Contents
How is gene fusion detected?
We detect gene fusions of transcripts within and across chromosomes. This detection is based on paired-end reads that are uniquely mapped to transcripts from different loci. The approach consists of four steps. These are: filtering, clustering, inclusion of splice-junction information and scoring.
What does RNA-Seq detect?
In addition to mRNA transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as miRNA, tRNA, and ribosomal profiling. RNA-Seq can also be used to determine exon/intron boundaries and verify or amend previously annotated 5′ and 3′ gene boundaries.
What is RNA-Seq data used for?
RNA sequencing (RNA-Seq) uses the capabilities of high-throughput sequencing methods to provide insight into the transcriptome of a cell. Compared to previous Sanger sequencing- and microarray-based methods, RNA-Seq provides far higher coverage and greater resolution of the dynamic nature of the transcriptome.
Does RNA-Seq measure gene expression?
RNA-seq is a novel methodology based on NGS that enables to investigate differential gene expression at high resolution. In RNA-seq studies, gene expression levels are measured by counts, i.e. by the number of reads mapped on each gene.
What causes gene fusion?
A fusion gene is a hybrid gene formed from two previously independent genes. It can occur as a result of translocation, interstitial deletion, or chromosomal inversion.
Can DNA sequencing detect gene fusion?
Many bioinformatic approaches have been developed to detect fusion mutations including whole-genome sequencing, targeted-based hybridization capture, and transcriptome-based approaches. Here we describe the most commonly used experimental methods to sequence and identify gene fusions using either DNA or RNA.
Why is RNA-seq better than microarray?
“mRNA-Seq offers improved specificity, so it’s better at detecting transcripts, and specifically isoforms, than microarrays. It’s also more sensitive in detecting differential expression and offers increased dynamic range.”
Is RNA-seq reliable?
We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed for all examined platforms, including qPCR.
How do you analyze RNA-seq?
For most RNA‐seq studies, the data analyses consist of the following key steps [5, 6]: (1) quality check and preprocessing of raw sequence reads, (2) mapping reads to a reference genome or transcriptome, (3) counting reads mapped to individual genes or transcripts, (4) identification of differential expression (DE) …
Is translocation a fusion?
A fusion gene is a hybrid gene formed from two previously independent genes. It can occur as a result of translocation, interstitial deletion, or chromosomal inversion. Fusion genes have been found to be prevalent in all main types of human neoplasia.
What is NTRK gene fusion?
jeen FYOO-zhun) A mutation (change) that occurs when a piece of the chromosome containing a gene called NTRK breaks off and joins with a gene on another chromosome. NTRK gene fusions lead to abnormal proteins called TRK fusion proteins, which may cause cancer cells to grow.
How is RNA sequencing used to detect fusion genes?
The advent of RNA sequencing (RNA-seq) technology allows us to efficiently discover novel fusion genes. Many tools have been developed for detecting fusion transcripts using RNA-seq data, and their comparisons are available in several recent publications [ 9, 10 ].
How are two types of RNA seq used for chimeric junction detection?
In addition, the use of one or two kinds of reads for chimeric junction detection allows one to define 3 classes of approaches: (1) the whole paired-end approach, (2) the direct fragmentation approach, and (3) the paired-end + fragmentation approach [ 41 ]. Two types of RNA-seq reads for chimera detection.
Which is an important application of RNA-Seq?
Nowadays, RNA-Sequencing technology 1 is playing an important role in characterizing the whole transcriptome in any given sample. Quantification of gene expression, identification of novel transcripts and detection of fusion transcripts are the major applications of RNA-Seq.
How is chimpipe used to detect fusion genes?
ChimPipe combines discordant paired-end reads and split-reads to detect any kind of chimeras, including those originating from polymerase read-through, and shows an excellent trade-off between sensitivity and precision. The chimeras found by ChimPipe can be validated in-vitro with high accuracy.