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Blood. 2016 Jun 16;127(24):3004-14. doi: 10.1182/blood-2015-08-664649. Epub 2016 Mar 10.

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

Author information

1
Foundation Medicine, Cambridge, MA;
2
Leukemia Service, Department of Medicine, Human Oncology and Pathogenesis Program.
3
Cancer Biology and Genetics Program, Lymphoma Service, Department of Medicine.
4
Human Oncology and Pathogenesis Program.
5
Cancer Biology and Genetics Program, Leukemia Center, Department of Pediatrics, and.
6
Leukemia Center.
7
Lymphoma Service, Department of Medicine.
8
Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY;
9
Department of Medicine (Oncology), Albert Einstein College of Medicine, Yeshiva University, New York, NY;
10
Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN;
11
Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY;
12
Foundation Medicine, Cambridge, MA; Division of Hematology and Oncology, Tufts University Medical Center, Boston, MA; and.
13
Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY; Division of Hematologic Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.
14
Leukemia Service, Department of Medicine, Human Oncology and Pathogenesis Program, Leukemia Center.

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.

PMID:
26966091
PMCID:
PMC4968346
DOI:
10.1182/blood-2015-08-664649
[Indexed for MEDLINE]
Free PMC Article

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