Child was diagnosed as GBS and treated with intravenous immunoglobulin. Child recovered completely on follow-up. GBS should be considered as a differential diagnosis in acute onset respiratory failure with neuromuscular weakness in infants.

p16 hypermethylation: a biomarker for increased esophageal cancer susceptibility in high incidence region of North East India.

Esophageal cancer is one of the most common cancers in North East India. The molecular mechanisms of esophageal cancer susceptibility in North East India have not been fully understood. There is a need for identification of biomarkers to identify people at risk of esophageal cancer. p16 is an essential G1 cell cycle regulatory gene whose loss of function is associated with carcinogenesis. Therefore, we conducted this study to determine the prevalence of p16 gene methylation in patients with esophageal cancer to assess the feasibility of using gene methylation as a biomarker. A total of 100 newly diagnosed esophageal cancer cases along with equal number of age, sex, and ethnicity-matched controls were included in this study. Methylation-specific PCR was used to determine the p16 methylation status. Aberrant promoter methylation of the p16 gene was detected in 81 of 100 (81%) esophageal cancer cases. Hypermethylation of p16 gene was found to be influenced by lifestyle factors. Betel quid and tobacco chewing habit synergistically with p16 methylation elevated the risk for esophageal cancer development (adjusted odds ratio (OR) = 6.88, 95% confidence interval (CI) = 1.64-28.81, p = 0.003 for betel quid chewing and adjusted OR = 7.02, 95% CI = 1.87-26.38, p = 0.001 for tobacco chewing). Further, intake of green leafy vegetables and fruits lowered the risk of esophageal cancer (adjusted OR = 0.16, 95 % CI = 0.04-0.58, p = 0.05 for green leafy vegetables and adjusted OR = 0.15, 95% CI = 0.04-0.64, p = 0.01 for fruits). Thus, p16 hypermethylation may aid as a biomarker in identifying habitués at greater risk for esophageal cancer susceptibility in high incidence region of North East India.

Promoter methylation of MGMT gene in serum of patients with esophageal squamous cell carcinoma in North East India.

BACKGROUND: Promoter hypermethylation is a common event in human cancer. O6-methylguanine-DNA methyltransferase (MGMT) is a gene involved in DNA repair, which is methylated in a variety of cancers. We aimed to explore the methylation status of MGMT gene among the North Eastern population where esophageal cancer incidence and exposure to carcinogens like nitrosamines is high. MATERIALS AND METHODS: A total of 100 newly diagnosed esophageal cancer cases along with equal number of age, sex and ethnicity matched controls were included in this study. Methylation specific PCR was used to determine the MGMT methylation status in serum samples. RESULTS: Aberrant promoter methylation of the MGMT gene was detected in 70% of esophageal cancer cases. Hypermethylation of MGMT gene was found to be influenced by environmental factors like betel quid and tobacco which contain potent carcinogens like nitrosamines. Tobacco chewing and tobacco smoking habit synergistically with MGMT methylation elevated the risk for esophageal cancer development [adjusted OR=5.02, 95% CI=1.35-18.74; p=0.010 for tobacco chewing and Adjusted OR=3.00, 95% CI=1.22-7.36; p=0.014 for tobacco smoking]. CONCLUSIONS: Results suggest that the DNA hypermethylation of MGMT is an important mechanism for MGMT gene silencing resulting in esophageal cancer development and is influenced by the environmental factors. Thus MGMT hypermethylation can be used as a biomarker for esophageal cancer in high incidence region of North East India.

Orbitocranial complications of acute sinusitis in children.

BACKGROUND: Orbitocranial complications (OCCs) of sinusitis are uncommon but potentially life threatening. OCCs carry high morbidity, mortality, and significant long-term sequelae. Late recognition leads to even worse outcomes. OBJECTIVE: To present four case reports showing that aggressive management of complications of sinusitis-like OCC decreases long-term sequelae and mortality in pediatric patients. CASE REPORTS: Four pediatric patients diagnosed with OCC were treated at our institution from April 2012 to March 2013. Three were boys and one was a girl; ages ranged from 4-14 years. Magnetic resonance imaging and computed tomography were the most useful imaging modalities. All patients received broad-spectrum antibiotics. Additional interventions consisted of endoscopic sinus surgery, subdural empyema drainage, and orbital decompression. CONCLUSION: The difficult complications of acute sinusitis in the pediatric age group should be anticipated, recognized early, and aggressively managed to prevent morbidity and a fatal outcome.

