Announcement of population data Mitochondrial DNA control region variation in a population sample from Hong Kong, China Jodi A. Irwin a,*, Jessica L. Saunier a, Philip Beh b, Katharine M. Strouss a, Carla D. Paintner a, Thomas J. Parsons a,1 a Armed Forces DNA Identification Laboratory, 1413 Research Boulevard, Building 101, Rockville, MD 20850, United States b Department of Pathology, The University of Hong Kong, 3/F, University Pathology Building, Queen Mary Hospital, Hong Kong Population: 377 blood samples were obtained from residents of urban Hong Kong with diverse Chinese ancestry. Extraction: Genomic DNA was extracted from 6 mm punches of dried blood on filter paper using the Qiagen QIAmp DNA kit and a custom protocol on a Qiagen 9604 robotic platform. Additional details of the approach are described in [1,2]. PCR amplification and sequencing: PCR amplification and amplicon re-sequencing reactions were performed as described in [1,2], using an automated approach for data generation and a highly redundant sequencing strategy to provide adequate sequence coverage. At nearly all positions, two forward and two reverse strands verified each base. In those cases for which sequence quality diminished following long polycytosine tracts, multiple primers were used to abut the C-stretches and provide full reads through the region. Analysis of data: Electropherograms were evaluated in Sequencher version 4.1.4Fb19 (GeneCodes, Ann Arbor, MI) by three scientists: two at the Armed Forces DNA Identification Laboratory and one at the Institute of Legal Medicine in Innsbruck Austria. Differences from the rCRS [3,4] were transferred electro- nically from Sequencher into a master database, where the imported data were verified. Finalized data were then compared to documented sequence chemistry artifacts [5] in order to help ensure data quality. As a final quality control measure, the haplotypes were represented as a median-joining network [6], calculated and drawn with Network 4.5. In order to visualize this rather large dataset, a number of highly variable sites were filtered, the data were pre-processed using star contraction [7], and only the network containing the shortest trees [8] was evaluated for character conflicts or polymorphisms that could potentially reflect errors in the data. Genetic diversity indices were generated by a custom software package LISA (Laboratory Information Systems Applications, Future Technologies Inc. Fairfax, VA). Hypervariable C-stretch length variants at sites 16193, 309 and 573 were ignored in the analyses. In addition, for all comparisons within and between populations, point heteroplasmies were considered to be con- sistent with each of the bases present at the heteroplasmic site. Sequences were assigned to mitochondrial DNA haplogroups on the basis of differences from the rCRS that are either diagnostic of, or associated with, specific mtDNA lineages [9���18]. A number of control region sites that are known to mutate frequently are often associated with haplogroups observed in this data set. Thus, some assignments, such as D5, D4a, and M10, should be considered tentative due to the fact that the polymorphisms used for these classifications occur at one or more of the following highly recurrent positions: 16129, 16189, 150, 152 and 16311. Access to data: Sequences were evaluated using the EMPOP QC software. All haplotypes passed the quality checks and will be made available in the EMPOP database (www.empop.org) under Forensic Science International: Genetics 3 (2009) e119���e125 A R T I C L E I N F O Article history: Received 2 September 2008 Accepted 27 October 2008 Keywords: Mitochondrial DNA Control region China A B S T R A C T Entire mitochondrial control region