IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes.

With the advent of next-generation sequencing, large-scale initiatives for mining whole genomes and exomes have been employed to better understand global or population-level genetic architecture. India encompasses more than 17% of the world population with extensive genetic diversity, but is under-represented in the global sequencing datasets. This gave us the impetus to perform and analyze the whole genome sequencing of 1029 healthy Indian individuals under the pilot phase of the 'IndiGen' program. We generated a compendium of 55,898,122 single allelic genetic variants from geographically distinct Indian genomes and calculated the allele frequency, allele count, allele number, along with the number of heterozygous or homozygous individuals. In the present study, these variants were systematically annotated using publicly available population databases and can be accessed through a browsable online database named as 'IndiGenomes' http://clingen.igib.res.in/indigen/. The IndiGenomes database will help clinicians and researchers in exploring the genetic component underlying medical conditions. Till date, this is the most comprehensive genetic variant resource for the Indian population and is made freely available for academic utility. The resource has also been accessed extensively by the worldwide community since it's launch.

Role of podoplanin, E-cadherin, Ki-67 in the dissemination of tumor cells in ovarian surface epithelial carcinoma-An immunohistochemical study.

BACKGROUND/AIM: To understand the biological behaviour, ovarian carcinoma should be approached as a complex tissue composed of tumor cells, ECM proteins, endothelial cells, fibroblasts, inflammatory cells and lymphatics. We aimed to investigate the role of proliferation index of the tumor cells, cell adheshion molecules and lymphangiogenesis in the dissemination of tumor in ovarian surface epithelial carcinomas using suitable antibodies. MATERIALS AND METHODS: Fifty-nine cases of ovarian carcinoma were assessed immunohistochemically to quantify the intratumoral and peritumoral LVD, podoplanin expression in stroma, E-cadherin expression and proliferation index of the tumor cells. Descriptive statistics were done stratifying the cases into early stage(FIGO-I) and advanced stage (FIGO-II,III,IV).Receiver operating curve was applied to determine the cut off of intratumoral LVD, peritumoral LVD, Ki-67 to discriminate early stage and advanced stage disease and the cut offs were validated by generating regression model. RESULTS: Intratumoral LVD (p = 0.001), peritumoral LVD (p = 0.000), high Ki-67 (p = 0.000), podoplanin expressing cancer associated fibroblasts (p = 0.002) and macrophages expressing podoplanin (p = 0.003) were significantly associated with advanced stage disease. Intratumoral LVD, peritumoral LVD and Ki67 at cut offs of 3.5, 9.5 and 30 % emerged as discriminators of early stage disease from advanced stage disease by ROC curve analysis. Peritumoral LVD > 9.5 had the highest odds of advanced disease (OR-33.948, CI-4.631-38.622). CONCLUSION: OSECs with intratumoral LVD > 3.5, peritumoral LVD > 9.5 and Ki-67 > 30 % should be considered for aggressive chemotherapy and frequent follow-up. Peritumoral LVD and podoplanin expression in components of tumor stroma have a determinant role in tumor dissemination in OSEC.

Methodology for the early identification of neurodevelopmental disorders in the primary and preschool children in rural India by applying intervention module developed for teachers.

Objective: Neurodevelopmental disorders NDD are neurologic processing problems that interfere with learning in children. Primary and preschool teachers who are essential links in public health reach out to such children do not receive any formal training to identify these disorders. Hence, a primary and preschool level intervention addressing the issue is proposed. Materials and Methods: Primary and preschool teachers of government and government-aided schools and Anganwadi/preschools in the Model Rural Health Research Unit Tirunelveli field practice area will be assigned into two groups. The training module will be developed and validated using neurodevelopmental screening tool (NDST). Before identifying the students using the NDST, the teachers in Group A will get training using the module. Group B is the control group, in which untrained teachers administer the NDST to the children and then will be trained. Neurologists will assess the same children over 1 year. Results: The effectiveness of teacher training for the early detection of children with NDD will be assessed. Thus, the validity of the screening for NDD by the teachers will be estimated. Conclusion: If successful, the module can be incorporated into the Rashtriya Bal Swasthya Karyakram program of India for the early identification of children with NDD.

Sociocultural and drug-related factors associated with adherence to iron-folic acid supplementation among pregnant women - A mixed-methods study.

