Coupled models of genomic surveillance and evolving pandemics with applications for timely public health interventions.

Disease surveillance systems provide early warnings of disease outbreaks before they become public health emergencies. However, pandemics containment would be challenging due to the complex immunity landscape created by multiple variants. Genomic surveillance is critical for detecting novel variants with diverse characteristics and importation/emergence times. Yet, a systematic study incorporating genomic monitoring, situation assessment, and intervention strategies is lacking in the literature. We formulate an integrated computational modeling framework to study a realistic course of action based on sequencing, analysis, and response. We study the effects of the second variant's importation time, its infectiousness advantage and, its cross-infection on the novel variant's detection time, and the resulting intervention scenarios to contain epidemics driven by two-variants dynamics. Our results illustrate the limitation in the intervention's effectiveness due to the variants' competing dynamics and provide the following insights: i) There is a set of importation times that yields the worst detection time for the second variant, which depends on the first variant's basic reproductive number; ii) When the second variant is imported relatively early with respect to the first variant, the cross-infection level does not impact the detection time of the second variant. We found that depending on the target metric, the best outcomes are attained under different interventions' regimes. Our results emphasize the importance of sustained enforcement of Non-Pharmaceutical Interventions on preventing epidemic resurgence due to importation/emergence of novel variants. We also discuss how our methods can be used to study when a novel variant emerges within a population.

Consensus guidelines on management of oral potentially malignant disorders.

Oral cancer is usually preceded by oral potentially malignant disorders (OPMDs) and early detection can downstage the disease. The majority of OPMDs are asymptomatic in early stages and can be detected on routine oral examination. Though only a proportion of OPMDs may transform to oral squamous cell carcinoma (OSCC), they may serve as a surrogate clinical lesion to identify individuals at risk of developing OSCC. Currently, there is a scarcity of scientific evidence on specific interventions and management of OPMDs and there is no consensus regarding their management. A consensus meeting with a panel of experts was convened to frame guidelines for clinical practices and recommendations for management strategies for OPMDs. A review of literature from medical databases was conducted to provide the best possible evidence and provide recommendations in management of OPMDs.

Reimagining India's Health System: Technology Levers for Universal Health Care.

Just as the COVID-19 pandemic highlighted the inadequacies of our current health systems and rekindled the debate around universal health care, the Lancet Citizens' Commission on Reimagining India's Health System was launched in late 2020. As a part of the commission, we articulated how technology can enable universal health care. We begin by stating the foundational values-a set of normative statements-that should underpin the use of technology in our health systems. Then, after summarising the paradigm shifts necessary to achieve citizen-centred universal health care, we articulate five 'technology levers' to enable those shifts. Finally, we describe the intersections and synergies between technology and the other pillars of health systems, namely, human resources, financing, governance and citizens' engagement.

Comparison of Fixed- and Variable-Loop Button Fixation in Arthroscopic Anterior Cruciate Ligament Reconstruction.

Introduction With the advent of fixed- and variable-loop suspensory fixation devices for arthroscopic anterior cruciate ligament (ACL) reconstruction, a maximum number of grafts can be placed within the femoral tunnel. Although several biomechanical studies have been conducted comparing these two devices, only a few comparative clinical studies are available. This study was conducted to compare the functional outcomes of arthroscopic ACL reconstruction using fixed-loop devices with those of variable-loop devices by determining their effect on graft laxity clinical assessment and patient-reported outcome scores. Methodology Out of 32 patients (27 males and five females) who underwent primary ACL reconstruction using tripled hamstring autograft, fixed- and variable-loop devices were used for 13 and 19 patients, respectively. Thirteen patients in each group were evaluated over a period of one year using the Lysholm knee score. Six patients in the variable-loop group had only six months of follow-up. Anterior drawer and Lachman tests were performed at six-month and one-year follow-ups, respectively. Results The mean ages of patients in the fixed- and variable-loop groups were 34.5[Formula: see text]11 and 34.1[Formula: see text]9.1 years, respectively. The Lysholm knee score at six weeks was fair in 7.7% of the patients in the fixed-loop group when compared to 52.6% of those in the variable-loop group (p<0.05). All the other parameters were comparable between the two groups. One patient in each group had ligament laxity at six-month and one-year follow-up, respectively. Conclusion This study showed no statistically significant difference in graft laxity or functional outcomes of arthroscopic ACL reconstruction with fixed- and variable-loop devices, except for a better patient-reported outcome score in the variable-loop group at six weeks of follow-up. Hence, there is a need for more comparative studies in this direction.

Validation of whole genome sequencing from dried blood spots.

