The Next Generation Sequencing (UFS-NGS) Unit at the University of the Free State (UFS) – in a bid to advance genomics initiatives, training, and services – recently acquired new state-of-the-art technology with a wide range of advantages, including educational enhancement and cutting-edge research on food security and healthcare applications and impact.
The NextSeq 2000 platform boasts a higher capacity of up to 350 and 550 gigabytes of data on the P3 and the recently released P4 flow cell, respectively, with a unique chemistry coupled with a variety of built-in applications. Its flexibility will allow the university to cater for both state-funded research projects and private collaborations, positioning the institution as a hub for cutting-edge genomics research and innovation.
Prof Martin Nyaga, Head of the UFS-NGS Unit and Associate Professor in the Division of Virology, says acquiring such a next-level genomic instrument is a game changer and a step forward in the unit’s agenda to advance genomic research initiatives, produce quality research data, and add to our vision of becoming a reputable genomic hub in Africa.
The NextSeq 2000 platform was launched by Prof Vasu Reddy, Vice-Chancellor: Research and Internationalisation, Prof Gert van Zyl, Dean: Faculty of Health Sciences, and Dr Glen Taylor, Senior Director: Directorate Research Development (DRD), on 8 April 2024.
Hands-on experience for researchers and students
“Over the years, the UFS-NGS Unit has generated several thousands of whole genome/targeted sequences and metagenomic data sets of various pathogens, including rotaviruses and coronaviruses, among others, using the Illumina MiSeq. The NextSeq 2000 will not only be a research tool, but also an educational asset.
“This will serve to provide students and researchers with hands-on experience in genomics and molecular biology, equipping them with practical skills necessary for careers in various scientific and medical, biomedical, and agricultural disciplines that are relevant both nationally and globally. It will further enable collaborative genomic research initiatives among researchers at the UFS and globally, especially in Africa,” says Prof Nyaga.
The UFS-NGS Unit team, which previously operated on a MiSeq™ sequencing platform, has already received hands-on training from the Illumina channel partner in South Africa, SEPARATIONS – led by Drs Justin Mills and Natasha Kitchin – which was a huge success. Several successful runs have since been sequenced using the P3 flow cells, generating more than 350 gigabytes of metagenomics data through this robust platform.
Critical for research quality and diagnostic precision
Acquiring this instrument, explains Prof Nyaga, was a sensible decision for the university, particularly given the existing familiarity with Illumina technology through the MiSeq platform.
“Its versatility caters to diverse research applications aligning with varied research needs, including but not limited to agricultural and biomedical sciences, vaccine efficacy studies, human cancer research, and the studies on transmittable diseases. Its high-throughput sequencing capabilities enable researchers to delve deep into the genetic makeup of tumour samples and identify critical mutations and markers linked to cancer development.”
Prof Nyaga says this knowledge is vital for tailoring personalised treatments and gaining insights into the underlying mechanisms of diseases, ultimately enhancing patient outcomes and, where applied in agricultural sciences, enhances food security.
Moreover, the NextSeq 2000 data accuracy ensures the reliability of genetic analyses, which is critical to maintaining research quality and diagnostic precision, and its scalability future-proofs the institution’s capacity as our research endeavours grow. It empowers both the faculties of Health Sciences, and Natural and Agricultural Sciences, as well as the broader research network, to conduct groundbreaking studies and publish high-impact research papers.
This, in turn, will attract top-tier talent and multiple funding opportunities. The NextSeq 2000's ability to sequence rare and underrepresented clinical samples from the Free State and beyond, will enable research to address health disparities, enhance diagnostics for region-specific diseases, and contribute to a more equitable health-care system. This aligns seamlessly with Vision 130 to champion global health initiatives and foster societal well-being.
Additionally, routine diagnostics can stand to benefit significantly from the NextSeq 2000's capabilities. Its high-throughput sequencing and enhanced accuracy can streamline diagnostic processes, reducing patient waiting times and improving diagnostic precision. The result is better patient care and treatment outcomes.
• The UFS-NGS Unit organises annual data and bioinformatics workshops to enhance usage of genomics data produced by the sequencing platforms available in the UFS-NGS Unit. Researchers applying these techniques are encouraged to click here and apply for the 2024 bioinformatics workshop and a genomics clinical forum.