mtDNAmanager: A Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Young, Hwan Young ^a   Song, Injee ^b   Ha, Eunho ^c   Cho, Sung Bae ^b   Yang, Woo Ick ^a   Shin, Kyoung Jin ^a  

^a Yonsei University College of Medicine   (South Korea)

^b Yonsei University   (South Korea)

^c Yonsei University Wonju   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS RESOURCES; DATABASE SCREENINGS; MITOCHONDRIAL DNA; MITOCHONDRIAL DNA (MTDNA); MTDNA SEQUENCE; NUCLEOTIDE POLYMORPHISMS; RECENT RESEARCHES; WEB-BASED TOOLS;

BIOINFORMATICS; BIOLOGY; DIAGNOSIS; DNA; INFORMATION MANAGEMENT; QUERY PROCESSING;

QUALITY CONTROL;

MITOCHONDRIAL DNA;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENETIC DATABASE; GENETICS; HAPLOTYPE; INTERNET; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; REGULATOR GENE;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA, MITOCHONDRIAL; HAPLOTYPES; INTERNET; LOCUS CONTROL REGION; MOLECULAR SEQUENCE DATA; PHYLOGENY; RESEARCH DESIGN; SOFTWARE;

EID: 58249113948     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-483     Document Type: Article

References (65)

