Available Population Databases

MtDNA typing results on samples from unknown sources are most useful if they are evaluated in comparison to a known sample or a database. Databases of more than 1000 unrelated individuals now exist and have been compiled from multiple population groups (Handt et al. 1998, Budowle et al. 1999, Attimonelli et al. 2000, Wittig et al. 2000, Röhl et al. 2001, Monson et al. 2002). The size of the database is important because without recombination between mtDNA molecules, an mtDNA sequence is treated as a single locus (i.e., haplotype instead of genotype).

The largest compiled database described to date contains HV1 and HV2 sequences from 14 138 individuals (Röhl et al. 2001). This information was collated from 103 mtDNA publications prior to January 2000, 13 data sets published in 2000 and 2001, and two unpublished data sets. Authors of the original publications were contacted in an effort to confirm and correct sequence errors, eliminate duplications, and harmonize nomenclatures, but not every query was answered. Of the 116 publications, 90 required some kind of change to correct errors or adjust nomenclature illustrating the challenge of compiling accurate mtDNA sequence databases. The authors conclude that their annotated database probably still contains errors and that while it can be used for qualitative identification of relevant reference populations for a given mtDNA type, the determination of a 'legally defensible' frequency estimate of an mtDNA type within a population should be performed with higher-quality data yet to be produced (Röhl et al. 2001).

The FBI has compiled the mtDNA Population Database also known as CODISmt (Monson et al. 2002) for the purpose of being able to determine a legally defensible frequency estimate. The CODISmt database has a forensic and a published literature component to it (Miller and Budowle 2001) in order to separate data obtained from laboratories following validated forensic protocols and academic research laboratories where data quality is not reviewed as carefully prior to publication.

The forensic database contains 4839 mtDNA profiles from 14 different populations (Table 10.6). These samples have been sequenced and the electrophero-grams carefully reviewed across positions 16024-16365 for HV1 and positions 73-340 for HV2. Several publications have come out of analysis of mtDNA profiles contained within the various populations as summarized in Table 10.6.

Table 10.6

Summary of high quality forensic profiles present in the FBI Laboratory's mtDNA Population Database now called CODISmt when it was released to the public in April 2002 (Monson et al. 2002).

Population Name

Number of Profiles

Data Analysis on Group

African-American

Apache

Caucasian

China/Taiwan

Egypt

Guam

Hispanic

India

Japan

Korea

Navajo

Pakistan

Sierra Leone

Thailand

Total

1148 180 1655

356 48 87 686 19 163 182 146 8

109 52 4839

Budowle et al. (1999)

Budowle et al. (2002b)

Allard et al. (2004)

Budowle et al. (1999) Allard et al. (2004) Budowle et al. (2002b)

An additional 6106 published profiles have been compiled from the literature with annotated population information (Miller et al. 1996, Miller and Budowle 2001). For classification of mtDNA profiles, a standard 14-character nucleotide sequence identifier was assigned to each profile where the first three characters represent the country of origin, the second three characters the group or ethnic affiliation, and the final six characters are sequential acquisition numbers (Miller and Budowle 2001, Monson et al. 2002).

Both of these databases were publicly released in April 2002 in a Microsoft Access format and can be downloaded from the FBI web site along with an analysis tool named MitoSearch (Monson et al. 2002). MitoSearch can examine the population data sets listed in Table 10.6 for specific mtDNA sequences, which are entered based on differences from the Cambridge Reference Sequence. The software returns the number of times that the specified profile appears in each population group. For example, the mtDNA type 16129A, 263G, 309del, 315.1C occurs twice in 1148 African-American profiles, twice in 1655 Caucasian profiles, and not at all in 686 Hispanic profiles.

The European forensic mtDNA sequencing community has also been actively engaged in developing new high quality population databases for forensic and human identity testing applications. A European DNA Profiling Group mitochondrial DNA population database project (EMPOP) has been launched to construct a high quality mtDNA database that eventually can be accessed online at http://www.empop.org.

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