دورية أكاديمية
Mitochondrial genome sequence analysis: A custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy
| العنوان: | Mitochondrial genome sequence analysis: A custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy |
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| المؤلفون: | Xie Hongbo M, Perin Juan C, Schurr Theodore G, Dulik Matthew C, Zhadanov Sergey I, Baur Joseph A, King Michael P, Place Emily, Clarke Colleen, Grauer Michael, Schug Jonathan, Santani Avni, Albano Anthony, Kim Cecilia, Procaccio Vincent, Hakonarson Hakon, Gai Xiaowu, Falk Marni J |
| المصدر: | BMC Bioinformatics, Vol 12, Iss 1, p 402 (2011) |
| بيانات النشر: | BMC |
| سنة النشر: | 2011 |
| المجموعة: | Directory of Open Access Journals: DOAJ Articles |
| مصطلحات موضوعية: | Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5 |
| الوصف: | Background 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. Results 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. Conclusions 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 ... |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| تدمد: | 1471-2105 |
| العلاقة: | http://www.biomedcentral.com/1471-2105/12/402Test; https://doaj.org/toc/1471-2105Test; https://doaj.org/article/dcffdad225634636bea90407e1fae4caTest |
| DOI: | 10.1186/1471-2105-12-402 |
| الإتاحة: | https://doi.org/10.1186/1471-2105-12-402Test https://doaj.org/article/dcffdad225634636bea90407e1fae4caTest |
| رقم الانضمام: | edsbas.A7EB7876 |
| قاعدة البيانات: | BASE |
Full Text Finder | تدمد: | 14712105 |
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| DOI: | 10.1186/1471-2105-12-402 |