1. Bandelt HJ Salas A Bravi C Problems in FBI mtDNA database Science 2004, 305:1402-1404. 10.1126/science.305.5689.1402b 15353782
2. Budowle B Polanskey D FBI mtDNA database: A cogent perspective Science 2005, 307:8450-847. 10.1126/science.307.5711.845c 15705827
3. Salas A Carracedo A Macaulay V Richards M Bandelt HJ A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics Biochem Biophys Res Commun 2005, 335:891-899. 10.1016/j.bbrc.2005.07.161 16102729
4. Bandelt HJ Lahermo P Richards M Macaulay V Detecting errors in mtDNA data by phylogenetic analysis Int J Legal Med 2001, 115:64-69. 10.1007/ s004140100228 11724431
5. Bandelt HJ Quintana-Murci L Salas A Macaulay V The fingerprint of phantom mutations in mitochondrial DNA data Am J Hum Genet 2002, 71:1150-1160. 385090 12384858 10.1086/344397
6. Attimonelli M Accetturo M Santamaria M Lascaro D Scioscia G Pappadà G Russo L Zanchetta L Tommaseo-Ponzetta M HmtDB, a human mitochondrial genomic resource based on variability studies supporting population genetics and biomedical research BMC Bioinformatics 2005, 6:S4. 1866381 16351753 10.1186/1471-2105-6-S4-S4
7. The European DNA Profiling Group (EDNAP) MtDNA Population Database (EMPOP) http://www.empop.org
8. Parson W Dür A EMPOP-A forensic mtDNA database Forensic Sci Int Gene 2007, 1:88-92. 10.1016/j.fsigen.2007.01.018
9. Andrews RM Kubacka I Chinnery PF Lightowlers RN Turnbull DM Howell N Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA Nat Genet 1999, 23:147. 10.1038/13779 10508508
10. Macaulay V Richards M Hickey E Vega E Cruciani F Guida V Scozzari R Bonné-Tamir B Sykes B Torroni A The emerging tree of West Eurasian mtDNAs: A synthesis of control-region sequences and RFLPs Am J Hum Genet 1999, 64:232-249. 1377722 9915963 10.1086/302204
11. Helgason A Hickey E Goodacre S Bosnes V Stefánsson K Ward R Sykes B mtDNA and the islands of the North Atlantic: Estimating the proportions of Norse and Gaelic ancestry Am J Hum Genet 2001, 68:723-737. 1274484 11179019 10.1086/318785
12. Kivisild T Tolk HV Parik J Wang Y Papiha SS Bandelt HJ Villems R The emerging limbs and twigs of the East Asian mtDNA tree Mol Biol Evol 2002, 19:1737-1751. 12270900
13. Salas A Richards M De la Fe T Lareu MV Sobrino B Sánchez-Diz P Macaulay V Carracedo A The making of the African mtDNA landscape Am J Hum Genet 2002, 71:1082-1111. 385086 12395296 10.1086/344348
14. Kong QP Yao YG Liu M Shen SP Chen C Zhu CL Palanichamy MG Zhang YP Mitochondrial DNA sequence polymorphisms of five ethnic populations from northern China Hum Genet 2003, 113:391-405. 10.1007/s00439-003-1004-7 12938036
15. Kong QP Yao YG Sun C Bandelt HJ Zhu CL Zhang YP Phylogeny of East Asian mitochondrial DNA lineages inferred from complete sequences Am J Hum Genet 2003, 73:671-676. 1180693 12870132 10.1086/377718
16. Reidla M Kivisild T Metspalu E Kaldma K Tambets K Tolk HV Parik J Loogväli EL Derenko M Malyarchuk B Bermisheva M Zhadanov S Pennarun E Gubina M Golubenko M Damba L Fedorova S Gusar V Grechanina E Mikerezi I Moisan JP Chaventré A Khusnutdinova E Osipova L Stepanov V Voevoda M Achilli A Rengo C Rickards O De Stefano GF Papiha S Beckman L Janicijevic B Rudan P Anagnou N Michalodimitrakis E Koziel S Usanga E Geberhiwot T Herrnstadt C Howell N Torroni A Villems R Origin and diffusion of mtDNA haplogroup X Am J Hum Genet 2003, 73:1178-1190. 1180497 14574647 10.1086/379380
17. Achilli A Rengo C Magri C Battaglia V Olivieri A Scozzari R Cruciani F Zeviani M Briem E Carelli V Moral P Dugoujon JM Roostalu U Loogväli EL Kivisild T Bandelt HJ Richards M Villems R Santachiara-Benerecetti AS Semino O Torroni A The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool Am J Hum Genet 2004, 75:910-918. 1182122 15382008 10.1086/425590
18. Kivisild T Reidla M Metspalu E Rosa A Brehm A Pennarun E Parik J Geberhiwot T Usanga E Villems R Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears Am J Hum Genet 2004, 75:752-770. 1182106 15457403 10.1086/425161
