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Research and Technology - Forensic Science Communications - January 2005

Research and Technology - Forensic Science Communications - January 2005

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January 2005 - Volume 7 - Number 1

Research and Technology

Summary of the Findings of a Quality Review of the Scientific Working Group on DNA Analysis Methods Mitochondrial DNA Database

Deborah Polanskey
Forensic mtDNA Examiner
DNA Analysis Unit 2

Bruce Budowle
Senior Biological Sciences Program Advisor
Laboratory
Federal Bureau of Investigation
Quantico, Virginia

Introduction I Database I Analysis I Summary I References

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

Allard, M. W., Wilson, M. R., Monson, K. L., and Budowle, B. Characterization of the Caucasian haplogroups present in the SWGDAM forensic mtDNA dataset for 1771 human control region sequences, Journal of Forensic Sciences (2003) 47:1215-1223.

Allard, M. W., Wilson, M. R., Monson, K. L., and Budowle, B. Control region sequences for East Asian individuals in the Scientific Working Group on DNA Analysis Methods forensic mtDNA dataset,
Legal Medicine (2004) 6:11-24.

Anderson, S., Bankier, A. T., Barrell, B., de Bruijin, M. H. L., Coulson, A. R., Drouin, I. C., Eperon, I. C., Nierlick, D. P., Roe, B. A., Sanger, F., Schreier, P. M., Smith, A. J. H., Staden, R., and Young, I. G. Sequence and organization of the mitochondrial genome,
Nature (1981) 290:457-465.

Andrews, R. M., Kubacka, I., Chinnery, P. F., Lightowlers, R. N., Turnbull, D. M., and Howell, N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA,
Nature Genetics (1999) 23(2):147.

Bandelt, H. J., Lahermo, P., Richards, M., and Macaulay, V. Detecting errors in mtDNA data by phylogenetic analysis,
International Journal of Legal Medicine (2001) 115:64-69.

Bar, W., Brinkmann, B., Budowle, B., Carracedo, A., Gill, P., Holland, M., Lincoln, P., Mayr, W., Morling, N., Olaisen, B., Schneider, P. M., Tully, G., and Wilson, M. DNA Commission of the International Society for Forensic Genetics: Guideline for mitochondrial DNA typing,
International Journal of Legal Medicine (2000) 113(4):193-196.

Budowle, B., Allard, M. W., Wilson, M. R., and Chakraborty, R. Forensic and mitochondrial DNA: Applications, debated and foundations,
Annual Review of Genomics and Human Genetics (2003) 4:119-141.

Budowle, B., Polanskey, D., Allard, M. W., and Chakraborty, R. Addressing the use of phylogenetic analysis for identification of sequence in error in the SWGDAM mitochondrial DNA database,
Journal of Forensic Sciences (in press).

Miller, K. W. P. and Budowle, B. Compendium of human mitochondrial DNA control region: Development of an international standard forensic database,
Croatian Medical Journal (2001) 42(3):315-327.

Monson, K. L., Miller, K. W. P., Wilson, M. R., DiZinno, J. A., and Budowle, B. The mtDNA population database: An integrated software and database resource for forensic comparison.
Forensic Science Communications [Online]. (April 2002). Available: http://www.fbi.gov/hq/lab/fsc/backissu/april2002/miller1.htm.

Scientific Working Group on DNA Analysis, Guidelines for mitochondrial DNA (mtDNA) nucleotide sequence interpretation,
Forensic Science Communications [Online]. (April 2003). Available: http://www.fbi.gov/hq/lab/fsc/backissu/april2003/swgdammitodna.htm.

Wilson, M. R., Allard, M. W., Monson, K. L., Miller, K. W. P., and Budowle, B. Recommendations for consistent treatment of length variants in the human mitochondrial DNA control region, Forensic Science International (2002A) 129:35-42.

Wilson, M. R., Allard, M. W., Monson, K. L., Miller, K. W. P., and Budowle, B. Further discussion of the consistent treatment of length variants in the human mitochondrial DNA control region,
Forensic Science Communications [Online]. (October 2002B). Available: http://www.fbi.gov/hq/lab/fsc/backissu/oct2002/wilson.htm.

Yao, Y. G., Bravi, C., and Bandelt, H. G. Call for mtDNA data quality control in forensic science,
Forensic Science International (2004) 141:1-6.