Illumina, Grail, and Leading Cancer Centers Develop Ultra-Deep NGS Liquid Biopsy for Advanced NSCLC

In 2016, the FDA approved the first blood-based cancer genetic testing technology for detecting non-small cell lung cancer (NSCLC)EGFRGene Mutations Usher in a New Era of Liquid Biopsy.In NSCLC,EGFRThe mutation frequency of genes is very high, clearlyEGFRGene status is crucial for guiding subsequent targeted therapy in patients with non-small cell lung cancer (NSCLC). In large-scale cancer studies,Due to the approximately 14% failure rate of tissue biopsy NGS testing methods, it is not possible toTo meet clinical needs. Some scientists believe that,The detection method combining liquid biopsy, NGS, and machine learning is highly likely to compensate for the limitations of tissue biopsy and help guide treatment choices for cancer patients.

Recently,Scientists from Memorial Sloan Kettering Cancer Center, MD Anderson Cancer Center, and Dana-Farber Cancer Institute, in collaboration with research teams from Illumina and GRAIL, jointly developed a novel liquid biopsy method for detecting gene mutations in non-small cell lung cancer (NSCLC)—an ultra-deep cfDNA NGS analysis method (Ultra-deep next-generation sequencing of plasma cfDNA). This method can detect advancedMultiple aspects of NSCLCDriver mutation targets and drug-resistant mutations, with high sensitivity and specificity.In certain cases, this method can play a critical role when tissue biopsy data are insufficient for analysis. Recently, the related research findings were published inAnnals of OncologyOn.

It is reported that this liquid biopsy method utilizes Illumina’s “ultra-deep NGS” technology. Researchers canUltra-deep NGS sequencing of plasma cfDNA and white blood cells was performed using a hybrid capture panel covering 37 lung cancer-related genes, with a sequencing depth of 50,000×., enabling the detection of low-frequency variants. Simultaneously, white blood cells are sequenced to filter out non-cancer signals such as clonal hematopoiesis. The resulting sequencing data are ultimately analyzed using GRAIL’s machine learning algorithms to identify driver mutations.

Figure: Workflow of ultra-deep NGS targeted detection of cfDNA

In the study, scientists conducted genetic testing on 127 patients with advanced metastatic non-small cell lung cancer (NSCLC). The patients were divided into three groups,Group 1 consisted of patients with known cancer driver mutations identified through tissue-based genotyping;Group 2 consisted of patients with tissue NGS testing negative for driver mutations;Group 3 consists of patients with insufficient tissue testing data or unknown driver factors.The researchers calculated the clinical sensitivity and specificity of plasma testing for known carcinogenic factors, compared the results with tissue genotyping, and performed orthogonal ddPCR validation in a cohort of NSCLC patients.

Research has found that,This method is capable of detecting variants with an allele frequency of 0.14%.cfDNA-based genotyping is consistent with tissue biopsy-based genotyping in most cases. Study data showed that cancer driver gene mutations were identified by tissue biopsy in 91 patients, and ultra-deep cfDNA NGS analysis was able to detect these mutations in 68 of them.True Positive Rate: 75%。

Bob Li, an MSK medical oncologist leading the study, stated, “Among the 19 patients in whom tissue biopsy did not detect mutations,Ultra-Deep cfDNA NGS Analysis MethodNo abnormalities were detected, indicating that the method has no false positives.True Negative Rate was 100%。”

Figure: Number of patients with driver or resistance mutations detected in tumor tissue and plasma, along with sensitivity and specificity.

Meanwhile, researchers alsoThe tumor tissue was considered insufficient for genotyping.This method was evaluated in 17 patients. Based on the test analysis,Ultra-Deep cfDNA NGS AnalysisMethods identified 4 patients among themKRASmutation, with one patient confirmed by tissue biopsy. Furthermore, in 23 cases of acquired resistanceEGFRIn patients with mutations, the novel liquid biopsy method can detect multiple drug-resistance mutations, includingEGFR T790MandC797SMutations andERBB 2Amplification.

Bob Li stated that a 75% detection rate indicates that tissue biopsy may still be necessary. However, to formulate treatment plans earlier, liquid biopsy can be performed first. Therefore, when traditional tissue biopsy is not feasible, liquid biopsy may also serve as a valuable alternative.

The research findings indicate that, in the treatment of lung cancer,Ultra-deep NGS liquid biopsy can play an important auxiliary role in tissue biopsy by detecting a broad spectrum of driver and resistance mutations in NSCLC, enabling genotyping when tissue biopsy data are insufficient.Provided robust evidence supporting the potential clinical utility of plasma-based NGS testing and the clinical validity of cfDNA in the treatment and interventional studies of lung cancer.

Scientists have been exploring new methods to improve the sensitivity of liquid biopsy. For early detection of multiple types of cancer, GRAIL is working hard to develop highly sensitive blood tests. At the ASCO conference in June 2018, GRAIL presented data from its Circulating Cell-free Genome Atlas (CCGA) project. The research data showed that the detection rate of its liquid biopsy method for lung adenocarcinoma, squamous cell lung cancer, and small cell lung cancer ranged from 59% to 92%, with a false positive rate of less than 2%.

Currently, some liquid biopsy technologies primarily identify oncogenic mutations by detecting cell-free DNA (cfDNA), thereby assisting and guiding physicians in selecting treatment regimens. However, a joint review by the American Society of Clinical Oncology (ASCO) and the College of American Pathologists (CAP) concluded that it is premature to apply cfDNA testing in routine clinical practice, as existing studies have their own limitations and require further validation. This study creatively integrates liquid biopsy, next-generation sequencing (NGS), and machine learning, offering new insights for cancer therapy research. It is hoped that with advances in sequencing technology, scientists will develop more sensitive detection methods, enabling liquid biopsy to benefit a broader population of cancer patients.

References:

1.Ultra-deep next-generation sequencing of plasma cell-free DNA in patients with advanced lung cancers: results from the Actionable Genome Consortium

https://academic.oup.com/annonc/advance-article/doi/10.1093/annonc/mdz046/5390576

2. A liquid biopsy that combines Illumina’s ‘ultradeep’ sequencing with Grail’s machine learning

https://www.fiercebiotech.com/research/combining-illumina-s-ultra-deep-sequencing-grail-s-machine-learning-liquid-biopsy

3. Illumina-Sponsored Study Finds Liquid Biopsy Complements Tissue-Based Genotyping in Lung Cancer

https://www.genomeweb.com/liquid-biopsy/illumina-sponsored-study-finds-liquid-biopsy-complements-tissue-based-genotyping-lung#.XJxp6SJ742w