Mosaic Chromosomal Alterations Research Articles

Determinants of mosaic chromosomal alteration fitness

Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate as PACER scores for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our mCA fitness estimates, derived by aggregating per-individual PACER scores, were correlated (R2 = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using population-level distributions of clonal fraction. Among individuals with JAK2 V617F clonal hematopoiesis of indeterminate potential or mCAs affecting the JAK2 gene on chromosome 9, PACER score was strongly correlated with erythrocyte count. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified a TCL1A locus variant associated with mCA clonal expansion rate, with suggestive variants in NRIP1 and TERT.

Abstract 4849: Mosaic chromosomal alterations in a prospective cohort of Mexican Americans for cancer risk and genetic insights

Abstract Introduction: In this study, we aim to explore mosaic chromosomal alterations (mCA) and their implications in cancer risk among Mexican Americans (MA) - an expanding yet historically underrepresented ethnic minority in the U.S. In addition, we propose to develop a novel method that identifies high mutant cell fraction (MCF) copy-neutral Loss of heterozygosity (cn-LOH). At sufficiently high MCF, these will look like runs of homozygosity (ROH) and may be missed by current mCA detection techniques that rely on identified germline heterozygote genotypes. Our preliminary findings revealed frequent and widespread homozygosity across the genome, predominantly in short regions (<10 Mb), although some exceeded 100 Mb. Our objective is to advance mCA detection techniques, differentiating cn-LOH from ROH, to deepen our understanding of mCA. Methods: We analyzed SNP array data from blood and saliva samples of 1657 individuals, focusing on cancer and chronic disease risk ages, from the Mano a Mano Mexican American Cohort Study. We applied hapLOH and MoChA, both haplotype-based methods, to detect mCA. To identify high-MCF cn-LOH, we first scanned for observed ROH using PLINK. Separately, we develop a statistical framework through simulations to differentiate high-MCF cn-LOH from ROH. We considered multiple methods; initially, we built a statistical framework using a hypothesis-testing approach (H0: ROH; H1: cn-LOH), where we compared the “B allele” frequency information within observed ROH. To split this information and obtain our groups, we used population genetic principles. Secondly, we classified our events, calculating the likelihood ratio of our statistical hypotheses. Finally, we explored a haplotype-based imputation approach that leverages flanking diploid region information. Results: We identified numerous mCA, predominantly in individuals without cancer. Simulations showed effective classification in larger homozygosity regions (>10 Mb), guiding our methodological focus on detecting shorter high-MCF regions. Not surprisingly, extremely high MCFs (0.99-1) presented challenges in accurate identification. Conclusion and Future Directions: To improve our mCA results description, we will thoroughly characterize and study their association with cancer phenotypes and environmental exposures. We are in the process of genotyping the entire cohort, which consists of over 25,000 participants. To date, our cohort includes 909 cancer cases, of which 262 are hematological malignancies. We sought to design a unique method that differentiates high-MCF cn-LOH from observed ROH, improving current mCA discovery. Our focus is on small regions as they provide limited information to infer event types. Our next step is to characterize and validate our results, especially in pathologically normal samples, as a way of identifying potential biomarkers of interest. Citation Format: Jessica Valdebenito, Justin Wong, Dahwei Chang, Henry Gomez, Kevin T Nead, Yasminka Jakubek, Paul Scheet. Mosaic chromosomal alterations in a prospective cohort of Mexican Americans for cancer risk and genetic insights [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4849.

Abstract 3954: Increased mosaic chromosomal alterations among survivors of childhood acute myeloid leukemia

Abstract Background: We previously characterized point mutations of clonal hematopoiesis (CH) including single nucleotide variants or small insertion/deletions residing in a set of cancer-related genes (e.g., DNMT3A and TET2), and found that CH point mutations occurred at a much higher prevalence in childhood cancer survivors (CCS) than in age-sex-race matched community controls. However, mosaic chromosomal alterations (mCAs), another form of CH with megabase-scale structural alterations (copy gain, copy loss and copy-neutral loss of heterozygosity), have not been examined. Methods: Detection of mCAs was performed on whole-genome sequencing (WGS, 30X) data from 5-year CCS with the Mosaic Chromosomal Alterations (MoChA) caller which utilizes phased genotypes, coverage, and B allele frequency (BAF) at heterozygous sites (HETS). We implemented the pipeline established by the TOPMed consortium to detect low mutant cell fractions (CF ≥1%). Variant filtration criteria: minor allele frequency <1%, the read depth of either allele <5, and only one variant retained in each 1Kb window. Called mCA filtration criteria: <100 HETS; lod score <5; relative coverage >2.9 or BAF deviation >0.16 and relative coverage >2.5. Autosomal mCAs (CF ≥1%, HETS >100 and length >1Mb) retained. Multivariable Cox models evaluated the association between mCAs and specific late-effects including all-cause mortality, obesity, myocardial infarction (MI) or cardiomyopathy (CMP); multivariable logistic models evaluated the association between mCAs and childhood cancer diagnoses. All models were adjusted for age, sex and therapeutic exposures. Results: In our evaluation of 4,330 CCS (median age at blood draw: 26.8 years) and 433 controls (33.6 years) with WGS data from the St. Jude Lifetime Cohort, the prevalence of mCAs was slightly higher among CCS than community controls (4.83% vs. 4.16%). Among CCS, mCAs were associated with therapeutic exposures (alkylating agents: odds ratio [OR]=1.48, 95% CI=1.09-2.00; antimetabolites: 1.53, 1.02-2.31; corticosteroids: 0.60, 0.40-0.91). In contrast to recent mCA studies in the general population, we observed no co-occurrence with CH point mutations, and no associations with late-effects including all-cause mortality, obesity, MI or CMP. Interestingly, mCAs were significantly associated with the primary diagnosis of acute myeloid leukemia (AML, OR=2.86, 95% CI=1.63-5.01). Furthermore, this finding was replicated in 2898 5-year survivors from the Childhood Cancer Survivor Study (OR=3.77, 95% CI=1.94-7.33). Conclusion: mCAs were not associated with age-related morbidities and mortality among CCS. However, we identified a striking association between mCAs and previous diagnoses of AML independent of treatment exposures. If validated among AML patients at the time of diagnosis, mCAs, which reflect the underlying genome instability, may serve as a diagnostic biomarker for AML. Citation Format: Xijun Zhang, Na Qin, Qian Dong, Cheng Chen, John Easton, Heather Mulder, Xiang Chen, Kyla Shelton, Cindy Im, Yutaka Yasui, Greg Armstrong, Kirsten K. Ness, Melissa M. Hudson, Paul Auer, Jinghui Zhang, Zhaoming Wang. Increased mosaic chromosomal alterations among survivors of childhood acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3954.

