Using target capture sequencing detect microsatellite instability(MSI), tumor mutational burden(TMB) and POLE/POLD1 mutations in colorectal cancer.

2018 ◽  
Vol 36 (15_suppl) ◽  
pp. e15012-e15012
Author(s):  
Jing Wang ◽  
Dan Liu ◽  
Huanwen M. Wu ◽  
Yuting Yi ◽  
Yan-Fang Guan ◽  
...  
2019 ◽  
Vol 3 (2) ◽  
Author(s):  
Rebecca C Poulos ◽  
Dilmi Perera ◽  
Deborah Packham ◽  
Anushi Shah ◽  
Caroline Janitz ◽  
...  

Abstract Background Genetic testing of cancer samples primarily focuses on protein-coding regions, despite most mutations arising in noncoding DNA. Noncoding mutations can be pathogenic if they disrupt gene regulation, but the benefits of assessing promoter mutations in driver genes by panel testing has not yet been established. This is especially the case in colorectal cancer, for which few putative driver variants at regulatory elements have been reported. Methods We designed a unique target capture sequencing panel of 39 colorectal cancer driver genes and their promoters, together with more than 35 megabases of regulatory elements focusing on gene promoters. Using this panel, we sequenced 95 colorectal cancer and matched normal samples at high depth, averaging 170× and 82× coverage, respectively. Results Our target capture sequencing design enabled improved coverage and variant detection across captured regions. We found cases with hereditary defects in mismatch and base excision repair due to deleterious germline coding variants, and we identified mutational spectra consistent with these repair deficiencies. Focusing on gene promoters and other regulatory regions, we found little evidence for base or region-specific recurrence of functional somatic mutations. Promoter elements, including TERT, harbored few mutations, with none showing strong functional evidence. Recurrent regulatory mutations were rare in our sequenced regions in colorectal cancer, though we highlight some candidate mutations for future functional studies. Conclusions Our study supports recent findings that regulatory driver mutations are rare in many cancer types and suggests that the inclusion of promoter regions into cancer panel testing is currently likely to have limited clinical utility in colorectal cancer.


2019 ◽  
Vol 37 (14) ◽  
pp. 1217-1227 ◽  
Author(s):  
Federico Innocenti ◽  
Fang-Shu Ou ◽  
Xueping Qu ◽  
Tyler J. Zemla ◽  
Donna Niedzwiecki ◽  
...  

PURPOSE CALGB/SWOG 80405 was a randomized phase III trial that found no statistically significant difference in overall survival (OS) in patients with first-line metastatic colorectal cancer treated with chemotherapy plus either bevacizumab or cetuximab. Primary tumor DNA from 843 patients has been used to discover genetic markers of OS. PATIENTS AND METHODS Gene mutations were determined by polymerase chain reaction. Microsatellite status was determined by genotyping of microsatellites. Tumor mutational burden (TMB) was determined by next-generation sequencing. Cox proportional hazard models were used, with adjusting factors. Interaction of molecular alterations with either the bevacizumab or the cetuximab arms was tested. RESULTS Patients with high TMB in their tumors had longer OS than did patients with low TMB (hazard ratio [HR], 0.73 [95% CI, 0.57 to 0.95]; P = .02). In patients with microsatellite instability–high (MSI-H) tumors, longer OS was observed in the bevacizumab arm than in the cetuximab arm (HR, 0.13 [95% CI, 0.06 to 0.30]; interaction P < .001 for interaction between microsatellite status and the two arms). Patients with BRAF mutant tumors had shorter OS than did patients with wild-type (WT) tumors (HR, 2.01 [95% CI, 1.49 to 2.71]; P < .001). Patients with extended RAS mutant tumors had shorter OS than did patients with WT tumors (HR, 1.52 [95% CI, 1.26 to 1.84]; P < .001). Patients with triple-negative tumors (WT for NRAS/ KRAS/ BRAF) had a median OS of 35.9 months (95% CI, 33.0 to 38.8 months) versus 22.2 months (95% CI, 19.6 to 24.4 months ) in patients with at least one mutated gene in their tumors ( P < .001). CONCLUSION In patients with metastatic colorectal cancer treated in first line, low TMB, and BRAF and RAS mutations are negative prognostic factors. Patients with MSI-H tumors benefited more from bevacizumab than from cetuximab, and studies to confirm this effect of MSI-H are warranted.


