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 M. 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

Research output: Contribution to journalArticle

101 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)3004-3014
Number of pages11
JournalBlood
Volume127
Issue number24
DOIs
StatePublished - 2016

Fingerprint

DNA Fingerprinting
Gene Fusion
Hematologic Neoplasms
Assays
Fusion reactions
Genes
RNA
DNA
Substitution reactions
Clinical laboratories
Paraffin
Formaldehyde
Bone Marrow
Bone
Blood
Therapeutics
Throughput
Pathologists

ASJC Scopus subject areas

  • Immunology
  • Biochemistry
  • Hematology
  • Cell Biology

Cite this

He, J., Abdel-Wahab, O., Nahas, M. K., Wang, K., Rampal, R. K., Intlekofer, A. M., ... 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

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

In: Blood, Vol. 127, No. 24, 2016, p. 3004-3014.

Research output: Contribution to journalArticle

He, J, Abdel-Wahab, O, Nahas, MK, Wang, K, Rampal, RK, Intlekofer, AM, Patel, J, Krivstov, A, Frampton, GM, Young, LE, Zhong, S, Bailey, M, White, JR, Roels, S, Deffenbaugh, J, Fichtenholtz, A, Brennan, T, Rosenzweig, M, Pelak, K, Knapp, KM, Brennan, KW, Donahue, AL, Young, G, Garcia, L, Beckstrom, ST, Zhao, M, White, E, Banning, V, Buell, J, Iwanik, K, Ross, JS, Morosini, D, Younes, A, Hanash, AM, Paietta, EM, Roberts, K, Mullighan, C, Dogan, A, Armstrong, SA, Mughal, T, Vergilio, JA, Labrecque, E, Erlich, R, Vietz, C, Yelensky, R, Stephens, PJ, Miller, VA, Van Den Brink, MRM, Otto, GA, Lipson, D & Levine, RL 2016, 'Integrated genomic DNA/RNA profiling of hematologic malignancies in the clinical setting', Blood, vol. 127, no. 24, pp. 3004-3014. https://doi.org/10.1182/blood-2015-08-664649
He J, Abdel-Wahab O, Nahas MK, Wang K, Rampal RK, Intlekofer AM et al. Integrated genomic DNA/RNA profiling of hematologic malignancies in the clinical setting. Blood. 2016;127(24):3004-3014. https://doi.org/10.1182/blood-2015-08-664649
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 M. ; 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. / Integrated genomic DNA/RNA profiling of hematologic malignancies in the clinical setting. In: Blood. 2016 ; Vol. 127, No. 24. pp. 3004-3014.
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AU - Abdel-Wahab, Omar

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AU - Rampal, Raajit K.

AU - Intlekofer, Andrew M.

AU - Patel, Jay

AU - Krivstov, Andrei

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AU - Young, Lauren E.

AU - Zhong, Shan

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AU - Brennan, Timothy

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AU - Pelak, Kimberly

AU - Knapp, Kristina M.

AU - Brennan, Kristina W.

AU - Donahue, Amy L.

AU - Young, Geneva

AU - Garcia, Lazaro

AU - Beckstrom, Selmira T.

AU - Zhao, Mandy

AU - White, Emily

AU - Banning, Vera

AU - Buell, Jamie

AU - Iwanik, Kiel

AU - Ross, Jeffrey S.

AU - Morosini, Deborah

AU - Younes, Anas

AU - Hanash, Alan M.

AU - Paietta, Elisabeth M.

AU - Roberts, Kathryn

AU - Mullighan, Charles

AU - Dogan, Ahmet

AU - Armstrong, Scott A.

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AU - Miller, Vincent A.

AU - Van Den Brink, Marcel R M

AU - Otto, Geoff A.

AU - Lipson, Doron

AU - Levine, Ross L.

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