{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T20:35:05Z","timestamp":1761597305945},"reference-count":20,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Mitochondrial genome sequence analysis is critical to the diagnostic evaluation of mitochondrial disease. Existing methodologies differ widely in throughput, complexity, cost efficiency, and sensitivity of heteroplasmy detection. Affymetrix MitoChip v2.0, which uses a sequencing-by-genotyping technology, allows potentially accurate and high-throughput sequencing of the entire human mitochondrial genome to be completed in a cost-effective fashion. However, the relatively low call rate achieved using existing software tools has limited the wide adoption of this platform for either clinical or research applications. Here, we report the design and development of a custom bioinformatics software pipeline that achieves a much improved call rate and accuracy for the Affymetrix MitoChip v2.0 platform. We used this custom pipeline to analyze MitoChip v2.0 data from 24 DNA samples representing a broad range of tissue types (18 whole blood, 3 skeletal muscle, 3 cell lines), mutations (a 5.8 kilobase pair deletion and 6 known heteroplasmic mutations), and haplogroup origins. All results were compared to those obtained by at least one other mitochondrial DNA sequence analysis method, including Sanger sequencing, denaturing HPLC-based heteroduplex analysis, and\/or the Illumina Genome Analyzer II next generation sequencing platform.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>An average call rate of 99.75% was achieved across all samples with our custom pipeline. Comparison of calls for 15 samples characterized previously by Sanger sequencing revealed a total of 29 discordant calls, which translates to an estimated 0.012% for the base call error rate. We successfully identified 4 known heteroplasmic mutations and 24 other potential heteroplasmic mutations across 20 samples that passed quality control.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Affymetrix MitoChip v2.0 analysis using our optimized MitoChip Filtering Protocol (MFP) bioinformatics pipeline now offers the high sensitivity and accuracy needed for reliable, high-throughput and cost-efficient whole mitochondrial genome sequencing. This approach provides a viable alternative of potential utility for both clinical diagnostic and research applications to traditional Sanger and other emerging sequencing technologies for whole mitochondrial genome analysis.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-402","type":"journal-article","created":{"date-parts":[[2011,10,19]],"date-time":"2011-10-19T18:21:18Z","timestamp":1319048478000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Mitochondrial genome sequence analysis: A custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy"],"prefix":"10.1186","volume":"12","author":[{"given":"Hongbo M","family":"Xie","sequence":"first","affiliation":[]},{"given":"Juan C","family":"Perin","sequence":"additional","affiliation":[]},{"given":"Theodore G","family":"Schurr","sequence":"additional","affiliation":[]},{"given":"Matthew C","family":"Dulik","sequence":"additional","affiliation":[]},{"given":"Sergey I","family":"Zhadanov","sequence":"additional","affiliation":[]},{"given":"Joseph A","family":"Baur","sequence":"additional","affiliation":[]},{"given":"Michael P","family":"King","sequence":"additional","affiliation":[]},{"given":"Emily","family":"Place","sequence":"additional","affiliation":[]},{"given":"Colleen","family":"Clarke","sequence":"additional","affiliation":[]},{"given":"Michael","family":"Grauer","sequence":"additional","affiliation":[]},{"given":"Jonathan","family":"Schug","sequence":"additional","affiliation":[]},{"given":"Avni","family":"Santani","sequence":"additional","affiliation":[]},{"given":"Anthony","family":"Albano","sequence":"additional","affiliation":[]},{"given":"Cecilia","family":"Kim","sequence":"additional","affiliation":[]},{"given":"Vincent","family":"Procaccio","sequence":"additional","affiliation":[]},{"given":"Hakon","family":"Hakonarson","sequence":"additional","affiliation":[]},{"given":"Xiaowu","family":"Gai","sequence":"additional","affiliation":[]},{"given":"Marni J","family":"Falk","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,10,19]]},"reference":[{"issue":"5","key":"4955_CR1","doi-asserted-by":"publisher","first-page":"812","DOI":"10.1101\/gr.2228504","volume":"14","author":"A Maitra","year":"2004","unstructured":"Maitra A, Cohen Y, Gillespie SE, Mambo E, Fukushima N, Hoque MO, Shah N, Goggins M, Califano J, Sidransky D: The Human MitoChip: a high-throughput sequencing microarray for mitochondrial mutation detection. Genome Res. 2004, 14 (5): 812-819. 