Mosaic chromosomal alterations in blood are associated with an increased risk of Alzheimer’s disease
Open accessAbstract
Mosaic chromosomal alterations (mCAs) in blood, a form of clonal hematopoiesis, have been linked to various diseases, but their role in Alzheimer’s disease (AD) remains unclear. We analyzed blood whole-genome sequencing (WGS) data from 24,049 individuals in the Alzheimer’s Disease Sequencing Project and found that autosomal mCAs were significantly associated with increased AD risk (odds ratio = 1.27; P = 1.3 × 10 −5 ). This association varied by ancestry, mCA subtype, APOE ε4 allele status, and chromosomal location. Using matched blood WGS and brain single-nucleus RNA-seq data, we identified microglia-annotated cells in the brain carrying the same mCAs found in blood. These findings suggest that blood mCAs may contribute to AD pathogenesis, potentially through infiltration into the brain and influencing local immune response.
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Recent evidence identifies peripheral somatic clones within human brain-resident microglia.
“This mechanism is supported by recent evidence identifying peripheral somatic clones within human brain-resident microglia [34]”
From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]
The Main section reports microglia-annotated brain cells carrying the same mosaic chromosomal alterations as cells in blood, supporting the presence of peripheral somatic alterations in that cell population. It does not establish that these cells are brain-resident microglia: the authors say the finding raises the possibility that blood-derived monocytes entered the brain. (LLM, conf=0.87)
Experimental — accuracy not yet measuredMechanistic insights provide a plausible biological framework for the heterogeneous and sometimes contradictory epidemiological findings observed across studies, particularly those derived from shared cohorts such as the ADSP.
“These mechanistic insights provide a plausible biological framework for the heterogeneous and sometimes contradictory epidemiological findings observed across studies, particularly those derived from shared cohorts such as the ADSP [10,13,34].”
From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]
The Main section reports contrasting findings: an earlier multicohort study found CHIP protective against Alzheimer’s disease, whereas this paper finds CHIP associated with increased risk. It also proposes a possible microglial mechanism and analyzes ADSP data. It does not establish that this mechanism explains differences across epidemiological studies, particularly studies using shared ADSP cohorts; that framework is the citing authors’ interpretation. (LLM, conf=0.82)
Experimental — accuracy not yet measuredThe impact of somatic mosaicism on the brain depends heavily on the specific genetic architecture of the clonal expansion.
“Collectively, these findings suggest that the impact of somatic mosaicism on the brain depends heavily on the specific genetic architecture of the clonal expansion.”
From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]
The Main section reports that Alzheimer’s disease risk associations differ by mCA type and chromosomal location, supporting the idea that genetic features matter. But the paper measures associations with Alzheimer’s disease, not whether the genetic architecture of a clonal expansion determines its impact on the brain; the Main section also says a causal relationship and the biological relevance of the brain-cell findings require further study. No page numbers are available in our copy. (LLM, conf=0.82)
Experimental — accuracy not yet measuredThree independent analytical frameworks have been applied to the same ADSP cohort, yielding disparate results.
“Notably, three independent analytical frameworks have now been applied to the same ADSP cohort, yielding disparate results.”
From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]
The Methods section (page unavailable) confirms that this paper analyzes the ADSP release R4 cohort. The Main section reports an increased AD risk associated with CHIP in its data and contrasts this with a previously reported protective effect, but it does not identify three independent analytical frameworks applied to the same ADSP cohort or compare their results. (LLM, conf=0.82)
Experimental — accuracy not yet measuredIdentical mCA clones were identified within a subset of brain-resident microglia exhibiting a pro-inflammatory transcriptional profile, providing direct evidence that large-scale somatic mosaicism in the blood can mirror pathological immune states in the CNS.
“the study identified identical mCA clones within a subset of brain-resident microglia that exhibited a pro-inflammatory transcriptional profile characterized by the upregulation of MHC-II processing genes and markers of cellular senescence, providing direct evidence that large-scale somatic mosaicism in the blood can mirror pathological immune states in the CNS [34].”
From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]
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Experimental — accuracy not yet measured
Gene-specific effects, clonal burden, host genetic background, and neurovascular integrity all shape whether CHIP-derived immune cells exert protective or pathogenic influences in the aging brain.
“Gene-specific effects, clonal burden, host genetic background, and neurovascular integrity all shape whether CHIP-derived immune cells exert protective or pathogenic influences in the aging brain [10,11,13,19,33,34].”
From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]
The Main section (page unavailable) reports differing associations for CHIP and other forms of clonal hematopoiesis with Alzheimer’s disease. It also finds that mCA-associated risk varies by APOE genotype and number of mCAs. Those findings lend partial support to the proposed role of genetic background and burden, but the paper does not establish that gene-specific CHIP effects or neurovascular integrity determine whether CHIP-derived brain immune cells are protective or pathogenic. (LLM, conf=0.82)
Experimental — accuracy not yet measuredAutosomal mosaic chromosomal alterations are associated with increased AD risk and are detectable in both blood and brain-resident microglia, implicating shared vascular and immune mechanisms.
“Recent whole-genome sequencing analyses demonstrate that autosomal mosaic chromosomal alterations are also associated with increased AD risk and are detectable in both blood and brain-resident microglia, implicating shared vascular and immune mechanisms [34,46].”
From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]
The Abstract and Main section report an association between autosomal mCAs in blood and increased AD risk, and identify brain microglia-annotated cells carrying the same alterations. They suggest a possible effect on local immune response, but do not establish a shared vascular mechanism. The Main section also cautions that contamination by circulating blood cells cannot be ruled out, so the finding does not establish that the altered cells are brain-resident microglia. (LLM, conf=0.87)
Experimental — accuracy not yet measuredMosaic chromosomal alterations, including loss of the Y chromosome, are strongly associated with cardiovascular disease, stroke, and dementia risk.
