A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape

Elisabeth Castellanos,Conxi Lázaro,Ignacio Blanco,Manuel Perucho,Lidia Feliubadaló,Marta Pineda,Eva Tornero,Lauro Sumoy,Sheila Santín,Eduard Serra,Matilde Navarro,Joan Brunet,Inma Rosas,Jesús Del Valle,Gabi Capellá,Raquel Pluvinet,Juan Velasco,Bernat Gel

doi:10.1038/srep39348

Abstract

We wanted to implement an NGS strategy to globally analyze hereditary cancer with diagnostic quality while retaining the same degree of understanding and control we had in pre-NGS strategies. To do this, we developed the I2HCP panel, a custom bait library covering 122 hereditary cancer genes. We improved bait design, tested different NGS platforms and created a clinically driven custom data analysis pipeline. The I2HCP panel was developed using a training set of hereditary colorectal cancer, hereditary breast and ovarian cancer and neurofibromatosis patients and reached an accuracy, analytical sensitivity and specificity greater than 99%, which was maintained in a validation set. I2HCP changed our diagnostic approach, involving clinicians and a genetic diagnostics team from panel design to reporting. The new strategy improved diagnostic sensitivity, solved uncertain clinical diagnoses and identified mutations in new genes. We assessed the genetic variation in the complete set of hereditary cancer genes, revealing a complex variation landscape that coexists with the disease-causing mutation. We developed, validated and implemented a custom NGS-based strategy for hereditary cancer diagnostics that improved our previous workflows. Additionally, the existence of a rich genetic variation in hereditary cancer genes favors the use of this panel to investigate their role in cancer risk.

Highlights

Recommendations and standards have been published to guide the development, validation and implementation of next-generation sequencing (NGS)-based clinical genetic testing[15,16,17,18,19,20,21,22]
This activity encompasses all types of hereditary cancer (HC) syndromes, we work mainly with hereditary colorectal cancer (Familial Adenomatous Polyposis, FAP, and Hereditary Non-Polyposis Colorectal Cancer, HNPCC), hereditary breast and ovarian cancer (HBOC) and neurofibromatoses Type 1 and Type 2 (NF1, NF2) and related disorders such as RASopathies and Phakomatoses
Homogenize diagnostic procedures for different conditions and preserve understanding and control over the complete workflow, we developed a comprehensive custom NGS-based diagnostic strategy to be implemented in the routine diagnostics scenario applicable to most of the genes involved in hereditary cancer and related disorders, to other initiatives (Mainstreaming Cancer Genetics)[27]

Summary

Introduction

Recommendations and standards have been published to guide the development, validation and implementation of NGS-based clinical genetic testing[15,16,17,18,19,20,21,22]. The diagnostic activity of the ICO-IMPPC Joint Program for Hereditary Cancer focuses on the detection and interpretation of all inherited genetic variants that confer a higher risk of developing cancer. This activity encompasses all types of hereditary cancer (HC) syndromes, we work mainly with hereditary colorectal cancer (Familial Adenomatous Polyposis, FAP, and Hereditary Non-Polyposis Colorectal Cancer, HNPCC), hereditary breast and ovarian cancer (HBOC) and neurofibromatoses Type 1 and Type 2 (NF1, NF2) and related disorders such as RASopathies and Phakomatoses. Our aim was to develop a tool and a diagnostic strategy that would ensure the desired sequencing quality, provide great flexibility in the bioinformatic analysis to enhance clinical utility, and enable us to gather global data on the genetic variation of hereditary cancer

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Conclusion