As part of the deal, ArcherDX will develop a series of diagnostic tests by using its anchored multiplex PCR (AMP) chemistry, which will run on the Illumina MiSeqDx instrument.
The tests being developed will be used in the current and future clinical trials.
ArcherDX CEO Dr Jason Myers said: "The ArcherDX-Illumina partnership enables our vision of creating a companion test aligned to the current and next generations of targeted therapies, rather than a single companion diagnostic targeting a single targeted therapy.
"This will dramatically improve patient outcomes and lower the sample and cost burdens of clinical sequencing in the future."
Illumina oncology market development vice president Dr John Leite said: "Illumina is committed to enabling the development of companion diagnostics using NGS."
Last December, Illumina signed an agreement with Novogene to jointly develop next-generation sequencing (NGS) system for reproductive health and oncology applications.
Under the terms of the deal, Illumina sequencers technology will be combined with Novogene’s advanced clinical application development capabilities.
ArcherDX produces NGS assays to generate sequencing libraries for detecting gene fusions, point mutations, CNVs and RNA abundance.