sequences were generated from 377 unrelated individuals from urban Hong Kong. In line with other control region datasets from China, the sample from Hong Kong exhibited significant genetic diversity that was reflected in a random match probability of 0.19% and a mean pairwise difference of 13.14. A total of 305 haplotypes were identified, of which 262 were unique. These sequences will be made publicly available to serve as forensic mtDNA reference data for China. �� 2008 Elsevier Ireland Ltd. All rights reserved. * Corresponding author. Tel.: +1 301 319 0244 fax: +1 301 295 5932. E-mail address: jodi.a.irwin@us.army.mil (J.A. Irwin). 1 Present address: International Commission on Missing Persons, Alipasina �� 45A, 71000 Sarajevo, Bosnia and Herzegovina. Contents lists available at ScienceDirect Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig 1872-4973/$ ��� see front matter �� 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2008.10.008

Table 1 mtDNA haplotypes, and haplogroup associations, in a population sample from Hong Kong, China. For samples possessing length heteroplasmy, the haplotypes listed below represent the major component. # Individuals Haplogroup Haplotype 8 M7b1 16129A 16192T 16223T 16297C 73G 150T 199C 263G 309.1C 315.1C 489C 3 D/G 16092C 16223T 16362C 16519C 73G 263G 309.1C 315.1C 489C 3 D4a3a 16093C 16129A 16223T 16249C 16362C 73G 152C 237G 263G 309.1C 315.1C 489C 3 F1a1 16129A 16162G 16172C 16304C 16519C 73G 249- 263G 309.1C 315.1C 523- 524- 3 F1a1 16129A 16162G 16172C 16304C 16362C 16399G 16519C 73G 249- 263G 315.1C 523- 524- 3 F1a1c 16129A 16162G 16172C 16304C 73G 150T 249- 263G 315.1C 523- 524- 548T 3 M7b 16223T 16297C 73G 150T 199C 204C 263G 309.1C 315.1C 489C 2 A 16126C 16223T 16234T 16290T 16319A 16519C 73G 235G 263G 315.1C 523- 524- 2 B4b1a2a 16136C 16183C 16189C 16193.1C 16217C 16309G 16354T 16519C 73G 207A 263G 315.1C 499A 2 B5a 16140C 16183C 16189C 16193.1C 16266A 16519C 73G 210G 263G 309.1C 309.2C 315.1C 523- 524- 2 B5a 16140C 16183C 16189C 16193.1C 16266A 16519C 73G 210G 263G 309.1C 315.1C 523- 524- 2 C 16093C 16172C 16223T 16298C 16327T 16519C 73G 249- 263G 309.1C 315.1C 489C 2 D/G 16223T 16362C 16519C 73G 263G 315.1C 489C 2 D/G 16362C 73G 152C 195C 263G 309.1C 315.1C 489C 2 D4a 16129A 16223T 16263C 16362C 16519C 73G 152C 263G 309.1C 309.2C 315.1C 489C 507C 2 D5a 16092C 16164G 16167T 16172C 16182C 16183C 16189C 16223T 16266T 16293G 16362C 73G 150T 263G 315.1C 489C 523- 524- 2 D5b 16182C 16183C 16189C 16223T 16362C 73G 150T 263G 309.1C 315.1C 456T 489C 2 F 16304C 16362C 16399G 16497G 73G 146C 152C 207A 249- 263G 309.1C 315.1C 2 F1a 16108T 16129A 16162G 16172C 16304C 16519C 73G 93G 249- 263G 315.1C 523- 524- 2 F1a 16129A 16172C 16304C 16519C 73G 249- 263G 315.1C 523- 524- 2 F1a1a 16108T 16129A 16162G 16172C 16304C 16519C 73G 195C 249- 263G 309.1C 315.1C 523- 524- 2 F1c 16111T 16129A 16266T 16304C 16519C 73G 152C 249- 263G 309.1C 309.2C 315.1C 523- 524- 2 F2a 16092A 16291T 16304C 73G 249- 263G 309.1C 315.1C 523- 524- 2 M7b 16223T 16297C 73G 150T 199C 204C 263G 315.1C 489C 2 M7b1 16129A 16192T 16223T 16297C 16519C 73G 150T 199C 263G 309.1C 315.1C 489C 2 M7b1 16129A 16192T 16223T 16297C 73G 150T 194- 199C 263G 309.1C 309.2C 315.1C 489C 2 M7c3 16519C 73G 146A 199C 204C 263G 309.1C 315.1C 489C 523- 524- 2 M9a���b? 16223T 16240G 16362C 73G 153G 263G 309.1C 309.2C 315.1C 489C 2 R9b 16304C 16309G 16390A 16519C 73G 183G 263G 315.1C 523- 524- 2 U2 16051G 16182C 16183C 16189C 16519C 73G 152C 214G 263G 315.1C 356.1C 2 Z 16185T 16223T 16260T 16298C 73G 151T 152C 249- 263G 309.1C 315.1C 489C 1 A 16124C 16223T 16290T 16319A 16519C 73G 235G 263G 309.1C 315.1C 318C 523- 524- 1 A 16125A 16223T 16290T 16311C 16319A 16362C 73G 152C 235G 263G 309.1C 309.2C 315.1C 