NGS in Molecular Diagnostics

The first NGS system was approved for clinical use by the FDA only in 2013. Hence, the market segment is quite new, even though a significant industry exists for LDTs performed as testing services on NGS platforms by certified clinical labs. The current IVD market available in clinical sequencing consists largely of sales of NGS systems to reference and specialty genetics labs, including instruments, library preparation and sequencing reagents, and other consumables.

Currently, NGS technologies that are mainly used in clinical laboratories are Illumina and Ion Torrent systems. The Ion Torrent Personal Genome Machine (PGM) was launched in 2011 by Life Technologies (now part of Thermo Fisher). The more popular Illumina benchtops for diagnostic purpose are MiSeq (launched in 2011), MiniSeq (launched in 2016), and iSeq100 (launched in 2017). The Ion Torrent exploited the emulsion PCR using native dNTP chemistry that releases hydrogen ions during base incorporation by DNA polymerase and a modified silicon chip detecting the pH modification. Illumina technology, on the other hand, is based on the existing Solexa sequencing by synthesis (SBS) chemistry with the use of very small flow-cells, reduced imaging time, and fast sequencing process.

While polymerase chain reaction (PCR) technology has been at the forefront of diagnostics during the COVID-19 pandemic, sequencing has been at the forefront of understanding the SARS-CoV-2 virus responsible for the disease. In many regions, a set percentage of samples must be sequenced.

Kalorama extensively covers next-generation sequencing in its report – Molecular Diagnostics The World Market for Molecular Diagnostics Tests, 11th Edition. Clinical nucleic acid sequencing diagnostics stand apart from other molecular diagnostics tests such as NAATs since clinical sequencing results are not limited by probe specificity and they permit reading of the sequence. While NAAT probes may miss aberrant sequences containing SNPs, software-driven, open interpretation of clinical sequencing enables a more flexible and comprehensive

NGS and COVID-19

Sequencing has been an essential tool for the development of strategies and therapeutics in the fight against COVID-19, and sequencing-based rapid and high-throughput diagnostics for COVID-19 are in development. Sequencing technology suppliers are collaborating with researchers to develop sequencing-based diagnostic tools. For example, several groups are using Illumina’s next-generation sequencing (NGS) technology to develop ultrahigh-throughput COVID-19 diagnostic testing. Illumina received EUA for its COVIDSeq test in June 2020.

In April 2021, Translational Genomics Research Institute (TGen) and Jumpcode Genomics announced a collaboration to develop COVID-19 tests using a combination of NGS and CRISPR.

Oxford Nanopore has also been developing COVID-19 diagnostics using portable sequencing platforms. In May, the company announced the development of Lampore, an end-to-end assay for the detection of SARS-CoV-2. Lampore is designed as a rapid, low-cost, and scalable assay that can be used in both high-throughput labs and decentralized locations.

In May 2020, DNAe, a company relatively new to the sequencing market, announced that it is developing a point-of-need SARS-CoV-2 test using its silicon transistor-based Lidia-SEQ platform. The company is currently developing the test as part of a contract with the U.S. Biomedical Advanced Research and Development Authority potentially worth $51.9 million. In April, the U.S. Food and Drug Administration (FDA) designated the system and its first assay for detecting the infection that causes sepsis a breakthrough device. Under the breakthrough device program, the FDA supports and helps accelerate the development of novel diagnostics technologies.

NGS and Companion Diagnostics

There has been a number of developments in next-generation sequencing and companion diagnostics:

In September 2022, Qiagen and Neuron23 announced an agreement to develop a NGS based companion diagnostic for Neuron23’s brain penetrant leucine-rich repeat kinase (LRRK2) inhibitor for Parkinson’s disease; it is planned to be developed using the NextSeq 500 System.

In June 2022, the FDA approved Foundation Medicine’s FoundationOne CDx as a companion diagnostic (CDx) for Roche’s Rozlytrek (entrectinib); it is used to identify patients with ROS1 fusion-positive NSCLC, or patients with NTRK fusion-positive cancers, for whom treatment with Rozlytrek may be appropriate.

In May 2022, Illumina announced the addition of a companion diagnostic (CDx) indication to its CE-marked in vitro diagnostic TruSight Oncology (TSO) Comprehensive (EU) test.