BACKGROUND: The National Family Health Survey of India (NFHS-5) revealed a lapse in the advancement of mitigating anemia despite free supplementation of iron-folic acid tablets (IFAT) and improvement in IFAT coverage during pregnancy. The local sociocultural beliefs and community perspective toward IFAT are pivotal in reducing the gap between IFAT coverage and consumption. Hence, we proposed the study to assess adherence to IFAT among rural pregnant women and explore the associated factors. MATERIALS AND METHODS: The present study was conducted as a mixed-methods study with a sequential exploratory design in a rural setting of the Model Rural Health Research Unit (MRHRU) from October 2020 to May 2021. Ten focus group discussions (FGDs; 8 - antenatal women, 1 - mother/mother-in-law, and 1 - health care worker) were conducted, and framework analysis was done to identify themes followed by a quantitative survey with a semi-structured questionnaire among antenatal women (n = 236). Logistic regression was used to analyze factors associated with adherence. RESULTS: The major themes that emerged from FGDs were the sociocultural factors (gender norms, communal fallacies), lack of awareness, and drug-related factors (unpalatability, misperceptions, and experienced side effects). Around 57% were adherent to IFAT. Side effects experienced on IFAT intake (P = 0.001, OR = 2.33), misconceptions regarding IFAT, like weight gain in IFAT use (P = 0.001, OR = 2.86), a big baby with IFAT use (P = 0.000, OR = 5.93) negatively influenced adherence. CONCLUSIONS: The significant gaps between IFAT coverage and consumption surrounded the unpleasant odor and stench of IFAT, side effects, lack of individualized counseling, and misperceptions regarding IFAT use.

Psychosocial Problems of Rural Indian Women Practising Breast Self-Examination - a Community-Based Study from Southern India.

Introduction: Globally, breast cancer affects 2.5 million people annually. Younger women with advanced-stage cancers had a lower survival rate, but early detection enhanced survival chances by 27 to 47%. Breast self-examination (BSE) has led to early detection and higher rates of benign biopsies. Studies evaluating the psychosocial impact of BSE are few in India which has been attempted in the present study. Methods: The community-based descriptive cross-sectional study was conducted among rural women aged 30 years and above, who have done BSE at least once without present or prior breast abnormalities in the field practice area of Model Rural Health Research Unit, Tirunelveli. The research questionnaire was developed based on the findings of focus group discussion (FGD) on the same objective in the study area. Results: Among 379 participants, 146 (38.5%) felt confident in their BSE knowledge, 28.2% (n=107) and 5.5% (n=21) of the respondents experienced anxiety and depression while practising BSE, respectively. There is a significant difference between the mean anxiety levels (p-value=0.002) and depression (p-value=0.013) of individuals who have detected anomalies during BSE and those who have not. Conclusion: Regular counselling has to improve knowledge about BSE, like the timing and method of examination, and decreases the anxiety and depression level.

A Novel Subset of Triple-Negative Breast Cancers with Unique Histology and Immunohistochemical Expression.

Background & Objective: Triple-Negative Breast Carcinoma (TNBC) is characterized by an absence of estrogen receptor, progesterone receptor and HER2 neu expression, with distinct molecular, histological and clinical features, aggressive clinical course and a poor prognosis. The objective was to evaluate the expression of Cytokeratin5/6 (CK 5/6), Epidermal Growth Factor Receptor 1 (EGFR 1), E-cadherin and Androgen receptor in tissue sections of TNBC. Methods: All modified radical mastectomy samples received negative for the three markers were subjected to further studies with CK5/6, EGFR 1, E- cadherin and Androgen receptor staining. The clinical and pathological data were tabulated and statistically analysed using the Chi-square test, and cross-tabulation was done to assess the correlation between these markers. Results: Of 94 samples classified as TNBC, 31 (33%) were positive for CK 5/6, 47 (50%) for EGFR, 32 (34%) for E Cadherin and Androgen receptor, respectively. We had one positive patient for all four markers, 13 patients were negative for all four. Thirty-five cases were positive for only one marker, 32 were positive for two markers, and 13 were positive for three markers. Analysis revealed certain interesting patterns, namely - E cadherin was the most common isolated marker expressed in our cohort of TNBC with 15 of 35 positives. Conclusion: This study highlights the presence of a unique subtype of TNBC, which are negative for all the four markers studied here, with unique histomorphology of absent tumour necrosis and stromal lymphocytic infiltration being unique.

Micronutrient Deficiency in Pregnancy: Time to Think Beyond Iron and Folic Acid Supplementation.

Background: Micronutrients play an important role in influencing pregnancy outcomes. Anemia is common among pregnant women against which iron and folic acid supplementation programs are already in action. The study aimed to estimate the prevalence of anemic and selected micronutrient status among pregnant women. Materials and Methods: It is a community-based cross-sectional study. The study was carried out among pregnant women registered in Primary Health Center, Kallur, Tirunelveli district, Tamil Nadu, India, using a semi-structured data capture tool. The blood samples were collected following standard procedure. Results: The micronutrient status among 139 pregnant women were selenium <1%, copper <1%, zinc 11.5%, iodine 14.4%, Vitamin B12 41.7%, and ferritin 42.4%. Vitamin B12, zinc, and selenium levels showed a significant difference with reference values among the three trimesters. Iron and folic acid supplementation was followed by 58.7% of pregnant women. Multiple micronutrient deficiency with anemia was found among 54.6%. Conclusion: Anemia and micronutrient deficiency are high among pregnant women in this region. Since iron and folic acid supplementation strategies are already being implemented by the government, it is high time that we extend our health policy beyond that and plan for micronutrient supplementation as well.

