Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers

The utility of cancer whole genome and transcriptome sequencing (cWGTS) in oncology is increasingly recognized. However, implementation of cWGTS is challenged by the need to deliver results within clinically relevant timeframes, concerns about assay sensitivity, reporting and prioritization of findings. In a prospective research study we develop a workflow that reports comprehensive cWGTS results in 9 days. Comparison of cWGTS to diagnostic panel assays demonstrates the potential of cWGTS to capture all clinically reported mutations with comparable sensitivity in a single workflow. Benchmarking identifies a minimum of 80× as optimal depth for clinical WGS sequencing. Integration of germline, somatic DNA and RNA-seq data enable data-driven variant prioritization and reporting, with oncogenic findings reported in 54% more patients than standard of care. These results establish key technical considerations for the implementation of cWGTS as an integrated test in clinical oncology.

Cancer whole-genome and transcriptome sequencing (cWGTS) has been challenging to implement in clinical settings. Here, the authors develop a workflow to deliver robust cWGTS analyses and reports within clinically-relevant timeframes for paediatric, adolescent and young adult solid tumour patients.

Impact of concomitant immunosuppression on the presentation and prognosis of patients with melanoma

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Background: Melanoma has been reported to be susceptible to immune control. Therefore, we hypothesized that concomitant immune suppression might impact the course of the disease. Methods: We examined the Beth Israel Deaconess Medical Center Cutaneous Oncology Program database for pts with immune suppression at the time of melanoma diagnosis. The demographics and stage of these pts were compared to those in the database as a whole. In addition, 3 controls matched for age, gender, stage and tumor location were identified for each case and disease outcome was compared between cases and controls. Results: 19 pts were identified with melanoma and concomitant immune suppression in a database of 1820 melanoma pts. Other diagnoses included renal transplant (4) inflammatory arthritis (8), Multiple Sclerosis (2), and ulcerative colitis (3). Immunosuppressive meds included methotrexate, azothioprine, cyclosporine, prednisone, infliximab, and natalizumab. Melanoma stages at diagnosis were in situ 1, IB 7, IIA 1, IIB 1, IIIB 3, IIIC 5, and IV 1. Compared to the database as a whole, cases were more likely to be female (84% vs 45%) and have a higher disease stage (42% stage IIIB/C vs 26%). In addition, more cases appeared to have an amelanotic primary (21% vs. 5.4%) or an atypical mole syndrome (21% vs 10.2%). For pts who relapsed, the cases had a shorter disease free interval (DFI) (2.1 vs 9.7 yrs) than the controls. At a median f/up of 52 mos, 37% of the cases had relapsed and all of these pts had died. At a median f/up of 76 mos, 30% of the controls had relapsed yet only 47% of these pts had died. As a consequence, cases appeared more likely to have died of their disease than controls (42% vs 23%) (p=0.10). Conclusions: Compared to the general melanoma population, pts with concomitant immune suppression appear more likely to be female, have an amelanotic primary or atypical mole syndrome and more advanced disease at presentation. Although pts with concomitant immune suppression are equally likely to relapse compared to matched controls, those that relapse appear to have a shorter DFI and to be less likely to be salvaged, suggesting more aggressive tumor behavior in this setting. Thus, diagnosis and treatment of a primary melanoma at an early stage appears especially important in an immunosuppressed population.

No significant financial relationships to disclose.