Despite these important insights, the relationship between different CH events, infectious risk and infectious disease severity has not been studied. The presence of co-existing medical comorbidities known to correlate with Covid-19 severity including diabetes, COPD, asthma, hypertension and cardiovascular disease, were ascertained from ICD-9 and ICD-10 billing codes. However, the majority of mutations in CH appear to occur outside of canonical cancer driver genes11,12. 
In a fixed effects meta-analysis of odds-ratio estimates from the multivariable logistic regression models employed in each separate cohort analysis, the presence of CH was associated with an increased risk of severe Covid-19 (OR=1.85, 95%=1.15-2.99, p=0.01) (Figure 1). R.L.L. Subjects who had an active malignancy at the time of blood draw were excluded. Subjects had a tumor and blood sample (as a matched normal control) sequenced using MSK-IMPACT, an FDA-authorized hybridization capture-based next-generation sequencing assay encompassing all protein-coding exons from the canonical transcript of 341, 410, or 468 cancer-associated genes (Supplementary Table 4). These provinces had the highest numbers of Covid-19 cases during the period14. This association trended towards statistical significance in patients with any CH mutation and a maximum VAF<5% (OR=1.75, 95% CI=0.97-3.17, p=0.06: Extended Data Figures 2-4). Sequencing reads were trimmed with SeqPrep (v0.3) and Sickle (v1.33) and aligned to the human genome (hg19) using BWA-MEM (v0.7.10). In a large cancer patient cohort, CH is also associated with other severe infections, namely Streptococcus/Enterococccus and Clostridium difficile infections. P30 CA008748), the Marie Josee and Henry R Kravis Center for Molecular Oncology, Cycle for Survival, and MSK Molecular Diagnostics Service. Future investigation including functional studies will be important to clarify the mechanisms underlying the association between CH and infection risk and to develop potential interventional strategies to attenuate inflammation, clonal expansion, and infectious sequelae in patients with and without cancer. a) Number of CH mutations among those with severe and non-severe Covid-19 b) VAF of CH mutations by Covid-19 severity and infection status. Blood was drawn following confirmation of Covid-19 positivity. Professor Koh Youngil of the Department of Hematology and Oncology at SNUH stated, "We have confirmed that clonal hematopoiesis, which has been attracting attention as a biomarker for cardiovascular disease and cancer, has a close relationship with the severity of COVID-19." 
Summary statistics for a fixed effects meta-analysis are shown. Preprints are preliminary research reports that have not been certified by peer review. Teng Gao; Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York. 
), V Foundation (E.P. 
There were seven subjects with Covid-19 for whom there was minimal documentation of clinical course following Covid-19 infection and these individuals were excluded. Shown are the results from logistic regression comparing the odds ratios of severe Covid-19 among those with one or more CH mutations <5% VAF compared to no CH and CH with a VAF >5% and no CH. Our study included patients from two separate cohorts: Among the 1,636 patients with solid tumors tested for clonal hematopoiesis at the Memorial Sloan Kettering Cancer Center, the research team found 413 patients positive for COVID-19 and also tested 112 healthy patients without cancer who had been hospitalized for COVID-19 at four tertiary medical institutions in Korea, including Seoul National University Hospital. Summary statistics for a fixed effects meta-analysis are shown. All models were adjusted for age, gender, race, smoking, tumor type, and cumulative exposure to cytotoxic chemotherapy prior to blood draw and after blood draw as previously described10. is a member of the board of directors of Personal Genome Diagnostics (PGDx) and Jounce Therapeutics; is a paid consultant to PGDx and Neophore; is an uncompensated consultant for Merck (with the exception of travel and research support for clinical trials); is an inventor of multiple licensed patents related to technology for circulating tumor DNA analyses and mismatch repair deficiency for diagnosis and therapy from Johns Hopkins University, some of which are associated with equity or royalty payments directly to Johns Hopkins and L.A.D. 
Alternatively, this could represent a novel pathophysiology that links CH-induced changes in hematopoietic stem, progenitor, and lymphoid cell function with immune regulation and infection response. The strength of the association between CH and severe Covid-19 was similar among patients with one CH mutation (OR=1.78, 95% CI=1.0-3.1, p=0.04) and multiple CH mutations (OR=2.0, 95% CI=1.0-3.8, p=0.04). Clonal hematopoiesis is associated with risk of severe Covid-19, Department of Medicine, Washington University, Department of Internal Medicine, Seoul National University Hospital, Center for Precision Medicine, Seoul National University Hospital, Department of Medicine, Memorial Sloan Kettering Cancer Center, Department of Pathology, Memorial Sloan Kettering Cancer Center, Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Department of Internal Medicine, National Medical Center, Department of Internal Medicine, Seoul National University Bundang Hospital, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, Department of Pathology and Molecular Medicine, Queens University, Cardiovascular Research Center, Massachusetts General Hospital, Department of Medicine, Brigham and Womens Hospital, Harvard Medical School, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Clinical Genetics Research Lab, Department of Medicine, Memorial Sloan Kettering Cancer CenterS. These subjects were also excluded. Our exploratory analysis suggests that the relationship between CH and Covid-19 and CH and Clostridium difficile infection may be partly driven by non-driver CH. Median coverage in the blood samples was 497x, and median coverage in the tumors was 790x. In order to explore the association between particular mutation types and Covid-19 severity, we performed a stratified analysis of Covid-19 severity by PD-CH versus non-PD CH status. These findings suggest a relationship between CH and risk of severe infections that warrants further investigation.
Most non-PD mutations in Covid-19 positive cases occurred in non-recurrently mutated genes (65% at MSK and 76.9% in KoCH, Supplementary Figure 1). When stratified by CH-mutation characteristics, patients with two or more CH-mutations had a stronger association with Clostridium difficile infection (OR=3.4, 95% CI=1.8-6.3, p=210-4) compared to patients with one CH-mutation (OR=1.4, 95% CI=0.8-2.7, p=0.28). A significant association was observed between non-PD CH and severe Covid-19 (OR=2.01, 95% CI=1.15-3.50, p=0.02), as well as between silent (synonymous) CH and severe Covid-19 (OR=2.58, 95% CI 1.01-6.61, p=0.05). He added "Clonal hematopoiesis could be used as an index to predict the severe progression of COVID-19.". Shown are the results from logistic regression comparing the odds ratios of severe Covid-19 among those with one mutation and those with two or more mutations. Association between maximum VAF of CH-mutation(s) and Covid-19 severity.
Hypoxia requiring supplemental oxygen was defined as supplemental oxygen device >1 L with O2 <94% resulting from Covid-19 infection. Subjects who were billed using a ICD9/10 code within the phecode for the first time following their sequencing blood draw with evidence of CH were considered to have an incident infection. We thank the Global Science experimental Data hub Center (GSDC) and Korea Research Environment Open NETwork (KREONET) service for data computing and network provided by the Korea Institute of Science and Technology Information (KISTI).Work performed at Memorial Sloan Kettering Cancer Center was supported in part by the Cancer Center Support Grant (grant no. Of these patients, 1,626 were tested for SARS-CoV-2 (the virus that causes Covid-19) RNA between March 1st 2020 and July 1st 2020; 403 (24.8%) individuals tested positive for SARS-CoV-2 (Methods and Table 1). CH was significantly (FDR-corrected p-value<0.10) associated with the onset of two infection subclasses: Clostridium difficile infection (HR=2.0, 95% CI: 1.2-3.3, p=6103) and Streptococcus/Enterococcus infection (HR=1.5, 95% CI=1.1-2.1, p=5103).
L.A.D. Association between CH and risk of infection in solid tumor patients. Models were adjusted for age, gender, race, smoking, diabetes, cardiovascular disease, COPD/asthma, cancer primary site (if history of malignancy), exposure to cytotoxic cancer therapy for the MSK and Korea Consortia. M.F.B is on the advisory board for Roche and recieves research support from Illumina. All authors contributed to the writing of the manuscript and approved it for submission. 
B) Association between CH subtype defined by putative driver status and risk of Clostridium Difficle and Streptococcus/Enterococcus infection using cox proportional hazards regression. 
In summary, we show in cancer and non-cancer patients that CH is associated with increased Covid-19 severity. Summary statistics for a fixed effects meta-analysis are shown. The association between CH and Clostridium difficile infection was significant for mutations with a VAF of >5% (OR=2.5, 95% CI=1.4-4.6, p=0.002) but not mutations with a VAF of 2-5% (OR=1.6, 95% CI=0.8-3.1, p=0.17). The date of blood draw (used for MSK-IMPACT sequencing) served as the onset date for this time-to-event analysis; the end-date was the date of billing code entry for the infectious disease subtype phecode, death or last follow-up, whichever came first. Moreover, systemic infections and the resultant inflammatory signals can lead to increased clonal fitness of TET2 mutant cells and clonal expansion10,17,18. For Insertions and deletions in-house InDel caller was used26. Following the 10:1 rule regarding the number of covariates in a multivariable model in proportion to the number of events16, we excluded infection subclasses populated with less than 80 individuals. Single nucleotide variants (SNVs) were called using Mutect and VarDict. is on the supervisory board of Qiagen and is a scientific advisor to Loxo, Imago, C4 Therapeutics and Isoplexis which include equity interest. The mutational events that drive CH overlap with known drivers of hematologic malignancies.
We used multivariable logistic regression to evaluate for an association between clonal hematopoiesis and Covid-19 severity adjusting for age (measured as a continuous variable), gender, race, smoking history and co-existing medical comorbidities including diabetes, COPD/asthma and cardiovascular disease all classified as per Table 1. All NGS libraries were prepared using the Agilent SureSelect XT HS and XT Low input enzymatic fragmentation kit. This was done separately for the MSK and KoCH cohorts due to limitations of data sharing. Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence, Age-Related Clonal Hematopoiesis Associated with Adverse Outcomes, Prediction of acute myeloid leukaemia risk in healthy individuals, Somatic mutations precede acute myeloid leukemia years before diagnosis, Genetic Interleukin 6 Signaling Deficiency Attenuates Cardiovascular Risk in Clonal Hematopoiesis, Inherited causes of clonal haematopoiesis in 97,691 whole genomes, An inflammatory cytokine signature predicts COVID-19 severity and survival, Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study, Tet2-Mediated Clonal Hematopoiesis Accelerates Heart Failure Through a Mechanism Involving the IL-1/NLRP3 Inflammasome, Inhibition of Inflammatory Signaling in Tet2 Mutant Preleukemic Cells Mitigates Stress-Induced Abnormalities and Clonal Hematopoiesis, Clonal hematopoiesis, with and without candidate driver mutations, is common in the elderly, Synonymous mutations reveal genome-wide driver mutation rates in healthy tissues, Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations, Chromosomal alterations among age-related haematopoietic clones in Japan, Identification of Clonal Hematopoiesis Mutations in Solid Tumor Patients Undergoing Unpaired Next-Generation Sequencing Assays, Clonal hematopoiesis