Genotyping by mass spectrometric analysis of short DNA fragments

Steven J. Laken; Peta E. Jackson; Kenneth W. Kinzler; Bert Vogelstein; Paul T. Strickland; John D. Groopman; Marlin D. Friesen

doi:10.1038/4333

Genotyping by mass spectrometric analysis of short DNA fragments

Steven J. Laken, Peta E. Jackson, Kenneth W. Kinzler, Bert Vogelstein, Paul T. Strickland, John D. Groopman, Marlin D. Friesen

Research output: Contribution to journal › Article › peer-review

97 Scopus citations

Abstract

A method has been developed to produce small DNA fragments from PCR products for analysis of defined DNA variations by mass spectrometry. The genomic region to be analyzed is PCR-amplified with primers containing a sequence for the type IIS restriction endonuclease Bpml. Bpml digestion of the resultant PCR products yields fragments as small as seven bases, which are then analyzed by electrospray ionization mass spectrometry. The approach was validated using seven different variants within the APC tumor suppressor gene, in which a perfect correlation was obtained with DNA sequencing. Both the sense and antisense strands were analyzed independently, and several variants can be analyzed simultaneously. These results provide the basis for a generally applicable and highly accurate method that directly queries the mass of variant DNA sequences.

Original language	English (US)
Pages (from-to)	1352-1356
Number of pages	5
Journal	Nature biotechnology
Volume	16
Issue number	13
DOIs	https://doi.org/10.1038/4333
State	Published - Dec 1998

Keywords

Genomics
Single nucleotide polymorphisms
Type IIS restriction endonuclease

ASJC Scopus subject areas

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Molecular Medicine
Biomedical Engineering

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10.1038/4333

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title = "Genotyping by mass spectrometric analysis of short DNA fragments",

abstract = "A method has been developed to produce small DNA fragments from PCR products for analysis of defined DNA variations by mass spectrometry. The genomic region to be analyzed is PCR-amplified with primers containing a sequence for the type IIS restriction endonuclease Bpml. Bpml digestion of the resultant PCR products yields fragments as small as seven bases, which are then analyzed by electrospray ionization mass spectrometry. The approach was validated using seven different variants within the APC tumor suppressor gene, in which a perfect correlation was obtained with DNA sequencing. Both the sense and antisense strands were analyzed independently, and several variants can be analyzed simultaneously. These results provide the basis for a generally applicable and highly accurate method that directly queries the mass of variant DNA sequences.",

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AU - Laken, Steven J.

AU - Jackson, Peta E.

AU - Kinzler, Kenneth W.

AU - Vogelstein, Bert

AU - Strickland, Paul T.

AU - Groopman, John D.

AU - Friesen, Marlin D.

PY - 1998/12

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AB - A method has been developed to produce small DNA fragments from PCR products for analysis of defined DNA variations by mass spectrometry. The genomic region to be analyzed is PCR-amplified with primers containing a sequence for the type IIS restriction endonuclease Bpml. Bpml digestion of the resultant PCR products yields fragments as small as seven bases, which are then analyzed by electrospray ionization mass spectrometry. The approach was validated using seven different variants within the APC tumor suppressor gene, in which a perfect correlation was obtained with DNA sequencing. Both the sense and antisense strands were analyzed independently, and several variants can be analyzed simultaneously. These results provide the basis for a generally applicable and highly accurate method that directly queries the mass of variant DNA sequences.

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KW - Single nucleotide polymorphisms

KW - Type IIS restriction endonuclease

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Genotyping by mass spectrometric analysis of short DNA fragments

Abstract

Keywords

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