Publications by authors named "Sravya Bhamidipati"
Background: Copy number variation (CNV) is a class of genomic Structural Variation (SV) that underlie genomic disorders and can have profound implications for health. Short-read genome sequencing (sr-GS) enables CNV calling for genomic intervals of variable size and across multiple phenotypes. However, unresolved challenges include an overwhelming number of false-positive calls due to systematic biases from non-uniform read coverage and collapsed calls resulting from the abundance of paralogous segments and repetitive elements in the human genome.
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- - Respiratory syncytial virus (RSV) and human noroviruses (HuNoV) are major pathogens that cause respiratory and gastrointestinal infections respectively, making it essential to generate full-length genome sequences for studying their diversity and tracking variants.
- - The study developed oligonucleotide probe sets from numerous viral isolate sequences, which were utilized in a capture enrichment sequencing workflow to analyze samples, significantly improving the quality of viral genome recovery.
- - The results showed that over 99% of RSV genomes and over 96% of HuNoV genomes were complete post-capture, demonstrating the effectiveness of this method for comprehensive genome sequencing and monitoring emerging variants.
The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a complex genomic rearrangement (CGR). Although it has been identified as an important pathogenic DNA mutation signature in genomic disorders and cancer genomes, its architecture remains unresolved. Here, we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the DNA of 24 patients identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted structural variant (SV) haplotypes.
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- Researchers compiled a comprehensive catalog of 355,667 structural variants (SVs) from DNA data, with over half being novel, to better understand the relationship between SVs and diseases.
- The study involved rigorous methods to ensure high-quality variant identification, showing over 90% accuracy compared to previous genetic assemblies.
- This catalog reveals significant connections between SVs and various health traits, identifying 690 specific regions that may influence medically relevant genes, providing a crucial resource for disease research.
Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.
View Article and Find Full Text PDFBackground: Cryptosporidium parvum is an apicomplexan parasite commonly found across many host species with a global infection prevalence in human populations of 7.6%. Understanding its diversity and genomic makeup can help in fighting established infections and prohibiting further transmission.
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