2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A25-A25
Author(s):  
Charles Schneider ◽  
Michael Krainock ◽  
Meenakshi Malhotra ◽  
Paul Billings ◽  
Alexey Aleshin

BackgroundHigh microsatellite instability (MSI-H) in metastatic colorectal cancer (mCRC) is associated with a beneficial response to immunotherapy. Additionally, within MSI-H cancers, tumor mutational burden (TMB) is independently predictive of immunotherapy responsiveness.1 Durable responses to therapy have been demonstrated in patients with MSI-H mCRC treated with Nivolumab and Ipilimumab.2 However, less is known about treatment responsiveness in patients with high mutational burden mCRC that demonstrates microsatellite stability (MSI-L).MethodsWe report on a 55-year-old female with a PALB-2 germline mutation who presented with a right-sided colonic adenocarcinoma with the involvement of the omentum and liver. The patient received 6 cycles of neoadjuvant FOLFOX, followed by an extended right hemicolectomy, omentectomy, and partial liver resection. The surgical specimen revealed a moderately differentiated adenocarcinoma in the cecum demonstrating a poor response to chemotherapy, 0/23 lymph nodes positive, one focus of adenocarcinoma in the liver with clear margins, and focal omental involvement with adenocarcinoma. The patient subsequently underwent 6 cycles of ‘adjuvant’ FOLFOX, with Oxaliplatin omitted after 3 cycles secondary to peripheral neuropathy. Soon after the patient experienced a recurrence that involved the anterior abdominal wall, between the peritoneum, and stomach, which was subsequently resected with negative margins. Molecular profiling of this metastatic focus revealed a TMB of 15.4 mutations per megabase, proficient Mismatch Repair (pMMR), a PDL1 CPS score of 26, and microsatellite stable (MSS) status. First, ctDNA analysis was performed at the time of recurrence and was found to be positive. Based on the TMB score of 15.4 and an elevated PDL1 score, the patient was initiated on Nivolumab and Ipilimumab. ctDNA measurements were obtained at the patient‘s request.ResultsDNA assessment performed after surgery and prior to initiation of immunotherapy revealed an approximate doubling of ctDNA levels, measured in mean tumor molecules (MTM) per mL of plasma, every month. During this period of time and correlating with the rise in ctDNA levels, the patient developed a new and enlarging FDG avid cardiophrenic lymph node. Following 2 cycles of Nivolumab and Ipilimumab, the FDG avid lymph node completely resolved and ctDNA clearance was observed (figure 1).Abstract 26 Figure 1ctDNA time-course demonstrating ctDNA kineticsTime-point A represents the initial ctDNA assay, performed at the time of resection of peritoneal metastasis. An additional time-point (B) drawn a month later reveals a further increase in ctDNA. Time-point C represents a peak in ctDNA levels, concomitant with the new emergence of a PET avid cardiophrenic lymph node. Combination Immunotherapy (IO) was begun shortly after time-point C. Time-point D represents ctDNA clearance and radiographic resolution of lymph node metastasis after two cycles of IO. MTM/mL - mean tumor molecules/milliliter of plasmaConclusionsHere we present a case of ctDNA clearance correlating with a radiographic resolution of metastatic disease in a patient with MSS mCRC. The data is provocative and suggests a possible contributory role of ctDNA-based testing as an additional monitoring parameter to measure disease-responsiveness to immunotherapy. Further investigation is warranted.Ethics ApprovalN/AConsentN/AReferencesSchrock AB, Ouyang C, Sandhu J, Sokol E, Jin D, Ross J8, Miller VA, Lim D, Amanam l, Chao J, Catenacci D, Cho M, Braiteh 7, Klempner SJ, Ali 8M, Fakih M. Tumor mutational burden is predictive of response to immune checkpoint inhibitors in MSl-high metastatic colorectal cancer. Ann Oncol 2019;30(7):1096–1103Overman MJ, et al. Durable Clinical/Benefit With Nivolumab Plus lpilimumab in DNA Mismatch Repair-Deficient/Microsatellite Instability-High Metastatic Colorectal Cancer. Clin Oncol 2018;36(8):773–779.


BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jian Xiao ◽  
Wenyun Li ◽  
Yan Huang ◽  
Mengli Huang ◽  
Shanshan Li ◽  
...  

Abstract Background Mismatch repair (MMR)/microsatellite instability (MSI) and tumor mutational burden (TMB) are independent biomarkers that complement each other for predicting immune checkpoint inhibitors (ICIs) efficacy. Here we aim to establish a strategy that integrates MSI and TMB determination for colorectal cancer (CRC) in one single assay. Methods Surgical or biopsy specimens retrospectively collected from CRC patients were subjected to NGS analysis. Immunohistochemistry (IHC) and polymerase chain reaction (PCR) were also used to determine MMR/MSI for those having enough tissues. The NGS-MSI method was validated against IHC and PCR. The MSI-high (MSI-H) or microsatellite stable (MSS) groups were further stratified based on tumor mutational burden, followed by validation using the The Cancer Genome Atlas (TCGA) CRC dataset. Immune microenvironment was evaluated for each subgroup be profiling the expression of immune signatures. Results Tissues from 430 CRC patients were analyzed using a 381-gene NGS panel. Alterations in KRAS, NRAS, BRAF, and HER2 occurred at a significantly higher incidence among MSI-H tumors than in MSS patients (83.6% vs. 58.4%, p = 0.0003). A subset comprising 98 tumors were tested for MSI/MMR using all three techniques, where NGS proved to be 99.0 and 93.9% concordant with PCR and IHC, respectively. Four of the 7 IHC-PCR discordant cases had low TMB (1.1–8.1 muts/Mb) and were confirmed to have been misdiagnosed by IHC. Intriguingly, 4 of the 66 MSS tumors (as determined by NGS) were defined as TMB-high (TMB-H) using a cut-off of 29 mut/Mb. Likewise, 15 of the 456 MSS tumors in the TCGA CRC cohort were also TMB-H with a cut-off of 9 muts/Mb. Expression of immune signatures across subgroups (MSS-TMB-H, MSI-H-TMB-H, and MSS-TMB-L) confirmed that the microenvironment of the MSS-TMB-H tumors was similar to that of the MSI-H-TMB-H tumors, but significantly more immune-responsive than that of the MSS-TMB-L tumors, indicating that MSI combined with TMB may be more precise than MSI alone for immune microenvironment prediction. Conclusion This study demonstrated that NGS panel-based method is both robust and tissue-efficient for comprehensive molecular diagnosis of CRC. It also underscores the importance of combining MSI and TMB information for discerning patients with different microenvironment.


