During the testing of alternative primers for the Y chromosome short tandem repeat marker DYS19, a duplicated region of the Y chromosome was discovered. The duplicated sequence is contained within GenBank accession AC006335 and has a high degree of homology with the DYS19 flanking region (GenBank accession AC017019) but without the polymorphic TAGA repeat. Bioinformatic approaches have been taken to try and understand the implications of this homolog to enable improved primer design for DYS19. Sequence alignments and careful placement of primers in order to obtain specific amplification of the DYS19 locus are discussed in the context of all previously published primer sets. Since the DYS19 locus is part of the widely used minimal haplotype, its robust amplification is highly desirable particularly in multiplex reactions. The discovery of this duplicated region of the Y chromosome shows the value of newly available human genome sequence information for assay design and the importance of using sequence queries and alignments in the primer design process.
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Sequence-based mutation patterns at 41 Y chromosomal STRs in 2 548 father-son pairs.
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School of Forensic Science and Technology, Criminal Investigation Police University of China, Shenyang, China.
Unlabelled: A total of 2 548 unrelated healthy father-son pairs from a Northern Han Chinese population were genotyped at 41 Y chromosomal short tandem repeat (Y-STRs) including DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS444, DYS447, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS522, DYS549, DYS533, DYS557, DYS570, DYS576, DYS593, DYS596, DYS627, DYS635, DYS643, DYS645, Y-GATA-H4, DYF387S1a/b, DYF404S1a/b, DYS385a/b, and DYS527a/b. In 2 548 father samples, 2 387 unique haplotypes were detected with the haplotype diversity and discrimination capacity values of 0.999 956 608 and 0.
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Universidad de Buenos Aires - Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas (SHDG), Junin 956, Ciudad Autónoma de Buenos Aires 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Argentina.
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National Institute of Standards and Technology, 100 Bureau Drive, M/S 8314, Gaithersburg, MD 20899, USA.
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Next-generation sequencing (NGS) can produce massively parallel sequencing (MPS) data for many targeted regions with a high depth of coverage, suggesting its successful application to the amplicons of forensic genetic markers. In the present study, we evaluated the practical utility of MPS in Y-chromosome short tandem repeat (Y-STR) analysis using a multiplex polymerase chain reaction (PCR) system. The multiplex PCR system simultaneously amplified 24 Y-chromosomal markers, including the PowerPlex Y23 loci (DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and YGATAH4) and the M175 marker with the small-sized amplicons ranging from 85 to 253bp.
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Laboratory for Forensic Genetics and Molecular Archaeology, K.U. Leuven, Campus Gasthuisberg O&N, Herestraat 49--bus 602, B-3000 Leuven, Belgium.
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