east asian mtdna haplogroup determination in koreans
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East Asian mtDNA haplogroup determination in Koreans: Haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis Hwan Young Lee, Ji-Eun Yoo, Myung Jin Park, Ukhee Chung, Kyoung-Jin Shin, Chong-Youl

  1. East Asian mtDNA haplogroup determination in Koreans: Haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis Hwan Young Lee, Ji-Eun Yoo, Myung Jin Park, Ukhee Chung, Kyoung-Jin Shin, Chong-Youl Kim Department of Forensic Medicine, College of Medicine, Yonsei University, Seoul, Korea Human Identification Research Institute, Yonsei University, Seoul, Korea ISFG 2005 Korean mtDNA database establishment and haplogroup assignment � A high quality mtDNA control region sequence database was established in 593 Koreans ( http://forensic.yonsei.ac.kr/ ) � Based on shared haplogroup-specific polymorphisms in control region sequence, 592 mtDNAs (99.8%) were classified into various East Asian haplogroups or subhaplogroups � Statistical parameters were calculated using “ mtDNA Star ” ( K-J Shin, Yonsei University, unpublished ) ISFG 2005 1

  2. mtDNA haplogroup determination has practical value in forensic field � Sequencing and documenting processes are prone to copying errors (e.g. base shift, reference bias, phantom mutations, base misscoring, artifactual recombination) � As mtDNA evolves along a tree, assigning new mtDNA types to a spot in the global mtDNA tree can prevent potential errors in mtDNA database � Phylogenetic analysis is the key tool in understanding the structure of the mtDNA data ISFG 2005 The ideal approach is confirmation of diagnostic coding region SNP � Previously identified control region mutation motifs cannot exactly define major haplogroups and their subhaplogroups without complementation of coding region information � As an example, D4, G and M9 mtDNA are not distinguishable only with control region sequence polymorphisms Sample Haplogroup Control region sequence BF4229 D4 16223 16362 16519 73 263 309.1C 315.1C 489 523d 524d 385 G 16223 16362 16519 73 263 309.1C 315.1C 489 476 G 16078T 16179 16223 16234 16362 16519 73 152 263 309.1C 309.2C 315.1C 489 BF4102 M9 16223 16234 16274 16362 73 153 263 315.1C 489 409 G 16189 16223 16269 16278 16362 73 260 263 284 309.1C 309.2C 315.1C 489 BF4271 D4 16172Y 16189 16223 16278 16362 73 263 309.1C 315.1C 489 573.1C 573.2C 573.3C 573.pC ISFG 2005 2

  3. Design of three multiplex systems for coding region SNP scoring � Multiplex I 115 bp 130 bp 145 bp 160 bp 100 bp D5 M10 Multiplex M11 D4 N9 M9 M A PCR A N9 M Multiplex M9 M10M11 SNaPshot D4 D5 8 3 0 7 1 2 4 7 6 9 SNP site 0 9 9 4 9 1 4 6 3 4 7 6 7 4 4 4 8 7 8 5 0 0 1 1 1 ISFG 2005 Design of three multiplex systems for coding region SNP scoring � Multiplex II 100 bp 115 bp 130 bp 145 bp 160 bp G Multiplex M7 M8 R9 B R D PCR D G R9 M8 R B Multiplex M7 SNaPshot 3 3 4 6 5 0 l e 3 7 8 2 9 0 d SNP site 9 8 8 8 1 7 3 p 4 4 9 7 2 b 1 9 ISFG 2005 3

