Optimizing the number of variants tracked to follow disease burden with circulating tumor DNA assays in metastatic colorectal cancer.

Background: The number of somatic mutations detectable in circulating tumor DNA (ctDNA) is highly heterogeneous in metastatic colorectal cancer (mCRC). The optimal number of mutations required to assess disease kinetics is relevant and remains poorly understood. Objectives: To determine whether increasing panel breadth (the number of tracked variants in a ctDNA assay) would alter the sensitivity in detecting ctDNA in patients with mCRC. Design: We used archival tissue sequencing to perform an in silico assessment of the optimal number of tracked mutations to detect and monitor disease kinetics in mCRC using sequencing data from the Canadian Cancer Trials Group CO.26 trial. Methods: For each patient, 1, 2, 4, 8, 12, or 16 of the most clonal (highest variant allele frequency) somatic variants were selected from archival tissue-based whole-exome sequencing and assessed for the proportion of variants detected in matched ctDNA at baseline, week 8, and progression timepoints. Results: Data from 110 patients were analyzed. Genes most frequently encountered among the top four highest VAF variants in archival tissue were TP53 (51.9% of patients), APC (43.3%), KRAS (42.3%), and SMAD4 (9.6%). While the frequency of detecting at least one tracked variant increased when expanding beyond variant pool sizes of 1 and 2 in baseline (p = 0.0030) and progression (p = 0.0030) ctDNA samples, we observed no significant benefit to increases in variant pool size past four variants in any of the ctDNA timepoints (p < 0.05). Conclusion: While increasing panel breadth beyond two tracked variants improved variant re-detection in ctDNA samples from patients with treatment refractory mCRC, increases beyond four tracked variants yielded no significant improvement in variant re-detection.

Preponderance of sonic hedgehog pathway activation characterizes adult medulloblastoma.

Medulloblastoma (MB) represents approximately 4% of adult brain tumours, and as such is a poorly studied disease. Although many adult MB are treated using paediatric MB protocols, the reported outcomes are inferior to those observed in children. It remains unclear whether biologic differences underlie these clinical observations. We investigated the molecular characteristics of 31 adult MB. Twelve and 19 adult MB were respectively examined using Affymetrix-HG-U133-plus-2.0-genechips and immunohistochemical analyses. 26/31 (84%) of adult MB examined by gene expression and/or immunohistochemical analysis showed evidence of sonic hedgehog (SHH) pathway activation. A comparison of adult and paediatric MB showed that most adult tumours cluster within the SHH-active subgroup of paediatric MB. The preponderance of SHH activity in adult MB tumours was also shown by positive SFRP1 immunostaining in 16/19 adult paraffin-embedded adult MB tumour blocks. A smaller proportion of adult tumours exhibited evidence of WNT pathway activation, as confirmed by nuclear ß-catenin staining (9.7%; 3/31). Notably, we found PTCH1 gene mutation in 4/8 samples tested. Similar to children, adult MB has abnormalities in developmental signalling pathways including SHH and WNT. Importantly, we found a preponderance of SHH pathway activation amongst MB tumours in adults. This SHH signature does not appear to correlate with a long-term favourable outcome. Differences in molecular profiles exist between adult and paediatric SHH-driven MB and further investigations are needed to better characterize age-related molecular profiles in this subgroup.

Immune response to conjugated meningococcal C vaccine in pediatric oncology patients.

BACKGROUND: Following outbreaks of meningococcal disease in Quebec in 1991-1993 and 2000-2001, a mass vaccination campaign was performed. In 2001-2002, children aged 2 months to 20 years were immunized with the Meningococcal CRM197 vaccine (Menjugate). We examined the response of pediatric oncology patients during or following maintenance chemotherapy and post-bone-marrow transplantation to Meningococcal C vaccine. PROCEDURE: This was an open label descriptive study of a cohort of patients from the oncology clinic at the Montreal Children's Hospital. A positive vaccine response was defined as a fourfold increase in specific IgG from baseline and a bactericidal assay using human complement (hBCA) titer >1:4. RESULTS: Of the 25 patients with ALL, 13 had a serologic response (average 60-fold increase). The serologic responders had a higher mean B cell count (0.262) compared to non-responders 0.068 x 10.9/L [t(23) = 2.843 (P < 0.05)]. Eleven of the 12 non-responders and 4 of the responders were on maintenance chemotherapy. In addition, two of the five patients post-bone-marrow transplant, responded. Fifteen of the 34 patients (44%) had an adequate hBCA response (mean titer 61). The group included 14/18 serologic responders with hBCA response (P < 0.001) and 16/17 non-serologic responders with no hBCA response (P < 0.001). CONCLUSIONS: Meningococcal C-conjugate vaccine produced variable responses in children with common cancers. Proximity to chemotherapy and total B cell number may help predict likelihood of response.