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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

(2018) PLOS ONE. 13(4).
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Organization
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.
Keywords
GENERATION, ABERRATIONS, ANEUPLOIDY, ALIGNMENT, EMBRYOS

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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. 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.
@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},
  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},
}

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