European researchers have identified a group of genes that behave as potential modifiers in cystic fibrosis (CF) patients with a F508del mutation in the CFTR gene — a discovery that may lead to new ways to treat the disease. Their study, “Transcriptomic profile ...
Read More »RNA-Seq solves patients’ diagnostic mysteries
Recent advances in large-scale clinical DNA sequencing have led to genetic diagnoses for many rare disease patients, but the diagnosis rate based on these approaches is still far from perfect. On average, clinicians are unable to provide a genetic diagnosis ...
Read More »Commonly used RNA-seq alignment and variant calling programs perform poorly in detecting intermediate long indels (>2 bases) that are clinically actionable
Driver somatic mutations are a hallmark of a tumor that can be used for diagnosis and targeted therapy. Mutations are primarily detected from tumor DNA. As dynamic molecules of gene activities, transcriptome profiling by RNA sequence (RNA-seq) is becoming increasingly ...
Read More »MiRME – A new method to detect a wide range of miRNA mutation and editing sites from small RNA HTS profiles
Various types of mutation and editing (M/E) events in microRNAs (miRNAs) can change the stabilities of pre-miRNAs and/or complementarities between miRNAs and their targets. Small RNA (sRNA) high-throughput sequencing (HTS) profiles can contain many mutated and edited miRNAs. Systematic detection ...
Read More »The dark matter of the cancer genome has been largely neglected
Cancer is a disease of the genome caused by oncogene activation and tumor suppressor gene inhibition. Deep sequencing studies including large consortia such as TCGA and ICGC identified numerous tumor-specific mutations not only in protein-coding sequences but also in non-coding ...
Read More »eSNV-detect – a computational system to identify expressed single nucleotide variants from transcriptome sequencing data
Rapid development of next generation sequencing technology has enabled the identification of genomic alterations from short sequencing reads. There are a number of software pipelines available for calling single nucleotide variants from genomic DNA but, no comprehensive pipelines to identify, ...
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