Illumina and Thermo both have been collaborating with pharmaceutical companies to develop CDx assays. In 2017, Illumina received FDA approval for Praxis Extended RAS Panel test to run on MiSeqDx, which is a CDx test developed in partnership with Amgen that analyzes 56 variants in the KRAS and NRAS genes to test if metastatic colorectal cancer patients will benefit from Amgen’s Vectibix (panitumumab). In April 2021, Illumina and Kartos Therapeutics announced a partnership to co-develop a TP53 companion diagnostic (CDx) based on the content of Illumina’s comprehensive genomic profiling assay, TruSight Oncology 500 (TSO 500). In January 2021, Illumina and Myriad Genetics agreed to create a kit-based version of the myChoice oncology companion diagnostic (CDx) test for international markets; to develop and commercialize kits globally for the assessment of homologous recombination deficiency (HRD) along with other proprietary biomarkers; using a combination of TruSight Oncology content and myChoice.

In March 2021, Illumina and Intermountain Precision Genomics agreed to create a comprehensive germline genetic testing and somatic tumor offering that combines Myriad’s hereditary cancer and companion diagnostic tests with Intermountain Precision Genomics’ laboratory services, utilizing the TheraMap test—powered by the TruSight Oncology 500 (TSO 500) NGS test from Illumina.

Thermo Fisher has also been actively focusing on CDx market opportunities. In 2017, the company received FDA approval for its OncomineDx Target Test. This NGS-based multiplex CDx test simultaneously evaluates patient tumor samples for biomarkers associated with targeted therapies for non-small cell lung cancer (NSCLC). The test was the first NGS-based IVD for NSCLC and was developed in partnership with Pfizer and Novartis. Results on three genes included enable the identification of patients eligible for treatment with combined therapy of Tafinlar and Mekinist, XALKORI, or IRESSA. The test panel currently covers 46 cancer-driver gene variants evaluation. The company is expanding the clinical utility of the test by partnering with more pharmaceutical companies. For instance, Thermo Fisher signed agreements with Daiichi Sankyo and Takeda Pharmaceuticals in May 2018.

In February 2021, Qiagen and Inovio Pharmaceuticals announced an extension of their partnership with a new master collaboration agreement to develop liquid biopsy-based companion diagnostic products based on NGS to complement Inovio’s therapies; for use on Illumina NextSeq 550 Dx.

In general, CDx is a major focus in the clinical NGS market segment. Between 2014 and 2018, 26 significant CDx products were approved by FDA. Roche received the maximum number of product approvals during this period, based on its FoundationOneCDx and Ventana ALK (D5F3) CDx Assays. Agilent Technologies, Inc. registered the second-highest number of product launches in the past four years, primarily through its Dako range of CDx products.

Nine of the 26 CDx approvals between 2014 and 2018 were for NSCLC. Considering the growing lung cancer incidences worldwide, which is estimated to be over 2.2 million in 2018, the demand for lung cancer diagnostics and drugs can be expected to rise in future. The reimbursement landscape for these tests also looks better. In April 2018, The Centers for Medicare & Medicaid Services have announced that NGS–based CDx will be covered for beneficiaries with advanced cancer. Both these factors, in addition to the major collaborations focused on NGS in the global CDx markets, are expected to drive the market for NGS-based cancer diagnostics.

The number of players in the CDx segment is expected to increase in the coming years. In the United States, CLIA allows manufacturers to skip the FDA-approval process, by proving the effectiveness of a new CDx product to be similar to an already FDA-approved CDx product. This process allows several manufacturers to commercialize their products. However, there are several measures that are being currently undertaken by the FDA to curb this, which would consequently lead to a decrease in the number of players in the overall market owing to pricing pressure. Regulatory bodies in other markets such as the EMA (Europe), CFDA (China), and MHLW & PMA (Japan), have also been aligning their regulatory processes with that of the FDA, to unify the overall regulatory process for CDx. In Europe, there is higher availability of CE- marked clinical sequencing kits. In the Chinese market, it is mandatory that all clinical sequencing services be performed using CFDA-approved sequencing kits and systems.