- Course Introduction
- 01: Evidence & DNA
- 02: Forensic Biology
- 03: DNA Extraction & Quantitation
- 04: DNA Amplification
- 05: Amplified DNA Product Separation
- 06: STR Data Analysis & Interpretation
- 07: Population Genetics & Statistics
- 08: Communicating Results
- 09: Other DNA Markers & Technologies
- Course Resources
- Laboratory Training Manual
President's DNA Initiative
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Advancing Justice Through DNA Technology
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Advancing Justice Through DNA Technology
DNA Analyst Training
Y-STR Markers
Home > Other DNA Markers & Technologies > Other Nuclear DNA Markers and Technologies > Y-STRs > Y-STR Markers
A variety of polymorphic genetic markers have been identified in the euchromatin portion of the Y-chromosome, including a number of STR and SNP loci and a single hypervariable minisatellite locus. A number of candidate Y-SNP loci have been identified, but they suffer from a limited discrimination potential and their implementation in forensic casework is dependent upon the development of additional markers and appropriately validated detection technologies. The hypervariable minisatellite, MSY1, is the most polymorphic single locus system found on the Y-chromosome but difficulties with the required minisatellite variant repeat (MVR) technique have discouraged its operational use. Y-STR loci, on the other hand, offer a number of advantages including good discrimination potential, ease of analysis and a number of available candidate loci amenable to multiplex analysis.
Although more than three hundred STR loci have been described on the Y-chromosome a much more limited number have been appropriately evaluated for forensic casework use and some of these have presented a particular challenge for assay design. The Y-STR loci comprise di-, tri-, tetra-, and penta-nucleotide repeats with the di-nucleotides exhibiting the most polymorphism but an excessively high level of stutter artifacts.15 Due to their evolutionary relatedness, many homologous sequences are found on both the X and Y-chromosomes, which can confound the analysis of mixed male/female specimens. Additionally, some of the loci are bi-local in the sense that one or both of the primer sites and associated tandem repeats are duplicated upstream or downstream of the parent sequence. In these particular cases, two alleles are co-amplified, and there is some, but not complete, correlation between the alleles at both loci. Importantly, sample quantity limitations with forensic specimens require that candidate Y-STR loci be analyzed together in a parallel fashion by incorporating them into a multiplex PCR assay format, the design of which can be complicated by some of the aforementioned factors.
A major international multi-center study of 13 candidate Y-STR markers in 1997 resulted in recommendations for the use of nine core loci for standard forensic haplotyping (designated the minimal haplotype loci, MHL or minHt).16 The nine MHL loci include:
- DYS19
- DYS 385 (a)
- DYS 385 (b)
- DYS389 I
- DYS389 II
- DYS390
- DYS391
- DYS392
- DYS393
Subsequent to the development of the MHL loci, additional microsatellite loci were described that proved to have utility in forensic genetics. In January 2003 the Scientific Working Group on DNA Analysis Methods (SWGDAM) recommended for US forensic casework use a set of eleven core loci that included the MHL loci plus DYS 438 and DYS 439.
Click here to read about the SWGDAM recommended core loci in the Forensic Science Communications, July 2004 publication.
Commercial kit vendors in the US have incorporated the SWGDAM core loci into their Y-STR multiplex systems (ABI, Promega and Reliagene) which comprise eleven (Reliagene’s Y-PLEX-12TM), twelve (Promega’s PowerPlex YTM) or seventeen (Applied Biosystems’ Y-FilerTM ) Y-STR loci (see Table). These kits have been fully validated for forensic use according to the SWGDAM developmental validation guidelines. The kits have been designed to perform with a high degree of specificity for Y-chromosome sequences in the presence of a vast excess of X-chromosomal DNA from a female, despite the previously described extensive sequence homology between both chromosomes.
Click here to read the Revised Validation Guildelines by SWGDAM in July 2004.
Loci Comprising the MHL, SWGDAM Core Sets and Commercial Kits |
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Minimal Haplotype Loci |
SWGDAM Core Loci |
Reliagene’s Y-PLEX-12™ |
Promega’s PowerPlex Y™ |
Applied Biosystems’ Y-Filer™ |
DYS 19 DYS 385 a,b DYS 389I DYS 389II DYS 390 DYS 391 DYS 392 DYS 393
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DYS 19 DYS 385 a,b DYS 389I DYS 389II DYS 390 DYS 391 DYS 392 DYS 393 DYS 438 DYS 439
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AMEL DYS 19 DYS 385 a,b DYS 389I DYS 389II DYS 390 DYS 391 DYS 392 DYS 393 DYS 438 DYS 439
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DYS 19 DYS 385 a,b DYS 389I DYS 389I DYS 390 DYS 391 DYS 392 DYS 393 DYS 438 DYS 439 DYS 437
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DYS 19 DYS 385 a,b DYS 389I DYS 389II DYS 390 DYS 391 DYS 392 DYS 393 DYS 438 DYS 439 DYS 437 DYS 448 DYS 456 DYS 458 DYS 635 Y-GATA-H4 |
