scholarly journals MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

2013 ◽  
Vol 30 (7) ◽  
pp. 1015-1016 ◽  
Author(s):  
Beifang Niu ◽  
Kai Ye ◽  
Qunyuan Zhang ◽  
Charles Lu ◽  
Mingchao Xie ◽  
...  
2020 ◽  
Author(s):  
Beatrice Knudsen ◽  
Fangjin Huang ◽  
Hisashi Tanaka ◽  
Joanne Rutgers

Abstract Purpose: Tumors with mutations in the exonuclease domain of POLE are associated with ultrahigh mutation rates. POLE mutant tumors are best characterized in intestinal and uterine cancers and are associated with a prominent immune infiltrate and favorable prognosis. To determine whether mutations in other DNA polymerases cooperate with POLE mutations to generate the ultramutator phenotype, we analyzed exome sequence data from 15 cancer types with POLE mutations in The Cancer Genome Atlas (TCGA).Results: 36% of POLE mutant tumors, predominantly colorectal, stomach and endometrial cancers carried mutations in POLQ (E/Q) and/or POLZ/REV3L (E/Z). Mutation burden, microsatellite instability (MSI) status, tumor stage, disease free survival and immune scores were evaluated in these tumors. Compared to the POLE-only mutant tumors, tumors with E/Q, E/Z, and E/Q/Z mutations possessed significantly higher overall mutation frequencies (p < 0.001) and increased frequencies of mutations within the POLE exonuclease domain (p = 0.013). E/Q, E/Z, and E/Q/Z mutant colorectal, stomach and endometrial tumors within the TCGA cohort demonstrated 100% disease-free survival, even if mutations occurred outside the POLE exonuclease domain (p = 0.003). However, immune scores were related to microsatellite instability (MSI) and not POLE mutation status, suggesting that mechanisms in addition to host immune response may contribute to the prolonged disease-free survival.Conclusion: Our results demonstrate that POLE mutant tumors can be further substratified for outcomes prediction based on additional mutations in POLQ and ERV3L.


2001 ◽  
Vol 120 (5) ◽  
pp. A295-A295
Author(s):  
D CHANG ◽  
A GOEL ◽  
L RICCIARDIELLO ◽  
C ARNOLD ◽  
C BOLAND

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.


2008 ◽  
Vol 31 (4) ◽  
pp. 12
Author(s):  
A J Hyde ◽  
D Fontaine ◽  
R C Green ◽  
M Simms ◽  
P S Parfrey ◽  
...  

Background: Lynch Syndrome is an autosomal dominant trait that accounts forapproximately 3% of all cases of colorectal cancer (CRC). It is caused by mutations in DNA mismatch repair (MMR) genes, most commonly MLH1 or MSH2. These MMR defects cause high levels of microsatellite instability (MSI-H) in the tumours. MSI testing of all CRCs to identify potential Lynch Syndrome cases is not practical, so the Bethesda Guidelines, which use clinical and pathological features, were created to identify those tumours most likely to be MSI-H^1. In 2007 Jenkins et. al. created MsPath, a tool based on the pathological features described in the rarely used 3^rd Bethesda criterion, to improve prediction of MSI-H tumours among CRC cases diagnosed before age 60 years^2. Methods: We collected a population-based cohort of 716 CRC cases diagnosed before age 75 years in Newfoundland. For each of these cases we collected family history, performed MSI analysis, and scored a number of pathological features for the purpose of evaluating the accuracy of the Bethesda Criteria and MsPath at predicting MSI-H tumours. Results: Our work validates the MsPath tool in the Newfoundland population for the same age group used to create the tool. We found it identified MSI-H cases with a sensitivity of 95% and specificity of 35% in our population of CRCcases diagnosed before age 60 years (n=290). We also tested this tool on our older population of CRCcases, diagnosed at ages 60 to 74 years (n=426). We found it to be at least as predictive in this population,with a sensitivity of 95% and a specificity of 42%. We then used our entire cohort (N=716) to compare MsPath with the other Bethesda criteria.Bethesda criteria 1, 2, 4 and 5 together predicted MSI-H cases with a sensitivity of 67% and a specificity of 51%. MsPath was better at identifying these cases, with a sensitivity of 95% and a specificity of 39%. Conclusions: We conclude that MsPath can be extended to include patients diagnosed with CRC before age 75 years. As well, we have found that MsPath is a better predictive tool than the Revised Bethesda Guidelines for identifying MSI-H cases within a population-based setting of colorectal cancer. References: 1. Umar, A. et. al. J Natl Cancer Inst 2004;96:261-8 2.Jenkins, M.A. et. al. Gastroenterology 2007;133:48-56


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