Comparison Of Fmbio Ii And Abi 310 Instrument Platforms

There are advantages and disadvantages to any approach taken for DNA typing. The primary instrument platforms covered in this chapter, namely the FMBIO II Gel Imager and ABI Prism 310 Genetic Analyzer, are compared in Table 14.2. The steps surrounding the FMBIO are more labor intensive since the sample loading is not as automated as the ABI 310. However, the FMBIO is capable of about 10 times the throughput of the ABI 310 on a per instrument basis, and therefore on a similar throughput scale as the 16-capillary ABI 3100 instrument.

Parameter

FMBIO II/III Gel Scanner

ABI Prism 310 CE System

STR kit solution for 13 CODIS core loci

Fluorescent dyes detected

Laser wavelength used to excite fluorophores

Instrument cost

Batch size (including allelic ladders)

Sample throughput

Sample data collection time

PowerPlex® 1.1 and 2.1 or PowerPlex® 16 BIO (Promega Corporation)

Fluorescein, JOE, TMR, CXR, Rhodamine Red, Texas Red

532 nm (Nd:YAG solid-state laser); additional 635 nm and 488 nm with FMBIO III+

25 per gel

(depends on comb used)

20 or more gels/scanner/day (~450 samples/day)

15 minutes to scan gel

Profiler Plus™ and COfiler™ or Identifiler™ (Applied Biosystems) or PowerPlex® 16 (Promega Corporation)

488 nm and 514.5nm (Argon ion gas laser)

48 or 96 per tray

48 samples/24 hour period

~30 minutes per sample

Table 14.2

Comparison of FMBIO II and ABI 310 detection formats.

Computer type

Macintosh® or Windows NT/2000

Macintosh® or Windows NT/2000

Table 14.2

(Continued)

Parameter

FMBIO II/III Gel Scanner

ABI Prism 310 CE System

Data collection software

Readlmage or FMBIO Ill Image Scanner

Peak sizing software FMBIO® Analysis Genotyping software STaR Call™ Data file size

Accessories needed

Lifetime of gel or capillary for re-use

Primary advantage of approach sample

Gel electrophoresis apparatus, glass gel plates, acrylamide, loading dye, comb

2-5 runs

Capable of high volume sample processing because separation and detection are separate and many samples can be run in parallel on each gel

ABI 310 Data Collection

GeneScan® (or GeneMapper/D)

Genotyper® (or GeneMapper/D)

~200 kb/sample (GeneScan) ~100 kb/sample (Genotyper)

Capillary, POP-4 polymer, tubes, septa tube caps

~100-300 runs

Automated sample processing with no gel pouring or loading required

REFERENCES AND ADDITIONAL READING

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Buel, E., Schwartz, M. and LaFountain, M.J. (1998) Journal of Forensic Sciences, 43, 164-170.

Butler, J.M., McCord, B.R., Jung, J.M. and Allen, R.O. (1994) BioTechniques, 17, 1062-1070.

Butler, J.M. (1995) Sizing and quantitation of polymerase chain reaction products by capillary electrophoresis for use in DNA typing. PhD Dissertation, University of Virginia, Charlottesville.

Butler, J.M., Buel, E., Crivellente, F. and McCord, B.R. (2004) Electrophoresis, 25, 1397-1412.

Butler, J.M. (2004) Short tandem repeat analysis for human identity testing. Current Protocols in Human Genetics, John Wiley & Sons, Hoboken, NJ, Unit 14.8, (Supplement 41), pp.14.8.1-14.8.22.

Gill, P., Koumi, P. and Allen, H. (2001) Electrophoresis, 22, 2670-2678.

Isenberg, A.R., Allen, R.O., Keys, K.M., Smerick, J.B., Budowle, B. and McCord, B.R. (1998) Electrophoresis, 19, 94-100.

Lazaruk, K., Walsh, P.S., Oaks, F., Gilbert, D., Rosenblum, B.B., Menchen, S., Scheibler, D., Wenz, H.M., Holt, C. and Wallin, J. (1998) Electrophoresis, 19, 86-93.

Lins, A.M., Micka, K.A., Sprecher, C.J., Taylor, J.A., Bacher, J.W., Rabbach, D., Bever, R.A., Creacy, S. and Schümm, J.W. (1998) Journal of Forensic Sciences, 43, 1168-1180.

Mansfield, E.S., Vainer, M., Enad, S., Barker, D.L., Harris, D., Rappaport, E. and Fortina, P. (1996) Genome Research, 6, 893-903.

Mansfield, E.S., Robertson, J.M., Vainer, M., Isenberg, A.R., Frazier, R.R., Ferguson, K., Chow, S., Harris, D.W., Barker, D.L., Gill, P.D., Budowle, B. and McCord, B.R. (1998) Electrophoresis, 19, 101-107.

McCord, B.R., Jung, J.M. and Holleran, E.A. (1993a) Journal of Liquid Chromatography, 16, 1963-1981.

McCord, B.R., McClure, D.L. and Jung, J.M. (1993b) Journal of Chromatography A, 652, 75-82.

McCord, B.R. (2003) Troubleshooting capillary electrophoresis systems. Profiles in DNA, 6 (2); Available at: http://www.promega.com/profiles/602/ ProfilesInDNA_602_10.pdf.

Madabhushi, R.S. (1998) Electrophoresis, 19, 224-230.

Micka, K.A., Amiott, E.A., Hockenberry, T.L., Sprecher, C.J., Lins, A.M., Rabbach, D.R., Taylor, J.A., Bacher, J.W., Glidewell, D.E., Gibson, S.D., Crouse, C.A. and Schumm, J.W. (1999) Journal of Forensic Sciences, 44, 1243-1257.

Promega Corporation (1997) GenePrint® Fluorescent STR Systems Technical Manual. Madison, Wisconsin: Promega Corporation.

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Rosenblum, B.B., Oaks, F., Menchen, S. and Johnson, B. (1997) Nucleic Acids Research 25, 3925-3929.

Schumm, J.W., Lins, A.M., Micka, K.A., Sprecher, C.J., Rabbach, D. and Bacher, J.W. (1996) Proceedings from the First European Symposium on Human Identification, pp. 90-104. Madison, Wisconsin: Promega Corporation.

Schumm, J.W., Sprecher, C.J., Lins, A.M., Micka, K.A., Rabbach, D.R., Taylor, J.A., Tereba, A. and Bacher, J.W. (1997) Proceedings of the Eighth International Symposium on Human Identification, pp. 78-84. Madison, Wisconsin: Promega Corporation.

Sgueglia, J. B., Geiger, S. and Davis, J. (2003) Analytical and Bioanalytical Chemistry, 376, 1247-1254.

Steadman, G.W. (2000) Survey of DNA Crime Laboratories, 1998. Bureau of Justice Statistics, Special Report February 2000, U.S. Department of Justice.

Tereba, A., Micka, K.A. and Schumm, J.W. (1998) BioTechniques, 25, 892-897.

Wang, Y., Ju, J., Carpenter, B.A., Atherton, J.M., Sensabaugh, G.F. and Mathies, R.A. (1995) Analytical Chemistry, 67, 1197-1203.

Wenz, H.M., Robertson, J.M., Menchen, S., Oaks, F., Demorest, D.M., Scheibler, D., Rosenblum, B.B., Wike, C., Gilbert, D.A. and Efcavitch, J.W. (1998) Genome Research, 8, 69-80.

CHAPTER 15

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