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

Na Li; Li Wang; Hui Wang; Minyue Ma; Xiaohong Wang; Yi Li; Wenke Zhang; Jianguang Zhang; David S. Cram; Yuanqing Yao

doi:10.1016/j.jgg.2015.03.001

Volume 42 Issue 4

Apr. 2015

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Article Navigation > Journal of Genetics and Genomics > 2015 > 42(4): 151-159

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

doi: 10.1016/j.jgg.2015.03.001

a
Department of Gynecology and Obstetrics, Reproductive Medicine Center, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
b
Department of Obstetrics and Gynecology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China
c
Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing 100853, China
d
Berry Genomics, C., Limited, Beijing 100015, China

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Corresponding author: E-mail address: david.cram@berrygenomics.com (David S. Cram); E-mail address: yqyao_ghpla@163.com (Yuanqing Yao)
Received Date: 2014-10-20
Accepted Date: 2015-03-08
Rev Recd Date: 2015-03-06

Available Online: 2015-03-14

Publish Date: 2015-04-20

Abstract

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

These two authors contributed equally to this work.

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References(32)

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