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Y-SNP Typing of U.S. African American and Caucasian Samples Using Allele-Specific ∗ Hybridization and Primer Extension

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Y-SNP Typing of U.S. African American and Caucasian Samples Using Allele-Specific ∗ Hybridization and Primer Extension JForensic Sci, July 2004, Vol. 49, No. 4 Paper ID JFS2003303 Available online at: www.astm.org Peter M. Vallone,1 Ph.D. and John M. Butler,1 Ph.D. Y-SNP Typing of U.S. African American and Caucasian Samples Using Allele-Specific ∗ Hybridization and Primer Extension ABSTRACT: Multiplex analysis of genetic markers has become increasingly important in a number of fields, including DNA diagnostics and human identity testing. Two methods for examination of single nucleotide polymorphisms (SNPs) with a potential for a high degree of multiplex analysis of markers are primer extension with fluorescence detection, and allele-specific hybridization using flow cytometry. In this paper, we examined 50 different SNPs on the Y-chromosome using three primer extension multiplexes and five hybridization multiplex assays. For certain loci, the allele-specific hybridization method exhibited sizable background signal from the absent alternate allele. However, 100% concordance (>2000 alleles) was observed in ten markers that were typed using both methods. A total of 18 unique haplogroups out of a possible 45 were observed in a group of 229 U.S. African American and Caucasian males with the majority of samples being assigned into 2 of the 18 haplogroups. KEYWORDS: forensic science, Y-chromosome, single nucleotide polymorphism, SNP typing, Y-SNPs, SNaPshot, primer extension, Luminex, allele-specific hybridization In recent years, single nucleotide polymorphisms (SNPs) have kit to type 50 Y-SNP markers in more than 200 individuals. In become more widely used in a variety of applications, including addition, by examining ten of the Y-SNPs with both methods, we medical diagnostics, population genetics, and human identity test- were able to assess concordance in more than 2000 allele calls ing (1,2). The ability to analyze a number of SNP markers in paral- between primer extension and hybridization approaches. lel relies on multiplex amplification and detection formats (3). Two SNP detection formats capable of multiplex analysis are allele- specific primer extension (ASPE) and allele-specific hybridiza- Methods tion (ASH), which we use here to examine variation along the U.S. African American and Caucasian DNA Samples Y-chromosome. The lack of recombination along most of the Y-chromosome Anonymous liquid blood samples with self-identified ethnicities makes it a useful tool in human evolutionary studies and assess- were purchased from Interstate Blood Bank, Inc. (Memphis, TN) ing male migration patterns (4–10). Y-chromosome markers have and Millennium Biotech, Inc. (Ft. Lauderdale, FL) and extracted also been used in attempts to address some interesting historical using a modified salting out procedure (19). Carll Ladd from the questions (11,12). Analysis of Y-SNP markers has typically been Connecticut Forensic Laboratory (Meriden, CT) kindly provided done with manual techniques such as restriction digestion of PCR extracted DNA for 20 U.S. Caucasian and 20 African American products (10,13) or by procedures that can only examine one or samplesusedaspartofthisstudy.TheextractedDNAwasquantified two markers simultaneously such as allele-specific PCR (7), dena- using ultraviolet (UV) spectrophotometry followed by a PicoGreen turing high performance liquid chromatography (5), melting curve assay (20) to adjust concentrations to approximately 1 ng/µL. All analysis (14), and real-time PCR (15). More recently, microarrays samples were examined with 15 autosomal short tandem repeats and (16), time-of-flight mass spectrometry (17), and fluorescent primer the amelogenin sex-typing marker using the AmpFSTR Identifiler extension (10,18) have been applied to Y-SNP analysis in order to Kit to verify that each sample was unique (21). A total of 229 male type multiple markers in parallel. samples were typed (115 African Americans and 114 Caucasians). In an effort to evaluate the usefulness of Y-chromosome SNP markers for human identity applications, we constructed several novel multiplex ASPE assays and utilized a new commercial ASH Y-SNP Markers A total of 50 Y-chromosome biallelic markers were used to cover all 18 major haplogroups (A-R) recognized by the Y-chromosome 1 Biotechnology Division, National Institute of Standards and Technology, consortium (YCC) (22,23). Table 1 contains a summary of the Y- Gaithersburg, MD 20899-8311. ∗ SNP markers used in this