10.1101\/gr.2228504.","journal-title":"Genome Res"},{"issue":"4","key":"4955_CR2","doi-asserted-by":"publisher","first-page":"476","DOI":"10.2353\/jmoldx.2006.060008","volume":"8","author":"S Zhou","year":"2006","unstructured":"Zhou S, Kassauei K, Cutler DJ, Kennedy GC, Sidransky D, Maitra A, Califano J: An oligonucleotide microarray for high-throughput sequencing of the mitochondrial genome. J Mol Diagn. 2006, 8 (4): 476-482. 10.2353\/jmoldx.2006.060008.","journal-title":"J Mol Diagn"},{"issue":"11","key":"4955_CR3","doi-asserted-by":"crossref","first-page":"1913","DOI":"10.1101\/gr.197201","volume":"11","author":"DJ Cutler","year":"2001","unstructured":"Cutler DJ, Zwick ME, Carrasquillo MM, Yohn CT, Tobin KP, Kashuk C, Mathews DJ, Shah NA, Eichler EE, Warrington JA: High-throughput variation detection and genotyping using microarrays. Genome Res. 2001, 11 (11): 1913-1925.","journal-title":"Genome Res"},{"issue":"1","key":"4955_CR4","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1002\/humu.20816","volume":"30","author":"A Hartmann","year":"2009","unstructured":"Hartmann A, Thieme M, Nanduri LK, Stempfl T, Moehle C, Kivisild T, Oefner PJ: Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes. Hum Mutat. 2009, 30 (1): 115-122. 10.1002\/humu.20816.","journal-title":"Hum Mutat"},{"issue":"21","key":"4955_CR5","doi-asserted-by":"publisher","first-page":"e148","DOI":"10.1093\/nar\/gkm918","volume":"35","author":"GA Pandya","year":"2007","unstructured":"Pandya GA, Holmes MH, Sunkara S, Sparks A, Bai Y, Verratti K, Saeed K, Venepally P, Jarrahi B, Fleischmann RD: A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform. Nucleic Acids Res. 2007, 35 (21): e148-10.1093\/nar\/gkm918.","journal-title":"Nucleic Acids Res"},{"issue":"1-2","key":"4955_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.cccn.2004.11.003","volume":"354","author":"LJ Wong","year":"2005","unstructured":"Wong LJ, Boles RG: Mitochondrial DNA analysis in clinical laboratory diagnostics. Clin Chim Acta. 2005, 354 (1-2): 1-20. 10.1016\/j.cccn.2004.11.003.","journal-title":"Clin Chim Acta"},{"issue":"3","key":"4955_CR7","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1089\/gte.2005.9.190","volume":"9","author":"HE White","year":"2005","unstructured":"White HE, Durston VJ, Seller A, Fratter C, Harvey JF, Cross NC: Accurate detection and quantitation of heteroplasmic mitochondrial point mutations by pyrosequencing. Genet Test. 2005, 9 (3): 190-199. 10.1089\/gte.2005.9.190.","journal-title":"Genet Test"},{"issue":"6","key":"4955_CR8","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1086\/425871","volume":"75","author":"MG Palanichamy","year":"2004","unstructured":"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 (6): 966-978. 10.1086\/425871.","journal-title":"Am J Hum Genet"},{"key":"4955_CR9","volume-title":"How to Detect and Handle Outliers","author":"B Iglewicz","year":"1993","unstructured":"Iglewicz B, Hoaglin DC: How to Detect and Handle Outliers. 1993, Milwaukee, WI: American Society for Quality Control"},{"key":"4955_CR10","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1186\/1471-2105-10-440","volume":"10","author":"M Thieme","year":"2009","unstructured":"Thieme M, Lottaz C, Niederstatter H, Parson W, Spang R, Oefner PJ: ReseqChip: automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly. BMC Bioinformatics. 2009, 10: 440-10.1186\/1471-2105-10-440.","journal-title":"BMC Bioinformatics"},{"issue":"11","key":"4955_CR11","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1038\/sj.ejhg.5201891","volume":"15","author":"M Leveque","year":"2007","unstructured":"Leveque M, Marlin S, Jonard L, Procaccio V, Reynier P, Amati-Bonneau P, Baulande S, Pierron D, Lacombe D, Duriez F: Whole mitochondrial genome screening in maternally inherited non-syndromic hearing impairment using a microarray resequencing mitochondrial DNA chip. Eur J Hum Genet. 