2018 ◽  
Author(s):  
Rebecca C Poulos ◽  
Dilmi Perera ◽  
Deborah Packham ◽  
Anushi Shah ◽  
Caroline Janitz ◽  
...  

AbstractLarge-scale whole cancer-genome sequencing projects have led to the identification of a handful of cis-regulatory driver mutations in cancer genomes. However, recent studies have demonstrated that very large cancer cohorts will be required in order to identify low frequency non-coding drivers. To further this endeavour, in this study, we performed highdepth sequencing across 95 colorectal cancers and matched normal samples using a unique target capture sequencing (TCS) assay focusing on over 35 megabases of gene regulatory elements. We first assessed coverage and variant detection capability from our TCS data, and compared this with a sample that was additionally whole-genome sequenced (WGS). TCS enabled substantially deeper sequencing and thus we detected 51% more somatic single nucleotide variants (n = 2,457) and 144% more somatic insertions and deletions (n = 39) by TCS than WGS. Variants obtained from TCS data were suitable for somatic mutational signature detection, enabling us to define the signatures associated with germline deleterious variants in MSH6 and MUTYH in samples within our cohort. Finally, we surveyed regulatory mutations to find putative drivers by assessing variant recurrence and function, identifying some regulatory variants that may influence oncogenesis. Our study demonstrates TCS to be a sequencing-efficient alternative to traditional WGS, enabling improved coverage and variant detection when seeking to identify variants at specific loci among larger cohorts. Interestingly, we found no candidate variants that have a clear driver function, suggesting that regulatory drivers may be rare in a colorectal cancer cohort of this size.Author SummaryIn recent years, some cancer research focus has turned towards the role of somatic mutations in the 98% of the genome that is non-coding. To investigate such mutations, we performed deep sequencing of regulatory regions and a selection of coding genes across 95 colorectal cancer and matched-normal samples. To determine the ability of our targeted deep sequencing methodology to accurately detect variants, we compared our results with those from a sample that was additionally whole-genome sequenced. We found target capture sequencing to enable greater sequencing depth, allowing the detection of 51% and 144% more somatic single nucleotide and insertion/deletion mutations, respectively. Our study here demonstrates target capture sequencing to be a useful approach for researchers seeking to identify variants at specific loci among larger cohorts. Our results also enabled the generation of mutational signatures, implicating deleterious germline single nucleotide variants in coding exons of MSH6 and MUTYH in samples within our cohort. Finally, we surveyed regulatory elements in search of somatic cancer driver mutations. We identified some regulatory variants that may influence oncogenesis, but found no candidate variants with clear driver function. These findings suggest that regulatory driver mutations may be rare in a colorectal cancer cohort of this size.


2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Lijun Xu ◽  
Qing Zheng

Abstract Background Tumor mutational burden (TMB) is a promising predictor, which could stratify colorectal cancer (CRC) patients based on the response to immune checkpoint inhibitors (ICIs). MicroRNAs (miRNAs) act as the key regulators of anti-cancer immune response. However, the relationship between TMB and miRNA expression profiles is not elucidated in CRC. Methods Differentially expressed miRNAs (DE miRNAs) between the TMBhigh group and the TMBlow group were identified for the CRC cohort of the TCGA database. In the training cohort, a miRNA-related expression signature for predicting TMB level was developed by the least absolute shrinkage and selection operator (LASSO) method and tested with reference to its discrimination, calibration, and decision curve analysis (DCA) in the validation cohort. Functional enrichment analysis of these TMB-related miRNAs was performed. The correlation between this miRNA-related expression signature and three immune checkpoints was analyzed. Results Twenty-one out of 43 DE miRNAs were identified as TMB-related miRNAs, which were used to develop a miRNA-related expression signature. This TMB-related miRNA signature demonstrated great discrimination (AUCtest set = 0.970), satisfactory calibration (P > 0.05), and clinical utility in the validation cohort. Functional enrichment results revealed that these TMB-related miRNAs were mainly involved in biological processes associated with immune response and signaling pathways related with cancer. This miRNA-related expression signature showed a median positive correlation with PD-L1 (R = 0.47, P < 0.05) and CTLA4 (R = 0.39, P < 0.05) and a low positive correlation with PD-1 (R = 0.16, P < 0.05). Conclusion This study presents a miRNA-related expression signature which could stratify CRC patients with different TMB levels.


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