and risk for atherosclerotic cardiovascular disease, Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host, Antibiotic treatment ameliorates Ten-eleven translocation 2 (TET2) loss-of-function associated hematological malignancies, Chemotherapy and COVID-19 Outcomes in Patients With Cancer, Clinical Characteristics of Coronavirus Disease 2019 in China, Coronavirus Disease 2019 (COVID-19) in Italy, Factors associated with hospital admission and critical illness among 5279 people with coronavirus disease 2019 in New York City: prospective cohort study, Clinical Course and Outcomes of 3,060 Patients with Coronavirus Disease 2019 in Korea, January-May 2020, Cancer therapy shapes the fitness landscape of clonal hematopoiesis, Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation, NPM1 as a potential therapeutic target for atypical teratoid/rhabdoid tumors, Endocrinology (including Diabetes Mellitus and Metabolic Disease), Intensive Care and Critical Care Medicine, Rehabilitation Medicine and Physical Therapy. Variant calling was performed using SNver(v0.4.1), LoFreq(v0.6.1), GATK UnifiedGenotyper(v2.3.9) for SNVs. The criterion for measuring COVID-19 severity was hypoxia, which has oxygen saturation below 94% and requires supplemental oxygen of 1L or more. We used multivariable logistic regression adjusting for covariates including age, smoking, prior Covid-19 related comorbidities, and prior cancer treatment to determine the association between severe Covid-19 and CH in each population. For both cohorts, the primary outcome was severe Covid-19 infection, defined as the presence of hypoxia requiring supplemental oxygen (oxygen device >1 L or hypoxia <94%). We annotated variants as oncogenic if they fulfilled any of the following criteria: 1) truncating variants in NF1, DNMT3A, TET2, IKZF1, RAD21, WT1, KMT2D, SH2B3, TP53, CEBPA, ASXL1, RUNX1, BCOR, KDM6A, STAG2, PHF6, KMT2C, PPM1D, ATM, ARID1A, ARID2, ASXL2, CHEK2, CREBBP, ETV6, EZH2, FBXW7, MGA, MPL, RB1, SETD2, SUZ12, ZRSR2 or in CALR exon 9; 2) any truncating mutations (nonsense, essential splice site or frameshift indel) in known tumor suppressor genes as per the Cancer Gene Census, OncoKB, or the scientific literature; 3) translation start site mutations in SH2B3; 4) TERT promoter mutations; 5) FLT3-ITDs; 6) in-frame indels in CALR, CEBPA, CHEK2, ETV6, EZH2; 7) any variant occurring in the COSMIC haematopoietic and lymphoid category greater than or equal to 10 times; 8) any variant reported as somatic at least 20 times in COSMIC; 9) any variant noted as potentially oncogenic in an in-house dataset of 7,000 individuals with myeloid neoplasm greater than or equal to 5 times; 10) any loci (defined by the amino acid location) reported as having at least 5 missense mutations and at least one exact mutational match in TopMed6. Clonal expansions characterized by non-driver mutational events could be facilitated by multiple mechanisms. 
Subjects who had a hematologic malignancy diagnosed after MSK-IMPACT testing or who had an active hematologic malignancy at the time of blood draw were excluded. Shown are the results from logistic regression adjusted for age, gender, race, smoking, diabetes, cardiovascular disease, COPD/asthma, cancer primary site (if history of malignancy), exposure to cytotoxic cancer therapy for the MSK and KoCH. 
Overall, CH was observed in 35% of Covid-19 positive cases at MSK and 21% in KoCH. For example, mutations in TET2 result in heightened secretion of several cytokines including IL-1/IL-6 signaling that may partially explain the increased risk of cardiovascular disease5,9,16. The sequencing test utilizes genomic DNA extracted from formalin fixed paraffin embedded (FFPE) tumor tissue as well as matched patient blood samples. received honoraria from Illumina. Many classes of genetic alterations, such as copy number events (CNVs), structural variants, non-coding, and epigenetic changes, are not detectable using the targeted panels included in this study. 
Laboratory-confirmed patients with Covid-19 between January and April 2020 in four tertiary hospitals in Republic of Korea were approached for consent to this study. CH was significantly associated with risk of Clostridium Difficile (HR=2.0, 95% CI: 1.2-3.3, p=6103) and Streptococcus/Enterococcus infections (HR=1.5, 95% CI=1.1-2.1, p=5103). All models were adjusted for age, gender, race, smoking, diabetes, cardiovascular disease, COPD/asthma, cancer primary site (if history of malignancy), exposure to cytotoxic cancer therapy. For solid tumor patients at MSK we also adjusted for primary tumor site (thoracic or non-thoracic cancer) and receipt of cytotoxic chemotherapy before and after IMPACT blood draw. We further explored the relationship between CH and risk of other infections in 14,211 solid tumor patients at MSK. Accumulation of mutations can lead to cancer or cardiovascular disease, attracting attention to it as an important biomarker for predicting patients prognosis. Accuracy of populated information was manually checked in the EMR by three independent physicians (K.B, M.F, A.S).
In particular, patients with clonal hematopoiesis without cancer-causing mutations had 2.01 times higher risk of severe COVID-19. Seoul National University Hospital (SNUH) Infectious Diseases Department Professor Kim Nam Joong and his team (Professor Koh Youngil, Department of Hematology and Oncology) announced on the 29th Oct 2021 that if a patient with clonal hematopoiesis is infected with COVID-19, the risk of getting severe is twice as high. In the MSK cohort, CH was observed in 51% and 30% of patients with severe versus non-severe Covid-19, respectively (adjusted OR: 1.85, 95% CI 1.10-3.12, Figure 1). The hematopoietic system is a key regulator of inflammation and immunity. Given the number of model covariates, we limited the analysis to 32 infection subclasses that affected at least 80 individuals (see Methods).