Abstract 2205: Modifiable risk factors are associated with clonal hematopoiesis

Abstract Observational studies have implicated modifiable factors like smoking, alcohol intake, physical activity (PA), and sleep to cancer risk. Clonal hematopoiesis (CH), marked by clonal expansions of mutated hematopoietic progenitors with mosaic chromosomal alterations (mCAs) or clonal hematopoiesis of indeterminate potential (CHIP), has been associated with the risk of serval cancers and may shed light the interplay between these factors and early preneoplastic hematopoietic expansion.Leveraging genotyping array and whole-exome sequencing data of leukocyte-derived DNA from 485,028 participants without hematologic malignancies in the UK Biobank (UKBB), we performed genome-wide characterization of two common forms of CH—mCAs and CHIP. To assess associations between social deprivation, self-reported modifiable risk factors, and CH risk, we employed multivariable logistic regression models adjusted for potential confounders including age, sex, smoking history, and genetic ancestry.We identified 11,826 (2.4%) individuals with autosomal mosaic chromosomal alterations (auto mCAs), 15,499 (3.2%) with loss of the X chromosome (mLOX), 43,044 (8.8%) with loss of the Y chromosome (mLOY) and 22,508 (4.6%) with CHIP. Individuals with any CH subtype were on average older than CH-free individuals (p < 9.11 × 10−52). Multivariable models identified a significant negative association between mLOY and social deprivation in England (1 SD change in score: OR = 0.968 [0.956-0.980], p = 4.88 × 10−7), suggesting modifiable risk factors could influence risk of mLOY. We observed a positive association with ever smoking and CH, which decreased with increased years since smoking cessation. Current smokers were at higher risk for auto mCAs (Odds ratio (OR) = 1.23, 95% Confidence Interval (CI):[1.16-1.31], P-value (p) = 2.63 × 10−11), mLOY (OR = 2.25, 95%CI: [2.17-2.33], p < 9.11 × 10−52), and CHIP (OR = 1.40,, 95%CI: [1.34-1.47] p < 9.11 × 10−52); and former smokers also exhibited significant associations for mLOY (OR = 1.16, 95%CI: [1.13-1.19], p = 2.97 × 10−32) and CHIP (OR = 1.11, 95%CI: [1.08-1.15], p = 2.75 × 10−13). Alcohol consumption was associated with a significant increase in the risk of mLOX in heavy drinkers (>2-3 drinks/day) compared to non-drinkers (OR = 1.16, 95%CI: [1.09-1.24], p = 1.21 × 10−5). Moderate and high PA levels (categorized as level 2 and 3 based on total activity), were positively associated with increased mLOY frequency (moderate: OR = 1.05, 95%CI: [1.02-1.08], p = 8.6 × 10−2, high: OR = 1.06, 95%CI: [1.03-1.08], p = 1.6 × 10−3). We observed no evidence for an association between sleep patterns and CH.Our investigation in a large cohort identified associations between CH and social deprivation, smoking, alcohol consumption and PA. As CH is an intermediate marker for hematologic cancer risk, our findings imply that modifiable exposures may contribute to hematologic cancer risk through clonal mechanisms. Citation Format: Corey D. Young, Aubrey K. Hubbard, Pedro Saint-Maurice, Irenaeus Chan, Kelly L. Bolton, Stephen J. Chanock, Charles Matthews, Steven C. Moore, Erikka Loftfield, Yin Cao, Mitchell J. Machiela, Duc Tran. Modifiable risk factors are associated with clonal hematopoiesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2205.

Abstract 7345: Double-strand break inference from mosaic chromosomal alterations

Abstract Double-strand breaks (DSBs) can cause alterations and rearrangements in chromosomes leading to large structural mutations. There have been previous efforts to identify DSBs in tumors and utilize these as a measure of homologous repair deficiency and response to therapy. In contrast, DSBs have not been well characterized in non-tumor human tissues. To address this void, we explore the distribution of DSBs in hematopoietic stem cells (HSCs) through the analyses of mosaic chromosomal alteration (mCA) breakpoints. Specifically, this work explores the relationship between the likelihood of DSB occurrences and the chromosomes on which they occur. Using data from the UK Biobank, mCA breakpoints were labeled as either DSBs or nonDSBs by proximity to telomeres and centromeres. mCA calls from the UK Biobank were obtained from Loh et al 2020. The START_MB_RANGE and END_MB_RANGE fields were treated as two separate breakpoint events for each entry in the data. Each of these breakpoint ranges was checked to see if it was close to either of the telomeres or to the centromere. Those falling within one Mb were categorized as mCA breakpoints that were likely not a result of DSBs, but rather missegregation of chromosomes or chromosome arms. Ranges that met either of these conditions were labeled “nonDSB” while ranges that did not were labeled “DSB.” These labeled data were processed in R using the Hmisc package. The 1-alpha binomial probability was calculated for the total number of DSBs versus the total number of breakpoint events. The point estimate for each chromosome was plotted along with the upper and lower confidence intervals. This work investigates the properties of DSBs. It is important to note that the observed putative DSBs are not representative of the frequency of DSBs in HSCs, since the resulting mutations can have different impacts on cellular fitness. This point is highlighted by our finding of increased putative DSBs on chromosome 13, as copy number changes involving the 13q14 locus are well documented drivers of chronic lymphocytic leukemia. In this investigation we observe that the proportion of putative DSBs is not correlated with chromosome length (p = 0.2). This result is likely due to the differential fitness effect of mCAs. However, it may also reflect differences in the likelihood of DSBs across the genome. We are currently working on methods from Machine Learning to further understand if there are genetic features which can predict DSBs which give rise to mCAs in HSCs. Citation Format: Abraham Dutch, Cody Bumgardner, Yasminka Jakubek. Double-strand break inference from mosaic chromosomal alterations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7345.

Abstract 3433: Characterization of co-occurring clonal hematopoiesis to identify high risk clones associated with hematologic cancer risk

Abstract Clonal hematopoiesis (CH) is the age-related clonal expansion of hematopoietic cells as a result of acquired mutations in driver genes, commonly referred to as clonal hematopoiesis of indeterminate potential (CHIP), or due to large-scale mosaic chromosomal alterations (mCAs). While the type and genomic location of CH exhibits varying associations with hematological parameters as well as lymphoid and myeloid malignancy risk, few studies have examined the co-occurrence of CH types. We characterized the frequency of co-occurring CH and examined the association of co-occurring CH with various cancer-related phenotypes to identify potential high-risk clones associated with hematologic cancer risk. We analyzed sequencing and genotyping array data from 453,807 participants in the UK Biobank to detect CHIP and mCAs. In total, 83,240 (18.3%) individuals had at least one detectable type of CH, with increasing age strongly associated with increasing frequency of CH (P < 2 × 10−16). The most common type of CH was mCAs (N= 67,081 (14.7%)), with mosaic loss of the Y (mLOY) and X (mLOX) chromosomes being most frequently observed in males and females, respectively. We noted inverse associations between mLOY or mLOX with autosomal mCAs, but positive associations between some autosomal mCAs (e.g., chr3 and chr18 mCAs). CHIP was detected in 20,354 (4.5%) individuals, with mutations in DNMT3A, TET2, and ASXL1 most common. Similar to mCAs, some forms of CHIP were inversely associated (e.g., DNMT3A CHIP with most other CHIP mutations) while others displayed positive associations (e.g., JAK2 CHIP with NFE2 CHIP), suggesting both instances of mutual exclusivity as well as cooperation. We likewise noted several instances of CHIP and mCAs co-occurring (e.g., MYD88 and chr18 mCAs) and overlapping (e.g., JAK2 and 9p24 mCAs) more frequently than expected. Compared to those with no CH, participants with CH had notable alterations in blood cell counts, leukocyte telomere length (LTL), and elevated hematologic cancer risk even after adjusting for age, sex, smoking, and genetic ancestry. Furthermore, co-occurring CH had more pronounced associations, with the greatest alterations and hematologic cancer risk generally noted in participants with overlapping CHIP and mCAs (e.g., MYD88 and 3p22 mCAs). These findings highlight substantial enrichment in CH co-occurrences, particularly in the positional overlap of CHIP and mCAs, and indicate an increased risk of hematological malignancies when CH types overlap (HR = 29.5, 95% CI [24.0, 36.3], P < 2 × 10−16). Overall, this study details the landscape of co-occurring CH and nominates high risk co-occurrences with strong implications for future hematological malignancy risk. Citation Format: Kara M. Barnao, Aubrey K. Hubbard, Weiyin Zhou, Irenaeus Chan, Duc Tran, Yin Cao, Stephen J. Chanock, Kelly L. Bolton, Mitchell J. Machiela. Characterization of co-occurring clonal hematopoiesis to identify high risk clones associated with hematologic cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3433.

Tumor Predisposing Post-Zygotic Chromosomal Alterations in Bladder Cancer-Insights from Histologically Normal Urothelium.

Bladder urothelial carcinoma (BLCA) is the 10th most common cancer with a low survival rate and strong male bias. We studied the field cancerization in BLCA using multi-sample- and multi-tissue-per-patient protocol for sensitive detection of autosomal post-zygotic chromosomal alterations and loss of chromosome Y (LOY). We analysed 277 samples of histologically normal urothelium, 145 tumors and 63 blood samples from 52 males and 15 females, using the in-house adapted Mosaic Chromosomal Alterations (MoChA) pipeline. This approach allows identification of the early aberrations in urothelium from BLCA patients. Overall, 45% of patients exhibited at least one alteration in at least one normal urothelium sample. Recurrence analysis resulted in 16 hotspots composed of either gains and copy number neutral loss of heterozygosity (CN-LOH) or deletions and CN-LOH, encompassing well-known and new BLCA cancer driver genes. Conservative assessment of LOY showed 29%, 27% and 18% of LOY-cells in tumors, blood and normal urothelium, respectively. We provide a proof of principle that our approach can characterize the earliest alterations preconditioning normal urothelium to BLCA development. Frequent LOY in blood and urothelium-derived tissues suggest its involvement in BLCA.

Driver mutation zygosity is a critical factor in predicting clonal hematopoiesis transformation risk

Clonal hematopoiesis (CH) can be caused by either single gene mutations (eg point mutations in JAK2 causing CHIP) or mosaic chromosomal alterations (e.g., loss of heterozygosity at chromosome 9p). CH is associated with a significantly increased risk of hematologic malignancies. However, the absolute rate of transformation on an annualized basis is low. Improved prognostication of transformation risk is urgently needed for routine clinical practice. We hypothesized that the co-occurrence of CHIP and mCAs at the same locus (e.g., transforming a heterozygous JAK2 CHIP mutation into a homozygous mutation through concomitant loss of heterozygosity at chromosome 9) might have important prognostic implications for malignancy transformation risk. We tested this hypothesis using our discovery cohort, the UK Biobank (n = 451,180), and subsequently validated it in the BioVU cohort (n = 91,335). We find that individuals with a concurrent somatic mutation and mCA were at significantly increased risk of hematologic malignancy (for example, In BioVU cohort incidence of hematologic malignancies is higher in individuals with co-occurring JAK2 V617F and 9p CN-LOH; HR = 54.76, 95% CI = 33.92–88.41, P < 0.001 vs. JAK2 V617F alone; HR = 44.05, 95% CI = 35.06–55.35, P < 0.001). Currently, the ‘zygosity’ of the CHIP mutation is not routinely reported in clinical assays or considered in prognosticating CHIP transformation risk. Based on these observations, we propose that clinical reports should include ‘zygosity’ status of CHIP mutations and that future prognostication systems should take mutation ‘zygosity’ into account.