19. Loogväli EL Roostalu U Malyarchuk BA Derenko MV Kivisild T Metspalu E Tambets K Reidla M Tolk HV Parik J Pennarun E Laos S Lunkina A Golubenko M Barac L Pericic M Balanovsky OP Gusar V Khusnutdinova EK Stepanov V Puzyrev V Rudan P Balanovska EV Grechanina E Richard C Moisan JP Chaventre A Anagnou NP Pappa KI Michalodimitrakis EN Claustres M Golge M Mikerezi I Usanga E Villems R Disuniting uniformity: A pied cladistic canvas of mtDNA haplogroup H in Eurasia Mol Biol Evol 2004, 21:2012-2021. 10.1093/molbev/msh209 15254257
20. Metspalu M Kivisild T Metspalu E Parik J Hudjashov G Kaldma K Serk P Karmin M Behar DM Gilbert MT Endicott P Mastana S Papiha SS Skorecki K Torroni A Villems R Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans BMC Genet 2004, 5:26. 516768 15339343 10.1186/1471-2156-5-26
21. Palanichamy MG Sun C Agrawal S Bandelt HJ Kong QP Khan F Wang CY Chaudhuri TK Palla V Zhang YP Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: Implications for the peopling of South Asia Am J Hum Genet 2004, 75:966-978. 1182158 15467980 10.1086/425871
22. Quintana-Murci L Chaix R Wells RS Behar DM Sayar H Scozzari R Rengo C Al-Zahery N Semino O Santachiara-Benerecetti AS Coppa A Ayub Q Mohyuddin A Tyler-Smith C Qasim Mehdi S Torroni A McElreavey K Where west meets east: The complex mtDNA landscape of the southwest and Central Asian corridor Am J Hum Genet 2004, 74:827-845. 1181978 15077202 10.1086/383236
23. Salas A Richards M Lareu MV Scozzari R Coppa A Torroni A Macaulay V Carracedo A The African diaspora: Mitochondrial DNA and the Atlantic slave trade Am J Hum Genet 2004, 74:454-465. 1182259 14872407 10.1086/ 382194
24. Tanaka M Cabrera VM González AM Larruga JM Takeyasu T Fuku N Guo LJ Hirose R Fujita Y Kurata M Shinoda K Umetsu K Yamada Y Oshida Y Sato Y Hattori N Mizuno Y Arai Y Hirose N Ohta S Ogawa O Tanaka Y Kawamori R Shamoto-Nagai M Maruyama W Shimokata H Suzuki R Shimodaira H Mitochondrial genome variation in eastern Asia and the peopling of Japan Genome Res 2004, 14:1832-1850. 524407 15466285 10.1101/gr.2286304
25. Yao YG Kong QP Wang CY Zhu CL Zhang YP Different matrilineal contributions to genetic structure of ethnic groups in the silk road region in china Mol Biol Evol 2004, 21:2265-2280. 10.1093/molbev/msh238 15317881
26. Achilli A Rengo C Battaglia V Pala M Olivieri A Fornarino S Magri C Scozzari R Babudri N Santachiara-Benerecetti AS Bandelt HJ Semino O Torroni A Saami and Berbers - an unexpected mitochondrial DNA link Am J Hum Genet 2005, 76:883-886. 1199377 15791543 10.1086/430073
27. Friedlaender J Schurr T Gentz F Koki G Friedlaender F Horvat G Babb P Cerchio S Kaestle F Schanfield M Deka R Yanagihara R Merriwether DA Expanding Southwest Pacific mitochondrial haplogroups P and Q Mol Biol Evol 2005, 22:1506-1517. 10.1093/molbev/msi142 15814828
28. Macaulay V Hill C Achilli A Rengo C Clarke D Meehan W Blackburn J Semino O Scozzari R Cruciani F Taha A Shaari NK Raja JM Ismail P Zainuddin Z Goodwin W Bulbeck D Bandelt HJ Oppenheimer S Torroni A Richards M Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes Science 2005, 308:1034-1036. 10.1126/ science.1109792 15890885
29. Merriwether DA Hodgson JA Friedlaender FR Allaby R Cerchio S Koki G Friedlaender JS Ancient mitochondrial M haplogroups identified in the Southwest Pacific Proc Natl Acad Sci USA 2005, 102:13034-13039. 1201611 16150714 10.1073/pnas.0506195102
30. Wen B Li H Gao S Mao X Gao Y Li F Zhang F He Y Dong Y Zhang Y Huang W Jin J Xiao C Lu D Chakraborty R Su B Deka R Jin L Genetic structure of Hmong-Mien speaking populations in East Asia as revealed by mtDNA lineages Mol Biol Evol 2005, 22:725-734. 10.1093/molbev/msi055 15548747
31. Behar DM Metspalu E Kivisild T Achilli A Hadid Y Tzur S Pereira L Amorim A Quintana-Murci L Majamaa K Herrnstadt C Howell N Balanovsky O Kutuev I Pshenichnov A Gurwitz D Bonne-Tamir B Torroni A Villems R Skorecki K The matrilineal ancestry of Ashkenazi Jewry: Portrait of a recent founder event Am J Hum Genet 2006, 78:487-497. 1380291 16404693 10.1086/500307
32. Hill C Soares P Mormina M Macaulay V Meehan W Blackburn J Clarke D Raja JM Ismail P Bulbeck D Oppenheimer S Richards M Phylogeography and ethnogenesis of aboriginal Southeast Asians Mol Biol Evol 2006, 23:2480-2491. 10.1093/molbev/msl124 16982817
