Section
E-PS-MD-01-001
Automation meets reliability: use of Oncomine
TM
Precision Assay on the Genexus TM
System for accurate identification of cancer biomarkers in FFPE and liquid biopsy samples
J. Schageman* , T. Jayaweera, N. Siepert, B. Hradecky, E. Ostrowska, I. Casuga, K. Lea, P. Kshatriya, J. Gu, R. Cao, A. Cheng, K. Bramlett
*Thermo Fisher Scientific, Austin, TX, United States
Background & objectives: We report the use of the Oncomine TM Precision Assay (OPA) with the Genexus TM System which provides a fast, accurate and comprehensive genetic profile across 50 key genes using DNA and RNA from FFPE tissues or liquid biopsy samples.
Methods: Contrived and clinical research samples with known variants were used for the OPA FFPE and liquid biopsy workflows (n = 30). NA quantification was completed using the Genexus TM purification instrument’s Qubit TM feature after purification. Extracted NA was transferred to the Genexus TM sequencer for library preparation, sequencing, variant and QC reporting using the onboard Ion Torrent™ analysis software.
Results: The OPA assay only required 10ng of DNA and RNA from FFPE samples and 20ng of cfTNA from liquid biopsy samples. Genexus TM purification instrument onboard quantitation data showed successful extraction of NA exceeding the required yields for library preparation. Excess NA was automatically aliquoted into an archive plate and stored for future use. Sequencing results for four samples of FFPE or liquid biopsy were reported within 24 hours. Both Control and clinical research samples showed expected assay metrics including read coverage, molecular coverage, and uniformity. The results reported all expected variants at correct allele frequencies, including BRAF V600E, KRAS G12C, PIK3CA N345K, and AKT1 E17K.
Conclusion: The Genexus TM system provides a user-friendly workflow with automated NA purification, quantitation, sample dilution, library preparation, sequencing, and data analysis with minimal hands-on time that can be performed with limited expertise to obtain results within 24 hours. Reliable identification of variants from control and clinical research samples of FFPE and liquid biopsy origin with optimal assay metrics demonstrates the successful use of the OPA assay and Genexus TM system that can be confidently used in clinical oncology research.
E-PS-MD-01-002
RAS/BRAF mutations in colorectal cancer : assessment of its status in a north African population compared to European population
H. Douik* , G. Sahraoui, L. Charfi, R. Doghri, I. Nasri, D. Benghezala, L. Chaabane, R. Ben Ghorbel, A. Ben Amara, K. Mrad
*Salah Azaiz Institute of Cancer, Tunisia
Background & objectives: Kras/Nras/Braf mutation screening is recommended in metastatic colorectal cancer for personalized medicine therapy. Since epidemiology of colorectal cancer in north African population is different from European population, we aimed to compare mutational status in the two populations.
Methods: Ras/Braf screening was achieved using the Idylla technologies on formalin fixed paraffin embedded tissue sections. Spotting areas with the greatest amount of tumoral cells was performed on HE slides. A threshold of 10% tumoral cells was required. Then, 1 x 5 μm tissue section was prepared from the corresponding paraffin block.
Results: We tested Ras and Braf mutations in a series of 250 colorectal patients with or without metastasis.
Our results showed 58% of Ras (Kras and Nras) mutations and 3% of Braf V600 mutations. 56% of mutations were present in metastatic colorectal patients and 44% in non metastatic colorectal patients. Moreover it seems that we could not predict the type of mutation according to any histologic classification.
Conclusion: Ras/Braf mutation frequency in our population approaches occidental series.
E-PS-MD-01-003
Molecular markers in group 3 and group 4 medulloblastomas
A.I. Vicenteño León* , C. Barrera Velázquez, F. Chico Ponce de León, L. Cabrera Muñoz, M. Pérez Peña Díaz Conti, G. Baay Guzmán, A. Rodríguez Velasco, S. Juárez Méndez, M. Monreal Lazcano, S. Sadowinski Pine, A. Escobar Sánchez, V. González Carranza, S. Torres García, J. García Quintana, P. Eguía Aguilar
*Departamento de Patología Clínica y Experimental, Hospital Infantil de México Federico Gómez (HIMFG), Mexico
Background & objectives: Together, group 3 and group 4 medulloblastomas represent up to 70% of paediatric cases; however, their distinction can be challenging. The objective of the study is to evaluate five genes reported as potentially discriminated amongst both groups.
Methods: Seventy-five patients diagnosed with medulloblastoma and treated at Hospital Infantil de México Federico Gómez were included. Molecular classification was assessed by Polymerase Chain Reaction, based on 22 gene panel proposed by Northcott et al 2012, plus ANO2, DISC1, ARHGAP18, GMR8, PRDM6. The expression of the novel genes was evaluated between the four groups and compared with four cerebellar control samples.
Results: Using the 22 subgroup signature genes, samples were classified as 8/75 wingless, 27/75 sonic hedgehog, 22/75 group 3, and 18/75 group 4 medulloblastomas.
Thereafter, when compared between the four subgroups, mean fold change values for ANO2 were 4.00, 1.20, 8.46 and 10.18; for DISC1 were 17.36, 15.22, 12.28 and 19.72; for ARHGAP18 were 2.52, 4.28, 14.71 and 8.59; for GRM8 were 152.9, 814.7, 230.6 and 1381.9; and, for PRDM6 were 16.21, 11.57, 19.26, and 27.40, for wingless, sonic hedgehog, group 3, and group 4, respectively.
Consequently, the overexpression of ANO2, DISC1, GRM8 and PRDM6 were consistent with group 4, while overexpression of ARHGAP18 with group 3 subgroup assignment.
Conclusion: This study confirms differential expression of the five genes analysed between the four main molecular subgroups of medulloblastoma, furthermore, help to differentiate amongst groups 3 and 4.
Outputs provide continued support for group 3 and group 4 distinction. Next step is to validate the set of genes by methylation or with an independent validation cohort of medulloblastomas. Supplementary studies may also provide insights to facilitate groups 3 and 4 subtypification using the evaluated genes.
Funding: Governmental grants (Fondos Federales México HIM/2018/092).