South Asian medical cohorts reveal strong founder effects and high rates of homozygosity

The benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927 individuals from isolated South Asian populations. We characterize population structure in South Asia and describe a genotyping array (SARGAM) and imputation reference panel that are optimized for South Asian genomes. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of rare homozygotes that reach 100 times that seen in outbred populations. Founder effects increase the power to associate functional variants with disease processes and make South Asia a uniquely powerful place for population-scale genetic studies.

Seasonal distribution of microplastics in surface waters of the Northern Indian Ocean

Seven expeditions were carried out during pre-monsoon, monsoon and post monsoon in 2018-2019 for marine plastic collection in surface waters of Northern Indian Ocean. PE and PP (83 %) is the dominant type of polymer found in the surface waters. Colored particles account for 67 % of all particles, with fibre/line accounting for 86 %. The average (Mean ± SD) microplastics concentration in the Northern Indian Ocean during pre-monsoon is 15,200 ± 7999 no./km², Monsoon is 18,223 ± 14,725 no./km² and post monsoon is 72,381 ± 77,692 no./km². BoB during pre-monsoon and post monsoon the microplastic concentration remains same except in the northern BoB this change is caused due to weak winds. Microplastics concentration varied both spatially, temporal and heterogeneity in nature. These differences are caused by effect of wind and seasonal reversal of currents. Microplastics collected in the anticyclonic eddy are 129,000 no./km².

Neonatal diabetes with a rare LRBA mutation

Neonatal diabetes mellitus (NDM) is characterised by onset of persistent hyperglycaemia within the first 6 months of life. NDM is frequently caused by a mutation in a single gene affecting pancreatic beta cell function. We report an infant, born to a non-consanguineous couple, who presented with osmotic symptoms and diabetic ketoacidosis. The genetic analysis showed a mutation in LRBA (lipopolysaccharide-responsive and beige-like anchor protein) gene. We highlight the importance of considering genetic analysis in every infant with NDM, to understand the nature of genetic mutation, associated comorbidities, response to glibenclamide and future prognosis.

High prevalence of asymptomatic left ventricular diastolic dysfunction and its detection among South Asian patients with Type 2 Diabetes Mellitus compared with White Europeans

Background

Heart failure (HF) is an important manifestation of Type 2 Diabetes (T2D). The development of HF in T2D may be preceded by Stage B HF. Asymptomatic left ventricular impairment, especially left ventricular diastolic dysfunction (LVDD), is a defining early feature of Stage B HF. Detection of Stage B HF is crucial as it provides an opportune target for intervention with cardio-protective therapy to prevent the development of symptomatic HF in T2D. The risk of T2DM is higher in South Asian populations resulting in increased risk of macrovascular and microvascular complications. The prevalence of Stage B HF in South Asian patients with T2DM is not known.

Purpose

(i) To compare the prevalence of Stage B HF in South Asians in India compared with White Europeans in Scotland; (ii) To test the role of NT-proBNP in identifying Stage B HF

Methods

This study involved the comparison between two independently conducted, cross-sectional studies. The patients were asymptomatic patients with T2DM with no prior history of cardiovascular disease from Chennai, India (n=246) and Tayside, Scotland (n=246). All patients underwent transthoracic echocardiogram (echo) examination to detect the presence of structural and functional echo features of Stage B HF: left atrial enlargement (LAE), left ventricular hypertrophy (LVH), LVDD and LV systolic dysfunction (LVSD). Receiver operating curves (ROC) were used to determine the predictive ability of NT-proBNP to predict LAE/LVDD/LVD/LVSD.

