Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene

Department of Medicine, Washington University, St Louis, Missouri, USA.
JAMA The Journal of the American Medical Association (Impact Factor: 35.29). 04/2011; 305(15):1577-84. DOI: 10.1001/jama.2011.497
Source: PubMed


Whole-genome sequencing is becoming increasingly available for research purposes, but it has not yet been routinely used for clinical diagnosis.
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.
Clinical relevance of whole-genome sequencing and time to communicate validated results to the treating physician.
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.
Whole-genome sequencing can identify cytogenetically invisible oncogenes in a clinically relevant time frame.

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Available from: Shashikant Kulkarni, Sep 29, 2015
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    • "More recently, NGS has been employed in order to provide new insight into the genetic mechanisms of cancer, as the technology enables the exploration of tumor genomes in previously infeasible levels of detail. Among many examples, researchers have used it to examine the patterns of genomic alteration in non-small-cell carcinoma [4] and melanoma cell lines [5], to discover novel and possibly tumorigenic mutations in the acute myeloid leukemia genome [6], and have even used findings to inform clinical treatment of a patient with acute promyelocytic leukemia [7]. "
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    • "As a result, ES/WGS have quickly been transitioned from use as a research tool to use in clinical service labs as an alternative to targeted genetic testing. Several widely publicized examples in which these tools have been used to facilitate a clinical diagnosis have further engendered enthusiasm for adopting ES/ WGS into clinical practice [Bainbridge et al., 2011; Welch et al., 2011; Worthey et al., 2011]. We are similarly enthused, but such swift translation of ES/WGS into clinical settings raises important questions such as: (1) under what circumstances is ES/ WGS likely to be of greatest clinical benefit, (2) how can informed consent for ES/WGS effectively be obtained, (3) what are reasonable options to offer for sharing individual ES/WGS (iES/WGS) results, (4) how should iES/WGS results be managed for providers and families, and (5) how can providers' and families' expectations about risk profiling using ES/WGS be managed. "
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    American Journal of Medical Genetics Part A 05/2013; 161(5):935-50. DOI:10.1002/ajmg.a.35942 · 2.16 Impact Factor
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    • "NGS has already been applied in the clinic for cancer diagnosis and prognosis. For example, whole genome sequencing identified a novel insertional fusion that created a classic bcr3 PML-RARA fusion gene for a patient with acute myeloid leukemia and the findings altered the treatment plan for the patient [33]. By sequencing the tumor genome of a patient, clinicians are able to design patient-specific probes that uses DNA in the patient’s blood serum to monitor the progress of a patient’s treatment and detect for any signs of relapse [27-31]. "
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