Structural variation of the human genome: mechanisms, assays, and role in male infertility

References

• Andersson, M., Page, D.C., Pettay, D., Subrt, I., Turleau, C., de Grouchy, J., (1988) Y;autosome translocations and mosaicism in the aetiology of 45, X maleness: assignment of fertility factor to distal Yq11. Hum Genet 79:2–7.
   PubMed Web of Science ®Google Scholar
• Arnemann, J., Epplen, J.T., Cooke, H.J., Sauermann, U., Engel, W., Schmidtke, J. (1987) A human Y-chromosomal DNA sequence expressed in testicular tissue. Nucleic Acids Res 15:8713–8724.
   PubMed Web of Science ®Google Scholar
• Bailey, J.A., Gu, Z., Clark, R.A., Reinert, K., Samonte, R.V., Schwartz, S., (2002) Recent segmental duplications in the human genome. Science 297:1003–1007.
   Google Scholar
• Balaresque, P., Bowden, G.R., Parkin, E.J., Omran, G.A., Heyer, E., Quintana-Murci, L., (2008) Dynamic nature of the proximal AZFc region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis. Hum Mutat 29:1171–1180.
   PubMed Web of Science ®Google Scholar
• Barbouti, A., Stankiewicz, P., Nusbaum, C., Cuomo, C., Cook, A., Hoglund, M., (2004) The breakpoint region of the most common isochromosome, i(17q), in human neoplasia is characterized by a complex genomic architecture with large, palindromic, low-copy repeats. Am J Hum Genet 74:1–10.
   PubMed Web of Science ®Google Scholar
• Beck, C.R., Collier, P., Macfarlane, C., Malig, M., Kidd, J.M., Eichler, E.E., (2010) LINE-1 retrotransposition activity in human genomes. Cell 141:1159–1170.
   PubMed Web of Science ®Google Scholar
• Bi, W., Park, S.S., Shaw, C.J., Withers, M.A., Patel, P.I., Lupski, J.R. (2003) Reciprocal crossovers and a positional preference for strand exchange in recombination events resulting in deletion or duplication of chromosome 17p11.2. Am J Hum Genet 73:1302–1315.
   PubMedGoogle Scholar
• Blanco, P., Shlumukova, M., Sargent, C.A., Jobling, M.A., Affara, N., Hurles, M.E. (2000) Divergent outcomes of intrachromosomal recombination on the human Y chromosome: male infertility and recurrent polymorphism. J Med Genet 37:752–758.
   PubMed Web of Science ®Google Scholar
• Bosch, E., Jobling, M.A. (2003) Duplications of the AZFa region of the human Y chromosome are mediated by homologous recombination between HERVs and are compatible with male fertility. Hum Mol Genet 12:341–347.
   PubMed Web of Science ®Google Scholar
• Bruder, C.E., Piotrowski, A., Gijsbers, A.A., Andersson, R., Erickson, S., Diaz de Stahl, T., (2008) Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles. Am J Hum Genet 82:763–771.
   PubMed Web of Science ®Google Scholar
• Carvalho, C.M., Lupski, J.R. (2008) Copy number variation at the breakpoint region of isochromosome 17q. Genome Res 18:1724–1732.
   PubMed Web of Science ®Google Scholar
• Carvalho, C.M., Santos, F.R. (2005) Human Y-chromosome variation and male dysfunction. J Mol Genet Med 1:63–75.
   PubMedGoogle Scholar
• Carvalho, C.M., Zhang, F., Liu, P., Patel, A., Sahoo, T., Bacino, C.A., (2009) Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching. Hum Mol Genet 18:2188–2203.
   PubMed Web of Science ®Google Scholar
• Carvalho, C.M., Zuccherato, L.W., Bastos-Rodrigues, L., Santos, F.R., Pena, S.D. (2006a) No association found between gr/gr deletions and infertility in Brazilian males. Mol Hum Reprod 12:269–273.
   PubMed Web of Science ®Google Scholar
• Carvalho, C.M., Zuccherato, L.W., Fujisawa, M., Shirakawa, T., Ribeiro-dos-Santos, A.K., Santos, S.E., (2006b) Study of AZFc partial deletion gr/gr in fertile and infertile Japanese males. J Hum Genet 51:794–799.