  4. Design of three multiplex systems for coding region SNP scoring � Multiplex III 115 bp 130 bp 145 bp 160 bp 100 bp D4 D4e Multiplex D4J D4b D4g D4a PCR D4g D4a Multiplex D4e D4 D4j D4b SNaPshot 9 0 0 5 1 6 1 7 2 1 0 9 SNP site 0 9 0 7 6 2 3 4 8 8 1 1 1 1 1 ISFG 2005 Control region motifs for East Asian haplogroups were identified Haplogroup HV1 HV2 HV3 etc D4 16223-16362 489 B4 M8 D5 16183C-16189-16217 16189-16223-16362 16223-16298 150 489 489 D4a 16129-16223-16362 152 (16519), 489 16182C-16183C-16189-16217-16261 (16519), 523d-524d D5a1 M8a B4a 16182C-16183C-16189-16223-16362 16184-16223-16298-16319 150-309d 16390-68-489 489 D4b1 16223-16319-16362 489-523d-524d 16136-16183C-16189-16217 (16223)-16298-16327 D5a2 B4b1 C 16182Y-16183C-16189-16223-16266-16362 150 489-523d-524d 16519, 499 456-489 D4b2* 16223-16362 489-523d-524d B4d 16183C-16185-16189d-16217-16234 16223-16260-16298 546 pre-Z D5b 16189-16223-16362 150 249d 456-489 16519, 489 D4b2b (16223)-16362 194 16519, 489-523d-524d Z B4c1a 16183C-16189-16217-16311 152-249d 16519 D5c 16188.1C-16193.1C-16362 16185-16223-16260-16298 150-152 489 489 D4d B4c1b 16140-16183C-16189-16217-16274-16335 16245-16362 489 M9 150 489 G 16223-16362 16223-16234-16362 152-249d (or 247d) 489 D4e* 16223-16362 489 G1a B4c1c 16183C-16189-16217-16311 150-195-214 16519, 489 M9a 16223-16325-16362 16223-16234-16316-16362 150 489 D4e1 16223-16362 94 489 B4f 16168-16172-16183C-16189-16217-16249-16325 200 16390 16497, 489, 523d-524d-573.pC M10a G1b 16184-16214-16223-16362 16129-16223-16311-16357 489 D4g1 16129-16140-16187-16189-16266R 16223-16278-16362 489-573.pC B5a1 M10b 93-210 16519, 523d-524d G2a1 16189-16223-16278-16362 16066-16223-16311 489 489-573.pC D4h* 16223-16362 489 B5b 16140-16183C-16189-16243 16519, 523d-524d, (or 513d-514d) G2a1a M11 16223-16227-16278-(16362) 16223 215-318-326 489 489 A D4h1 16223-16290-16319 16174-16223-16362 235 146-183 489 G2a2 F 16051-16150-16223-16278-16362 (16304) 249d 489 D4h2 A4 16223-16290-16319-16362 16174-16223-16311-16362 235 152 523d-524d 489 G2a3 F1ac 16223-16278-16303-16362 16129-16304 249d 489 16519, 523d-524d 16187-16223-16290-16319 A5 D4i 16223-16294-16362 235 523d-524d 489 G2a4 F1a1 16204-16223-16278-16362 (16129)-16162-16172-(16304) 249d 489 (16519), 523d-524d N9a 16223-16257A-16261 150 D4j* 16223-16362 489 G3a F1a2 16223-16274-16362 16172-16284-16304-16311 143-152 249d 489 16390-16519, 523d-524d 150 D4j1 N9a1 16129-16223-16257A-16261 16184-16223-16311-16362 489 F1c M7a 16209-16223 16111-16129-16304 152-249d 489 16519, 523d-524d N9a2 16172-16223-16257A-(16261) 150 D4k1 16192-16223 195 489 M7a1 F1b 16209-16223-16324 16183C-16189-16304 249d 489-(523d-524d) 16519, 523d-524d 16172-16223-16257A-16261 150 D4k2 N9a2a 16223-16274-16290-16319-16362 195 16497 489 M7b1 F1b1 16129-16192-16223-16297 (16182C)-16183C-16189-16232A-16249-16304-16311 150-199 249d 489 (16519), 523d-524d N9b 16183C-16189-16223 16519 D4m 16244-16362 489 M7b2 16129-16189-16223-16297-16298 16291-16304 150-199 249d 489 F2a Y1b 16126-16231-16266 146 16519 D4n 16223-16355A-16362 489 146-199 M7c 16223 16519, 489-523d-524d R11 16189-16311 185-189 Y2 16126-16231-16311 482 16519, 489-523d-524d (or 513d-514d) M7c1 16223-16295 (146)-199 ISFG 2005 4

