In honor of the discovery of the double helix structure of DNA by James Watson and Francis Crick in 1953 and the completion of the Human Genome Project in 2003, we celebrate the 25th of April as International DNA Day. While acknowledging all great efforts by the brilliant minds that pushed the genetic innovation, it is a day we not only look into the core of the cell but also ahead to the leaps that are still to be taken in the field of genetic analysis and application. These two milestones mark great leaps taken then but much has happened in between and since.
The code of life
As the carrier of genetic information from one generation to the next, DNA is as old as humanity itself. It is only relatively recently that we understand the implications of the molecule and even more recently how to gather information about diseases, heredity and genetic alterations. While this information is of great value to researchers, it has found its impact on diseases and applications paving the way towards a more personalized treatment approach and renewed insights in what was considered established knowledge. Technologies used in the 80s, 90s and 00s to complete the Human Genome Project have been replaced by quicker and cheaper options, making the techniques of genome analysis more accessible for research and diagnostic purposes.
The Human Genome Project (HGP) was an effort initiated in 1990 in the United States with the intentions to sequence the euchromatic regions of the nuclear genome, which makes up approximately 92.1% of the total human genome. When in 1977 Sanger reported his method for determining the order of nucleotides in DNA, the options for genetic innovations and research opened. In the same year, the first human gene was isolated and sequenced. It was not until the development of whole-genome shotgun sequencing technique combined with the data processing computer algorithms developed at The Institute for Genomic Research (TIGR) that high amount of sequencing data could be produced and processed. When after several years of working on the HGP, only 5% of the genome was sequenced in 1998, a step was taken to ensure the set goals (finished by 2005) remained possible. In that year PE Biosystems (now Applied Biosystems, a Thermo Fisher Company) developed an automated high throughput capillary DNA sequencer, the ABI PRISM 3700 DNA Analyzer. This sped up the progression, but another factor played a bigger role in the increased speed: Celera. Celera is a private company that joined the effort to sequence the human genome but contrary to the publicly funded HGP, they did not want to make the data publicly available. This motivated the publicly funded effort to speed up the publication of the data, later Celera changed its standpoint and made its data available under certain circumstances.
This all led to the publication of the initial ‘working draft’ of the whole human genome in 2001. To ensure that the researchers had the worlds’ attention, the article was published in Nature and in Science and both the US president Bill Clinton and UK prime minister Tony Blair gave speeches about the subject. In April 2003, researchers published the final sequencing mapping, it was determined that 99% of the euchromatic human genome was sequenced with a 99.99% accuracy. Leaving approximately 8% of the total genome still unaccounted for.
The logo of the Human Genome Project (source: Human Genome Project, U.S. Department of Energy)
The covers of Nature and Science with the publication of the initial human genome in 2001 (Source: Nature, Science)
It took several steps to fill all the unresolved gaps, a publication in 2009 by the Genome Reference Consortium showed an updated version leaving approximately 300 gaps. This was brought down to 160 gaps by 2015 and to 79 gaps by 2020, still accounting for 5% of the human genome. Subsequently, the Telomere-to-Telomere consortium focused on sequencing the most troublesome chromosome: the Y-chromosome. This is filled with genetic repeats and has a high variability between males. Eventually, Rhie et al. published the successful sequencing of the missing regions in the Y-chromosome, achieving full sequencing of all 24 human chromosomes.
Decoding the first humans – a local hero
Sequencing the first human genomes was a costly expense, among the memorable names of the first humans that had their DNA sequenced were James Watson (discoverer of the DNA helix shape in 1953) and Craig Venter (founder of Celera). In 2009, Stanford professor Stephen Quake reported that he was able to sequence his DNA for less than $50,000 and with a team of just two other people. Highlighting that the advancements that were made reduced the pricing from several million dollars and a team of 250 people to a far smaller investment. But another major step was taken the year before, with a Leiden local hero in the lead.
It was in 2008 that the genome of a female joined the sequencing mix. A Dutch clinical geneticist working at the Leiden Genome Technology Center of the Leiden University Medical Center, had her DNA sequenced not only as the first woman in the world but also as the first person in Europe. After four males, Dr. Marjolein Kriek, a clinical geneticist, provided her DNA to be sequenced as the fifth person in the world. The aim was to show deeper insights into X-chromosome variability, so a total of 22 billion base pairs were read on Illumina 1G equipment. Because the sequencing was done in between other projects, it took 6 months to complete with a cost of €40.000.- (not including in-depth bioinformatic analysis).
GenomeScans’ predecessor ServiceXS was closely related to the project and was honoured to contribute to the sequencing effort of Dr. Krieks’ DNA. Afterward, her sequence has been turned into an art piece that stands at the Radboud University in Nijmegen, depicting the printed version of her whole genetic make-up.
Statue of dr. Marjolein Kriek (Source: Wikimedia)
The Genetic code of dr. Marjolein Kriek as depicted on the statue (Copyright: Bas van Vlijmen)
The next generation
The reduction in necessary investment (both monetary and personnel) that was experienced between the first full sequencing and that of Dr. Kriek has continued over the past years. With the most recent Next Generation Sequencing techniques, we can sequence a full genome in 2 weeks for less than a €1.000.-.
Next Generation Sequencing is a term used for a group of advanced sequencing technologies that allow for rapid and high throughput sequencing of RNA and DNA. Several different technologies have been developed by different providers with a range of applications. Sequencing by Synthesis (SBS) uses fluorescent labels and is applied by Illumina, Single-Molecule Real-Time (SMRT) sequencing is developed by PacBio and also uses fluorescence but only (as the name implies) a single molecule in real time. Nanopore Sequencing is developed by Oxford Nanopore and uses a difference in electrical current to determine the sequence of the molecule.
Even though that sounds positive, the question remains what good it can do for people that are experiencing healthcare issues. Due to the previous high cost of whole genome sequencing, GenomeScan would perform focussed panels based on the disease indication of a patient to determine what type of complications have arisen. “It is like reading only a few chapters of a whole story” says GenomeScan CEO Kees van den Berg. “When we perform whole genome sequencing, we read the entire book, and we can provide the full story of a patient. We can indicate if there are any additional complications, providing the healthcare professionals with the right answers to aid in decision making. Due to the increased availability of whole genome sequencing, it will become cheaper than to perform several different tests and will eventually provide more data. This trend can already be observed in health insurance providers because they see the benefits and make whole genome sequencing standard care for some indications. I am confident that this will be the future of diagnostics”.
