Tangye, S. G. et al. Human inborn errors of immunity: 2022 update on the classification from the International Union of Immunological Societies Expert Committee. J. Clin. Immunol. 42, 1473–1507 (2022).
Google Scholar
Gruber, C. & Bogunovic, D. Incomplete penetrance in primary immunodeficiency: a skeleton in the closet. Hum. Genet. 139, 745–757 (2020).
Google Scholar
Gimelbrant, A., Hutchinson, J. N., Thompson, B. R. & Chess, A. Widespread monoallelic expression on human autosomes. Science 318, 1136–1140 (2007).
Google Scholar
Chess, A. Monoallelic gene expression in mammals. Annu. Rev. Genet. 50, 317–327 (2016).
Google Scholar
Nag, A. et al. Chromatin signature of widespread monoallelic expression. eLife 2, e01256 (2013).
Google Scholar
da Rocha, S. T. & Gendrel, A. V. The influence of DNA methylation on monoallelic expression. Essays Biochem. 63, 663–676 (2019).
Google Scholar
Bousfiha, A. A. et al. Primary immunodeficiency diseases worldwide: more common than generally thought. J. Clin. Immunol. 33, 1–7 (2013).
Google Scholar
Wengler, G. S. et al. High prevalence of nonsense, frame shift, and splice-site mutations in 16 patients with full-blown Wiskott–Aldrich syndrome. Blood 86, 3648–3654 (1995).
Google Scholar
Gámez-Díaz, L. et al. The extended phenotype of LPS-responsive beige-like anchor protein (LRBA) deficiency. J. Allergy Clin. Immunol. 137, 223–230 (2016).
Google Scholar
Fieschi, C. et al. Low penetrance, broad resistance, and favorable outcome of interleukin 12 receptor β1 deficiency: medical and immunological implications. J. Exp. Med. 197, 527–535 (2003).
Google Scholar
Schwab, C. et al. Phenotype, penetrance, and treatment of 133 cytotoxic T-lymphocyte antigen 4-insufficient subjects. J. Allergy Clin. Immunol. 142, 1932–1946 (2018).
Google Scholar
Timberlake, A. T. et al. Two locus inheritance of non-syndromic midline craniosynostosis via rare SMAD6 and common BMP2 alleles. eLife 5, e20125 (2016).
Google Scholar
Spaan, A. N. et al. Human OTULIN haploinsufficiency impairs cell-intrinsic immunity to staphylococcal α-toxin. Science 376, eabm6380 (2022).
Google Scholar
Israel, L. et al. Human adaptive immunity rescues an inborn error of innate immunity. Cell 168, 789–800.e10 (2017).
Google Scholar
Castel, S. E. et al. Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk. Nat. Genet. 50, 1327–1334 (2018).
Google Scholar
Buzby, J. S., Williams, S. A., Schaffer, L., Head, S. R. & Nugent, D. J. Allele-specific wild-type TP53 expression in the unaffected carrier parent of children with Li–Fraumeni syndrome. Cancer Genet. 211, 9–17 (2017).
Google Scholar
Lyon, M. F. Gene action in the X-chromosome (Mus musculus L.). Nature 190, 372–373 (1961).
Google Scholar
Brown, C. et al. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature 349, 38–44 (1991).
Google Scholar
Barlow, D. P. Gametic imprinting in mammals. Science 270, 1610–1613 (1995).
Google Scholar
Chess, A., Simon, I., Cedar, H., & Axel, R. Allelic inactivation regulates olfactory receptor gene expression. Cell 78, 823–834 (1994).
Google Scholar
Gimelbrant, A. A., Ensminger, A. W., Qi, P., Zucker, J. & Chess, A. Monoallelic expression and asynchronous replication of p120 catenin in mouse and human cells. J. Biol. Chem. 280, 1354–1359 (2005).
Google Scholar
Davie, J. M., Paul, W. E., Mage, R. G., & Goldman, M. B. Membrane-associated immunoglobulin of rabbit peripheral blood lymphocytes: allelic exclusion at the b locus. Proc. Natl Acad. Sci. USA 68, 430–434 (2024).
Google Scholar
Gascoigne, N. R. J. & Alam, S. M. Allelic exclusion of the T cell receptor α-chain: developmental regulation of a post-translational event. Semin. Immunol. 11, 337–347 (1999).
Google Scholar
Reinius, B. & Sandberg, R. Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation. Nat. Rev. Genet. 16, 653–664 (2015).
Google Scholar
Deng, Q., Ramsköld, D., Reinius, B. & Sandberg, R. Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 343, 193–196 (2014).
Google Scholar
Marion-Poll, L. et al. Locus specific epigenetic modalities of random allelic expression imbalance. Nat. Commun. 12, 5330 (2021).
