Clone-Based Systematic Haplotyping (CSH): A Procedure for Physical Haplotyping of Whole Genomes

Burgtorf, Carola; Kepper, Pamela; Hoehe, Margret R.; Schmitt, Carsten; Reinhardt, Richard; Lehrach, Hans; Sauer, Sascha

doi:10.1101/gr.1442303

Cited by 51 publications

(40 citation statements)

References 23 publications

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“…Long-range haplotyping over several kilobases would require cumbersome walking from one fragment to the adjacent fragment. Recently, we have developed a molecular haplotyping method in which the alleles of SNPs are statistically separated by a cloning approach using a pooling strategy and subsequently determining the phase of SNPs by multiplexed GOOD assays [55]. We have termed the procedure ''Clone-based Systematic Haplotyping'' (CSH).…”

Section: Molecular Haplotypingmentioning

confidence: 99%

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

Sauer

2006

Clinica Chimica Acta

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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

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Section: Molecular Haplotypingmentioning

confidence: 99%

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

Sauer

2006

Clinica Chimica Acta

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“…In many cases particularly to improve power of genetic analysis several SNPs in close proximity have to be considered as one group defined as the haplotype [40], the phase of SNP alleles on a single chromosome, which can be more meaningful than the single SNP information. The haplotype can be either determined using prediction algorithms or-when this is not accurately feasible due to large numbers and high heterozygosity of SNPs-by employing molecular haplotyping procedures, such as "clone-based systematic haplotyping" (CSH) [45].…”

Section: Typing Of Dna Markersmentioning

confidence: 99%

Genome Projects and the Functional-Genomic Era

Sauer

Konthur

Lehrach

2005

CCHTS

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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.

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“…For example, one process called the clone-based systematic haplotyping combined the high throughput platforms of cosmid library tiling, PCR and sequencing in a 96-well format that allowed rapid haplotyping of SNPs separated by about 50kb (Burgtorf et al 2003). The integration of various existing platforms and the further development of additional techniques into these high throughput platforms should make direct haplotyping analysis increasingly affordable.…”

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confidence: 99%

Extracting Haplotypes from Diploid Organisms

2006

Current Issues in Molecular Biology

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Each diploid organism has two alleles at every gene locus. In sexual organisms such as most plants, animals and fungi, the two alleles in an individual may be genetically very different from each other. DNA sequence data from individual alleles (called a haplotype) can provide powerful information to address a variety of biological questions and guide many practical applications. The advancement in molecular technology and computational tools in the last decade has made obtaining large-scale haplotypes feasible. This review summarizes the two basic approaches for obtaining haplotypes and discusses the associated techniques and methods. The first approach is to experimentally obtain diploid sequence information and then use computer algorithms to infer haplotypes. The second approach is to obtain haplotype sequences directly through experimentation. The advantages and disadvantages of each approach are discussed. I then discussed a specific example on how the direct approach was used to obtain haplotype information to address several fundamental biological questions of a pathogenic yeast. With increasing sophistication in both bioinformatics tools and high-throughput molecular techniques, haplotype analysis is becoming an integrated component in biomedical research.

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Clone-Based Systematic Haplotyping (CSH): A Procedure for Physical Haplotyping of Whole Genomes

Cited by 51 publications

References 23 publications

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

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

Genome Projects and the Functional-Genomic Era

Extracting Haplotypes from Diploid Organisms

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