The Genetic Determinants and Genomic Consequences of Non-Leukemogenic Somatic Point Mutations (2024)

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View ORCID ProfileJoshua S. Weinstock, View ORCID ProfileSharjeel A. Chaudhry, Maria Ioannou, Maria Viskadourou, View ORCID ProfilePaula Reventun, View ORCID ProfileYasminka A. Jakubek, View ORCID ProfileL. Alexander Liggett, Cecelia Laurie, Jai G. Broome, Alyna Khan, View ORCID ProfileKent D. Taylor, View ORCID ProfileXiuqing Guo, Patricia A. Peyser, Eric Boerwinkle, View ORCID ProfileNathalie Chami, View ORCID ProfileEimear E. Kenny, View ORCID ProfileRuth J. Loos, Bruce M. Psaty, Tracy P. Russell, View ORCID ProfileJennifer A. Brody, View ORCID ProfileJeong H. Yun, View ORCID ProfileMichael H. Cho, Ramachandran S. Vasan, View ORCID ProfileSharon L. Kardia, View ORCID ProfileJennifer A. Smith, View ORCID ProfileLaura M. Raffield, Aurelian Bidulescu, Emily O’Brien, Mariza de Andrade, View ORCID ProfileJerome I. Rotter, View ORCID ProfileStephen S. Rich, Russell P. Tracy, View ORCID ProfileYii Der Ida Chen, View ORCID ProfileC. Charles Gu, View ORCID ProfileChao A. Hsiung, View ORCID ProfileCharles Kooperberg, Bernhard Haring, Rami Nassir, Rasika Mathias, Alex Reiner, View ORCID ProfileVijay Sankaran, Charles J. Lowenstein, Thomas W. Blackwell, Goncalo R. Abecasis, View ORCID ProfileAlbert V. Smith, View ORCID ProfileHyun M. Kang, View ORCID ProfilePradeep Natarajan, Siddhartha Jaiswal, Alexander Bick, Wendy S. Post, Paul Scheet, Paul Auer, View ORCID ProfileTheodoros Karantanos, Alexis Battle, Marios Arvanitis

doi: https://doi.org/10.1101/2024.08.22.24312319

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Abstract

Clonal hematopoiesis (CH) is defined by the expansion of a lineage of genetically identical cells in blood. Genetic lesions that confer a fitness advantage, such as point mutations or mosaic chromosomal alterations (mCAs) in genes associated with hematologic malignancy, are frequent mediators of CH. However, recent analyses of both single cell-derived colonies of hematopoietic cells and population sequencing cohorts have revealed CH frequently occurs in the absence of known driver genetic lesions. To characterize CH without known driver genetic lesions, we used 51,399 deeply sequenced whole genomes from the NHLBI TOPMed sequencing initiative to perform simultaneous germline and somatic mutation analyses among individuals without leukemogenic point mutations (LPM), which we term CH-LPMneg. We quantified CH by estimating the total mutation burden. Because estimating somatic mutation burden without a paired-tissue sample is challenging, we developed a novel statistical method, the Genomic and Epigenomic informed Mutation (GEM) rate, that uses external genomic and epigenomic data sources to distinguish artifactual signals from true somatic mutations. We performed a genome-wide association study of GEM to discover the germline determinants of CH-LPMneg. After fine-mapping and variant-to-gene analyses, we identified seven genes associated with CH-LPMneg (TCL1A, TERT, SMC4, NRIP1, PRDM16, MSRA, SCARB1), and one locus associated with a sex-associated mutation pathway (SRGAP2C). We performed a secondary analysis excluding individuals with mCAs, finding that the genetic architecture was largely unaffected by their inclusion. Functional analyses of SMC4 and NRIP1 implicated altered HSC self-renewal and proliferation as the primary mediator of mutation burden in blood. We then performed comprehensive multi-tissue transcriptomic analyses, finding that the expression levels of 404 genes are associated with GEM. Finally, we performed phenotypic association meta-analyses across four cohorts, finding that GEM is associated with increased white blood cell count and increased risk for incident peripheral artery disease, but is not significantly associated with incident stroke or coronary disease events. Overall, we develop GEM for quantifying mutation burden from WGS without a paired-tissue sample and use GEM to discover the genetic, genomic, and phenotypic correlates of CH-LPMneg.

Competing Interest Statement

L.M.R. is a consultant for the TOPMed Administrative Coordinating Center (through Westat). B.M.P. serves on the Steering Committee of the Yale Open Data Access Project funded by Johnson & Johnson. J.Y. reports grant support from Bayer. M.C. reports grant support from Bayer and GSK, Consulting and speaking fees from Illumina and AstraZeneca. A.G.B., P.N, and S.J. are cofounders, equity holders, and on the scientific advisory board of TenSixteen Bio. G.R.A. is an employee of Regeneron Pharmaceuticals and receives salary, stock and stock options as compensation.

Funding Statement

Whole genome sequencing (WGS) for the Trans-Omics in Precision Medicine (TOPMed) program was supported by the National Heart, Lung and Blood Institute (NHLBI). See Supplementary Information 1 for study omics support information. Centralized read mapping and genotype calling, along with variant quality metrics and filtering were provided by the TOPMed Informatics Research Center (3R01HL-117626-02S1; contract HHSN268201800002I). Phenotype harmonization, data management, sample-identity quality control and general study coordination were provided by the TOPMed Data Coordinating Center (R01HL-120393; U01HL-120393; contract HHSN268201800001I). We thank the studies and participants who provided biological samples and data for TOPMed. The full study-specific acknowledgments are included in Supplementary Cohort Acknowledgements.

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Ethics committee/IRB of Johns Hopkins University gave ethical approval for this work

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Footnotes

  • This revised manuscript includes a correction for a typographical error.

Data Availability

Individual whole-genome sequence data for TOPMed whole genomes, individual-level harmonized phenotypes and the CHIP variant call sets used in this analysis are available through restricted access via the dbGaP TOPMed Exchange Area available to TOPMed investigators.

Copyright

The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.

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PostedAugust 26, 2024.

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The Genetic Determinants and Genomic Consequences of Non-Leukemogenic Somatic Point Mutations (2024)
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