title: Rapid detection of germline mutations for hereditary gastrointestinal polyposis/cancers using HaloPlex target enrichment and high-throughput sequencing technologies.
abstract: Genetic testing for hereditary colorectal polyposis/cancers has become increasingly important. Therefore, the development of a timesaving diagnostic platform is indispensable for clinical practice. We designed and validated target enrichment sequencing for 20 genes implicated in familial gastrointestinal polyposis/cancers in 32 cases with previously confirmed mutations using the HaloPlex enrichment system and MiSeq. We demonstrated that HaloPlex captured the targeted regions with a high efficiency (99.66 % for covered target regions, and 99.998 % for breadth of coverage), and MiSeq achieved a high sequencing accuracy (98.6 % for the concordant rate with SNP arrays). Using this approach, we correctly identified 33/33 (100 %) confirmed alterations including SNV, small INDELs and large deletions, and insertions in APC, BMPR1A, EPCAM, MLH1, MSH2, MSH6, PMS2, and SKT11. Our approach yielded the sequences of 20 target genes in a single experiment, and correctly identified all previously known mutations. Our results indicate that our approach successfully detected a wide range of genetic variations in a short turnaround time and with a small sample size for the rapid screening of known causative gene mutations of inherited colon cancer, such as familial adenomatous polyposis, Lynch syndrome, Peutz-Jeghers syndrome, and Juvenile polyposis syndrome.
authors.affiliation: Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan.
authors.forename: Masakazu
authors.initials: M
authors.lastname: Kohda
authors.affiliation: Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Kamoda, Kawagoe City, Saitama, 350-8550, Japan.|Department of Organ Regulatory Surgery, Fukushima Medical University, Fukushima, 960-1295, Japan.
authors.forename: Kensuke
authors.initials: K
authors.lastname: Kumamoto
authors.affiliation: Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan.
authors.forename: Hidetaka
authors.initials: H
authors.lastname: Eguchi
authors.affiliation: Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan.
authors.forename: Tomoko
authors.initials: T
authors.lastname: Hirata
authors.affiliation: Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan.
authors.forename: Yuhki
authors.initials: Y
authors.lastname: Tada
authors.affiliation: Department of Surgery, Iwakuni Clinical Center, Yamaguchi, 740-8510, Japan.
authors.forename: Kohji
authors.initials: K
authors.lastname: Tanakaya
authors.affiliation: Divisions of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, 362-0806, Japan.
authors.forename: Kiwamu
authors.initials: K
authors.lastname: Akagi
authors.affiliation: Department of Organ Regulatory Surgery, Fukushima Medical University, Fukushima, 960-1295, Japan.
authors.forename: Seiichi
authors.initials: S
authors.lastname: Takenoshita
authors.affiliation: Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Kamoda, Kawagoe City, Saitama, 350-8550, Japan.
authors.forename: Takeo
authors.initials: T
authors.lastname: Iwama
authors.affiliation: Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Kamoda, Kawagoe City, Saitama, 350-8550, Japan. 05hishi@saitama-med.ac.jp.
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Ishida
authors.affiliation: Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan. okazaki@saitama-med.ac.jp.
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Okazaki
mesh_terms: D011125:Adenomatous Polyposis Coli / Q000235:genetics; D003123:Colorectal Neoplasms, Hereditary Nonpolyposis / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods*; D005770:Gastrointestinal Neoplasms / Q000235:genetics*; D020440:Gene Duplication; D018095:Germ-Line Mutation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D044483:Intestinal Polyposis / Q000151:congenital / Q000235:genetics; D009386:Neoplastic Syndromes, Hereditary / Q000235:genetics; D010580:Peutz-Jeghers Syndrome / Q000235:genetics; D015203:Reproducibility of Results; D017384:Sequence Deletion
keywords: Colorectal cancer; Familial adenomatous polyposis; Hereditary gastrointestinal polyposis; Lynch syndrome; Mismatch repair genes
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