Sarcomas are among the most genetically diverse cancers, comprising more than 100 distinct subtypes, each with its own molecular characteristics. Unlike many solid tumours, sarcomas are frequently defined by complex genomic alterations such as gene fusions, copy number variations (CNVs), internal tandem duplications (ITDs) and structural rearrangements. As a result, accurate molecular profiling has become an increasingly important part of diagnosis, classification and research.

As part of our Sarcoma Awareness series, this week we’re highlighting GeneFirst’s partnership with BiOligo, a leading manufacturer of high-quality oligonucleotides and raw materials for molecular diagnostics. Together we’re exploring some of the technical factors that underpin reliable NGS assays and why the quality of the oligos used within the assay can have a significant impact on performance.

Sarcoma Presents Unique Challenges for NGS

Developing robust NGS assays for sarcoma is far from straightforward. Many clinically important genomic alterations occur in challenging genomic regions or involve complex structural changes that require highly sensitive and reproducible detection.

One of the greatest challenges is the detection of gene fusions. Rearrangements involving genes such as EWSR1, FUS, CIC and SS18 are recognised hallmarks of several sarcoma subtypes, yet fusion partners and breakpoint locations can vary considerably between patients. Detecting these alterations reliably requires both well-designed assays and consistently manufactured, high-quality oligonucleotides.

Sarcoma testing also frequently involves copy number alterations, including amplification of MDM2 and CDK4 or deletion of CDKN2A. These analyses rely on consistent uniformity of sequencing coverage, making consistency across oligonucleotide pools particularly important.

To add further complexity, many clinically relevant targets are located within regions of unusually high GC content or repetitive DNA sequences, making them inherently difficult to analyse. At the same time, many clinical samples are derived from FFPE tissue, where DNA and RNA are often fragmented and degraded.

Why Oligonucleotide Quality Matters

Although different targeted sequencing technologies use different enrichment strategies – including ATOM-Seq, anchored PCR, amplicon-based sequencing and hybridisation capture – they all rely on high-quality oligonucleotides at critical stages of the workflow.

Whether functioning as primers, molecular tags or capture probes, the quality, purity and consistency of oligonucleotides can influence:

• Sensitivity for detecting clinically relevant variants

• Specificity and level of off-target sequencing

• Coverage uniformity across target regions

• Reproducibility between samples and sequencing runs

• Overall confidence in molecular results

Even a well-designed assay can be affected if the underlying oligonucleotides exhibit sequence errors, poor purity or inconsistent representation within complex pools.

At GeneFirst, we recognise that assay performance depends not only on innovative assay design but also on the quality of every component within the workflow. That's why we've partnered with BiOligo, a leading manufacturer of high-quality oligonucleotides and molecular diagnostic raw materials, to highlight the important role that oligo quality plays in supporting advanced NGS applications.

BiOligo works with assay developers across a broad range of sequencing technologies, supplying oligonucleotides manufactured to deliver high sequence fidelity, excellent pool uniformity and consistent batch-to-batch performance. These attributes help support applications ranging from fusion detection, mutation profiling and copy number analysis to the development of robust oncology assays.

Looking Ahead

Precision oncology relies on more than advanced sequencing technologies; it relies on quality throughout the entire workflow. By working with leading partners such as BiOligo, GeneFirst is committed to supporting the development of robust, reliable NGS assays that help researchers and laboratories detect complex genomic alterations with confidence. For sarcoma testing where complex structural alterations and challenging clinical samples are common, high-quality oligonucleotides provide an important foundation for generating robust and reproducible sequencing data.

If you'd like to learn more about BiOligo and its products or discuss your assay development needs, please visit our website or contact us at info@genefirst.com

About BiOligo

BiOligo is a leading manufacturer of high-quality custom oligonucleotides and molecular diagnostic raw materials, supporting researchers, assay developers and diagnostics companies worldwide. With expertise in oligonucleotide synthesis, complex oligo pools and custom manufacturing, BiOligo helps enable the development of robust molecular assays and next-generation sequencing (NGS) applications through a commitment to quality, consistency and technical excellence.

About GeneFirst

GeneFirst Ltd is a UK-based molecular diagnostics company focused on advancing cancer screening and oncology testing through innovative molecular technologies. The company develops and manufactures diagnostic solutions that support the early detection, monitoring and management of cancer, helping laboratories and healthcare providers improve patient outcomes.

Media Contact

Winnie Wu

Chief Operations Officer

GeneFirst Ltd

Email: winnie.wu@genefirst.com

Website: www.genefirst.com