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Germline Results From Tumor-Normal Sequencing Guides Precision Therapy in Advanced Cancer Patients

NEW YORK – Employing tumor-normal sequencing, researchers have demonstrated that a significant number of advanced cancer patients learned germline findings that informed the treatment they received.

In one study, involving 12,000 patients treated at Memorial Sloan Kettering Cancer Center, researchers identified nearly 600 patients with recurrent or metastatic cancer who had actionable germline mutations, and 44 percent of them received targeted drugs either as part of the standard of care or as part of a research protocol.

Presenting the findings at the American Society of Clinical Oncology's virtual annual meeting, MSK's Zsofia Stadler said her group's study represents the most comprehensive assessment of the clinical utility of germline variants for guiding targeted therapy decisions in advanced cancer patients. This study, she said, demonstrates the "the importance of germline analysis for cancer treatment." 

In another study, presented at the same meeting, researchers from the University of Michigan investigated the prevalence of actionable germline mutations in a cohort of around 1,000 patients, and found that 49 patients, or close to 5 percent, had therapeutically targetable germline mutations.

The findings from these two studies are timely given that cancer patients are increasingly having their tumors sequenced in the hopes of identifying precision therapy options. Studies have shown that after tumor profiling, approximately 10 percent of patients received results based on which they can receive precision drugs. Patients' tumors are often profiled using next-generation sequencing (NGS) panels that gauge hundreds of genes and also pick up clinically significant germline mutations, but often these findings are censored and not reported back to or discussed with the patient. This is likely because there is a perception that germline genetic mutations, which have been historically important for inherited cancer risk assessment, don't really impact the immediate care of patients.

"We know the identification of germline alterations has important implications for our cancer patients, including implementation of appropriate cancer surveillance measures, potential risk-reducing measures, and of course predictive genetic testing for at-risk relatives," said Stadler. "However, less is known about the clinical impact of germline findings on targeted cancer treatment."

At MSK, cancer patients can have their tumors profiled with the MSK-IMPACT NGS panel which gauges more than 400 genes. The goal of this testing, Stadler said, is to identify genetic mutations in the tumor that can be targeted with treatments. To do this, the cancer center sequences a patient's tumor tissue and normal blood sample, compares the detected mutations, and subtracts out the germline variants that occur in every cell in the body, not just the tumor. At the end of this process, only the somatic mutations found in the tumor are reported.

Starting in 2015, patients at MSK who received testing with MSK-IMPACT could provide consent under an institutional review board-approved protocol to receive separate germline testing for 88 genes associated with increased cancer risk. Between 2015 and 2019, nearly 12,000 patients agreed to this additional testing to learn if they harbored likely pathogenic or pathogenic mutations in any of these genes. If patients had pathogenic findings, this was noted in their medical record, which investigators then reviewed to assess whether the mutations could inform treatment.

Around half of these 12,000 tested patients had breast, prostate, pancreatic, or colorectal cancers, while the rest of the patients had a variety of rarer tumor types. Approximately 2,000 patients, or 17 percent, had likely pathogenic or pathogenic mutations, 682 of whom had mutations in high- or moderate-penetrance genes.

In terms of therapeutic actionability, Stadler and colleagues identified targetable mutations in 849 patients, or 7 percent. Since PARP inhibitors now can be given to patients with BRCA1 or BRCA2 mutations with certain types of cancers, mutations in these genes comprised more than half of the actionable findings. Nearly 20 percent of mutations were in Lynch syndrome genes, which can guide immunotherapy use.

MSK classifies the actionability of somatic variants detected by MSK-IMPACT using a three-tier system that emerged in the process of garnering FDA authorization for the panel. In authorizing that test, the FDA released a three-tier framework to help labs determine what information they could accurately communicate in test reports based on the evidence underlying detected biomarkers. The same system can also help oncologists prioritize which findings are most informative for their patient's care from the long list of genetic mutations often identified by these tests. 

In the FDA's framework, tier 1 biomarkers are those that the agency has given companion diagnostic status based on evidence showing that they can determine which patients will or will not respond to a drug. Tier 2 biomarkers are "cancer mutations with evidence of clinical significance" that doctors can use in the care of cancer patients in line with guidelines and other information. Tier 3 biomarkers are "cancer mutations with potential clinical significance," which can help direct patients to clinical trials.

Since germline variations don't have a widely accepted system of classification for therapeutic actionability, Stadler and colleagues adapted this three-tier system for somatic variants to weigh the evidence on the 88 cancer risk genes. While 849 patients, or 7 percent, had targetable germline mutations in tier 1 and 2 genes, using all three tiers, around 1,000 patients, or nearly 9 percent, had germline mutations with therapeutic significance.