BACKGROUND: Dried blood spots (DBS) are a relatively inexpensive source of nucleic acids and are easy to collect, transport, and store in large-scale field surveys, especially in resource-limited settings. However, their performance in whole-genome sequencing (WGS) relative to that of venous blood DNA has not been analyzed for various downstream applications. METHODS: This study compares the WGS performance of DBS paired with venous blood samples collected from 12 subjects. RESULTS: Results of standard quality checks of coverage, base quality, and mapping quality were found to be near identical between DBS and venous blood. Concordance for single-nucleotide variants, insertions and deletions, and copy number variants was high between these two sample types. Additionally, downstream analyses typical of population-based studies were performed, such as mitochondrial heteroplasmy detection, haplotype analysis, mitochondrial copy number changes, and determination of telomere lengths. The absolute mitochondrial copy number values were higher for DBS than for venous blood, though the trend in sample-to-sample variation was similar between DBS and blood. Telomere length estimates in most DBS samples were on par with those from venous blood. CONCLUSION: DBS samples can serve as a robust and feasible alternative to venous blood for studies requiring WGS analysis.

Health Heatmap of India: An Open Data Platform.

Health Heatmap of India is an open data platform built for bringing together data from diverse sources and facilitating visualization, analysis, and insight building from such data. In this paper, we describe the context and need for such an open data platform and describe the technical aspects of building it. The beta site of the portal is available at https://healthheatmapindia.org.

Multi-gene testing in neurological disorders showed an improved diagnostic yield: data from over 1000 Indian patients.

BACKGROUND: Neurological disorders are clinically heterogeneous group of disorders and are major causes of disability and death. Several of these disorders are caused due to genetic aberration. A precise and confirmatory diagnosis in the patients in a timely manner is essential for appropriate therapeutic and management strategies. Due to the complexity of the clinical presentations across various neurological disorders, arriving at an accurate diagnosis remains a challenge. METHODS: We sequenced 1012 unrelated patients from India with suspected neurological disorders, using TruSight One panel. Genetic variations were identified using the Strand NGS software and interpreted using the StrandOmics platform. RESULTS: We were able to detect mutations in 197 genes in 405 (40%) cases and 178 mutations were novel. The highest diagnostic rate was observed among patients with muscular dystrophy (64%) followed by leukodystrophy and ataxia (43%, each). In our cohort, 26% of the patients who received definitive diagnosis were primarily referred with complex neurological phenotypes with no suggestive diagnosis. In terms of mutations types, 62.8% were truncating and in addition, 13.4% were structural variants, which are also likely to cause loss of function. CONCLUSION: In our study, we observed an improved performance of multi-gene panel testing, with an overall diagnostic yield of 40%. Furthermore, we show that NGS (next-generation sequencing)-based testing is comprehensive and can detect all types of variants including structural variants. It can be considered as a single-platform genetic test for neurological disorders that can provide a swift and definitive diagnosis in a cost-effective manner.

Organization for rare diseases India (ORDI) - addressing the challenges and opportunities for the Indian rare diseases' community.

In order to address the unmet needs and create opportunities that benefit patients with rare disease in India, a group of volunteers created a not-for-profit organization named Organization for Rare Diseases India (ORDI; www.ordindia.org). ORDI plans to represent the collective voice and advocate the needs of patients with rare diseases and other stakeholders in India. The ORDI team members come from diverse backgrounds such as genetics, molecular diagnostics, drug development, bioinformatics, communications, information technology, patient advocacy and public service. ORDI builds on the lessons learned from numerous similar organizations in the USA, European Union and disease-specific rare disease foundations in India. In this review, we provide a background on the landscape of rare diseases and the organizations that are active in this area globally and in India. We discuss the unique challenges in tackling rare diseases in India, and highlight the unmet needs of the key stakeholders of rare diseases. Finally, we define the vision, mission, goals and objectives of ORDI, identify the key developments in the health care context in India and welcome community feedback and comments on our approach.

A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes.

We collaborate in a research program aimed at creating a rigorous framework, experimental infrastructure, and computational environment for understanding, experimenting with, manipulating, and modifying a diverse set of fundamental biological processes at multiple scales and spatio-temporal modes. The novelty of our research is based on an approach that (i) requires coevolution of experimental science and theoretical techniques and (ii) exploits a certain universality in biology guided by a parsimonious model of evolutionary mechanisms operating at the genomic level and manifesting at the proteomic, transcriptomic, phylogenic, and other higher levels. Our current program in "systems biology" endeavors to marry large-scale biological experiments with the tools to ponder and reason about large, complex, and subtle natural systems. To achieve this ambitious goal, ideas and concepts are combined from many different fields: biological experimentation, applied mathematical modeling, computational reasoning schemes, and large-scale numerical and symbolic simulations. From a biological viewpoint, the basic issues are many: (i) understanding common and shared structural motifs among biological processes; (ii) modeling biological noise due to interactions among a small number of key molecules or loss of synchrony; (iii) explaining the robustness of these systems in spite of such noise; and (iv) cataloging multistatic behavior and adaptation exhibited by many biological processes.