Epidemiological distribution of mosaic loss of chromosome Y in adult men in 10 areas in China and its prospective association with lung cancer

Objective: To detect the prevalence of mosaic loss of chromosome Y in adult men in ten study areas in China, describe the epidemiological distribution of mosaic loss of chromosome Y (mLOY) carriers and assess its prospective association with lung cancer. Methods: Based on the data from baseline survey, genetic analysis and follow-up (as of December 31, 2018) from China Kadoorie Biobank, we used Mosaic Chromosomal Alterations pipeline to detect mLOY carriers in 10 areas in China and described the epidemiological characteristics of mLOY carriers in adult men, including age, area distribution, lifestyle and disease history. We used multivariate logistic regression model to identify the potential relevant factor of mLOY. Cox proportional hazard regression model was fitted to assess the prospective association of mLOY with lung cancer. Stratification analysis were conducted to evaluate the potential modification effects of smoking and age. We also conducted mediation analysis to assess the mediating effect of mLOY in the association between smoking and lung cancer. Results: A total of 42 859 adult men were included in our analysis, in whom 2 458 mLOY carriers were detected (5.7%). The detection rate increased with age (P<0.05). The detection rate was higher in urban area (7.3%±0.2%) than that in rural area (4.7%±0.1%). The results of logistic regression analysis indicated that smoking might be a risk factor for the detection of mLOY (OR=1.49, 95%CI:1.36-1.64). After follow-up for average 11.1 years, 1 041 lung cancer cases were observed. The prospective analysis showed that mLOY carriers had an increased risk for lung cancer by 24% compared with non-mLOY carriers (HR=1.24, 95%CI:1.01-1.52) and expanded mLOY carriers (mLOY cell proportion ≥10%) had an increased risk for lung cancer by 50% (HR=1.50, 95%CI:1.13-2.00). Stratification analysis showed no modification effects of smoking and age in the association between mLOY and lung cancer (interaction P>0.05). Mediation analysis showed that mLOY could be a mediating factor in the association between smoking and lung cancer, the estimated effect was 0.09 (0.01-0.17). Conclusions: There were significant differences in the detection rate of mLOY in adult men with different social-economic characteristics and lifestyles in ten areas in China. Besides, mLOY carriers, especially expanded mLOY carriers, had increased risk for lung cancer and mLOY might be a mediating factor in the association between smoking and lung cancer.

Mosaic chromosomal alterations in peripheral blood leukocytes of children in sub-Saharan Africa

In high-income countries, mosaic chromosomal alterations in peripheral blood leukocytes are associated with an elevated risk of adverse health outcomes, including hematologic malignancies. We investigate mosaic chromosomal alterations in sub-Saharan Africa among 931 children with Burkitt lymphoma, an aggressive lymphoma commonly characterized by immunoglobulin-MYC chromosomal rearrangements, 3822 Burkitt lymphoma-free children, and 674 cancer-free men from Ghana. We find autosomal and X chromosome mosaic chromosomal alterations in 3.4% and 1.7% of Burkitt lymphoma-free children, and 8.4% and 3.7% of children with Burkitt lymphoma (P-values = 5.7×10−11 and 3.74×10−2, respectively). Autosomal mosaic chromosomal alterations are detected in 14.0% of Ghanaian men and increase with age. Mosaic chromosomal alterations in Burkitt lymphoma cases include gains on chromosomes 1q and 8, the latter spanning MYC, while mosaic chromosomal alterations in Burkitt lymphoma-free children include copy-neutral loss of heterozygosity on chromosomes 10, 14, and 16. Our results highlight mosaic chromosomal alterations in sub-Saharan African populations as a promising area of research.

Mosaic Chromosomal Alterations and Monoclonal B-Cell Lymphocytosis: Relationship and Risk of Hematologic Malignancies

Background: Monoclonal B-cell lymphocytosis (MBL) is a precursor condition to chronic lymphocytic leukemia (CLL) characterized by the presence of circulating monoclonal B-cell populations in the peripheral blood of otherwise healthy individuals. MBL increases risk of several adverse clinical outcomes, including development of hematological malignancies. Mosaic chromosomal alterations (mCAs) are a form of clonal hematopoiesis which affect large segments of DNA and include gains, losses, and copy number neutral loss of heterozygosity events. mCAs can be detected from SNP-array genotyping. Prior work has suggested mCAs as a potent risk factor for hematological malignancies. However, the nature of the relationship between mCAs and MBL is unknown. We sought to determine 1) the association between mCAs and MBL and 2) their combined effect on risk of hematological malignancies, in a large, prospectively collected, and well-annotated cohort of individuals with known MBL, mCA, and clinical outcomes. Methods: We examined the prevalence of mCA in a cohort of individuals from the Mayo Clinic Biobank who were screened for MBL using a sensitive eight-color flow cytometry assay. We classified MBL by the size of the clone relative to total B-cells, with high count (HC) defined as those individuals who had a percent clonal B-cell count ≥85% out of total B-cell count and low-count (LC) otherwise. Autosomal mCAs were detected from whole blood DNA collected at the time of MBL screening using a SNP-array-based assay. The MoChA pipeline was used to identify mCA events. Logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CIs). To examine incident hematological cancers, we identified and validated all hematological cancers through medical record abstraction using the International Statistical Classification of Diseases codes. Cox regression was used to calculate hazard ratios (HR) and 95% CIs, stratified by MBL status or autosomal mCA status. All models were adjusted for age and sex. Results: We evaluated the prevalence of autosomal mCA in 3,764 individuals (792 individuals with MBL of whom 64 had HC-MBL and 2,972 without MBL). The prevalence of autosomal mCA was 7.7% ( n=288) with a median mCA cell fraction of 0.09 (range 0.01-1). Among those with and without MBL overall, the prevalence of mCA was 15.5% ( n=123) and 5.6% ( n=165), respectively (Figure 1). Compared to those without an autosomal mCA, individuals with an autosomal mCA were 2.4-fold more likely to have MBL (95% CI 1.9-3.2; P =2.0x10 -11; Figure 1). CLL-associated mCA (i.e., those commonly altered in CLL including trisomy 12 and deletion of 6q, 11q, 13q, and 17p) were present in 42 individuals, of whom 38 (90.5%) had MBL overall and 30 (71.4%) individuals had HC-MBL. Compared to those without a CLL-associated mCA, individuals with a CLL-associated mCA were 539.39-fold more likely to have HC-MBL (95% CI 190.3-1975.9; P &amp;lt;2.0x10 -16) and 6.7-fold more likely to have LC-MBL (95% CI 2.0-26.5; P =0.0031; Figure 1). Next, we evaluated the relationship between MBL and mCA with risk of developing a hematologic malignancy in 3,009 individuals with follow-up data (median 10 years). Forty-one individuals developed an incident hematological malignancy (68.3% lymphoid). When we evaluated the effect of autosomal mCA stratified by MBL status we observed elevated but non-significant risk of hematological malignancies (Figure 2). When we evaluated the effect of MBL stratified by autosomal mCA status we observed elevated and significant increased risk of developing a hematological malignancy (Figure 2). Conclusions: We found that the presence of an autosomal mCA is highly associated with having MBL. In particular, &amp;gt;90% of CLL-associated mCA carriers had MBL with ~7- and ~540-fold increased association for LC- and HC-MBL, respectively. These results suggest that almost all individuals in large biobanks with CLL-associated mCAs have undiagnosed MBL. However, not all individuals with MBL have an mCA. When evaluating risk of hematological malignancies, we found autosomal mCAs had &amp;gt;2-fold elevated but non-significant effects when stratified by MBL status while MBL remained a significant risk factor regardless of autosomal mCA status. Collectively these results support that MBL remains an important risk factor and suggests that mCAs hold potential to identify a subgroup of individuals at greater risk of developing a hematological malignancy.

