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Identification of causative genetic locus of a large family with hearing loss

Research Project

Project/Area Number 25462637
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Otorhinolaryngology
Research InstitutionChiba University (2015)
Kyoto University (2013)

Principal Investigator

Sekine Akihiro  千葉大学, 予防医学センター, 教授 (30425631)

Co-Investigator(Kenkyū-buntansha) OKANO Takayuki  京都大学, 医学部附属病院, 助教 (60642931)
Co-Investigator(Renkei-kenkyūsha) KITAJIRI Shinichiro  京都大学, 医学部附属病院, 助教 (00532970)
YAMAMOTO Norio  京都大学, 医学部附属病院, 助教 (70378644)
TAKEMURA Ryo  千葉大学, 医学部附属病院, 特任助教 (50747516)
KITAHARA Terue  千葉大学, 予防医学センター, 特任研究員 (70761162)
MASHIMO Yoichi  千葉大学, 大学院医学研究院, 技術職員 (90422253)
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2015: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2014: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2013: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Keywords遺伝性難聴 / パラメトリック連鎖解析 / 大家系 / 全ゲノム解析 / 原因未知 / 難聴 / 原因遺伝子 / ゲノム解析 / パラメトリック解析
Outline of Final Research Achievements

To identify the causative genetic loci in a large family (affected:12, unaffected:24) with hereditary hearing loss, we performed a parametric linkage analysis using variations detected by whole genome sequencing (HiSeq) and genome wide association study (affected vs unaffected individuals) by human Omni2.5M+exon array. Highest LOD score (2.01~2.71) by parametric linkage mapping was observed a 79kb region in chr13p. Also, 79Mb (p value~1x10-6, odds ratio~14.4) in chr13p included the preceding 79kb was indicated the sole candidate region by genome wide association study. Therefore, sequencing of target 79kb region by PacBioRSII, and succeeded in narrowing the 4 loci included a causative locus exhibiting mutually high linkage disequilibrium.

Report

(3 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2013 Research-status Report
  • Research Products

    (32 results)

All 2016 2015 2014 2013 Other

All Journal Article (24 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 24 results,  Open Access: 14 results,  Acknowledgement Compliant: 1 results) Presentation (6 results) (of which Invited: 3 results) Book (1 results) Remarks (1 results)

  • [Journal Article] Mouth Breathing, another Risk Factor for Asthma: the Nagahama Study.2016

    • Author(s)
      Yumi I, Matsumoto H, Nagasaki T, Kanemitsu Y, Murase K, Ito I, Oguma T, Muro S, Asai K, Tabara Y, Takahashi K, Bessho K, Sekine A, Kosugi S, Yamada R, Nakayama T, Matsuda F, Niimi A, Chin K, Mishima M; Nagahama Study Group.
    • Journal Title

      Allergy

      Volume: 未定 Issue: 7 Pages: 1031-1036

    • DOI

      10.1111/all.12885

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Synergistic association of elevated serum free fatty acid and glucose levels with large arterial stiffness in a general population: The Nagahama Study2016

    • Author(s)
      Yasuharu Tabara, Yoshimitsu Takahashi, Kazuya Setoh, Takahisa Kawaguchi, Norimoto Gotoh, Chikashi Terao, Ryo Yamada, Shinji Kosugi, Akihiro Sekine, Takeo Nakayama, Fumihiko Matsuda, on behalf of the Nagahama Study group.
    • Journal Title

      M E T A B O L I S M C L I N I C A L A N D E X P E R I M E N T A L

      Volume: 65 Issue: 1 Pages: 66-72

    • DOI

      10.1016/j.metabol.2015.10.011

    • NAID

      120005698009

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development of a simple genotyping method for the HLA-A∗31:01-tagging SNP in Japanese2015

    • Author(s)
      Maekawa K, Nakamura R, Kaniwa N, Mizusawa S, Kitamoto A, Kitamoto T, Ukaji M, Matsuzawa Y, Sugiyama E, Uchida Y, Kurose K, Ueta M, Sotozono C, Ikeda H, Yagami A, Matsukura S, Kinoshita S, Muramatsu M, Ikezawa Z, Sekine A, Furuya H, Takahashi Y, Matsunaga K, Aihara M, Saito Y
    • Journal Title

      Pharmacogenomics.

