High-resolution human papillomavirus genotyping by MALDI-TOF mass spectrometry.
We describe a matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS)-based assay for human papillomavirus (HPV) genotyping--the restriction fragment mass polymorphism (RFMP) assay, which is based on mass measurement of genotype-specific oligonucleotide fragments generated by TypeIIS restriction endonuclease cleavage after recognition sites have been introduced by PCR amplification. The use of a TypeIIS restriction enzyme makes the RFMP assay independent of sequence and applicable to a wide variety of HPV genotypes, because these enzymes have cleavage sites at a fixed distance from their recognition sites. After PCR amplification, samples are subjected to restriction enzyme digestion with FokI and BtsCI and desalting using Oasis purification plates, followed by analysis by MALDI-TOF MS. Overall, the protocol is simple, takes approximately 4-4.5 h and can accurately detect and identify at least 74 different HPV genotypes.
Hong
Sun Pyo
SP
R&D Center, GeneMatrix Inc, Yongin 446-913, Korea.
Shin
Soo-Kyung
SK
Lee
Eun Hee
EH
Kim
Eun Ok
EO
Ji
Seung Il
SI
Chung
Hyun Jae
HJ
Park
Sun Nie
SN
Yoo
Wangdon
W
Folk
William R
WR
Kim
Soo-Ok
SO
D020029:Base Pairing; D001483:Base Sequence; D005838:Genotype; D052162:Human papillomavirus 16 / Q000235:genetics*; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000235:genetics; D012150:Polymorphism, Restriction Fragment Length / Q000235:genetics*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
D009841:Oligonucleotides