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

May 2004
Office of the Inspector General

Glossary of Terms and Acronyms

Act: the DNA Identification Act of 1994 (Act) was the vehicle whereby Congress authorized the creation of CODIS, and directed the FBI to establish the Board. The Act also directed that the guidelines issued by TWGDAM would be deemed to be national standards until the FBI issued its own standards pursuant to the Act.

Allele: the characteristics of a single copy of a specific gene, or of a single copy of a specific location on a chromosome, is referred to as an allele. For example, one copy of a specific STR region might have 10 repeats, while the other copy might have 11 repeats. These would represent two alleles of that STR region.

Allelic ladder: contains the more common alleles in the general population for specific chromosomal locations. Allelic ladders are used like molecular rulers to help "measure" the lengths of the fragments in the reference and evidentiary samples. The Genotyper® software compares the peaks in the evidentiary or reference sample to the peaks in the allelic ladder at that same location.

Amplification: the replication of extracted DNA so that the DNA can be detected by an analyzer or a capillary electrophoresis machine. Amplification is the third of five stages in the PCR/STR analysis process.

ASCLD/LAB: the American Society of Crime Laboratory Directors/Laboratory Accreditation Board is one of the organizations that provides accreditation for labs. The organization performs a thorough inspection of the laboratory before it grants accreditation.

Board: the FBI established the DNA Advisory Board (Board), in response to a Congressional mandate within the Act, to develop national quality assurance standards that would ensure that the operations of CODIS participants met minimum quality standards. The Board was formally constituted on March 10, 1995, and was comprised of members of a variety of forensic and science organizations. The Board's mission was to develop quality assurance standards for laboratories and analysts that examine DNA.

Capillary electrophoresis: the form of electrophoresis employed by the DNAUI. Its distinguishing characteristic is that the electrophoresis occurs inside a capillary tube (a very thin glass tube) with a sieving material inside, rather than on a piece of gelatinous material. Capillary electrophoresis is an automated process that analyzes many DNA samples and requires minimal involvement by DNA scientists after the initial set-up procedures are completed.

Chromosomes: chromosomes store information in the chemical structure of DNA much like a book or a compact disk. The nucleus contains 46 chromosomes, two copies of each of the 23 different human chromosomes. One copy of each chromosome is inherited from an individual's mother and one copy is inherited from an individual's father, giving a child DNA characteristics of both its mother and father.

Combined DNA Index System (CODIS): provides a framework for storing, maintaining, tracking, and searching DNA specimen information. CODIS refers to the entire system of DNA databases (convicted offender database, forensic database, victim database, etc.) maintained at the national, state, and local levels. CODIS currently consists of three distinct levels: the National DNA Index System, State DNA Index System, and Local DNA Index System.

Deoxyribonucleic Acid (DNA): DNA is found in almost all living cells, and carries the encoded information necessary for building and maintaining life. This encoded information is what makes each person an individual. DNA consists of two strands of molecules that wrap around each other to resemble a twisted ladder whose sides are connected by rungs of chemicals called bases. There are four kinds of these chemical bases (also called nucleotides), and the order in which they are arranged is called the DNA sequence. It is this unique sequence that is determined when a DNA sample is typed.

DNA Profile: a set of DNA identification characteristics, i.e., the particular chemical bases at specific DNA locations, which permit the DNA of one person to be distinguishable from that of another person.

DNA Sample: a body tissue or fluid sample (blood, a skin cell sample, or semen, for example) that can be subjected to DNA analysis.

DNA Typing: the process by which a DNA sample is examined and a DNA profile is produced.

DNAUI: the DNA Analysis Unit I (DNAUI) identifies and characterizes body fluids and body fluid stains recovered as evidence in violent crimes using traditional serological techniques and related biochemical analysis. These stains are analyzed and compared to results from the known body fluid samples submitted by the victim(s) and/or suspected perpetrator(s).

Electrophoresis: a process whereby DNA fragments are sorted according to length (i.e., number of short tandem repeats). In general, the process involves: 1) Adding DNA to one end of a piece of gelatinous material which contains tiny holes that allows the material to function as a molecular sieve; 2) applying an electric current to the material, causing the DNA fragments to move; and 3) determining the size of the DNA fragments by comparing the distance each fragment moved to the distances moved by the fragments of known size. Since it is easier for smaller fragments to move through the material, the smaller fragments move farther than the larger fragments. As a result, at the end of electrophoresis the DNA fragments are sorted by size. Electrophoresis is the fourth of five stages in the PCR/STR analysis process.

Examiner (Analyst): an individual who conducts or directs the analysis of forensic casework samples, interprets data, and reaches conclusions. In the context of the DNAUI, the Examiner collects supporting documentation from the Serologist and PCR Biologist for the work performed by each, interprets the data that resulted from that work, draws conclusions about those results, and writes a report describing those conclusions.

