Enhanced sensitivity of CpG island search and primer design based on predicted CpG island position. (May 2018)
- Record Type:
- Journal Article
- Title:
- Enhanced sensitivity of CpG island search and primer design based on predicted CpG island position. (May 2018)
- Main Title:
- Enhanced sensitivity of CpG island search and primer design based on predicted CpG island position
- Authors:
- Park, Hyun-Chul
Ahn, Eu-Ree
Jung, Ju Yeon
Park, Ji-Hye
Lee, Jee Won
Lim, Si-Keun
Kim, Won - Abstract:
- Abstract: DNA methylation has important biological roles, such as gene expression regulation, as well as practical applications in forensics, such as in body fluid identification and age estimation. DNA methylation often occurs in the CpG site, and methylation within the CpG islands affects various cellular functions and is related to tissue-specific identification. Several programs have been developed to identify CpG islands; however, the size, location, and number of predicted CpG islands are not identical due to different search algorithms. In addition, they only provide structural information for predicted CpG islands without experimental information, such as primer design. We developed an analysis pipeline package, CpGPNP, to integrate CpG island prediction and primer design. CpGPNP predicts CpG islands more accurately and sensitively than other programs, and designs primers easily based on the predicted CpG island locations. The primer design function included standard, bisulfite, and methylation-specific PCR to identify the methylation of particular CpG sites. In this study, we performed CpG island prediction on all chromosomes and compared CpG island search performance of CpGPNP with other CpG island prediction programs. In addition, we compared the position of primers designed for a specific region within the predicted CpG island using other bisulfite PCR primer programs. The primers designed by CpGPNP were used to experimentally verify the amplification of theAbstract: DNA methylation has important biological roles, such as gene expression regulation, as well as practical applications in forensics, such as in body fluid identification and age estimation. DNA methylation often occurs in the CpG site, and methylation within the CpG islands affects various cellular functions and is related to tissue-specific identification. Several programs have been developed to identify CpG islands; however, the size, location, and number of predicted CpG islands are not identical due to different search algorithms. In addition, they only provide structural information for predicted CpG islands without experimental information, such as primer design. We developed an analysis pipeline package, CpGPNP, to integrate CpG island prediction and primer design. CpGPNP predicts CpG islands more accurately and sensitively than other programs, and designs primers easily based on the predicted CpG island locations. The primer design function included standard, bisulfite, and methylation-specific PCR to identify the methylation of particular CpG sites. In this study, we performed CpG island prediction on all chromosomes and compared CpG island search performance of CpGPNP with other CpG island prediction programs. In addition, we compared the position of primers designed for a specific region within the predicted CpG island using other bisulfite PCR primer programs. The primers designed by CpGPNP were used to experimentally verify the amplification of the target region of markers for body fluid identification and age estimation. CpGPNP is freely available at http://forensicdna.kr/cpgpnp/ . … (more)
- Is Part Of:
- Forensic science international. Volume 34(2018)
- Journal:
- Forensic science international
- Issue:
- Volume 34(2018)
- Issue Display:
- Volume 34, Issue 2018 (2018)
- Year:
- 2018
- Volume:
- 34
- Issue:
- 2018
- Issue Sort Value:
- 2018-0034-2018-0000
- Page Start:
- 134
- Page End:
- 140
- Publication Date:
- 2018-05
- Subjects:
- CpG island -- Prediction -- Methylation -- Primer design -- CpG site
Forensic genetics -- Periodicals
Génétique légale -- Périodiques
Forensic genetics
Electronic journals
Periodicals
614.1 - Journal URLs:
- http://www.clinicalkey.com.au/dura/browse/journalIssue/18724973 ↗
http://www.clinicalkey.com/dura/browse/journalIssue/18724973 ↗
http://www.sciencedirect.com/science/journal/18724973 ↗
http://www.elsevier.com/journals ↗ - DOI:
- 10.1016/j.fsigen.2018.02.013 ↗
- Languages:
- English
- ISSNs:
- 1872-4973
- Deposit Type:
- Legaldeposit
- View Content:
- Available online (eLD content is only available in our Reading Rooms) ↗
- Physical Locations:
- British Library DSC - 3987.764050
British Library DSC - BLDSS-3PM
British Library HMNTS - ELD Digital store - Ingest File:
- 23116.xml