title: Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method.
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.
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
authors.forename: Lieselot
authors.initials: L
authors.lastname: Deleye
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
authors.forename: Dieter
authors.initials: D
authors.lastname: De Coninck
authors.affiliation: Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium.
authors.forename: Christodoulos
authors.initials: C
authors.lastname: Christodoulou
authors.affiliation: Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium.
authors.forename: Tom
authors.initials: T
authors.lastname: Sante
authors.affiliation: Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium.
authors.forename: Annelies
authors.initials: A
authors.lastname: Dheedene
authors.affiliation: Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium.
authors.forename: Björn
authors.initials: B
authors.lastname: Heindryckx
authors.affiliation: Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium.
authors.forename: Etienne
authors.initials: E
authors.lastname: Van den Abbeel
authors.affiliation: Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium.
authors.forename: Petra
authors.initials: P
authors.lastname: De Sutter
authors.affiliation: Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium.
authors.forename: Björn
authors.initials: B
authors.lastname: Menten
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
authors.forename: Dieter
authors.initials: D
authors.lastname: Deforce
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
authors.forename: Filip
authors.initials: F
authors.lastname: Van Nieuwerburgh
mesh_terms: D002460:Cell Line; D002877:Chromosomes, Human / Q000235:genetics; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D005260:Female; D018628:Gene Dosage; D015723:Gene Library; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D021141:Nucleic Acid Amplification Techniques; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis