Liya Xu, PhD

Photo of Liya Xu, PhD
Title(s)Assistant Professor of Research Ophthalmology
SchoolKeck School of Medicine of Usc
Address4640 West Sunset Blvd
Off Campus
Los Angeles CA 90027
Phone+1 213 740 9945
ORCID ORCID Icon0000-0002-5501-2039 Additional info
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    Dr. Liya Xu is a research ophthalmologist and ocular cancer investigator whose research focuses on developing liquid biopsy and multi-omics approaches to improve the diagnosis, risk stratification, and biological understanding of ocular malignancies. Her laboratory uses aqueous humor as a tumor-proximal source of molecular information and integrates genomic, epigenomic, fragmentomic, proteomic, and extracellular vesicle analyses to characterize tumor biology and disease evolution.

    Her research spans both pediatric and adult ocular cancers, with a particular focus on retinoblastoma and uveal melanoma. In retinoblastoma, her work seeks to define genomic trajectories of tumor evolution and develop minimally invasive approaches for molecular characterization and clinical risk assessment. In uveal melanoma, her laboratory investigates the molecular features associated with early dissemination and metastatic risk by integrating tumor, aqueous humor, and circulating blood-based biomarkers.

    A central goal of her research program is to establish liquid biopsy as a high-resolution molecular sensor of ocular and systemic disease, translating multi-omic discoveries into clinically useful biomarkers and precision tools for ocular oncology.

    Collapse Biography 
    Collapse awards and honors
    Knight Templar Eye Foundation (KTEF)2021  - 2023Pediatric Ophthalmology Career-Starter Research Grant
    The Saban Research Institute, Children's Hospital Los Angeles2022  - 2024Research Career Development Award (RCDA)
    University of Southern California2024  - 2025Dean's Pilot Research Award
    University of Southern California2025  - 2026Wright Foundation

    Collapse Research 
    Collapse Featured Publications
    Collapse research activities and funding
    Dissecting Inter-Compartmental Tumor-Host Communication Driving Early Dissemination in Uveal Melanoma.
    NIH R01CA311805May 5, 2026 - Apr 1, 2031
    Role: Principal Investigator
    Establishing Cutoff for Minimal Residual Intraocular Disease in Retinoblastoma Using Extracellular Vesicles From Aqueous Humor Liquid Biopsy
    DoD HT9425-25-1-0563Aug 1, 2025 - Jul 31, 2028
    Role: Principle Investigator
    Development of a Novel Aqueous Humor-Based Multiplex Assay for Uveal Melanoma Metastatic Risk Prediction
    NIH R41CA291243Sep 5, 2024 - Aug 31, 2025
    Role: Principal Investigator

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    Completed SC CTSI Mentor Training: Yes

    Collapse Bibliographic 
    Collapse publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Aqueous Humor Liquid Biopsy Identifies Murine Double Minute 4 Segmental Gain in Retinoblastoma: Implications for Chemotherapy Response and Precision Oncology. JCO Precis Oncol. 2025 Aug; 9:e2500250. Huang E, Sirivolu S, Yellapantula V, Kale P, Kuhn P, Hicks J, Brown B, Paniagua H, Pandya D, Shah R, Berry JL, Xu L. PMID: 40834326; PMCID: PMC12379781.
      View in: PubMed   Mentions: 1     Fields:    
    2. Minimum Technical Preanalytical, Patient, and Clinical Context Data Elements for Cerebrospinal Fluid Liquid Biopsy: Recommendations for Public Database Submissions. JCO Precis Oncol. 2025 Jun; 9:e2400921. Bagley SJ, Beaubier N, Balaj L, Bettegowda C, Carpenter E, Carter BS, Corner A, Dittamore R, Grossman RL, Hickman RA, Kuhn P, LeBlang S, Lichtenberg T, Mansouri A, Miller A, Ngo T, Rood BR, Till J, Xu L, Leiman LC. PMID: 40570259; PMCID: PMC12203979.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    3. The use of aqueous humor cfDNA for low-pass whole genome sequencing as a clinical test to identify intraocular retinoblastoma recurrence. ScienceBank. 2025; 2025. Chigane D, Pandya D, Brown B, Lin M, Tseng A, Shah R, Jubran R, Snider M, Peng P, Singh M, Yellapantula V, Biegel JA, Xu L, Berry JL. PMID: 41716777; PMCID: PMC12914873.
      View in: PubMed   Mentions:
    4. Retinoblastoma: Aqueous humor liquid biopsy. Taiwan J Ophthalmol. 2025 Jan-Mar; 15(1):55-61. Sanchez GM, Chigane D, Lin M, Xu L, Yellapantula V, Berry JL. PMID: 40213298; PMCID: PMC11981557.
      View in: PubMed   Mentions: 2  
    5. Safety Assessment of Aqueous Humor Liquid Biopsy in Retinoblastoma: A Multicenter Study of 1203 Procedures. Ophthalmology. 2026 03; 133(3):326-332. Chigane D, Pandya D, Singh M, Brown B, Lin M, Xu L, Stacey AW, Bonnell AC, Hubbard GB, Grossniklaus H, Skalet AH, Bellsmith KN, Lally SE, Simão-Rafael M, Muñoz CJ, Català-Mora J, Malaise D, Lumbroso-Le Rouic L, Matet A, Chantada GL, Cassoux N, Shields CL, Berry JL. PMID: 40118155; PMCID: PMC12519347.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    6. Dynamics of microRNA secreted via extracellular vesicles during the maturation of embryonic stem cell-derived retinal pigment epithelium. J Extracell Biol. 2024 Sep; 3(9):e70001. Pollalis D, Nair GKG, Leung J, Bloemhof CM, Bailey JK, Pennington BO, Kelly KR, Khan AI, Yeh AK, Sundaram KS, Clegg DO, Peng CC, Xu L, Georgescu C, Wren JD, Lee SY. PMID: 39281021; PMCID: PMC11393772.
      View in: PubMed   Mentions: 5  
    7. Single-cell somatic copy number alteration profiling of vitreous humor seeds in retinoblastoma. Ophthalmic Genet. 2024 12; 45(6):646-649. Sirivolu S, Schmidt MJ, Prabakar RK, Kuhn P, Hicks J, Berry JL, Xu L. PMID: 39016001; PMCID: PMC11598666.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    8. Aqueous VEGF-A Levels as a Liquid Biopsy Biomarker of Retinoblastoma Vitreous Seed Response to Therapy. Invest Ophthalmol Vis Sci. 2024 06 03; 65(6):18. Daniels AB, Sishtla KL, Bogan CM, Pierce JM, Chen SC, Xu L, Berry JL, Corson TW. PMID: 38861274; PMCID: PMC11174092.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimals
    9. Liquid Biopsy Profiling with Multiple Tests in Patients with Metastatic Breast Cancer. J Mol Pathol (Basel). 2024 Jun; 5(2):199-214. Higa N, Welter L, Xu L, Kolatkar A, Bramlett KS, Gjoerup OV, Graf R, Huang RSP, Leary RJ, Lee Y, Perkins JG, Riker AI, Singh AP, Tafra L, Tweed CK, Shriver CD, Hicks J, Kuhn P. PMID: 41614092; PMCID: PMC12851560.
      View in: PubMed   Mentions:
    10. Isolation and Characterization of Extracellular Vesicles Through Orthogonal Approaches for the Development of Intraocular EV Therapy. Invest Ophthalmol Vis Sci. 2024 Mar 05; 65(3):6. Leung J, Pollalis D, Nair GKG, Bailey JK, Pennington BO, Khan AI, Kelly KR, Yeh AK, Sundaram KS, Clegg DO, Peng CC, Xu L, Lee SY. PMID: 38466285; PMCID: PMC10929743.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    11. Correlating somatic copy number alteration in aqueous humour cfDNA with chemotherapy history, eye salvage and pathological features in retinoblastoma. Br J Ophthalmol. 2024 02 21; 108(3):449-456. Luo Y, Xu M, Yang L, Yao Y, Berry JL, Xu L, Wen X, He X, Han M, Fan X, Fan J, Jia R. PMID: 36931696; PMCID: PMC10505245.