Clonal Hematopoiesis Associated with Rheumatoid Arthritis

Introduction: Clonal hematopoiesis (CH) becomes common with age and can play a role in the pathophysiology of inflammatory diseases by modifying immune cell function. CH is characterized by the presence of somatic mutations in genes such as DNMT3A and TET2 (CH of indeterminate potential, CHIP), and as mosaic chromosomal alterations (mCAs). While CHIP, particularly in the context of TET2 mutations, can promote inflammation in cardiovascular diseases, the association between clonal hematopoiesis and autoimmunity has not been comprehensively studied to date. Rheumatoid arthritis (RA) is one of the most common autoimmune diseases primarily affecting joints. Seropositive RA is defined by the presence of anti-cyclic citrullinated peptide antibodies (ACPA) and/or rheumatoid factor (RF), whereas seronegative RA is a more heterogeneous inflammatory disease entity involving patients with clinical RA manifestations in the absence of ACPA and RF. Understanding of the association between CH and inflammatory processes may yield novel insights into prevention and management of autoimmune diseases. Methods: To comprehensively evaluate the association between CH and autoimmune diseases, we identified CHIP variants in whole exome sequencing (WES) data from the FINRISK study (N=10 129). We also detected mCAs and CHIP in the nationwide FinnGen study (N=340 173), where we manually identified CHIP carriers as outliers in SNP intensity plots at known CHIP loci in DNA microarray data. Only known CHIP loci with variant prevalence comparable to UK Biobank WES data and significant positive associations with age and hematological malignancies were included for downstream analyses. To further characterize the link between CHIP and RA phenotypes, we performed targeted panel sequencing of 69 myeloid driver genes in 675 RA patient blood samples (91% collected at diagnosis) and 60 healthy controls. We studied the association between CH and RA in multivariable models excluding participants with prevalent hematologic malignancies and adjusting for sex, age, smoking, and principal components of ancestry. We performed uni- and multivariable analyses to evaluate the link between CHIP and RA patient phenotypes. Results: We identified CHIP in 381 (3.8%) FINRISK participants. As expected, the prevalence of CHIP increased with age, and CHIP variants were associated with prevalent and incident hematologic malignancies. C-reactive protein values were higher in participants with CHIP (P&amp;lt;0.001). In multivariable models, CHIP status (OR 1.98, 1.13-3.45, P=0.017) was more common in participants with questionnaire-based history of RA (N=151) (Fig 1A). In the FinnGen study, CHIP carrier status was associated with prevalent autoimmune diseases (OR 1.26, 1.05-1.53, P=0.015). We validated the association between prevalent RA (N=10 990) and CHIP carrier status (N=2 393) in the FinnGen study (OR 1.58, 1.18-2.13, P=0.002) (Fig 1A). In particular, CHIP (OR 2.17, 1.40-3.36, P&amp;lt;0.001), and GNB1 variants (OR 4.71, 1.87-11.82, P=0.001) were associated with the seronegative RA, whereas DNMT3A was associated with seropositive RA (OR 1.83, 1.08-3.09, P=0.024). We observed no association between autosomal mCAs and RA. Using targeted panel sequencing, we found CHIP in 22% (146/675) of RA patients. RA patients with CHIP variants were older than those without a CHIP variant (median, 69 vs 63 years, P&amp;lt;0.001). Erythrocyte sedimentation rate (ESR) was higher in those with CHIP (median, 42.5 vs 26.0 mm/h, P=0.043). RA patients with TET2 variants were more likely to have seronegative disease compared with TET2 wild-type patients (proportion of seronegative patients, 56% vs 33%, OR 2.62; P=0.008) (Fig 1B). The association remained significant (OR 2.38, 1.14-4.96, P=0.02) when adjusting for age, sex, and smoking. Evaluation of longitudinal disease outcomes by CHIP status are currently ongoing. Conclusion: CHIP variants were more common in participants with prevalent RA in two population-level cohorts, and the association was specific to seronegative RA in the large FinnGen cohort. In newly diagnosed RA patients, TET2 mutations were more common in seronegative than in seropositive RA. While the causality and the functional basis of these observations remain to be explored in future studies, our results provide additional evidence for the association between CHIP and inflammation in various disease contexts, including autoimmune diseases.