Genomic analysis of patients in a South Indian Community with autosomal dominant cortical tremor, myoclonus and epilepsy suggests a founder repeat expansion mutation in the SAMD12 gene.

Autosomal Dominant Cortical Tremor, Myoclonus and Epilepsy is a non-progressive disorder characterized by distal tremors. Autosomal Dominant Cortical Tremor, Myoclonus and Epilepsy has been reported globally with different genetic predispositions of autosomal dominant inheritance with a high degree of penetrance. In south India, Autosomal Dominant Cortical Tremor, Myoclonus and Epilepsy has been reported in a large cohort of 48 families, in which the genetic defect was not identified. This report pertains to the whole-genome analysis of four individuals followed by repeat-primed PCR for 102 patients from a familial cohort of 325 individuals. All the patients underwent extensive clinical evaluation including neuropsychological examinations. The whole-genome sequencing was done for two affected and two unaffected individuals, belonging to two different families. The whole-genome sequencing analysis revealed the repeat expansion of TTTTA and TTTCA in intron 4 of the SAMD12 gene located on chromosome 8 in the patients affected with Autosomal Dominant Cortical Tremor, Myoclonus and Epilepsy, whereas the unaffected family members were negative for the similar expansion. Further, the repeat-primed PCR analysis of 102 patients showed the expansion of the TTTCA repeats in the intron 4 of SAMD12 gene. All patients registered for this study belong to a single community called "Nadar" whose nativity is confined to the southern districts of India, with reported unique genetic characteristics. This is the largest and most comprehensive single report on clinically and genetically characterized Autosomal Dominant Cortical Tremor, Myoclonus and Epilepsy patients belonging to a unique ethnic group worldwide.

Pharmacogenomic landscape of COVID-19 therapies from Indian population genomes.

Aim: Numerous drugs are being widely prescribed for COVID-19 treatment without any direct evidence for the drug safety/efficacy in patients across diverse ethnic populations. Materials & methods: We analyzed whole genomes of 1029 Indian individuals (IndiGen) to understand the extent of drug-gene (pharmacogenetic), drug-drug and drug-drug-gene interactions associated with COVID-19 therapy in the Indian population. Results: We identified 30 clinically significant pharmacogenetic variants and 73 predicted deleterious pharmacogenetic variants. COVID-19-associated pharmacogenes were substantially overlapped with those of metabolic disorder therapeutics. CYP3A4, ABCB1 and ALB are the most shared pharmacogenes. Fifteen COVID-19 therapeutics were predicted as likely drug-drug interaction candidates when used with four CYP inhibitor drugs. Conclusion: Our findings provide actionable insights for future validation studies and improved clinical decisions for COVID-19 therapy in Indians.

Genetic epidemiology of autoinflammatory disease variants in Indian population from 1029 whole genomes.

BACKGROUND: Autoinflammatory disorders are the group of inherited inflammatory disorders caused due to the genetic defect in the genes that regulates innate immune systems. These have been clinically characterized based on the duration and occurrence of unprovoked fever, skin rash, and patient's ancestry. There are several autoinflammatory disorders that are found to be prevalent in a specific population and whose disease genetic epidemiology within the population has been well understood. However, India has a limited number of genetic studies reported for autoinflammatory disorders till date. The whole genome sequencing and analysis of 1029 Indian individuals performed under the IndiGen project persuaded us to perform the genetic epidemiology of the autoinflammatory disorders in India. RESULTS: We have systematically annotated the genetic variants of 56 genes implicated in autoinflammatory disorder. These genetic variants were reclassified into five categories (i.e., pathogenic, likely pathogenic, benign, likely benign, and variant of uncertain significance (VUS)) according to the American College of Medical Genetics and Association of Molecular pathology (ACMG-AMP) guidelines. Our analysis revealed 20 pathogenic and likely pathogenic variants with significant differences in the allele frequency compared with the global population. We also found six causal founder variants in the IndiGen dataset belonging to different ancestry. We have performed haplotype prediction analysis for founder mutations haplotype that reveals the admixture of the South Asian population with other populations. The cumulative carrier frequency of the autoinflammatory disorder in India was found to be 3.5% which is much higher than reported. CONCLUSION: With such frequency in the Indian population, there is a great need for awareness among clinicians as well as the general public regarding the autoinflammatory disorder. To the best of our knowledge, this is the first and most comprehensive population scale genetic epidemiological study being reported from India.