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    12. Aqueous Humor Liquid Biopsy as a Companion Diagnostic for Retinoblastoma: Implications for Diagnosis, Prognosis, and Therapeutic Options: Five Years of Progress. Am J Ophthalmol. 2024 07; 263:188-205. Berry JL, Pike S, Shah R, Reid MW, Peng CC, Wang Y, Yellapantula V, Biegel J, Kuhn P, Hicks J, Xu L. PMID: 38040321; PMCID: PMC11148850.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    13. Multicentre analysis of nucleic acid quantification using aqueous humour liquid biopsy in uveal melanoma: implications for clinical testing. Can J Ophthalmol. 2025 02; 60(1):e23-e31. Pike SB, Reid MW, Peng CC, Chang C, Xu BY, Gombos DS, Patel S, Xu L, Berry JL. PMID: 38036045; PMCID: PMC11128479.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    14. Simultaneous Copy Number Alteration and Single-Nucleotide Variation Analysis in Matched Aqueous Humor and Tumor Samples in Children with Retinoblastoma. Int J Mol Sci. 2023 May 11; 24(10). Schmidt MJ, Prabakar RK, Pike S, Yellapantula V, Peng CC, Kuhn P, Hicks J, Xu L, Berry JL. PMID: 37239954; PMCID: PMC10218537.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    15. Diagnostic Aqueous Humor Proteome Predicts Metastatic Potential in Uveal Melanoma. Int J Mol Sci. 2023 Apr 06; 24(7). Peng CC, Sirivolu S, Pike S, Kim ME, Reiser B, Li HT, Liang G, Xu L, Berry JL. PMID: 37047796; PMCID: PMC10094875.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    16. Contrived Materials and a Data Set for the Evaluation of Liquid Biopsy Tests: A Blood Profiling Atlas in Cancer (BLOODPAC) Community Study. J Mol Diagn. 2023 03; 25(3):143-155. Hernandez KM, Bramlett KS, Agius P, Baden J, Cao R, Clement O, Corner AS, Craft J, Dean DA, Dry JR, Grigaityte K, Grossman RL, Hicks J, Higa N, Holzer TR, Jensen J, Johann DJ, Katz S, Kolatkar A, Keynton JL, Lee JSH, Maar D, Martini JF, Meyer CG, Roberts PC, Ryder M, Salvatore L, Schageman JJ, Somiari S, Stetson D, Stern M, Xu L, Leiman LC. PMID: 36828596.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    17. Combined low-pass whole genome and targeted sequencing in liquid biopsies for pediatric solid tumors. NPJ Precis Oncol. 2023 Feb 20; 7(1):21. Christodoulou E, Yellapantula V, O'Halloran K, Xu L, Berry JL, Cotter JA, Zdanowicz A, Mascarenhas L, Amatruda JF, Ostrow D, Bootwalla M, Gai X, Navid F, Biegel JA. PMID: 36805676; PMCID: PMC9941464.
      View in: PubMed   Mentions: 37  
    18. A Multicenter Analysis of Nucleic Acid Quantification Using Aqueous Humor Liquid Biopsy in Retinoblastoma: Implications for Clinical Testing. Ophthalmol Sci. 2023 Sep; 3(3):100289. Im DH, Pike S, Reid MW, Peng CC, Sirivolu S, Grossniklaus HE, Hubbard GB, Skalet AH, Bellsmith KN, Shields CL, Lally SE, Stacey AW, Reiser BJ, Nagiel A, Shah R, Xu L, Berry JL. PMID: 37025945; PMCID: PMC10070901.
      View in: PubMed   Mentions: 13  
    19. Non-synonymous, synonymous, and non-coding nucleotide variants contribute to recurrently altered biological processes during retinoblastoma progression. Genes Chromosomes Cancer. 2023 05; 62(5):275-289. Stachelek K, Harutyunyan N, Lee S, Beck A, Kim J, Xu L, Berry JL, Nagiel A, Reynolds CP, Murphree AL, Lee TC, Aparicio JG, Cobrinik D. PMID: 36550020; PMCID: PMC10006380.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    20. Chromosome 6p amplification detected in blood cell-free DNA in advanced intraocular retinoblastoma. Ophthalmic Genet. 2022 12; 43(6):866-870. Sirivolu S, Xu L, Warren M, Prabakar RK, Shah R, Kuhn P, Hicks J, Berry JL. PMID: 36342106; PMCID: PMC9877166.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    21. Malignant teratoid intraocular ciliary body medulloepithelioma in a 5-year-old male with corresponding somatic copy number alteration profile of aqueous humor cell-free DNA. Ophthalmic Genet. 2022 12; 43(6):855-861. Pike S, Iyengar R, Peng CC, Chevez-Barrios P, Brown B, Shah R, Biegel J, Yellapantula V, Nagiel A, Reiser BJ, Xu L, Berry JL. PMID: 36314385; PMCID: PMC9877122.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    22. Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy. Nat Commun. 2022 09 21; 13(1):5523. Li HT, Xu L, Weisenberger DJ, Li M, Zhou W, Peng CC, Stachelek K, Cobrinik D, Liang G, Berry JL. PMID: 36130950; PMCID: PMC9492718.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    23. Identification of epithelial and mesenchymal circulating tumor cells in clonal lineage of an aggressive prostate cancer case. NPJ Precis Oncol. 2022 Jun 21; 6(1):41. Chai S, Ruiz-Velasco C, Naghdloo A, Pore M, Singh M, Matsumoto N, Kolatkar A, Xu L, Shishido S, Aparicio A, Zurita AJ, Hicks J, Kuhn P. PMID: 35729213; PMCID: PMC9213535.
