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Massively parallel sequencing of micro-manipulated cells targeting a comprehensive panel of disease-causing genes: A comparative evaluation of upstream whole-genome amplification methods

Lieselot Deleye UGent, Yannick Gansemans UGent, Dieter De Coninck, Filip Van Nieuwerburgh UGent and Dieter Deforce UGent (2018) PLOS ONE. 13(4).
abstract
Single Gene Disorders (SGD) are still routinely diagnosed using PCR-based assays that need to be developed and validated for each individual disease-specific gene fragment. The TruSight One sequencing panel currently covers 12 Mb of genomic content, including 4813 genes associated with a clinical phenotype. When only a limited number of cells are available, whole genome amplification (WGA) is required prior to DNA target capture techniques such as the TruSight One panel. In this study, we compared 4 different WGA methods in combination with the TruSight One sequencing panel to perform single nucleotide polymorphism (SNP) genotyping starting from 3 micro-manipulated cells. This setting simulates clinical settings such as day-5 blastocyst biopsy for Preimplantation Genetic Testing (PGT), liquid biopsy of circulating tumor cells (CTCs) and cancer-cell profiling. Bulk cell samples were processed alongside these WGA samples to serve as a performance reference. Target coverage, coverage uniformity and SNP calling accuracy obtained using any of the WGA, is inferior to the results obtained on bulk cell samples. However, results after REPLI-g come close. Compared to the other WGA methods, the method using REPLI-g WGA results in a better coverage of the targeted genomic regions with a more uniform read depth. Consequently, this method also results in a more accurate SNP calling and could be considered for clinical genotyping of a limited number of cells.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
keyword
GENERATION, ABERRATIONS, ANEUPLOIDY, ALIGNMENT, EMBRYOS
journal title
PLOS ONE
PLoS One
volume
13
issue
4
article number
e0196334
pages
12 pages
publisher
Public Library Science
place of publication
San francisco
Web of Science type
Article
Web of Science id
000431007600064
ISSN
1932-6203
DOI
10.1371/journal.pone.0196334
language
English
UGent publication?
yes
classification
U
id
8561818
handle
http://hdl.handle.net/1854/LU-8561818
date created
2018-05-15 09:57:52
date last changed
2018-05-15 09:57:57
@article{8561818,
  abstract     = {Single Gene Disorders (SGD) are still routinely diagnosed using PCR-based assays that need to be developed and validated for each individual disease-specific gene fragment. The TruSight One sequencing panel currently covers 12 Mb of genomic content, including 4813 genes associated with a clinical phenotype. When only a limited number of cells are available, whole genome amplification (WGA) is required prior to DNA target capture techniques such as the TruSight One panel. In this study, we compared 4 different WGA methods in combination with the TruSight One sequencing panel to perform single nucleotide polymorphism (SNP) genotyping starting from 3 micro-manipulated cells. This setting simulates clinical settings such as day-5 blastocyst biopsy for Preimplantation Genetic Testing (PGT), liquid biopsy of circulating tumor cells (CTCs) and cancer-cell profiling. Bulk cell samples were processed alongside these WGA samples to serve as a performance reference. Target coverage, coverage uniformity and SNP calling accuracy obtained using any of the WGA, is inferior to the results obtained on bulk cell samples. However, results after REPLI-g come close. Compared to the other WGA methods, the method using REPLI-g WGA results in a better coverage of the targeted genomic regions with a more uniform read depth. Consequently, this method also results in a more accurate SNP calling and could be considered for clinical genotyping of a limited number of cells.},
  articleno    = {e0196334},
  author       = {Deleye, Lieselot and Gansemans, Yannick and De Coninck, Dieter and Van Nieuwerburgh, Filip and Deforce, Dieter},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  keyword      = {GENERATION,ABERRATIONS,ANEUPLOIDY,ALIGNMENT,EMBRYOS},
  language     = {eng},
  number       = {4},
  pages        = {12},
  publisher    = {Public Library Science},
  title        = {Massively parallel sequencing of micro-manipulated cells targeting a comprehensive panel of disease-causing genes: A comparative evaluation of upstream whole-genome amplification methods},
  url          = {http://dx.doi.org/10.1371/journal.pone.0196334},
  volume       = {13},
  year         = {2018},
}

Chicago
Deleye, Lieselot, Yannick Gansemans, Dieter De Coninck, Filip Van Nieuwerburgh, and Dieter Deforce. 2018. “Massively Parallel Sequencing of Micro-manipulated Cells Targeting a Comprehensive Panel of Disease-causing Genes: A Comparative Evaluation of Upstream Whole-genome Amplification Methods.” Plos One 13 (4).
APA
Deleye, L., Gansemans, Y., De Coninck, D., Van Nieuwerburgh, F., & Deforce, D. (2018). Massively parallel sequencing of micro-manipulated cells targeting a comprehensive panel of disease-causing genes: A comparative evaluation of upstream whole-genome amplification methods. PLOS ONE, 13(4).
Vancouver
1.
Deleye L, Gansemans Y, De Coninck D, Van Nieuwerburgh F, Deforce D. Massively parallel sequencing of micro-manipulated cells targeting a comprehensive panel of disease-causing genes: A comparative evaluation of upstream whole-genome amplification methods. PLOS ONE. San francisco: Public Library Science; 2018;13(4).
MLA
Deleye, Lieselot, Yannick Gansemans, Dieter De Coninck, et al. “Massively Parallel Sequencing of Micro-manipulated Cells Targeting a Comprehensive Panel of Disease-causing Genes: A Comparative Evaluation of Upstream Whole-genome Amplification Methods.” PLOS ONE 13.4 (2018): n. pag. Print.