title: Integrated next-generation sequencing analysis of whole exome and 409 cancer-related genes.
abstract: The use of next-generation sequencing (NGS) techniques to analyze the genomes of cancer cells has identified numerous genomic alterations, including single-base substitutions, small insertions and deletions, amplification, recombination, and epigenetic modifications. NGS contributes to the clinical management of patients as well as new discoveries that identify the mechanisms of tumorigenesis. Moreover, analysis of gene panels targeting actionable mutations enhances efforts to optimize the selection of chemotherapeutic regimens. However, whole genome sequencing takes several days and costs at least $10,000, depending on sequence coverage. Therefore, laboratories with relatively limited resources must employ a more economical approach. For this purpose, we conducted an integrated nucleotide sequence analysis of a panel of 409-cancer related genes (409-CRG) combined with whole exome sequencing (WES). Analysis of the 409-CRG panel detected low-frequency variants with high sensitivity, and WES identified moderate and high frequency somatic variants as well as germline variants.
authors.affiliation: Cancer Diagnostics Reseach Division, Shizuoka Cancer Center Research Institute.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Shimoda
authors.forename: Takeshi
authors.initials: T
authors.lastname: Nagashima
authors.forename: Kenichi
authors.initials: K
authors.lastname: Urakami
authors.forename: Tomoe
authors.initials: T
authors.lastname: Tanabe
authors.forename: Junko
authors.initials: J
authors.lastname: Saito
authors.forename: Akane
authors.initials: A
authors.lastname: Naruoka
authors.forename: Masakuni
authors.initials: M
authors.lastname: Serizawa
authors.forename: Tohru
authors.initials: T
authors.lastname: Mochizuki
authors.forename: Keiichi
authors.initials: K
authors.lastname: Ohshima
authors.forename: Sumiko
authors.initials: S
authors.lastname: Ohnami
authors.forename: Shumpei
authors.initials: S
authors.lastname: Ohnami
authors.forename: Masatoshi
authors.initials: M
authors.lastname: Kusuhara
authors.forename: Ken
authors.initials: K
authors.lastname: Yamaguchi
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D055028:Comparative Genomic Hybridization; D019295:Computational Biology / Q000379:methods; D059472:Exome; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide