Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry

Fu, Dong-Jing; Tang, Kai; Braun, A.; Reuter, Dirk; Darnhofer-Demar, Brigitte; Little, Damon P.; O’Donnell, Maryanne J.; Cantor, Charles R.; Köster, Hubert

doi:10.1038/nbt0498-381

Cited by 130 publications

(57 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Conventional methods include single strand conformation polymorphism analysis (Orita et al 1989), gel-based restriction fragment length polymorphism (RFLP), allele-specific oligonucleotide (ASO) hybridization (Saiki et al 1989), oligonucleotide ligation assay (OLA) (Landegren et al 1988), and primer extension assay (Syvanen et al 1990). New technologies (e.g., chips, mass spectrometry, slides) have been developed and incorporated into the detection and readout of allele signals based on either hybridization or enzymatic discrimination (Livak et al 1995;Chen et al 1997;Fu et al 1998;Tyagi et al 1998;Chen et al 1999;Gilles et al 1999).…”

mentioning

confidence: 99%

A Microsphere-Based Assay for Multiplexed Single Nucleotide Polymorphism Analysis Using Single Base Chain Extension

Chen¹,

Iannone²,

Li³

et al. 2000

Genome Res.

201

127

View full text Add to dashboard Cite

A rapid, high throughput readout for single-nucleotide polymorphism (SNP) analysis was developed employing single base chain extension and cytometric analysis of an array of fluorescent microspheres. An array of fluorescent microspheres was coupled with uniquely identifying sequences, termed complementary ZipCodes (cZipCodes), which allowed for multiplexing possibilities. For a given assay, querying a polymorphic base involved extending an oligonucleotide containing both a ZipCode and a SNP-specific sequence with a DNA polymerase and a pair of fluoresceinated dideoxynucleotides. To capture the reaction products for analysis, the ZipCode portion of the oligonucleotide was hybridized with its cZipCodes on the microsphere. Flow cytometry was used for microsphere decoding and SNP typing by detecting the fluorescein label captured on the microspheres. In addition to multiplexing capability, the ZipCode system allows multiple sets of SNPs to be analyzed by a limited set of cZipCode-attached microspheres. A standard set of non-cross reactive ZipCodes was established experimentally and the accuracy of the system was validated by comparison with genotypes determined by other technologies. From a total of 58 SNPs, 55 SNPs were successfully analyzed in the first pass using this assay format and all 181 genotypes across the 55 SNPs were correct. These data demonstrate that the microsphere-based single base chain extension (SBCE) method is a sensitive and reliable assay. It can be readily adapted to an automated, high-throughput genotyping system.

show abstract

mentioning

confidence: 99%

A Microsphere-Based Assay for Multiplexed Single Nucleotide Polymorphism Analysis Using Single Base Chain Extension

Chen¹,

Iannone²,

Li³

et al. 2000

Genome Res.

201

127

View full text Add to dashboard Cite

show abstract

“…In the mid-90s, several approaches combined enzymatic Sanger-sequencing or related procedures with MALDI readout to provide an efficient alternative to relatively slow slabgel or capillary-based technology [36,37]. However, it became apparent that the highlighted problems with MALDI such as limited size range of detection, fragmentation, adduct formation, and resolution severely impeded to accurately and efficiently analyse DNA sequence ladders.…”

Section: Snp Genotyping By Maldimentioning

confidence: 99%

Typing of single nucleotide polymorphisms by MALDI mass spectrometry: Principles and diagnostic applications

