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Identification of the short arm of the Y chromosome by cytogenetic and molecular analyses


Isochromosome Y is one of the structural anomalies of the Y chromosome associated with a 45,X cell line and a broad spectrum of phenotypes. We present a case of de novo 46,X,+mar detected in a 17-yearold male patient. He had shortening of the right leg, bilateral breast enlargement, pubic, underarm and facial hair development, small penis and testicles, low serum cortisol, ACTH and total testosterone levels, normal LH value, high FSH value, normal testicles and epididymis, minimal left varicocele. The chromosome aberration was detected by cytogenetic analysis. Cytogenetic and molecular analysis was performed by conventional karyotyping and quantitative florescence PCR, respectively. The molecular analyses by PCR detected the presence of the SRY and AMXY genes, confirming the presence of the short arm of the Y chromosome. PCR demonstrated that the marker chromosome is of Y origin and corresponds to an authentic isochromosome for the short arm of the Y chromosome, i(Yp). We suggest that the structural alteration of the Y chromosome was a new mutation, which occurred in the initial mitotic division of the embryo, originally 46,XY. The result of accurate evaluation provides correct sex assignment and the prevention of the neoplastic degeneration of a dysgenetic gonad. The karyotype 46,X,i(Yp) indicates that the patient is preserving the SRY gene.

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  1. Hsu, L.Y., Phenotype/karyotype correlations of Y chromosome aneuploidy with emphasis on structural aberrations in postnatally diagnosed cases, Am. J. Med. Genet., 1994, vol. 53, no. 2, pp. 108–140.

    CAS  Article  PubMed  Google Scholar 

  2. Kelly, T.E., Franco, J.B., Rogol, A., Golden, W.L., Discordant phenotypes and 45,X/46,X,idic(Y), J. Med. Genet., 1998, vol. 35, no. 10, pp. 862–864.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  3. Reddy, K.S. and Sulcova, V., Pathogenetics of 45,X/46,XY gonadal mosaicism, Cytogenet. Cell Genet., 1998, vol. 82, no. 1–2, pp. 52–57.

    CAS  Article  PubMed  Google Scholar 

  4. Quilter, C.R., Nathwani, N., Conway, G.S., Stanhope, R., Ralph, D., Bahadur, G., Serhal, P., Taylor, K., and Delhanty, J.D., A comparative study between infertile males and patients with Turner syndrome to determine the influence of sex chromosome mosaicism and the breakpoints of structurally abnormal Y chromosomes on phenotypic sex, J. Med. Genet., 2002, vol. 39, no. 12, e80.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  5. Infertility in the Male, Lipshultz, L.I. and Howards, S.S., Eds., St Louis, Mosby, 1997.

  6. Van Golde, R.J., Wetzels, A.M., de Graaf, R., Tuerlings, J.H., Braat, D.D., and Kremer J.A., Decreased fertilization rate and embryo quality after ICSI in oligozoospermic men with microdeletions in the azoospermia factor c region of the Y chromosome. Hum. Reprod., 2001, vol. 16, no. 2, pp. 289–292.

    Article  PubMed  Google Scholar 

  7. Mittal, R.D., Singh, G., Srivastava, A., Pradhan, M., Kesari, A., Makker, A., and Mittal, B., Y chromosome micro-deletions in idiopathic infertility from Northern India, Ann. Genet., 2004, vol.47, no. 4, pp. 331–337.

    Article  PubMed  Google Scholar 

  8. Dada, R., Gupta, N.P., and Kucheria, K., Yq microdeletions–azoospermia factor candidate genes and spermatogenic arrest, J. Biomol. Tech., 2004, vol. 15, no. 3, pp. 176–183.

    PubMed  PubMed Central  Google Scholar 

  9. Van Assche, E., Bonduelle, M., Tournaye, H., Joris, H., Verheyen, G., Deyroey, P., Van Steirteghem, A., and Liebaers, I., Cytogenetics of infertile men, Hum. Reprod., 1996, vol.11, Suppl. 4, pp.1–24.

    Article  PubMed  Google Scholar 

  10. Robinson, D.O., Dalton, P., Jacobs, P.A., Mosse, K., Power, M.M., Skuse, D.H., and Crolla, J.A., Molecular and FISH analysis of structurally abnormal Y chromosomes in patients with Turner syndrome, J. Med. Genet., 1999, vol. 36, no. 4, pp. 279–284.

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Álvarez-Nava, F., Soto, M., Martinez, M.C., Prieto, M., and Alvarez, Z., FISH and PCR analyses in three patients with 45,X/46,X,idic(Y) karyotype: clinical and pathologic spectrum, Ann. Genet., 2003, vol. 46, no. 4, pp. 443–448.

    Article  PubMed  Google Scholar 

  12. DesGroseilliers, M., Beaulieu Bergeron, M., Brochu, P., Lemyre, E., and Lemieux, N., Phenotypic variability in isodicentric Y patients: study of nine cases, Clin. Genet., 2006, vol. 70, no. 2, pp. 145–150.

    CAS  Article  PubMed  Google Scholar 

  13. Davis, RM., Localisation of male determining factors in man: a thorough review of structural anomalies of the Y chromosome, J. Med. Genet., 1981, vol. 18, no. 3, pp. 161–195.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  14. Fitch, N., Richer, C.L., Pinsky, L., and Kahn, A., Deletion of the long arm of the Y chromosome and review of Y chromosome abnormalities, Am. J. Med. Genet., 1985, vol. 20, no. 1, pp. 31–42.

    CAS  Article  PubMed  Google Scholar 

  15. Guedes, A.D., Bianco, B., Lipay, M.V., Brunoni, D., de Lourdes Chauffaille, M., and Verreschi, I.T., Determination of the sexual phenotype in a child with 45,X/46,X,Idic(Yp) mosaicism: importance of the relative proportion of the 45,X line in gonadal tissue, Am. J. Med. Genet., 2006, vol. 140A, no. 17, pp. 1871–1875.

    CAS  Article  PubMed  Google Scholar 

  16. DiNapoli, L., and Capel, B., SRY and the standoff in sex determination, Mol. Endocrinol., 2008, vol. 22, no. 1, pp. 1–9.

    CAS  Article  PubMed  Google Scholar 

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Correspondence to Osman Demirhan.

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Demirhan, O., Yilmaz, M.B., Tanriverdi, N. et al. Identification of the short arm of the Y chromosome by cytogenetic and molecular analyses. Cytol. Genet. 51, 60–64 (2017).

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  • Y isochromosome
  • SRY gene
  • azospermia
  • QF-PCR