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Whole genome sequencing identifies ANXA3 and MTHFR mutations in a large family with an unknown equinus deformity associated genetic disorder

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Abstract

The aim of this study was to characterize a previously uncharacterized genetic disorder associated with equinus deformity in a large Chinese family at the genetic level. Blood samples were obtained and whole genome sequencing was performed. Differential gene variants were identified and potential impacts on protein structure were predicted. Based on the control sample, several diseases associated variants were identified and selected for further validation. One of the potential variants identified was a ANXA3 gene [chr4, c.C820T(p.R274*)] variant. Further bioinformatic analysis showed that the observed mutation could lead to a three-dimensional conformational change. Moreover, a MTHFR variant that is different from variants associated with clubfoot was also identified. Bioinformatic analysis showed that this mutation could alter the protein binding region. These findings imply that this uncharacterized genetic disorder is not clubfoot, despite sharing some similar symptoms. Furthermore, specific CNV profiles were identified in association with the diseased samples, thus further speaking to the complexity of this multigenerational disorder. This study examined a previously uncharacterized genetic disorder appearing similar to clubfoot and yet having distinct features. Following whole genome sequencing and comparative analysis, several differential gene variants were identified to enable a further distinction from clubfoot. It is hoped that these findings will provide further insight into this disorder and other similar disorders.

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Acknowledgments

This work was supported by the project of the National Natural Science Foundation of China (No. 61271054), the key project of Nanjing public health bureau (No. ZKX13038, 201308036), Science and Technology Development Fund Key Project of Nanjing Medical University (No. 2013NJMU095), and the project of Nanjing Children’s Hospital Affiliated to Nanjing Medical University (No. ETYY2013032).

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    Authors and Affiliations

    1. Department of Orthopaedic, Nanjing Children’s Hospital Affiliated to Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210008, Jiangsu, China

      Zhiqun Zhang, Lei Ni & Yue Lou

    2. Department of Internal Neurology, Nanjing Red Cross Hospital, Nanjing, 210001, Jiangsu, China

      Zhuqing Kong

    3. Nanjing Decode Genomics Biotechnology Co., Ltd., Nanjing, 210019, Jiangsu, China

      Miao Zhu & Wenxiang Lu

    4. School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, Jiangsu, China

      Yunfei Bai

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    1. Zhiqun Zhang
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    Correspondence to Yunfei Bai or Yue Lou.

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    Zhiqun Zhang and Zhuqing Kong have contributed equally to this work.

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    Fig. S1 An example of PCR validation result (TIFF 706 kb)

    11033_2016_4047_MOESM2_ESM.tif

    Fig. S2 Chromatograms of HIST1H3A and its predicted three-dimensional structure. HIST1H3A-W indicates the wild type, and HIST1H3A-M indicates the gene with mutation site. Note: although the chromatograms of HIST1H3A-M (heterozygote) showed consistent sequence with HIST1H3A-W, their three-dimensional structures were also predicted and compared (TIFF 1709 kb)

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    Zhang, Z., Kong, Z., Zhu, M. et al. Whole genome sequencing identifies ANXA3 and MTHFR mutations in a large family with an unknown equinus deformity associated genetic disorder. Mol Biol Rep 43, 1147–1155 (2016). https://doi.org/10.1007/s11033-016-4047-2

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    • DOI: https://doi.org/10.1007/s11033-016-4047-2

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