Analysis of MLPA Data Using Novel Software Coffalyser.NET by MRC-Holland

Abstract

Genetic knowledge has increased tremendously in the last years, filling gaps and giving answers that were inaccessible before. Medical genetics seeks to understand how genetic variation relates to human health and disease (National Center for Biotechnology Information, 2008). Although genetics plays a larger role in general, the knowledge of the genetic origins of disease has increased our understanding of illnesses caused by abnormalities in the genes or chromosomes, offering the potential to improve the diagnosis and treatment of patients. Normally, every person carries two copies of every gene (with the exception of genes related to sex-linked traits), which cells can translate into a functional protein. The presence of mutant forms of genes (mutations, copy number changes, insertion/deletions and chromosomal alterations) may affect several processes concerning the production of these proteins often resulting in the development of genetic disorders. Genetic disease is either caused by changes in the DNA of somatic cells in the body or it is inherited, e.g. by mutations in the germ cells of the parents. Genetic testing is "the analysis of, chromosomes (DNA), proteins, and certain metabolites in order to detect heritable disease-related genotypes, mutations, phenotypes, or karyotypes for clinical purposes (Holtzman et al, 2002). In order to make this suitable for routine diagnostics dedicated, affordable, fast, easy-to-interpret and simple-to-use genetic tests are necessary. This allows scientists to easily access information that for instance can be used to: confirm or rule out a suspected genetic condition or help determine a person's chance of developing or passing on a genetic disorder. Several hundred genetic tests are currently in use, and more are being developed (Sequeiros et al, 2008). The Multiplex Ligationdependent Probe Amplification (MLPA) is a PCR-based technique, which allows the detecting of copy number changes in DNA or RNA. MLPA can quantify up to 50 nucleic acid sequences or genes in one simple reaction, with a resolution down to the single nucleotide level (Schouten et al., 2002) needing only 20 ng of DNA. The MLPA procedure itself needs little hands on work allowing up to 96 samples to be handled simultaneously while results can be obtained within 24 hours. These properties make it a very efficient technique for medium-throughput screening of many different diseases in both a research and diagnostic settings (Ahn et al, 2007).