Children’s Hospital of Philadelphia researchers develop new RNA sequencing platform for diagnosing rare diseases
The technology, called STRIPE, enables cost-effective, scalable analysis of full-length RNA molecules to reveal disease-causing genetic variants and provide molecular diagnoses for previously undiagnosed patients Researchers from Children’s Hospital of Philadelphia (CHOP) developed a new RNA sequencing strategy that ...
longcallR – SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads
Understanding how genes are expressed is not just about which genes are turned on or off, but also how different versions of those genes are produced. A team led by researcher at the Dana-Farber Cancer Institute have developed a ...
scSNViz – visualization and analysis of cell-specific expressed SNVs
Single-cell RNA sequencing has transformed how researchers study complex tissues by revealing differences in gene expression from one cell to the next. But understanding variation goes beyond expression alone. Cells can differ in the genetic variants they express, including ...
Researchers develop deep-learning tools to transform cancer diagnosis and genomic research
Researchers from the Faculty of Engineering at The University of Hong Kong (HKU) have developed two innovative deep-learning algorithms, ClairS-TO and Clair3-RNA, that significantly advance genetic mutation detection in cancer diagnostics and RNA-based genomic studies. The pioneering research team, ...
RNA-MosaicHunter – accurate detection of somatic single-nucleotide variants from bulk RNA-seq data
Somatic variants are changes in the DNA that occur after conception, and they have been linked not only to cancer, but also to a range of developmental, aging-related, and neurological disorders. While many tools have been developed to find ...
Clair3-RNA – a deep learning-based small variant caller for long-read RNA sequencing data
Understanding how genes vary and which RNA isoforms are produced is key to modern biology and medicine. Long-read RNA sequencing makes this possible by reading entire RNA molecules in one piece, but it also introduces a challenge, the data ...
MUTE-Seq – ultrasensitive method to detect low-frequency cancer mutations
MUTE-Seq is a new liquid-biopsy method powered by an engineered ultra-precise CRISPR enzyme, FnCas9-AF2, which can distinguish single-base mismatches across all sgRNA positions with near-zero off-target activity. By selectively removing wild-type DNA before sequencing, it boosts true mutant signals ...
VarRNA – variant calling from RNA-Seq data
Understanding how genetic variants influence cancer is one of the major challenges in modern biomedical research. These variants can drive tumor growth, affect how a cancer behaves, and even determine how well a patient responds to treatment. In a ...
VarRNA – variant calling from RNA-Seq data
Understanding how genetic changes drive cancer is one of the biggest challenges in biomedical research. Traditionally, scientists look at DNA to find these changes, but now researchers are turning to RNA for even more answers. A team led by ...
FLAIR2 – detecting haplotype-specific transcript variation in long reads
RNA sequencing (RNA-seq) has transformed our ability to study RNA, the molecule that plays a crucial role in translating genetic information from...
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