title: MonoSeq Variant Caller Reveals Novel Mononucleotide Run Indel Mutations in Tumors with Defective DNA Mismatch Repair.
abstract: Next-generation sequencing has revolutionized cancer genetics, but accurately detecting mutations in repetitive DNA sequences, especially mononucleotide runs, remains a challenge. This is a particular concern for tumors with defective mismatch repair (MMR) that accumulate strand-slippage mutations. We developed MonoSeq to improve indel mutation detection in mononucleotide runs, and used MonoSeq to investigate strand-slippage mutations in endometrial cancers, a tumor type that has frequent loss of MMR. We performed extensive Sanger sequencing to validate both clonal and subclonal MonoSeq mutation calls. Eighty-one regions containing mononucleotide runs were sequenced in 540 primary endometrial cancers (223 with defective MMR). Our analyses revealed that the overall mutation rate in MMR-deficient tumors was 20-30-fold higher than in MMR-normal tumors. MonoSeq analysis identified several previously unreported mutations, including a novel hotspot in an A7 run in the terminal exon of ARID5B.The ARID5B indel mutations were seen in both MMR-deficient and MMR-normal tumors, suggesting biologic selection. The analysis of tumor mRNAs revealed the presence of mutant transcripts that could result in translation of neopeptides. Improved detection of mononucleotide run strand-slippage mutations has clear implications for comprehensive mutation detection in tumors with defective MMR. Indel frameshift mutations and the resultant antigenic peptides could help guide immunotherapy strategies.
authors.affiliation: James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Walker
authors.affiliation: James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH.
authors.forename: Mario A
authors.initials: MA
authors.lastname: Miranda
authors.affiliation: James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: O'Hern
authors.affiliation: James Comprehensive Cancer Center and the Department of Internal Medicine, Ohio State University, Columbus, Ohio.
authors.forename: James S
authors.initials: JS
authors.lastname: Blachly
authors.affiliation: James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH.
authors.forename: Cassandra L
authors.initials: CL
authors.lastname: Moyer
authors.affiliation: Siteman Cancer Center and the Department of Surgery, Washington University School of Medicine, St. Louis, MO.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Ivanovich
authors.affiliation: James Comprehensive Cancer Center, Ohio State University, Columbus, OH.
authors.forename: Karl W
authors.initials: KW
authors.lastname: Kroll
authors.affiliation: James Comprehensive Cancer Center, Ohio State University, Columbus, OH.
authors.forename: Ann-Kathrin
authors.initials: AK
authors.lastname: Eisfeld
authors.affiliation: James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH.
authors.forename: Caroline E
authors.initials: CE
authors.lastname: Sapp
authors.affiliation: Siteman Cancer Center and the Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO.
authors.forename: David G
authors.initials: DG
authors.lastname: Mutch
authors.affiliation: James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH.
authors.forename: David E
authors.initials: DE
authors.lastname: Cohn
authors.affiliation: Department of Physics, Department of Chemistry and Biochemistry, Department of Internal Medicine, Ohio State University, Columbus, OH.
authors.forename: Ralf
authors.initials: R
authors.lastname: Bundschuh
authors.affiliation: James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH. paul.goodfellow@osumc.edu.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Goodfellow
mesh_terms: D000465:Algorithms; D053843:DNA Mismatch Repair; D004268:DNA-Binding Proteins / Q000235:genetics*; D016889:Endometrial Neoplasms / Q000235:genetics*; D005260:Female; D016368:Frameshift Mutation; D020869:Gene Expression Profiling / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D054643:INDEL Mutation; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics*
chemical_list: C503805:ARID5B protein, human; D004268:DNA-Binding Proteins; D014157:Transcription Factors
keywords: endometrial cancer; microsatellite instability; mononucleotide run; next-generation sequencing