Results

The prevalence of Stage B HF was high in South-Asian patients with T2DM (median age of 55 [49, 62] with a high prevalence of LVDD (5% had LVH, 7.3% had LAE, 70% had LVDD and 0% had LVSD (Figure 1B). 10% of the South Asian patients had at least 2 factors contributing to Stage B HF and these patients had higher NT-proBNP titres (703.4 [500.0, 949.2] vs 423.7 [35.0, 754.2], p<0.001). ROC curves show that NT-proBNP can predict these participants with 2 or more echo features [Figure 2B, AUC: 0.7043 (0.6159, 0.7928) p<0.05]. The prevalence of Stage B HF among White Europeans (median age of 67 [61, 72].) was lower compared with South Asian patients: 15% had LVH, 13% had LAE, 19% had LVDD and 2% had LVSD (Figure 1A). 8% of White Europeans had at least 2 factors contributing to Stage B HF and these had higher NT-proBNP titres (368.9 [154.6, 1087.8] vs 186.8 [79.7, 411.5], p=0.02). ROC curves show that NT-proBNP can predict participants with 2 or more factors [Figure 2A, AUC: 0.6399 (0.5122, 0.7676) p<0.05].

Conclusion

Our study has shown that South Asian patients with T2DM have a high prevalence of Stage B HF compared with White Europeans and that the predominant Stage B HF feature is LVDD.

We also found that NTproBNP could potentially be used to detect Stage B HF and help identify at-risk patients for cardio-protective therapy such as SGLT2 inhibitor therapy that has been shown to prevent the development of future HF events.

Funding Acknowledgement

Type of funding sources: None.

Seasonal temperature variability observed at abyssal depths in the Arabian Sea

The abyssal ocean is generally considered an aseasonal environment decoupled from the variabilities observed at and just below the ocean's surface. Herein, we describe the first in-situ timeseries record of seasonal warming and cooling in the Arabian Sea at a depth of 4000 m. The seasonal cycle was observed over the nearly four-year-long record (from November 2018 to March 2022). The abyssal seasonal temperature cycle also exhibited noticeable interannual variability. We investigate whether or not surface processes influence the near-seabed temperature through deep meridional overturning circulation modulated by the Indian monsoon or by Rossby wave propagation. We also consider if bottom water circulation variability and discharge of the dense Persian Gulf and Red Sea Water may contribute to the observed seasonality.

Young-onset diabetes in Asian Indians is associated with lower measured and genetically determined beta cell function

AIMS/HYPOTHESIS

South Asians in general, and Asian Indians in particular, have higher risk of type 2 diabetes compared with white Europeans, and a younger age of onset. The reasons for the younger age of onset in relation to obesity, beta cell function and insulin sensitivity are under-explored.

METHODS

Two cohorts of Asian Indians, the ICMR-INDIAB cohort (Indian Council of Medical Research-India Diabetes Study) and the DMDSC cohort (Dr Mohan's Diabetes Specialties Centre), and one of white Europeans, the ESDC (East Scotland Diabetes Cohort), were used. Using a cross-sectional design, we examined the comparative prevalence of healthy, overweight and obese participants with young-onset diabetes, classified according to their BMI. We explored the role of clinically measured beta cell function in diabetes onset in Asian Indians. Finally, the comparative distribution of a partitioned polygenic score (pPS) for risk of diabetes due to poor beta cell function was examined. Replication of the genetic findings was sought using data from the UK Biobank.

RESULTS

The prevalence of young-onset diabetes with normal BMI was 9.3% amongst white Europeans and 24-39% amongst Asian Indians. In Asian Indians with young-onset diabetes, after adjustment for family history of type 2 diabetes, sex, insulin sensitivity and HDL-cholesterol, stimulated C-peptide was 492 pmol/ml (IQR 353-616, p<0.0001) lower in lean compared with obese individuals. Asian Indians in our study, and South Asians from the UK Biobank, had a higher number of risk alleles than white Europeans. After weighting the pPS for beta cell function, Asian Indians have lower genetically determined beta cell function than white Europeans (p<0.0001). The pPS was associated with age of diagnosis in Asian Indians but not in white Europeans. The pPS explained 2% of the variation in clinically measured beta cell function, and 1.2%, 0.97%, and 0.36% of variance in age of diabetes amongst Asian Indians with normal BMI, or classified as overweight and obese BMI, respectively.

CONCLUSIONS/INTERPRETATION

The prevalence of lean BMI in young-onset diabetes is over two times higher in Asian Indians compared with white Europeans. This phenotype of lean, young-onset diabetes appears driven in part by lower beta cell function. We demonstrate that Asian Indians with diabetes also have lower genetically determined beta cell function.

