scholarly journals Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures

2017 ◽  
Author(s):  
Javad Noorbakhsh ◽  
Jeffrey H. Chuang
Keyword(s):  
Allele Frequency ◽  
Somatic Mutations ◽  
Cancer Genome ◽  
Allele Frequencies ◽  
The Cancer Genome Atlas ◽  
Neutral Evolution ◽  
Evolutionary Models ◽  
Cancer Genome Atlas ◽  
Limit Power ◽  
Genome Atlas

We read with great interest the paper by Williams, et. al.[1], who argued for neutral evolution in tumors by analyzing The Cancer Genome Atlas (TCGA) data. They supported this conclusion by showing high R2 values for fits to a neutral evolution model predicting M ∝ 1 / f, where M is the number of somatic mutations with allele frequency ≥ f. However, we believe a conclusion of neutrality must be treated cautiously, as high R2 values are consistent with many evolutionary models.

scholarly journals Exceptional Chemotherapy Response in Metastatic Colorectal Cancer Associated With Hyper-Indel–Hypermutated Cancer Genome and Comutation of POLD1 and MLH1

2017 ◽  
pp. 1-12
Author(s):  
Manish R. Sharma ◽  
James T. Auman ◽  
Nirali M. Patel ◽  
Juneko E. Grilley-Olson ◽  
Xiaobei Zhao ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Colon Cancer ◽  
Somatic Mutation ◽  
Mutation Rate ◽  
Germ Line ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Response To Chemotherapy ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Purpose A 73-year-old woman with metastatic colon cancer experienced a complete response to chemotherapy with dose-intensified irinotecan that has been durable for 5 years. We sequenced her tumor and germ line DNA and looked for similar patterns in publicly available genomic data from patients with colorectal cancer. Patients and Methods Tumor DNA was obtained from a biopsy before therapy, and germ line DNA was obtained from blood. Tumor and germline DNA were sequenced using a commercial panel with approximately 250 genes. Whole-genome amplification and exome sequencing were performed for POLE and POLD1. A POLD1 mutation was confirmed by Sanger sequencing. The somatic mutation and clinical annotation data files from the colon (n = 461) and rectal (n = 171) adenocarcinoma data sets were downloaded from The Cancer Genome Atlas data portal and analyzed for patterns of mutations and clinical outcomes in patients with POLE- and/or POLD1-mutated tumors. Results The pattern of alterations included APC biallelic inactivation and microsatellite instability high (MSI-H) phenotype, with somatic inactivation of MLH1 and hypermutation (estimated mutation rate > 200 per megabase). The extremely high mutation rate led us to investigate additional mechanisms for hypermutation, including loss of function of POLE. POLE was unaltered, but a related gene not typically associated with somatic mutation in colon cancer, POLD1, had a somatic mutation c.2171G>A [p.Gly724Glu]. Additionally, we noted that the high mutation rate was largely composed of dinucleotide deletions. A similar pattern of hypermutation (dinucleotide deletions, POLD1 mutations, MSI-H) was found in tumors from The Cancer Genome Atlas. Conclusion POLD1 mutation with associated MSI-H and hyper-indel–hypermutated cancer genome characterizes a previously unrecognized variant of colon cancer that was found in this patient with an exceptional response to chemotherapy.

scholarly journals The construction and analysis of ceRNA networks in invasive breast cancer: a study based on The Cancer Genome Atlas

2018 ◽  
Vol Volume 11 ◽  
pp. 1-11 ◽  
Author(s):  
Chundi Gao ◽  
Huayao Li ◽  
Jing Zhuang ◽  
HongXiu Zhang ◽  
Kejia Wang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Invasive Breast Cancer ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Cancer Genome Atlas ◽  
Genome Atlas

scholarly journals Molecular Correlates of Metastasis by Systematic Pan-Cancer Analysis Across The Cancer Genome Atlas

2018 ◽  
Vol 17 (2) ◽  
pp. 476-487 ◽  
Author(s):  
Fengju Chen ◽  
Yiqun Zhang ◽  
Sooryanarayana Varambally ◽  
Chad J. Creighton
Keyword(s):  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Cancer Genome Atlas ◽  
Pan Cancer ◽  
Genome Atlas

scholarly journals Large-scale profiling of microRNAs for The Cancer Genome Atlas

2015 ◽  
Vol 44 (1) ◽  
pp. e3-e3 ◽  
Author(s):  
Andy Chu ◽  
Gordon Robertson ◽  
Denise Brooks ◽  
Andrew J. Mungall ◽  
Inanc Birol ◽  
...  
Keyword(s):  
Large Scale ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Cancer Genome Atlas ◽  
Genome Atlas

scholarly journals Response to Comment on “DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification”

Science ◽  
2018 ◽  
Vol 361 (6409) ◽  
pp. eaat0958 ◽  
Author(s):  
Lixin Chen ◽  
Pingfang Liu ◽  
Thomas C. Evans ◽  
Laurence M. Ettwiller
Keyword(s):  
Dna Damage ◽  
Oxidative Damage ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Sequencing Errors ◽  
Cancer Genome Atlas ◽  
Genome Atlas ◽  
Variant Identification

Following the Comment of Stewart et al., we repeated our analysis on sequencing runs from The Cancer Genome Atlas (TCGA) using their suggested parameters. We found signs of oxidative damage in all sequence contexts and irrespective of the sequencing date, reaffirming that DNA damage affects mutation-calling pipelines in their ability to accurately identify somatic variations.

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