Abdool Karim Q, Abdool Karim SS, Frohlich JA, Grobler AC, Baxter C, Mansoor LE et al (2010) Effectiveness and safety of tenofovir gel, an antiretroviral microbicide, for the prevention of HIV infection in women. Science 329(5996):1168–1174

Article  CAS  PubMed  PubMed Central  Google Scholar 

Avnir Y, Tallarico AS, Zhu Q, Bennett AS, Connelly G, Sheehan J et al (2014) Molecular signatures of hemagglutinin stem-directed heterosubtypic human neutralizing antibodies against influenza A viruses. PLoS Pathog 10(5):e1004103

Article  PubMed  PubMed Central  Google Scholar 

Avnir Y, Watson CT, Glanville J, Peterson EC, Tallarico AS, Bennett AS et al (2016) IGHV1-69 polymorphism modulates anti-influenza antibody repertoires, correlates with IGHV utilization shifts and varies by ethnicity. Sci Rep 6(1):20842

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boyd SD, Gaëta BA, Jackson KJ, Fire AZ, Marshall EL, Merker JD et al (1950) 2010 Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements. J Immunol Baltim Md 184(12):6986–92

Google Scholar 

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T et al (2019) Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun 16(10):1784

Article  Google Scholar 

Choudhury A, Aron S, Botigué LR, Sengupta D, Botha G, Bensellak T et al (2020) High-depth African genomes inform human migration and health. Nature 586(7831):741–748

Article  CAS  PubMed  PubMed Central  Google Scholar 

Corcoran MM, Phad GE, Bernat NV, Stahl-Hennig C, Sumida N, Persson MAA et al (2016) Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity. Nat Commun 7:13642

Article  CAS  PubMed  PubMed Central  Google Scholar 

Corrie BD, Marthandan N, Zimonja B, Jaglale J, Zhou Y, Barr E et al (2018) iReceptor: a platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories. Immunol Rev 284(1):24–41

Article  CAS  PubMed  PubMed Central  Google Scholar 

Doria-Rose NA, Schramm CA, Gorman J, Moore PL, Bhiman JN, DeKosky BJ et al (2014) Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies. Nature 509(7498):55–62

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gidoni M, Snir O, Peres A, Polak P, Lindeman I, Mikocziova I et al (2019) Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping. Nat Commun 10(1):628

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hardt U, Corcoran MM, Narang S, Malmström V, Padyukov L, Karlsson Hedestam GB (2023) Analysis of IGH allele content in a sample group of rheumatoid arthritis patients demonstrates unrevealed population heterogeneity. Front Immunol 14:1073414

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huang Y, Thörnqvist L, Ohlin M (2021) Computational inference, validation, and Analysis of 5'UTR-leader sequences of alleles of immunoglobulin heavy chain variable genes. Front Immunol 12:730105. https://doi.org/10.3389/fimmu.2021.730105

Jackson KJL, Liu Y, Roskin KM, Glanville J, Hoh RA, Seo K et al (2014) Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements. Cell Host Microbe 16(1):105–114

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kenter AL, Watson CT, Spille JH (2021) Igh locus polymorphism may dictate topological chromatin conformation and V gene usage in the Ig repertoire. Front Immunol 12:682589

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lab H (2010) FASTX toolkit. Hannon Lab Cold Spring Harbor, NY

Lees W, Busse CE, Corcoran M, Ohlin M, Scheepers C, Matsen FA IV et al (2020) OGRDB: a reference database of inferred immune receptor genes. Nucleic Acids Res 48(D1):D964–D970

Article  CAS  PubMed  Google Scholar 

Lefranc MP, Giudicelli V, Duroux P, Jabado-Michaloud J, Folch G, Aouinti S et al (2015) IMGT, the international ImMunoGeneTics information system 25 years on. Nucleic Acids Res 43:D413-422

Article  CAS  PubMed  Google Scholar 

Lefranc MP (2014) Immunoglobulin and T cell receptor genes: IMGT(®) and the birth and rise of immunoinformatics. Front Immunol 5:22. https://doi.org/10.3389/fimmu.2014.00022

Lefranc M-P, Lefranc G (2001) The immunoglobulin factsBook, Academic Press, p 458

Manso T, Folch G, Giudicelli V, Jabado-Michaloud J, Kushwaha A, Nguefack Ngoune V et al (2022) IMGT® databases, related tools and web resources through three main axes of research and development. Nucleic Acids Res 50(D1):D1262–D1272

Article  CAS  PubMed  Google Scholar 

Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17(1):10–2

Article  Google Scholar 

May A, Hazelhurst S, Li Y, Norris SA, Govind N, Tikly M et al (2013) Genetic diversity in black South Africans from Soweto. BMC Genomics 14:644

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mikocziova I, Gidoni M, Lindeman I, Peres A, Snir O, Yaari G et al (2020) Polymorphisms in human immunoglobulin heavy chain variable genes and their upstream regions. Nucleic Acids Res 48(10):5499–5510

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mikocziova I, Greiff V, Sollid LM (2021a) Immunoglobulin germline gene variation and its impact on human disease. Genes Immun 22(4):205–217

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mikocziova I, Peres A, Gidoni M, Greiff V, Yaari G, Sollid LM (2021) Germline polymorphisms and alternative splicing of human immunoglobulin light chain genes. iScience 103192. https://doi.org/10.1016/j.isci.2021.103192

Mor M, Werbner M, Alter J, Safra M, Chomsky E, Lee JC et al (2021) Multi-clonal SARS-CoV-2 neutralization by antibodies isolated from severe COVID-19 convalescent donors. PLoS Pathog 17(2):e1009165

Article  CAS  PubMed  PubMed Central  Google Scholar 

Moyo T, Kitchin D, Moore PL (2020) Targeting the N332-supersite of the HIV-1 envelope for vaccine design. Expert Opin Ther Targets 24(6):499–509

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nielsen SCA, Yang F, Jackson KJL, Hoh RA, Röltgen K, Jean GH et al (2020) Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2. Cell Host Microbe 28(4):516-525.e5

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ohlin M (2021) Poorly expressed alleles of several human immunoglobulin heavy chain variable genes are common in the human population. Front Immunol 11:603980. https://doi.org/10.3389/fimmu.2020.603980

Ohlin M, Scheepers C, Corcoran M, Lees WD, Busse CE, Bagnara D et al (2019) Inferred allelic variants of immunoglobulin receptor genes: a system for their evaluation, documentation, and naming. Front Immunol 10:435

Article  CAS  PubMed  PubMed Central  Google Scholar 

Omer A, Shemesh O, Peres A, Polak P, Shepherd AJ, Watson CT et al (2020) VDJbase: an adaptive immune receptor genotype and haplotype database. Nucleic Acids Res 48(D1):D1051–D1056

Article  CAS  PubMed  Google Scholar 

Pappas L, Foglierini M, Piccoli L, Kallewaard NL, Turrini F, Silacci C et al (2014) Rapid development of broadly influenza neutralizing antibodies through redundant mutations. Nature 516(7531):418–422

Article  CAS  PubMed  Google Scholar 

Pennell M, Rodriguez OL, Watson CT, Greiff V (2023) The evolutionary and functional significance of germline immunoglobulin gene variation. Trends Immunol 44(1):7–21

Article  CAS  PubMed  Google Scholar 

Peres A, Gidoni M, Polak P, Yaari G (2019) RAbHIT: R antibody haplotype inference tool. Bioinforma Oxf Engl 35(22):4840–4842

Article  CAS  Google Scholar