Role of household exposure, dietary habits and glutathione S-Transferases M1, T1 polymorphisms in susceptibility to lung cancer among women in Mizoram India.

BACKGROUND: A case-control study was conducted to evaluate the effect of household exposure, dietary habits, smoking and Glutathione S-Transferases M1, T1 polymorphisms on lung cancer among women in Mizoram, India. MATERIALS AND METHODS: We selected 230 newly diagnosed primary lung cases and 460 controls from women in Mizoram. Multivariate logistic regression analysis was performed to estimate adjusted odds ratio (OR). RESULTS: Exposure of cooking oil fumes (p<0.003), wood as heating source for cooking (p=0.004), kitchen inside living room (p=0.001), improper ventilated house (p=0.003), roasting of soda in kitchen (p=0.001), current smokers of tobacco (p=0.043), intake of smoked fish (p=0.006), smoked meat (p=0.001), Soda (p<0.001) and GSTM1 null genotype (p=0.003) were significantly associated with increased risk of lung cancer among women in Mizoram. Significantly protective effect was observed for intake of bamboo shoots (p=<0.001) and egg (p<0.001). A clear increase in dose response gradient was observed for total cooking dish years. Risk for lung cancer tends to increase with collegial effect of indoor environmental sources (p=0.022). Significant correlation was also observed for interaction of GST polymorphisms with some of dietary habits. CONCLUSIONS: We confirmed the important role of exposure of cooking oil emission and wood smoke, intake of smoked meat, smoked fish and soda (an alkali preparation used as food additives in Mizoram) and tobacco consumption for increase risk of lung cancer among Women in Mizoram.

Interaction of XRCC1 and XPD gene polymorphisms with lifestyle and environmental factors regarding susceptibility to lung cancer in a high incidence population in North East India.

BACKGROUND: This study aimed to explore the role of XRCC1 (Arg399Gln) and XPD (Lys751Gln) gene polymorphisms, lifestyle and environmental factors as well as their possible interactions in propensity to develop lung cancer in a population with high incidence from North East India. MATERIALS AND METHODS: A total of 272 lung cancer cases and 544 controls were collected and XRCC1 (Arg399Gln) and XPD (Lys751Gln) genotypes were analyzed using a polymerase chain reaction based restriction fragment length polymorphism assay. Conditional multiple logistic regression analysis was used to calculate adjusted odds ratios and 95% confidence intervals after adjusting for confounding factors. RESULTS: The combined Gln/Gln genotype of XRCC1 and XPD genes (OR=2.78, CI=1.05-7.38; p=0.040) was significantly associated with increased risk for lung cancer. Interaction of XRCC1Gln/Gln genotype with exposure of wood combustion (OR=2.56, CI=1.16-5.66; p=0.020), exposure of cooking oil fumes (OR=3.45, CI=1.39-8.58; p=0.008) and tobacco smoking (OR=2.54, CI=1.21-5.32; p=0.014) and interaction of XPD with betel quid chewing (OR=2.31, CI=1.23-4.32; p=0.009) and tobacco smoking (OR=2.13, CI=1.12-4.05; p=0.022) were found to be significantly associated with increased risk for lung cancer. CONCLUSIONS: Gln/Gln alleles of both XRCC1 and XPD genes appear to amplify the effects of household exposure, smoking and betel quid chewing on lung cancer risk in the study population.

Genetic analysis in Bartter syndrome from India.

Bartter syndrome is a group of inherited, salt-losing tubulopathies presenting as hypokalemic metabolic alkalosis with normotensive hyperreninemia and hyperaldosteronism. Around 150 cases have been reported in literature till now. Mutations leading to salt losing tubulopathies are not routinely tested in Indian population. The authors have done the genetic analysis for the first time in the Bartter syndrome on two cases from India. First case was antenatal Bartter syndrome presenting with massive polyuria and hyperkalemia. Mutational analysis revealed compound heterozygous mutations in KCNJ1(ROMK) gene [p(Leu220Phe), p(Thr191Pro)]. Second case had a phenotypic presentation of classical Bartter syndrome however, genetic analysis revealed only heterozygous novel mutation in SLC12A gene p(Ala232Thr). Bartter syndrome is a clinical diagnosis and genetic analysis is recommended for prognostication and genetic counseling.