Extraction: a process whereby chemicals are used to release or remove DNA from evidence. Extraction is the first of five stages in the PCR/STR analysis process.

Forensic Database: consists of DNA profiles from persons whose identities are not known with certainty and who left DNA at the scene of a crime or whose DNA was carried away from it. For example, a DNA profile may be developed from a bloody knife found at a crime scene or found in a trash dumpster.

Genes: each chromosome contains many genes, which are the portions of the chromosome that code for personally identifying characteristics, like hair color or eye color. It has been estimated that only 2 to 3 percent of the information in a chromosome is organized into genes.

GeneScan®: a component of the proprietary software that accompanies the capillary electrophoresis machines used by the DNAUI. The GeneScan® software allows scientists to view and process the raw, unanalyzed data that documents everything the laser of the electrophoresis machine detects, including background noise that is common in electrophoresis instruments. GeneScan® is a registered trademark of Applied Biosystems.

Genotyper®: a component of the proprietary software that accompanies the capillary electrophoresis machines used by the DNAUI. Genotyper® allows the forensic scientist to take the processed GeneScan® data and display it in a format that applies allele designations to the profile fragments, and to focus his or her review on the results of the control and evidence samples. Genotyper® is a registered trademark of Applied Biosystems.

Guide: the FBI created a standardized DNA audit guide (Guide), with input from the Board, ASCLD-LAB, and NFSTC, to ensure that auditors of local, state, and federal DNA laboratories are thorough and interpret the quality assurance standards consistently. The FBI offers Guide training for auditors, including those representing accrediting and certifying organizations such as ASCLD-LAB and NFSTC. For an audit to fulfill the quality assurance standards' external audit requirement, it must be conducted in accordance with the Guide and by an auditor trained in its use.

Internal Size Standard: contains DNA fragments of known sizes that provide reference points for determining the length of a sample's DNA fragments. GeneScan® software uses the internal size standard to help the software as it determines the lengths of the DNA fragments detected during electrophoresis.

Investigations Aided: the primary measuring unit that the FBI uses to quantify the success of CODIS. An investigation is aided when a DNA match through CODIS either identifies a potential suspect or links crimes together, but only when the DNA match provides new information that would not have been otherwise developed.

Known DNA sample: a DNA sample for which the source is known. These samples are generally obtained from the victim and/or suspected perpetrator of a crime, as well as from other persons whose DNA might be reflected when samples of the evidence are analyzed (could include a boyfriend, husband, or other third-party). These samples are also referred to as reference samples, since they serve as a reference to which the unknown DNA samples are compared with the goal of identifying the source of the unknown DNA samples.

Mitochondrial DNA: DNA found in the mitochondria of a cell. Mitochondria are about the size of bacteria and are scattered throughout a cell outside its nucleus. Since there are between 500 to 1,000 mitochondria in every cell, as opposed to one nucleus, mitochondrial DNA analysis affords a better chance of a DNA profile than nuclear DNA analysis in cases where a sample is decayed or degraded, such as skeletal remains that have been exposed to the elements for years.

National DNA Index System (NDIS): the FBI-maintained national component to CODIS. NDIS contains DNA profiles uploaded from approved SDIS laboratories.

NDIS Requirements: the NDIS office has issued programmatic rules that govern the exchange of information for NDIS participants and has established standards for the submission of DNA data, collectively referred to as NDIS Requirements. The NDIS requirements are found in the Memorandum of Understanding (MOU) that is established between the FBI and each NDIS participant. The MOU requires that signatories comply with general requirements already established (i.e., federal legislation, the Forensic and Offender Standards) as well as requirements specific to the national index that accompany the MOU in three appendices: NDIS Responsibilities (Appendix A); NDIS Data Acceptance Standards (Appendix B); and the NDIS Procedures Manual (Appendix C).

Negative Control: the negative control contains all of the reagents used for amplification. DNA from the evidence is not added to the negative control, though the contents are amplified. The purpose of the negative control is to reveal any contamination that is present in the reagents or introduced during the testing process.

NFSTC: the National Forensic Science Technology Center (NFSTC) is one of two primary accreditation or certification entities for forensic and offender DNA laboratories.

NIST: the National Institute of Standards and Technology.

Nuclear DNA: DNA found in the nucleus of a cell. The nucleus is the cell's control center. Nuclear DNA contains the entire genetic make-up of a person, including inherited traits such as eye color or height. There is only one group of nuclear DNA per cell, since each cell has only one nucleus. Since nuclear DNA is sensitive to environmental conditions, it can be difficult to obtain useable nuclear DNA from deteriorated and/or old crime scene samples. The alternative to nuclear DNA analysis is mitochondrial DNA analysis.

