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Estimating carrier frequencies of newborn screening disorders using a whole-genome reference panel of 3552 Japanese individuals

Human Genetics volume 138, pages 389–409 (2019)Cite this article

Abstract

Incidence rates of Mendelian diseases vary among ethnic groups, and frequencies of variant types of causative genes also vary among human populations. In this study, we examined to what extent we can predict population frequencies of recessive disorders from genomic data, and explored better strategies for variant interpretation and classification. We used a whole-genome reference panel from 3552 general Japanese individuals constructed by the Tohoku Medical Megabank Organization (ToMMo). Focusing on 32 genes for 17 congenital metabolic disorders included in newborn screening (NBS) in Japan, we identified reported and predicted pathogenic variants through variant annotation, interpretation, and multiple ways of classifications. The estimated carrier frequencies were compared with those from the Japanese NBS data based on 1,949,987 newborns from a previous study. The estimated carrier frequency based on genomic data with a recent guideline of variant interpretation for the PAH gene, in which defects cause hyperphenylalaninemia (HPA) and phenylketonuria (PKU), provided a closer estimate to that by the observed incidence than the other methods. In contrast, the estimated carrier frequencies for SLC25A13, which causes citrin deficiency, were much higher compared with the incidence rate. The results varied greatly among the 11 NBS diseases with single responsible genes; the possible reasons for departures from the carrier frequencies by reported incidence rates were discussed. Of note, (1) the number of pathogenic variants increases by including additional lines of evidence, (2) common variants with mild effects also contribute to the actual frequency of patients, and (3) penetrance of each variant remains unclear.

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Acknowledgements

We are indebted to all volunteers who participated in this Tohoku Medical Megabank project. We would like to acknowledge all members associated with this project; the member list is available at the following web site: http://www.megabank.tohoku.ac.jp/english/a171201/. This work was supported in part by the Tohoku Medical Megabank Project from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and the Reconstruction Agency; the Japan Agency for Medical Research and Development (AMED; Grant Numbers JP18km0105001 and JP18km0105002) for Tohoku University. All computational resources were provided by the Tohoku University Tohoku Medical Megabank Organization (ToMMo) supercomputer system (http://sc.megabank.tohoku.ac.jp/en), which is supported by Facilitation of R&D Platform for AMED Genome Medicine Support conducted by AMED (Grant Number JP18km0405001). This research is also supported by the Center of Innovation Program from Japan Science and Technology Agency, JST.

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Affiliations

  1. Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan

    Yumi Yamaguchi-Kabata, Jun Yasuda, Akira Uruno, Kazuro Shimokawa, Seizo Koshiba, Yoichi Suzuki, Nobuo Fuse, Hiroshi Kawame, Shu Tadaka, Masao Nagasaki, Kaname Kojima, Fumiki Katsuoka, Kazuki Kumada, Osamu Tanabe, Gen Tamiya, Nobuo Yaegashi, Kengo Kinoshita, Masayuki Yamamoto & Shigeo Kure

  2. Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan

    Yumi Yamaguchi-Kabata, Jun Yasuda, Akira Uruno, Yoichi Suzuki, Nobuo Fuse, Hiroshi Kawame, Masao Nagasaki, Kaname Kojima, Fumiki Katsuoka, Osamu Tanabe, Gen Tamiya, Nobuo Yaegashi, Masayuki Yamamoto & Shigeo Kure

  3. Present address: Miygai Cancer Center Research Institute, 47-1, Noda-yama,, Medeshima-shiode, Natori, 981-1293, Japan

    Jun Yasuda

  4. Present address: Ageo Central General Hospital, 1-10-10 Kashiwa-za, Ageo, 362-8588, Japan

    Yoichi Suzuki

  5. Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579, Japan

    Masao Nagasaki, Kaname Kojima & Kengo Kinoshita

  6. Present address: Radiation Effects Research Foundation Hiroshima Laboratory, 5-2 Hijiyama Park, Minami-ku, Hiroshima, 732-0815, Japan

    Osamu Tanabe

  7. Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Nihonbashi 1-chome Mitsui Building, 15th floor, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan

    Gen Tamiya

  8. Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan

    Kengo Kinoshita

  9. Advanced Research center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan

    Kengo Kinoshita & Masayuki Yamamoto

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  1. Yumi Yamaguchi-Kabata
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  2. Jun Yasuda
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Correspondence to Yumi Yamaguchi-Kabata or Kengo Kinoshita.

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Yamaguchi-Kabata, Y., Yasuda, J., Uruno, A. et al. Estimating carrier frequencies of newborn screening disorders using a whole-genome reference panel of 3552 Japanese individuals. Hum Genet 138, 389–409 (2019). https://doi.org/10.1007/s00439-019-01998-7

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