ICRmax: An optimized approach to detect tumor-specific interchromosomal rearrangements for clinical application

Author(s)

Donnard, Elisa R. ^{[1, 2]} ; Carpinetti, Paola A. ^{[1, 2]} ; Navarro, Fabio C. P. ^{[1, 2]} ; Perez, Rodrigo O. ^{[3, 4]} ; Habr-Gama, Angelita ^[4] ; Parmigiani, Raphael B. ^[1] ; Camargo, Anamaria A. ^{[1, 3]} ; Galante, Pedro A. F. ^[1]

Affiliation

^[1] Hosp Sirio Libanes, Ctr Mol Oncol, Sao Paulo - Brazil

^[2] Univ Sao Paulo, Inst Quim, Dept Bioquim, BR-01498 Sao Paulo - Brazil

^[3] Ludwig Inst Canc Res, Sao Paulo - Brazil

^[4] Inst Angelita & Joaquim Gama, Sao Paulo - Brazil

• Document type: Journal article
• Source: Genomics; v. 105, n. 5-6, p. 265-272, MAY 2015.
• Web of Science Citations: 2

Abstract

Somatically acquired chromosomal rearrangements occur at early stages during tumorigenesis and can be used to indirectly detect tumor cells, serving as highly sensitive and tumor-specific biomarkers. Advances in high-throughput sequencing have allowed the genome-wide identification of patient-specific chromosomal rearrangements to be used as personalized biomarkers to efficiently assess response to treatment, detect residual disease and monitor disease recurrence. However, sequencing and data processing costs still represent major obstacles for the widespread application of personalized biomarkers in oncology. We developed a computational pipeline (ICRmax) for the cost-effective identification of a minimal set of tumor-specific interchromosomal rearrangements (ICRs). We examined ICRmax performance on sequencing data from rectal tumors and simulated data achieving an average accuracy of 68% for ICR identification. ICRmax identifies ICRs from low-coverage sequenced tumors, eliminates the need to sequence a matched normal tissue and significantly reduces the costs that limit the utilization of personalized biomarkers in the clinical setting. (C) 2015 The Authors. Published by Elsevier Inc. (AU)

• FAPESP's process: 11/50684-8 - Neoadjuvant treatment in rectal cancer: identification of a genic signature capable of predicting response to treatment and the development of personalized biomarkers for assessing minimal residual disease
• Grantee: Anamaria Aranha Camargo
• Support Opportunities: Regular Research Grants
• FAPESP's process: 10/12658-2 - Analysis of biomarkers in rectal tumors through next-generation sequencing
• Grantee: Elisa Rennó Donnard Moreira
• Support Opportunities: Scholarships in Brazil - Doctorate