Genomic Technology Core

Mission

The Genomic Technology Core develops novel single-cell genomic methods for investigating rheumatic disease cellular function. The core provides consultation on experimental design, service models for sample processing, and state-of-the-art genomics workflows all within centralized data management systems to ensure trustworthy, reproducible results. 

 

GT Core

 

Specifically, the GT Core will:

  1. Develop a state-of-the-art laboratory information management system (LIMS) for tracking biospecimen data for rheumatic disease patients throughout the entire process from sample acquisition to data generation.
  2. Consolidate the storage and management of the numerous existing rheumatic disease biospecimen collections and facilitate the processing, storage, and management of future biospecimens collected from rheumatic disease patients, from childhood to old age.    
  3. Assemble a panel of experts in genomics and other molecular technologies (including immunologic and proteomic phenotyping) who will provide consultative services related to the appropriate application of genomics and molecular phenotyping of biospecimens for Center rheumatic disease projects.
  4. Serve as a liaison between investigators and other UCSF laboratory personnel to ensure that high quality genomics and molecular phenotyping data are generated and distributed to the IB Core for integration with clinical data and statistical analysis.

 

Recent Publications:

  1. LaFlam TN, Billesbølle CB, Dinh T, Wolfreys FD, Lu E, Matteson T, An J, Xu Y, Singhal A, Brandes N, Ntranos V, Manglik A, Cyster JG, Ye CJ. Phenotypic pleiotropy of missense variants in human B cell confinement receptor P2RY8. Cell Genom. 2025 Nov 12;5(11):100981. doi: 10.1016/j.xgen.2025.100981. Epub 2025 Sep 9. PubMed PMID: 40930105; PubMed Central PMCID: PMC12648108.

  1. Horton MK, Nititham J, Taylor KE, Katz P, Ye CJ, Yazdany J, Dall'Era M, Hurabielle C, Barcellos LF, Criswell LA, Lanata CM. Changes in DNA methylation are associated with systemic lupus erythematosus flare remission and clinical subtypes. Clin Epigenetics. 2024 Dec 18;16(1):181. doi: 10.1186/s13148-024-01792-x. PubMed PMID: 39696438; PubMed Central PMCID: PMC11656870.

  1. McCarthy EE, Yu S, Perlmutter N, Nakao Y, Naito R, Lin C, Riekher V, DeRisi J, Ye CJ, Weiss A, Ashouri JF. Endogenous antigens shape the transcriptome and TCR repertoire in an autoimmune arthritis model. J Clin Invest. 2024 Nov 26;135(2). doi: 10.1172/JCI174647. PubMed PMID: 39589811; PubMed Central PMCID: PMC11735108.

  1. Kim MC, Gate R, Lee DS, Tolopko A, Lu A, Gordon E, Shifrut E, Garcia-Nieto PE, Marson A, Ntranos V, Ye CJ. Method of moments framework for differential expression analysis of single-cell RNA sequencing data. Cell. 2024 Oct 31;187(22):6393-6410.e16. doi: 10.1016/j.cell.2024.09.044. Epub 2024 Oct 24. PubMed PMID: 39454576; PubMed Central PMCID: PMC11556465.

  1. IGVF Consortium. Deciphering the impact of genomic variation on function. Nature. 2024 Sep;633(8028):47-57. doi: 10.1038/s41586-024-07510-0. Epub 2024 Sep 4. Review. PubMed PMID: 39232149; PubMed Central PMCID: PMC11973978.

  1. Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, Steinhart Z, Satpathy AT, Pollard KS, Corn JE, Bernstein BE, Ye CJ, Marson A. Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nat Genet. 2024 Jun;56(6):1156-1167. doi: 10.1038/s41588-024-01743-5. Epub 2024 May 29. PubMed PMID: 38811842; PubMed Central PMCID: PMC11176074.

  1. Neavin D, Senabouth A, Arora H, Lee JTH, Ripoll-Cladellas A, sc-eQTLGen Consortium, Franke L, Prabhakar S, Ye CJ, McCarthy DJ, Melé M, Hemberg M, Powell JE. Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods. Genome Biol. 2024 Apr 15;25(1):94. doi: 10.1186/s13059-024-03224-8. PubMed PMID: 38622708; PubMed Central PMCID: PMC11020463.

  1. Zhou Z, Du J, Wang J, Liu L, Gordon MG, Ye CJ, Powell JE, Li MJ, Rao S. SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues. Database (Oxford). 2024 Mar 9;2024. doi: 10.1093/database/baae010. PubMed PMID: 38459946; PubMed Central PMCID: PMC10924434.

  1. Mennillo E, Kim YJ, Lee G, Rusu I, Patel RK, Dorman LC, Flynn E, Li S, Bain JL, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein ML, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho SJ, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG. Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis. Nat Commun. 2024 Feb 19;15(1):1493. doi: 10.1038/s41467-024-45665-6. PubMed PMID: 38374043; PubMed Central PMCID: PMC10876948.

  1. Hurabielle C, LaFlam TN, Gearing M, Ye CJ. Functional genomics in inborn errors of immunity. Immunol Rev. 2024 Mar;322(1):53-70. doi: 10.1111/imr.13309. Epub 2024 Feb 8. Review. PubMed PMID: 38329267; PubMed Central PMCID: PMC10950534.

  1. Strober BJ, Tayeb K, Popp J, Qi G, Gordon MG, Perez R, Ye CJ, Battle A. SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models. Genome Biol. 2024 Jan 22;25(1):28. doi: 10.1186/s13059-023-03152-z. PubMed PMID: 38254214; PubMed Central PMCID: PMC10801966.