Diagnostic challenge using new methods in exome-negative patients

• Project/Area Number: 18K07864
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 52050:Embryonic medicine and pediatrics-related
• Research Institution: Kanagawa Children's Medical Center (Clinical Research Institute)
• Principal Investigator: Enomoto Yumi 地方独立行政法人神奈川県立病院機構神奈川県立こども医療センター(臨床研究所), 臨床研究所, 研究員 (20506290)
• Project Period (FY): 2018-04-01 – 2022-03-31
• Project Status: Completed (Fiscal Year 2021)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2020: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2019: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2018: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
• Keywords: 全ゲノムシーケンス / 先天異常 / エクソン外変異 / 複雑構造変異 / エクソームシーケンス / イントロン変異 / トランスポゾン挿入変異 / 先天性疾患 / ultraconserved elements / トポロジー関連ドメイン / 発症メカニズム

Outline of Final Research Achievements

We performed whole genome sequencing (WGS) in exome-negative patients. WGS identified causal variants in two patients. One patient had a de novo variant in deep intronic region of the gene related his clinical features. Our functional study revealed that the variant resulted in aberrant splicing. The other patient (Rubinstein-Taybi syndrome) had scattered deletions including a partial 5’-untranslated region of CREBBP, but all coding exons in CREBBP were intact (two normal copies). Both variants were not identified by exome sequencing. This study using WGS identified the causative variants and elucidated the mechanism of disease in exome-negative patients.

Academic Significance and Societal Importance of the Research Achievements

エクソーム解析では原因不明だった患者を対象に、全ゲノムシーケンスを用いた変異の探索を行った。結果、２名の患者の原因変異および疾患発症メカニズムを明らかにすることができた。本研究にてエクソーム解析の限界、全ゲノムシーケンス解析の可能性および課題が示された。今後の臨床シーケンス、遺伝学的研究の有用なデータになると思われる。

Research Products

• [Journal Article] Divergent variant patterns among 19 patients with Rubinstein-Taybi syndrome uncovered by comprehensive genetic analysis including whole genome sequencing (2022)
  • Author(s): Enomoto Y, Yokoi T, Tsurusaki Y, Murakami H, Tominaga M, Minatogawa M, Abe-Hatano C, Kuroda Y, Ohashi I, Ida K, Shiiya S, Kumaki T, Naruto T, Mitsui J, Harada N, Kido Y, Kurosawa K
  • Journal Title: Clinical Genetics Volume: 101 Issue: 3 Pages: 335-345
  • DOI: 10.1111/cge.14103
  • Peer Reviewed
• [Presentation] Complex rearrangements of CREBBP detected in patients with Rubinstein-Taybi syndrome (RSTS) (2019)
  • Author(s): Enomoto Y, Tsurusaki Y, Kuroda Y, Murakami H, Kimura Y, Shiiya S, Naruto T, Kido Y, Kurosawa K
  • Organizer: American Society Of Human Genetics 69th Annual Meeting
  • Int'l Joint Research
• [Presentation] エクソーム解析で疾患原因不明の患者に対する 新手法による原因解明の試み (2019)
  • Author(s): 榎本友美, 黒澤健司
  • Organizer: 2019年度「先進ゲノム支援」拡大班会議
• [Presentation] Whole exome sequence identified the deletion in 5' UTR or upstream intronic region of CREBBP in a patient with Rubinstein-Taybi syndrome (2018)
  • Author(s): Enomoto Y, Tsurusaki Y, Kuroda Y, Murakami H, Ida K, Umegae M, Harada N, Kimura Y, Naruto T, Kurosawa K
  • Organizer: American Society Of Human Genetics 68th Annual Meeting
  • Int'l Joint Research
• [Presentation] The variety of phenotype in patients with rare Japanese-origin homozygous deletion in RECQL4 (2018)
  • Author(s): Enomoto Y, Tsurusaki Y, Kuroda Y, Murakami H, Umegae M, Kimura Y, Naruto T, Shimokaze T, Kurosawa K
  • Organizer: 日本人類遺伝学会第63回大会