Liya Xu, PhD

Liya Xu received her PhD in Neuroscience from University of Southern California 2010. Subsequently, she joined Biomedical Pioneering Innovation Center (BIOPIC) of Peking University to lead the development of one-step next generation sequencing (NGS) based Preimplantation Genetic Diagnosis (PGD) for simultaneous avoidance of monogenic disease and chromosome abnormality. Since 2017, her collaboration with Dr. Jesse Berry has been focusing on developing aqueous humor (AH) as a surrogate tumor biopsy for retinoblastoma (RB). It holds the potential to unlock a new era of precision medicine that will transform the way to detect RB, guide the management and prognosis for RB and lead to alternative treatment regimens that offer a personalized approach to medicine for these children with a greater chance of saving the eye.

Dr. Xu’s research concentrates on integrating patient, model system, and high-content single particle data to translate clinically observed correlations into a mechanistic understanding of the physical and biological underpinning of the dynamics of ocular cancers, specifically retinoblastoma. Two complementary research projects address the laboratory’s aims of 1) developing the clinical utility of aqueous humors (AH) as liquid biopsy platform for ocular cancer management; and 2) characterizing the tumor circulome of aqueous humor from RB eyes with multi-omics approaches.

• Knight Templar Eye Foundation (KTEF): Pediatric Ophthalmology Career-Starter Research Grant, 2021

• 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. . View in PubMed
• Aqueous Humor Liquid Biopsy as a Companion Diagnostic for Retinoblastoma: Implications for Diagnosis, Prognosis, and Therapeutic Options: Five Years of Progress Am J Ophthalmol. 2023 Nov 30; 263:188-205. . View in PubMed
• Multicentre analysis of nucleic acid quantification using aqueous humour liquid biopsy in uveal melanoma: implications for clinical testing Can J Ophthalmol. 2023 Nov 27. . View in PubMed
• 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. . View in PubMed
• 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). . View in PubMed
• Diagnostic Aqueous Humor Proteome Predicts Metastatic Potential in Uveal Melanoma Int J Mol Sci. 2023 Apr 06; 24(7). . View in PubMed
• Correlating somatic copy number alteration in aqueous humour cfDNA with chemotherapy history, eye salvage and pathological features in retinoblastoma Br J Ophthalmol. 2023 Mar 17. . View in PubMed
• Combined low-pass whole genome and targeted sequencing in liquid biopsies for pediatric solid tumors NPJ Precis Oncol. 2023 Feb 20; 7(1):21. . View in PubMed
• 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. . View in PubMed
• 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. . View in PubMed
• 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. . View in PubMed
• 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. . View in PubMed
• 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. . View in PubMed
• Chromosome 6p amplification detected in blood cell-free DNA in advanced intraocular retinoblastoma Ophthalmic Genet. 2022 12; 43(6):866-870. . View in PubMed
• Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy Nat Commun. 2022 09 21; 13(1):5523. . View in PubMed
• Aqueous Humor as a Liquid Biopsy for Retinoblastoma: Clear Corneal Paracentesis and Genomic Analysis J Vis Exp. 2021 09 07; (175). . View in PubMed
• Author Correction: SMURF-seq: efficient copy number profiling on long-read sequencers Genome Biol. 2020 Aug 25; 21(1):214. . View in PubMed
• 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). . View in PubMed
• Aqueous Humor Is Superior to Blood as a Liquid Biopsy for Retinoblastoma Ophthalmology. 2020 04; 127(4):552-554. . View in PubMed
• 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. . View in PubMed
• SMURF-seq: efficient copy number profiling on long-read sequencers Genome Biol. 2019 07 08; 20(1):134. . View in PubMed
• 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. . View in PubMed
• 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. . View in PubMed
• Mutagenesis and cysteine scanning of transmembrane domain 10 of the human dipeptide transporter Pharm Res. 2009 Oct; 26(10):2358-66. . View in PubMed
• 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. . View in PubMed

• Berry, Jesse
• Cobrinik, David
• Jubran, Rima
• Kuhn, Peter
• Belson, Paula
• Rao, Narsing
• Goldkorn, Amir
• Lenz, Heinz-Josef
• Krailo, Mark
• Shah, Rachana