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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17(1):10–2
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
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
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
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
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
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
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
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
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
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
Peres A, Gidoni M, Polak P, Yaari G (2019) RAbHIT: R antibody haplotype inference tool. Bioinforma Oxf Engl 35(22):4840–4842
Richardson SI, Moore PL (2019) The antibody response in HIV-1-infected donors. Curr Opin HIV AIDS 14(4):233–239
PubMed PubMed Central Google Scholar
Rodriguez OL, Gibson WS, Parks T, Emery M, Powell J, Strahl M et al (2020) A novel framework for characterizing genomic haplotype diversity in the human immunoglobulin heavy chain locus. Front Immunol 11:2136
CAS PubMed PubMed Central Google Scholar
Rodriguez OL, Safonova Y, Silver CA, Shields K, Gibson WS, Kos JT et al (2023) Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire. Nat Commun 14(1):4419
CAS PubMed PubMed Central Google Scholar
Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584
PubMed PubMed Central Google Scholar
Safonova Y, Shin SB, Kramer L, Reecy J, Watson CT, Smith TPL et al (2022) Variations in antibody repertoires correlate with vaccine responses. Genome Res 32(4):791–804
CAS PubMed PubMed Central Google Scholar
Scheepers C, Shrestha RK, Lambson BE, Jackson KJL, Wright IA, Naicker D et al (2015) Ability to develop broadly neutralizing HIV-1 antibodies is not restricted by the germline Ig gene repertoire. J Immunol 194(9). https://doi.org/10.4049/jimmunol.1500118
Sengupta D, Choudhury A, Fortes-Lima C, Aron S, Whitelaw G, Bostoen K et al (2020) Genetic-substructure and complex demographic history of South African Bantu speakers.
Comments (0)