SEGF: A Novel Method for Gene Fusion Detection from Single-End Next-Generation Sequencing Data

Genes
Hai XuShidong Xu

Abstract

With the development and application of next-generation sequencing (NGS) and target capture technology, the demand for an effective analysis method to accurately detect gene fusion from high-throughput data is growing. Hence, we developed a novel fusion gene analyzing method called single-end gene fusion (SEGF) by starting with single-end DNA-seq data. This approach takes raw sequencing data as input, and integrates the commonly used alignment approach basic local alignment search tool (BLAST) and short oligonucleotide analysis package (SOAP) with stringent passing filters to achieve successful fusion gene detection. To evaluate SEGF, we compared it with four other fusion gene discovery analysis methods by analyzing sequencing results of 23 standard DNA samples and DNA extracted from 286 lung cancer formalin fixed paraffin embedded (FFPE) samples. The results generated by SEGF indicated that it not only detected the fusion genes from standard samples and clinical samples, but also had the highest accuracy and sensitivity among the five compared methods. In addition, SEGF was capable of detecting complex gene fusion types from single-end NGS sequencing data compared with other methods. By using SEGF to acquire gene fusion inform...Continue Reading

References

Jan 2, 2008·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Kentaro InamuraYuichi Ishikawa
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 6, 2009·Bioinformatics·Ruiqiang LiJun Wang
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Feb 14, 2012·Nature Medicine·Kengo TakeuchiYuichi Ishikawa
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Jan 15, 2015·Nucleic Acids Research·Melanie SchirmerChristopher Quince

❮ Previous
Next ❯

Citations

Jul 31, 2020·Diagnostics·Rossella Bruno, Gabriella Fontanini

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
DNA-seq
Illumina sequencing

Software Mentioned

Fusion and
SEGF
MEM
CREST
Short Oligonucleotide Analysis Package ( SOAP )
BLAST
SOAP
ALN
Chromosomal Translocation Enumeration and Recovery Algorithm (...
BWA

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Methods : a Companion to Methods in Enzymology
Ditte AndreasenPeter Mouritzen
Methods in Molecular Biology
Emma M Quinn, Ross McManus
© 2022 Meta ULC. All rights reserved