Biology subjects

Rudy, G.

Publications and source records attributed to Rudy, G..

3 recordsLinked to original sources

bioRxiv2024

Analyzing Performance of Twist Bioscience Exome Enrichment with Spike-in CNV Backbone Panels at Various Probe Densities Leveraging Golden Helix VS-CNV Analysis Software

Clinical Whole Exome Sequencing (WES) offers a high diagnostic yield test by detecting pathogenic variants in all coding genes of the human genome. WES is poised to consolidate multiple genetic tests by accurately identifying Copy Number Variation (CNV) events, typically necessitating microarray analysis. However, standard commercial exome kits are typically limited to targeting exon coding regions, leaving significant gaps in coverage between genes, which could hinder comprehensive CNV detection. To convert microarray CNV calling with NGS, advances in both assay design and computational methods are needed. Addressing the need for comprehensive coverage, Twist Bioscience has developed an enhanced Exome 2.0 Plus Comprehensive Exome Spike-in panel with added CNV "backbone" probes. These probes target common SNPs polymorphic in multiple populations and are evenly distributed in the intergenic and intronic regions, with three varying densities at 25 kb, 50 kb, and 100 kb intervals from highest to lowest resolution respectively. Concurrently, Golden Helix has developed a multi-modal CNV caller designed specifically for target-capture NGS data to detect single-exon to whole-chromosome aneuploidy CNV events. This study evaluates the combined efficacy of the backbone-probe enhanced exome capture kit and VS-CNV 2.6 in identifying known CNVs using the Coriell CNVPANEL01 reference set. The integration of the enhanced capture kit with VS-CNV 2.6 achieved a 100% sensitivity rate for the detection of known CNV events at all three probe densities. The application of best-practice quality metrics, annotations, and filters was shown to have a minimal impact on this high sensitivity. These findings underscore the potential of the augmented Twist Exome in tandem with the VS-CNV caller and VarSeqs annotation and filtering capabilities. This combination presents a promising alternative to conventional microarray assays, potentially consolidating WES and CNV into a single assay obviating the need for additional testing in clinical CNV detection. The studys results advocate for the implementation of this integrated approach as a more efficient and equally sensitive method for CNV analysis in a clinical setting.

bioinformatics↗

bioRxiv2023

Phage DNA polymerase prevents on-target damage and enhances precision of CRISPR editing

Common unintended chromosomal alterations induced by CRISPR/Cas9 in mammalian cells, particularly on-target large deletions and chromosomal translocations present a safety challenge for genome editing. Base editing and prime editing that can precisely introduce desired edits without double-stranded breaks and exogenous DNA templates face their own challenges. Thus, there is still an unmet need to develop safer and more efficient editing tools. We screened diverse DNA polymerases of distinct origins and identified T4 DNA polymerase derived from phage T4 that greatly prevents undesired on-target large deletions and chromosomal translocations while increasing the proportion of precise 1- to 2-base-pair insertions generated during CRISPR/Cas9 editing (termed CasPlus). CasPlus induced substantially fewer on-target large deletions while increasing the efficiency to correct common frameshift mutations in DMD (exon 52 deletion) and restored higher level of dystrophin expression than Cas9-alone in human induced pluripotent stem cell-derived cardiomyocytes. Moreover, CasPlus can greatly reduce the frequency of on-target large deletions in mouse germline editing. In multiplexed guide RNAs mediating gene editing, CasPlus represses chromosomal translocations while maintaining gene disruption efficiency that is higher or comparable to Cas9 in primary human T cells. Therefore, CasPlus offers a safer and more efficient gene editing strategy to treat pathogenic variants or to introduce genetic modifications in human applications.

bioengineering↗

bioRxiv2020

Analysis of 46,046 SARS-CoV-2 whole-genomes leveraging principal component analysis (PCA)

Since the beginning of the global SARS-CoV-2 pandemic, there have been a number of efforts to understand the mutations and clusters of genetic lines of the SARS-CoV-2 virus. Until now, phylogenetic analysis methods have been used for this purpose. Here we show that Principal Component Analysis (PCA), which is widely used in population genetics, can not only help us to understand existing findings about the mutation processes of the virus, but can also provide even deeper insights into these processes while being less sensitive to sequencing gaps. Here we describe a comprehensive analysis of a 46,046 SARS-CoV-2 genome sequence dataset downloaded from the GISAID database in June of this year. SummaryPCA provides deep insights into the analysis of large data sets of SARS-CoV-2 genomes, revealing virus lineages that have thus far been unnoticed.

bioinformatics↗