The researchers used the more stringent criteria — germline mutations in tier 1 and 2 genes — to try to guide treatment decisions for nearly 600 patients with recurrent or metastatic cancer. Ultimately, 44 percent received targeted drugs either as part of the standard of care or as part of a research protocol. Patients who received treatment had germline mutations in a variety of genes, though alterations in BRCA1 and BRCA2 drove a lot of the therapeutic decisions in the study.

As such, researchers explored this subset of patients in more detail. Of the 175 patients with BRCA1/2 germline mutations, 57 percent were classified as tier 1 mutations because patients had breast or ovarian cancer and were able to receive PARP inhibitors that had been FDA approved for their molecularly defined indication. More than 40 percent — including 21 percent of pancreatic cancer patients and 11 percent of prostate cancer patients — received PARP inhibitors under a research protocol. Since this study, however, the FDA has approved PARP inhibitors for BRCA-mutated pancreatic and prostate cancer

"With the emergence of novel targeted treatments with new FDA indications, the therapeutic actionability of germline variants is likely to increase over time," Stadler said.

Germline testing for all advanced cancer patients?

The study led by Erin Cobain from the University of Michigan similarly demonstrated the clinical utility of germline findings from tumor testing, though on a smaller scale. The researchers conducted targeted exome sequencing for 1,700 genes and transcriptome sequencing on tumor and normal samples from approximately 1,000 patients with advanced solid tumors. Pathogenic germline variants were identified in 160 patients, or 16 percent. Of the deleterious cancer risk mutations identified during this process, 92 percent were not known before patients were tested as part of this protocol, "which indicates that current clinical criteria may not identify all patients at risk for cancer predisposition," Cobain said.

Close to 5 percent of patients had biomarkers that could inform their treatment, such as defects in DNA repair genes, which can be treated with PARP inhibitors, and mutations in mismatch repair gene defects that can be used to prescribe immunotherapy. Significant proportions of patients with rare tumors had pathogenic variants, such as 20 percent of sarcomas, 17 percent of hepatobiliary cancers, and 16 percent of cancers of unknown primary. Cobain highlighted that some of these patients with these rare tumors had germline mutations that could potentially be therapeutically targeted, which is important given the limited treatment options in these settings. 

Ultimately, 11 patients received PARP inhibitors and immunotherapies based on germline findings. Two patients had a complete response, one had a partial response, and five had stable disease. Of the three patients who had progressive disease, two were breast cancer patients with germline ATM mutations treated with PARP inhibitors, and the third was a pancreatic cancer patient with a BRCA1 mutation who received a PARP inhibitor.

The results of this study "support consideration of directed germline testing in all patients with metastatic solid tumors to identify defects in DNA repair with therapeutic targets," Cobain said.

Needs infrastructure

To Funda Meric-Bernstam from MD Anderson Cancer Center, both of these studies demonstrate that if cancer centers are doing tumor/normal sequencing and looking for germline variants of clinical significance, they may not have to look too hard. However, she clarified that its also not "easy" to identify and report germline variants in this context. "This requires a lab to both analyze the normal [samples] and call pathogenic and likely pathogenic variants," she said.

Currently, there isn't a standardized method among tumor sequencing labs when it comes to dealing with germline findings. Some labs conduct only tumor testing, others conduct tumor-normal analysis but subtract germline findings, and still others perform tumor-normal testing and report only a subset of germline findings. Even if a lab sequencing only tumor tissue, tests will identify mutations in genes that are more likely to have occurred in the germline.

Meric-Bernstam noted that although the studies at MSK and the University of Michigan were done under IRB-approved protocols, in the real world when tumor sequencing is done, most patients aren't asked if they want to learn germline findings. "You really need infrastructure to return [results], to counsel, and to offer cascade testing," she said. "You need to facilitate the analysis of normal [samples] so you can ensure findings can be acted upon in a timely fashion, especially in patients with advanced disease. You need to have infrastructure in place for treatment matching and treatments available."

Though there are technical and infrastructural challenges to reporting out germline findings in the context of cancer tumor sequencing, genetics experts are increasingly of the opinion that it is no longer ethical to mask these findings, particularly given their increasingly important role in therapy selection as demonstrated by the ASCO studies. The American College of Medical Genetics and Genomics last month published a set of points that clinicians and genomics labs should consider when presumed germline variants are flagged during tumor sequencing. 

Recognizing the varying practices in the field in this regard, the ACMG in its publication told genetic testing labs to be transparent about their ability to detect germline variants from tumor testing, as well as their reporting practices. Additionally, the ACMG told clinicians to take the opportunity when ordering tumor testing to evaluate the patient for clinical signs of an underlying hereditary cancer syndrome that may require germline testing.

According to Douglas Stewart, who is lead author of the ACMG paper and is a senior investigator within the National Cancer Institutes' Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, the aim of the association is to promote best practices. But it is also the association's hope, he recently said in an interview, that the issues laid out in the paper will start a discussion in the field about how "to capitalize on this huge opportunity of identifying germline variation in tumor sequencing so that it benefits as many people as possible."