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STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods

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Abstract
The growing interest in liquid biopsies for cancer research and cell-based non-invasive prenatal testing (NIPT) invigorates the need for improved single cell analysis. In these applications, target cells are extremely rare and fragile in peripheral circulation, which makes the genetic analysis very challenging. To overcome these challenges, cell stabilization and unbiased whole genome amplification are required. This study investigates the performance of four WGA methods on single or a limited number of cells after 24 hour of Streck Cell-Free DNA BCT preservation. The suitability of the DNA, amplified with Ampli1, DOPlify, PicoPLEX and REPLI-g, was assessed for both short tandem repeat (STR) profiling and copy number variant (CNV) analysis after shallow whole genome massively parallel sequencing (MPS). Results demonstrate that Ampli1, DOPlify and PicoPLEX perform well for both applications, with some differences between the methods. Samples amplified with REPLI-g did not result in suitable STR or CNV profiles, indicating that this WGA method is not able to generate high quality DNA after Streck Cell-Free DNA BCT stabilization of the cells.
Keywords
GENETIC DIAGNOSIS, DNA, ABERRATIONS, NUCLEAR

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Chicago
Vander Plaetsen, Ann-Sophie, Lieselot Deleye, Senne Cornelis, Laurentijn Tilleman, Filip Van Nieuwerburgh, and Dieter Deforce. 2017. “STR Profiling and Copy Number Variation Analysis on Single, Preserved Cells Using Current Whole Genome Amplification Methods.” Scientific Reports 7.
APA
Vander Plaetsen, A.-S., Deleye, L., Cornelis, S., Tilleman, L., Van Nieuwerburgh, F., & Deforce, D. (2017). STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods. SCIENTIFIC REPORTS, 7.
Vancouver
1.
Vander Plaetsen A-S, Deleye L, Cornelis S, Tilleman L, Van Nieuwerburgh F, Deforce D. STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods. SCIENTIFIC REPORTS. 2017;7.
MLA
Vander Plaetsen, Ann-Sophie, Lieselot Deleye, Senne Cornelis, et al. “STR Profiling and Copy Number Variation Analysis on Single, Preserved Cells Using Current Whole Genome Amplification Methods.” SCIENTIFIC REPORTS 7 (2017): n. pag. Print.
@article{8544217,
  abstract     = {The growing interest in liquid biopsies for cancer research and cell-based non-invasive prenatal testing (NIPT) invigorates the need for improved single cell analysis. In these applications, target cells are extremely rare and fragile in peripheral circulation, which makes the genetic analysis very challenging. To overcome these challenges, cell stabilization and unbiased whole genome amplification are required. This study investigates the performance of four WGA methods on single or a limited number of cells after 24 hour of Streck Cell-Free DNA BCT preservation. The suitability of the DNA, amplified with Ampli1, DOPlify, PicoPLEX and REPLI-g, was assessed for both short tandem repeat (STR) profiling and copy number variant (CNV) analysis after shallow whole genome massively parallel sequencing (MPS). Results demonstrate that Ampli1, DOPlify and PicoPLEX perform well for both applications, with some differences between the methods. Samples amplified with REPLI-g did not result in suitable STR or CNV profiles, indicating that this WGA method is not able to generate high quality DNA after Streck Cell-Free DNA BCT stabilization of the cells.},
  articleno    = {17189},
  author       = {Vander Plaetsen, Ann-Sophie and Deleye, Lieselot and Cornelis, Senne and Tilleman, Laurentijn and Van Nieuwerburgh, Filip and Deforce, Dieter},
  issn         = {2045-2322},
  journal      = {SCIENTIFIC REPORTS},
  language     = {eng},
  pages        = {9},
  title        = {STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods},
  url          = {http://dx.doi.org/10.1038/s41598-017-17525-5},
  volume       = {7},
  year         = {2017},
}

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