Phenylhydrazine hydrochloride induced dosedependent embryo cytotoxicity in zebrafish.

Phenylhydrazine hydrochloride (PHZ) is a chemical compound. PHZ and its derivatives were used firstly as antipyretics, treatment of blood disorders such as polycythaemia Vera. For many years phenyl hydrazine was used for experimental induction of anaemia in animal models. However, this compound is reported to cause damage to red blood cells, potentially resulting in anaemia and consequential secondary involvement of other tissues, such as the spleen and liver. Recent studies suggest that PHZ cause genotoxicity in mice models. The aim of our study is to study the effect of PHZ in embryonic and larval stage of zebra fish model. Zebra fish embryos and larvae were used in this study. Working concentration prepared from 0.05 gm of PHZ stock solution. The embryos and larvae were exposed to different concentrations of PHZ (0.1, 0.3, 0.5, 0.7 0.9, 1.0, 3.0, 5.0, 7.0 9.0 and 10.0 µg/mL) and (0.1, 0.3, 0.5, 0.7, 0.9 and 1.0 µg/mL) respectively. Survival rate, mortality rate, hatching rate and phenotypic anomalies were studied in developing embryos. Heart rate and apoptosis were evaluated to assess the PHZ toxicity in larval stage of Zebra fish. Statistical analysis was performed by Pearson correlation and P values < 0.05 were considered statistically significant. The LC50of PHZ in embryo and larvae was found to be 0.7µg/mL. PHZ treated embryos showed that survival rate was decreased during 72hpf. In the case of mortality, 0.7 µg/mL and above concentration mortality rate was significantly increased between 48 and 72 hpf and the none embryos survived after 72 hpf. We observed delayed hatching rate in treated embryos when compared to control embryos. 0.5 µg/mL treated larvae showed significantly (p<0.05) decreased heart rate 20% at 96 hrs. Phenotype anomalies such as enlarged yolk sac, yolk sac split, pericardial edema, notochord anomaly appeared at higher concentration of PHZ treated embryos. Acridine orange fluorescence staining revealed that high apoptotic cells were detected at caudal fin region of larvae on day 3 at a concentration of 0.7µg/mL treated group. Our study suggests that PHZ causes multiple phenotypic abnormalities and toxicity on zebrafish embryos and larvae with respect of dose and time dependent manner.

Biliary Cystadenoma: A Case Report.

Biliary cystadenoma is a rare cystic neoplasms of liver that usually occurs in middle-aged women characterized by multiloculated cysts with internal septae and mural nodules. Unilocular biliary cystadenomas are rare and are difficult to differentiate from other cysts by radiology. Biliary cystadenomas are slow growing benign lesions that are easily resectable with a reported recurrence rate of 90% when the resection is incomplete. We present a case of 65-year-old male with unilocular biliary cystadenoma with mesenchymal stroma who presented with abdominal pain and distension. Laparotomy followed by cystectomy was done and postoperative period was uneventful with no abnormal biochemical, heamatological or imaging findings. Preoperative radio-imaging techniques may not always be helpful in arriving at a specific diagnosis in such cases. Hence thorough sampling and a careful histopathological examination is considered gold standard for specific diagnosis.

Hemophagocytic lymphohistiocytosis syndrome in Dengue hemorrhagic fever.

Hemophagocytic lymphohistiocytosis (HLH) is a life threatening florid activation of macrophages of the lymphoreticular system. It is reported to be associated with dengue in children in India and carries a high mortality. Patients present with high fever, worsening blood cell counts, splenomegaly, abnormal liver enzymes with features of liver failure, coagulopathy and neurological complications. The diagnosis is according to "Diagnostic Guidelines for HLH 2004", based on a triad of clinical, blood parameters and bone marrow cytology. In the present study, data of 212 children admitted with dengue were analyzed. Of 212 children, 31 children were classified as suspect HLH and advised bone marrow evaluation; of whom 23 children had marrow evidence of HLH. Worsening of blood cell counts were recorded in all children with a mean platelet count of 58,303.03 cells/cumm, low hematocrit in 95.65 %, low mean hemoglobin level of 8.37 g/dL, high erythrocyte sedimentation rate (ESR) and prolonged pro-thrombin time/international normalization ratio (PT/INR). Serum triglycerides, ferritin and transaminases were high. Of the 23 children, 19 patients received intravenous immunoglobulin (IVIG) and all of these children recovered. Dengue with multi-organ dysfunction is commonly concurrent to HLH in the marrow and hence, an early diagnosis based on clinical, laboratory and bone marrow evaluation is significant. A bone marrow evaluation confirms the diagnosis of HLH.