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$ export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins && bcftools +mocha
$ export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins && bcftools	plugin mocha
$ bcftools +$BCFTOOLS_PLUGINS/mocha.so
$ bcftools plugin $BCFTOOLS_PLUGINS/mocha.so

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Publications

2024

• Otsuka, I. et al. Increased somatic mosaicism in autosomal and X chromosomes for suicide death. Molecular Psychiatry (2024) doi:10.1038/s41380-024-02718-y
• Ormond, C. et al. Whole genome sequencing study of identical twins discordant for psychosis. Translational Psychiatry (2024) doi:10.1038/s41398-024-02982-0
• Desai, P. et al. Association of clonal hematopoiesis and mosaic chromosomal alterations with solid malignancy incidence and mortality. Cancer (2024) doi:10.1002/cncr.35455
• Chang, K. et al. The Contribution of Mosaic Chromosomal Alterations to Schizophrenia. Biological Psychiatry (2024) doi:10.1016/j.biopsych.2024.06.015
• Lim, J. et al. Associations between mosaic loss of sex chromosomes and incident hospitalization for atrial fibrillation in the United Kingdom. medRxiv (2024) doi:10.1101/2024.05.29.24308171
• Liu, A. et al. Genetic drivers and cellular selection of female mosaic X chromosome loss. Nature (2024) doi:10.1038/s41586-024-07533-7
• Pershad, Y. et al. Determinants of mosaic chromosomal alteration fitness. Nat Commun. (2024) doi:10.1038/s41467-024-48190-8
• Francis, M. et al. Multi-ancestry genome-wide association meta-analysis of mosaic loss of chromosome Y in the Million Veteran Program identifies 167 novel loci. medRxiv (2024) doi:10.1101/2024.04.24.24306301
• Kishtagari, A. et al. Driver mutation zygosity is a critical factor in predicting clonal hematopoiesis transformation risk. Blood Cancer Journal (2024) doi:10.1038/s41408-023-00974-9

2023

• Rafati, M. et al. JAK2V617F mutation and associated chromosomal alterations in primary and secondary myelofibrosis and post-HCT outcomes. Blood Advances (2023) doi:10.1182/bloodadvances.2023010882
• Chang, V. C. et al. Glyphosate Use and Mosaic Loss of Chromosome Y among Male Farmers in the Agricultural Health Study. Environmental Health Perspectives (2023) doi:10.1289/EHP12834
• Zhou, W. et al. Mosaic chromosomal alterations in peripheral blood leukocytes of children in sub-Saharan Africa. Nature Communications (2023) doi:10.1038/s41467-023-43881-0
• Jakubek, Y. A. et al. Mosaic chromosomal alterations in blood across ancestries using whole-genome sequencing. Nature Genetics (2023) doi:10.1038/s41588-023-01553-1
• Ressler, A. K. et al. Single-nucleus DNA sequencing reveals hidden somatic loss-of-heterozygosity in Cerebral Cavernous Malformations. Nature Communications (2023) doi:10.1038/s41467-023-42908-w
• Brown, W. B. et al. Shared and distinct genetic etiologies for different types of clonal hematopoiesis. Nature Communications (2023) doi:10.1038/s41467-023-41315-5
• Rodriguez-Meira, A. et al. Single-cell multi-omics identifies chronic inflammation as a driver of TP53-mutant leukemic evolution. Nature Genetics (2023) doi:10.1038/s41588-023-01480-1
• Eberhardt, R. Y. et al. Detection of mosaic chromosomal alterations in children with severe developmental disorders recruited to the DDD study. Genetics in Medicine Open (2023) doi:10.1016/j.gimo.2023.100836
• Babadi, M. et al. GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data. Nature Genetics (2023) doi:10.1038/s41588-023-01449-0
• Kamphuis, P. et al. Clonal Hematopoiesis Defined by Somatic Mutations Infrequently Co-occurs With Mosaic Loss of the Y Chromosome in a Population-based Cohort. Hemasphere (2023) doi:10.1097/HS9.0000000000000956
• Hubbard, A. K. et al. Serum biomarkers are altered in UK Biobank participants with mosaic chromosomal alterations. Human Molecular Genetics (2023) doi:10.1093/hmg/ddad133
• Cheng, C. et al. Mosaic Chromosomal Alterations Are Associated With Increased Lung Cancer Risk: Insight From the INTEGRAL-ILCCO Cohort Analysis. Journal of Thoracic Oncology (2023) doi:10.1016/j.jtho.2023.05.001
• Wright, C. et al. Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland. New England Journal of Medicine (2023) doi:10.1056/NEJMoa2209046
• Watson, C. J. et al. Mutation rates and fitness consequences of mosaic chromosomal alterations in blood. Nature Genetics (2023) doi:10.1038/s41588-023-01490-z
• Maury, E. A. et al. Schizophrenia-associated somatic copy-number variants from 12,834 cases reveal recurrent NRXN1 and ABCB11 disruptions. Cell Genomics (2022) doi:10.1016/j.xgen.2023.100356
• Dawoud, A. A. Z. et al. Age-related loss of chromosome Y is associated with levels of sex hormone binding globulin and clonal hematopoiesis defined by TET2, TP53, and CBL mutations. Human Genetics (2023) doi:10.1126/sciadv.ade9746
• Wong, W. J. et al. Clonal hematopoiesis and risk of chronic liver disease. Nature (2023) doi:10.1038/s41586-023-05857-4
• Lin, S. et al. Mosaic chromosomal alterations detected in men living with HIV and the relationship to non-Hodgkin lymphoma. AIDS (2023) doi:10.1097/QAD.0000000000003545
• Kessler, M. D. et al. Common and rare variant associations with clonal haematopoiesis phenotypes. Nature (2023) doi:10.1038/s41586-022-05448-9

