Automated solid-phase extraction for purification of single nucleotide polymorphism genotyping products prior to matrix-assisted laser desorption/ionisation time-of-flight mass spectrometric analysis

Sauer, Sascha; Kepper, Pamela; SMYRA, A; Dahl, Andreas; FERSE, F; Lehrach, Hans; Reinhardt, Richard

doi:10.1016/s0021-9673(04)01273-7

Cited by 8 publications

(5 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…With 1 fmol, we were at the detection limit. Mean S/N ratios obtained with our slides were thus similar to those obtained with microZipTips and OASIS HLB purification, with HPA as matrix, and with anchor-chip MALDI targets (21 ). Examples of the detection ranges for our approach with different amounts of oligonucleotides are shown in Fig.…”

Section: Resultssupporting

confidence: 72%

See 1 more Smart Citation

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Analysis of DNA on Microarrays

et al. 2006

View full text Add to dashboard Cite

Background: Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is a powerful tool in biomolecule analysis with a wide range of application possibilities, including genotyping of singlebase variations (also known as single-nucleotide polymorphisms, or SNPs) for candidate gene studies and diagnostic typing of DNA markers. We tested a method that does not require stringent purification of the nucleic acids and/or the use of modification chemistry before mass spectrometry analysis. Methods: We used an alternative direct analysis approach that allows MALDI analysis of crude DNA samples printed on microscope slides densely coated with primary amino groups that efficiently bind negatively charged DNA. After simple washing of the slides, we applied MALDI matrix and used a conventional MALDI mass spectrometer to detect DNA products. Results: We analyzed crude oligonucleotide samples and performed automated genotyping of single-base variations in 72 DNA samples. Conclusion: This procedure offers an operational short-cut compared with standard MALDI procedures for preparation of oligonucleotides, including purification, and thus is an efficient tool for genotyping applications, particularly those requiring accurate, flexible, and rapid data generation and medium throughput.

show abstract

Section: Resultssupporting

confidence: 72%

“…These 69 MALDI spectra were all of sufficient quality for accurate and easy diagnostic allele calling. In our hands, this yield is similar to conventional approaches using an HPA matrix preparation (21 ). Because of poor spectra quality, 3 spectra could not be determined.…”

Section: Single-base Variation Genotyping Using Aminomodified Microscsupporting

confidence: 58%

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Analysis of DNA on Microarrays

et al. 2006

View full text Add to dashboard Cite

show abstract

“…Therefore much more operational time is needed than in competing assays such as TaqMani. Future developments of mass spectrometric SNP typing methods should focus on shortening and simplifying reaction sequences [46]. Such improvements can be crucial for diagnostic applications in clinical practice.…”

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

“…One can roughly define the (cost-) efficiency of the different methods by the number of SNPs and DNAs under investigation. While array-based methods [41,46,47] combined with high-multiplex generation of SNP products including molecular bondcoding are efficient when analysing several thousand SNPs at a time in hundreds of DNA samples, solution based approaches such as TaqMan using fluorescence detection [48], or mass spectrometry based procedures [49][50][51][52][53] are rather economical in candidate gene studies where several ten to hundred SNPs have to be typed in cohorts of several thousand DNAs. Many of the SNP typing methods are continuously optimised in terms of throughput, cost efficiency and applicability.…”

Section: Typing Of Dna Markersmentioning

confidence: 99%

Genome Projects and the Functional-Genomic Era

Sauer

Konthur

Lehrach

2005

CCHTS

View full text Add to dashboard Cite

The problems we face today in public health as a result of the -fortunately -increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.

show abstract

Automated solid-phase extraction for purification of single nucleotide polymorphism genotyping products prior to matrix-assisted laser desorption/ionisation time-of-flight mass spectrometric analysis

Cited by 8 publications

References 0 publications

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Analysis of DNA on Microarrays

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Analysis of DNA on Microarrays

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

Genome Projects and the Functional-Genomic Era

Contact Info

Product

Resources

About