Xiaoxu Yang, Ph.D.

Research Focus

Our lab is focused on the biological questions that genomic mosaicism can help us answer. From a fertilized egg, all our cells constantly acquire mutations. Our body repairs most mutations, but some mutations remain in our genome and get passed from cell to cell during embryonic development, upon tissue self-renewal, or after environmental exposure. The distribution of these mutations leads to the phenomenon of genomic mosaicism. We developed DeepMosaic (Yang et al., Nat Biotech 2023), MosaicBase (Yang et al., GPB 2020), and other computational resources to understand genomic mosaicism. We are interested in the impact of genomic mosaicism in the father's sperm on the offspring, such as the life-long impact on their genetic health (Yang et al., Cell 2021), or how the environment and behavior are shaping the mutational landscape. We would also like to use genomic mosaicism as a 'genetic paint' to trace back human development in different tissue and cell types both in normal conditions (Breuss et al., Nature 2022, Chung et al., Nature 2024) and disease settings.

Representative Publications

  1. Chung C*, Yang X*, Hevner RF, Kennedy K, Vong KI, LiuY, Patel A, Nedururi R, Barton ST, Noel G, Barrows C, Stanley V, Mittal S, Breuss MW, Schlachetzki JCM, Kingsmore SF, and Gleeson JG. 2024. Cell-type-resolved mosaicism reveals clonal dynamics of the human forebrain. Nature. PMID: 37961480.

  2. Yang X#,*, Xu X*, Breuss MW, Antaki D, Ball LL, Chung C, Shen J, Li C, George RD, Wang Y, Bae T, Cheng Y, Abyzov A, Wei L, Alexandrov LB, Sebat JL, NIMH Brain Somatic Mosaicism Network, and Gleeson JG#. 2023. Control-independent mosaic single nucleotide variant detection with DeepMosaic. Nature Biotechnology. PMID: 36593400.

  3. Chung C*, Yang X*, Bae T, Vong KI, Mittal S, Donkels C, Phillips HW, Li Z, Marsh APL, Breuss MW, Ball LL, Garcia CAB, George RD, Gu J, Xu M, Barrows C, James KN, Stanley V, Nidhiry AS, Khoury S, Howe G, Riley E, Xu X, Copeland B, Wang Y, Kim SH, Kang H-C, Schulze-Bonhage A, Smyth MD, Sattar S, Nespeca M, Gonda DD, Imai K, Takahashi Y, Chen H-H, Tsai J-W, Conti V, Guerrini R, Devinsky O, Silva WA, Machado HR, Mathern GW, Abyzov A, Baldassari S, Baulac S, Brain Somatic Mosaicism Network, and Gleeson JG. 2023. Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Nature Genetics (cover story) PMID: 36635388.

  4. Breuss MW*, Yang X*, Schlachetzki JCM*, Antaki D*, Lana AJ, Chung C, Chai G, Stanley V, Song Q, Newmeyer TF, Nguyen A, O'Brien S, Hoeksema MA, Cao B, Nott A, McEvoy-Venneri J, Pasillas MP, Barton ST, Copeland BR, Nahas S, Karaan LVD, Ding Y, Brain Somatic Mosaicism Network, Glass CK, and Gleeson JG. 2022. Somatic Mosaicism Reveals Clonal Distributions of Neocortical Development. NaturePMID: 35444276.

  5. Breuss MW*,#, Yang X*, Stanley V, McEvoy-Venneri J, Xu X, Morales AJ, and Gleeson JG#. 2022. Unbiased mosaic variant assessment in sperm: a cohort study to test predictability of transmission. eLifePMID: 35787314.

  6. Yang X*, Breuss MW*, Xu X, Antaki D, James KN, Stanley V, Ball LL, George RD, Wirth SA, Cao B, Nguyen A, McEvoy-Venneri J, Chai G, Nahas S, Kraan LVD, Ding Y, Sebat JL, and Gleeson JG. 2021. Developmental and temporal characteristics of clonal sperm mosaicism. Cell. PMID: 34388390.

  7. Yang X*, Yang C*, Zheng X*, Xiong L, Tao Y, Wang M, Ye AY, Wu Q, Dou Y, Luo J, Wei L#, and Huang AY#. 2020. MosaicBase: A knowledgebase for postzygotic mosaic variants for non-cancer diseases and asymptomatic human individuals. Genomics Proteomics BioinformaticsPMID: 32911083.

  8. Liu A*, Yang XX*, Yang XL*, Wu Q, Zhang J, Sun D, Yang Z, Jiang Y, Wu X, Wei L#, and Zhang Y#. 2019. Mosaicism and incomplete penetrance of PCDH19 mutations. J. Med. GenetPMID: 30287595.

  9. Yang XL*, Yang XX*, Chen J, Li S, Zeng Q, Huang AY, Ye AY, Yu Z, Wang S, Jiang Y, Wu X, Wu Q#, Wei L#, and Zhang Y#. 2019. ATP1A3 mosaicism in families with alternating hemiplegia of childhood. Clin. GenetPMID: 30891744.

  10. Zhang Q*, Yang X*, Wang J*, Li J*, Wu Q, Wen Y, Zhao Y, Zhang X, He Y, Wu X, Yu S, Wei L#, and Bao X#.2018. Genomic mosaicism in the pathogenesis and inheritance of a Rett syndrome cohort. Genet. Med. PMID: 30405208.

  11. Huang AY*,#, Yang X*, and Wang S, Zheng X, Wu Q, Ye AY, and Wei L#. 2018. Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs. PLoS Genet. PMID: 29763432.

  12. Yang X*, Liu A*, Xu X, Yang X, Zeng Q, Ye AY, Yu Z, Wang S, Huang AY, Wu X, Wu Q#, Wei L#, and Zhang Y#. 2017. Genomic mosaicism in paternal sperm and multiple parental tissues in a Dravet syndrome cohort. Sci. Rep. PMID: 29142202.

  13. Xu X*, Yang X*, Wu Q*, Liu A, Yang X, Ye AY, Huang AY, Li J, Wang M, Yu Z, Wang S, Zhang Z, Wu X, Wei L#, and Zhang Y#. 2015. Amplicon resequencing identified parental mosaicism for approximately 10% of ‘de novo’ SCN1A mutations in children with Dravet syndrome. Hum. MutatPMID: 26096185.

Complete list at MyBibliography

Contact Information

Email: u6055394@utah.edu



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