“Mosaic chromosomal alterations, including loss of the Y chromosome (LOY), are strongly associated with cardiovascular disease, stroke, and dementia risk [34,44,45].”
From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]
The Main section reports an association between blood mCAs and Alzheimer’s disease and notes a previously reported association between LOY and Alzheimer’s disease. It links clonal hematopoiesis broadly—not mCAs or LOY specifically—to cardiovascular disease, and does not address stroke risk. The evidence supports the Alzheimer’s component, but not the full set of associations claimed. (LLM, conf=0.87)
Experimental — accuracy not yet measuredAutosomal mCAs have recently been identified within brain-resident microglia.
“Further supporting this central accumulation, autosomal mCAs have recently been identified within brain-resident microglia”
From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]
The Main section reports mCAs in microglia-annotated cells from brain single-nucleus data, supporting identification in cells classified as microglia. It does not establish that those cells were brain-resident microglia: the authors suggest they may derive from blood monocytes and say contamination by circulating blood cells cannot be ruled out. Page numbers are not provided in our copy. (LLM, conf=0.85)
Experimental — accuracy not yet measuredCHIP-associated mutations can be detected in microglia resident in the brain and correlate with peripheral clonal burden, but this phenomenon appears to fluctuate and is context-dependent.
“While recent evidence demonstrates that CHIP-associated mutations can be detected in microglia resident in the brain and correlate with peripheral clonal burden, this phenomenon appears to fluctuate and is context-dependent [10,34].”
From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]
The Main section reports the same blood mosaic chromosomal alterations (mCAs) in microglia-annotated cells and a correlation in their cell fractions in the primary dataset, but not in the replication dataset. It attributes the finding about CHIP mutations to a previous study; its own correlated finding concerns mCAs, not CHIP-associated mutations. The limitations section also says circulating-blood-cell contamination cannot be ruled out, so residence in brain microglia is not established, and the cross-sectional results do not show fluctuation over time. (LLM, conf=0.88)
Experimental — accuracy not yet measuredDistinct forms of somatic clonal expansion converge on vascular and inflammatory pathways that critically shape phenotypes of dementia.
“Together, these findings suggest that distinct forms of somatic clonal expansion converge on vascular and inflammatory pathways that critically shape phenotypes of dementia.”
From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]
The Main section reports that blood mCAs and CHIP were independently associated with Alzheimer’s disease, and suggests that mCA-bearing cells may influence the brain’s local immune response. It also notes a general link between clonal hematopoiesis and cardiovascular disease. It does not establish that distinct forms converge on vascular and inflammatory pathways or that those pathways critically shape dementia phenotypes. (LLM, conf=0.85)
Experimental — accuracy not yet measuredThese somatic clones integrate into the neuroinflammatory landscape and potentially outcompete wild-type cells under pathological conditions.
“indicating that these somatic clones integrate into the neuroinflammatory landscape and potentially outcompete wild-type cells under pathological conditions [34].”
From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]
The Main section (page not provided) finds blood-associated chromosomal alterations in microglia-annotated brain cells and enrichment of those cells in a redox-related microglial state, supporting their presence in the brain’s disease-relevant cellular landscape. It does not show that the clones outcompete wild-type cells under pathological conditions. (LLM, conf=0.84)
Experimental — accuracy not yet measuredLarge CHIP clones in the ADSP cohort have been associated with reduced AD risk and attenuated neuropathology, while smaller clones, mosaic chromosomal alterations, and specific genetic contexts may have increased susceptibility.
“While large CHIP clones in the ADSP cohort have been associated with a reduced AD risk and attenuated neuropathology [10], smaller clones, mosaic chromosomal alterations [34], and specific genetic contexts, most notably APOE stratification, may have increased susceptibility [13].”
From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]
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- Authors
- Naito, T., Hirata, K., Jang, B., Lakhani, C. M., Buonfiglioli, A., Lee, W.-P., Valladares, O., Wang, L.-S., Okada, Y., Won, H.-H., Papapetrou, E. P., Marro, S. G., Knowles, D. A., & Raj, T.
- Affiliations
- New York Genome Center (US)
- Icahn School of Medicine at Mount Sinai (US)
- Samsung Medical Center (KR)
- University of Pennsylvania (US)
- RIKEN Center for Integrative Medical Sciences (JP)
- Tisch Cancer Institute (US)
- Corresponding author
- Naito, Tatsuhiko
- ORCID
- Venue
- medRxiv
- Publisher
- openRxiv
- Published
- 2025-06-04
- PMC
- PMC12155033
- OpenAlex
- W4411016607
- Cited by
- 4
- References
- 6
- Citations by year
- 2026: 2 · 2025: 2
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- medRxiv (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by)
- Funders
- BrightFocus Foundation
- Georgia Clinical and Translational Science Alliance (UL1TR004419)
- National Institutes of Health (1r21ag063130-01a1, 1s10od026880-01, 1rf1ag065926-01a1, 1r56ag055824-01a1, 1s10od030463-01, AG066514, NIA R01-AG054005, RF1-AG065926, UL1TR004419)
- Japan Society for the Promotion of Science
- National Institute on Aging (U01AG058635, R21-AG063130, U01AG068880, NIA R21-AG063130, R01AG054005, R56AG088669, R56- AG055824, RF1-AG065926, P30AG066514)
- National Institute of Neurological Disorders and Stroke (U54NS123743, R01NS116006)
- National Center for Advancing Translational Sciences (S10OD026880, S10OD030463)
- Topics
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- mosaic chromosomal alterations, clonal hematopoiesis, Alzheimer's disease risk, microglia, APOE ε4, ancestry differences, neuroinflammation
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