2022

• Levin, M. G. et al. Genetics of smoking and risk of clonal hematopoiesis. Nature Scientific Reports (2022) doi:10.1038/s41598-022-09604-z
• Qin, N. et al. Association of the interaction between mosaic chromosomal alterations and polygenic risk score with the risk of lung cancer: an array-based case-control association and prospective cohort study. The Lancet Oncology (2022) doi:10.1016/S1470-2045(22)00600-3
• Brown, D. W. et al. Germline-somatic JAK2 interactions are associated with clonal expansion in myelofibrosis. Nature Communications (2022) doi:10.1038/s41467-022-32986-7
• McReynolds, L. J. et al. Genetic testing in severe aplastic anemia is required for optimal hematopoietic cell transplant outcomes. Blood (2022) doi:10.1182/blood.2022016508
• Uddin, M. et al. Germline genomic and phenomic landscape of clonal hematopoiesis in 323,1121 individuals. medRxiv (2022) doi:10.1101/2022.07.29.22278015
• Genovese, G. et al. Chromosomal phase improves aneuploidy detection in non-invasive prenatal testing at low fetal DNA fractions. Nature Scientific Reports (2022) doi:10.1038/s41598-022-14049-5
• Merkle, F. T. et al. Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation. Cell Stem Cell (2022) doi:10.1016/j.stem.2022.01.011
• López-Rivera, J. A. et al. The genomic landscape across 474 surgically accessible epileptogenic human brain lesions. Brain (2022) doi:10.1093/brain/awac376
• Walsh, K. et al. Clonal Hematopoiesis Analyses in Clinical, Epidemiologic, and Genetic Aging Studies to Unravel Underlying Mechanisms of Age-Related Dysfunction in Humans. frontiers in Aging (2022) doi:10.3389/fragi.2022.841796
• Balagué-Dobón, L. et al. Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure. Briefings in Bioinformatics (2022) doi:10.1093/bib/bbac043

2021

• Honigberg, M. C. et al. Premature Menopause, Clonal Hematopoiesis, and Coronary Artery Disease in Postmenopausal Women. Circulation (2021) doi:10.1161/CIRCULATIONAHA.120.051775
• Lin, S. et al. Incident disease associations with mosaic chromosomal alterations on autosomes, X and Y chromosomes: insights from a phenome-wide association study in the UK Biobank. Cell & Bioscience (2021) doi:10.1186/s13578-021-00651-z
• Saiki, R et al. Combined landscape of single-nucleotide variants and copy number alterations in clonal hematopoiesis. Nature Medicine (2021) doi:10.1038/s41591-021-01411-9
• Koskela, J. T. et al. Genetic variant in SPDL1 reveals novel mechanism linking pulmonary fibrosis risk and cancer protection. medRxiv (2021) doi:10.1101/2021.05.07.21255988
• Niroula, A. et al. Distinction of lymphoid and myeloid clonal hematopoiesis. Nat Med (2021) doi:10.1038/s41591-021-01521-4
• Glessner, J.T. et al. MONTAGE: a new tool for high-throughput detection of mosaic copy number variation. BMC Genomics (2021) doi:10.1186/s12864-021-07395-7
• Sherman, M. A. et al. Large mosaic copy number variations confer autism risk. Nat Neurosci (2021) doi:10.1038/s41593-020-00766-5
• Zekavat S., et al. Hematopoietic mosaic chromosomal alterations increase the risk for diverse types of infection. Nat Medicine (2021) doi:10.1038/s41591-021-01371-0

2020

• Lin, S.-H. et al. Mosaic chromosome Y loss is associated with alterations in blood cell counts in UK Biobank men. Sci Rep 10, 3655 (2020) doi:10.1038/s41598-020-59963-8
• Brown, D. W. et al. Genetically predicted telomere length is associated with clonal somatic copy number alterations in peripheral leukocytes. PLoS Genet 16, e1009078 (2020).doi:10.1371/journal.pgen.1009078
• Hagg S., et al. Deciphering the genetic and epidemiological landscape of mitochondrial DNA abundance. Hum Genetics (2020) doi:10.1007/s00439-020-02249-w
• Terao, C. et al. The genomic landscape of clonal hematopoiesis in Japan. Nature (2020) doi:10.1038/s41586-020-2426-2
• Loh, P.-R., Genovese, G. & McCarroll, S. A. Monogenic and polygenic inheritance become instruments for clonal selection. Nature (2020) doi:10.1038/s41586-020-2430-6

2019

• Thompson, D. J. et al. Genetic predisposition to mosaic Y chromosome loss in blood. Nature 575, 652-657 (2019) doi:10.1038/s41586-019-1765-3

2018

• Loh, P.-R. et al. Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations. Nature 559, 350-355 (2018) doi:10.1038/s41586-018-0321-x

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