Dr Im Hogyune of Genome Opinion Inc, who was in charge of genetic information analysis in this study, said, Genome Opinion Inc is studying the effects of clonal hematopoiesis on various diseases and developing clonal hematopoiesis diagnostic technology. He also added, We will focus on research and development so that this technology can lead not only to diagnosis but also methods of treatment., [Picture] From left: Prof Kim Nam Joong & Professor Koh Youngil.
The full statistical rationale is further described in the Methods section. Demographics, smoking history, exposure to oncologic therapy and primary tumor site were extracted from the electronic health record. The first cohort was composed of patients with solid tumors treated at Memorial Sloan Kettering Cancer Center (MSK) with blood previously sequenced using MSK-IMPACT, a previously validated targeted gene panel capturing all commonly mutated CH-associated genes (Supplementary Table 1)24. The minimal clinical and genetic data frame used to generate all analyses presented in this paper are available by request and will be made publicly available upon acceptance to a peer-reviewed journal.
Billing codes were highly accurate in identifying the presence of the respective infectious disease (concordance >95%). ), European Hematology Association (E.P. E.P receives research funding from Celgene.D.G and has received honoraria for speaking and scientific advisory engagements with Celgene, Prime Oncology, Novartis, Illumina and Kyowa Hakko Kirin and is a co-founder in Isabl Technologies. The mean depth of coverage of samples was higher than 800x. The severity of Covid-19 is also associated with advanced age, cardiovascular and malignant comorbidities, and elevated circulating IL-6 levels; features which are seen with age-associated CH1923. Preprints posted online allow authors to receive rapid feedback and the entire scientific community can appraise the work for themselves and respond appropriately.
All called mutations were genotyped in the patient-matched tumor sample. Patient Bill of Rights and Responsibilities, Seoul National University Hospital opens outpatient department of clinical genomic medicine, Hepatitis B: the sooner the antiviral treatment, the better.
We used Cox proportional hazards regression to estimate the hazard ratio for risk of infection among those with CH compared to CH negative individuals. This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. The majority of CH mutations were classified as PD-CH (52% in the MSK cohort and 67% in the KoCH dataset). - Analysis of 525 COVID patients registered with domestic and overseas clonal hematopoietic consortium, - Cancer biomarker clonal hematopoiesis can be used as a predictive index for the severity of COVID-19. Variant calling for each blood sample was performed unmatched, using a pooled control sample of DNA from 10 unrelated individuals as a comparator. For example, chromosomal aneuploidies result in a predisposition for lymphoid fate specification and transformation13,14 while point mutations in DNMT3A result in increased myeloid differentiation6,15. This will need to be further studied in larger cohorts. 
K.L.B, R.P, T.G, A.S, M.B,Y.K,H.I,C.S, A.Z led the generation and analysis of sequencing data. The criterion for measuring COVID-19 severity was hypoxia, which has oxygen saturation below 94% and requires supplemental oxygen of 1L or more. 
The terms of all of these arrangements are being managed by Johns Hopkins and Memorial Sloan Kettering in accordance with their conflict of interest policies. There was not a statistically-significant association between PD-CH and severe Covid-19 infection (OR=1.15, 95% CI=0.61-2.02, p=0.77: Extend ed Data Figure 1). Among 515 individuals with Covid-19 from Memorial Sloan Kettering (MSK) and the Korean Clonal Hematopoiesis (KoCH) consortia, we found that CH was associated with severe Covid-19 outcomes (OR=1.9, 95%=1.2-2.9, p=0.01). K.L.B, M.F, J.J., A.S., Y.K, H.I, C.S, S.K,H.S,A.Z, performed statistical analyses and/or participated in data interpretation. ), and the Cancer Colorectal Cancer Dream Team Translational Research Grant (SU2C-AACR-DT22-17 to L.D.). Mutations were annotated with VEP(version 86) and OncoKb. Those who were billed for an ICD9/10 code within the phecode prior to blood draw were removed from the analysis of that phecode. A.Z. He has received honoraria from Roche, Lilly and Amgen for invited lectures and from Gilead for grant reviews. Heterogeneity also exists across CH phenotypes by driver gene in regards to its impact on inflammatory signaling6. Those comments are posted alongside the preprints for anyone to read them and serve as a post publication assessment. MSK-IMPACT contains most of the commonly reported CH genes with the exception that earlier versions of the panel did not contain PPM1D or SRSF2. 
We then performed a fixed-effects meta-analysis to estimate the association in the overall population. Patients with a maximum CH variant allele frequency (VAF) of >5% showed a significant association with severe Covid-19 (OR=1.9, 95% CI=1.0-3.4, p=0.04). Blood-derived DNA was sequenced using a custom panel of 89 genes frequently mutated in CH. All the statistical analyses were performed with the use of the R statistical package (www.r-project.org). MSK-IMPACT is validated and approved for clinical use by New York State Department of Health Clinical Laboratory Evaluation Program. Acquired mutations that lead to clonal expansion are common in the normal aging hematopoietic system (clonal hematopoiesis, or CH), yet are known to alter stem/progenitor and lymphoid function and response to environmental stressors, including systemic infections5,6,9,10. Clonal hematopoiesis refers to a condition in which acquired mutations occur in hematopoietic stem cells responsible for blood production. Using a previously established phenome-wide-association study (Phe-WAS) methodology25, we mapped patient ICD-9 and ICD-10 billing codes to categories of infectious disease. They should not be relied on to guide clinical practice or health-related behavior and should not be reported in news media as established information. Pooled libraries were sequenced on an Illumina HiSeq 2500 with 2100bp paired-end reads. He receives research support from and consulted for Celgene and Roche and has consulted for Lilly, Janssen, Astellas, Morphosys and Novartis.
