Chapter 15 New Technologies and Automation ©2002 Academic Press

Anal. Biochem. 1999, 270, Rapid Microchip CE Separation Whitehead Institute Fluorescein-labeled PCR Products TMR-labeled PCR Products Allelic ladders mixed with samples for genotyping purposes PowerPlex™ 1.1 Rapid Microchip CE Result ©2002 Academic Press

Microchip CE PNAS (1997) 94: Mass Spectrometry Int. J. Legal Med. (1998) 112: Hybridization Arrays Nucleic Acids Res. (2000) 28: e17 Data courtesy of Jim Schumm Capillary Electrophoresis Electrophoresis. (1998) 19: Gels Data courtesy of Bill Hudlow J. Forensic Sci. (1998) 43: Nucleic Acids Res. (1999) 27: e36 Capillary Arrays Various STR Typing Technologies

STR Analysis by Hybridization on Microchips ©2002 Academic Press

STR allele containing 6 repeat units Hybridization between probes and STR allele Capture Probe (attached to chip) Reporter Probe (fluorescent dye attached) Schematic of Nanogen STR Chip Assay Locus D Locus C Locus B Locus A Alleles (Repeat #) Locus A = 6,8 Locus B = 3,4 Locus C = 6,8 Locus D = 6,6 ©2002 Academic Press

Acceleration Region Detector Ion Extractor Drift Region Electric-Field Free Pulsed Laser Beam High-Density Sample Array DNA Reaction Products (Size separated and drifting to the detector) X-Y sample control DNA separations occur in microseconds! Total analysis is 5-10 seconds per sample because multiple spectra are collected and averaged Schematic of Time-of-Flight Mass Spectrometry Process ©2002 Academic Press

ABI 310 Result 9.3 allele: 1071 sec 10 allele: 1073 sec ABI 310 Result 9.3 allele: 1071 sec 10 allele: 1073 sec Mass Spec Result 9.3 allele:  sec 10 allele:  sec Mass Spec Result 9.3 allele:  sec 10 allele:  sec Allele 10 COfiler TM size: 187 bp MS size: 83 bp Redesigned primers for mass spec work TH01 Alleles: CE vs. Mass Spec ©2002 Academic Press

Robot Sample Preparation On-board thermal cycler with plate handler PCR set-up and 310/3100 plate loading STR results with automation ©2002 Academic Press