Molecular Diagnostics of Primary Immunodeficiencies: Benefits and Future Challenges

  • Mirjam van der Burg
  • Menno C. Van Zelm
  • Jacques J.M. Van Dongen
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 634)


Primary immunodeficiencies (PID) are inherited disorders with defects in one or more components of the immune system. According to the latest classification, they can be divided in eight subgroups (See Table 1) (Geha et al. 2007). Although many PID are the result of a single gene mutation, making a molecular diagnosis for a patient can be difficult. Over 135 candidate PID genes have been identified, but the prevalence of most of the genetic defects is low. Furthermore, different genetic defects can result in a similar clinical presentation, whereas patients with different defects in the same gene can present with diverse clinical pictures. Therefore, it is important to take stepwise approach for the diagnosis of PID. First, the patient needs to be evaluated clinically and immunologically using the international multistage diagnostic protocol, designed by the European Society for Immunodeficiencies (ESID) for patient-centered screening for primary immunodeficiency (De...


Primary Immunodeficiency Molecular Diagnostics Common Variable Immunodeficiency CVID Patient Human Gene Mutation Database 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Aiuti, A., Slavin, S., Aker, M., Ficara, F., Deola, S., Mortellaro, A., Morecki, S., Andolfi, G., Tabucchi, A., Carlucci, F., Marinello, E., Cattaneo, F., Vai, S., Servida, P., Miniero, R., Roncarolo, M. G., Bordignon, C. 2002. Correction of ADA-SCID by stem cell gene therapy combined with nonmyeloablative conditioning. Science 296:2410–2413PubMedCrossRefGoogle Scholar
  2. Antonarakis, S. E., Krawczak, M., Cooper, D. N. 2000. Disease-causing mutations in the human genome. Eur. J. Pediatr. 159 Suppl 3:S173–178PubMedCrossRefGoogle Scholar
  3. Bordignon, C., Notarangelo, L. D., Nobili, N., Ferrari, G., Casorati, G., Panina, P., Mazzolari, E., Maggioni, D., Rossi, C., Servida, P., Ugazio, A. G., Mavilio, F. 1995. Gene therapy in peripheral blood lymphocytes and bone marrow for ADA- immunodeficient patients. Science 270:470–475PubMedCrossRefGoogle Scholar
  4. Cavazzana-Calvo, M., Hacein-Bey, S., de Saint Basile, G., Gross, F., Yvon, E., Nusbaum, P., Selz, F., Hue, C., Certain, S., Casanova, J. L., Bousso, P., Deist, F. L., Fischer, A. 2000. Gene therapy of human severe combined immunodeficiency (SCID)-X1 disease. Science 288:669–672PubMedCrossRefGoogle Scholar
  5. Cooper, D. N., Youssoufian, H. 1988. The CpG dinucleotide and human genetic disease. Hum. Genet. 78:151–155PubMedCrossRefGoogle Scholar
  6. De Vries, E. 2006. Patient-centred screening for primary immunodeficiency: a multi-stage diagnostic protocol designed for non-immunologists. Clin. Exp. Immunol. 145:204–214PubMedCrossRefGoogle Scholar
  7. Den Dunnen, J. T., Antonarakis, S. E. 2000. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum. Mutat. 15:7–12CrossRefGoogle Scholar
  8. Geha, R. S., Notarangelo, L. D., Casanova, J. L., Chapel, H., Conley, M. E., Fischer, A., Hammarstrom, L., Nonoyama, S., Ochs, H. D., Puck, J. M., Roifman, C., Seger, R., Wedgwood, J. 2007. Primary immunodeficiency diseases: an update from the International Union of Immunological Societies Primary Immunodeficiency Diseases Classification Committee. J. Allergy. Clin. Immunol. 120:776–794PubMedCrossRefGoogle Scholar
  9. Green, P. M., Montandon, A. J., Bentley, D. R., Ljung, R., Nilsson, I. M., Giannelli, F. 1990. The incidence and distribution of CpG—TpG transitions in the coagulation factor IX gene. A fresh look at CpG mutational hotspots. Nucleic. Acids. Res. 18:3227–3231PubMedCrossRefGoogle Scholar
  10. Grimbacher, B., Hutloff, A., Schlesier, M., Glocker, E., Warnatz, K., Drager, R., Eibel, H., Fischer, B., Schaffer, A. A., Mages, H. W., Kroczek, R. A., Peter, H. H. 2003. Homozygous loss of ICOS is associated with adult-onset common variable immunodeficiency. Nat. Immunol. 4:261–268PubMedCrossRefGoogle Scholar