33. Kong QP Bandelt HJ Sun C Yao YG Salas A Achilli A Wang CY Zhong L Zhu CL Wu SF Torroni A Zhang YP Updating the East Asian mtDNA phylogeny: A prerequisite for the identification of pathogenic mutations Hum Mol Genet 2006, 15:2076-2086. 10.1093/hmg/ddl130 16714301
34. Lee HY Yoo JE Park MJ Chung U Kim CY Shin KJ East Asian mtDNA haplogroup determination in Koreans: Haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis Electrophoresis 2006, 27:4408-4418. 10.1002/elps.200600151 17058303
35. Olivieri A Achilli A Pala M Battaglia V Fornarino S Al-Zahery N Scozzari R Cruciani F Behar DM Dugoujon JM Coudray C Santachiara-Benerecetti AS Semino O Bandelt HJ Torroni A The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa Science 2006, 314:1767-1770. 10.1126/ science.1135566 17170302
36. Pierson MJ Martinez-Arias R Holland BR Gemmell NJ Hurles ME Penny D Deciphering past human population movements in Oceania: Provably optimal trees of 127 mtDNA genomes Mol Biol Evol 2006, 23:1966-1975. 10.1093/ molbev/msl063 16855009
37. Sun C Kong QP Palanichamy MG Agrawal S Bandelt HJ Yao YG Khan F Zhu CL Chaudhuri TK Zhang YP The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes Mol Biol Evol 2006, 23:683-690. 10.1093/molbev/msj078 16361303
38. Thangaraj K Chaubey G Singh VK Vanniarajan A Thanseem I Reddy AG Singh L In situ origin of deep rooting lineages of mitochondrial macrohaplogroup 'M' in India BMC Genomics 2006, 7:151. 1534032 16776823 10.1186/ 1471-2164-7-151
39. Thanseem I Thangaraj K Chaubey G Singh VK Bhaskar LV Reddy BM Reddy AG Singh L Genetic affinities among the lower castes and tribal groups of India: Inference from Y chromosome and mitochondrial DNA BMC Genet 2006, 7:42. 1569435 16893451 10.1186/1471-2156-7-42
40. Derenko M Malyarchuk B Grzybowski T Denisova G Dambueva I Perkova M Dorzhu C Luzina F Lee HK Vanecek T Villems R Zakharov I Phylogeographic analysis of mitochondrial DNA in northern Asian populations Am J Hum Genet 2007, 81:1025-1041. 2265662 17924343 10.1086/522933
41. Friedlaender JS Friedlaender FR Hodgson JA Stoltz M Koki G Horvat G Zhadanov S Schurr TG Merriwether DA Melanesian mtDNA complexity PLoS ONE 2007, 2:e248. 1803017 17327912 10.1371/journal.pone.0000248
42. Hill C Soares P Mormina M Macaulay V Clarke D Blumbach PB Vizuete-Forster M Forster P Bulbeck D Oppenheimer S Richards M A mitochondrial stratigraphy for island southeast Asia Am J Hum Genet 2007, 80:29-43. 1876738 17160892 10.1086/510412
43. Hudjashov G Kivisild T Underhill PA Endicott P Sanchez JJ Lin AA Shen P Oefner P Renfrew C Villems R Forster P Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis Proc Natl Acad Sci USA 2007, 104:8726-8730. 1885570 17496137 10.1073/ pnas.0702928104
44. Reddy BM Langstieh BT Kumar V Nagaraja T Reddy AN Meka A Reddy AG Thangaraj K Singh L Austro-Asiatic tribes of Northeast India provide hitherto missing genetic link between South and Southeast Asia PLoS ONE 2007, 2:e1141. 2065843 17989774 10.1371/journal.pone.0001141
45. Roostalu U Kutuev I Loogväli EL Metspalu E Tambets K Reidla M Khusnutdinova EK Usanga E Kivisild T Villems R Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: The Near Eastern and Caucasian perspective Mol Biol Evol 2007, 24:436-448. 10.1093/molbev/msl173 17099056
46. Achilli A Perego UA Bravi CM Coble MD Kong QP Woodward SR Salas A Torroni A Bandelt HJ The phylogeny of the four pan-American MtDNA haplogroups: Implications for evolutionary and disease studies PLoS ONE 2008, 3:e1764. 2258150 18335039 10.1371/journal.pone.0001764
47. Malyarchuk B Grzybowski T Derenko M Perkova M Vanecek T Lazur J Gomolcak P Tsybovsky I Mitochondrial DNA phylogeny in Eastern and Western Slavs Mol Biol Evol 2008, 25:1651-1658. 10.1093/molbev/msn114 18477584
48. Malyarchuk BA Perkova MA Derenko MV Vanecek T Lazur J Gomolcak P Mitochondrial DNA variability in Slovaks, with application to the Roma origin Ann Hum Genet 2008, 72:228-40. 10.1111/j.1469-1809.2007.00410.x 18205894
