Biomedical subjects

Lata Rani

Publications and source records attributed to Lata Rani.

3 recordsLinked to original sources

PubMed2026

CHITRA: an interactive visualization tool for comparative genomic rearrangement analysis.

MOTIVATION: The increasing availability of chromosome-scale genome assemblies has fuelled a renewed interest in studying chromosomal evolution and rearrangements. Synteny visualization plays a critical role in understanding genome organization, structural variations, and evolutionary relationships. However, existing tools often have steep learning curves, produce static plots, or are limited in their ability to analyse multiple genomes simultaneously. There is a growing need for an intuitive and interactive visualization tool that can effectively explore syntenic relationships and chromosomal rearrangements. RESULTS: Here, we present CHITRA, a web-based interactive tool designed to visualize synteny blocks, chromosomal rearrangements, and breakpoints in both linear and circular styles. CHITRA-enables real-time exploration of genome structural variations with an intuitive graphical interface, customizable visualization options, and high-resolution export capabilities for publication-ready figures. The tool supports chromosome- and scaffold-level assemblies and allows users to filter, highlight, and interactively examine syntenic relationships. AVAILABILITY AND IMPLEMENTATION: CHITRA is freely available at https://chitra.bioinformaticsonline.com/, with comprehensive documentation at https://chitra.bioinformaticsonline.com/docs. The source code is open-source and accessible on GitHub at https://github.com/pranjalpruthi/CHITRA.

Journal Article↗

PubMed2025

Genomic Alterations in Multiple Myeloma: A Comprehensive Landscape.

UNLABELLED: Multiple myeloma (MM) is a biologically heterogeneous plasma cell malignancy in which cytogenetic abnormalities play a key role in disease prognosis. This study evaluates the spectrum of genomic aberrations in newly diagnosed multiple myeloma (NDMM) patients, with a focus on high-risk cytogenetic profiles, including double-hit (DHMM), and triple-hit multiple myeloma (THMM). This is a retrospective analysis of NDMM patients, reviewing clinical and laboratory data for baseline characteristics, cytogenetics, therapy, and outcomes. Patients were categorized based on the cytogenetic abnormalities. Double-hit MM was defined by the coexistence of two high-risk abnormalities and triple-hit MM was defined by coexistence of three or more high-risk abnormalities. Survival outcomes were assessed using Kaplan-Meier analysis and Cox regression models using SigmaPlot (version 15). A total of 314 NDMM cases (205 Male: 109 Female; median age 58 years) enrolled between 2014 and 2021 were evaluated. Using the Revised International Staging System (R2-ISS), most patients were in stage 2 (41.1%) and stage 3 (38.2%). Cytogenetic analysis revealed one or more high-risk abnormalities in 43% of cases. Among the high-risk group, one, two and three or more high-risk abnormalities were observed in 89 (28%), 35 (11%), and 11 (4%) patients, respectively. THMM cases exhibited the poorest outcomes [median overall survival (OS):7 months], in comparison to DHMM (OS: 33 months), SHMM (OS: 40 months), and patients without high-risk features (OS: 60 months). Cox regression analysis confirmed that THMM patients had a 3.6-fold increased risk of death (HR: 3.677; 95% CI: 2.219-7.915; p < 0.001) and 4-fold increased risk of progression (HR: 4.191; 95% CI: 1.897-7.126; p < 0.001) compared to patients without any high-risk abnormalities. Among 67 patients undergoing autologous stem cell transplant (ASCT), high risk abnormalities were significantly associated with shorter OS (HR: 2.409; 95% CI: 1.094-5.291; p = 0.029, 111 months for ASCT without high-risk vs. 78 months for ASCT with high- risk abnormalities) and shortened PFS (HR: 2.379; 95% CI: 1.285-4.403; p = 0.006, 85 months for ASCT without high-risk vs. 34 months with high-risk abnormalities). Double and triple-hit MM constitute 14.6% of NDMM cases, indicating poor survival and early disease progression. Comprehensive cytogenetic profiling at diagnosis and post-ASCT has the potential to improve risk stratification and guide individualized treatment strategies for high-risk MM patients. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s12288-025-02284-5.

Cytogenetic↗

PubMed2023

Phylogeny and evolution of SARS-CoV-2 during Delta and Omicron variant waves in India.

SARS-CoV-2 evolution has continued to generate variants, responsible for new pandemic waves locally and globally. Varying disease presentation and severity has been ascribed to inherent variant characteristics and vaccine immunity. This study analyzed genomic data from 305 whole genome sequences from SARS-CoV-2 patients before and through the third wave in India. Delta variant was reported in patients without comorbidity (97%), while Omicron BA.2 was reported in patients with comorbidity (77%). Tissue adaptation studies brought forth higher propensity of Omicron variants to bronchial tissue than lung, contrary to observation in Delta variants from Delhi. Study of codon usage pattern distinguished the prevalent variants, clustering them separately, Omicron BA.2 isolated in February grouped away from December strains, and all BA.2 after December acquired a new mutation S959P in ORF1b (44.3% of BA.2 in the study) indicating ongoing evolution. Loss of critical spike mutations in Omicron BA.2 and gain of immune evasion mutations including G142D, reported in Delta but absent in BA.1, and S371F instead of S371L in BA.1 could explain very brief period of BA.1 in December 2021, followed by complete replacement by BA.2. Higher propensity of Omicron variants to bronchial tissue, probably ensured increased transmission while Omicron BA.2 became the prevalent variant possibly due to evolutionary trade-off. Virus evolution continues to shape the epidemic and its culmination.Communicated by Ramaswamy H. Sarma.

SARS-CoV-2↗