The FBI DNA Laboratory: A Review of Protocol and Practice Vulnerabilities

May 2004
Office of the Inspector General

Appendix I

As noted in Chapter Two, Section I.D, the primers used during the amplification process contain different fluorescent labels, which allow the lasers in the capillary electrophoresis machine to detect and differentiate the various DNA fragments separated during capillary electrophoresis. The label on each primer determines the color in which the results are displayed on both computer monitors and printouts. At the present time, the fluorescent labels produce peaks that are blue, green, and yellow. The yellow peaks are usually displayed in black on the Genescan^® and Genotyper^® printouts, with the remaining peaks printed in the corresponding color. In addition, the internal lane standard peaks are always displayed in red.

At the present time, two amplification kits¹ are required for forensic scientists to test the 13 chromosomal locations that comprise a DNA profile. Scientists also test a 14th location, known as amelogenin, which indicates the sex of the DNA contributor. One amplification kit, Profiler Plus,™ contains the reagents necessary to test ten chromosomal locations. The fluorescent labels in this kit produce results that are shown in blue for three chromosomal locations, four locations are shown in green, and three locations are called yellow even though they display in black. The COfiler™ amplification kit displays the results for two chromosomal locations in blue, four locations are displayed in green, and one location representing the yellow peaks is displayed in black. Three chromosomal locations are tested with both the Profiler Plus™ and COfiler™ kits, which gives forensic scientists points of comparison to ensure the results are consistent between the two kits.

The Genescan^® graphic for the positive control in Appendix 2 reflects the DNA profile of a sample used as a positive control by a CODIS participating laboratory. The following table represents the allele calls that correspond to the electrophoresis results shown in that graphic.

Example of a DNA Profile

Applied Biosystems Analysis Kit	Chromosomal Location	Alleles Present in DNA Sample	Genotyper® Printout
AmpFlSTR® Profiler Plus™ PCR Amplification Kit	D3S1358	14, 15	Page 141
	VWA	17, 18
	FGA	23, 24
	Amelogenin	X, X	Page 141
	D8S1179	13, 13
	D21S11	30, 30
	D18S51	15, 19
	D5S818	11, 11	Page 142
	D13S317	11, 11
	D7S820	10, 11
AmpFlSTR® COfiler™ PCR Amplification Kit	D3S1358	14, 15	Page 142
	D16S539	11, 12
	Amelogenin	X, X	Page 143
	THO1	8, 9.3
	TPOX	8, 8
	CSF1PO	10, 12
	D7S820	10, 11	Page 143

The following pages contain the Genotyper^® printouts supporting the allelic values listed in the above chart. These printouts reflect the fact that Genotyper^® reformats the Genescan^® data and allows the forensic scientist that reviews the data to review only the specific peaks required for data interpretation, including (but not limited to) the specific peaks from the DNA sample and the allelic ladders. The background noise is filtered out in the Genotyper^® view.

Genotyper® View: Profiler Ladder with Positive Control Allele call [Images not available electronically]

1. In this report, we focus on the amplification kits manufactured by Applied Biosystems because they are used by the DNAUI. Some state and local DNA laboratories use kits manufactured by other companies. These kits examine the same chromosomal locations and produce the same type of data as the kits discussed here.