Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study

Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA.
Science translational medicine (Impact Factor: 15.84). 11/2011; 3(111):111ra121. DOI: 10.1126/scitranslmed.3003161
Source: PubMed


Individual cancers harbor a set of genetic aberrations that can be informative for identifying rational therapies currently available or in clinical trials. We implemented a pilot study to explore the practical challenges of applying high-throughput sequencing in clinical oncology. We enrolled patients with advanced or refractory cancer who were eligible for clinical trials. For each patient, we performed whole-genome sequencing of the tumor, targeted whole-exome sequencing of tumor and normal DNA, and transcriptome sequencing (RNA-Seq) of the tumor to identify potentially informative mutations in a clinically relevant time frame of 3 to 4 weeks. With this approach, we detected several classes of cancer mutations including structural rearrangements, copy number alterations, point mutations, and gene expression alterations. A multidisciplinary Sequencing Tumor Board (STB) deliberated on the clinical interpretation of the sequencing results obtained. We tested our sequencing strategy on human prostate cancer xenografts. Next, we enrolled two patients into the clinical protocol and were able to review the results at our STB within 24 days of biopsy. The first patient had metastatic colorectal cancer in which we identified somatic point mutations in NRAS, TP53, AURKA, FAS, and MYH11, plus amplification and overexpression of cyclin-dependent kinase 8 (CDK8). The second patient had malignant melanoma, in which we identified a somatic point mutation in HRAS and a structural rearrangement affecting CDKN2C. The STB identified the CDK8 amplification and Ras mutation as providing a rationale for clinical trials with CDK inhibitors or MEK (mitogen-activated or extracellular signal-regulated protein kinase kinase) and PI3K (phosphatidylinositol 3-kinase) inhibitors, respectively. Integrative high-throughput sequencing of patients with advanced cancer generates a comprehensive, individual mutational landscape to facilitate biomarker-driven clinical trials in oncology.

19 Reads
  • Source
    • "Personalized CRC patient treatment based on characterizing the individual tumors by high throughput sequencing strategies has been attempted [12]. Most studies reporting sequencing data have been with panels of select genes, or with cell lines, patient derived xenografts, or primary tumors removed at surgery [13]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Background The outcome of patients with metastatic colorectal carcinoma (mCRC) following first line therapy is poor, with median survival of less than one year. The purpose of this study was to identify candidate therapeutically targetable somatic events in mCRC patient samples by whole genome sequencing (WGS), so as to obtain targeted treatment strategies for individual patients. Methods Four patients were recruited, all of whom had received > 2 prior therapy regimens. Percutaneous needle biopsies of metastases were performed with whole blood collection for the extraction of constitutional DNA. One tumor was not included in this study as the quality of tumor tissue was not sufficient for further analysis. WGS was performed using Illumina paired end chemistry on HiSeq2000 sequencing systems, which yielded coverage of greater than 30X for all samples. NGS data were processed and analyzed to detect somatic genomic alterations including point mutations, indels, copy number alterations, translocations and rearrangements. Results All 3 tumor samples had KRAS mutations, while 2 tumors contained mutations in the APC gene and the PIK3CA gene. Although we did not identify a TCF7L2-VTI1A translocation, we did detect a TCF7L2 mutation in one tumor. Among the other interesting mutated genes was INPPL1, an important gene involved in PI3 kinase signaling. Functional studies demonstrated that inhibition of INPPL1 reduced growth of CRC cells, suggesting that INPPL1 may promote growth in CRC. Conclusions Our study further supports potential molecularly defined therapeutic contexts that might provide insights into treatment strategies for refractory mCRC. New insights into the role of INPPL1 in colon tumor cell growth have also been identified. Continued development of appropriate targeted agents towards specific events may be warranted to help improve outcomes in CRC.
    BMC Medical Genomics 06/2014; 7(1):36. DOI:10.1186/1755-8794-7-36 · 2.87 Impact Factor
  • Source
    • "To test the practicality of NGS in clinical situations , Roychowdhury et al. sequenced the whole genome and transcriptome of tumors and targeted whole-exome of tumors and normal DNA in two patients with advanced or refractory cancer (one metastatic colorectal cancer and one metastatic melanoma) (Roychowdhury et al., 2011). A multidisciplinary board deliberated on the clinical consequences of genomic alterations, and within 24 days of biopsy, personalized treatments were designed (Roychowdhury et al., 2011). Although most of the findings in this pilot study were not clinically significant , the approach proved NGS to be clinically relevant and practical in terms of cost and time. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Advances in the management of patients with head and neck squamous cell carcinoma (HNSCC) have not significantly changed the prognosis of this tumor over the past five decades. Molecular heterogeneity of HNSCC and its association with HPV, in addition to the increase in the number of cancers arising in traditionally low-risk patients, are among some of the obstacles to the successful management of this group of tumors. Massively parallel sequencing, otherwise known as next-generation sequencing (NGS), is rapidly changing conventional patient management by providing detailed information about each patient's genome and transcriptome. Despite major advances in technology and a significant reduction in the cost of sequencing, NGS remains mainly limited to research facilities. In addition, there are only a few published studies that have utilized this technology in HNSCC. This paper aims to report briefly on current commercially available NGS platforms and discuss their clinical applications, ethical considerations, and utilization in personalized patient care, particularly as this relates to head and neck cancer.
    Journal of dental research 02/2014; 93(5). DOI:10.1177/0022034514524783 · 4.14 Impact Factor
  • Source
    • "Each sample was to found to have a clinically meaningful mutation, which included KRAS, BRAF, PIK3CA, or CTNNB1, in addition to common tumor-suppressor genes. WGS and WES were performed for two patients with advanced cancer treated at the University of Michigan by Roychowdhury and colleagues [44]. The patient with CRC was found to have multiple somatic mutations along with CDK8 overexpression and amplification, whereas the patient with melanoma had a somatic mutation in HRAS with a structural rearrangement in CDKN2C. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Large-scale collaborative initiatives using next-generation DNA sequencing and other high-throughput technologies have begun to characterize the genomic landscape of breast cancer. These landmark studies have identified infrequent driver mutations that are potential targets for therapeutic intervention with approved or investigational drug treatments, among other important discoveries. Recently, many institutions have launched molecular screening programs that apply high-throughput genomic technologies to patients with advanced solid malignancies, including breast cancer, to inform clinical decision-making. This article provides an overview of the recent molecular insights in breast cancer, including potentially actionable somatic alterations, the technological platforms currently available in a clinical diagnostics setting to detect these alterations, and ongoing institutional or regional molecular screening programs in advanced breast cancer.
    Breast cancer research: BCR 10/2013; 15(5):R97. DOI:10.1186/bcr3558 · 5.49 Impact Factor
Show more