Abstract 1114: Genomics in cancer patient care: Bench to bedside and beyond
Authors: Sharanya Raghunath, David Loughmiller, Aimee Shamo, Jackie Wayne, Patrick Bradley, Jason Gillman, Gary Stone, Derrick Haslem, Lincoln Nadauld, Pravin J. Mishra
Journal: Cancer Research (2015)

Abstract Burgeoning sequencing technologies and the slow pace to use genomics data clinically has been largely hampered by lack of unestablished clinical utilities. There is an immediate need to store, analyze and retrieve meaningful clinical information from high throughput genomics data. At Intermountain Cancer Genomics (ICG) we created a complete translational pipeline that integrates these major core aspects: a clinical laboratory that generates data targeted within our gene panel, a bioinformatics pipeline that accounts for the quality of the data and further generates a set of variants that can be interpreted and targeted clinically to improve the quality of a patient's life. At the ICG clinical laboratory we have developed a comprehensive ICG100 targeted sequencing panel under CLIA-CAP guidelines. DNA extracted from patient's tumor specimen gets sequenced for the entire coding region of 96 cancer-related genes which are often altered in cancer. These targeted regions are sequenced on Illumina's MiSeq sequencing platform using an in-solution, oligo-capture sequencing method. This test offers high coverage (&amp;gt;100X) and detects all classes of genomic alterations, including indels, translocations, copy number alterations (CNAs), and point mutations across the exons of 96 genes. This approach is viable and well-suited for all sample types including FFPE, fresh tissue and plasma. We have developed a comprehensive bio-analytics pipeline that accommodates the diverse variants generated by the unique sequencing chemistry. Comparison of ICG100 to a commercially available CLIA-certified sequencing test that also detects copy number alterations, reveals high concordance across the spectrum of variant types. In addition, the ICG100 test detected 10 additional CNAs across 6 separate samples that were not identified in the commercially available test, suggesting an increased sensitivity with ICG100. This integrated service utilizes a collaborative molecular tumor board that consist of subject expert scientists and physicians. Interdisciplinary tumor board suggests effective treatment options based on genomics data and clinical relevance. ‘Actionable’ genomic alterations are categorized as such if linked to an approved therapy in the solid tumor examined or another solid tumor. This test can be ordered by oncologist through a simple web-based interface where genomic results and molecular tumor board interpretation can be viewed. Additionally, oncologists can make a treatment selection and order drug at their convenience. The ICG100 test therefore not only is cost-effective but offers higher sensitivity, coverage, superior ability for clinical management with identification of actionable CNAs, genomics-driven personalized treatment and precision cancer care. Citation Format: Sharanya Raghunath, David Loughmiller, Aimee Shamo, Jackie Wayne, Patrick Bradley, Jason Gillman, Gary Stone, Derrick Haslem, Lincoln Nadauld, Pravin J. Mishra. Genomics in cancer patient care: Bench to bedside and beyond. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1114. doi:10.1158/1538-7445.AM2015-1114