Illumina, Inc. and Loxo Oncology announced a global strategic partnership to develop and commercialize a multi-gene panel for broad tumour profiling, resulting in a distributable, next-generation sequencing (NGS) based companion diagnostic (CDx) with a pan-cancer indication. The co-development partnership will seek approval for a version of the Illumina TruSight Tumor 170 as a companion diagnostic (CDx) for Loxo Oncology's larotrectinib, which targets NTRK gene fusions, and LOXO-292, which targets RET gene alterations, across tumor types.

TruSight Tumor 170 is a comprehensive, state-of-the-art, next-generation sequencing test that interrogates point mutations, fusions, amplifications and splice variants in 170 genes associated with common solid tumours. The CDx version of TruSight Tumor 170 will allow local laboratories to provide referring physicians with comprehensive genomic information, so that patients can be matched to the most appropriate therapeutic options. This version of TruSight Tumor 170 will run on the NextSeq 550Dx platform.

"We are leveraging our leadership in next-generation sequencing to deliver in-vitro diagnostic solutions to improve the management of cancer patients in the clinic," said Garret Hampton, Ph.D., executive vice president of clinical genomics at Illumina. "To this end, we are partnering with leading biotechnology companies, such as Loxo Oncology, to develop companion diagnostics for best-in-class therapeutics. Distributable diagnostic solutions, such as a CDx version of TruSight Tumor 170, in combination with the NextSeq 550Dx platform, will enable labs to perform precision medicine testing in-house."

Under the partnership, the companies will collaborate to validate a CDx version of TruSight Tumor 170 for NTRK fusions and RET fusions/mutations as a Class III FDA-approved diagnostic in conjunction with larotrectinib and LOXO-292, respectively. The companies are also planning to broaden the clinical utility of the full panel by obtaining regulatory approval for the other assay content, to be marketed as a tumour profiling test. Illumina will lead regulatory activities related to the Class III plans for NTRK and RET, the Class II plans for the tumour profiling content and CE marking.

"We are very excited to announce this collaboration with Illumina, the world's leader in NGS technology," said Jacob Van Naarden, chief business officer of Loxo Oncology. "We have piloted numerous NGS assays, and the Illumina TruSight Tumor 170 assay has consistently demonstrated robust performance with its assessment of both DNA and RNA, including highly sensitive gene fusion detection. The broad 170-gene assay content has the potential to deliver meaningful insights from a single tumour specimen, identifying patients with NTRK fusions, RET fusions, RET mutations, and many other actionable tumor alterations. Furthermore, we believe that this collaboration will improve patient access to high-quality NGS testing because pathologists will be able to run TruSight Tumor 170 locally and receive reimbursement."

TruSight Tumor 170 currently serves as the foundation for a comprehensive research use oncology menu, including:  170 unique genes informed by partnering pharmaceutical companies, academic community leaders and industry guidance enable broad tumour profiling; Integrated workflow allowing more comprehensive testing while preserving precious samples by evaluating DNA and RNA in one integrated protocol with only 40ng from FFPE samples; Underlying assay method to serve as a standard for oncology testing and will be deployed across a variety of applications including Immuno-Oncology and liquid biopsy.

Larotrectinib is a potent, oral and highly selective tropomyosin receptor kinase (TRK) inhibitor. The investigational new drug is in clinical development for the treatment of patients with cancers that harbour a neurotrophic tyrosine receptor kinase (NTRK) gene fusion. Growing research suggests that the NTRK genes, which encode for TRKs, can become abnormally fused to other genes, resulting in growth signals that can lead to cancer in many sites of the body. In clinical trials, larotrectinib demonstrated marked and durable anti-tumour activity in TRK fusion cancer regardless of patient age or tumor type. In an analysis of 55 RECIST-evaluable adult and paediatric patients with NTRK gene fusions, larotrectinib demonstrated an 80 per cent investigator-assessed confirmed overall response rate (ORR) and a 75 per cent centrally-assessed confirmed ORR, across many different types of solid tumours. Larotrectinib was well tolerated; the majority of all adverse events were grade 1 or 2. There were no treatment-related grade 4 or 5 events, and no treatment-related grade 3 adverse events occurred in more than 5% of patients.

Larotrectinib has been granted Breakthrough Therapy Designation, Rare Pediatric Disease Designation and Orphan Drug Designation by the US FDA.

In November 2017, Loxo Oncology and Bayer entered into an exclusive global collaboration for the development and commercialization of larotrectinib and LOXO-195, a next-generation TRK inhibitor. Bayer and Loxo Oncology will jointly develop the two products with Loxo Oncology leading the ongoing clinical studies as well as the filing in the U.S., and Bayer leading ex-US regulatory activities and worldwide commercial activities. In the US, Loxo Oncology and Bayer will co-promote the products.

LOXO-292 is a potent, oral and selective investigational new drug in clinical development for the treatment of patients with cancers that harbour abnormalities in the rearranged during transfection (RET) kinase. RET fusions have been identified in approximately 2% of non-small cell lung cancer, 10-20% of papillary thyroid cancer, and a subset of colon and other cancers. RET point mutations account for approximately 60% of medullary thyroid cancer. Both RET fusion and select RET mutated cancers are primarily dependent on this single activated kinase for their proliferation and survival. This dependency, often referred to as "oncogene addiction," renders such tumours highly susceptible to small molecule inhibitors targeting RET. LOXO-292 was designed to inhibit native RET signaling as well as anticipated acquired resistance mechanisms that could otherwise limit the activity of this therapeutic approach. LOXO-292 is currently being studied in a Phase 1 trial.

Illumina is improving human health by unlocking the power of the genome. The company focus on innovation has established us as the global leader in DNA sequencing and array-based technologies, serving customers in the research, clinical, and applied markets.

Loxo Oncology is a biopharmaceutical company innovating the development of highly selective medicines for patients with genetically defined cancers.