Familial Cancer

, Volume 15, Issue 4, pp 553–562 | Cite as

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

  • Masakazu Kohda
  • Kensuke Kumamoto
  • Hidetaka Eguchi
  • Tomoko Hirata
  • Yuhki Tada
  • Kohji Tanakaya
  • Kiwamu Akagi
  • Seiichi Takenoshita
  • Takeo Iwama
  • Hideyuki IshidaEmail author
  • Yasushi OkazakiEmail author
Original Article


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.


Hereditary gastrointestinal polyposis Colorectal cancer Familial adenomatous polyposis Lynch syndrome Mismatch repair genes 



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.

Compliance with ethical standards

Conflict of interest

None of the authors have conflict of interest.

Supplementary material

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Supplementary material 1 (PDF 411 kb)
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Supplementary material 2 (PDF 11 kb)
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Supplementary material 3 (XLSX 22 kb)
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Supplementary material 4 (XLSX 26 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Masakazu Kohda
    • 1
  • Kensuke Kumamoto
    • 2
    • 3
  • Hidetaka Eguchi
    • 1
  • Tomoko Hirata
    • 1
  • Yuhki Tada
    • 1
  • Kohji Tanakaya
    • 4
  • Kiwamu Akagi
    • 5
  • Seiichi Takenoshita
    • 3
  • Takeo Iwama
    • 2
  • Hideyuki Ishida
    • 2
    Email author
  • Yasushi Okazaki
    • 1
    Email author
  1. 1.Division of Translational Research, Research Center for Genomic MedicineSaitama Medical UniversityHidakaJapan
  2. 2.Department of Digestive Tract and General Surgery, Saitama Medical CenterSaitama Medical UniversityKamoda, Kawagoe CityJapan
  3. 3.Department of Organ Regulatory SurgeryFukushima Medical UniversityFukushimaJapan
  4. 4.Department of SurgeryIwakuni Clinical CenterYamaguchiJapan
  5. 5.Divisions of Molecular Diagnosis and Cancer PreventionSaitama Cancer CenterSaitamaJapan

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