2007, 15 (11): 1145-1155. 10.1038\/sj.ejhg.5201891.","journal-title":"Eur J Hum Genet"},{"issue":"3","key":"4955_CR12","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1093\/bioinformatics\/btp666","volume":"26","author":"I Milne","year":"2010","unstructured":"Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F, Marshall D: Tablet--next generation sequence assembly visualization. Bioinformatics. 2010, 26 (3): 401-402. 10.1093\/bioinformatics\/btp666.","journal-title":"Bioinformatics"},{"key":"4955_CR13","first-page":"Unit 19 16","volume":"Chapter 19","author":"J Wang","year":"2011","unstructured":"Wang J, Venegas V, Li F, Wong LJ: Analysis of mitochondrial DNA point mutation heteroplasmy by ARMS quantitative PCR. Curr Protoc Hum Genet. 2011, Chapter 19: Unit 19 16-","journal-title":"Curr Protoc Hum Genet"},{"issue":"5806","key":"4955_CR14","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/290457a0","volume":"290","author":"S Anderson","year":"1981","unstructured":"Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F: Sequence and organization of the human mitochondrial genome. Nature. 1981, 290 (5806): 457-465. 10.1038\/290457a0.","journal-title":"Nature"},{"issue":"2","key":"4955_CR15","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1038\/13779","volume":"23","author":"RM Andrews","year":"1999","unstructured":"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 (2): 147-10.1038\/13779.","journal-title":"Nat Genet"},{"issue":"5","key":"4955_CR16","doi-asserted-by":"publisher","first-page":"1130","DOI":"10.1016\/j.ajhg.2008.04.002","volume":"82","author":"DM Behar","year":"2008","unstructured":"Behar DM, Villems R, Soodyall H, Blue-Smith J, Pereira L, Metspalu E, Scozzari R, Makkan H, Tzur S, Comas D: The dawn of human matrilineal diversity. Am J Hum Genet. 2008, 82 (5): 1130-1140. 10.1016\/j.ajhg.2008.04.002.","journal-title":"Am J Hum Genet"},{"issue":"6","key":"4955_CR17","doi-asserted-by":"publisher","first-page":"e104","DOI":"10.1371\/journal.pgen.0030104","volume":"3","author":"DM Behar","year":"2007","unstructured":"Behar DM, Rosset S, Blue-Smith J, Balanovsky O, Tzur S, Comas D, Mitchell RJ, Quintana-Murci L, Tyler-Smith C, Wells RS: The Genographic Project public participation mitochondrial DNA database. PLoS Genet. 2007, 3 (6): e104-10.1371\/journal.pgen.0030104.","journal-title":"PLoS Genet"},{"issue":"7319","key":"4955_CR18","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1038\/nature09534","volume":"467","author":"RM Durbin","year":"2010","unstructured":"Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Gibbs RA, Hurles ME, McVean GA: A map of human genome variation from population-scale sequencing. Nature. 2010, 467 (7319): 1061-1073. 10.1038\/nature09534.","journal-title":"Nature"},{"issue":"2","key":"4955_CR19","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1016\/j.ajhg.2010.07.014","volume":"87","author":"M Li","year":"2010","unstructured":"Li M, Schonberg A, Schaefer M, Schroeder R, Nasidze I, Stoneking M: Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am J Hum Genet. 2010, 87 (2): 237-249. 10.1016\/j.ajhg.2010.07.014.","journal-title":"Am J Hum Genet"},{"issue":"4","key":"4955_CR20","doi-asserted-by":"publisher","first-page":"287","DOI":"10.2144\/000113389","volume":"48","author":"S Tang","year":"2010","unstructured":"Tang S, Huang T: Characterization of mitochondrial DNA heteroplasmy using a parallel sequencing system. Biotechniques. 2010, 48 (4): 287-296. 10.2144\/000113389.","journal-title":"Biotechniques"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-402.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T17:47:21Z","timestamp":1630518441000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-402"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,10,19]]},"references-count":20,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4955"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-402","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,10,19]]},"assertion":[{"value":"25 May 2011","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 October 2011","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 October 2011","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"402"}}