Integrated genomic DNA/RNA profiling of hematologic malignancies in the clinical setting

Jie He, Omar Abdel-Wahab, Michelle K. Nahas, Kai Wang, Raajit K. Rampal, Andrew M. Intlekofer, Jay Patel, Andrei Krivstov, Garrett M. Frampton, Lauren E. Young, Shan Zhong, Mark Bailey, Jared R. White, Steven Roels, Jason Deffenbaugh, Alex Fichtenholtz, Timothy Brennan, Mark Rosenzweig, Kimberly Pelak, Kristina M. KnappKristina W. Brennan, Amy L. Donahue, Geneva Young, Lazaro Garcia, Selmira T. Beckstrom, Mandy Zhao, Emily White, Vera Banning, Jamie Buell, Kiel Iwanik, Jeffrey S. Ross, Deborah Morosini, Anas Younes, Alan M. Hanash, Elisabeth Paietta, Kathryn Roberts, Charles Mullighan, Ahmet Dogan, Scott A. Armstrong, Tariq Mughal, Jo Anne Vergilio, Elaine Labrecque, Rachel Erlich, Christine Vietz, Roman Yelensky, Philip J. Stephens, Vincent A. Miller, Marcel R.M. Van Den Brink, Geoff A. Otto, Doron Lipson, Ross L. Levine

106 Scopus citations

Abstract

The spectrum of somatic alterations in hematologic malignancies includes substitutions, insertions/deletions (indels), copy number alterations (CNAs), and a wide range of gene fusions; no current clinically available single assay captures the different types of alterations. We developed a novel next-generation sequencing-based assay to identify all classes of genomic alterations using archived formalin-fixed paraffin-embedded blood and bone marrow samples with high accuracy in a clinically relevant time frame, which is performed in our Clinical Laboratory Improvement Amendments-certified College of American Pathologists-accredited laboratory. Targeted capture of DNA/RNA and next-generation sequencing reliably identifies substitutions, indels, CNAs, and gene fusions, with similar accuracy to lower-throughput assays that focus on specific genes and types of genomic alterations. Profiling of 3696 samples identified recurrent somatic alterations that impact diagnosis, prognosis, and therapy selection. This comprehensive genomic profiling approach has proved effective in detecting all types of genomic alterations, including fusion transcripts, which increases the ability to identify clinically relevant genomic alterations with therapeutic relevance.

Cite this

He, J., Abdel-Wahab, O., Nahas, M. K., Wang, K., Rampal, R. K., Intlekofer, A. M., Patel, J., Krivstov, A., Frampton, G. M., Young, L. E., Zhong, S., Bailey, M., White, J. R., Roels, S., Deffenbaugh, J., Fichtenholtz, A., Brennan, T., Rosenzweig, M., Pelak, K., ... Levine, R. L. (2016). Integrated genomic DNA/RNA profiling of hematologic malignancies in the clinical setting. Blood, 127(24), 3004-3014. https://doi.org/10.1182/blood-2015-08-664649