  11. Hacein-Bey-Abina, S., Le Deist, F., Carlier, F., Bouneaud, C., Hue, C., De Villartay, J. P., Thrasher, A. J., Wulffraat, N., Sorensen, R., Dupuis-Girod, S., Fischer, A., Davies, E. G., Kuis, W., Leiva, L., Cavazzana-Calvo, M. 2002. Sustained correction of X-linked severe combined immunodeficiency by ex vivo gene therapy. N. Engl. J. Med. 346:1185–1193PubMedCrossRefGoogle Scholar
  12. Hacein-Bey-Abina, S., Von Kalle, C., Schmidt, M., McCormack, M. P., Wulffraat, N., Leboulch, P., Lim, A., Osborne, C. S., Pawliuk, R., Morillon, E., Sorensen, R., Forster, A., Fraser, P., Cohen, J. I., de Saint Basile, G., Alexander, I., Wintergerst, U., Frebourg, T., Aurias, A., Stoppa-Lyonnet, D., Romana, S., Radford-Weiss, I., Gross, F., Valensi, F., Delabesse, E., Macintyre, E., Sigaux, F., Soulier, J., Leiva, L. E., Wissler, M., Prinz, C., Rabbitts, T. H., Le Deist, F., Fischer, A., Cavazzana-Calvo, M. 2003. LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1. Science 302:415–419PubMedCrossRefGoogle Scholar
  13. Hamosh, A., Scott, A. F., Amberger, J. S., Bocchini, C. A., McKusick, V. A. 2005. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic. Acids. Res. 33:D514–517PubMedCrossRefGoogle Scholar
  14. Kanegane, H., Agematsu, K., Futatani, T., Sira, M. M., Suga, K., Sekiguchi, T., van Zelm, M. C., Miyawaki, T. 2007. Novel mutations in a Japanese patient with CD19 deficiency. Genes. Immun. 8:663–670PubMedCrossRefGoogle Scholar
  15. Kimura, H., Iyehara-Ogawa, H., Kato, T. 1994. Slippage--misalignment: to what extent does it contribute to mammalian cell mutagenesis? Mutagenesis 9:395–400PubMedCrossRefGoogle Scholar
  16. Krawczak, M., Cooper, D. N. 1991. Gene deletions causing human genetic disease: mechanisms of mutagenesis and the role of the local DNA sequence environment. Hum. Genet. 86:425–441PubMedCrossRefGoogle Scholar
  17. Kunkel, T. A. 1990. Misalignment-mediated DNA synthesis errors. Biochemistry 29:8003–8011PubMedCrossRefGoogle Scholar
  18. Kunkel, T. A., Soni, A. 1988. Mutagenesis by transient misalignment. J. Biol. Chem. 263:14784–14789PubMedGoogle Scholar
  19. Maki, H. 2002. Origins of spontaneous mutations: specificity and directionality of base-substitution, frameshift, and sequence-substitution mutageneses. Annu. Rev. Genet. 36:279–303PubMedCrossRefGoogle Scholar
  20. McNaughton, J. C., Cockburn, D. J., Hughes, G., Jones, W. A., Laing, N. G., Ray, P. N., Stockwell, P. A., Petersen, G. B. 1998. Is gene deletion in eukaryotes sequence-dependent? A study of nine deletion junctions and nineteen other deletion breakpoints in intron 7 of the human dystrophin gene. Gene 222:41–51PubMedCrossRefGoogle Scholar
  21. Moshous, D., Pannetier, C., Chasseval Rd, R., Deist Fl, F., Cavazzana-Calvo, M., Romana, S., Macintyre, E., Canioni, D., Brousse, N., Fischer, A., Casanova, J. L., Villartay, J. P. 2003. Partial T and B lymphocyte immunodeficiency and predisposition to lymphoma in patients with hypomorphic mutations in Artemis. J. Clin. Invest. 111:381–387.PubMedGoogle Scholar
  22. Noordzij, J. G., De Bruin-Versteeg, S., Comans-Bitter, W. M., Hartwig, N. G., Hendriks, R. W., De Groot, R., Van Dongen, J. J. M. 2002a. Composition of precursor B-cell compartment in bone marrow from patients with X-linked agammaglobulinemia compared with healthy children. Pediatr. Res. 51:159–168Google Scholar
  23. Noordzij, J. G., De Bruin-Versteeg, S., Hartwig, N. G., Weemaes, C. M., Gerritsen, E. J. A., Bernatowska, E., Van Lierde, S., De Groot, R., Van Dongen, J. J. M. 2002b. XLA patients with BTK splice-site mutations produce low levels of wild-type BTK transcripts. J. Clin. Immunol. 22:306–318Google Scholar
  24. Noordzij, J. G., De Bruin-Versteeg, S., Verkaik, N. S., Vossen, J. M. J. J., De Groot, R., Bernatowska, E., Langerak, A. W., Van Gent, D. C., Van Dongen, J. J. M. 2002c. The immunophenotypic and immunogenotypic B-cell differentiation arrest in bone marrow of RAG deficient SCID patients corresponds to residual recombination activities of mutated RAG proteins. Blood 100:2145–2152Google Scholar
