MSY Breakpoint Mapper       Home | Breakpoint Mapper | User Guide | Publications | Page Laboratory | Contact


Human MSY sequence

  • The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes.
    Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, Chinwalla A, Delehaunty A, Delehaunty K, Du H, Fewell G, Fulton L, Fulton R, Graves T, Hou SF, Latrielle P, Leonard S, Mardis E, Maupin R, McPherson J, Miner T, Nash W, Nguyen C, Ozersky P, Pepin K, Rock S, Rohlfing T, Scott K, Schultz B, Strong C, Tin-Wollam A, Yang SP, Waterston RH, Wilson RK, Rozen S, Page DC (2003) Nature 423: 825-837.

  • Abundant gene conversion between arms of palindromes in human and ape Y chromosomes.
    Rozen S, Skaletsky H, Marszalek JD, Minx PJ, Cordum HS, Waterston RH, Wilson RK, Page DC (2003) Nature 423: 873-6.

  • Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome.
    Kirsch S, Weiss B, Miner TL, Waterston RH, Clark RA, Eichler EE, Munch C, Schempp W, Rappold G (2005) Genome Res 15: 195-204.

  • A physical map of the human Y chromosome.
    Tilford CA, Kuroda-Kawaguchi T, Skaletsky H, Rozen S, Brown LG, Rosenberg M, McPherson JD, Wylie K, Sekhon M, Kucaba TA, Waterston RH, Page DC (2001) Nature 409: 943-5.

Deletion mapping
  • The human Y chromosome: a 43-interval map based on naturally occurring deletions.
    Vollrath D, Foote S, Hilton A, Brown LG, Beer-Romero P, Bogan JS, Page DC (1992) Science 258: 52-9.

Primer design
Structural polymorphism
  • High mutation rates have driven extensive structural polymorphism among human Y chromosomes.
    Repping S, van Daalen SK, Brown LG, Korver CM, Lange J, Marszalek JD, Pyntikova T, van der Veen F, Skaletsky H, Page DC, Rozen S (2006) Nat Genet 38: 463-7.

AZFa deletions
  • Deletion of azoospermia factor a (AZFa) region of human Y chromosome caused by recombination between HERV15 proviruses.
    Sun C, Skaletsky H, Rozen S, Gromoll J, Nieschlag E, Oates R, Page DC (2000) Hum Mol Genet 9: 2291-6.

  • Two long homologous retroviral sequence blocks in proximal Yq11 cause AZFa microdeletions as a result of intrachromosomal recombination events.
    Kamp C, Hirschmann P, Voss H, Huellen K, Vogt PH (2000) Hum Mol Genet 9: 2563-2572.

  • Divergent outcomes of intrachromosomal recombination on the human Y chromosome: male infertility and recurrent polymorphism.
    Blanco P, Shlumukova M, Sargent CA, Jobling MA, Affara N, Hurles ME (2000) J Med Genet 37: 752-8.

P5-P1 deletions (formerly AZFb)
  • Recombination between palindromes P5 and P1 on the human Y chromosome causes massive deletions and spermatogenic failure.
    Repping S, Skaletsky H, Lange J, Silber S, Van Der Veen F, Oates RD, Page DC, Rozen S (2002) Am J Hum Genet 71: 906-922.

AZFc deletions
  • The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men.
    Kuroda-Kawaguchi T, Skaletsky H, Brown LG, Minx PJ, Cordum HS, Waterston RH, Wilson RK, Silber S, Oates R, Rozen S, Page DC (2001) Nat Genet 29: 279-286.

gr/gr and b1/b3 deletions
  • Polymorphism for a 1.6-Mb deletion of the human Y chromosome persists through balance between recurrent mutation and haploid selection.
    Repping S, Skaletsky H, Brown L, van Daalen SK, Korver CM, Pyntikova T, Kuroda-Kawaguchi T, de Vries JW, Oates RD, Silber S, van der Veen F, Page DC, Rozen S (2003) Nat Genet 35: 247-251.

b2/b3 deletions
  • A large AZFc deletion removes DAZ3/DAZ4 and nearby genes from men in Y haplogroup N.
    Fernandes S, Paracchini S, Meyer LH, Floridia G, Tyler-Smith C, Vogt PH (2004) Am J Hum Genet 74: 180-7.

  • A family of human Y chromosomes has dispersed throughout northern Eurasia despite a 1.8-Mb deletion in the azoospermia factor c region.
    Repping S, van Daalen SK, Korver CM, Brown LG, Marszalek JD, Gianotten J, Oates RD, Silber S, van der Veen F, Page DC, Rozen S (2004) Genomics 83:1046-1052.

TSPY-TSPY deletions
  • Structural variation on the short arm of the human Y chromosome: recurrent multigene deletions encompassing Amelogenin Y.
    Jobling MA, Lo IC, Turner DJ, Bowden GR, Lee AC, Xue Y, Carvalho-Silva D, Hurles ME, Adams SM, Chang YM, Kraaijenbrink T, Henke J, Guanti G, McKeown B, van Oorschot RA, Mitchell RJ, de Knijff P, Tyler-Smith C, Parkin EJ (2007) Hum Mol Genet 16: 307-316.

Isodicentric Y chromosomes and Y isochromosomes
  • Isodicentric Y chromosomes and sex disorders as byproducts of homologous recombination that maintains palindromes.
    Lange J, Skaletsky H, van Daalen SKM, Embry SL, Korver CM, Brown LG, Oates RD, Silber S, Repping S, Page DC (2009) Cell 138: 855-869.

PseudoisoY chromosomes
  • Intrachromosomal homologous recombination between inverted amplicons on opposing Y-chromosome arms.
    Lange J, Noordam MJ, van Daalen SK, Skaletsky H, Clark BA, Macville MV, Page DC, Repping S (2012) Genomics 102: 257-264.