In a fixed effects meta-analysis of odds-ratio estimates from the multivariable logistic regression models employed in each separate cohort analysis, the presence of CH was associated with an increased risk of severe Covid-19 (OR=1.85, 95%=1.15-2.99, p=0.01) (Figure 1). R.L.L. Subjects who had an active malignancy at the time of blood draw were excluded. Subjects had a tumor and blood sample (as a matched normal control) sequenced using MSK-IMPACT, an FDA-authorized hybridization capture-based next-generation sequencing assay encompassing all protein-coding exons from the canonical transcript of 341, 410, or 468 cancer-associated genes (Supplementary Table 4). These provinces had the highest numbers of Covid-19 cases during the period14. This association trended towards statistical significance in patients with any CH mutation and a maximum VAF<5% (OR=1.75, 95% CI=0.97-3.17, p=0.06: Extended Data Figures 2-4). Sequencing reads were trimmed with SeqPrep (v0.3) and Sickle (v1.33) and aligned to the human genome (hg19) using BWA-MEM (v0.7.10). In a large cancer patient cohort, CH is also associated with other severe infections, namely Streptococcus/Enterococccus and Clostridium difficile infections. P30 CA008748), the Marie Josee and Henry R Kravis Center for Molecular Oncology, Cycle for Survival, and MSK Molecular Diagnostics Service. Future investigation including functional studies will be important to clarify the mechanisms underlying the association between CH and infection risk and to develop potential interventional strategies to attenuate inflammation, clonal expansion, and infectious sequelae in patients with and without cancer. a) Number of CH mutations among those with severe and non-severe Covid-19 b) VAF of CH mutations by Covid-19 severity and infection status. Blood was drawn following confirmation of Covid-19 positivity. Professor Koh Youngil of the Department of Hematology and Oncology at SNUH stated, "We have confirmed that clonal hematopoiesis, which has been attracting attention as a biomarker for cardiovascular disease and cancer, has a close relationship with the severity of COVID-19." Summary statistics for a fixed effects meta-analysis are shown. Preprints are preliminary research reports that have not been certified by peer review. Teng Gao; Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York. ), V Foundation (E.P. There were seven subjects with Covid-19 for whom there was minimal documentation of clinical course following Covid-19 infection and these individuals were excluded. Shown are the results from logistic regression comparing the odds ratios of severe Covid-19 among those with one or more CH mutations <5% VAF compared to no CH and CH with a VAF >5% and no CH. Our study included patients from two separate cohorts: Among the 1,636 patients with solid tumors tested for clonal hematopoiesis at the Memorial Sloan Kettering Cancer Center, the research team found 413 patients positive for COVID-19 and also tested 112 healthy patients without cancer who had been hospitalized for COVID-19 at four tertiary medical institutions in Korea, including Seoul National University Hospital. Summary statistics for a fixed effects meta-analysis are shown. All models were adjusted for age, gender, race, smoking, tumor type, and cumulative exposure to cytotoxic chemotherapy prior to blood draw and after blood draw as previously described10. is a member of the board of directors of Personal Genome Diagnostics (PGDx) and Jounce Therapeutics; is a paid consultant to PGDx and Neophore; is an uncompensated consultant for Merck (with the exception of travel and research support for clinical trials); is an inventor of multiple licensed patents related to technology for circulating tumor DNA analyses and mismatch repair deficiency for diagnosis and therapy from Johns Hopkins University, some of which are associated with equity or royalty payments directly to Johns Hopkins and L.A.D. Alternatively, this could represent a novel pathophysiology that links CH-induced changes in hematopoietic stem, progenitor, and lymphoid cell function with immune regulation and infection response. The strength of the association between CH and severe Covid-19 was similar among patients with one CH mutation (OR=1.78, 95% CI=1.0-3.1, p=0.04) and multiple CH mutations (OR=2.0, 95% CI=1.0-3.8, p=0.04). Clonal hematopoiesis is associated with risk of severe Covid-19, Department of Medicine, Washington University, Department of Internal Medicine, Seoul National University Hospital, Center for Precision Medicine, Seoul National University Hospital, Department of Medicine, Memorial Sloan Kettering Cancer Center, Department of Pathology, Memorial Sloan Kettering Cancer Center, Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Department of Internal Medicine, National Medical Center, Department of Internal Medicine, Seoul National University Bundang Hospital, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, Department of Pathology and Molecular Medicine, Queens University, Cardiovascular Research Center, Massachusetts General Hospital, Department of Medicine, Brigham and Womens Hospital, Harvard Medical School, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Clinical Genetics Research Lab, Department of Medicine, Memorial Sloan Kettering Cancer CenterS. These subjects were also excluded. Our exploratory analysis suggests that the relationship between CH and Covid-19 and CH and Clostridium difficile infection may be partly driven by non-driver CH. Median coverage in the blood samples was 497x, and median coverage in the tumors was 790x. In order to explore the association between particular mutation types and Covid-19 severity, we performed a stratified analysis of Covid-19 severity by PD-CH versus non-PD CH status. These findings suggest a relationship between CH and risk of severe infections that warrants further investigation.
