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.

Performance of a TthPrimPol-based whole genome amplification kit for copy number alteration detection using massively parallel sequencing

“…The variance of the read counts per window across the genome for the current TruePrime samples is a lot higher compared to the variance in the previously analyzed SurePlex samples3 (p = 0.015; Fig. 4).…”

“…The setup of this study was equal to the SurePlex study3, except for the WGA method used. The same cell line and cell isolation techniques were used.…”

“…The variability in distribution of the reads across the genome and the ability to correctly detect chromosomal aneuploidies and large CNAs was assessed and the results were compared to a study from Deleye et al 3 in which the performance of Picoplex/SurePlex and MALBAC WGA was studied in a similar setting.…”

Detection of Activating Estrogen Receptor Gene (ESR1) Mutations in Single Circulating Tumor Cells

“…Moreover, an improved ability of MALBAC in SNP variant identification has been recently reported, with better performance in uniformity and reproducibility [48]. Other methods, like SurePlex allows for a better copy number alterations (CNAs) detection, with a more uniformity amplification across the genome [49]. These observations led us to endorse MALBAC as the technique to be used in genotyping the ESR1 gene.…”

Shallow whole genome sequencing is well suited for the detection of chromosomal aberrations in human blastocysts

“…Probably due to the amplification bias introduced by the WGA protocol more sequencing is needed to obtain a similar resolution (21). Although several new WGA methods have been described, we and other investigators have shown that the SurePlex method used in the present study introduces the least amplification bias (22). Although MPS is a technique that allows scaling, the WGA is currently the limiting factor in achieving higher resolution copy number profiles when starting from a single or a limited number of cells.…”