Comparison of whole genome amplification methods for further quantitative analysis with microarray-based comparative genomic hybridization.
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.


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 amplifying genomic 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.


CONCLUSIONS
The amplified DNA products generated by LM-PCR best reflect the original genomic DNA.
Lee
Yun-Shien
YS
Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Gwei-ShanHsiang, Tao-Yuan 333, Taiwan.
Tsai
Chi-Neu
CN
Tsai
Chia-Lung
CL
Chang
Shuenn-Dyh
SD
Hsueh
Ding-Wei
DW
Liu
Chun-Ting
CT
Ma
Chung-Chun
CC
Lin
Seng-Hsuan
SH
Wang
Tzu-Hao
TH
Wang
Hsin-Shih
HS
D000650:Amnion / Q000166:cytology; D045744:Cell Line, Tumor; D020732:Cytogenetic Analysis / Q000379:methods; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D005838:Genotype; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011247:Pregnancy; D019836:Preimplantation Diagnosis / Q000379:methods*