OGC: the FBI's Office of General Counsel.

OPR: the FBI's Office of Professional Responsibility.

PCR Biologist: in the context of the DNAUI, the PCR Biologist is the staff member responsible for completing the PCR analysis process and providing to an Examiner the results of that process from which they can draw conclusions and report results. Included within this process is the completion of extraction, quantification, amplification, and electrophoresis.

Polymerase Chain Reaction (PCR): a method used to replicate specific portions of the DNA strands. The DNA is heated, causing the two strands to separate like a zipper. The two DNA halves are then cooled and mixed with a special enzyme. The result of this process is the creation of two DNA strands identical to each other and to the original DNA strand. This process is repeated many times to replicate a desired DNA sequence millions of times in a matter of hours. PCR is especially valuable because it does not require high quality or large quantities of DNA. Also, this method lends itself to automation and less labor-intensive typing. The PCR/STR analysis process includes five stages, which are extraction, quantification, amplification, electrophoresis, and data interpretation.

Positive Control: the positive control contains the reagents necessary for amplification plus DNA from a source for which the DNA profile is known. Since the DNA scientists know the correct test results for the positive control, it allows them to determine the accuracy and performance of the amplification and analysis processes.

Primers: short synthetic pieces of DNA designed to match places where human DNA is both repetitive and highly variable. Primers identify the starting and ending points of a DNA fragment that is to be duplicated with PCR. The primers also prime (or stimulate) the synthesis reaction when the DNA fragments are duplicated. The primers contain fluorescent labels so that they may be detected by lasers during electrophoresis.

Quantification: the process whereby the concentration of extracted DNA in a sample is measured, and the second of five stages in the PCR/STR analysis process.

Reagent: a substance that is used (as in detecting or measuring a component, in preparing a product, or in developing photographs) because of its chemical or biological activity.

Reagent Blank: the reagent blank contains all of the reagents used to process an item of evidence from extraction through electrophoresis. DNA from the evidence is not added to the reagent blanks, though their contents are amplified. The purpose of the reagent blank is to reveal any contamination that is present in the reagents or introduced during the testing process.

QAS: refers to the Quality Assurance Standards issued by the FBI Director upon the recommendation of the DNA Advisory Board. Quality Assurance refers to measures that are taken by labs to monitor, verify, and document performance. Two sets of QAS exist: QAS for Convicted Offender DNA Databasing Laboratories, effective April 1, 1999; and QAS for Forensic DNA Testing Laboratories, effective October 1, 1998.

SDIS: State DNA Index System containing the state-level DNA records uploaded from local laboratory sites within the state. SDIS is the state's repository of DNA identification records and is under the control of state authorities. The SDIS laboratory serves as the central point of contact for access to NDIS. The DNAUI serves as the SDIS laboratory for the FBI.

Serologist: a Serologist performs testing to determine what body fluids are present on the evidence and whether it is possible to extract DNA from it. In the DNAUI, the Serologist also assists with the initial and final evidence inventories, and is responsible for transferring to the PCR Biologist body-fluid stained evidence items and related case file documentation.

Short Tandem Repeats: short repeating units of identical chemical sequences arranged in direct succession in a particular region of the DNA.

Short Tandem Repeat Analysis (STR): refers to a DNA typing method that utilizes PCR technology to quickly amplify and analyze sections of DNA that contain short tandem repeats. This method allows a high level of discrimination, since 13 chromosomal locations are examined and subsequently compared with other samples.

SWGDAM: TWGDAM was renamed the Scientific Working Group on DNA Analysis Methods (SWGDAM) after the Office of Justice Programs created short-term technical working groups that began to be confused by members of the DNA community with the FBI's long-term technical working groups. Since being renamed, SWGDAM has produced additional guidance for the forensic community, including guidelines for data interpretation, training, quality assurance, and health and safety audits.

TWGDAM: the Technical Working Group on DNA Analysis Methods (TWGDAM) was the one of several technical working groups sponsored by the FBI to examine DNA's forensic science applications. TWGDAM was established in 1989 with representatives from 12 laboratories, and focused specifically on the development of forensic DNA methods. Later that same year, TWGDAM developed and published a set of quality guidelines for forensic DNA laboratories, and updated those guidelines in 1991 and in 1995.

Unknown DNA Sample: a sample of DNA for which the source is not known. Unknown DNA samples are also referred to as questioned samples. Unknown DNA samples are taken from evidence items submitted to a laboratory, that are analyzed by the laboratory and compared to a known DNA sample to determine whether the source of the unknown DNA sample can be identified.