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Sequence-based diagnostics – Methods & Applications

Sequence-based diagnostics analyzes the DNA or RNA sequence of an organism to detect diseases, identify pathogens, and precisely characterize genetic alterations.

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Things worth knowing about "Sequence-based diagnostics"

Sequence-based diagnostics analyzes the DNA or RNA sequence of an organism to detect diseases, identify pathogens, and precisely characterize genetic alterations.

What is sequence-based diagnostics?

Sequence-based diagnostics is a modern approach in laboratory medicine and molecular biology that determines the precise order of nucleotides – the DNA or RNA sequence – of an organism, pathogen, or human genome. Using state-of-the-art sequencing technologies, genetic information is read and analyzed with high accuracy. The resulting data allows clinicians to draw conclusions about diseases, pathogen types, resistance mechanisms, and individual genetic risk profiles.

Methods of sequence-based diagnostics

Several technology generations and approaches are used in sequence-based diagnostics:

Sanger sequencing

Sanger sequencing is one of the oldest and most well-established methods. It is suitable for targeted analysis of individual genes or short DNA segments and is considered the gold standard for confirming point mutations.

Next-Generation Sequencing (NGS)

Next-Generation Sequencing (NGS), also known as high-throughput sequencing, enables the parallel sequencing of millions of DNA fragments simultaneously. It is used for:

Whole genome sequencing (WGS)
Whole exome sequencing (WES) – analysis of all protein-coding regions
Targeted panel diagnostics – examination of defined gene groups
Transcriptome analysis (RNA-Seq) – measurement of gene expression

Nanopore sequencing

Nanopore sequencing is a newer technology capable of reading long DNA strands in real time. It is increasingly used for rapid pathogen identification, for example during outbreak situations.

Fields of application

Sequence-based diagnostics is applied across numerous medical disciplines:

Infectious disease diagnostics

By sequencing the genetic material of bacteria, viruses, or fungi, pathogens can be precisely identified, outbreak chains can be traced, and antibiotic resistance mechanisms can be detected at the genetic level. This was of major importance during the COVID-19 pandemic for variant surveillance.

Oncology

In cancer diagnostics, sequencing enables the identification of somatic mutations, gene fusions, and copy number variations in tumor cells. This is critical for selecting targeted therapies (precision oncology) and assessing treatment response.

Human genetics and rare diseases

In cases of unexplained illness, particularly in children, exome or genome sequencing enables the identification of germline mutations responsible for rare hereditary conditions. The diagnostic yield in this patient group ranges from 25 to 50 percent depending on the study.

Prenatal diagnostics

Non-invasive prenatal tests (NIPT) use sequence-based methods to analyze cell-free fetal DNA in maternal blood and detect chromosomal abnormalities such as trisomy 21 at an early stage.

Pharmacogenomics

Sequence-based diagnostics can identify genetic variants that influence individual responses to specific medications, supporting personalized prescribing with optimal efficacy and reduced risk of adverse effects.

Diagnostic workflow

The typical workflow of a sequence-based diagnostic investigation includes the following steps:

Sample collection: Blood, tissue, swab, urine, or other biological material
DNA or RNA extraction: Isolation of genetic material from the sample
Library preparation: Processing of nucleic acids for the sequencing workflow
Sequencing: Execution of the actual sequence analysis in the laboratory
Bioinformatic analysis: Processing and interpretation of raw data using specialized algorithms
Diagnostic report: Clinical interpretation and communication of results to the treating physician

Advantages and limitations

Advantages

Very high sensitivity and specificity
Ability to simultaneously analyze thousands of genes
Identification of previously unknown variants
Foundation for precision medicine
Increasingly cost-effective and rapidly available

Limitations and challenges

Large data volumes require specialized bioinformatic analysis
Variants of uncertain significance (VUS) complicate clinical interpretation
Data privacy and ethical concerns regarding the storage of genetic data
Not all laboratories have the required technical and bioinformatic infrastructure

References

Mardis, E.R. (2019): The impact of next-generation sequencing technology on genetics. In: Trends in Genetics, 24(3):133–141. DOI: 10.1016/j.tig.2007.12.007
European Parliament and Council of the EU: Regulation (EU) 2017/746 on in vitro diagnostic medical devices (IVDR) – European Commission, 2017.
Biesecker, L.G. & Green, R.C. (2014): Diagnostic Clinical Genome and Exome Sequencing. In: New England Journal of Medicine, 370(25):2418–2425. DOI: 10.1056/NEJMra1312543

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