Oxford Nanopore’s devices with 4bases kits will enable decentralised, flexible scalability with a significant decrease in turnaround time for clinical researchers in Italy and Switzerland, with a first target of same-day BRCA1 and BRCA2 analysis.

Oxford Nanopore Technologies plc (Oxford Nanopore) and 4bases, a Switzerland-based company, specialising in kits for sequencing and bioinformatic tools, today announce a collaboration to make available 4bases kits with Oxford Nanopore sequencing technology. While appropriate for a broad range of human and cancer genomic analyses, a first target is to enable same day sample-to-answer results for the analysis of the BRCA1 and BRCA2 genes.

BRCA1 and BRCA2 4bases kits are compatible with Oxford Nanopore’s devices, which start from $1000 for a MinION starter pack, expanding access to accurate, fast and affordable sequencing for any laboratory across Italy and Switzerland.

Internal studies using an extensive set of commercial samples have shown 100% concordance identifying the known genetic variants present within the BRCA1 and BRCA2 genes of these samples. These variants, which include single nucleotide variants and larger changes, are associated with increased cancer risk. The performance of the kits is equivalent to that of existing gold-standard methods, such as short-read sequencing, MLPA and Sanger sequencing. Research studies using clinical samples are underway in multiple sites.

Sequencing BRCA1 and BRCA2 

Mutations in BRCA1 and BRCA2 genes can significantly increase the risk of developing breast and ovarian cancers. Early identification of mutational carriers enables appropriate risk stratifications which can lead to important survival benefits. Additionally, highly effective treatment options such as PARPi (Poly(ADP-ribose) polymerase inhibition) have now been approved for certain cancer patients harbouring BRCA1 and BRCA2 genetic mutations.

In healthcare, routine BRCA1 and BRCA2 genetic testing currently performed for both cancer prevention and treatment are highly centralised and can have a turnaround time ranging from a few weeks to months, depending on the need to batch multiple samples. In certain cases, the long turnaround time can lead to making clinical decisions (like surgical treatment decisions) without the result at hand which can later have strong implications for patients harbouring BRCA mutations.

To address an unmet need for workflows that can rapidly sequence BRCA1 and BRCA2, in matter of hours or day(s), Oxford Nanopore and 4bases will release an end-to-end research workflow using 4bases kits and Oxford Nanopore sequencing technology.

The 4bases kit targets the BRCA1 and BRCA2 genes through PCR generating short amplicons compatible with Oxford Nanopore’s built-in short fragment mode (SFM) sequencing and, following nanopore library prep and sequencing, the software identifies variants present in these genes to provide a report listing the mutations to the end user.

Gordon Sanghera, CEO, Oxford Nanopore Technologies, commented:  

“We are delighted to be working with 4bases on this important work to deliver distributed and accessible sequencing to scientists in Italy and Switzerland. In the first instance, we are excited to see how the combination of 4bases and nanopore sequencing will enable rapid characterisation of the BRCA1 and BRCA2 genes and significantly decrease the time to answer. As our collaboration develops we will see this expanded across the breadth of the 4bases portfolio and this will have a large impact on many research areas.”   

Fabio Grandi, CEO, 4bases, commented:

“With now over 10 years of activity in the field of next generation sequencing, we at 4bases have witnessed every step of what we can call a revolution, leading to an always faster and more comprehensive acquisition of genomic data to the increasing benefit of clinicians involved with precision medicine. Our solutions are now used on a worldwide basis with the main sequencing systems and are now specifically adapted to the new Oxford Nanopore sequencing technology. After the development of 4eVAR, our new bioinformatics tool, completed last year, this strategic collaboration represents a new and exciting milestone in the 4bases development.”