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The Combined DNA Index System (CODIS) is the United States national DNA database created and maintained by the Federal Bureau of Investigation. CODIS consists of three levels of information; Local DNA Index Systems (LDIS) where DNA profiles originate, State DNA Index Systems (SDIS) which allows for laboratories within states to share information, and the National DNA Index System (NDIS) which allows states to compare DNA information with one another.
The CODIS software contains multiple different databases depending on the type of information being searched against. Examples of these databases include, missing persons, convicted offenders, and forensic samples collected from crime scenes. Each state, and the federal system, has different laws for collection, upload, and analysis of information contained within their database. However, for privacy reasons, the CODIS database does not contain any personal identifying information, such as the name associated with the DNA profile. The uploading agency is notified of any hits to their samples and are tasked with the dissemination of personal information pursuant to their laws.
The creation of a national DNA database within the U.S. was first mention by the Technical Working Group on DNA Analysis Methods (TWGDAM) in 1989. In 1990, the FBI began a pilot DNA databasing program with 14 state and local laboratories. In 1994, Congress passed the DNA Identification Act which authorized the FBI to create a national DNA database of convicted offenders as well as separate databases for missing persons and forensic samples collected from crime scenes. The Act also required that laboratories participating in the CODIS program maintain accreditation from an independent nonprofit organization that is actively involved in the forensic fields and that scientists processing DNA samples for submission into CODIS maintain proficiency and are routinely tested to ensure the quality of the profiles being uploaded into the database. The national level of CODIS (NDIS) was implemented in October 1998. Today, all 50 states, the District of Columbia, federal law enforcement, the Army Laboratory, and Puerto Rico participate in national sharing of DNA profiles.
The CODIS database contains several different indexes for the storage of DNA profile information. For assistance in criminal investigations three indexes exist: the offender index, which contains DNA profiles of those convicted of crimes; the arrestee index, which contains profiles of those arrestee of crimes pursuit to the laws of the particular state; and the forensic index, which contains profiles collected from a crime scene. Additional indexes, such as the unidentified human remain index, the missing persons index, and the biological relatives of missing persons index, are used to assist in identifying missing persons.
The bulk of identifications using CODIS rely on short tandem repeats (STRs) that are scattered throughout the human genome and on statistics that are used to calculate the rarity of that specific profile in the population. STRs are a type of copy-number variation and comprise a sequence of nucleotide base pairs that is repeated over and over again. At each location tested during DNA analysis, also known as a locus (plural loci), a person has two sets of repeats, one from the father and one from the mother. Each set is measured and the number of repeat copies is recorded. If both strands, inherited from the parents, contain the same number of repeats at that locus the person is said to be homozygous at that locus. If the repeat numbers differ they are said to be heterozygous. Every possible difference at a locus is an allele. This repeat determination is performed across a number of loci and the repeat values is the DNA profile that is uploaded to CODIS. As of January 1, 2017, requirements for upload to national level for known offender profiles is 20 loci.
Alternatively, CODIS allows for the upload of mitochondrial DNA (mtDNA) information into the missing persons indexes. Since mtDNA is passed down from mother to offspring it can be used to link remains to still living relatives who have the same mtDNA.
Prior to January 1, 2017, the national level of CODIS required that known offender profiles have a set of 13 loci called the "CODIS core". Since then, the requirement has expanded to include seven additional loci. Partial profiles are also allowed in CODIS in separate indexes and are common in crime scene samples that are degraded or are mixtures of multiple individuals. Upload of these profiles to the national level of CODIS requires at least eight of the core loci to be present as well as a profile rarity of 1 in 10 million (calculated using population statistics).
Loci that fall within a gene are named after the gene. For example TPOX, is named after the human thyroid peroxidase gene. Loci that do not fall within genes are given a standard naming scheme for uniformity. These loci are named D + the chromosome the locus is on + S + the order in which the location on that chromosome was described. For example, D3S1358 is on the third chromosome and is the 1358th location described. The CODIS core are listed below; loci with asterisks are the new core and were added to the list in January 2017.
The loci used in CODIS were chosen because they are in regions of noncoding DNA, sections that do not code for proteins. These sections should not be able to tell investigators any additional information about the person such as their hair or eye color, or their race. However, new advancements in the understanding of genetic markers and ancestry have indicated that the CODIS loci may actually contain some phenotypic information.
While the U.S. database is not directly connected to any other country, the underlying CODIS software is used by other agencies around the world. As of April 2016[update], the CODIS software is used by 90 international laboratories in 50 countries. International police agencies that want to search the U.S. database can submit a request to the FBI for review. If the request is reasonable and the profile being searched would meet inclusionary standards for a U.S. profile, such as number of loci, the request can be searched at the national level or forwarded to any states where reasonable suspicion exists that they may be present in that level of the database.
The CODIS database originally was primarily used to collect DNA of convicted sex offenders. Over time, this has expanded. Currently all fifty states have mandatory DNA collection from certain felony offenses such as sexual assault and homicide. Other states have gone further in collecting DNA samples from juveniles and all suspects arrested. In California, as a result of Proposition 69 in 2004, all suspects arrested for a felony, as well as some individuals convicted of misdemeanors, had their DNA collected starting in 2009. In addition to this, all members of the US Armed Services who are convicted at a Special court martial and above are ordered to provide DNA samples, even if their crime has no civilian equivalent (for example adultery).
Currently, the ACLU is concerned with the increased use of collecting DNA from arrested suspects rather than DNA testing for convicted felons. Along with the ACLU, civil libertarians oppose the use of a DNA database for privacy concerns as well as possible institutionalized discrimination policies in collection.