study according to their physical position Contribution of the U.S. National Institute of Standards and Technology. Certain commercial equipment, instruments, and materials are identified in order along the Y-chromosome.These positions were identified using am- to specify experimental procedures as completely as possible. In no case does plicon sequences for the 50 Y-SNPs with the BLAST-Like Align- such identification imply a recommendation or endorsement by the National ment Tool (BLAT): http://genome.ucsc.edu/cgi-bin/hgBlat. Of the Institute of Standards and Technology nor does it imply that any of the materials, 50 Y-SNPs, 18 was typed by three hexaplex allele specific primer instruments, or equipment identified are necessarily the best available for the purpose. extension assays. An additional set of 42 Y-SNP loci was typed by Received 6 Sept. 2003; and in revised form 21 Dec. 2003, 6 March 2004. an ASH assay described below. Ten of the Y-SNP loci probed were accepted 6 March 2004; published XXXX. redundant between the two sets. Copyright C 2004 by ASTM International, 100 Barr Harbor Drive, PO Box C700, West Conshohocken, PA 19428-2959. 723 724 JOURNAL OF FORENSIC SCIENCES TABLE 1—Summary information about the 50 Y-chromosome SNP markers used in this study. The BLAT position designates the exact position along the reference Y-chromosome defined by the Human Genome Project (April 2003). The Y Chromosome Consortium (YCC) haplogroup (Hg) defined by the various Y-SNPs are listed along with the multiplex used to type the samples. The Hg listed for each marker is the Hg defined by typing that Y-SNP alone. Multiplexes 1–5 come from the Marligen Y-SNP ASH kit while multiplexes A, B and C are performed using ASPE assays developed in-house. The polymorphisms are listed with the ancestral allele first followed by the derived allele. The two Right-hand columns tabulate the ratio of ancestral:derived allele frequencies for a particular Y-SNP in the 115 African American and 114 Caucasian samples. The sequence immediately surrounding Y-SNP P25 occurs an additional two times on the Y-chromosome at the positions indicated (P25b and P25c). Y Position (Mb) SNP Name YCC Hg Defined Multiplex Polymorphism African American (N = 115) Caucasian (N = 114) 2,562,931 SRY+465 O2b 4 C->T 1.00/0.00 1.00/0.00 2,564,927 SRY10831a,b B-R, R1a 5 A->G, G->A 0.01/0.99, 1.00/0.00 0.00/1.00, 0.95/0.05 2,566,620 SRY9138 K1 4 C->T 1.00/0.00 1.00/0.00 2,642,605 M130 (RPS4Y) C 3 C->T 1.00/0.00 1.00/0.00 13,407,330 M2 E3a 2 A->G 0.42/0.58 1.00/0.00 13,413,670 DYS391 E3 2 C->G 0.40/0.60 0.96/0.04 14,124,138 M168 C-R 1 C->T 0.03/0.97 0.00/1.00 14,157,939 M170 I 3, A A->C 0.96/0.04 0.79/0.21 14,179,223 M182 B2 2 C->T 0.99/0.01 1.00/0.00 14,232,730 Tat N3 4 T->C 1.00/0.00 0.99/0.01 14,264,427 M174 D 3, A T->C 1.00/0.00 1.00/0.00 14,279,781 M172 J2 3, A T->G 1.00/0.00 0.95/0.05 14,337,676 M201 G 3 G->T 0.99/0.01 0.97/0.03 14,340,899 M198 R1a1 C C->T 1.00/0.00 0.95/0.05 14,818,875 M175 O 1 −5bp (+/−) 1.00/0.00 1.00/0.00 14,892,152 M207 R 1 A->G 0.73/0.27 0.35/0.65 18,343,057 M3 Q3 4, B C->T 1.00/0.00 1.00/0.00 20,806,634 M5 M 4 C->T 1.00/0.00 1.00/0.00 20,807,275 P3 A2 2 G->A 1.00/0.00 1.00/0.00 20,903,048 M153 R1b6 5 T->A 1.00/0.00 0.99/0.01 20,926,945 M9 K-R B C->G 0.72/0.28 0.33/0.67 20,927,335 M11 L 3, B A->G 1.00/0.00 1.00/0.00 20,929,850 M18 R1b1 5 +2bp (−/+) 1.00/0.00 1.00/0.00 20,936,442 M31 A1 2 G->C 0.99/0.01 1.00/0.00 20,937,124 M32 A3 2 T->C 1.00/0.00 1.00/0.00 20,937,138 M33 E1 2, B A->C 0.97/0.03 1.00/0.00 20,938,391 M35 E3b 2, B G->C 0.98/0.02 0.97/0.03 20,948,239 M37 R1b2 5 C->T 1.00/0.00 1.00/0.00 20,949,887 M52 H 3 A->C 1.00/0.00 1.00/0.00 20,959,373 M119 O1 4, A A->C 1.00/0.00 1.00/0.00 20,961,146 M137 J2c C T->C 1.00/0.00 1.00/0.00 20,961,189 M124 P1 4, C C->T 1.00/0.00 1.00/0.00 20,961,274 M123 E3b3 C G->A 1.00/0.00 1.00/0.00 20,961,362 M122 O3 C T->C 1.00/0.00 1.00/0.00 20,961,382 M166 J2f2 C G->A 1.00/0.00 1.00/0.00 20,964,647 M112 B2b A G->A 1.00/0.00 1.00/0.00 20,975,939 M146 B1 2 A->C 1.00/0.00 1.00/0.00 21,063,528 M42 B-R 1 A->T 0.01/0.99 0.00/1.00 21,064,475 M45 P-R 1 G->A 0.73/0.27 0.35/0.65 21,064,542 M157 R1a1b 5 A->C 1.00/0.00 1.00/0.00 21,066,207 M150 B2a 2 C->T 0.99/0.01 1.00/0.00 21,074,761 M60 B 1 +1bp (−/+) 0.99/0.01 1.00/0.00 21,086,865 M75 E2 2, A G->A 0.97/0.03 1.00/0.00 21,090,746 M69 H B T->C 1.00/0.00 1.00/0.00 21,102,797 M87 R1a1c 5 T->C 1.00/0.00 1.00/0.00 21,114,001 M89 F-R 1 C->T 0.68/0.32 0.04/0.96 21,134,846 M94 B-R 1 C->A 0.01/0.99 0.00/1.00 21,135,132 M95 O2a 4 C->T 1.00/0.00 1.00/0.00 22,653,504 P4 A2 2 C->T 1.00/0.00 1.00/0.00 24,142,855 P25a R1b 5 C->A 0.77/0.23 0.48/0.52 25,868,376 P25b ..
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