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Unfolding of hidden white blood cell count phenotypes for gene discovery using latent class mixed modeling

Genes & Immunity volume 20, pages 555–565 (2019)Cite this article

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Abstract

Resting-state white blood cell (WBC) count is a marker of inflammation and immune system health. There is evidence that WBC count is not fixed over time and there is heterogeneity in WBC trajectory that is associated with morbidity and mortality. Latent class mixed modeling (LCMM) is a method that can identify unobserved heterogeneity in longitudinal data and attempts to classify individuals into groups based on a linear model of repeated measurements. We applied LCMM to repeated WBC count measures derived from electronic medical records of participants of the National Human Genetics Research Institute (NHRGI) electronic MEdical Record and GEnomics (eMERGE) network study, revealing two WBC count trajectory phenotypes. Advancing these phenotypes to GWAS, we found genetic associations between trajectory class membership and regions on chromosome 1p34.3 and chromosome 11q13.4. The chromosome 1 region contains CSF3R, which encodes the granulocyte colony-stimulating factor receptor. This protein is a major factor in neutrophil stimulation and proliferation. The association on chromosome 11 contain genes RNF169 and XRRA1; both involved in the regulation of double-strand break DNA repair.

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Acknowledgements

The eMERGE Network was initiated and funded by NHGRI through the following grants:

Phase III: U01HG8657 (Kaiser Permanente Washington, formerly Group Health Cooperative/University of Washington, Seattle); U01HG8685 (Brigham and Women’s Hospital); U01HG8672 (Vanderbilt University Medical Center); U01HG8666 (Cincinnati Children’s Hospital Medical Center); U01HG6379 (Mayo Clinic); U01HG8679 (Geisinger Clinic); U01HG8680 (Columbia University Health Sciences); U01HG8684 (Children’s Hospital of Philadelphia); U01HG8673 (Northwestern University); U01HG8701 (Vanderbilt University Medical Center serving as the Coordinating Center); U01HG8676 (Partners Healthcare/Broad Institute); and U01HG8664 (Baylor College of Medicine).

Phase II: U01HG006828 (Cincinnati Children’s Hospital Medical Center/Boston Children’s Hospital); U01HG006830 (Children’s Hospital of Philadelphia); U01HG006389 (Essentia Institute of Rural Health, Marshfield Clinic Research Foundation and Pennsylvania State University); U01HG006382 (Geisinger Clinic); U01HG006375 (Group Health Cooperative/University of Washington); U01HG006379 (Mayo Clinic); U01HG006380 (Icahn School of Medicine at Mount Sinai); U01HG006388 (Northwestern University); U01HG006378 (Vanderbilt University Medical Center); U01HG006385 (Vanderbilt University Medical Center serving as the Coordinating Center), U01HG004438 (CIDR) and U01HG004424 (the Broad Institute) serving as Genotyping Centers, and U01HG004438 (CIDR) serving as a Sequencing Center.

Phase I: U01-HG-004610 (Group Health Cooperative/University of Washington); U01-HG-004608 (Marshfield Clinic Research Foundation and Vanderbilt University Medical Center); U01-HG-04599 (Mayo Clinic); U01HG004609 (Northwestern University); U01-HG-04603 (Vanderbilt University Medical Center, also serving as the Administrative Coordinating Center); U01HG004438 (CIDR) and U01HG004424 (the Broad Institute) serving as Genotyping Centers.

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Authors and Affiliations

  1. Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, WA, 98109, USA

    Taryn O. Hall, Ian B. Stanaway & David R. Crosslin

  2. Kaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, WA, 98109, USA

    David S. Carrell & Eric B. Larson

  3. Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, TN, 37235, USA

    Robert J. Carroll & Joshua C. Denny

  4. Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA

    Hakon Hakonarson & Frank D. Mentch

  5. Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA

    Peggy L. Peissig

  6. Geisinger Research, Rockville, MD, 20850, USA

    Sarah A. Pendergrass

  7. Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, 98105, USA

    Elisabeth A. Rosenthal & Gail P. Jarvik

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  1. Taryn O. Hall
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Hall, T.O., Stanaway, I.B., Carrell, D.S. et al. Unfolding of hidden white blood cell count phenotypes for gene discovery using latent class mixed modeling. Genes Immun 20, 555–565 (2019). https://doi.org/10.1038/s41435-018-0051-y

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