      Volume: 16 Issue: 15 Pages: 1689

    • DOI

      10.2217/pgs.15.115

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Knee Pain and Low Back Pain Additively Disturb Sleep in the General Population: A Cross-Sectional Analysis of the Nagahama Study.2015

    • Author(s)
      Murase K, Tabara Y, Ito H, Kobayashi M, Takahashi Y, Setoh K, Kawaguchi T, Muro S, Kadotani H, Kosugi S, Sekine A, Yamada R, Nakayama T, Mishima M, Matsuda S, Matsuda F, Chin K.
    • Journal Title

      PLoS One

      Volume: 10 Issue: 10 Pages: e0140058-e0140058

    • DOI

      10.1371/journal.pone.0140058

    • NAID

      120005756275

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Descriptive epidemiology of spot urine sodium-to-potassium ratio clarified close relationship with blood pressure level: the Nagahama study.2015

    • Author(s)
      Tabara Y, Takahashi Y, Kumagai K, Setoh K, Kawaguchi T, Takahashi M, Muraoka Y, Tsujikawa A, Gotoh N, Terao C, Yamada R, Kosugi S, Sekine A, Yoshimura N, Nakayama T, Matsuda F; Nagahama study group.
    • Journal Title

      J Hypertens

      Volume: 33 Issue: 12 Pages: 2407-13

    • DOI

      10.1097/hjh.0000000000000734

    • NAID

      120005712944

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] MMP20 and ARMS2/HTRA1 are Associated with Neovascular Lesion Size in Age-Related Macular Degeneration2015

    • Author(s)
      Akagi-Kurashige Y, Yamashiro K, Gotoh N, Miyake M, Morooka S, Yoshikawa M, Nakata I, Kumagai K, Tsujikawa A, Yamada R, Matsuda F, Saito M, Iida T, Sugahara M, Kurimoto Y, Cheng CY, Khor CC, Wong TY, Yoshimura N; Nagahama Cohort Research Group
    • Journal Title

      Ophthalmology

      Volume: 122 Issue: 11 Pages: 2295-2302

    • DOI

      10.1016/j.ophtha.2015.07.032

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Three missense variants of metabolic syndrome-related genes are associated with alpha-1 antitrypsin levels.2015

    • Author(s)
      146.Three missense variants of metabolic syndrome-related genes are associated with alpha-1 antitrypsin levels. Setoh K, Terao C, Muro S, Kawaguchi T, Tabara Y, Takahashi M, Nakayama T, Kosugi S, Sekine A, Yamada R, Mishima M, Matsuda F.
    • Journal Title

      Nat Commun

      Volume: 6 Issue: 1 Pages: 7754-7754

    • DOI

      10.1038/ncomms8754

    • NAID

      120005743662

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 7C.07: ASSOCIATION OF SERUM FREE FATTY ACID LEVEL WITH REDUCED REFLECTION PRESSURE WAVE MAGNITUDE AND CENTRAL BLOOD PRESSURE: THE NAGAHAMA STUDY.2015

    • Author(s)
      Tabara Y, Takahashi Y, Kawaguchi T, Setoh K, Terao C, Yamada R, Kosugi S, Sekine A, Nakayama T, Matsuda F.
    • Journal Title

      J Hypertens

      Volume: 33 Suppl Issue: Supplement 1 Pages: e98-e98

    • DOI

      10.1097/01.hjh.0000467614.38730.87

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Identification of myopia-associated WNT7B polymorphisms provides insights into the mechanism underlying the development of myopia.2015

    • Author(s)
      Miyake M, Yamashiro K, Tabara Y, Suda K, Morooka S, Nakanishi H, Khor CC, Chen P, Qiao F, Nakata I, Akagi-Kurashige Y, Gotoh N, Tsujikawa A, Meguro A, Kusuhara S, Polasek O, Hayward C, Wright AF, Campbell H, Mizuki N, et al
    • Journal Title

      Nat Commun

      Volume: 印刷中 Issue: 1 Pages: 6689-6689

    • DOI

      10.1038/ncomms7689

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Significant association of periodontal disease with anti-citrullinated peptide antibody in a Japanese healthy population-the Nagahama study.2015

    • Author(s)
      C Terao, K Asai; M Hashimoto; T Yamazaki; K Ohmura; A Yamaguchi; K Takahashi; N Takei; T Ishii; T Kawaguchi; Y Tabara; M Takahashi; T Nakayama; S Kosugi; A Sekine; T Fujii; R Yamada; T Mimori; F Matsuda; K Bessho, Nagahama Study Group.
    • Journal Title

      Journal of Autoimmunity

      Volume: 59 Pages: 85-90

    • DOI

      10.1016/j.jaut.2015.03.002

    • NAID

      120005601013

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Calcium, ARMS2 Genotype, and Chlamydia Pneumoniae Infection in Early Age-Related Macular Degeneration: a Multivariate Analysis from the Nagahama Study.2015

    • Author(s)
      Nakata I, Yamashiro K, Kawaguchi T, Nakanishi H, Akagi-Kurashige Y, Miyake M, Tsujikawa A, Yamada R, Matsuda F, Yoshimura N; Nagahama Study Group.
    • Journal Title

      Sci Rep.