Clonal Hematopoiesis and Venous Thromboembolism in the UK Biobank

Background: Patients with myeloid malignancies have an increased risk of thrombosis, but less is known about the risk of thrombosis in clonal hematopoiesis of indeterminate potential (CHIP). We evaluated genotype-specific associations between CHIP and both prevalent and incident venous thromboembolism (VTE) in the largest such analysis to date of the UK Biobank. Methods: We examined 425,573 individuals without a prevalent hematologic malignancy diagnosis from the UK Biobank. Whole exome sequencing and single nucleotide polymorphism array data were analyzed to identify individuals with CHIP and/or mosaic chromosomal alterations (mCA), respectively. Prevalent and incident VTE cases were ascertained with respect to the time of DNA sampling. VTE events were identified based on ICD10 codes, including but not limited to, pulmonary embolism, phlebitis/thrombophlebitis of deep veins of lower veins, portal vein thrombosis, and Budd Chiari syndrome. Median follow-up time for incident VTE was 11.8 years. Associations of CHIP and VTE were assessed using logistic regression for prevalent analyses and Cox proportional hazards for incident analyses. The association analyses were adjusted for age at the time of DNA sampling, sex, Caucasian ancestry, genetic principal components, ever smoked status, and body mass index (BMI) as covariates. Results: Prevalent VTE and CHIP: While CHIP overall was not associated with an increased risk of prevalent VTE (odds ratio (OR) 1.06; 95% CI 0.87-1.28, P= 0.56) (Figure 1), JAK2-mutant CHIP and JAK2 CHIP with loss of heterozygosity at the JAK2 locus (LOH 9p) were powerfully associated with increased risk of thrombosis, OR = 7.49 (95% CI 3.02-18.56, P=1.41e-05) and 6.74 (95% CI 1.62-28.08; P=8.71e-03). Having both CHIP and autosomal mCA was associated with a nominally increased risk of VTE (OR 1.76; 95% CI 1.02-3.06, P= 0.04). Otherwise, non- JAK2 CHIP , ASXL1 CHIP , TET2 CHIP , DNMT3A CHIP were not associated with increased prevalent VTE, regardless of clone size. Incident VTE and CHIP: CHIP was modestly associated with incident VTE with a hazard ratio of 1.15 (1.03-1.28; P=0.01), and CHIP with a larger clone size (VAF &amp;gt; 10%) was associated with a hazard ratio of 1.22 (95% CI 1.08-1.39; P= 0.001) (Figure 2). Consistent with our analysis of prevalent VTE, JAK2-CHIP and JAK2-CHIP with LOH 9p were strongly associated with incident VTE with hazard ratios of 3.76 (95% CI 1.79-7.9, P= 0.0004) and 4.89 (95% CI 1.84-13.04; P=0.0015). Other associations, including overall CHIP, CHIP with VAF &amp;gt;10%, CHIP together with autosomal mCA, autosomal mCA, non- JAK2 CHIP, TET2 CHIP with VAF &amp;gt;10%, showed modest increased hazard ratios between 1 and 2. Conclusions: In this study of risk of thrombosis in the UK Biobank, CHIP was not significantly associated with prevalent VTE and was modestly associated incident VTE. Among CHIP genotypes analyzed, only JAK2 mutations were significantly associated with both prevalent and incident VTE risk (OR 7.49 and HR 3.76, respectively). JAK2-mutant CHIP may be an undetected contributor to cases of VTE and may have therapeutic implications.

Clonal Hematopoiesis in Cartilage-Hair Hypoplasia

Background: Cartilage-hair hypoplasia (CHH) is an autosomal recessive disorder characterized by short stature, hypotrichosis, combined immunodeficiency, and macrocytic anemia. CHH is caused by germline mutations in the RMRP gene encoding the RNA component of the mitochondrial RNA processing endoribonuclease. CHH is heavily enriched in the Finnish (1 in 23000 births) and the Amish (1 in 1340 births) populations. Transient macrocytic anemia is common in children with CHH, whereas severe hypoplastic macrocytic anemia is only present in 10% of pediatric CHH patients and can be treated with allogeneic hematopoietic stem cell transplantation (HSCT). The mechanism behind hypoplastic anemia in CHH is unknown: while erythroid differentiation from hematopoietic stem cells is impaired in vitro in CHH, immune dysregulation may also play a role in this phenotype. Clonal hematopoiesis is a common phenomenon of aging. Patients with inherited and immune-mediated bone marrow failure (BMF) show distinct spectra of clonal hematopoiesis mutations, reflecting context-specific selection of hematopoietic stem cell clones. However, the spectrum of clonal hematopoiesis is yet to be characterized in CHH. Methods: To assess the landscape of somatic alterations in hematopoietic cells in CHH, we performed whole exome sequencing (WES) on twelve bone marrow samples of four pediatric (age 4 to 13 years) and eight adult (age 20 to 52 years) unrelated subjects with CHH. Three children with CHH had severe hypoplastic anemia at the time of DNA sampling and three patients underwent HSCT during follow-up. Seven adults with CHH had normal blood counts and no severe immune phenotypes despite other clinical manifestations of CHH. Matched skin fibroblast samples were available for five CHH adults in the cohort for whom we performed tumor-normal variant calling. For the remaining cases, variant calling was based on tumor-only samples and stringent filtering to exclude germline variants. Additionally, we queried the FINRISK dataset, a Finnish cohort comprising WES and SNP microarray data from 10 129 participants, for the presence of CHH associated RMRP variants and evaluated their association with clonal hematopoiesis of indeterminate potential (CHIP) and mosaic chromosomal alterations (mCAs). Results: The median WES coverage of the bone marrow samples was 445x (347-505). Eleven out of 12 patients were homozygous for the RMRP founder variant n.71A&amp;gt;G and one patient was compound heterozygous for two pathogenic RMRP variants. We observed no somatic reversion of the germline RMRP variants. Two pediatric patients had variants in the CHIP genes: CHH1 (age 13 years) with TP53 hotspot variant R175C (variant allele frequency, VAF 0.006) and CHH2 (age 4 years) with BCORL1 P1681Qfs*20 (VAF 0.025). One fifty-year-old patient had a DNMT3A splicing variant c.1555-1G&amp;gt;C (VAF 0.022), likely consistent with CHIP observed in older general population. To identify clonal hematopoiesis outside the classical CHIP genes, we performed conservative filtering of the remaining somatic variant calls, resulting in a list of 36 high-confidence coding variants (VAF &amp;gt;0.02). These variants were present in 10 out of 12 patients; no recurrent genetic alterations were observed. Finally, the analysis of the FINRISK dataset revealed eleven participants with RMRP disease-associated variants; each participant had one heterozygous RMRP variant. No enrichment of CHIP variants or mCAs were observed in carriers of RMRP variants. Conclusion: We observed TP53 and BCORL1 mutations in the bone marrow samples of pediatric patients with CHH. In comparison to other CHIP-associated conditions, BCORL1 variants are disproportionately represented in immune-mediated aplastic anemia, potentially suggestive of similar immune-mediated origin of hypoplastic anemia in CHH. TP53 mutations are abundant in inherited BMF syndromes; however and in contrast to classical inherited BMF syndromes, CHH is not associated with increased risk of myeloid malignancies. No enrichment of classical or non-classical clonal hematopoiesis mutations were observed in adults with clinical CHH diagnosis or in RMRP variant carriers in the population-level FINRISK cohort. This is consistent with transient selection pressure on hematopoietic stem cells in childhood CHH. To our knowledge, our study is the first attempt to characterize the spectrum of clonal hematopoiesis in CHH.

