Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene, April 20, 2011, Welch et al. 305 (15): 1577 — JAMA

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Preliminary Communication

Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion OncogeneJohn S. Welch, MD, PhD; Peter Westervelt, MD, PhD; Li Ding, PhD; David E. Larson, PhD; Jeffery M. Klco, MD, PhD; Shashikant Kulkarni, PhD; John Wallis, PhD; Ken Chen, PhD; Jacqueline E. Payton, MD, PhD; Robert S. Fulton, MS; Joelle Veizer, BS; Heather Schmidt, BS; Tammi L. Vickery, BS; Sharon Heath; Mark A. Watson, MD, PhD; Michael H. Tomasson, MD; Daniel C. Link, MD; Timothy A. Graubert, MD; John F. DiPersio, MD, PhD; Elaine R. Mardis, PhD; Timothy J. Ley, MD; Richard K. Wilson, PhD


[+] Author Affiliations

Author Affiliations: Departments of Medicine (Drs Welch, Westervelt, Tomasson, Link, Graubert, DiPersio, and Ley and Ms Heath), Pathology and Immunology (Drs Klco, Kulkarni, Payton, and Watson), Genetics (Drs Kulkarni, Mardis, Ley, and Wilson), and Pediatrics (Dr Kulkarni), and Genome Institute (Drs Ding, Larson, Wallis, Chen, Watson, Mardis, Ley, and Wilson and Mr Fulton and Mss Veizer, Schmidt, and Vickery), Washington University, St Louis, Missouri.


Abstract
Context
Whole-genome sequencing is becoming increasingly available for research purposes, but it has not yet been routinely used for clinical diagnosis.

Objective
To determine whether whole-genome sequencing can identify cryptic, actionable mutations in a clinically relevant time frame.


Design, Setting, and Patient
We were referred a difficult diagnostic case of acute promyelocytic leukemia with no pathogenic X-RARA fusion identified by routine metaphase cytogenetics or interphase fluorescence in situ hybridization (FISH). The case patient was enrolled in an institutional review board–approved protocol, with consent specifically tailored to the implications of whole-genome sequencing. The protocol uses a “movable firewall” that maintains patient anonymity within the entire research team but allows the research team to communicate medically relevant information to the treating physician.


Main Outcome Measures
Clinical relevance of whole-genome sequencing and time to communicate validated results to the treating physician.


Results
Massively parallel paired-end sequencing allowed identification of a cytogenetically cryptic event: a 77-kilobase segment from chromosome 15 was inserted en bloc into the second intron of the RARA gene on chromosome 17, resulting in a classic bcr3 PML-RARA fusion gene. Reverse transcription polymerase chain reaction sequencing subsequently validated the expression of the fusion transcript. Novel FISH probes identified 2 additional cases of t(15;17)–negative acute promyelocytic leukemia that had cytogenetically invisible insertions. Whole-genome sequencing and validation were completed in 7 weeks and changed the treatment plan for the patient.


Conclusion
Whole-genome sequencing can identify cytogenetically invisible oncogenes in a clinically relevant time frame.

KEYWORDS: EARLY DIAGNOSIS, GENOME, HUMAN, LEUKEMIA, MYELOID, ACUTE, LEUKEMIA, PROMYELOCYTIC, ACUTE, ONCOGENE PROTEINS, FUSION, ONCOGENES, SEQUENCE ANALYSIS, DNA, TIME FACTORS.

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Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene, April 20, 2011, Welch et al. 305 (15): 1577 — JAMA