      Volume: 5 Issue: 1 Pages: 9345-9345

    • DOI

      10.1038/srep09345

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] IKZF1, a new susceptibility gene for cold medicine-related Stevens-Johnson syndrome/toxic epidermal necrolysis with severe mucosal involvement2015

    • Author(s)
      Ueta M, Sawai H, Sotozono C, Hitomi Y, Kaniwa N, Kim MK, Seo KY, Yoon KC, Joo CK, Kannabiran C, Wakamatsu TH, Sangwan V, Rathi V, Basu S, Ozeki T, Mushiroda T, Sugiyama E, Maekawa K, Nakamura R, Aihara M, Matsunaga K, Sekine A, Gomes JÁP, Hamuro J, Saito Y, Kubo M, Kinoshita S, Tokunaga K.
    • Journal Title

      J. Allergy Clin. Immunol.

      Volume: 135 Issue: 6 Pages: 1538

    • DOI

      10.1016/j.jaci.2014.12.1916

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Central blood pressure relates more strongly to retinal arteriolar narrowing than brachial blood pressure: the Nagahama Study.2015

    • Author(s)
      Kumagai K1, Tabara Y, Yamashiro K, Miyake M, Akagi-Kurashige Y, Oishi M, Yoshikawa M, Kimura Y, Tsujikawa A, Takahashi Y, Setoh K, Kawaguchi T, Terao C, Yamada R, Kosugi S, Sekine A, Nakayama T, Matsuda F, Yoshimura N; Nagahama Study group
    • Journal Title

      J Hypertens

      Volume: 33 Issue: 2 Pages: 323-9

    • DOI

      10.1097/hjh.0000000000000391

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] An association between anti-nuclear antibodies and HLA class II locus and heterogeneous characteristics of staining patterns: The Nagahama Study.2014

    • Author(s)
      Terao C, Ohmura K, Yamada R, Kawaguchi T, Shimizu M, Tabara Y, Takahashi M, Setoh K, Nakayama T, Kosugi S, Sekine A, Matsuda F, Tsuneyo Mimori T on behalf of the Nagahama Study Group.
    • Journal Title

      Arthritis Rheumatol.

      Volume: 66 Issue: 3_suppl Pages: 3395-403

    • DOI

      10.1177/0022034514559127

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Airflow limitation in smokers is associated with arterial stiffness: The Nagahama Study.2014

    • Author(s)
      Tabara Y., Muro S., Takahashi Y., Setoh K., Kawaguchi T., Terao C., Kosugi S., Sekine A., Yamada R., Nakayama T., Mishima M., Matsuda F. : Nagahama Study Group.
    • Journal Title

      Atherosclerosis

      Volume: 232 Pages: 59-64

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Association between the cholesteryl ester transfer protein gene and polypoidal choroidal vasculopathy.2013

    • Author(s)
      Nakata I., Yamashiro K., Kawaguchi T., Gotoh N., Nakanishi H., Akagi-Kurashige Y., Miyake M., Tsujikawa A., Oishi A., Saito M., Iida T., Yamada R., Matsuda F., Yoshimura N..; Nagahama Study Group.
    • Journal Title

      Invest Ophthalmol Vis Sci.

      Volume: 54 Pages: 6068-6073

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Prevalence and characteristics of age-related macular degeneration in the Japanese population: the Nagahama study.2013

    • Author(s)
      Nakata I., Yamashiro K., Nakanishi H., Akagi-Kurashige Y., Miyake M., Tsujikawa A., Matsuda F., Yoshimura N. ; Nagahama Cohort Research Group.
    • Journal Title

      Am J Ophthalmol.

      Volume: 156 Pages: 1002-1009

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Mastication and risk for diabetes in a Japanese population: a cross-sectional study.2013

    • Author(s)
      Yamazaki T., Yamori M., Asai K., Nakano-Araki I., Yamaguchi A., Takahashi K., Sekine A., Matsuda F., Kosugi S., Nakayama T., Inagaki N., Bessho K.; Nagahama Study Collaboration Group.
    • Journal Title

      PLoS One.

      Volume: 8

    • NAID

      120005296012

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Association of Longer QT Interval With Arterial Waveform and Lower Pulse Pressure Amplification: The Nagahama Study.2013

    • Author(s)
      Tabara Y., Takahashi Y., Kohara K., Setoh K., Kawaguchi T., Terao C., Igase M., Yamada R., Kosugi S., Sekine A., Miki T., Nakayama T., Matsuda F.; Nagahama Study Group.
    • Journal Title

      Am. J. Hypertens.

