{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T11:12:37Z","timestamp":1768821157369,"version":"3.49.0"},"reference-count":97,"publisher":"MDPI AG","issue":"21","license":[{"start":{"date-parts":[[2021,11,6]],"date-time":"2021-11-06T00:00:00Z","timestamp":1636156800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","doi-asserted-by":"publisher","award":["PAC-PRECISE LISBOA-01-0145-FEDER-016394"],"award-info":[{"award-number":["PAC-PRECISE LISBOA-01-0145-FEDER-016394"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000890","name":"National Multiple Sclerosis Society","doi-asserted-by":"publisher","award":["PP-1712-29466"],"award-info":[{"award-number":["PP-1712-29466"]}],"id":[{"id":"10.13039\/100000890","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA) research. The Applied Biosystems\u2122 Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific, USA) is an innovative library preparation kit suitable for degraded samples and low DNA input. However, its bioinformatic processing occurs in the enterprise Ion Torrent Suite\u2122 Software (TSS), yielding BAM files aligned to an unorthodox version of the revised Cambridge Reference Sequence (rCRS), with a heteroplasmy threshold level of 10%. Here, we present an alternative customizable pipeline, the PrecisionCallerPipeline (PCP), for processing samples with the correct rCRS output after Ion Torrent sequencing with the Precision ID library kit. Using 18 samples (3 original samples and 15 mixtures) derived from the 1000 Genomes Project, we achieved overall improved performance metrics in comparison with the proprietary TSS, with optimal performance at a 2.5% heteroplasmy threshold. We further validated our findings with 50 samples from an ongoing independent cohort of stroke patients, with PCP finding 98.31% of TSS\u2019s variants (TSS found 57.92% of PCP\u2019s variants), with a significant correlation between the variant levels of variants found with both pipelines.<\/jats:p>","DOI":"10.3390\/ijms222112031","type":"journal-article","created":{"date-parts":[[2021,11,7]],"date-time":"2021-11-07T20:41:14Z","timestamp":1636317674000},"page":"12031","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel"],"prefix":"10.3390","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3946-3868","authenticated-orcid":false,"given":"Filipe","family":"Cortes-Figueiredo","sequence":"first","affiliation":[{"name":"VMorais Lab\u2014Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal"},{"name":"NeuroCure Clinical Research Center, Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, 10117 Berlin, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0074-0741","authenticated-orcid":false,"given":"Filipa S.","family":"Carvalho","sequence":"additional","affiliation":[{"name":"VMorais Lab\u2014Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6913-5526","authenticated-orcid":false,"given":"Ana Catarina","family":"Fonseca","sequence":"additional","affiliation":[{"name":"Jos\u00e9 Ferro Lab\u2014Clinical Research in Non-communicable Neurological Diseases, Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal"},{"name":"Servi\u00e7o de Neurologia, Hospital de Santa Maria, Centro Hospitalar Universit\u00e1rio Lisboa Norte, 1649-035 Lisbon, Portugal"}]},{"given":"Friedemann","family":"Paul","sequence":"additional","affiliation":[{"name":"NeuroCure Clinical Research Center, Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, 10117 Berlin, Germany"},{"name":"Experimental and Clinical Research Center, Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin and Max Delbr\u00fcck Center for Molecular Medicine, 13125 Berlin, Germany"}]},{"given":"Jos\u00e9 M.","family":"Ferro","sequence":"additional","affiliation":[{"name":"Jos\u00e9 Ferro Lab\u2014Clinical Research in Non-communicable Neurological Diseases, Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal"},{"name":"Servi\u00e7o de Neurologia, Hospital de Santa Maria, Centro Hospitalar Universit\u00e1rio Lisboa Norte, 1649-035 Lisbon, Portugal"}]},{"given":"Sebastian","family":"Sch\u00f6nherr","sequence":"additional","affiliation":[{"name":"Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2871-8669","authenticated-orcid":false,"given":"Hansi","family":"Weissensteiner","sequence":"additional","affiliation":[{"name":"Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0830-0548","authenticated-orcid":false,"given":"Vanessa A.","family":"Morais","sequence":"additional","affiliation":[{"name":"VMorais Lab\u2014Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2021,11,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1038\/nrg1606","article-title":"Mitochondrial DNA Mutations in Human Disease","volume":"6","author":"Taylor","year":"2005","journal-title":"Nat. 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