PMC:2668061 / 9877-12295 JSONTXT

{"project":"2_test","denotations":[{"id":"19061982-16759179-2048673","span":{"begin":139,"end":141},"obj":"16759179"},{"id":"19061982-16759179-2048674","span":{"begin":311,"end":313},"obj":"16759179"},{"id":"19061982-16759179-2048675","span":{"begin":461,"end":463},"obj":"16759179"},{"id":"19061982-16026953-2048676","span":{"begin":970,"end":972},"obj":"16026953"},{"id":"19061982-16759179-2048677","span":{"begin":1178,"end":1180},"obj":"16759179"},{"id":"19061982-11827954-2048678","span":{"begin":1396,"end":1398},"obj":"11827954"},{"id":"19061982-11827954-2048679","span":{"begin":1735,"end":1737},"obj":"11827954"},{"id":"19061982-12897772-2048680","span":{"begin":1757,"end":1759},"obj":"12897772"},{"id":"19061982-11852201-2048681","span":{"begin":2245,"end":2247},"obj":"11852201"},{"id":"19061982-11852201-2048682","span":{"begin":2352,"end":2354},"obj":"11852201"}],"text":"Y Chromosome Haplotyping\nBinary markers (Figure 1) on the nonrecombining region of the Y chromosome were typed in hierarchical multiplexes,43 via the SNaPshot minisequencing procedure (Applied Biosystems) and an ABI3100 Genetic Analyzer (Applied Biosystems). All samples were initially analyzed with multiplex I43 (containing the markers M9, M69, M89, M145, M170, M172, M201, and 12f2). Samples derived for M9 (haplogroup [hg] K) were analyzed with multiplex II43 (containing M17, M45, M173, M207, P25, and SRY10831). Two individuals derived for M45 but ancestral for M207 (hgP∗[xR]) were analyzed with the markers MEH2 and M3 and could thus be assigned to hgQ∗(xQ3). Samples derived for M173 but ancestral for SRY10831.2 and M17 (hgR1∗[xR1a]) were further analyzed with multiplex IV—which, to our knowledge, is previously unpublished—containing the markers M65, M153, M222, M269, and SRY-2627. Ten individuals carry reversions of the marker P25 through gene conversion,44 and the allelic state of this marker in these chromosomes is therefore ignored for the purposes of this study. Samples derived for M145 within multiplex I (in hgDE) were further analyzed with multiplex III43 (containing M33, M35, M75, M78, M81, M96, M123, and P2), and the marker M2 was also analyzed as appropriate. Previously unreported primers were designed on the basis of published information about polymorphic sites.45 Note that hgR2 (R-M124) is reported in Figure 1, because it was detected in the Sephardic Jewish sample (Table S1, available online), but was not typed in the Iberian samples, because all chromosomes derived for M207 (hgR) were also derived for M173 (hgR1).\nNomenclature of haplogroups is in accordance with the Y Chromosome Consortium,45 uses updated names,40 and is given in Figure 1. We employ shorthand names as follows: E3b∗ refers to E3b∗(xE3b1, E3b2, E3b3), also known as E-M35∗(xM78, M81, M123); and R1b3∗ refers to R1b3∗(xR1b3b, R1b3d, R1b3f, R1b3g), also known as R-M269∗(xM65, M153, SRY-2627, M222).\nNineteen Y-chromosomal STRs (DYS19, DYS385a/b, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, DYS460, DYS461, DYS462) were typed in three multiplexes, as described previously,46 on an ABI3100 Genetic Analyzer (Applied Biosystems). Allele nomenclature is as reported by Bosch et al.,46 and DYS385a and DYS385b were omitted from statistical analyses."}