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Development of Y STR Megaplex Assays



R Schoske, John Butler, Peter Vallone, Margaret C. Kline, M. Prinz, A J. Redd, M F. Hammer


Y Chromosome short tandem repeat markers have a number of applications in human identity testing including typing the perpetrator of sexual assault cases without differential extraction and tracing paternal lineages for missing person investigations. In order for Y STR systems to become more widely accepted within the forensic DNA typing community, population studies and robust assays are required. We have focused on developing new Y STR multiplexes that can provide a high degree of discrimination between unrelated males. The Y STR markers we are working with include hexanucleotide repeat DYS448, penanucleotides DYS438, DYS446, DYS447, DYS450, tetranucleotide repeat DYS19, DYS385 I/II, DYS389 I/II, DYS390, DYS391, DYS393, DYS437, DYS439, DYS441, DYS442, GATA A7.1, GATA H4, GO9411, trinucleotides DYS388, DYS392, DYS426 and the dinucleotide repeat YCAII. Primers for the markers DYS385, DYS389 and YCAII target duplicated regions of the Y chromosome and thus can produce two polymorphic peaks with each primer set. The multiplexes we are developing are the first to include all of the European 11-locus extended haplotype in a single reaction.We have compared our results to the commercially available Y-Plex 6 kit from Reliagene that amplifies 6 Y STRs. In order to improve the power of discrimination for Y chromosome tests, we have developed strategies for rapidly preparing multiplex PCR assays that utilize both four and five dye chemistries for detection and permit simultaneous amplification of 20 or more Y STR markers in a single reaction. Primer design issues will be reviewed, as will our efforts to avoid any homology with X chromosome sequences. Primers have been redesigned from previously published work with these Y STR markers in order to make them more compatible in a multiplex amplification. Results will be shown using our new Y STR multiplex from 3 different laboratories. In addition, allele ranges for each of the Y STR markers have been well characterized in a diverse set of world population samples.
Proceedings Title
Twelfth International Symposium on Human Identification - 2001
Conference Dates
October 10-13, 2001
Conference Location
Biloxi, MS, US


high throughput DNA testing, multiplex PCR, Y-STR markers


Schoske, R. , Butler, J. , Vallone, P. , Kline, M. , Prinz, M. , Redd, A. and Hammer, M. (2001), Development of Y STR Megaplex Assays, Twelfth International Symposium on Human Identification - 2001, Biloxi, MS, US (Accessed April 17, 2024)
Created November 30, 2001, Updated October 15, 2021