Most non-PD mutations in Covid-19 positive cases occurred in non-recurrently mutated genes (65% at MSK and 76.9% in KoCH, Supplementary Figure 1). When stratified by CH-mutation characteristics, patients with two or more CH-mutations had a stronger association with Clostridium difficile infection (OR=3.4, 95% CI=1.8-6.3, p=210-4) compared to patients with one CH-mutation (OR=1.4, 95% CI=0.8-2.7, p=0.28). A significant association was observed between non-PD CH and severe Covid-19 (OR=2.01, 95% CI=1.15-3.50, p=0.02), as well as between silent (synonymous) CH and severe Covid-19 (OR=2.58, 95% CI 1.01-6.61, p=0.05). He added "Clonal hematopoiesis could be used as an index to predict the severe progression of COVID-19.". Shown are the results from logistic regression comparing the odds ratios of severe Covid-19 among those with one mutation and those with two or more mutations. Association between maximum VAF of CH-mutation(s) and Covid-19 severity.
Hypoxia requiring supplemental oxygen was defined as supplemental oxygen device >1 L with O2 <94% resulting from Covid-19 infection. Subjects who were billed using a ICD9/10 code within the phecode for the first time following their sequencing blood draw with evidence of CH were considered to have an incident infection. We thank the Global Science experimental Data hub Center (GSDC) and Korea Research Environment Open NETwork (KREONET) service for data computing and network provided by the Korea Institute of Science and Technology Information (KISTI).Work performed at Memorial Sloan Kettering Cancer Center was supported in part by the Cancer Center Support Grant (grant no. Of these patients, 1,626 were tested for SARS-CoV-2 (the virus that causes Covid-19) RNA between March 1st 2020 and July 1st 2020; 403 (24.8%) individuals tested positive for SARS-CoV-2 (Methods and Table 1). CH was significantly (FDR-corrected p-value<0.10) associated with the onset of two infection subclasses: Clostridium difficile infection (HR=2.0, 95% CI: 1.2-3.3, p=6103) and Streptococcus/Enterococcus infection (HR=1.5, 95% CI=1.1-2.1, p=5103).
L.A.D. Association between CH and risk of infection in solid tumor patients. Models were adjusted for age, gender, race, smoking, diabetes, cardiovascular disease, COPD/asthma, cancer primary site (if history of malignancy), exposure to cytotoxic cancer therapy for the MSK and Korea Consortia. M.F.B is on the advisory board for Roche and recieves research support from Illumina. All authors contributed to the writing of the manuscript and approved it for submission. B) Association between CH subtype defined by putative driver status and risk of Clostridium Difficle and Streptococcus/Enterococcus infection using cox proportional hazards regression. In summary, we show in cancer and non-cancer patients that CH is associated with increased Covid-19 severity. Summary statistics for a fixed effects meta-analysis are shown. The association between CH and Clostridium difficile infection was significant for mutations with a VAF of >5% (OR=2.5, 95% CI=1.4-4.6, p=0.002) but not mutations with a VAF of 2-5% (OR=1.6, 95% CI=0.8-3.1, p=0.17). The date of blood draw (used for MSK-IMPACT sequencing) served as the onset date for this time-to-event analysis; the end-date was the date of billing code entry for the infectious disease subtype phecode, death or last follow-up, whichever came first. Moreover, systemic infections and the resultant inflammatory signals can lead to increased clonal fitness of TET2 mutant cells and clonal expansion10,17,18. For Insertions and deletions in-house InDel caller was used26. Following the 10:1 rule regarding the number of covariates in a multivariable model in proportion to the number of events16, we excluded infection subclasses populated with less than 80 individuals. Single nucleotide variants (SNVs) were called using Mutect and VarDict. is on the supervisory board of Qiagen and is a scientific advisor to Loxo, Imago, C4 Therapeutics and Isoplexis which include equity interest. The mutational events that drive CH overlap with known drivers of hematologic malignancies. We used multivariable logistic regression to evaluate for an association between clonal hematopoiesis and Covid-19 severity adjusting for age (measured as a continuous variable), gender, race, smoking history and co-existing medical comorbidities including diabetes, COPD/asthma and cardiovascular disease all classified as per Table 1. All NGS libraries were prepared using the Agilent SureSelect XT HS and XT Low input enzymatic fragmentation kit. This was done separately for the MSK and KoCH cohorts due to limitations of data sharing. Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence, Age-Related Clonal Hematopoiesis Associated with Adverse Outcomes, Prediction of acute myeloid leukaemia risk in healthy individuals, Somatic mutations precede acute myeloid leukemia years before diagnosis, Genetic Interleukin 6 Signaling Deficiency Attenuates Cardiovascular Risk in Clonal Hematopoiesis, Inherited causes of clonal haematopoiesis in 97,691 whole genomes, An inflammatory cytokine signature predicts COVID-19 severity and survival, Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study, Tet2-Mediated Clonal Hematopoiesis Accelerates Heart Failure Through a Mechanism Involving the IL-1/NLRP3 Inflammasome, Inhibition of Inflammatory Signaling in Tet2 Mutant Preleukemic Cells Mitigates Stress-Induced Abnormalities and Clonal Hematopoiesis, Clonal hematopoiesis, with and without candidate driver mutations, is common in the elderly, Synonymous mutations reveal genome-wide driver mutation rates in healthy tissues, Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations, Chromosomal alterations among age-related haematopoietic clones in Japan, Identification of Clonal Hematopoiesis Mutations in Solid Tumor Patients Undergoing Unpaired Next-Generation Sequencing Assays, Clonal hematopoiesis