Clonal Hematopoiesis Is Associated with Severe COVID-19 Enhancing Inflammatory Responses in Myeloid Cells

Background Clonal hematopoiesis (CH) is prevalent among aged populations and highlighted because its association with not only hematological malignancies but various benign diseases (e.g. cardiovascular diseases). Of particular interest among these diseases is COVID-19. To date, the association between severe COVID-19 and CH-related gene mutations or mosaic chromosomal alterations (mCAs) was examined using biobank samples taken long before the pandemic and the association has not been tested in a sufficiently large cohort of patients on the basis of CH evaluated at the time of COVID-19 diagnosis. Moreover, no study examined the joint effect of gene mutations and mCAs. The mechanism of the association between severe COVID-19 and CH has not been addressed either. Methods To address these issues we enrolled a total of 4,541 patients with COVID-19, of whom 54% had a severe infection. We performed targeted-capture sequencing of 42 CH-related genes and SNP-array analysis to detect CH-related mutations and mCAs. We also performed RNA-seq (n=987) of whole blood samples and plasma proteomic analysis (n=1,200) using the Olink technology to investigate the effect of biological consequence of CH, which was applied to understand the underlying mechanism of sever COVID-19. Results We identified gene mutations and mCAs in 16.3% and 6.2% of COVID-19 patients, respectively. They coexisted in 2.4% patients. As reported in CH in normal individuals, most frequent alterations included mutations in DNMT3A (7.6%), TET2 (4.1%), ASXL1 (1.4%), PPM1D (1.7%), and mCAs such as 14qUPD, and del(20q). To evaluate the risk of severe COVID-19 conferred by CH, we compared the age-stratified frequencies of CH between severe and non-severe COVID-19 patients (Figure, a). Focusing on CH in ≧10% clonal fractions, CH was significantly enriched in severe COVID-19 in elderly patients, we detected a significant enrichment of cases with both gene mutations and mCAs and isolated gene mutations, but not that of isolated mCAs, in severe cases. Multivariable logistic regression analysis with adjustment for age and sex revealed the significant association of CH defined either CH-mutations or mCA with severe COVID-19 with an odds ratio (OR) of 1.34 [95%CI=1.03-1.84] in patients aged ≥65 years. Particularly, CH defined by combined gene mutations and mCAs conferred a remarkable increase in the risk of severe COVID-19 [OR=12.1, 95%CI=1.61-90.6], suggesting the presence of their synergistic impact on severe COVID-19. To elucidate the underlying mechanism of the observed association between severe COVID-19 and CH, we next evaluated the transcriptomic/proteomic features of severe COVID-19 and CH (Figure, b). In severe COVID-19, multiple inflammatory pathways including IFN-α/γ, TNF-α, and IL-6 responses were consistently up-regulated in both transcriptomic and proteomic analysis. Similar to these features of severe COVID-19, CH was also associated with inflammatory response and IFN-α/γ responses in RNA expression while the impact of CH on protein expression was not prominent. To further clarify the transcriptomic features of severe COVID-19 and CH, we performed deconvolution analysis of gene expression to estimate the fraction of each cell component and cell-type-specific expression profiles. Severe COVID-19 was characterized by elevated fractions of neutrophils, activated dendritic cells (DCs), and decreased fractions of several types of lymphocytes, while only a marginal increase of activated DCs was observed in CH. Cell-type-specific pathway analysis revealed up-regulations of inflammatory responses and IL-6/TNF-a signaling in neutrophils/monocytes were associated with both severe COVID-19 and CH independently, suggesting that CH might be involved in the development of severe COVID-19 through the augmentation of inflammatory responses in these myeloid cells, which are further augmented by increased neutrophils induced by COVID-19 independent of CH. Conclusion CH was significantly associated with an increased risk of severe COVID-19, particularly when the patients had both gene mutations and mCAs, where the augmented inflammatory responses by myeloid cells can be a mechanism of severe COVID-19 risk conferred by CH. Our findings highlight the link between the mechanism of severe COVID-19 and the biological effects of CH.

Genetic Determinants of Clonal Hematopoiesis and Progression to Hematologic Malignancies in 479,117 Individuals

Clonal hematopoiesis (CH), while common with aging, confers a high relative risk of hematologic malignancy (HM). Genome-wide association studies have identified multiple germline predisposition loci for CH but many have an unclear functional role. Here we characterized the contribution of pathogenic/likely pathogenic germline variants (PGVs) to CH and its progression to HM using the UK Biobank (UKBB) as a discovery cohort (N=454,859) with validation in Memorial Sloan Kettering IMPACT and The Cancer Genome Atlas (N=24,258). We profiled whole exome sequencing (WES) for PGVs in 240 cancer predisposition genes.We simultaneously analyzedWES for CH driven by single nucleotide variants/indels and SNP array data for mosaic chromosomal alterations. Overall, 8.9% of individuals in the UKBB harbored PGVs in genes with a dominant inheritance mode (5.2% in HM-related genes). To identify germline CH predisposition genes, we performed multivariable logistic regression with adjustment for age, sex, race, smoking and prior cancer type. Our analyses focused on heterozygous PGVs in both dominant and recessive genes since the majority of participants carried one deleterious variant. We found PGVs in 15 genes (8 are novel) increased the risk of CH (FDR corrected p-value &amp;lt;0.05), including 3 recessive genes that haven't been shown to confer a phenotype in the heterozygous state (Figure 1). Prominently featured pathways include DNA damage repair/sensing, telomere maintenance, RAS, JAK/STAT signaling, and hematopoietic cell differentiation/development. Through pairwise analysis, we identified 102 additional germline genes predisposing to CH in specific genes/genetic regions; Out of 61 germline genes with ≥1 carrier who developed CH in replication cohorts, we replicated 55 genes (30 were significant with p&amp;lt;0.05 and 25 were directionally consistent). Overrepresented pathways include immune regulation ( e.g.UNC13D, DOCK8 and ADA), homologous recombination deficiency ( e.g.FANCARAD51D, BRIP1 and BRCA1) among others. We observed heterogeneity in CH patterns for different germline genes. We used a recently published method ( Watson et al., Science, 2020) to quantify the fitness advantage of specific CH mutations among PGV carriers compared to non-carriers based on the distributions of variant allele frequency. We found that some associations between PGVs and CH appeared driven by selection including PGVs in ATM, MPL, and TP53 and CH overlapping the same gene/genetic region and PGVs in CHEK2 and DNMT3A CH. Other CH predisposition genes like POT1 were associated with multiple CH events across the genome, suggesting that tolerance of genetic instability rather than selection accounts for their associations with CH. During 14-years of follow-up, 4,596 UKBB participants developed HM. 18 CH predisposition genes were also associated with HM, including several genes not previously linked to HM in the heterozygous state ( e.g.CTC1, BLM, and WNR). To characterize the interaction between PGVs and CH on HM risk, we performed stratified analyses by mutational status. We observed synergistic effect between PGVs and CH on HM risk whereby CH carriers with PGVs have a higher risk of developing HM (HR [95%CI]: 1.30 [1.14-1.48]) compared to those without PGVs. We looked into specific HM predisposition genes and found this synergistic effect was consistent across most genes (Figure 2). We further grouped PGV carriers into those acquired high risk CH (CH in specific gene/genetic region showing moderate/strong association with the mutated germline gene) and those acquired low risk CH (showing weak or no association). Compared to non-carriers, PGV carriers who developed high risk CH showed high risk of myeloid (24.2 [19.3-30.5]) and lymphoid malignancies (6.3 [5.2-7.7]), whereas the risk for myeloid (1.5 [1.3-1.8]) and lymphoid malignancies (2.5 [1.8-3.4]) were weaker among PGV carriers with low risk CH. In summary, we identifyseveral novel genes/pathways predisposing to CH and its progression to HMs. The association between germline genetic background and CH is explained by a combination of selection for specific somatic events and increased mutational acquisition/tolerance. High risk CH mutations vary by germline genetic background emphasizing the need for patient specific models of CH risk. These findings highlight the importance of germline-CH interactions in determining the risk of CH progression to HMs.

