Taiwanese Journal of Obstetrics and Gynecology
Volume 47, Issue 1 , Pages 32-41, March 2008

Comparison of Whole Genome Amplification Methods for Further Quantitative Analysis with Microarray-based Comparative Genomic Hybridization

  • Yun-Shien Lee

      Affiliations

    • Genomic Medicine Research Core Laboratory, ChangGung Memorial Hospital, Tao-Yuan, Taiwan
    • Department of Biotechnology, Ming-Chuan University, Tao-Yuan, Taiwan
    • ,
  • Chi-Neu Tsai

      Affiliations

    • Graduate Institute of Clinical Medical Sciences, College of Medicine, Tao-Yuan, Taiwan
    • ,
  • Chia-Lung Tsai

      Affiliations

    • Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, ChangGung University, Tao-Yuan, Taiwan
    • ,
  • Shuenn-Dyh Chang

      Affiliations

    • Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, ChangGung University, Tao-Yuan, Taiwan
    • ,
  • Ding-Wei Hsueh

      Affiliations

    • Genomic Medicine Research Core Laboratory, ChangGung Memorial Hospital, Tao-Yuan, Taiwan
    • ,
  • Chun-Ting Liu

      Affiliations

    • Genomic Medicine Research Core Laboratory, ChangGung Memorial Hospital, Tao-Yuan, Taiwan
    • ,
  • Chung-Chun Ma

      Affiliations

    • Genomic Medicine Research Core Laboratory, ChangGung Memorial Hospital, Tao-Yuan, Taiwan
    • ,
  • Seng-Hsuan Lin

      Affiliations

    • Genomic Medicine Research Core Laboratory, ChangGung Memorial Hospital, Tao-Yuan, Taiwan
    • ,
  • Tzu-Hao Wang

      Affiliations

    • Genomic Medicine Research Core Laboratory, ChangGung Memorial Hospital, Tao-Yuan, Taiwan
    • Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, ChangGung University, Tao-Yuan, Taiwan
    • Corresponding Author InformationCorrespondence to: Dr Tzu-Hao Wang, Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, 5 Fu-Hsing Street, Gwei-Shan Hsiang, Tao-Yuan 333, Taiwan
    • ,
  • Hsin-Shih Wang

      Affiliations

    • Graduate Institute of Clinical Medical Sciences, College of Medicine, Tao-Yuan, Taiwan
    • Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, ChangGung University, Tao-Yuan, Taiwan

Accepted 29 November 2007.

Article Outline

Summary 

Objective

Whole genome amplification (WGA) is a crucial procedure for genomic DNA analysis from limited sources, such as in forensic analysis, embryo biopsy for preimplantation genetic diagnosis, or needle aspiration biopsies. Several strategies for WGA have been developed for either genotyping or microarray-based comparative genome hybridization (array-CGH) during the past decade. Nevertheless, there were few studies in which various WGA methods had been performed side-by-side and results evaluated with multiple methods.

Materials and Methods

Ease of performance, qualitative accuracy, and quantitative fidelity of different WGA methods, such as degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), ligation-mediated PCR (LM-PCR) and strand displacement amplification (SDA), were compared in amplifyinggenomic DNA derived from karyotype-confirmed amniocytes and the cancer cell line SAOS2.

Results

Using analysis with microsatellite markers, single nucleotide polymorphism markers, and array-CGH, our results suggested that: (1) genomic DNA amplified from DOP-PCR resulted in false positive and negative results by analysis with array-CGH; (2) SDA is the easiest performance method among the three WGA methods; and (3) amplified DNA products generated by LM-PCR best reflect the original genomic DNA.

Conclusion

The amplified DNA products generated by LM-PCR best reflect the original genomic DNA.

Key Words:  array-CGH , DOP-PCR , LM-PCR , SDA , whole genome amplification

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PII: S1028-4559(08)60052-2

doi:10.1016/S1028-4559(08)60052-2

Taiwanese Journal of Obstetrics and Gynecology
Volume 47, Issue 1 , Pages 32-41, March 2008

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