Supplementary Information for
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.
Polymorphism for a 1.6-Mb deletion of the human Y chromosome persists through balance between recurrent mutation and haploid selection.
Nature Genetics 35, 247 (2003)
- Supplementary Table 1 Men with STS results indicating likely gr/gr deletion: they lackedsY1291 but possessed sY1161, sY1191, sY1206, and sY1201 (Fig. 1a, main text).
- Supplementary Table 2 Initial screen, prevalence of the gr/gr deletion by Y haplotype. Thegr/gr deletion was found in five Y haplotypes present in both groups of men (spermatogenicfailure and unknown spermatogenic phenotype). These five haplotypes are shaded. In all fivehaplotypes the frequency of the gr/gr deletion allele is higher among men with spermatogenic failure.
- Supplementary Table 3 Proportions of Y haplotypes among cases and controls in theassociation study are statistically indistinguishable.
- Supplementary Table 4 Association study, prevalence of the gr/gr deletion by Y haplotype.The gr/gr deletion was found in three Y haplotypes present in both cases and controls. Thesethree haplotypes are shaded. In all three haplotypes the frequency of the gr/gr deletion allele is higher among men with spermatogenic failure.
- Supplementary Table 5 Sources of “Y-diversity” samples (unknown spermatogenicphenotype) tested in initial screen.
- Supplementary Table 6 References for polymorphisms defining the Y haplotypes andgenealogy in Figure 4 (main text), Supplementary Tables 1–4, Supplementary Table 7 and Supplementary Figure 1.
- Supplementary Table 7 Polymorphisms defining Y haplotypes in Supplementary Tables 2–4.
- Figure S1 Y genealogy from Fig. 4 (main text) with Y Chromosome Consortium (YCC) branch designations (Genome Res. 12, 339-348, 2002)
- Supplementary Note Includes:
- Supplementary Note 1. Stratification is unlikely to explain association of the gr/gr deletion withspermatogenic failure.
- Supplementary Note 2. Branch D2b Y chromosomes, the YAP insertion in Japan, and the gr/grdeletion.
- Supplementary Note 3. What proportion of Y chromosomes might be gr/gr-deleted in theabsence of selection?
- Supplementary Note 4. Exploratory estimate of the effect of the gr/gr deletion on fitness.
- Supplementary Note 5. Alternative analysis, including gr/gr deletions with b2/b4 duplication or47,XYY karyotype.
- Supplementary References.