Butler2003b_Y_chromosome_Required_paper

Butler2003b_Y_chromosome_Required_paper - Recent...

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1042-7201/15-02/July 2003/91–111/$10.50 • Copyright © 2003 Central Police University Press Recent Developments in Y-Short Tandem Repeat and Y-Single Nucleotide Polymorphism Analysis J. M. Butler National Institute of Standards and Technology Gaithersburg, Maryland United States of America TABLE OF CONTENTS INTRODUCTION . ........................................................................................ 92 I. Y-SHORT TANDEM REPEAT MARKERS . .............................................. 93 A. Marker Discovery . ................................................................................. 93 B. Chromosomal Locations of Markers . .................................................... 93 C. Characteristics of New Markers . ........................................................... 95 D. Population Studies . ................................................................................ 95 E. Genetic Genealogy Studies. ................................................................... 96 II. Y-SHORT TANDEM REPEAT TYPING ASSAYS AND KITS . ............... 98 A. Approaches to Reliable Genotyping. ..................................................... 98 B. Multiplex Polymerase Chain Reaction . ................................................. 98 C. National Institute of Standard and Technology Multiplex Assays. ....... 98 D. Commercial Kits. ................................................................................. 100 III. Y-SINGLE NUCLEOTIDE POLYMORPHISM MARKERS AND TYPING ASSAYS . ..................................................................................... 100 A. Available Markers . .............................................................................. 100 B. Unified Nomenclature for Y-Single Nucleotide Polymorphism Haplogroups . ....................................................................................... 102 C. Typing Technologies . .......................................................................... 102 D. SNaPshot Assay. .................................................................................. 102 E. Luminex Assay . ................................................................................... 103 F. Optimal Y-Single Nucleotide Polymorphism Markers . ...................... 104 IV. REFERENCE MATERIALS AND STANDARDIZATION . ..................... 104 A. Available Reference Materials . ........................................................... 105 B. Allele Nomenclature Issues . ................................................................ 106 C. Validation and Interlaboratory Studies. ............................................... 106 CONCLUSIONS . ........................................................................................ 107 ACKNOWLEDGMENTS . .......................................................................... 107 REFERENCES . ........................................................................................... 107 ABOUT THE AUTHOR . ............................................................................ 111
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Forensic Science Review Volume Fifteen Number Two July 2003 Recent Developments in Y-Short Tandem Repeat and Y- Single Nucleotide Polymorphism Analysis a REFERENCE: Butler JM: Recent developments in Y-single tandem repeat and Y-single nucleotide polymorphism analysis; Forensic Sci Rev 15:91; 2003. ABSTRACT: This article reviews new genetic markers on the Y-chromosome and methods for analyzing these short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci. Relative chromosomal locations for over 50 Y-chromosome STRs (Y-STRs) are described along with their repeat motif and allele range characteristics based on published population studies. Multiplex assays for typing many of these markers in a parallel fashion are discussed, as are newly available commercial Y-STR kits. Approximately 250 SNP markers are now catalogued along the Y-chromosome (Y-SNPs) with a unified haplogroup nomenclature describing their relative relationships. Technologies for typing these Y-SNPs are reviewed including primer extension and allele-specific hybridization methods. Finally, available reference materials for standardization of allele calls, Y-STR allele nomenclature issues, and published validation and interlaboratory studies are reviewed. KEY WORDS: Forensic DNA typing, Luminex, multiplex PCR, SNaPshot, standard reference materials, STR nomenclature issues, Y-Chromosome, Y-SNP, Y-STR. forensic analysis of sexual assault evidence [6,16,18,36,37, 45,66,67,68,73,85,87,88], conducting missing persons investigations [21], performing deficient paternity testing [45,76,80], addressing historical questions [23], and supplementing genealogical research [48,89] ( Table 1 ).
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