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

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...

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Bibliographic Details
Published in:	Blood Vol. 127; no. 24; pp. 3004 - 3014
Main Authors:	He, Jie, Abdel-Wahab, Omar, Nahas, Michelle K., Wang, Kai, Rampal, Raajit K., Intlekofer, Andrew M., Patel, Jay, Krivstov, Andrei, Frampton, Garrett M., Young, Lauren E., Zhong, Shan, Bailey, Mark, White, Jared R., Roels, Steven, Deffenbaugh, Jason, Fichtenholtz, Alex, Brennan, Timothy, Rosenzweig, Mark, Pelak, Kimberly, Knapp, Kristina M., Brennan, Kristina W., Donahue, Amy L., Young, Geneva, Garcia, Lazaro, Beckstrom, Selmira T., Zhao, Mandy, White, Emily, Banning, Vera, Buell, Jamie, Iwanik, Kiel, Ross, Jeffrey S., Morosini, Deborah, Younes, Anas, Hanash, Alan M., Paietta, Elisabeth, Roberts, Kathryn, Mullighan, Charles, Dogan, Ahmet, Armstrong, Scott A., Mughal, Tariq, Vergilio, Jo-Anne, Labrecque, Elaine, Erlich, Rachel, Vietz, Christine, Yelensky, Roman, Stephens, Philip J., Miller, Vincent A., van den Brink, Marcel R.M., Otto, Geoff A., Lipson, Doron, Levine, Ross L.
Format:	Journal Article
Language:	English
Published:	United States Elsevier Inc 16-06-2016 American Society of Hematology
Subjects:	Chromosome Aberrations Clinical Laboratory Techniques - methods DNA Fingerprinting - methods DNA Mutational Analysis - methods DNA, Neoplasm - analysis Gene Expression Profiling - methods Gene Expression Regulation, Neoplastic Genomics - methods Hematologic Neoplasms - genetics Hematologic Neoplasms - metabolism Hematologic Neoplasms - pathology High-Throughput Nucleotide Sequencing Humans Lymphoid Neoplasia Mutation Polymorphism, Genetic RNA, Neoplasm - analysis Sensitivity and Specificity Systems Integration
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Summary:	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. •Novel clinically available comprehensive genomic profiling of both DNA and RNA in hematologic malignancies.•Profiling of 3696 clinical hematologic tumors identified somatic alterations that impact diagnosis, prognosis, and therapeutic selection.
Bibliography:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Undefined-1 ObjectType-Feature-3 content type line 23 J.H., O.A.-W., M.K.N., and K.W. contributed equally to this work.
ISSN:	0006-4971 1528-0020
DOI:	10.1182/blood-2015-08-664649