  5. Coding region SNP scoring is useful for molecular dissection of D4 haplogroup Haplogroup Freq.(%) Coding region SNP scoring using Multiplex III D4* 8.26 D4a 5.06 D4b 0.84 18 D4b1 1.69 Frequency distribution of haplogroups D4* 16 D4b2 3.71 determined by control region motifs 14 D4e 2.52 12 D4g 1.00 ) Frequency (% 10 D4j 2.35 8 6 D4a N9a2 B4B4a M7b2 4 D4b2 B4b1 A4 A5 B5b D5b F1b G2a1a M7c1 C G1a A D5a F1a N9a1 G3a M9a 2 M10 B5a Y1 M7a1 D* F1 D4b1 G2a2 ZM8a M* F D4b G2a1 M11 N9a D5 F2a G1b F1ac F1c R11 N9bY M7a M7b1 M7c M8CZ 0 Haplogroup ISFG 2005 Control region motifs for D4 subhaplogroups are identified Haplogroup HV1 HV2 HV3 etc D4 16223-16362 489 D4a 16129 -16223-16362 152 (16519)-489 D4b1 16223- 16319 -16362 489-523d-524d D4b2* 16223-16362 489-523d-524d D4b2b (16223)-16362 194 16519-489-523d-524d D4d 16245 -16362 489 D4e* 16223-16362 489 D4e1 16223-16362 94 489 D4g1 16223- 16278 -16362 489-573.pC D4h* 16223-16362 489 D4h1 16174 -16223-16362 146-183 489 D4h2 16174 -16223- 16311 -16362 152 489 D4i 16223- 16294 -16362 489 D4j* 16223-16362 489 D4j1 16184 -16223- 16311 -16362 489 D4k1 16192 -16223 195 489 D4k2 16223- 16274 - 16290 - 16319 -16362 195 489 D4m 16244 -16362 489 D4n 16223- 16355A -16362 489 ISFG 2005 5

  6. Coding region SNP scoring is indispensable in some haplogroups � One of G2a1 haplotype according to control region sequence was found to be D4g haplogroup, and 8 and 1 of D4 haplotypes turned out to be G and M9 haplogroups, respectively � D4 paragroups, e.g., D4*, D4b2*, D4e* and D4j*, which have a mutation motif 16223-16362-489, need coding region SNP scoring for exact haplogroup determination � Complementation of coding region SNP information to control region polymorphisms will lead to mtDNA data quality control and molecular dissection of haplogroups ISFG 2005 Multiplex systems are proved to be efficient in skeletal remain analysis � Efficiency test was performed in 101 skeletal remains from Korean War (1950~1953) victims � Small amplicon sizes enabled SNP score in old skeletal remains to be successfully analyzed without artifact 14668T D4 Multiplex I HV1-HV2-HV3 region sequence 4883T 16093- 16129 - 16223 - 16362 73- 152 -263-309.1C-315.1C D Multiplex II 489 14979C D4a Multiplex III ISFG 2005 6

  7. East Asian HG can be determined using “mtDNA Sequence Manager” � We have developed the haplogroup determining program, “ mtDNA Sequence Manager ” based on the collated control region mutation motifs for East Asian haplogroups or subhaplogroups � By using this program, 593 Korean mtDNAs and 101 Korean War victim mtDNAs can be classified into various East Asian haplogroups or subhaplogroups ( K-J Shin, Yonsei University, unpublished ) ISFG 2005 Concluding remarks � East Asian haplogroup determination is efficiently carried out using haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis � Identification of control region mutation motif and molecular dissection of haplogroups can be achieved by coding region SNP analysis � The 3 multiplex systems work well even in degraded samples and it will present a promising means for forensic and human genetics involving East Asian mtDNA haplogroups ISFG 2005 7

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