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Delivering genomic cancer data for clinical decisions

Analysis of a study published in a science journal   |   By Dr Philippa Brice   |   Published 27 April 2011
Study: Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene
By: Welch J.S. et al. (22 authors total)
In: The Journal of the American Medical Association
What this study set out to do:

Use whole-genome sequencing (WGS) to identify underlying genetic changes in a leukaemia patient rapidly enough to inform clinical decision-making 

How they went about it:

A patient in her thirties presented with a complex form of leukaemia. Clinicians were not able to determine which of two alternative types of disease was present, and hence which follow-up treatment to use. WGS was used to analyse tumour and normal skin cells from the patient in an attempt to provide a clear guide to treatment within 6-8 weeks.


The analysis revealed the presence of a mutation that had created an oncogenic fusion gene driving the leukaemia. Understanding the underlying molecular genetics of the cancer suggested that an alternative medical treatment was preferable, and the patient received chemotherapy rather than a stem cell transplant. 


WGS not only identified the key mutation of interest, but also all other mutations detected by standard means, and within a clinically relevant time-frame. It should soon be feasible to further reduce this to around 4 weeks. However, use in a normal medical context would require clinical standardisation of analysis and reporting. 

Our view:

This study looks at a new aspect of WGS analysis for clinical purposes, taking into account speed of reporting. In leukaemia the ideal follow-up treatment depends on the exact type of disease, but it must begin within a few weeks of the initial diagnosis and treatment, so time is of the essence. WGS could become a transformative tool in clinical cancer care, especially for complex cases, but the authors are right to differentiate between research and clinical settings, as the latter places new demands not only in terms of quality control, but also health professional education and communication. 

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