Introduction
The Scientific Working Group on DNA Analysis Methods mitochondrial
DNA (mtDNA) database is a resource for forensic analyses and research
purposes. The database is currently available to law enforcement
laboratories through the CODIS Missing Person Program and is called
the mtDNA Popstats Population Database. Non-CODIS participants can
access the database in Forensic Science Communications at
http://www.fbi.gov/hq/lab/fsc/backissu/april2002/miller1.htm.
Mitochondrial DNA Database
The Scientific Working Group on DNA Analysis Methods database consists
of mtDNA profiles of convenience samples provided by paternity,
university, and forensic laboratories. There are currently 5,071
mtDNA profiles in the database available to CODIS participating
laboratories. Of these profiles, 4,839 are in Forensic Science
Communications. The profiles in the database are designated
by differences with respect to the revised Cambridge Reference Sequence
(Anderson et al. 1981; Andrews et al. 1999). The nomenclature used
for defining differences with respect to the Cambridge Reference
Sequence is defined by Wilson et al. (2002A and B), which also is
recommended in the Guidelines for Mitochondrial DNA (mtDNA) Nucleotide
Sequence Interpretation (Scientific Working Group on DNA Analysis
2003).
At a minimum, profiles in the database contain sequences for hypervariable
region I (HVI, np 16024-16365) and hypervariable region II (HVII,
np 73-340) that have been sequenced in forward and reverse directions
(Bar et al. 2000). Identification numbers of the profiles provide,
if known, some information of population affinity and country source
(Miller and Budowle 2001; Monson et al. 2002).
Database Analysis
Phylogenetic and population genetic analyses of the Scientific
Working Group on DNA Analysis Methods database support using the
dataset to determine the rarity of a mtDNA sequence derived from
evidence (Allard et al. 2003; Allard et al. 2004; Budowle et al.
2003). Although the database has been validated for use, and all
known errors have been corrected, it is not entirely free of error.
In fact, it is unlikely that any mtDNA database contains no errors.
Most are due to man-made transcriptional errors (Budowle et al.
in press).
Phylogenetic analysis has been recommended as one method for detecting
some errors in databases (Bandelt et al. 2001; Yao et al. 2004).
A recent review of the Scientific Working Group on DNA Analysis
Methods database using phylogenetic analysis detected four transcriptional
errors, three odd concatenations, and two inadvertently modified
sequences (Budowle et al. in press). These errors were confirmed
by review of alignment data and/or reanalysis of the samples in
question. Once confirmed, the errors were corrected. The current
Scientific Working Group on DNA Analysis Methods database in CODIS
Missing Person Program and in Forensic Science Communications
has been revised to reflect the corrections.
Although phylogenetic analysis targets the sites that define haplogroups,
reviews of alignment data with respect to sequence-specific polymorphisms
should also be performed as part of quality assurance practices
for database management. A review of the alignment data and other
related documentation for each of the 5,071 profiles in the Scientific
Working Group on DNA Analysis Methods database was performed. The
alignment data were compared to entries in the database to verify
manual entries. The review revealed an additional 18 transcriptional
errors and one odd concatenation. These errors have been corrected
in CODIS Missing Person Program and in Forensic Science Communications.
A list of these errors is in Table 1. The effect on the estimation
of rarity for forensic casework was found to be nominal (data not
shown) and consistent with that described by Budowle et al. (in
press).
Press
here to view Table 1
The additional review of data and the use of phylogenetic analysis
to reduce the number of errors residing in the Scientific Working
Group on DNA Analysis Methods dataset cannot be overemphasized.
An automated means of data entry will be implemented to reduce,
if not eliminate, the transcriptional errors such as those described
in the review of the database. In an effort to continue to improve
the quality of the database, laboratories approved to contribute
profiles will be required to follow the Scientific Working Group
on DNA Analysis Methods guidelines for mtDNA sequencing and submit
electronic files or color printouts of sequence chromatograms. The
profiles, as a listing of differences with respect to the Cambridge
Reference Sequence, will be submitted in a common delineated message
format so that profiles can be added to the database in an automated
fashion.
Summary
Because of these continued quality assurance evaluations of the
Scientific Working Group on DNA Analysis Methods sequence data,
the database can be considered a reliable resource. The community
can have confidence in applying the database for forensic case analysis.
Part of the success in identifying errors has been due to public
availability and scrutiny of the database. The database will continue
to be available to the scientific community for review with the
intent of continuously improving quality.
References
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