and risk for atherosclerotic cardiovascular disease, Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host, Antibiotic treatment ameliorates Ten-eleven translocation 2 (TET2) loss-of-function associated hematological malignancies, Chemotherapy and COVID-19 Outcomes in Patients With Cancer, Clinical Characteristics of Coronavirus Disease 2019 in China, Coronavirus Disease 2019 (COVID-19) in Italy, Factors associated with hospital admission and critical illness among 5279 people with coronavirus disease 2019 in New York City: prospective cohort study, Clinical Course and Outcomes of 3,060 Patients with Coronavirus Disease 2019 in Korea, January-May 2020, Cancer therapy shapes the fitness landscape of clonal hematopoiesis, Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation, NPM1 as a potential therapeutic target for atypical teratoid/rhabdoid tumors, Endocrinology (including Diabetes Mellitus and Metabolic Disease), Intensive Care and Critical Care Medicine, Rehabilitation Medicine and Physical Therapy. Variant calling was performed using SNver(v0.4.1), LoFreq(v0.6.1), GATK UnifiedGenotyper(v2.3.9) for SNVs. The criterion for measuring COVID-19 severity was hypoxia, which has oxygen saturation below 94% and requires supplemental oxygen of 1L or more. We used multivariable logistic regression adjusting for covariates including age, smoking, prior Covid-19 related comorbidities, and prior cancer treatment to determine the association between severe Covid-19 and CH in each population. For both cohorts, the primary outcome was severe Covid-19 infection, defined as the presence of hypoxia requiring supplemental oxygen (oxygen device >1 L or hypoxia <94%). We annotated variants as oncogenic if they fulfilled any of the following criteria: 1) truncating variants in NF1, DNMT3A, TET2, IKZF1, RAD21, WT1, KMT2D, SH2B3, TP53, CEBPA, ASXL1, RUNX1, BCOR, KDM6A, STAG2, PHF6, KMT2C, PPM1D, ATM, ARID1A, ARID2, ASXL2, CHEK2, CREBBP, ETV6, EZH2, FBXW7, MGA, MPL, RB1, SETD2, SUZ12, ZRSR2 or in CALR exon 9; 2) any truncating mutations (nonsense, essential splice site or frameshift indel) in known tumor suppressor genes as per the Cancer Gene Census, OncoKB, or the scientific literature; 3) translation start site mutations in SH2B3; 4) TERT promoter mutations; 5) FLT3-ITDs; 6) in-frame indels in CALR, CEBPA, CHEK2, ETV6, EZH2; 7) any variant occurring in the COSMIC haematopoietic and lymphoid category greater than or equal to 10 times; 8) any variant reported as somatic at least 20 times in COSMIC; 9) any variant noted as potentially oncogenic in an in-house dataset of 7,000 individuals with myeloid neoplasm greater than or equal to 5 times; 10) any loci (defined by the amino acid location) reported as having at least 5 missense mutations and at least one exact mutational match in TopMed6. Clonal expansions characterized by non-driver mutational events could be facilitated by multiple mechanisms. Subjects who had a hematologic malignancy diagnosed after MSK-IMPACT testing or who had an active hematologic malignancy at the time of blood draw were excluded. Shown are the results from logistic regression adjusted for age, gender, race, smoking, diabetes, cardiovascular disease, COPD/asthma, cancer primary site (if history of malignancy), exposure to cytotoxic cancer therapy for the MSK and KoCH. Overall, CH was observed in 35% of Covid-19 positive cases at MSK and 21% in KoCH. For example, mutations in TET2 result in heightened secretion of several cytokines including IL-1/IL-6 signaling that may partially explain the increased risk of cardiovascular disease5,9,16. The sequencing test utilizes genomic DNA extracted from formalin fixed paraffin embedded (FFPE) tumor tissue as well as matched patient blood samples. received honoraria from Illumina. Many classes of genetic alterations, such as copy number events (CNVs), structural variants, non-coding, and epigenetic changes, are not detectable using the targeted panels included in this study. Laboratory-confirmed patients with Covid-19 between January and April 2020 in four tertiary hospitals in Republic of Korea were approached for consent to this study. CH was significantly associated with risk of Clostridium Difficile (HR=2.0, 95% CI: 1.2-3.3, p=6103) and Streptococcus/Enterococcus infections (HR=1.5, 95% CI=1.1-2.1, p=5103). All models were adjusted for age, gender, race, smoking, diabetes, cardiovascular disease, COPD/asthma, cancer primary site (if history of malignancy), exposure to cytotoxic cancer therapy. For solid tumor patients at MSK we also adjusted for primary tumor site (thoracic or non-thoracic cancer) and receipt of cytotoxic chemotherapy before and after IMPACT blood draw. We further explored the relationship between CH and risk of other infections in 14,211 solid tumor patients at MSK. Accumulation of mutations can lead to cancer or cardiovascular disease, attracting attention to it as an important biomarker for predicting patients prognosis. Accuracy of populated information was manually checked in the EMR by three independent physicians (K.B, M.F, A.S). In particular, patients with clonal hematopoiesis without cancer-causing mutations had 2.01 times higher risk of severe COVID-19. Seoul National University Hospital (SNUH) Infectious Diseases Department Professor Kim Nam Joong and his team (Professor Koh Youngil, Department of Hematology and Oncology) announced on the 29th Oct 2021 that if a patient with clonal hematopoiesis is infected with COVID-19, the risk of getting severe is twice as high. In the MSK cohort, CH was observed in 51% and 30% of patients with severe versus non-severe Covid-19, respectively (adjusted OR: 1.85, 95% CI 1.10-3.12, Figure 1). The hematopoietic system is a key regulator of inflammation and immunity. Given the number of model covariates, we limited the analysis to 32 infection subclasses that affected at least 80 individuals (see Methods).
