PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data

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Abrahamsson, SannaGothenburg University,Göteborgs universitet,Core Facilities, Bioinformatics,Core Facilities, Bioinformatics (author)

PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data

Article/chapterEnglish2022

Publisher, publication year, extent ...

2022-02-03
Springer Science and Business Media LLC,2022

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LIBRIS-ID:oai:gup.ub.gu.se/314161
https://gup.ub.gu.se/publication/314161URI
https://doi.org/10.1186/s12859-022-04583-4DOI

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Language:English

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Subject category:ref swepub-contenttype
Subject category:art swepub-publicationtype

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Background: Processed pseudogenes (PΨgs) are disabled gene copies that are transcribed and may affect expression of paralogous genes. Moreover, their insertion in the genome can disrupt the structure or the regulatory region of a gene, affecting its expression level. These events have been identified as occurring mutations during cancer development, thus being able to identify PΨgs and their location will improve their impact on diagnostic testing, not only in cancer but also in inherited disorders. Results: We have implemented PΨFinder (P-psy-finder), a tool that identifies PΨgs, annotates known ones and predicts their insertion site(s) in the genome. The tool screens alignment files and provides user-friendly summary reports and visualizations. To demonstrate its applicability, we scanned 218 DNA samples from patients screened for hereditary colorectal cancer. We detected 423 PΨgs distributed in 96% of the samples, comprising 7 different parent genes. Among these, we confirmed the well-known insertion site of the SMAD4-PΨg within the last intron of the SCAI gene in one sample. While for the ubiquitous CBX3-PΨg, present in 82.6% of the samples, we found it reversed inserted in the second intron of the C15ORF57 gene. Conclusions: PΨFinder is a tool that can automatically identify novel PΨgs from DNA sequencing data and determine their location in the genome with high sensitivity (95.92%). It generates high quality figures and tables that facilitate the interpretation of the results and can guide the experimental validation. PΨFinder is a complementary analysis to any mutational screening in the identification of disease-causing mutations within cancer and other diseases.

Subject headings and genre

MEDICIN OCH HÄLSOVETENSKAP Medicinsk bioteknologi Biomedicinsk laboratorievetenskap/teknologi hsv//swe
MEDICAL AND HEALTH SCIENCES Medical Biotechnology Biomedical Laboratory Science/Technology hsv//eng
NATURVETENSKAP Data- och informationsvetenskap Bioinformatik hsv//swe
NATURAL SCIENCES Computer and Information Sciences Bioinformatics hsv//eng
C15ORF57
CBX3
Colorectal cancer
DNA sequencing
Processed pseudogenes
SCAI
SMAD4

Added entries (persons, corporate bodies, meetings, titles ...)

Eiengård, FridaGothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för laboratoriemedicin,Department of Laboratory Medicine (author)
Rohlin, AnnaGothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för laboratoriemedicin,Department of Laboratory Medicine(Swepub:gu)xrohan (author)
Dávila López, MarcelaGothenburg University,Göteborgs universitet,Core Facilities, Bioinformatics,Core Facilities, Bioinformatics(Swepub:gu)xdavma (author)
Göteborgs universitetCore Facilities, Bioinformatics (creator_code:org_t)

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In:BMC Bioinformatics: Springer Science and Business Media LLC231471-2105

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