Minimal Haplotype Loci

The number of Y chromosome short tandem repeat (Y-STR) loci available for use in human identity testing has increased dramatically since the turn of the century and the availability of the human genome sequence. In the 1990s only a handful of Y-STR markers were characterized and available for use. At the beginning of 2002, only about 30 Y-STRs were available for researchers (Butler 2003). Since that time more than 200 new Y-STRs have been deposited in the Genome Database (GDB;; Kayser et al. 2004).

Yet even with a limited number of loci available at the time, a core set was selected in 1997 that continue to serve as 'minimal haplotype' loci (Kayser et al. 1997, Pascali et al. 1998). The minimal haplotype is defined by the single copy Y-STR loci DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, and the highly polymorphic multi-copy locus DYS385 a/b (Schneider et al. 1998). By means of a multicenter study, more than 4000 male DNA samples from 48 different subpopulation groups were studied with the single copy loci in the minimal haplotype set (de Knijff et al. 1997). This work formed the basis for what is now the online Y-STR Haplotype Reference Database (; that will be described in more detail below.

In January 2003, the U.S. Scientific Working Group on DNA Analysis Methods (SWGDAM) recommended use of the minimal haplotype loci plus two additional single-copy Y-STRs: DYS438 and DYS439 (Ayub et al. 2000). Information regarding these core loci may be found in Table 9.2. Although other Y-STRs will be added to databases as their value is demonstrated and they become part of commercially available kits, the original minimal haplotype loci and SWGDAM recommended Y-STRs are likely to dominate human identity applications in the coming years.





PCR Product








DYS393 3.04 AGAT

DYS19 9.44 TAGA

DYS391 13.41 TCTA

DYS437 13.78 TCTA

DYS439 13.83 AGAT

DYS389I/II 13.92

DYS438 14.25

DYS390 16.52

DYS385 a/b 20.00, 20.04 GAAA

DYS392 21.78 TAT






104-136 bp 232-268 bp 90-118 bp 183-199 bp 203-231 bp

TCTG TCTA 10-15/24-34 148-168bp/256-296bp 0.538 /0.675

TTTTC 8-12 101-121 bp 0.594

TCTA TCTG 18-27 191-227 bp 0.701

7-25 243-315 bp 0.838

7-18 294-327 bp 0.596

Table 9.2

Characteristics of minimal haplotype and SWGDAM-recommended Y-STR loci. Positions in megabases (Mb) along the Y chromosome were determined with the human genome reference sequence in January 2003 (see Butler 2003). Allele ranges are calculated from hit allelic ladders and do not represent the full range of alleles observed in world populations. PCR product sizes are those present in the PowerPleX® Y hit for the alleles listed. The STR diversity values are calculated from 244 U.S. Caucasian males (Schoske et al. 2004) and are useful to rank the relative informativeness of the loci. Note thatDYS437 is not one of the recommended loci but is present in the PowerPleX® Y kit.

Figure 9.5

Schematic illustration of how multiple PCR primer binding sites give rise to multi-copy PCR products for (a) DYS385a/b and (b) DYS389I/II. Arrows represent either forward F' or reverse 'R' primers. In the case of DYS385 a/b, the entire region around the STR repeat is duplicated and spaced about 40,775bp apart on the long arm of the Y chromosome. Thus, amplification with a single set of primers gives rise to one peak if the 'a' repeat region is equal in size to the 'b' repeat region or separate peaks if 'a' and 'b' differ in length. DYS389 possesses two primary repeat regions that are flanked on one side by a similar sequence. Widely used forward primers bind adjacent to both repeats generating amplicons that differ in size by ~120bp. Note thatDYS389II is inclusive of the DYS389I repeat region and therefore some analyses subtract DYS389II-DYS389I repeats.

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