Dr Im Hogyune of Genome Opinion Inc, who was in charge of genetic information analysis in this study, said, Genome Opinion Inc is studying the effects of clonal hematopoiesis on various diseases and developing clonal hematopoiesis diagnostic technology. He also added, We will focus on research and development so that this technology can lead not only to diagnosis but also methods of treatment., [Picture] From left: Prof Kim Nam Joong & Professor Koh Youngil.
The full statistical rationale is further described in the Methods section. Demographics, smoking history, exposure to oncologic therapy and primary tumor site were extracted from the electronic health record. The first cohort was composed of patients with solid tumors treated at Memorial Sloan Kettering Cancer Center (MSK) with blood previously sequenced using MSK-IMPACT, a previously validated targeted gene panel capturing all commonly mutated CH-associated genes (Supplementary Table 1)24. The minimal clinical and genetic data frame used to generate all analyses presented in this paper are available by request and will be made publicly available upon acceptance to a peer-reviewed journal. Billing codes were highly accurate in identifying the presence of the respective infectious disease (concordance >95%). ), European Hematology Association (E.P. E.P receives research funding from Celgene.D.G and has received honoraria for speaking and scientific advisory engagements with Celgene, Prime Oncology, Novartis, Illumina and Kyowa Hakko Kirin and is a co-founder in Isabl Technologies. The mean depth of coverage of samples was higher than 800x. The severity of Covid-19 is also associated with advanced age, cardiovascular and malignant comorbidities, and elevated circulating IL-6 levels; features which are seen with age-associated CH1923. Preprints posted online allow authors to receive rapid feedback and the entire scientific community can appraise the work for themselves and respond appropriately.
All called mutations were genotyped in the patient-matched tumor sample. Patient Bill of Rights and Responsibilities, Seoul National University Hospital opens outpatient department of clinical genomic medicine, Hepatitis B: the sooner the antiviral treatment, the better. We used Cox proportional hazards regression to estimate the hazard ratio for risk of infection among those with CH compared to CH negative individuals. This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. The majority of CH mutations were classified as PD-CH (52% in the MSK cohort and 67% in the KoCH dataset). - Analysis of 525 COVID patients registered with domestic and overseas clonal hematopoietic consortium, - Cancer biomarker clonal hematopoiesis can be used as a predictive index for the severity of COVID-19. Variant calling for each blood sample was performed unmatched, using a pooled control sample of DNA from 10 unrelated individuals as a comparator. For example, chromosomal aneuploidies result in a predisposition for lymphoid fate specification and transformation13,14 while point mutations in DNMT3A result in increased myeloid differentiation6,15. This will need to be further studied in larger cohorts. K.L.B, R.P, T.G, A.S, M.B,Y.K,H.I,C.S, A.Z led the generation and analysis of sequencing data. The criterion for measuring COVID-19 severity was hypoxia, which has oxygen saturation below 94% and requires supplemental oxygen of 1L or more. The terms of all of these arrangements are being managed by Johns Hopkins and Memorial Sloan Kettering in accordance with their conflict of interest policies. There was not a statistically-significant association between PD-CH and severe Covid-19 infection (OR=1.15, 95% CI=0.61-2.02, p=0.77: Extend ed Data Figure 1). Among 515 individuals with Covid-19 from Memorial Sloan Kettering (MSK) and the Korean Clonal Hematopoiesis (KoCH) consortia, we found that CH was associated with severe Covid-19 outcomes (OR=1.9, 95%=1.2-2.9, p=0.01). K.L.B, M.F, J.J., A.S., Y.K, H.I, C.S, S.K,H.S,A.Z, performed statistical analyses and/or participated in data interpretation. ), and the Cancer Colorectal Cancer Dream Team Translational Research Grant (SU2C-AACR-DT22-17 to L.D.). Mutations were annotated with VEP(version 86) and OncoKb. Those who were billed for an ICD9/10 code within the phecode prior to blood draw were removed from the analysis of that phecode. A.Z. He has received honoraria from Roche, Lilly and Amgen for invited lectures and from Gilead for grant reviews. Heterogeneity also exists across CH phenotypes by driver gene in regards to its impact on inflammatory signaling6. Those comments are posted alongside the preprints for anyone to read them and serve as a post publication assessment. MSK-IMPACT contains most of the commonly reported CH genes with the exception that earlier versions of the panel did not contain PPM1D or SRSF2. We then performed a fixed-effects meta-analysis to estimate the association in the overall population. Patients with a maximum CH variant allele frequency (VAF) of >5% showed a significant association with severe Covid-19 (OR=1.9, 95% CI=1.0-3.4, p=0.04). Blood-derived DNA was sequenced using a custom panel of 89 genes frequently mutated in CH. All the statistical analyses were performed with the use of the R statistical package (www.r-project.org). MSK-IMPACT is validated and approved for clinical use by New York State Department of Health Clinical Laboratory Evaluation Program. Acquired mutations that lead to clonal expansion are common in the normal aging hematopoietic system (clonal hematopoiesis, or CH), yet are known to alter stem/progenitor and lymphoid function and response to environmental stressors, including systemic infections5,6,9,10. Clonal hematopoiesis refers to a condition in which acquired mutations occur in hematopoietic stem cells responsible for blood production. Using a previously established phenome-wide-association study (Phe-WAS) methodology25, we mapped patient ICD-9 and ICD-10 billing codes to categories of infectious disease. They should not be relied on to guide clinical practice or health-related behavior and should not be reported in news media as established information. Pooled libraries were sequenced on an Illumina HiSeq 2500 with 2100bp paired-end reads. He receives research support from and consulted for Celgene and Roche and has consulted for Lilly, Janssen, Astellas, Morphosys and Novartis.