Shin Ito1, Ikuro Sato2, Mai Mochizuki3, Kazunori Yamaguchi1, Keiichi Tamai3, Takamichi Minato4, Nobuhiro Tanuma5, Hiroshi Shima5, Jun Yasuda6. 1. Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Miyagi, Japan. 2. Division of Pathology, Miyagi Cancer Center, Miyagi, Japan. 3. Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Miyagi, Japan. 4. Division of Gynecology, Miyagi Cancer Center, Miyagi, Japan. 5. Division of Cancer Chemotherapy, Miyagi Cancer Center Research Institute, Miyagi, Japan. 6. Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Miyagi, Japan; jun-ysauda@miyagi-pho.jp.
Abstract
BACKGROUND/AIM: Cancer profiling tests using formalin-fixed paraffin-embedded (FFPE) specimens with various conditions have become an essential tool for cancer treatment. The robustness of these tests needs to be addressed. MATERIALS AND METHODS: A cancer profiling test, NCC oncopanel, was tested with FFPE specimens from various tissues with different storage conditions and fixation lengths. Next generation sequencing was performed with Miseq and the data were assembled using the human reference genome hg19. RESULTS: Duration of storage and fixation affected the mapping statistics. Prolonged storage increased outward read paring and longer fixation rates caused increased singletons and unmapped reads. CONCLUSION: Our results indicate that a cancer profiling test with target capturing method, NCC oncopanel, shows robustness for FFPE cancer specimens with various storage conditions.
BACKGROUND/AIM: Cancer profiling tests using formalin-fixed paraffin-embedded (FFPE) specimens with various conditions have become an essential tool for cancer treatment. The robustness of these tests needs to be addressed. MATERIALS AND METHODS: A cancer profiling test, NCC oncopanel, was tested with FFPE specimens from various tissues with different storage conditions and fixation lengths. Next generation sequencing was performed with Miseq and the data were assembled using the human reference genome hg19. RESULTS: Duration of storage and fixation affected the mapping statistics. Prolonged storage increased outward read paring and longer fixation rates caused increased singletons and unmapped reads. CONCLUSION: Our results indicate that a cancer profiling test with target capturing method, NCC oncopanel, shows robustness for FFPE cancer specimens with various storage conditions.