Benjamini Y. and Hochberg Y. 1995 Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R Stat. Soc. Ser. B (Methodological) 57, 289–300.

MathSciNet  Google Scholar 

Chang C. C., Carson C. C., Tellier L. C., Vattikuti S., Purcell S. M. and Lee J. J. 2015 Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4, s13742–s14015.

Article  Google Scholar 

Chen D. D., Lu L. F., Xiong F., Wang X. L., Jiang J. Y., Zhang C. et al. 2022 Zebrafish CERKL enhances host TBK1 stability and simultaneously degrades viral protein via ubiquitination modulation. J. Immunol. 208, 2196–2206.

Article  CAS  PubMed  Google Scholar 

Chen W. H., Neuzil K. M., Boyce C. R., Pasetti M. F., Reymann M. K., Martellet L. et al. 2018 Safety and immunogenicity of a pentavalent meningococcal conjugate vaccine containing serogroups A, C, Y, W, and X in healthy adults: a phase 1, single-centre, double-blind, randomised, controlled study. Lancet Infect. Dis. 18, 1088–1096.

Article  CAS  PubMed  Google Scholar 

Coppiello G., Collantes M., Sirerol-Piquer M. S., Vandenwijngaert S., Schoors S., Swinnen M. et al. 2015 Meox2/Tcf15 heterodimers program the heart capillary endothelium for cardiac fatty acid uptake. Circulation 131, 815–826.

Article  CAS  PubMed  Google Scholar 

Das S., Forer L., Schönherr S., Sidore C., Locke A. E., Kwong A. et al. 2016 Next-generation genotype imputation service and methods. Nat. Genet. 48, 1284–1287.

Article  CAS  PubMed  Google Scholar 

Garg R., Akhade A. S., Yadav J. and Qadri A. 2015 MyD88-dependent pro-inflammatory activity in Vi polysaccharide vaccine against typhoid promotes Ab switching to IgG. Innate Immune. 21, 778–783.

Article  CAS  Google Scholar 

GBD 2017 Typhoid and Paratyphoid Collaborators 2019 The global burden of typhoid and paratyphoid fevers: a systematic analysis for the Global Burden of Disease Study 2017. Lancet Infect. Dis. 19, 369–381.

Article  Google Scholar 

Graf C., Zemann B., Rovina P., Urtz N., Schanzer A., Reuschel R. et al. 2008 Neutropenia with impaired immune response to Streptococcus pneumoniae in ceramide kinase-deficient mice. J. Immunol. 180, 3457–3466.

Article  CAS  PubMed  Google Scholar 

Hausmann O. N., Hu W. H., Keren-Raifman T., Witherow D. S., Wang Q., Levay K. et al. 2002 Spinal cord injury induces expression of RGS7 in microglia/macrophages in rats. Eur. J. Neurosci. 15, 602–612.

Article  PubMed  Google Scholar 

Jarret A., Jackson R., Duizer C., Healy M. E., Zhao J., Rone J. M. et al. 2020 Enteric nervous system-derived IL-18 orchestrates mucosal barrier immunity. Cell 180, 50–63.

Article  CAS  PubMed  Google Scholar 

Jin C., Gibani M. M., Moore M., Juel H. B., Jones E., Meiring J. et al. 2017 Efficacy and immunogenicity of a Vi-tetanus toxoid conjugate vaccine in the prevention of typhoid fever using a controlled human infection model of Salmonella Typhi: a randomised controlled, phase 2b trial. Lancet 390, 2472–2480.

Article  CAS  PubMed  Google Scholar 

Kennedy R. B., Ovsyannikova I. G., Haralambieva I. H., Lambert N. D., Pankratz V. S. and Poland G. A. 2014 Genome-wide SNP associations with rubella-specific cytokine responses in measles-mumps-rubella vaccine recipients. Immunogenetics 66, 493–499.

Article  CAS  PubMed  Google Scholar 

Kennedy R. B., Ovsyannikova I. G., Pankratz V. S., Haralambieva I. H., Vierkant R. A., Jacobson R. M. et al. 2012a Genome-wide genetic associations with IFNγ response to smallpox vaccine. Hum. Genet. 131, 1433–1451.

Article  CAS  PubMed  Google Scholar 

Kennedy R. B., Ovsyannikova I. G., Pankratz V. S., Haralambieva I. H., Vierkant R. A. and Poland G. A. 2012b Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients. Hum. Genet. 131, 1403–1421.

Article  CAS  PubMed  Google Scholar 

Kim M., Morales L. D., Jang I.-S., Cho Y.-Y. and Kim D. J. 2018 Protein Tyrosine Phosphatases as Potential Regulators of STAT3 Signaling. Int. J. Mol. Sci. 19, 2708.

Article  PubMed  Google Scholar 

Kim S., Lee K. S., Pak G. D., Excler J.-L., Sahastrabuddhe S., Marks F. et al. 2019 Spatial and temporal patterns of typhoid and paratyphoid fever outbreaks: A Worldwide Review, 1990–2018. Clin. Inf. Dis. 69, S499–S509.

Article  Google Scholar 

Lin H.-H., Chen H. L., Weng C.-C., Janapatla R. P., Chen C. L. and Chiu C.-H. 2021 Activation of apoptosis by Salmonella pathogenicity island-1 effectors through both intrinsic and extrinsic pathways in Salmonella-infected macrophages. J. Microbiol. Immunol. Inf. 54, 616–626.

Article  CAS  Google Scholar 

Li P., Shi D., Shen W., Shi S., Guo X., Li J. et al. 2022 Pilot genome-wide association study of antibody response to inactivated SARS-CoV-2 vaccines. Front. Immunol. 13, 1054147.

