ArticleNucleic acids research2011
Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 28 citations in OpenAlex.
- Activation of the cGAS-STING innate immune response in cells with deficient mitochondrial topoisomerase TOP1MT.Human molecular genetics · 2023Article
- Functional characterization of two variants of mitochondrial topoisomerase TOP1MT that impact regulation of the mitochondrial genome.The Journal of biological chemistry · 2022Article
- MUTYH: Not just polyposis.World journal of clinical oncology · 2020Review
- Isoforms of Base Excision Repair Enzymes Produced by Alternative Splicing.International journal of molecular sciences · 2019Review
- The peroxisomal Lon protease LonP2 in aging and disease: functions and comparisons with mitochondrial Lon protease LonP1.Biological reviews of the Cambridge Philosophical Society · 2017Review
- In silico prediction of physical protein interactions and characterization of interactome orphans.Nature methods · 2015Article
- APE2 is required for ATR-Chk1 checkpoint activation in response to oxidative stress.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Rare variant detection using family-based sequencing analysis.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- SRMA: an R package for resequencing array data analysis.Bioinformatics (Oxford, England) · 2012Article
- Coordinated regulation of mitochondrial topoisomerase IB with mitochondrial nuclear encoded genes and MYC.Nucleic acids research · 2011Article
- High-quality DNA sequence capture of 524 disease candidate genes.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Function and molecular mechanisms of APE2 in genome and epigenome integrity.Mutation research. Reviews in mutation researchReview
- The interface of transcription and DNA replication in the mitochondria.Biochimica et biophysica actaReview
Corrections and comments
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Authors and funding
14 authors at 7 institutions in 3 countries.
Funding
Abstract
A common goal in the discovery of rare functional DNA variants via medical resequencing is to incur a relatively lower proportion of false positive base-calls. We developed a novel statistical method for resequencing arrays (SRMA, sequence robust multi-array analysis) to increase the accuracy of detecting rare variants and reduce the costs in subsequent sequence verifications required in medical applications. SRMA includes single and multi-array analysis and accounts for technical variables as well as the possibility of both low- and high-frequency genomic variation. The confidence of each base-call was ranked using two quality measures. In comparison to Sanger capillary sequencing, we achieved a false discovery rate of 2% (false positive rate 1.2 × 10⁻⁵, false negative rate 5%), which is similar to automated second-generation sequencing technologies. Applied to the analysis of 39 nuclear candidate genes in disorders of mitochondrial DNA (mtDNA) maintenance, we confirmed mutations in the DNA polymerase gamma POLG in positive control cases, and identified novel rare variants in previously undiagnosed cases in the mitochondrial topoisomerase TOP1MT, the mismatch repair enzyme MUTYH, and the apurinic-apyrimidinic endonuclease APEX2. Some patients carried rare heterozygous variants in several functionally interacting genes, which could indicate synergistic genetic effects in these clinically similar disorders.
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Registered trials
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