      Volume: 26 Pages: 973-980

    • NAID

      120005474538

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Increased aortic wave reflection and smaller pulse pressure amplification in smokers and passive smokers confirmed by urinary cotinine levels: The Nagahama Study.2013

    • Author(s)
      Tabara Y., Takahashi Y., Setoh K., Muro S., Kawaguchi T., Terao C., Kosugi S., Sekine A., Yamada R., Mishima M., Nakayama T., Matsuda F.
    • Journal Title

      Int. J. Cardiol.

      Volume: 168 Pages: 2673-2677

    • NAID

      120005343927

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Prevalence of postmicturition urinary incontinence in Japanese men: Comparison with other types of incontinence.2013

    • Author(s)
      Yoshimura K., Nakayama T., Sekine A., Matsuda F., Kosugi S., Sugino Y., Yoshimura K., Ogawa O.
    • Journal Title

      Int. J .Urol.

      Volume: 20 Pages: 911-916

    • NAID

      10031195893

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] NUDT3 rs206936 is associated with body mass index in obese Japanese women.2013

    • Author(s)
      Kitamoto A. et al.
    • Journal Title

      Endocr. J.

      Volume: 60 Pages: 991-1000

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Genome-wide scan revealed that polymorphisms in the PNPLA3, SAMM50, and PARVB genes are associated with development and progression of nonalcoholic fatty liver disease in Japan.2013

    • Author(s)
      Kitamoto T., Kitamoto A., Yoneda M., Hyogo H., Ochi H., Nakamura T., Teranishi H., Mizusawa S., Ueno T., Chayama K., Nakajima A., Nakao K., Sekine A., Hotta K.
    • Journal Title

      Hum. Genet.

      Volume: 132 Pages: 783-792

    • NAID

      120005474457

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Replication study of 15 recently published Loci for body fat distribution in the Japanese population.2013

    • Author(s)
      Hotta K. et al.
    • Journal Title

      J. Atheroscler. Thromb.

      Volume: 20 Pages: 336-350

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Presentation] 特別講演1:弾性線維腫の大家系パラメトリック連鎖解析による原因遺伝子の探索2016

    • Author(s)
      関根章博、竹村亮、真下陽一、北原輝栄、藤原作平
    • Organizer
      第98回日本皮膚科学会大分地方会
    • Place of Presentation
      大分県労働福祉会館ソレイユ(大分県・大分市)
    • Year and Date
      2016-03-05
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] ショートリードを用いたWhole Genome Sequenceで得られた変異に対する評価.2015

    • Author(s)
      竹村亮, 北原輝栄, 関根章博
    • Organizer
      日本人類遺伝学会第60回大会
    • Place of Presentation
      京王プラザホテル(東京都・新宿)
    • Year and Date
      2015-10-16
    • Related Report
      2015 Annual Research Report
  • [Presentation] 遺伝カウンセリングに必要な全ゲノム解析情報の精度と検証2015

    • Author(s)
      関根章博、竹村亮、真下陽一、北原輝栄、山下泰生、羽田明
    • Organizer
      第39回日本遺伝カウンセリング学会各術集会
    • Place of Presentation
      三井ガーデンホテル千葉(千葉県・千葉市)
    • Year and Date
      2015-06-26
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 先天性難聴の遺伝学的検査における症例調査2013

    • Author(s)
      中國正祥、北尻真一郎、谷口美玲、岡野高之、村上裕美、関根章博、柴田有花、土屋 未央、小杉 眞司
    • Organizer
      日本人類遺伝学会第58回大会
    • Place of Presentation
      宮城県仙台
    • Related Report
      2013 Research-status Report
  • [Presentation] 医薬品副作用情報データベースを用いた横紋筋融解症の要因検討2013

    • Author(s)
      中國正祥、関根章博、水澤精穂、寺西啓、柴田有花、土屋実央、小杉眞司
    • Organizer
      第37回日本遺伝カウンセリング学会
    • Place of Presentation
      神奈川県川崎
    • Related Report
      2013 Research-status Report
  • [Presentation] Establishment of an accurate genome sequencing method combining next generation short-read (Hisq, Miseq) and long-read (PacBio) sequencers2013

    • Author(s)
      sekine A.
    • Organizer
      Okinawa International Projyect for Construction of Intellectual Cluster and Industry based on Advanced Genomic Research.
    • Place of Presentation
      okinawa naha
    • Related Report
      2013 Research-status Report
    • Invited
  • [Book] 最新内分泌代謝学「内分泌代謝疾患のゲノム、エピゲノム解析」2013

    • Author(s)
      関根章博(監修:中尾一和)
    • Publisher
      診断と治療社
    • Related Report
      2013 Research-status Report
  • [Remarks] 千葉大学予防医学センター

    • Related Report
      2015 Annual Research Report

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Published: 2014-07-25   Modified: 2019-07-29  

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