Google Scholar
Nag, A., Vigneau, S., Savova, V., Zwemer, L. M. & Gimelbrant, A. A. Chromatin signature identifies monoallelic gene expression across mammalian cell types. G3 5, 1713–1720 (2015).
Google Scholar
Xu, J. et al. Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells. Nat. Genet. 49, 377–386 (2017). 2017 493.
Google Scholar
Zhu, L. et al. scRNA-seq revealed the special TCR β & α V(D)J allelic inclusion rearrangement and the high proportion dual (or more) TCR-expressing cells. Cell Death Dis. 14, 487 (2023).
Google Scholar
Stubbington, M. J. T. et al. T cell fate and clonality inference from single-cell transcriptomes. Nat. Methods 13, 329–332 (2016).
Google Scholar
Tukiainen, T. et al. Landscape of X chromosome inactivation across human tissues. Nature 550, 244–248 (2017).
Google Scholar
Gupta, S. et al. RNA sequencing-based screen for reactivation of silenced alleles of autosomal genes. G3 12, jkab428 (2022).
Google Scholar
Vinogradova, S., Saksena, S. D., Ward, H. N., Vigneau, S. & Gimelbrant, A. A. MaGIC: a machine learning tool set and web application for monoallelic gene inference from chromatin. BMC Bioinformatics 20, 106 (2019).
Google Scholar
Ombrello, M. J. et al. Cold urticaria, immunodeficiency, and autoimmunity related to PLCG2 deletions. N. Engl. J. Med. 366, 330–338 (2012).
Google Scholar
CN, G. et al. Complex autoinflammatory syndrome unveils fundamental principles of JAK1 kinase transcriptional and biochemical function. Immunity 53, 672–684.e11 (2020).
Google Scholar
Del Bel, K. L. et al. JAK1 gain-of-function causes an autosomal dominant immune dysregulatory and hypereosinophilic syndrome. J. Allergy Clin. Immunol. 139, 2016–2020.e5 (2017).
Google Scholar
Horesh, M. E. et al. Individuals with JAK1 variants are affected by syndromic features encompassing autoimmunity, atopy, colitis, and dermatitis. J. Exp. Med. 221, e20232387 (2024).
Google Scholar
Gourdan, P. et al. Multifocal tuberculosis: a phenotype of Mendelian susceptibility to mycobacterial disease. Arch. Dis. Child. 109, 673–673 (2024).
Google Scholar
Dupuis, S. et al. Impairment of mycobacterial but not viral immunity by a germline human STAT1 mutation. Science 293, 300–303 (2001).
Google Scholar
Chapgier, A. et al. Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease. PLoS Genet. 2, e131 (2006).
Google Scholar
Liu, L. et al. Gain-of-function human STAT1 mutations impair IL-17 immunity and underlie chronic mucocutaneous candidiasis. J. Exp. Med. 208, 1635–1648 (2011).
Google Scholar
Okada, S. et al. Human STAT1 gain-of-function heterozygous mutations: chronic mucocutaneous candidiasis and type i interferonopathy. J. Clin. Immunol. 40, 1065–1081 (2020).
Google Scholar
Depner, M. et al. The extended clinical phenotype of 26 patients with chronic mucocutaneous candidiasis due to gain-of-function mutations in STAT1. J. Clin. Immunol. 36, 73–84 (2016).
Google Scholar
Ma, C. A. et al. Germline hypomorphic CARD11 mutations in severe atopic disease. Nat. Genet. 49, 1192–1201 (2017).
Google Scholar
Dorjbal, B. et al. Hypomorphic caspase activation and recruitment domain 11 (CARD11) mutations associated with diverse immunologic phenotypes with or without atopic disease. J. Allergy Clin. Immunol. 143, 1482–1495 (2019).
Google Scholar
Li, S. M. et al. Transcriptome-wide survey of mouse CNS-derived cells reveals monoallelic expression within novel gene families. PLoS ONE 7, e31751 (2012).
Google Scholar
Zwemer, L. M. et al. Autosomal monoallelic expression in the mouse. Genome Biol. 13, R10 (2012).
Google Scholar
Gendrel, A.-V. et al. Developmental dynamics and disease potential of random monoallelic gene expression. Dev. Cell 28, 366–380 (2014).
Google Scholar
Eckersley-Maslin, M. A. et al. Random monoallelic gene expression increases upon embryonic stem cell differentiation. Dev. Cell 28, 351–365 (2014).
Google Scholar
Borel, C. et al. Biased allelic expression in human primary fibroblast single cells. Am. J. Hum. Genet. 96, 70–80 (2015).
Google Scholar
Reinius, B. et al. Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq. Nat. Genet. 48, 1430–1435 (2016).
Google Scholar
Mendelevich, A. et al. Replicate sequencing libraries are important for quantification of allelic imbalance. Nat. Commun. 12, 3370 (2021).
Google Scholar
Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
Google Scholar
