Multiplex Y-STR Analysis

Abstract

Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.

What is claimed is: 
     
         1 . A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 
     
     
         2 . The amplification primer set of  claim 1 , wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 
     
     
         3 . The amplification primer set of  claim 2 , wherein the mobility-dependent analytical technique is capillary electrophoresis. 
     
     
         4 . The amplification primer set of  claim 1 , wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 
     
     
         5 . The amplification primer set of  claim 1 , further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 
     
     
         6 . The amplification primer set of  claim 1 , comprising 25 Y-STR markers. 
     
     
         7 . The amplification primer set of  claim 1 , wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 
     
     
         8 . The amplification primer set of  claim 7 , wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 
     
     
         9 . The amplification primer set of  claim 1 , wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 
     
     
         10 . The amplification primer set of  claim 1 , wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 
     
     
         11 . The amplification primer set of  claim 1 , further comprising at least 5 Y-STR markers which are rapidly mutating loci. 
     
     
         12 . The amplification primer set of  claim 11 , wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 
     
     
         13 . The amplification primer set of  claim 12 , wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 
     
     
         14 . The amplification primer set of  claim 1 , wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 
     
     
         15 . The amplification primer set of  claim 1 , wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 
     
     
         16 . A kit for co-amplifying a set of loci of at least one DNA sample comprising:
 a) the primers of  claim 1 ; and   b) optionally, a size standard.   
     
     
         17 . The kit of  claim 16 , wherein the size standard comprises an allelic ladder. 
     
     
         18 . A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
 contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and   amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs.   
     
     
         19 . The method of  claim 18 , further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 
     
     
         20 . The method of  claim 18 , wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 
     
     
         21 . The method of  claim 18 , wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 
     
     
         22 . The method of  claim 21 , wherein the set of amplification primers comprise primers for the amplification of the alleles of 27 Y-STR markers. 
     
     
         23 . The method of  claim 18 , wherein the primers are the primers of  claim 1 . 
     
     
         24 . The method of  claim 22 , wherein the 27 Y-STR markers are DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 
     
     
         25 . The method of  claim 22 , wherein the 27 Y-STR markers are DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4.