456T 523- 524- 576G 1 A 16126C 16223T 16234T 16290T 16319A 16445C 16519C 73G 235G 263G 315.1C 523- 524- 1 A 16126C 16223T 16234T 16290T 16319A 16519C 73G 235G 263G 309.1C 309.2C 315.1C 523- 524- 1 A 16126C 16235G 16290T 16319A 16519C 73G 235G 263G 315.1C 523- 524- 1 A 16166- 16223T 16290T 16319A 16362C 73G 152C 200G 204Y 235G 263G 309.1C 315.1C 523- 524- 1 A 16166- 16223T 16290T 16319A 16362C 73G 152C 200G 235G 263G 309.1C 309.2C 315.1C 523- 524- 1 A 16192T 16223T 16290T 16293C 16319A 16519C 73G 152C 235G 263G 309.1C 315.1C 523- 524- 1 A 16223T 16286T 16290T 16319A 16362C 73G 152C 204C 207A 235G 315.1C 523- 524- 554G 1 A 16223T 16290T 16293C 16319A 16519C 73G 152C 235G 263G 309.1C 315.1C 523- 524- 1 A 16223T 16290T 16293C 16319A 16519C 73G 152C 263G 309.1C 315.1C 523- 524- 1 A 16223T 16290T 16319A 16344T 16362C 73G 146C 152C 235G 263G 315.1C 523- 524- 573.1C 1 A5b 16126C 16223T 16235G 16290T 16319A 16519C 73G 235G 263G 315.1C 523- 524- 1 B? 16129A 16182C 16183C 16189C 16261T 73G 263G 309.1C 309.2C 315.1C 523- 524- 1 B4 16183C 16185T 16186Y 16189C 16217C 16234T 16519C 73G 151T 152C 197G 263G 309.1C 315.1C 546G 1 B4 16129A 16182C 16183C 16189C 16217C 16223T 16519C 73G 146C 150T 185A 189G 196C 263G 315.1C 513A 1 B4 16129A 16150T 16167T 16183C 16189C 16193.1C 16217C 16234T 16519C 73G 152C 263G 315.1C 556T 1 B4 16140C 16182C 16183C 16189C 16217C 16242A 16274A 16335G 16519C73G 146C 150T 263G 315.1C 456T 523- 524- 1 B4 16182C 16183C 16189C 16190Y 16217C 73G 214G 263G 309.1C 315.1C 368G 1 B4a 16092C 16182C 16183C 16189C 16217C 16224C 16261T 16399G 16519C 73G 263G 309.1C 309.2C 315.1C 523- 524- 1 B4a 16129A 16182C 16183C 16189C 16193.1C 16217C 16261T 16311C 73G 93G 263G 309- 315.1C 523- 524- 1 B4a 16129A 16182C 16183C 16189C 16217C 16261T 16311C 73G 263G 315.1C 523- 524- 1 B4a 16129A 16182C 16183C 16189C 16217C 16261T 16356C 73G 93G 263G 315.1C 513A 523- 524- 1 B4a 16129A 16182C 16183C 16189C 16217C 16261T 16519C 73G 263G 310C 314- 315- 523- 524- 1 B4a 16168T 16182C 16183C 16189C 16193.1C 16217C 16258C 16261T 16311C 16318T 16519C 73G 199Y 263G 309.1C 309.2C 315.1C 356.1C 523- 524- 1 B4a 16182C 16183C 16189C 16190T 16193.1C 16194C 16195C 16217C 16261T 16519C 73G 263G 302C 309.1C 309.2C 315.1C 393C 523- 524- 1 B4a 16182C 16183C 16189C 16193.1C 16217C 16261T 16299G 16355T 16390A 16519C 73G 263G 309.1C 309.2C 315.1C 1 B4a 16182C 16183C 16189C 16193.1C 16217C 16261T 73G 263G 309.1C 309.2C 315.1C 523- 524- 1 B4a 16182C 16183C 16189C 16217C 16261T 16274A 16299G 16519C 73G 150Y 193G 263G 309- 315.1C 523- 524- 1 B4b 16092C 16145A 16183C 16189C 16193.1C 16217C 16218T 16519C 73G 152C 204C 263G 309.1C 309.2C 315.1C 499A 524.1A 524.2C 1 B4b1 16136C 16154C 16183C 16189C 16193.1C 16217C 16218T 16223T 16519C 73G 249- 263G 309.1C 309.2C 309.3C 315.1C 499A 1 B4b1 16136C 16182C 16183C 16189C 16193.1C 16217C 16218T 16519C 73G 263G 309.1C 315.1C 499A 1 B4b1 16136C 16182C 16183C 16189C 16217C 16218T 16519C 73G 263G 309- 315.1C 499A 1 B4b1 16136C 16183C 16189C 16193.1C 16217C 16218T 16519C 73G 263G 309.1C 309.2C 315.1C 499A 1 B4b1 16136C 16183C 16189C 16217C 16519C 73G 207A 263G 315.1C 499A 523- 524- 1 B4b1a 16136C 16183C 16189C 16193.1C 16217C 16519C 73G 204C 207A 263G 309.1C 309.2C 315.1C 499A 1 B4b1a2a 16136C 16182M 16183C 16189C 16193.1C 16217C 16309G 16354T 16519C 73G 207A 263G 309.1C 309.2C 315.1C 499A 1 B4c1a1a 16086C 16129A 16162G 16182C 16183C 16189C 16193.1C 16217C 16311C 16519C 73G 263G 309.1C 315.1C 1 B4c1b 16113C 16140C 16182C 16183C 16189C 16193.1C 16217C 16274A 16519C 73G 146C 150T 263G 309.1C 309.2C 315.1C 1 B4c1b 16129A 16140C 16166G 16183C 16189C 16193.1C 16217C 16274A 16519C 73G 150T 194T 263G 309.1C 309.2C 315.1C J.A. Irwin et al. / Forensic Science International: Genetics 3 (2009) e119���e125 e120