ICT Aspects of Next-Generation-Sequencing Applied to Molecular Diagnostics

ICT Aspects of Next-Generation-Sequencing Applied to Molecular Diagnostics

Saskia Biskup (Institute for Clinical Genetics at Klinikum Stuttgart, Germany & CeGaT GmbH, Germany)
DOI: 10.4018/978-1-4666-3990-4.ch047
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Abstract

Next-Generation-Sequencing (NGS) techniques are currently on the rise. This is seen as a revolution by (most) geneticists. The wealth of data stemming from Next-Generation-Sequencing will without a doubt lead to significant advances in the field of molecular diagnostics. On the clinical side, this will be higher detection rates of the genetic causes of particular diseases in patients. On the scientific side, NGS techniques will lead to the discovering of genes related to certain diseases (see, for example, Mardis, et al., 2009; Haack, et al., 2010; Lupski, et al., 2010). However, these advances come at a price: geneticists will be confronted with different and new ICT issues related to NGS. Because of the so far unknown amount of data stemming from NGS, these ICT issues need to be taken seriously. The purpose of this chapter is to give an overview on the different ICT aspects that come with the introduction of Next-Generation-Sequencing in molecular diagnostics.
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Classical Molecular Diagnostics

For the last 10 years, molecular diagnostics used to be performed as follows: A medical doctor has a suspicion on a certain disease in a patient. To confirm the diagnosis the medical doctor sends a blood or DNA sample to a human geneticist. Often the human geneticist advises the medical doctor which gene should be tested. The human geneticist now isolates the DNA and amplifies the gene by Polymerase Chain Reaction (PCR). The PCR product is sequenced by means of Sanger Sequencing (Capillary Sequencers). The results are interpreted by the human geneticist and are summarized in a medical report. The medical report states if and to what degree a particular sequence variation is or might be related to actual or future illnesses. The human geneticist sends the medical report to the medical doctor requesting the genetic testing.

Note that by means of Sanger Sequencing it takes approx. 2 to 6 weeks to decipher one gene (depending on the number of exons per gene). The associated costs range from EUR 500 to EUR 4,000. However, many genetic diseases are diseases that can be caused by a sequence change in more than one possible candidate gene. Sometimes hundreds or even thousands of such candidate genes exist. In this case the classical Sanger approach of sequencing one candidate gene after the other is excessively expensive and extremely time consuming. Usually only the two or three most likely genes are deciphered. As a consequence in approx. 80-90% of clinically suspected genetic diseases the causative gene variation is not found by Sanger Sequencing.

Before turning our attention to diagnostic panels we need to discuss briefly why finding the genetic cause of a disease is important. Of course, the root cause of a genetic disease cannot be healed – simply because it is a genetic variation. This disease causing genetic variation is part of the DNA of every single cell in the body of the particular patient.

In the following we will describe the advantages of understanding the genetic cause of a disease by using hereditary eye diseases: Loss of vision affects several million people worldwide. The disease usually starts during adolescence, making an underlying genetic cause very likely. Thereafter the loss of sight progresses slowly and can take decades. As of today a total of more than 200 genes have been described that, when defective, might cause hereditary ophthalmic disease, see Berger et al. (2010). The list is expected to grow longer since thousands of all human genes are relevant to retinal function.

Key Terms in this Chapter

Next-Generation-Sequencing (NGS): High throughput sequencing using new techniques.

Genetic Testing: Sequencing of variants of the genome and interpretation with respect to human diseases.

Genetic Testing: Sequencing of variants of the genome and interpretation with respect to human diseases.

Next-Generation-Sequencing (NGS): High throughput sequencing using new techniques.

Diagnostic Panel: Massive parallel screening of all genes related to a certain disease by applying NGS techniques.

Sanger Sequencing: Classical, low error sequencing method using a capillary. Today the “gold standard” for molecular diagnostics.

Sanger Sequencing: Classical, low error sequencing method using a capillary. Today the “gold standard” for molecular diagnostics.

Diagnostic Panel: Massive parallel screening of all genes related to a certain disease by applying NGS techniques.

Mutation: Disease causing variant in the human genome.

Single Nucleotide Polymorphism (SNP): Variant that is more frequent than 5% in the population.

Single Nucleotide Polymorphism (SNP): Variant that is more frequent than 5% in the population.

Mutation: Disease causing variant in the human genome.

Exome: All coding regions of the genome.

Exome: All coding regions of the genome.

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