Mosaic chromosomal alterations in blood across ancestries using whole-genome sequencing

Megabase-scale mosaic chromosomal alterations (mCAs) in blood are prognostic markers for a host of human diseases. Here, to gain a better understanding of mCA rates in genetically diverse populations, we analyzed whole-genome sequencing data from 67,390 individuals from the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine program. We observed higher sensitivity with whole-genome sequencing data, compared with array-based data, in uncovering mCAs at low mutant cell fractions and found that individuals of European ancestry have the highest rates of autosomal mCAs and the lowest rates of chromosome X mCAs, compared with individuals of African or Hispanic ancestry. Although further studies in diverse populations will be needed to replicate our findings, we report three loci associated with loss of chromosome X, associations between autosomal mCAs and rare variants in DCPS, ADM17, PPP1R16B and TET2 and ancestry-specific variants in ATM and MPL with mCAs in cis.

A pan-tissue survey of mosaic chromosomal alterations in 948 individuals.

Genetic mutations accumulate in an organism's body throughout its lifetime. While somatic single-nucleotide variants have been well characterized in the human body, the patterns and consequences of large chromosomal alterations in normal tissues remain largely unknown. Here, we present a pan-tissue survey of mosaic chromosomal alterations (mCAs) in 948 healthy individuals from the Genotype-Tissue Expression project, augmenting RNA-based allelic imbalance estimation with haplotype phasing. We found that approximately a quarter of the individuals carry a clonally-expanded mCA in at least one tissue, with incidence strongly correlated with age. The prevalence and genome-wide patterns of mCAs vary considerably across tissue types, suggesting tissue-specific mutagenic exposure and selection pressures. The mCA landscapes in normal adrenal and pituitary glands resemble those in tumors arising from these tissues, whereas the same is not true for the esophagus and skin. Together, our findings show a widespread age-dependent emergence of mCAs across normal human tissues with intricate connections to tumorigenesis.

JAK2V617F mutation and associated chromosomal alterations in primary and secondary myelofibrosis and post-HCT outcomes

AbstractJAK2V617F is the most common driver mutation in primary or secondary myelofibrosis for which allogeneic hematopoietic cell transplantation (HCT) is the only curative treatment. Knowledge of the prognostic utility of JAK2 alterations in the HCT setting is limited. We identified all patients with MF who received HCT between 2000 and 2016 and had a pre-HCT blood sample (N = 973) available at the Center of International Blood and Marrow Transplant Research biorepository. PacBio sequencing and single nucleotide polymorphism–array genotyping were used to identify JAK2V617F mutation and associated mosaic chromosomal alterations (mCAs), respectively. Cox proportional hazard models were used for HCT outcome analyses. Genomic testing was complete for 924 patients with MF (634 primary MF [PMF], 135 postpolycythemia vera [PPV-MF], and 155 postessential thrombocytopenia [PET-MF]). JAK2V617F affected 562 patients (57.6% of PMF, 97% of PPV-MF, and 42.6% of PET-MF). Almost all patients with mCAs involving the JAK2 region (97.9%) were JAK2V617-positive. In PMF, JAK2V617F mutation status, allele burden, or identified mCAs were not associated with disease progression/relapse, nonrelapse mortality (NRM), or overall survival. Almost all PPV-MF were JAK2V617F-positive (97%), with no association between HCT outcomes and mutation allele burden or mCAs. In PET-MF, JAK2V617F high mutation allele burden (≥60%) was associated with excess risk of NRM, restricted to transplants received in the era of JAK inhibitors (2013-2016; hazard ratio = 7.65; 95% confidence interval = 2.10-27.82; P = .002). However, allele burden was not associated with post-HCT disease progression/relapse or survival. Our findings support the concept that HCT can mitigate the known negative effect of JAK2V617F in patients with MF, particularly for PMF and PPV-MF.

Mutation rates and fitness consequences of mosaic chromosomal alterations in blood

Mosaic chromosomal alterations (mCAs) are common in cancers and can arise decades before diagnosis. A quantitative understanding of the rate at which these events occur, and their functional consequences, could improve cancer risk prediction and our understanding of somatic evolution. Using mCA clone size estimates from the blood of approximately 500,000 UK Biobank participants, we estimate mutation rates and fitness consequences of acquired gain, loss and copy-neutral loss of heterozygosity events. Most mCAs have moderate to high fitness effects but occur at a low rate, being more than tenfold less common than equivalently fit single-nucleotide variants. Notable exceptions are mosaic loss of X and Y, which we estimate have roughly 1,000-fold higher mutation rates than autosomal mCAs. Although the way in which most mCAs increase in prevalence with age is consistent with constant growth rates, some mCAs exhibit different behavior, suggesting that their fitness may depend on inherited variants, extrinsic factors or distributions of fitness effects.