Whole genome sequencing

Whole genome sequencing (WGS) is a method for comprehensively analyzing the entire genome of an organism using next-generation sequencing (NGS). WGS is useful in various fields of research, including agricultural genomics, environmental sciences, cancer research, microbiology and developmental biology.

The principle of WGS is based on a very comprehensive genetic analysis, which is used in particular in research into rare diseases, diseases of unknown origin and tumors. The method is also used to decode the entire genome (approx. 3 billion base pairs in humans). The respective gene sample is compared with a reference genome using machine learning programs. This direct comparison allows genomic variants to be identified.

The introduction of NGS sequencing (Next Generation Sequencing) has made it possible to analyze the entire human genome (Whole Genome Sequencing, WGS) within a reasonable time frame. NGS is a technological advancement of classic Sanger sequencing. Whereas it used to be possible to read one DNA molecule at a time, NGS allows millions of different DNA segments to be read in parallel in a single analysis.

The entire nucleotide sequences (approx. 3 billion DNA building blocks) of all 23 chromosome pairs are sequenced (cut into small pieces), adapters are added to the ends of the fragments so that they can be attached to the sequencing platform. The fragments are amplified. The sequencing machine is located in the base sequence (ATCG) of each fragment. A computer reassembles the many fragments into a virtual overall picture. They can now be analyzed bioinformatically. Only a small fraction of the entire genome codes for proteins (the so-called exons) - 98% of the genome consists of non-coding DNA and includes introns, regulatory sequences and various repetitive sequences (see figure).

In principle, linking genomic data with phenotypic and clinical data offers "great opportunities for improving the understanding of complex (inflammatory) disease patterns in particular and also for the development of new therapeutic approaches". Genome databases are an important building block for identifying disease-causing mutations. According to recent studies, WGS has made it possible to find causal mutations in known disease-associated genes in around half of all patients with suspected genetic developmental disorders. To date, mutations are known in more than 4,000 of the 20,000 protein-coding human genes. This makes (comparative) genome, transcriptome and epigenome analyses possible.

Orphan diseases: Whole genome sequencing (WGS) is becoming the preferred method for the molecular genetic diagnosis of rare and unknown diseases and for the identification of relevant causes of cancer. Compared to other molecular genetic methods, WGS captures most genomic variation and eliminates the need for sequential genetic testing (Bagger FO et al. 2024).

Bacteriology: The complete genome sequence of a bacterial pathogen was first successfully determined in 1995. The complete nucleotide sequence of Haemophilus influenzae was determined using the chain termination method developed by Sanger et al. in 1977. This technology is labor-intensive, expensive and time-consuming. Since 2004, high-throughput next-generation sequencing technologies have been developed that enable highly efficient, time-saving and cost-effective whole genome sequencing (WGS) of all organisms, including bacterial pathogens. WGS technologies are used to identify bacterial species, strains and genotypes from cultured organisms and directly from clinical samples (Mustafa AS 2024. WGS has also contributed to the determination of antibiotic resistance through the detection of antimicrobial resistance genes and point mutations.

• Antimicrobial resistance (AMR): NGS has become an integral part of antimicrobial resistance (AMR) surveillance. The high throughput, now relatively low cost, high discriminatory power and fast turnaround time of WGS compared to classical biochemical methods mean that the technology is likely to remain a fundamental tool in AMR surveillance and for public health (Sørensen LH et al. 2021).

Some laboratories integrate internal NGS automation platforms, e.g. Falcon. This ensures seamless service workflows and remarkably high throughput. Automated and streamlined workflows and high-performance computing clusters now ensure that data is delivered promptly and without loss of quality, regardless of project size. The most modern sequencing platforms are Illumina, PacBio and Oxford Nanopore. The spatial transcriptomics service is supported by Visium CytAssist from 10X Genomics. All workers benefit from the latest platforms. Researchers can be offered the opportunity to carry out their projects using different sequencing strategies depending on the research application.

The latest generation of NGS technology is RNA sequencing (RNA-Seq). In its simplest form, RNA-Seq enables the determination of RNA molecules in a sample at the time of sampling. This enables a statement to be made about the activity of the genes recorded.

1. Bagger FO et al. (2024) Whole genome sequencing in clinical practice. BMC Med Genomics 17:39.
2. Marinova-Bulgaranova TV et al. (2025) Current Methods for Reliable Identification of Species in the Acinetobacter calcoaceticus-Acinetobacter baumannii Complex. Microorganisms 13:1819.
3. Mustafa AS (2024) Whole Genome Sequencing: Applications in Clinical Bacteriology. Med Princ Pract. 33:185-197.
4. Sørensen LH et al. (2021) Whole-genome sequencing for antimicrobial surveillance: species-specific quality thresholds and data evaluation from the network of the European Union Reference Laboratory for Antimicrobial Resistance genomic proficiency tests of 2021 and 2022. mSystems 9:e0016024.