   PubMed Web of Science ®Google Scholar
• Chance, P.F., Alderson, M.K., Leppig, K.A., Lensch, M.W., Matsunami, N., Smith, B., (1993) DNA deletion associated with hereditary neuropathy with liability to pressure palsies. Cell 72:143–151.
   PubMed Web of Science ®Google Scholar
• Chandley, A.C., Gosden, J.R., Hargreave, T.B., Spowart, G., Speed, R.M., McBeath, S. (1989) Deleted Yq in the sterile son of a man with a satellited Y chromosome (Yqs). J Med Genet 26:145–153.
   PubMed Web of Science ®Google Scholar
• Chen, K.S., Manian, P., Koeuth, T., Potocki, L., Zhao, Q., Chinault, A.C., (1997) Homologous recombination of a flanking repeat gene cluster is a mechanism for a common contiguous gene deletion syndrome. Nat Genet 17:154–163.
   PubMed Web of Science ®Google Scholar
• Conrad, D.F., Bird, C., Blackburne, B., Lindsay, S., Mamanova, L., Lee, C., (2010) Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nat Genet 42:385–391.
   PubMed Web of Science ®Google Scholar
• Costa, P., Goncalves, R., Ferras, C., Fernandes, S., Fernandes, A.T., Sousa, M., (2008) Identification of new breakpoints in AZFb and AZFc. Mol Hum Reprod 14:251–258.
   PubMed Web of Science ®Google Scholar
• de Kretser, D.M. (1997) Male infertility. Lancet 349:787–790.
   PubMed Web of Science ®Google Scholar
• Elghezal, H., Hidar, S., Braham, R., Denguezli, W., Ajina, M., Saad, A. (2006) Chromosome abnormalities in one thousand infertile males with nonobstructive sperm disorders. Fertil Steril 86:1792–1795.
   PubMed Web of Science ®Google Scholar
• Ewing, A.D., Kazazian, H.H. Jr., (2010) High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res 20:1262–1270.
   PubMed Web of Science ®Google Scholar
• Ferlin, A., Arredi, B., Speltra, E., Cazzadore, C., Selice, R., Garolla, A., (2007a) Molecular and clinical characterization of Y chromosome microdeletions in infertile men: a 10-year experience in Italy. J Clin Endocrinol Metab 92:762–770.
   PubMed Web of Science ®Google Scholar
• Ferlin, A., Moro, E., Rossi, A., Dallapiccola, B., Foresta, C. (2003) The human Y chromosome's azoospermia factor b (AZFb) region: sequence, structure, and deletion analysis in infertile men. J Med Genet 40:18–24.
   PubMed Web of Science ®Google Scholar
• Ferlin, A., Raicu, F., Gatta, V., Zuccarello, D., Palka, G., Foresta, C. (2007b) Male infertility: role of genetic background. Reprod Biomed Online 14:734–745.
   PubMed Web of Science ®Google Scholar
• Ferlin, A., Tessari, A., Ganz, F., Marchina, E., Barlati, S., Garolla, A., (2005) Association of partial AZFc region deletions with spermatogenic impairment and male infertility. J Med Genet 42:209–213.
   PubMed Web of Science ®Google Scholar
• Flores, M., Morales, L., Gonzaga-Jauregui, C., Dominguez-Vidana, R., Zepeda, C., Yanez, O., (2007) Recurrent DNA inversion rearrangements in the human genome. Proc Natl Acad Sci USA 104:6099–6106.
   PubMed Web of Science ®Google Scholar
• Foresta, C., Ferlin, A., Moro, E. (2000) Deletion and expression analysis of AZFa genes on the human Y chromosome revealed a major role for DBY in male infertility. Hum Mol Genet 9:1161–1169.
   PubMed Web of Science ®Google Scholar
• Gatta, V., Stuppia, L., Calabrese, G., Morizio, E., Guanciali-Franchi, P., Palka, G. (2002) A new case of Yq microdeletion transmitted from a normal father to two infertile sons. J Med Genet 39:E27.
   PubMedGoogle Scholar
• Giachini, C., Laface, I., Guarducci, E., Balercia, G., Forti, G., Krausz, C. (2008) Partial AZFc deletions and duplications: clinical correlates in the Italian population. Hum Genet 124:399–410.
   PubMed Web of Science ®Google Scholar
• Giachini, C., Nuti, F., Turner, D.J., Laface, I., Xue, Y., Daguin, F., (2009) TSPY1 copy number variation influences spermatogenesis and shows differences among Y lineages. J Clin Endocrinol Metab 94:4016–4022.
   PubMed Web of Science ®Google Scholar
• Gu, W., Zhang, F., Lupski, J.R. (2008) Mechanisms for human genomic rearrangements. Pathogenetics 1:4.
   PubMedGoogle Scholar
• Hastings, P.J., Ira, G., Lupski, J.R. (2009a) A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 5:e1000327.
   PubMed Web of Science ®Google Scholar
• Hastings, P.J., Lupski, J.R., Rosenberg, S.M., Ira, G. (2009b) Mechanisms of change in gene copy number. Nat Rev Genet 10:551–564.
   PubMed Web of Science ®Google Scholar
• Huang, C.R., Schneider, A.M., Lu, Y., Niranjan, T., Shen, P., Robinson, M.A., (2010) Mobile interspersed repeats are major structural variants in the human genome. Cell 141:1171–1182.
   PubMedGoogle Scholar
• Hurles, M.E., Willey, D., Matthews, L., Hussain, S.S. (2004) Origins of chromosomal rearrangement hotspots in the human genome: evidence from the AZFa deletion hotspots. Genome Biol 5:R55.
   Web of Science ®Google Scholar
• Inoue, K., Osaka, H., Thurston, V.C., Clarke, J.T., Yoneyama, A., Rosenbarker, L., (2002) Genomic rearrangements resulting in PLP1 deletion occur by nonhomologous end joining and cause different dysmyelinating phenotypes in males and females. Am J Hum Genet 71:838–853.
   PubMed Web of Science ®Google Scholar
• Iskow, R.C., McCabe, M.T., Mills, R.E., Torene, S., Pittard, W.S., Neuwald, A.F., (2010) Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 141:1253–1261.
   PubMed Web of Science ®Google Scholar
• Jobling, M.A. (2008) Copy number variation on the human Y chromosome. Cytogenet Genome Res 123:253–262.
   PubMed Web of Science ®Google Scholar
• Jobling, M.A., Lo, I.C., Turner, D.J., Bowden, G.R., Lee, A.C., Xue, Y., (2007) Structural variation on the short arm of the human Y chromosome: recurrent multigene deletions encompassing Amelogenin Y. Hum Mol Genet 16:307–316.
   PubMed Web of Science ®Google Scholar
• Jobling, M.A., Tyler-Smith, C. (2003) The human Y chromosome: an evolutionary marker comes of age. Nat Rev Genet 4:598–612.
   PubMed Web of Science ®Google Scholar
• Kamp, C., Hirschmann, P., Voss, H., Huellen, K., Vogt, P.H. (2000) Two long homologous retroviral sequence blocks in proximal Yq11 cause AZFa microdeletions as a result of intrachromosomal recombination events. Hum Mol Genet 9:2563–2572.
   PubMed Web of Science ®Google Scholar
• Kamp, C., Huellen, K., Fernandes, S., Sousa, M., Schlegel, P.N., Mielnik, A., (2001) High deletion frequency of the complete AZFa sequence in men with Sertoli-cell-only syndrome. Mol Hum Reprod 7:987–994.
   PubMed Web of Science ®Google Scholar
• Kee, K., Angeles, V.T., Flores, M., Nguyen, H.N., Reijo Pera, R.A. (2009) Human DAZL, DAZ and BOULE genes modulate primordial germ-cell and haploid gamete formation. Nature 462:222–225.
   PubMed Web of Science ®Google Scholar
• Krausz, C., Degl'Innocenti, S., Nuti, F., Morelli, A., Felici, F., Sansone, M., (2006) Natural transmission of USP9Y gene mutations: a new perspective on the role of AZFa genes in male fertility. Hum Mol Genet 15:2673–2681.
   PubMed Web of Science ®Google Scholar
• Kuhnert, B., Gromoll, J., Kostova, E., Tschanter, P., Luetjens, C.M., Simoni, M., (2004) Case report: natural transmission of an AZFc Y-chromosomal microdeletion from father to his sons. Hum Reprod 19:886–888.
   PubMed Web of Science ®Google Scholar
• Kuroda-Kawaguchi, T., Skaletsky, H., Brown, L.G., Minx, P.J., Cordum, H.S., Waterston, R.H., (2001) The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men. Nat Genet 29:279–286.
   PubMed Web of Science ®Google Scholar
• Lam, K.W., Jeffreys, A.J. (2006) Processes of copy-number change in human DNA: the dynamics of {alpha}-globin gene deletion. Proc Natl Acad Sci USA 103:8921–8927.
   PubMed Web of Science ®Google Scholar
• Lange, J., Skaletsky, H., van Daalen, S.K., Embry, S.L., Korver, C.M., Brown, L.G., (2009) Isodicentric Y chromosomes and sex disorders as byproducts of homologous recombination that maintains palindromes. Cell 138:855–869.
   PubMed Web of Science ®Google Scholar
• Lau, Y.F., Li, Y., Kido, T. (2009) Gonadoblastoma locus and the TSPY gene on the human Y chromosome. Birth Defects Res C Embryo Today 87:114–122.
   PubMedGoogle Scholar
• Lee, J.A., Carvalho, C.M., Lupski, J.R. (2007) A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131:1235–1247.
   PubMed Web of Science ®Google Scholar
• Lee, J.A., Inoue, K., Cheung, S.W., Shaw, C.A., Stankiewicz, P., Lupski, J.R. (2006) Role of genomic architecture in PLP1 duplication causing Pelizaeus-Merzbacher disease. Hum Mol Genet 15:2250–2265.
   PubMed Web of Science ®Google Scholar
• Lidegaard, O., Mikkelsen, A.L., Meldgaard, M., Brondum-Nielsen, K., Lindenberg, S. (1998) Severe male infertility. Impact of genetic factors on diagnosis and counselling. Acta Obstet Gynecol Scand 77:799–803.
   PubMed Web of Science ®Google Scholar
• Lieber, M.R. (2008) The mechanism of human nonhomologous DNA end joining. J Biol Chem 283:1–5.
   PubMed Web of Science ®Google Scholar
• Lindsay, S.J., Khajavi, M., Lupski, J.R., Hurles, M.E. (2006) A chromosomal rearrangement hotspot can be identified from population genetic variation and is coincident with a hotspot for allelic recombination. Am J Hum Genet 79:890–902.
   PubMed Web of Science ®Google Scholar
• Lu, C., Zhang, J., Li, Y., Xia, Y., Zhang, F., Wu, B., (2009) The b2/b3 subdeletion shows higher risk of spermatogenic failure and higher frequency of complete AZFc deletion than the gr/gr subdeletion in a Chinese population. Hum Mol Genet 18:1122–1130.
   PubMed Web of Science ®Google Scholar
• Luddi, A., Margollicci, M., Gambera, L., Serafini, F., Cioni, M., De Leo, V., (2009) Spermatogenesis in a man with complete deletion of USP9Y. N Engl J Med 360:881–885.
   PubMed Web of Science ®Google Scholar
• Lupski, J.R. (2010) Retrotransposition and structural variation in the human genome. Cell 141:1110–1112.
   PubMed Web of Science ®Google Scholar
• Lupski, J.R. (2009) Genomic disorders ten years on. Genome Med 1:42.
   PubMedGoogle Scholar
• Lupski, J.R. (2007) Genomic rearrangements and sporadic disease. Nat Genet 39:S43–47.
   PubMed Web of Science ®Google Scholar
• Lupski, J.R. (2004) Hotspots of homologous recombination in the human genome: not all homologous sequences are equal. Genome Biol 5:242.
   Google Scholar
• Lupski, J.R. (1998) Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet 14:417–422.
   PubMed Web of Science ®Google Scholar
• Lupski, J.R., de Oca-Luna, R.M., Slaugenhaupt, S., Pentao, L., Guzzetta, V., Trask, B.J., (1991) DNA duplication associated with Charcot-Marie-Tooth disease type 1A. Cell 66:219–232.
   PubMed Web of Science ®Google Scholar
• Lynch, M., Cram, D.S., Reilly, A., O'Bryan, M.K., Baker, H.W., de Kretser, D.M., (2005) The Y chromosome gr/gr subdeletion is associated with male infertility. Mol Hum Reprod 11:507–512.
   PubMed Web of Science ®Google Scholar
• Ma, K., Sharkey, A., Kirsch, S., Vogt, P., Keil, R., Hargreave, T.B., (1992) Towards the molecular localisation of the AZF locus: mapping of microdeletions in azoospermic men within 14 subintervals of interval 6 of the human Y chromosome. Hum Mol Genet 1:29–33.
   PubMed Web of Science ®Google Scholar
• Machev, N., Saut, N., Longepied, G., Terriou, P., Navarro, A., Levy, N., (2004) Sequence family variant loss from the AZFc interval of the human Y chromosome, but not gene copy loss, is strongly associated with male infertility. J Med Genet 41:814–825.
   PubMed Web of Science ®Google Scholar
• McLachlan, R.I., O'Bryan, M.K. (2010) Clinical Review#: State of the art for genetic testing of infertile men. J Clin Endocrinol Metab 95:1013–1024.
   PubMed Web of Science ®Google Scholar
• Mulhall, J.P., Reijo, R., Alagappan, R., Brown, L., Page, D., Carson, R., (1997) Azoospermic men with deletion of the DAZ gene cluster are capable of completing spermatogenesis: fertilization, normal embryonic development and pregnancy occur when retrieved testicular spermatozoa are used for intracytoplasmic sperm injection. Hum Reprod 12:503–508.
   PubMed Web of Science ®Google Scholar
• Myers, S., Freeman, C., Auton, A., Donnelly, P., McVean, G. (2008) A common sequence motif associated with recombination hot spots and genome instability in humans. Nat Genet 40:1124–1129.
   PubMed Web of Science ®Google Scholar
• Navarro-Costa, P., Goncalves, J., Plancha, C.E. (2010) The AZFc region of the Y chromosome: at the crossroads between genetic diversity and male infertility. Hum Reprod Update 16:525–542.
   PubMed Web of Science ®Google Scholar
• Nickkholgh, B., Noordam, M.J., Hovingh, S.E., van Pelt, A.M., van der Veen, F., Repping, S. (2010) Y chromosome TSPY copy numbers and semen quality. Fertil Steril 94:1744–1747.
   PubMed Web of Science ®Google Scholar
• O'Flynn O'Brien, K.L., Varghese, A.C., Agarwal, A. (2010) The genetic causes of male factor infertility: a review. Fertil Steril 93:1–12.
   PubMed Web of Science ®Google Scholar
• Ou, Z., Stankiewicz, P., Breman, A.M., Wiszniewska, J., Cooper, M.L., Shao, L., et al. Observation and prediction of recurrent human translocations mediated by NAHR between non-homologous chromosomes. Genome Res In press.
   Google Scholar
• Pang, M.G., Hoegerman, S.F., Cuticchia, A.J., Moon, S.Y., Doncel, G.F., Acosta, A.A., (1999) Detection of aneuploidy for chromosomes 4, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 21, X and Y by fluorescence in-situ hybridization in spermatozoa from nine patients with oligoasthenoteratozoospermia undergoing intracytoplasmic sperm injection. Hum Reprod 14:1266–1273.
   PubMed Web of Science ®Google Scholar
• Piotrowski, A., Bruder, C.E., Andersson, R., Diaz de Stahl, T., Menzel, U., Sandgren, J., (2008) Somatic mosaicism for copy number variation in differentiated human tissues. Hum Mutat 29:1118–1124.
   Google Scholar
• Potocki, L., Bi, W., Treadwell-Deering, D., Carvalho, C.M., Eifert, A., Friedman, E.M., (2007) Characterization of Potocki-Lupski syndrome (dup(17)(p11.2p11.2)) and delineation of a dosage-sensitive critical interval that can convey an autism phenotype. Am J Hum Genet 80:633–649.
   PubMed Web of Science ®Google Scholar
• Potocki, L., Chen, K.S., Park, S.S., Osterholm, D.E., Withers, M.A., Kimonis, V., (2000) Molecular mechanism for duplication 17p11.2- the homologous recombination reciprocal of the Smith-Magenis microdeletion. Nat Genet 24:84–87.
   PubMed Web of Science ®Google Scholar
• Reijo, R., Lee, T.Y., Salo, P., Alagappan, R., Brown, L.G., Rosenberg, M., (1995) Diverse spermatogenic defects in humans caused by Y chromosome deletions encompassing a novel RNA-binding protein gene. Nat Genet 10:383–393.
   PubMed Web of Science ®Google Scholar
• Reiter, L.T., Murakami, T., Koeuth, T., Pentao, L., Muzny, D.M., Gibbs, R.A., (1996) A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element. Nat Genet 12:288–297.
   PubMed Web of Science ®Google Scholar
• Repping, S., Skaletsky, H., Brown, L., van Daalen, S.K., Korver, C.M., Pyntikova, T., (2003) Polymorphism for a 1.6-Mb deletion of the human Y chromosome persists through balance between recurrent mutation and haploid selection. Nat Genet 35:247–251.
   PubMed Web of Science ®Google Scholar
• Repping, S., Skaletsky, H., Lange, J., Silber, S., Van Der Veen, F., Oates, R.D., (2002) Recombination between palindromes P5 and P1 on the human Y chromosome causes massive deletions and spermatogenic failure. Am J Hum Genet 71:906–922.
   PubMed Web of Science ®Google Scholar
• Repping, S., van Daalen, S.K., Brown, L.G., Korver, C.M., Lange, J., Marszalek, J.D., (2006) High mutation rates have driven extensive structural polymorphism among human Y chromosomes. Nat Genet 38:463–467.
   PubMed Web of Science ®Google Scholar
• Repping, S., van Daalen, S.K., Korver, C.M., Brown, L.G., Marszalek, J.D., Gianotten, J., (2004) A family of human Y chromosomes has dispersed throughout northern Eurasia despite a 1.8-Mb deletion in the azoospermia factor c region. Genomics 83:1046–1052.
   PubMed Web of Science ®Google Scholar
• Rozen, S., Skaletsky, H., Marszalek, J.D., Minx, P.J., Cordum, H.S., Waterston, R.H., (2003) Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423:873–876.
   PubMed Web of Science ®Google Scholar
• Santos, F.R., Pandya, A., Tyler-Smith, C. (1998) Reliability of DNA-based sex tests. Nat Genet 18:103.
   PubMed Web of Science ®Google Scholar
• Saxena, R., de Vries, J.W., Repping, S., Alagappan, R.K., Skaletsky, H., Brown, L.G., (2000) Four DAZ genes in two clusters found in the AZFc region of the human Y chromosome. Genomics 67:256–267.
   Google Scholar
• Schultz, N., Hamra, F.K., Garbers, D.L. (2003) A multitude of genes expressed solely in meiotic or postmeiotic spermatogenic cells offers a myriad of contraceptive targets. Proc Natl Acad Sci USA 100:12201–12206.
   PubMed Web of Science ®Google Scholar
• Shaw, C.J., Lupski, J.R. (2004) Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease. Hum Mol Genet 13(Spec No 1):R57–64.
   Google Scholar
• Skaletsky, H., Kuroda-Kawaguchi, T., Minx, P.J., Cordum, H.S., Hillier, L., Brown, L.G., (2003) The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423:825–837.
   PubMed Web of Science ®Google Scholar
• Slack, A., Thornton, P.C., Magner, D.B., Rosenberg, S.M., Hastings, P.J. (2006) On the mechanism of gene amplification induced under stress in Escherichia coli. PLoS Genet 2:e48.
   PubMed Web of Science ®Google Scholar
• Stankiewicz, P., Lupski, J.R. (2002) Genome architecture, rearrangements and genomic disorders. Trends Genet 18:74–82.
   PubMed Web of Science ®Google Scholar
• Sun, C., Skaletsky, H., Birren, B., Devon, K., Tang, Z., Silber, S., (1999) An azoospermic man with a de novo point mutation in the Y-chromosomal gene USP9Y. Nat Genet 23:429–432.
   PubMed Web of Science ®Google Scholar
• Sun, C., Skaletsky, H., Rozen, S., Gromoll, J., Nieschlag, E., Oates, R., (2000) Deletion of azoospermia factor a (AZFa) region of human Y chromosome caused by recombination between HERV15 proviruses. Hum Mol Genet 9:2291–2296.
   PubMed Web of Science ®Google Scholar
• Tiepolo, L., Zuffardi, O. (1976) Localization of factors controlling spermatogenesis in the nonfluorescent portion of the human Y chromosome long arm. Hum Genet 34:119–124.
   PubMed Web of Science ®Google Scholar
• Tilford, C.A., Kuroda-Kawaguchi, T., Skaletsky, H., Rozen, S., Brown, L.G., Rosenberg, M., (2001) A physical map of the human Y chromosome. Nature 409:943–945.
   PubMed Web of Science ®Google Scholar
• Tsuchiya, K., Reijo, R., Page, D.C., Disteche, C.M. (1995) Gonadoblastoma: molecular definition of the susceptibility region on the Y chromosome. Am J Hum Genet 57:1400–1407.
   PubMed Web of Science ®Google Scholar
• Turner, D.J., Miretti, M., Rajan, D., Fiegler, H., Carter, N.P., Blayney, M.L., (2008) Germline rates of de novo meiotic deletions and duplications causing several genomic disorders. Nat Genet 40:90–95.
   PubMed Web of Science ®Google Scholar
• Tyler-Smith, C., Taylor, L., Muller, U. (1988) Structure of a hypervariable tandemly repeated DNA sequence on the short arm of the human Y chromosome. J Mol Biol 203:837–848.
   PubMed Web of Science ®Google Scholar
• Underhill, P.A., Kivisild, T. (2007) Use of Y chromosome and mitochondrial DNA population structure in tracing human migrations. Annu Rev Genet 41:539–564.
   PubMed Web of Science ®Google Scholar
• Van Assche, E., Bonduelle, M., Tournaye, H., Joris, H., Verheyen, G., Devroey, P., (1996) Cytogenetics of infertile men. Hum Reprod 11( Suppl 4):1–24; discussion 25–26.
   Google Scholar
• Vergnaud, G., Page, D.C., Simmler, M.C., Brown, L., Rouyer, F., Noel, B., (1986) A deletion map of the human Y chromosome based on DNA hybridization. Am J Hum Genet 38:109–124.
   PubMed Web of Science ®Google Scholar
• Visser, L., Westerveld, G.H., Korver, C.M., van Daalen, S.K., Hovingh, S.E., Rozen, S., (2009) Y chromosome gr/gr deletions are a risk factor for low semen quality. Hum Reprod 24:2667–2673.
   PubMed Web of Science ®Google Scholar
• Vissers, L.E., Bhatt, S.S., Janssen, I.M., Xia, Z., Lalani, S.R., Pfundt, R., (2009) Rare pathogenic microdeletions and tandem duplications are microhomology-mediated and stimulated by local genomic architecture. Hum Mol Genet 18:3579–3593.
   PubMed Web of Science ®Google Scholar
• Vodicka, R., Vrtel, R., Dusek, L., Singh, A.R., Krizova, K., Svacinova, V., (2007) TSPY gene copy number as a potential new risk factor for male infertility. Reprod Biomed Online 14:579–587.
   PubMed Web of Science ®Google Scholar
• Vogt, P., Chandley, A.C., Hargreave, T.B., Keil, R., Ma, K., Sharkey, A. (1992) Microdeletions in interval 6 of the Y chromosome of males with idiopathic sterility point to disruption of AZF, a human spermatogenesis gene. Hum Genet 89:491–496.
   PubMed Web of Science ®Google Scholar
• Vogt, P.H., Edelmann, A., Kirsch, S., Henegariu, O., Hirschmann, P., Kiesewetter, F., (1996) Human Y chromosome azoospermia factors (AZF) mapped to different subregions in Yq11. Hum Mol Genet 5:933–943.
   PubMed Web of Science ®Google Scholar
• Walsh, T.J., Pera, R.R., Turek, P.J. (2009) The genetics of male infertility. Semin Reprod Med 27:124–136.
   PubMed Web of Science ®Google Scholar
• Woodward, K.J., Cundall, M., Sperle, K., Sistermans, E.A., Ross, M., Howell, G., (2005) Heterogeneous duplications in patients with Pelizaeus-Merzbacher disease suggest a mechanism of coupled homologous and nonhomologous recombination. Am J Hum Genet 77:966–987.
   PubMed Web of Science ®Google Scholar
• Wu, B., Lu, N.X., Xia, Y.K., Gu, A.H., Lu, C.C., Wang, W., (2007) A frequent Y chromosome b2/b3 subdeletion shows strong association with male infertility in Han-Chinese population. Hum Reprod 22:1107–1113.
   PubMed Web of Science ®Google Scholar
• Yang, Y., Ma, M.Y., Xiao, C.Y., Li, L., Li, S.W., Zhang, S.Z. (2008) Massive deletion in AZFb/b+c and azoospermia with Sertoli cell only and/or maturation arrest. Int J Androl 31:573–578.
   PubMedGoogle Scholar
• Yatsenko, A.N., Yatsenko, S.A., Weedin, J.W., Lawrence, A.E., Patel, A., Peacock, S., (2010) Comprehensive 5-year study of cytogenetic aberrations in 668 infertile men. J Urol 183:1636–1642.
   PubMed Web of Science ®Google Scholar
• Zhang, F., Carvalho, C.M., Lupski, J.R. (2009a) Complex human chromosomal and genomic rearrangements. Trends Genet 25:298–307.
   PubMed Web of Science ®Google Scholar
• Zhang, F., Khajavi, M., Connolly, A.M., Towne, C.F., Batish, S.D., Lupski, J.R. (2009b) The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans. Nat Genet 41:849–853.
   PubMed Web of Science ®Google Scholar
• Zhang, F., Li, Z., Wen, B., Jiang, J., Shao, M., Zhao, Y., (2006) A frequent partial AZFc deletion does not render an increased risk of spermatogenic impairment in East Asians. Ann Hum Genet 70:304–313.
   PubMed Web of Science ®Google Scholar
• Zhang, F., Lu, C., Li, Z., Xie, P., Xia, Y., Zhu, X., (2007) Partial deletions are associated with an increased risk of complete deletion in AZFc: a new insight into the role of partial AZFc deletions in male infertility. J Med Genet 44:437–444.
   PubMed Web of Science ®Google Scholar
• Zhang, F., Potocki, L., Sampson, J.B., Liu, P., Sanchez-Valle, A., Robbins-Furman, P., (2010a) Identification of uncommon recurrent Potocki-Lupski syndrome-associated duplications and the distribution of rearrangement types and mechanisms in PTLS. Am J Hum Genet 86:462–470.
   PubMed Web of Science ®Google Scholar
• Zhang, F., Seeman, P., Liu, P., Weterman, M.A., Gonzaga-Jauregui, C., Towne, C.F., (2010b) Mechanisms for nonrecurrent genomic rearrangements associated with CMT1A or HNPP: rare CNVs as a cause for missing heritability. Am J Hum Genet 86:892–903.
   PubMed Web of Science ®Google Scholar
• Zhang, J.S., Yang-Feng, T.L., Muller, U., Mohandas, T.K., de Jong, P.J., Lau, Y.F. (1992) Molecular isolation and characterization of an expressed gene from the human Y chromosome. Hum Mol Genet 1:717–726.
   PubMedGoogle Scholar