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J Genet Genomics. 2015 Apr 20;42(4):151-9. doi: 10.1016/j.jgg.2015.03.001. Epub 2015 Mar 14.

The Performance of Whole Genome Amplification Methods and Next-Generation Sequencing for Pre-Implantation Genetic Diagnosis of Chromosomal Abnormalities.

Author information

1
Department of Gynecology and Obstetrics, Reproductive Medicine Center, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China; Department of Obstetrics and Gynecology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China.
2
Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing 100853, China.
3
Department of Gynecology and Obstetrics, Reproductive Medicine Center, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China.
4
Berry Genomics, C., Limited, Beijing 100015, China.
5
Berry Genomics, C., Limited, Beijing 100015, China. Electronic address: david.cram@berrygenomics.com.
6
Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing 100853, China. Electronic address: yqyao_ghpla@163.com.

Abstract

Reliable and accurate pre-implantation genetic diagnosis (PGD) of patient's embryos by next-generation sequencing (NGS) is dependent on efficient whole genome amplification (WGA) of a representative biopsy sample. However, the performance of the current state of the art WGA methods has not been evaluated for sequencing. Using low template DNA (15 pg) and single cells, we showed that the two PCR-based WGA systems SurePlex and MALBAC are superior to the REPLI-g WGA multiple displacement amplification (MDA) system in terms of consistent and reproducible genome coverage and sequence bias across the 24 chromosomes, allowing better normalization of test to reference sequencing data. When copy number variation sequencing (CNV-Seq) was applied to single cell WGA products derived by either SurePlex or MALBAC amplification, we showed that known disease CNVs in the range of 3-15 Mb could be reliably and accurately detected at the correct genomic positions. These findings indicate that our CNV-Seq pipeline incorporating either SurePlex or MALBAC as the key initial WGA step is a powerful methodology for clinical PGD to identify euploid embryos in a patient's cohort for uterine transplantation.

KEYWORDS:

Copy number variation; Next-generation sequencing; Pre-implantation genetic diagnosis; Single cells; Whole genome amplification

PMID:
25953353
DOI:
10.1016/j.jgg.2015.03.001
[Indexed for MEDLINE]

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