ArticleInternational journal of molecular sciences2021
From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel.
Article in International journal of molecular sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Recent advances in drug treatment for prostate cancer.Japanese journal of radiology · 2025Review
- High frequency of mitochondrial DNA rearrangements in the peripheral blood of adults with intellectual disability.Journal of intellectual disability research : JIDR · 2025Article
- The Applied Genomics Development Strategy by the Croatian Academy of Sciences and Arts paves the way for the future development of applied genomics in Croatia.Croatian medical journal · 2024Article
- CD4Scientific reports · 2024Article
- Research of Mitochondrial Function, Structure, Dynamics and Intracellular Organization.International journal of molecular sciences · 2023Article
- Benchmarking Low-Frequency Variant Calling With Long-Read Data on Mitochondrial DNA.Frontiers in genetics · 2022Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
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™ 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™ 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's variants (TSS found 57.92% of PCP's variants), with a significant correlation between the variant levels of variants found with both pipelines.
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