      View in: PubMed   Mentions: 21  
    24. Disease characterization in liquid biopsy from HER2-mutated, non-amplified metastatic breast cancer patients treated with neratinib. NPJ Breast Cancer. 2022 Feb 18; 8(1):22. Shishido SN, Masson R, Xu L, Welter L, Prabakar RK, D' Souza A, Spicer D, Kang I, Jayachandran P, Hicks J, Lu J, Kuhn P. PMID: 35181666; PMCID: PMC8857263.
      View in: PubMed   Mentions: 14  
    25. Aqueous Humor as a Liquid Biopsy for Retinoblastoma: Clear Corneal Paracentesis and Genomic Analysis. J Vis Exp. 2021 09 07; (175). Kim ME, Xu L, Prabakar RK, Shen L, Peng CC, Kuhn P, Gai X, Hicks J, Berry JL. PMID: 34570090; PMCID: PMC9200366.
      View in: PubMed   Mentions: 23     Fields:    Translation:Humans
    26. Treatment response and tumor evolution: lessons from an extended series of multianalyte liquid biopsies in a metastatic breast cancer patient. Cold Spring Harb Mol Case Stud. 2020 12; 6(6). Welter L, Xu L, McKinley D, Dago AE, Prabakar RK, Restrepo-Vassalli S, Xu K, Rodriguez-Lee M, Kolatkar A, Nevarez R, Ruiz C, Nieva J, Kuhn P, Hicks J. PMID: 33203646; PMCID: PMC7784493.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    27. Author Correction: SMURF-seq: efficient copy number profiling on long-read sequencers. Genome Biol. 2020 Aug 25; 21(1):214. Prabakar RK, Xu L, Hicks J, Smith AD. PMID: 32843071; PMCID: PMC7447571.
      View in: PubMed   Mentions:    Fields:    
    28. Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients. J Mol Diagn. 2020 03; 22(3):319-337. Shishido SN, Welter L, Rodriguez-Lee M, Kolatkar A, Xu L, Ruiz C, Gerdtsson AS, Restrepo-Vassalli S, Carlsson A, Larsen J, Greenspan EJ, Hwang ES, Waitman KR, Nieva J, Bethel K, Hicks J, Kuhn P. PMID: 31978562; PMCID: PMC7103765.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    29. Aqueous Humor Is Superior to Blood as a Liquid Biopsy for Retinoblastoma. Ophthalmology. 2020 04; 127(4):552-554. Berry JL, Xu L, Polski A, Jubran R, Kuhn P, Kim JW, Hicks J. PMID: 31767439; PMCID: PMC7093221.
      View in: PubMed   Mentions: 36     Fields:    Translation:Humans
    30. SMURF-seq: efficient copy number profiling on long-read sequencers. Genome Biol. 2019 07 08; 20(1):134. Prabakar RK, Xu L, Hicks J, Smith AD. PMID: 31287019; PMCID: PMC6615205.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    31. Genomic cfDNA Analysis of Aqueous Humor in Retinoblastoma Predicts Eye Salvage: The Surrogate Tumor Biopsy for Retinoblastoma. Mol Cancer Res. 2018 11; 16(11):1701-1712. Berry JL, Xu L, Kooi I, Murphree AL, Prabakar RK, Reid M, Stachelek K, Le BHA, Welter L, Reiser BJ, Chévez-Barrios P, Jubran R, Lee TC, Kim JW, Kuhn P, Cobrinik D, Hicks J. PMID: 30061186; PMCID: PMC6214755.
      View in: PubMed   Mentions: 73     Fields:    Translation:Humans
    32. Functional role of the intracellular loop linking transmembrane domains 6 and 7 of the human dipeptide transporter hPEPT1. J Membr Biol. 2010 Dec; 238(1-3):43-9. Xu L, Li Y, Haworth IS, Davies DL. PMID: 21104182; PMCID: PMC3032433.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    33. Mutagenesis and cysteine scanning of transmembrane domain 10 of the human dipeptide transporter. Pharm Res. 2009 Oct; 26(10):2358-66. Xu L, Haworth IS, Kulkarni AA, Bolger MB, Davies DL. PMID: 19685173; PMCID: PMC2861424.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    34. Ethanol inhibits functional activity of the human intestinal dipeptide transporter hPepT1 expressed in Xenopus oocytes. Alcohol Clin Exp Res. 2008 May; 32(5):777-84. Li K, Xu L, Kulkarni AA, Perkins DI, Haworth IS, Davies DL. PMID: 18336632; PMCID: PMC2861421.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
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