49. Soares P Trejaut JA Loo JH Hill C Mormina M Lee CL Chen YM Hudjashov G Forster P Macaulay V Bulbeck D Oppenheimer S Lin M Richards MB Climate change and post-glacial human dispersals in southeast Asia Mol Biol Evol 2008, 25:1209-1218. 10.1093/molbev/msn068 18359946
50. Brandstätter A Niederstätter H Pavlic M Grubwieser P Parson W Generating population data for the EMPOP database-an overview of the mtDNA sequencing and data evaluation processes considering 273 Austrian control region sequences as example Forensic Sci Int 2007, 166:164-175. 10.1016/j.forsciint.2006.05.006 16829006
51. Just RS Diegoli TM Saunier JL Irwin JA Parsons TJ Complete mitochondrial genome sequences for 265 African American and U.S. "Hispanic" individuals Forensic Sci Int Gene 2008, 2:e45-e48. 10.1016/ j.fsigen.2007.12.001
52. Monson KL Miller KWP Wilson MR DiZinno JA Budowle B The mtDNA population database: An integrated software and database resource for forensic comparison Forensic Sci Commun 2002, 4.
53. Maruyama S Minaguchi K Saitou N Sequence polymorphisms of the mitochondrial DNA control region and phylogenetic analysis of mtDNA lineages in the Japanese population Int J Legal Med 2003, 117:218-225. 10.1007/s00414-003-0379-2 12845447
54. Brandstätter A Peterson CT Irwin JA Mpoke S Koech DK Parson W Parsons TJ Mitochondrial DNA control region sequences from Nairobi (Kenya): Inferring phylogenetic parameters for the establishment of a forensic database Int J Legal Med 2004, 118:294-306. 10.1007/ s00414-004-0466-z 15248073
55. Brandstätter A Klein R Duftner N Wiegand P Parson W Application of a quasi-median network analysis for the visualization of character conflicts to a population sample of mitochondrial DNA control region sequences from southern Germany (Ulm) Int J Legal Med 2006, 120:310-34. 10.1007/s00414-006-0114-x 16871406
56. Lee HY Yoo JE Park MJ Chung U Shin KJ Mitochondrial DNA control region sequences in Koreans: Identification of useful variable sites and phylogenetic analysis for mtDNA data quality control Int J Legal Med 2006, 120:5-14. 10.1007/s00414-005-0005-6 16177905
57. Alshamali F Brandstätter A Zimmermann B Parson W Mitochondrial DNA control region variation in Dubai, United Arab Emirates Forensic Sci Int Gene 2008, 2:e9-e10. 10.1016/j.fsigen.2007.08.005
58. Hedman M Brandstätter A Pimenoff V Sistonen P Palo JU Parson W Sajantila A Finnish mitochondrial DNA HVS-I and HVS-II population data Forensic Sci Int 2007, 172:171-178. 10.1016/j.forsciint.2006.09.012 17336475
59. Irwin J Egyed B Saunier J Szamosi G O'callaghan J Padar Z Parsons TJ Hungarian mtDNA population databases from Budapest and the Baranya county Roma Int J Legal Med 2007, 121:377-383. 10.1007/s00414-006-0128-4 17186294
60. Tetzlaff S Brandstätter A Wegener R Parson W Weirich V Mitochondrial DNA population data of HVS-I and HVS-II sequences from a northeast German sample Forensic Sci Int 2007, 172:218-224. 10.1016/ j.forsciint.2006.12.016 17331686
61. Lander N Rojas MG Chiurillo MA Ramirez JL Haplotype diversity in human mitochondrial DNA hypervariable regions I-III in the city of Caracas (Venezuela) Forensic Sci Int Gene 2008, 2:e61-e64. 10.1016/ j.fsigen.2007.12.009
62. Saunier JL Irwin JA Just RS O'Callaghan J Parsons TJ Mitochondrial control region sequences from a U.S. "Hispanic" population sample Forensic Sci Int Gene 2008, 2:e19-23. 10.1016/j.fsigen.2007.11.004
63. Balding DJ Nichols RA DNA profile match probability calculation: How to allow for population stratification, relatedness, database selection and single bands Forensic Sci Int 1994, 64:125-140. 10.1016/ 0379-0738(94)90222-4 8175083
64. Carracedo A Bär W Lincoln P Mayr W Morling N Olaisen B Schneider P Budowle B Brinkmann B Gill P Holland M Tully G Wilson M DNA commission of the international society for forensic genetics: Guidelines for mitochondrial DNA typing Forensic Sci Int 2000, 110:79-85. 10.1016/ S0379-0738(00)00161-4 10808096
65. Bandelt HJ Salas A Lutz-Bonengel S Artificial recombination in forensic mtDNA population databases Int J Legal Med 2004, 118:267-273. 10.1007/ s00414-004-0455-2 15257464