  25. Novoyatleva, T., Tang, Y., Rafalska, I., Stamm, S. 2006. Pre-mRNA missplicing as a cause of human disease. Prog. Mol. Subcell. Biol. 44:27–46PubMedCrossRefGoogle Scholar
  26. Piirila, H., Valiaho, J., Vihinen, M. 2006. Immunodeficiency mutation databases (IDbases). Hum. Mutat. 27:1200–1208PubMedCrossRefGoogle Scholar
  27. Rideout, W. M., 3rd, Coetzee, G. A., Olumi, A. F., Jones, P. A. 1990. 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science 249:1288–1290PubMedCrossRefGoogle Scholar
  28. Rogozin, I. B., Pavlov, Y. I. 2003. Theoretical analysis of mutation hotspots and their DNA sequence context specificity. Mutat. Res. 544:65–85PubMedCrossRefGoogle Scholar
  29. Salzer, U., Chapel, H. M., Webster, A. D., Pan-Hammarstrom, Q., Schmitt-Graeff, A., Schlesier, M., Peter, H. H., Rockstroh, J. K., Schneider, P., Schaffer, A. A., Hammarstrom, L., Grimbacher, B. 2005. Mutations in TNFRSF13B encoding TACI are associated with common variable immunodeficiency in humans. Nat. Genet. 37:820–828PubMedCrossRefGoogle Scholar
  30. Sellner, L. N., Taylor, G. R. 2004. MLPA and MAPH: new techniques for detection of gene deletions. Hum. Mutat. 23:413–419PubMedCrossRefGoogle Scholar
  31. Stenson, P. D., Ball, E. V., Mort, M., Phillips, A. D., Shiel, J. A., Thomas, N. S., Abeysinghe, S., Krawczak, M., Cooper, D. N. 2003. Human Gene Mutation Database (HGMD): 2003 update. Hum. Mutat. 21:577–581PubMedCrossRefGoogle Scholar
  32. Streisinger, G., Okada, Y., Emrich, J., Newton, J., Tsugita, A., Terzaghi, E., Inouye, M. 1966. Frameshift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthday. Cold Spring Harb. Symp. Quant. Biol. 31:77–84CrossRefGoogle Scholar
  33. Van der Burg, M., De Groot, R., Comans-Bitter, W. M., Den Hollander, J. C., Hooijkaas, H., Neijens, H. J., Berger, R. M. F., Oranje, A. P., Langerak, A. W., Van Dongen, J. J. M. 2000. Autoimmune lymphoproliferative syndrome (ALPS) in a child from consanguineous parents: a dominant or recessive disease? Pediatr. Res. 47:336–343PubMedCrossRefGoogle Scholar
  34. Van der Burg, M., van Veelen, L. R., Verkaik, N. S., Wiegant, W. W., Hartwig, N. G., Barendregt, B. H., Brugmans, L., Raams, A., Jaspers, N. G., Zdzienicka, M. Z., van Dongen, J. J. M., van Gent, D. C. 2006. A new type of radiosensitive T-B-NK+ severe combined immunodeficiency caused by a LIG4 mutation. J. Clin. Invest. 116:137–145PubMedCrossRefGoogle Scholar
  35. Van Zelm, M. C., Geertsema, C., Nieuwenhuis, N., de Ridder, D., Conley, M. E., Schiff, C., Tezcan, I., Bernatowska, E., Hartwig, N. G., Sanders, E. A., Litzman, J., Kondratenko, I., van Dongen, J. J. M., van der Burg, M. 2008. Gross deletions involving IGHM, BTK, or Artemis: a model for genomic lesions mediated by transposable elements. Am. J. Hum. Genet. 82:320–332PubMedCrossRefGoogle Scholar
  36. Van Zelm, M. C., Reisli, I., van der Burg, M., Castano, D., van Noesel, C. J., van Tol, M. J., Woellner, C., Grimbacher, B., Patino, P. J., van Dongen, J. J. M., Franco, J. L. 2006. An antibody-deficiency syndrome due to mutations in the CD19 gene. N. Engl. J. Med. 354:1901–1912PubMedCrossRefGoogle Scholar
  37. Youssoufian, H., Antonarakis, S. E., Bell, W., Griffin, A. M., Kazazian, H. H., Jr. 1988. Nonsense and missense mutations in hemophilia A: estimate of the relative mutation rate at CG dinucleotides. Am. J. Hum. Genet. 42:718–725PubMedGoogle Scholar
  38. Youssoufian, H., Kazazian, H. H., Jr., Phillips, D. G., Aronis, S., Tsiftis, G., Brown, V. A., Antonarakis, S. E. 1986. Recurrent mutations in haemophilia A give evidence for CpG mutation hotspots. Nature 324:380–382PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Mirjam van der Burg
    • 1
  • Menno C. Van Zelm
  • Jacques J.M. Van Dongen
  1. 1.Department of Immunology, Erasmus MCUniversity Medical Center RotterdamRotterdam

Personalised recommendations