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Published online before print April 14, 2003, 10.1101/gr.816903
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Vol 13, Issue 5, 954-964, May 2003

METHODS

Unbiased Whole-Genome Amplification Directly From Clinical Samples

Seiyu Hosono, A. Fawad Faruqi, Frank B. Dean, Yuefen Du, Zhenyu Sun, Xiaohong Wu, Jing Du, Stephen F. Kingsmore, Michael Egholm and Roger S. Lasken1

Molecular Staging, Inc., New Haven, Connecticut 06511, USA

Preparation of genomic DNA from clinical samples is a bottleneck in genotyping and DNA sequencing analysis and is frequently limited by the amount of specimen available. We use Multiple Displacement Amplification (MDA) to amplify the whole genome 10,000-fold directly from small amounts of whole blood, dried blood, buccal cells, cultured cells, and buffy coats specimens, generating large amounts of DNA for genetic testing. Genomic DNA was evenly amplified with complete coverage and consistent representation of all genes. All 47 loci analyzed from 44 individuals were represented in the amplified DNA at between 0.5- and 3.0-fold of the copy number in the starting genomic DNA template. A high-fidelity DNA polymerase ensures accurate representation of the DNA sequence. The amplified DNA was indistinguishable from the original genomic DNA template in 5 SNP and 10 microsatellite DNA assays on three different clinical sample types for 20 individuals. Amplification of genomic DNA directly from cells is highly reproducible, eliminates the need for DNA template purification, and allows genetic testing from small clinical samples. The low amplification bias of MDA represents a dramatic technical improvement in the ability to amplify a whole genome compared with older, PCR-based methods.

1 Corresponding author.

E-MAIL rogerl{at}molecularstaging.com; FAX: (203) 776-5276.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.816903. Article published online before print in April 2003.


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