What are junction spanning reads?
A read that spans a junction must have a match in the reference genome that is not shorter than its half length. Such a match then provides a seeding that can be used to identify a small genomic region for the search of the corresponding junction.
What is fusion detection?
Targeted Gene Fusion Detection Technology for NGS. A gene fusion is a hybrid gene formed from two previously independent genes. Fluorescence in situ hybridization (FISH) has been the gold standard for fusion detection, however it can only detect single mutations at a time and cannot detect novel fusion gene partners.
What are spanning reads?
Spanning reads contain one read located in different genes, while split reads indicates a single read overlapping on two different genes. The final step contains filtering and/or scoring systems to remove false positive fusion candidates.
How do you identify gene fusion?
To detect fusion genes, the current pipelines heavily depend on individual unmapped reads which harbor the fusion boundaries or discordant paired-end reads, in which each reads align against different genes, leading to neglecting the mate reads of unmapped reads or reads that span fusion boundaries.
What is a splice junction?
Splice-junction sequence signals are strongly conserved structural components of eukaryotic genes. These sequences border exon/intron junctions and aid in the process of removing introns by the RNA splicing machinery.
What are intron spanning reads?
**An intron-spanning read is an RNA read that originates from a single region of a transcript but it maps to two locations on the genome indicating the splice junction of two exons in the transcript.
What is a chimeric RNA unit?
Chimeric RNA, sometimes referred to as a fusion transcript, is composed of exons from two or more different genes that have the potential to encode novel proteins. These mRNAs are different from those produced by conventional splicing as they are produced by two or more gene loci.
What is RNA fusion?
Fusion transcript is a chimeric RNA encoded by a fusion gene or by two different genes by subsequent trans-splicing. Certain fusion transcripts are commonly produced by cancer cells, and detection of fusion transcripts is part of routine diagnostics of certain cancer types.
What is a split read?
Split reads: When one portion of an NGS read map to one location and other portion of the same read map to a different location of a genome. When the read both the portions is of equal length, this is called a balanced split.
What is transcriptional fusion?
Today fusions like these hisD fusions are often called transcriptional fusions. Such fusions do not result in the production of a hybrid protein but rather just place the gene(s) in question under the control of a different promoter.
How does gene fusion work?
Gene fusions are hybrid genes formed when two previously independent genes become juxtaposed. The fusion can result from structural rearrangements like translocations and deletions, transcription read-through of neighboring genes (1–3), or the trans- and cis-splicing of pre-mRNAs (4–8) (Figure 1).
What are RNA fusions?
How is fusionmap used to detect fusion genes?
Using FusionMap to characterize fusion genes in K562 chronic myeloid leukemia cell line, we further demonstrated its accuracy in fusion detection in both single-end RNA-Seq and gDNA-Seq datasets. These combined results show that FusionMap provides an accurate and systematic solution to detecting fusion events through junction-spanning reads.
How is fusionmap used in a NGS dataset?
FusionMap is designed to detect and align fusion junction-spanning reads to the genome directly. It can be applied to both paired-end and single-end NGS dataset starting from raw reads files or aligned BAM files (BAM files that keep unmapped reads). To save time, we only illustrate all following examples using Linux
How is fusionmap used in RNA Seq studies?
FusionMap can be applied to detect fusion junctions in both single- and paired-end datasets from either gDNA-Seq or RNA-Seq studies. Stop reading this article if you have an ArrayStudio License; you can run fusion detection easily through its GUI. Please read ArrayStudio guide and Oshell guide . Also Check FusionMap Change Log .
Which is the best definition of bioinformatics?
What is Bioinformatics? Bioinformatics is a dynamic and emerging field of science which deals with an amalgamation of several subjects. These subjects include Biology, Chemistry, Mathematics, Statistics and Computer Science. Bioinformatics focuses on developing new technologies in the fields of medicine, research and biotechnology.