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Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method

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Abstract
Current whole genome amplification (WGA) methods lead to amplification bias resulting in over-and under-represented regions in the genome. Nevertheless, certain WGA methods, such as SurePlex and subsequent arrayCGH analysis, make it possible to detect copy number alterations (CNAs) at a 10 Mb resolution. A more uniform WGA combined with massive parallel sequencing (MPS), however, could allow detection at higher resolution and lower cost. Recently, MALBAC, a new WGA method, claims unparalleled performance. Here, we compared the well-established SurePlex and MALBAC WGA for their ability to detect CNAs in MPS generated data and, in addition, compared PCR-free MPS library preparation with the standard enrichment PCR library preparation. Results showed that SurePlex amplification led to more uniformity across the genome, allowing for a better CNA detection with less false positives compared to MALBAC amplified samples. An even more uniform coverage was observed in samples following a PCR-free library preparation. In general, the combination of SurePlex and MPS led to the same chromosomal profile compared to a reference arrayCGH from unamplified genomic DNA, underlining the large potential of MPS techniques in CNA detection from a limited number of DNA material.
Keywords
ANEUPLOIDY, SINGLE-CELL, MICROARRAYS, EMBRYOS

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Chicago
Deleye, Lieselot, Dieter De Coninck, CHRISTODOULOS CHRISTODOULOU, Tom Sante, Annelies Dheedene, Björn Heindryckx, Etienne Van den Abbeel, et al. 2015. “Whole Genome Amplification with SurePlex Results in Better Copy Number Alteration Detection Using Sequencing Data Compared to the MALBAC Method.” Scientific Reports 5.
APA
Deleye, L., De Coninck, D., CHRISTODOULOU, C., Sante, T., Dheedene, A., Heindryckx, B., Van den Abbeel, E., et al. (2015). Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method. SCIENTIFIC REPORTS, 5.
Vancouver
1.
Deleye L, De Coninck D, CHRISTODOULOU C, Sante T, Dheedene A, Heindryckx B, et al. Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method. SCIENTIFIC REPORTS. 2015;5.
MLA
Deleye, Lieselot, Dieter De Coninck, CHRISTODOULOS CHRISTODOULOU, et al. “Whole Genome Amplification with SurePlex Results in Better Copy Number Alteration Detection Using Sequencing Data Compared to the MALBAC Method.” SCIENTIFIC REPORTS 5 (2015): n. pag. Print.
@article{6868639,
  abstract     = {Current whole genome amplification (WGA) methods lead to amplification bias resulting in over-and under-represented regions in the genome. Nevertheless, certain WGA methods, such as SurePlex and subsequent arrayCGH analysis, make it possible to detect copy number alterations (CNAs) at a 10 Mb resolution. A more uniform WGA combined with massive parallel sequencing (MPS), however, could allow detection at higher resolution and lower cost. Recently, MALBAC, a new WGA method, claims unparalleled performance. Here, we compared the well-established SurePlex and MALBAC WGA for their ability to detect CNAs in MPS generated data and, in addition, compared PCR-free MPS library preparation with the standard enrichment PCR library preparation. Results showed that SurePlex amplification led to more uniformity across the genome, allowing for a better CNA detection with less false positives compared to MALBAC amplified samples. An even more uniform coverage was observed in samples following a PCR-free library preparation. In general, the combination of SurePlex and MPS led to the same chromosomal profile compared to a reference arrayCGH from unamplified genomic DNA, underlining the large potential of MPS techniques in CNA detection from a limited number of DNA material.},
  articleno    = {11711},
  author       = {Deleye, Lieselot and De Coninck, Dieter and CHRISTODOULOU, CHRISTODOULOS and Sante, Tom and Dheedene, Annelies and Heindryckx, Bj{\"o}rn and Van den Abbeel, Etienne and De Sutter, Petra and Menten, Bj{\"o}rn and Deforce, Dieter and Van Nieuwerburgh, Filip},
  issn         = {2045-2322},
  journal      = {SCIENTIFIC REPORTS},
  keyword      = {ANEUPLOIDY,SINGLE-CELL,MICROARRAYS,EMBRYOS},
  language     = {eng},
  pages        = {13},
  title        = {Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method},
  url          = {http://dx.doi.org/10.1038/srep11711},
  volume       = {5},
  year         = {2015},
}

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