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).
Gruber, C. & Bogunovic, D. Incomplete penetrance in primary immunodeficiency: a skeleton in the closet. Hum. Genet. 139, 745–757 (2020).
Gimelbrant, A., Hutchinson, J. N., Thompson, B. R. & Chess, A. Widespread monoallelic expression on human autosomes. Science 318, 1136–1140 (2007).
Chess, A. Monoallelic gene expression in mammals. Annu. Rev. Genet. 50, 317–327 (2016).
Nag, A. et al. Chromatin signature of widespread monoallelic expression. eLife 2, e01256 (2013).
da Rocha, S. T. & Gendrel, A. V. The influence of DNA methylation on monoallelic expression. Essays Biochem. 63, 663–676 (2019).
Bousfiha, A. A. et al. Primary immunodeficiency diseases worldwide: more common than generally thought. J. Clin. Immunol. 33, 1–7 (2013).
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).
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).
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).
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).
Timberlake, A. T. et al. Two locus inheritance of non-syndromic midline craniosynostosis via rare SMAD6 and common BMP2 alleles. eLife 5, e20125 (2016).
Spaan, A. N. et al. Human OTULIN haploinsufficiency impairs cell-intrinsic immunity to staphylococcal α-toxin. Science 376, eabm6380 (2022).
Israel, L. et al. Human adaptive immunity rescues an inborn error of innate immunity. Cell 168, 789–800.e10 (2017).
Castel, S. E. et al. Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk. Nat. Genet. 50, 1327–1334 (2018).
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).
Lyon, M. F. Gene action in the X-chromosome (Mus musculus L.). Nature 190, 372–373 (1961).
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).
Barlow, D. P. Gametic imprinting in mammals. Science 270, 1610–1613 (1995).
Chess, A., Simon, I., Cedar, H., & Axel, R. Allelic inactivation regulates olfactory receptor gene expression. Cell 78, 823–834 (1994).
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).
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).
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).
Reinius, B. & Sandberg, R. Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation. Nat. Rev. Genet. 16, 653–664 (2015).
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).
Marion-Poll, L. et al. Locus specific epigenetic modalities of random allelic expression imbalance. Nat. Commun. 12, 5330 (2021).
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).
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.
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).
Stubbington, M. J. T. et al. T cell fate and clonality inference from single-cell transcriptomes. Nat. Methods 13, 329–332 (2016).
Tukiainen, T. et al. Landscape of X chromosome inactivation across human tissues. Nature 550, 244–248 (2017).
Gupta, S. et al. RNA sequencing-based screen for reactivation of silenced alleles of autosomal genes. G3 12, jkab428 (2022).
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).
Ombrello, M. J. et al. Cold urticaria, immunodeficiency, and autoimmunity related to PLCG2 deletions. N. Engl. J. Med. 366, 330–338 (2012).
CN, G. et al. Complex autoinflammatory syndrome unveils fundamental principles of JAK1 kinase transcriptional and biochemical function. Immunity 53, 672–684.e11 (2020).
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).
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).
Gourdan, P. et al. Multifocal tuberculosis: a phenotype of Mendelian susceptibility to mycobacterial disease. Arch. Dis. Child. 109, 673–673 (2024).
Dupuis, S. et al. Impairment of mycobacterial but not viral immunity by a germline human STAT1 mutation. Science 293, 300–303 (2001).
Chapgier, A. et al. Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease. PLoS Genet. 2, e131 (2006).
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).
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).
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).
Ma, C. A. et al. Germline hypomorphic CARD11 mutations in severe atopic disease. Nat. Genet. 49, 1192–1201 (2017).
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).
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).
Zwemer, L. M. et al. Autosomal monoallelic expression in the mouse. Genome Biol. 13, R10 (2012).
Gendrel, A.-V. et al. Developmental dynamics and disease potential of random monoallelic gene expression. Dev. Cell 28, 366–380 (2014).
Eckersley-Maslin, M. A. et al. Random monoallelic gene expression increases upon embryonic stem cell differentiation. Dev. Cell 28, 351–365 (2014).
Borel, C. et al. Biased allelic expression in human primary fibroblast single cells. Am. J. Hum. Genet. 96, 70–80 (2015).
Reinius, B. et al. Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq. Nat. Genet. 48, 1430–1435 (2016).
Mendelevich, A. et al. Replicate sequencing libraries are important for quantification of allelic imbalance. Nat. Commun. 12, 3370 (2021).
Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