Article  CAS  PubMed  Google Scholar 

Li S., Sullivan N. L., Rouphael N., Yu T., Banton S., Maddur M. S. et al. 2017 Metabolic phenotypes of response to vaccination in humans. Cell 169, 862–877.

Article  CAS  PubMed  Google Scholar 

Majumder P. P., Staats H. F., Sarkar-Roy N., Varma B., Ghosh T., Maiti S. et al. 2009 Genetic determinants of immune-response to a polysaccharide vaccine for typhoid. HUGO J. 3, 17–30.

Article  PubMed  Google Scholar 

Manoharan I., Swafford D., Shanmugam A., Patel N., Prasad P. D., Thangaraju M. et al. 2021 Activation of transcription factor 4 in dendritic cells controls Th1/Th17 responses and autoimmune neuroinflammation. J. Immunol. 207, 1428–1436.

Article  CAS  PubMed  Google Scholar 

Ma S., Wan X., Deng Z., Shi L., Hao C., Zhou Z. et al. 2017 Epigenetic regulator CXXC5 recruits DNA demethylase Tet2 to regulate TLR7/9-elicited IFN response in pDCs. J. Exp. Med. 214, 1471–1491.

Article  CAS  PubMed  Google Scholar 

Masuho I., Balaji S., Muntean B. S., Skamangas N. K., Chavali S., Tesmer J. J. G. et al. 2020 A global map of G protein signaling regulation by RGS proteins. Cell 183, 503–521.

Article  CAS  PubMed  Google Scholar 

Milet J., Sabbagh A., Migot-Nabias F., Luty A. J. F., Gaye O., Garcia A. et al. 2016 Genome-wide association study of antibody responses to Plasmodium falciparum candidate vaccine antigens. Genes Immu. 17, 110–117.

Article  CAS  Google Scholar 

Ng A. C. Y., Eisenberg J. M., Heath R. J. W., Huett A., Robinson M. C., Nau G. J. et al. 2011 Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity. Proc. Natl. Acad. Sci. USA 108, 4631–4638.

Article  ADS  CAS  PubMed  Google Scholar 

Ochiai R. L., Khan M. I., Soofi S. B., Sur D., Kanungo S., You Y. A. et al. 2014 Immune responses to Vi capsular polysaccharide typhoid vaccine in children 2 to 16 years old in Karachi, Pakistan, and Kolkata. India. Clin. Vaccine Immunol. 21, 661–666.

Article  PubMed  Google Scholar 

O’Connor D., Png E., Khor C. C., Snape M. D., Hill A. V. S., van der Klis F. et al. 2019 Common genetic variations associated with the persistence of immunity following childhood immunization. Cell Rep. 27, 3241–3253.

Article  PubMed  Google Scholar 

O’Connor D. and Pollard A. J. 2013 Characterizing vaccine responses using host genomic and transcriptomic analysis. Clin. Inf. Dis. 57, 860–869.

Article  Google Scholar 

Ovsyannikova I. G., Kennedy R. B., O’Byrne M., Jacobson R. M., Pankratz V. S. and Poland G. A. 2012 Genome-wide association study of antibody response to smallpox vaccine. Vaccine 30, 4182–4189.

Article  CAS  PubMed  Google Scholar 

Parween F., Yadav J. and Qadri A. 2019 The virulence polysaccharide of salmonella typhi suppresses activation of Rho family GTPases to limit inflammatory responses from epithelial cells. Front. Cell. Inf. Microbiol. 9, 141.

Article  CAS  Google Scholar 

Piccio L., Vermi W., Boles K. S., Fuchs A., Strader C. A., Facchetti F. et al. 2005 Adhesion of human T cells to antigen-presenting cells through SIRPβ2-CD47 interaction costimulates T-cell proliferation. Blood 105, 2421–2427.

Article  CAS  PubMed  Google Scholar 

Pickering M., Cumiskey D. and O’Connor J. J. 2005 Actions of TNF-alpha on glutamatergic synaptic transmission in the central nervous system. Exp. Physiol. 90, 663–670.

Article  CAS  PubMed  Google Scholar 

Piepoli A., Palmieri O., Maglietta R., Panza A., Cattaneo E., Latiano A. et al. 2012 The expression of leucine-rich repeat gene family members in colorectal cancer. Exp. Biol. Med. 237, 1123–1128.

Article  CAS  Google Scholar 

Price A. L., Patterson N. J., Plenge R. M., Weinblatt M. E., Shadick N. A. and Reich D. 2006 Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904–909.

Article  CAS  PubMed  Google Scholar 

Rodriguez-Fraticelli A. E., Weinreb C., Wang S.-W., Migueles R. P., Jankovic M., Usart M. et al. 2020 Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis. Nature 583, 585–589.

Article  ADS  CAS  PubMed  Google Scholar 

Sinha S., Renavikar P. S., Crawford M. P., Steward-Tharp S. M., Brate A., Tsalikian E. et al. 2020 Altered expression of SIRPγ on the T-cells of relapsing remitting multiple sclerosis and type 1 diabetes patients could potentiate effector responses from T-cells. PLoS One 15, e0238070.

Article  CAS  PubMed  Google Scholar 

Słomian D., Szyda J., Dobosz P., Stojak J., Michalska-Foryszewska A., Sypniewski M. et al. 2023 Better safe than sorry—Whole-genome sequencing indicates that missense variants are significant in susceptibility to COVID-19. PLoS One 18, e027