Sauer

2006

Clinica Chimica Acta

View full text Add to dashboard Cite

Background: After the completion of the human genome sequencing project human genetics has now shifted its focus to DNA variation. DNA variation analysis is considered to be a key in partly understanding the mechanisms of complex diseases or varying patient responses in drug treatment. One of the major goals in genetics is finding the DNA variants that can act as diagnostic markers for predisposition to specific diseases. Moreover, in microbiology DNA variation has long been known to help discriminate and identify bacterial strains and viruses. Diagnostics based on DNA or RNA detection might be advantageous as an early-stage indication can be provided. Methods: Many simple and efficient methods for the analysis of nucleic acids are already available. Consequently, the last few years have seen an increased in the use of large-scale analysis of nucleic acids, in basic DNA variation studies along with diagnostics. Mass spectrometry techniques such as matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) can be of great use for genome variation analysis. In particular high-throughput SNP analysis by MALDI can be performed using fully integrated platforms. Conclusions: Mass spectrometry-based procedures have promise for SNPs analysis especially for clinical diagnostics. D

show abstract

“…Various MS approaches have been developed for the measurement of levels of DNA methylation, including rapid screening of single nucleotide polymorphisms (SNPs), and quantitative allele studies. It has been used to monitor nucleotide digestion and DNA sequencing [121,122]. The commonly used approach involves bisulfite conversion of genomic DNA [80] followed by DNA sequencing, resulting in accurate determination of methylation status in genomic DNA.…”

Section: Matrix-assisted Laser Desorption/ionization Time-of-flight Mmentioning

confidence: 99%

Investigation of a Putative Estrogen-Imprinting Gene, Phosphodiesterase Type IV Variant (PDE4D4), in Determining Prostate Cancer Risk

Tang¹

2007

View full text Add to dashboard Cite

Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information Operations and Reports (0704-0188), 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. REPORT DATE (DD-MM-YYYY) 01-04-20072. REPORT TYPE (From -To) 15 Mar 06 -14 Mar 07 Annual DATES COVERED TITLE AND SUBTITLE NVESTIGATION OF A PUTATIVE ESTROGEN-IMPRINTING GENE, PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBERUniversity of Cincinnati Cincinnati OH 45221-0627 SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR'S ACRONYM(S) U.S. Army Medical Research and Materiel Command Fort Detrick, Maryland 21702-5012 SPONSOR/MONITOR'S REPORT NUMBER(S) DISTRIBUTION / AVAILABILITY STATEMENTApproved for Public Release; Distribution Unlimited SUPPLEMENTARY NOTES ABSTRACT:Estrogens are known to play a role in the initiation and progression of prostate cancer. Recently, environmental factors such as xenoestrogens have been reported on their prevalence of prostate diseases or cancers. Estrogen imprinting of the prostate gland is believed to associate with an increased incidence of prostatic lesions including inflammation, epithelial hyperplasia, squamous metaplasia, dysplasia and adenocarcinoma. And DNA methylation may be one of the possible mechanisms of the prostate reprogramming. By using one of the global methylation profiling techniques, MSRF, a gene called phosphodiesterase type IV variant 4 (PDE4D4) was shown to be hypomethylated following neonatal exposure to estradiol (EB) or bisphenol A (BPA). We further confirmed the persistence of PDE4D4 promoter hypomethylation and gene up-regulation in the adult life by using bisulfite genomic sequencing and real-time PCR. PDE4D4 has function of cAMP-degradation to maintain the second messenger, cAMP, in a narrow range of concentrations that is critical for growth and differentiation of the hormone target cells by activating several downstream signaling molecules. Taken together, these findings supported that PDE4D4 dysregulation, via CpG island hypomethylation, at its promoter regions in early life, by EB or BPA, can alter its expression and activity of the gene. Present data also suggested that PDE4D4 can be used as a biomarker for prostate cancer assessment. SUBJECT TERMSDNA methylation, phosphodiestera...

show abstract

Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry

Cited by 130 publications

References 28 publications

A Microsphere-Based Assay for Multiplexed Single Nucleotide Polymorphism Analysis Using Single Base Chain Extension

A Microsphere-Based Assay for Multiplexed Single Nucleotide Polymorphism Analysis Using Single Base Chain Extension

Typing of single nucleotide polymorphisms by MALDI mass spectrometry: Principles and diagnostic applications

Investigation of a Putative Estrogen-Imprinting Gene, Phosphodiesterase Type IV Variant (PDE4D4), in Determining Prostate Cancer Risk

Contact Info

Product

Resources

About