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

May 2004
Office of the Inspector General

Appendix II

Interpretation of DNA Analysis Data

As mentioned in Chapter Two, Section I.D, the manufacturer of the capillary electrophoresis machine developed proprietary software to display the test results and to aid in their interpretation. The software has two components, GeneScan® and Genotyper.® Data viewed in Genescan®, as appears below, is the raw, unanalyzed, collection data that documents everything the laser detected, including the background noise that is common in these types of instruments. The following graphic illustrates the appearance and content of this data for a DNA sample.

Screenshot of Genescan® software showing amplified DNA peaks.
Genescan® View: : raw data for a Positive Control (9947A) prepared according to protocol.
Peaks depicted in red originate from the internal size standard added to each sample.

Genotyper® takes this same data and displays it in a different format. With Genotyper®, the forensic scientist selects which peaks are displayed, choosing among the internal lane standard, the primer peaks, specific peaks from the DNA sample, and the allelic ladders. The background noise is filtered out in the Genotyper® view. With the exception of the red peaks, the primer peaks are those located between the brackets on the following illustration.

Screenshot of Genescan® software showing STR Primer Peaks.
Genescan® View: raw data for a Negative Control prepared according to protocol.
Peaks depicted in red originate from the internal size standard added to each sample.

In order to determine accurately the length of the sample's DNA fragments, an internal size standard is added to each sample before it undergoes capillary electrophoresis. As mentioned earlier, the internal size standard contains DNA fragments of known sizes that provide reference points for the software to use when determining the length of the sample's DNA fragments. The peaks corresponding to the internal size standard are shown as red peaks in both the Genescan® and Genotyper® printouts.

The Genotyper® software uses allelic ladders to assign allele calls, (i.e., determine which alleles correspond to the lengths of the sample's DNA fragments as determined by Genescan®). There is an allelic ladder for each chromosomal location tested. These ladders contain the most common alleles in the general population at each location. The Genotyper® software compares the peaks in the evidentiary or reference sample to the peaks in the allelic ladder at that same location. Genotyper® then assigns the corresponding allele designation to the evidentiary or reference peaks. The number of repeats in the DNA fragment determines the allele designation. For example, an allele call of 15 means the DNA fragment contains 15 repeats. The following illustration contains both the allelic ladders and two allele calls for a DNA sample. The DNA profile at two chromosomal locations for the sample shown below is: alleles 14 and 15 at location D3S1358, and alleles 11 and 12 at location D16S539.

Genotyper® View: COFiler Ladder
with Positive Control Allele call

[Image not available electronically]