WFS1 Gene-associated Diabetes Phenotypes and Identification of a Founder Mutation in Southern India

CONTEXT

Wolfram syndrome (WFS) is a rare autosomal recessive disorder characterized by juvenile-onset diabetes, diabetes insipidus, optic atrophy, deafness, and progressive neurodegeneration. However, due to the progressive nature of the disease and a lack of complete clinical manifestations, a confirmed diagnosis of WFS at the time of onset of diabetes is a challenge.

OBJECTIVE

With WFS1 rare heterozygous variants reported in diabetes, there is a need for comprehensive genetic screening strategies for the early diagnosis of WFS and delineating the phenotypic spectrum associated with the WFS1 gene variants in young-onset diabetes.

METHODS

This case series of 11 patients who were positive for WFS1 variants were identified with next-generation sequencing (NGS)-based screening of 17 genemonogenic diabetes panel. These results were further confirmed with Sanger sequencing.

RESULTS

9 out of 11 patients were homozygous for pathogenic/likely pathogenic variants in the WFS1 gene. Interestingly, 3 of these probands were positive for the novel WFS1 (NM_006005.3): c.1107_1108insA (p.Ala370Serfs*173) variant, and haplotype analysis suggested a founder effect in 3 families from Southern India. Additionally, we identified 2 patients with young-onset diabetes who were heterozygous for a likely pathogenic variant or a variant of uncertain significance in the WFS1 gene.

CONCLUSION

These results project the need for NGS-based parallel multigene testing as a tool for early diagnosis of WFS and identify heterozygous WFS1 variants implicated in young-onset diabetes.

Spatial and seasonal variations in coastal water characteristics at Kalpakkam, western Bay of Bengal, Southeast India: a multivariate statistical approach

A study was carried out in the coastal waters of Kalpakkam with the objectives to evaluate the seasonality in hydrobiological parameters in surface and bottom waters, and assess the anthropogenic stress and monsoonal flux on a spatiotemporal scale. The study covered an area of approximately 100 km² in the coastal environment. Relatively high values for pH, temperature, and TP were observed during the post-monsoon (POM) season. The monsoon (MON) season was linked with TN, ammonia, and DO concentrations as all these parameters have shown increased values during this season due to freshwater input. The summer (SUM) season was characterized by salinity, turbidity, nitrate, phosphate, and silicate, indicating a true marine environmental condition for plankton production. Principal component analysis (PCA) and cluster analysis (CA) indicated the presence of distinct coastal water masses with respect to seasons and sampling regions. The spatial pattern indicated the distinctness of the coastal nearshore water (CNW) and coastal offshore water (COW) with respect to water quality. The CNW was more dynamic due to direct external influence as compared to the relatively stable COW environment. Similarly, the study region in the northern part, which is continuously exposed to the backwater inputs and tourism activities, was statistically different from the southern part.

Multiple Sensory Modalities in Diurnal Geckos Is Associated with the Signaling Environment and Evolutionary Constraints

To be effective, animal signals need to be detectable in the environment, but their development and expression require resources. For multimodal communication, investment in elaborating traits in one modality could reduce the elaboration of traits in other modalities. In Cnemaspis geckos, chemical signals for conspecific communication pre-dated the evolution of visual signals, allowing us to examine the potential trade-off in signal elaboration and the current habitat associations with signal use. We studied five species of Cnemaspis and quantified visual (patch size, color characteristics) and chemical (secretory composition) traits in males, as well as key environmental parameters (temperature, humidity, light) in each of their habitats. Within species, we found some trade-off in the elaboration of signals, as the strength of several components in the visual and chemical modalities were negatively associated. Strength of some signal components in each modality was also independently associated with specific environmental parameters that affect their detection (visual traits) and persistence (chemical traits). Specifically, species with larger, brighter, and more saturated color patches were found in habitats where the brightness and chroma of light were lower. Furthermore, environments with higher substrate temperature and higher relative humidity harbored species that produced secretions with a higher percentage of saturated and aromatic compounds. Thus, the elaboration of multimodal signals in this group of Cnemaspis geckos seems to increase the efficiency of communication in the signaling-environment, but the strength of signals in different modalities is constrained by trade-offs in signal expression.

