Advanced search
1 file | 2.38 MB Add to list

WisecondorX : improved copy number detection for routine shallow whole-genome sequencing

Lennart Raman (UGent) , Annelies Dheedene (UGent) , Matthias De Smet (UGent) , Jo Van Dorpe (UGent) and Björn Menten (UGent)
(2019) NUCLEIC ACIDS RESEARCH. 47(4). p.1605-1614
Author
Organization
Abstract
Shallow whole-genome sequencing to infer copy number alterations (CNAs) in the human genome is rapidly becoming the method par excellence for routine diagnostic use. Numerous tools exist to deduce aberrations from massive parallel sequencing data, yet most are optimized for research and often fail to redeem paramount needs in a clinical setting. Optimally, a read depth-based analytical software should be able to deal with single-end and low-coverage datathis to make sequencing costs feasible. Other important factors include runtime, applicability to a variety of analyses and overall performance. We compared the most important aspect, being normalization, across six different CNA tools, selected for their assumed ability to satisfy the latter needs. In conclusion, WISECONDOR, which uses a within-sample normalization technique, undoubtedly produced the best results concerning variance, distributional assumptions and basic ability to detect true variations. Nonetheless, as is the case with every tool, WISECONDOR has limitations, which arise through its exclusiveness for non-invasive prenatal testing. Therefore, this work presents WisecondorX in addition, an improved WISECONDOR that enables its use for varying types of applications. WisecondorX is freely available at https://github.com/CenterForMedicalGeneticsGhent/WisecondorX.
Keywords
IDENTIFICATION, DIAGNOSIS, REGIONS

Downloads

  • gky1263.pdf
    • full text
    • |
    • open access
    • |
    • PDF
    • |
    • 2.38 MB

Citation

Please use this url to cite or link to this publication:

MLA
Raman, Lennart, et al. “WisecondorX : Improved Copy Number Detection for Routine Shallow Whole-Genome Sequencing.” NUCLEIC ACIDS RESEARCH, vol. 47, no. 4, 2019, pp. 1605–14.
APA
Raman, L., Dheedene, A., De Smet, M., Van Dorpe, J., & Menten, B. (2019). WisecondorX : improved copy number detection for routine shallow whole-genome sequencing. NUCLEIC ACIDS RESEARCH, 47(4), 1605–1614.
Chicago author-date
Raman, Lennart, Annelies Dheedene, Matthias De Smet, Jo Van Dorpe, and Björn Menten. 2019. “WisecondorX : Improved Copy Number Detection for Routine Shallow Whole-Genome Sequencing.” NUCLEIC ACIDS RESEARCH 47 (4): 1605–14.
Chicago author-date (all authors)
Raman, Lennart, Annelies Dheedene, Matthias De Smet, Jo Van Dorpe, and Björn Menten. 2019. “WisecondorX : Improved Copy Number Detection for Routine Shallow Whole-Genome Sequencing.” NUCLEIC ACIDS RESEARCH 47 (4): 1605–1614.
Vancouver
1.
Raman L, Dheedene A, De Smet M, Van Dorpe J, Menten B. WisecondorX : improved copy number detection for routine shallow whole-genome sequencing. NUCLEIC ACIDS RESEARCH. 2019;47(4):1605–14.
IEEE
[1]
L. Raman, A. Dheedene, M. De Smet, J. Van Dorpe, and B. Menten, “WisecondorX : improved copy number detection for routine shallow whole-genome sequencing,” NUCLEIC ACIDS RESEARCH, vol. 47, no. 4, pp. 1605–1614, 2019.
@article{8600819,
  abstract     = {Shallow whole-genome sequencing to infer copy number alterations (CNAs) in the human genome is rapidly becoming the method par excellence for routine diagnostic use. Numerous tools exist to deduce aberrations from massive parallel sequencing data, yet most are optimized for research and often fail to redeem paramount needs in a clinical setting. Optimally, a read depth-based analytical software should be able to deal with single-end and low-coverage datathis to make sequencing costs feasible. Other important factors include runtime, applicability to a variety of analyses and overall performance. We compared the most important aspect, being normalization, across six different CNA tools, selected for their assumed ability to satisfy the latter needs. In conclusion, WISECONDOR, which uses a within-sample normalization technique, undoubtedly produced the best results concerning variance, distributional assumptions and basic ability to detect true variations. Nonetheless, as is the case with every tool, WISECONDOR has limitations, which arise through its exclusiveness for non-invasive prenatal testing. Therefore, this work presents WisecondorX in addition, an improved WISECONDOR that enables its use for varying types of applications. WisecondorX is freely available at https://github.com/CenterForMedicalGeneticsGhent/WisecondorX.},
  author       = {Raman, Lennart and Dheedene, Annelies and De Smet, Matthias and Van Dorpe, Jo and Menten, Björn},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keywords     = {IDENTIFICATION,DIAGNOSIS,REGIONS},
  language     = {eng},
  number       = {4},
  pages        = {1605--1614},
  title        = {WisecondorX : improved copy number detection for routine shallow whole-genome sequencing},
  url          = {http://dx.doi.org/10.1093/nar/gky1263},
  volume       = {47},
  year         = {2019},
}

Altmetric
View in Altmetric
Web of Science
Times cited: