Intrachromosomal homologous recombination between inverted amplicons on opposing Y-chromosome arms

Julian Lange*, Michiel J. Noordam, Saskia K. M. van Daalen, Helen Skaletsky, Brian A. Clark, Merryn Macville, David C. Page, Sjoerd Repping

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


Amplicons - large, nearly identical repeats in direct or inverted orientation - are abundant in the male-specific region of the human Y chromosome (MSY) and provide targets for intrachromosomal non-allelic homologous recombination (NAHR). Thus far, NAHR events resulting in deletions, duplications, inversions, or isodicentric chromosomes have been reported only for amplicon pairs located exclusively on the short arm (Yp) or the long arm (Yq). Here we report our finding of four men with Y chromosomes that evidently formed by intrachromosomal NAHR between inverted repeat pairs comprising one amplicon on Yp and one amplicon on Yq. In two men with spermatogenic failure, sister-chromatid crossing-over resulted in pseudoisoYp chromosome formation and loss of distal Yq. In two men with normal spermatogenesis, intrachromatid crossing-over generated pericentric inversions. These findings highlight the recombinogenic nature of the MSY, as intrachromosomal NAHR occurs for nearly all Y-chromosome amplicon pairs, even those located on opposing chromosome arms.
Original languageEnglish
Pages (from-to)257-264
Issue number4
Publication statusPublished - Oct 2013


  • Human Y chromosome
  • Non-allelic homologous recombination
  • Structural variation
  • Male infertility

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