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Rapid detection of germline mutations for hereditary gastrointestinal polyposis/cancers using HaloPlex target enrichment and high-throughput sequencing technologies

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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.

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Funding

This study was supported in part by a grant-in-aid for the Support Project of the Strategic Research Center in Private Universities from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan awarded to the Saitama Medical University Research Center for Genomic Medicine.

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Authors and Affiliations

  1. Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan

    Masakazu Kohda, Hidetaka Eguchi, Tomoko Hirata, Yuhki Tada & Yasushi Okazaki

  2. Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Kamoda, Kawagoe City, Saitama, 350-8550, Japan

    Kensuke Kumamoto, Takeo Iwama & Hideyuki Ishida

  3. Department of Organ Regulatory Surgery, Fukushima Medical University, Fukushima, 960-1295, Japan

    Kensuke Kumamoto & Seiichi Takenoshita

  4. Department of Surgery, Iwakuni Clinical Center, Yamaguchi, 740-8510, Japan

    Kohji Tanakaya

  5. Divisions of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, 362-0806, Japan

    Kiwamu Akagi

Authors
  1. Masakazu Kohda
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  2. Kensuke Kumamoto
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  3. Hidetaka Eguchi
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  4. Tomoko Hirata
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  5. Yuhki Tada
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  6. Kohji Tanakaya
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  7. Kiwamu Akagi
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  8. Seiichi Takenoshita
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  9. Takeo Iwama
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  10. Hideyuki Ishida
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  11. Yasushi Okazaki
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Correspondence to Hideyuki Ishida or Yasushi Okazaki.

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None of the authors have conflict of interest.

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Masakazu Kohda and Kensuke Kumamoto are identical first authors.

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Kohda, M., Kumamoto, K., Eguchi, H. et al. Rapid detection of germline mutations for hereditary gastrointestinal polyposis/cancers using HaloPlex target enrichment and high-throughput sequencing technologies. Familial Cancer 15, 553–562 (2016). https://doi.org/10.1007/s10689-016-9872-x

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  • DOI: https://doi.org/10.1007/s10689-016-9872-x

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