Low-pass genome sequencing of LOUCY cell line. Homo sapiens

Massive parallel sequencing (MPS) techniques are rapidly evolving and continuously improving in accuracy, speed, and cost efficiency. An important factor determining the success of a sequencing run, is the whole genome amplification (WGA) of the DNA that has to be sequenced. The different currently available WGA methods lead to amplification bias resulting in over- and under-represented regions in the genome. Nevertheless, current WGA methods, such as SurePlex (Bluegnome) and subsequent aCGH analysis, make it possible to detect copy number variations (CNVs) at a 10 Mb resolution. A more uniform WGA combined with MPS instead of aCGH, however, could make it possible to screen at a higher resolution. Recently, a new Multiple Annealing and Looping Based Amplification Cycles (MALBAC) WGA method has been published, claiming unparalleled performance. The goal of this study was to compare the well-established SurePlex and MALBAC WGA for their ability to detect CNVs. Furthermore, we compared PCR-free MPS library preparation with the standard enrichment PCR library preparation. Samples consisting of either 1, 3 or 5 cells, in triplicate, were collected from the LOUCY lymphoblastoid cell line using micromanipulation and were amplified using both WGA methods. Illumina library preparation and sequencing was performed on the WGA products.