SAN FRANCISCO (GenomeWeb) – Nationwide Children's Hospital's Institute for Genomic Medicine is working to clinically validate a comprehensive cancer sequencing research protocol it has been running for the last year, with the goal of demonstrating the utility of genomic profiling and figuring out how to scale the methods it uses up for its pediatric cancer patients.
The institute, which is part of the Columbus, Ohio-based hospital, was launched in 2016, when it recruited Elaine Mardis and Rick Wilson from Washington University in St. Louis to head it up. From the start, the institute has had a dual research and clinical bent. Its initial clinical test was exome sequencing for children with congenital diseases, and it is now in the process of clinically validating its comprehensive cancer sequencing protocol.
Pediatric patients at Nationwide with rare or refractory cancers are eligible to enroll in the translational research study, which returns relevant findings to their physicians. Researchers perform exome sequencing on Illumina instruments, or in some cases whole-genome sequencing, on matched tumor/normal samples, as well as tumor transcriptome sequencing, said Catherine Cottrell, clinical laboratory director at the Institute for Genomic Medicine. Researchers also aim to consent parents when possible to obtaining any validated heritable germline findings.
The team began enrolling patients in January 2018. As of March, it had enrolled 59 patients and sequenced 47.
Cottrell described the approach as a "research-to-clinical continuum," where the genomic profile "lets us refine diagnosis, inform prognosis, determine therapeutic targets, and detect germline cancer predisposition alterations."
Aside from the comprehensive nature of the sequencing, another facet that sets it apart from other hospitals' cancer sequencing protocols is that it gives patients the option of receiving pathogenic findings within the set of 59 genes that the American College of Medical Genetics and Genomics has deemed actionable, as well as a limited number of carrier findings.
The researchers also further analyze patients' genomes using other technologies on a case-by-case basis, Cottrell said. Among those are Pacific Biosciences single-molecule sequencing to help elucidate complex structural variants, immune profiling on NanoString Technologies' gene expression platform.
Cottrell, along with Vincent Magrini, director of technology development at the genomic medicine institute, are leading the clinical validation of the paired tumor/normal exome sequencing protocol. The pipeline is an "enhanced exome," which includes Integrated DNA Technologies' xGen exome kit along with the IDT xGen CNV backbone panel to help identify copy number variants, and an IDT probe set that is enriched for known cancer regions. Cottrell added that the team is also working to validate the RNA-seq pipeline, "with early efforts focused on fusion detection."
The team first discusses the genomic profiling results among the cancer protocol steering committee, bioinformaticians, laboratory directors, and technical staff, Cottrell said. Then, they present the results, including relevant secondary and carrier findings, at a tumor board forum within the hospital. The tumor board is interdisciplinary and involves oncologists, surgeons, pathologists, radiologists, and other research and medical personnel, Cottrell said.
Thus far, Cottrell said they've found a number of medically meaningful findings, including somatic fusions in 13 individuals, targetable gene expression changes in 30, germline cancer predisposition variants in five, a pathogenic variant in one of the non-cancer-related ACMG 59 genes in one person, carrier variants in six, and a constitutional syndrome in four patients.
Cottrell said that more than 90 percent of the families have opted to receive the ACMG 59 and carrier findings. Analyzing parental samples, which they've been able to do in 40 cases, including 33 with samples from both parents, has been extremely valuable. In cases where a patient has a germline mutation, that's enabled the researchers to look for the same alteration in the parents, which can help inform future reproductive risk and enables genetic counseling of the parents about their own risk or potential risk to other family members.
One example included a 17-year-old female with meningeal melanoma as well as a neuropsychological disorder. An initial BRAF test was negative, while a chromosomal analysis identified a translocation, but it was unclear whether it was related to the patient's cancer or constitutional. The patient's brother and father had the same neuropsychological disorder, so the team moved on to do whole-genome sequencing and RNA-seq of the patient. They identified a hotspot alteration in an oncogene that is also known to be an activating event in melanoma. That alteration can lead to a second hit, including a loss within chromosome 3 or an inactivating mutation in the gene BAP1. The researchers did indeed find a loss-of-function mutation in BAP1 in the patient. Finally, they confirmed the previously identified translocation and are now further studying it to determine whether it could be related to the patient's neuropsychological disorder. The cancer-related findings were confirmed in a clinical setting and "informed clinical care," Cottrell said.
In a second case, an 18-year-old male came to Nationwide with symptoms of lethargy and vomiting. He had initially been diagnosed with medulloblastoma seven years ago, and had undergone resection, chemotherapy, and radiation at the initial diagnosis and again three years later when the tumor recurred. An imaging study identified a mass and a biopsy confirmed that the cancer had returned. The Nationwide team did exome sequencing and RNA-seq of both the initial tumor sample and the recurrent tumor. An analysis of copy number alterations "found no evidence of shared overlap, indicating the origin [of the recurrent tumor] may be different" from the original tumor. When analyzing the RNA-seq data, the researchers also noted very different expression patterns, indicating that the second tumor was not a recurrence but a totally different cancer type that was more similar to glioma than medulloblastoma. "This helped refine diagnosis and management for the patient," Cottrell said.
Cottrell said one lesson the team has learned is that " high-quality genomic profiling analyses can be effort- and time-intensive," which has implications for their ability to scale up to offer testing to more patients within Nationwide or potentially to patients at other hospitals and institutions. "Currently, it does take highly trained individuals with expertise," she said. However, she noted that the researchers have made headway on developing software pipelines and are continuing to refine those pipelines and make them more automated.
Such challenges are not unique to the Nationwide team. Recently, a number of researchers discussed challenges they've faced implementing precision oncology programs at academic medical centers, community hospitals, and integrated health systems, alike.
Like Cottrell, David Roth, director of the University of Pennsylvania's Center for Precision Medicine, noted that scaling up the center's cancer sequencing protocol will be a major challenge.
Cottrell also shared others' concerns regarding how to pay for the program. Currently, Nationwide's cancer sequencing is funded by the hospital, but the "goal is ultimately to make it a CLIA-validated reimbursable assay," Cottrell said. She anticipated the clinical validation would be completed within about one year.