Genetic Risk Factors in Drug-Induced Liver Injury Due to Isoniazid-Containing Antituberculosis Drug Regimens

Drug-induced liver injury (DILI) is a complication of treatment with antituberculosis (TB) drugs, especially in isoniazid (INH)-containing regimens. To investigate genetic risk factors, we performed a genomewide association study (GWAS) involving anti-TB DILI cases (55 Indian and 70 European) and controls (1,199 Indian and 10,397 European). Most cases were treated with a standard anti-TB drug regimen; all received INH. We imputed single nucleotide polymorphism and HLA genotypes and performed trans-ethnic meta-analysis on GWAS and candidate gene genotypes. GWAS found one significant association (rs117491755) in Europeans only. For HLA, HLA-B*52:01 was significant (meta-analysis odds ratio (OR) 2.67, 95% confidence interval (CI) 1.63-4.37, P = 9.4 × 10^-5 ). For N-acetyltransferase 2 (NAT2), NAT2*5 frequency was lower in cases (OR 0.69, 95% CI 0.57-0.83, P = 0.01). NAT2*6 and NAT2*7 were more common, with homozygotes for NAT2*6 and/or NAT2*7 enriched among cases (OR 1.89, 95% CI 0.84-4.22, P = 0.004). We conclude HLA genotype makes a small contribution to TB drug-related DILI and that the NAT2 contribution is complex, but consistent with previous reports when differences in the metabolic effect of NAT2*5 compared with those of NAT2*6 and NAT2*7 are considered.

White blood cell detection and classification using Euler’s Jenks optimized multinomial logistic neural networks

Due to the wide acceptance of White Blood Cells (WBCs) in disease diagnosis, detection and classification of WBC are hot topic. Existing methodologies have some drawbacks such as significant degree of error, higher accuracy, time bound and higher misclassification rate. A WBCs detection and classification called, Jenks Optimized Logistic Convolutional Neural Network (JO-LCNN) method has proposed. Initally, Eulers Principal Axis is used as a convolution model to obtain a rotation invariant form of image by differentiating the background and RBCs, then eliminating them which leaves only the WBCs. By eliminating the wanton features, inherent features are detected contributing to minimum misclassification rate. According to above, Jenks Optimization function is used as a pooling model to obtain feature map for lower resolution. Therefore JO-LCNN is used for removing tiny objects in image and complete nuclei. Finally, Multinomial Logistic classifier is used to classify five types of classes by means of loss function and updating weight according to the loss function, therefore classifying with higher accuracy rate. Using LISC database for WBCs with different parameters as classification accuracy, false positive rate and time complexity are performed. Result shows that JO-LCNN, efficiently improves accuracy with less time, misclassification rate than the state-of-art methods.

PheGWAS: a new dimension to visualize GWAS across multiple phenotypes

MOTIVATION

PheGWAS was developed to enhance exploration of phenome-wide pleiotropy at the genome-wide level through the efficient generation of a dynamic visualization combining Manhattan plots from GWAS with PheWAS to create a 3D 'landscape'. Pleiotropy in sub-surface GWAS significance strata can be explored in a sectional view plotted within user defined levels. Further complexity reduction is achieved by confining to a single chromosomal section. Comprehensive genomic and phenomic coordinates can be displayed.

RESULTS

PheGWAS is demonstrated using summary data from Global Lipids Genetics Consortium GWAS across multiple lipid traits. For single and multiple traits PheGWAS highlighted all 88 and 69 loci, respectively. Further, the genes and SNPs reported in Global Lipids Genetics Consortium were identified using additional functions implemented within PheGWAS. Not only is PheGWAS capable of identifying independent signals but also provides insights to local genetic correlation (verified using HESS) and in identifying the potential regions that share causal variants across phenotypes (verified using colocalization tests).

AVAILABILITY AND IMPLEMENTATION

The PheGWAS software and code are freely available at (https://github.com/georgeg0/PheGWAS).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.