Microarray-based DNA methylation profiling: technology and applications.

Axel Schumacher; Philipp Kapranov; Zachary Kaminsky; James Flanagan; Abbas Assadzadeh; Patrick Yau; Carl Virtanen; Neil Winegarden; Jill Cheng; Thomas Gingeras; Arturas Petronis

doi:10.1093/nar/gkj461

PubMed · 16428248

Microarray-based DNA methylation profiling: technology and applications.

Axel Schumacher·Philipp Kapranov·Zachary Kaminsky·James Flanagan·Abbas Assadzadeh·Patrick Yau·Carl Virtanen·Neil Winegarden·Jill Cheng·Thomas Gingeras·Arturas Petronis

View original source ↗Export metadata ↓

Abstract

This work is dedicated to the development of a technology for unbiased, high-throughput DNA methylation profiling of large genomic regions. In this method, unmethylated and methylated DNA fractions are enriched using a series of treatments with methylation sensitive restriction enzymes, and interrogated on microarrays. We have investigated various aspects of the technology including its replicability, informativeness, sensitivity and optimal PCR conditions using microarrays containing oligonucleotides representing 100 kb of genomic DNA derived from the chromosome 22 COMT region in addition to 12 192 element CpG island microarrays. Several new aspects of methylation profiling are provided, including the parallel identification of confounding effects of DNA sequence variation, the description of the principles of microarray design for epigenomic studies and the optimal choice of methylation sensitive restriction enzymes. We also demonstrate the advantages of using the unmethylated DNA fraction versus the methylated one, which substantially improve the chances of detecting DNA methylation differences. We applied this methodology for fine-mapping of methylation patterns of chromosomes 21 and 22 in eight individuals using tiling microarrays consisting of over 340 000 oligonucleotide probe pairs. The principles developed in this work will help to make epigenetic profiling of the entire human genome a routine procedure.

Explore related subjects

Chromosome Mapping Chromosomes, Human, Pair 21 Chromosomes, Human, Pair 22 CpG Islands DNA DNA Methylation Epigenesis, Genetic Genome, Human Genomics Humans Oligonucleotide Array Sequence Analysis Polymerase Chain Reaction Polymorphism, Single Nucleotide Reproducibility of Results Evaluation Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Axel Schumacher, Philipp Kapranov, Zachary Kaminsky, James Flanagan, Abbas Assadzadeh, Patrick Yau, Carl Virtanen, Neil Winegarden, Jill Cheng, Thomas Gingeras, Arturas Petronis. 2006-01-20. Microarray-based DNA methylation profiling: technology and applications.. https://doi.org/10.1093/nar%2Fgkj461

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2026

Mitotic karyotyping and FISH mapping of the gender-specific locus indicate an advanced XY system in Hippophae rhamnoides.

Hippophae rhamnoides ssp. turkestanica, a subdioecious plant inhabiting the cold desert of the Indian Himalaya, has gained immense recognition for its nutritional and medicinal values. In recent years, the plant species has proven to be a suitable system to understand the evolution of dioecy. Despite its biological significance, the cytogenetics of this dioecious plant is unclear due to various conflicting accounts of its X-Y chromosome system, particularly the length of Y-chromosome. In this study, we resolved these ambiguities through comprehensive cytogenetic analyses across diverse western Himalayan populations. Using morphometric analysis and fluorescence in situ hybridization (FISH) with a gender-specific marker (HRMSSR), we confirmed homomorphic XX chromosomes in females and heteromorphic sex-chromosomes in males with a notably smaller Y-chromosome. The investigation also revealed a predominant somatic chromosome number of 2n = 24, although minor deviations (2n = 18, 20, 22) appeared at the seed level. These findings highlight an evolutionarily advanced sex-chromosome system. This first detailed cytogenetic investigation of Himalayan Seabuckthorn provides critical insights into the chromosomal architecture, laying a crucial foundation for future evolutionary, genomic, and conservation studies in the species.

Chromosome Mapping↗

PubMed2007

The elusive goal of pedigree weights.

Non-parametric linkage analysis methods generally involve calculating an allele-sharing statistic for each pedigree in a data set, then standardizing and summing the statistics over pedigrees. Pedigrees of different sizes can be weighted differently in the sum, though it is perhaps most common to weight all standardized pedigree statistics equally. Most other common weighting schemes are based on the number of affected individuals in the pedigree. It is also possible to derive optimal weights, which maximize power to detect linkage under particular trait models. We started by investigating three different analytical and simulation-based methods to calculate power and derive optimal weights. We found that simulation methods produce noticeably more accurate power calculations than the other methods. However, although the different calculation methods give different "optimal" weights, the power at those weights is very similar. That is, the analytical calculation methods are sufficient for finding good weights even though the simulation methods are most appropriate for calculating power. In comparing optimal weights for different trait models, we found that the weights vary quite a bit with the model, such that optimal weights for one model are not necessarily powerful at all for other models. Finally, we studied the power of a number of general weighting schemes, and of some new ones that incorporate information on how closely the affected individuals are related. We were able to find some schemes that performed well in the sense of giving reasonably powerful weights for most of the trait models and pedigree types we considered.

Chromosome Mapping↗

PubMed2006

Molecular basis of human dentin diseases.

In recent years, substantial progress has been made regarding the molecular etiology of human structural tooth diseases that alter dentin matrix formation. These diseases have been classified into two major groups with subtypes: dentin dysplasia (DD) types I and II and dentinogenesis imperfecta (DGI) types I-III. Genetic linkage studies have identified the critical loci for DD-II, DGI-II, and DGI-II to human chromosome 4q21. Located within the common disease loci for these diseases is cluster of dentin/bone genes that includes osteopontin (OPN), bone sialoprotein (BSP), matrix extracellular phosphoglycoprotein (MEPE), dentin matrix protein 1 (DMP1), and dentin sialophosphoprotein (DSPP). To date, only mutations within dentin sialophosphoprotein have been associated with the pathogenesis of dentin diseases including DGI types-II and -III and DD-II. In this article, we overview the recent literature related to these dentin genetic diseases, their clinical features, and molecular pathogenesis.

Chromosome Mapping↗