Isolated severe bilateral bronchomalacia.

Airway malacia is uncommon condition having symptoms similar to common respiratory illnesses. Any child having persistent wheeze during infancy should be evaluated for airway malacia. The authors report a case of isolated severe bilateral bronchomalacia managed with tracheostomy and continuous positive pressure ventilation.

Association of a p53 codon 72 gene polymorphism with environmental factors and risk of lung cancer: a case control study in Mizoram and Manipur, a high incidence region in North East India.

BACKGROUND: A very high incidence of lung cancer is observed in Mizoram and Manipur, North East India. We conducted a population based case control study to establish associations of p53 codon 72 polymorphisms and interactions with environmental factors for this high incidence. MATERIAL AND METHODS: A total of 272 lung cancer cases and 544 controls matched for age (±5 years), sex and ethnicity were collected and p53 codon 72 polymorphism genotypes were analyzed using a polymerase chain based restriction fragment length polymorphism assay. We used conditional multiple logistic regression analysis to calculate adjusted odds ratios and 95% confidence intervals after adjusting for confounding factors. RESULTS: p53 Pro/Pro genotype was significantly associated with increased risk of lung cancer in the study population (adjusted OR=2.14, CI=1.35-3.38, p=0.001). Interactions of the p53 Pro/Pro genotype with exposure to wood smoke (adjusted OR=3.60, CI=1.85-6.98, p<0.001) and cooking oil fumes (adjusted OR=3.27, CI=1.55-6.87, p=0.002), betel quid chewing (adjusted OR=3.85, CI=1.96- 7.55, p<0.001), tobacco smoking (adjusted OR=4.42, CI=2.27-8.63, p<0.001) and alcohol consumption (adjusted OR=3.31, CI=1.10-10.03, p=0.034) were significant regarding the increased risk of lung cancer in the study population. CONCLUSIONS: The present study provided preliminary evidence that a p53 codon 72 polymorphism may effect lung cancer risk in the study population, interacting synergistically with environmental factors.

Interaction of tobacco smoking and chewing with Angiotensin converting enzyme (insertion/deletion) gene polymorphisms and risk of lung cancer in a high risk area from northeast India.

BACKGROUND: Association of angiotensin converting enzyme (ACE) gene polymorphisms with lung cancer susceptibility remains uncertain and varies with ethnicity. Northeast India represents a geographically, culturally, and ethnically isolated population. The area reports an especially high rate of tobacco usage in a variety of ways of consumption, compared with the rest of the Indian population. MATERIALS AND METHODS: We conducted a population based case control study in two major high risk region for lung cancer from Northeast India. A total of 151 consecutive lung cancer cases diagnosed histopathologically and equal numbers of controls were recruited with record of relevant sociodemographic information. Blood samples were collected and processed to identify ACE gene polymorphism. RESULTS: Significantly higher (40.4 % vs 29.1%, OR=1.97, CI=1.04-3.72; p=0.037) prevalence of the ACE II genotype was observed among lung cancer cases. Smoking was significantly associated with increased risk of lung cancer (OR=1.70, CI=1.02-2.81; p=0.041). An enhanced risk was also observed for interaction of ACE II genotype with tobacco smoking (OR=4.09, CI=1.51-11.05; p=0.005) and chewing (OR=3.68, CI=1.22-11.13; p=0.021). CONCLUSIONS: The present study indicates significant association s of the ACE II genotype with lung cancer in high risk Northeast India.

Pachymeningitis in a young child responded to antitubercular therapy: a case report.

Pachymeningitis is a rare disease of diverse etiology mainly affecting the adult population. Only 4 pediatric cases have been reported till now. We report the youngest child with pachymeningitis from India. Our case responded very well to antitubercular therapy with near complete recovery. Antitubercular therapy can be considered in children from endemic countries with hypertrophic pachymeningitis before labeling their condition as idiopathic hypertrophic pachymeningitis.

Ventriculo-peritoneal shunt: A rare cause of basal ganglia and thalamic abscess.

We report an 18-month-old female child with ventriculo-peritoneal shunt related thalamic abscess treated with stereotactic aspiration. Deep seated abscesses are complex due to difficult access and are associated with an increased risk of intra-ventricular rupture as well as antibiotic resistance, a fact which justifies a more aggressive and immediate neurosurgical management.