False-Positive Diagnosis of a Single, Large-Scale Mitochondrial DNA Deletion by Southern Blot Analysis: The Role of Neutral Polymorphisms

2004 ◽  
Vol 8 (4) ◽  
pp. 395-399 ◽  
Author(s):  
Marcus Deschauer ◽  
Anna Krasnianski ◽  
Stephan Zierz ◽  
Robert W. Taylor
2020 ◽  
Vol 48 (20) ◽  
pp. 11244-11258
Author(s):  
Gabriele A Fontana ◽  
Hailey L Gahlon

Abstract Deletions in mitochondrial DNA (mtDNA) are associated with diverse human pathologies including cancer, aging and mitochondrial disorders. Large-scale deletions span kilobases in length and the loss of these associated genes contributes to crippled oxidative phosphorylation and overall decline in mitochondrial fitness. There is not a united view for how mtDNA deletions are generated and the molecular mechanisms underlying this process are poorly understood. This review discusses the role of replication and repair in mtDNA deletion formation as well as nucleic acid motifs such as repeats, secondary structures, and DNA damage associated with deletion formation in the mitochondrial genome. We propose that while erroneous replication and repair can separately contribute to deletion formation, crosstalk between these pathways is also involved in generating deletions.


1991 ◽  
Vol 238 (3) ◽  
pp. 171-176 ◽  
Author(s):  
C. Geny ◽  
V. Cormier ◽  
C. Meyrignac ◽  
P. Cesaro ◽  
J. D. Degos ◽  
...  

2003 ◽  
Vol 49 (8) ◽  
pp. 1309-1317 ◽  
Author(s):  
Béatrice Chabi ◽  
Bénédicte Mousson de Camaret ◽  
Hervé Duborjal ◽  
Jean-Paul Issartel ◽  
Georges Stepien

Abstract Background: Many mitochondrial pathologies are quantitative disorders related to tissue-specific deletion, depletion, or overreplication of mitochondrial DNA (mtDNA). We developed an assay for the determination of mtDNA copy number by real-time quantitative PCR for the molecular diagnosis of such alterations. Methods: To determine altered mtDNA copy number in muscle from nine patients with single or multiple mtDNA deletions, we generated calibration curves from serial dilutions of cloned mtDNA probes specific to four different mitochondrial genes encoding either ribosomal (16S) or messenger (ND2, ND5, and ATPase6) RNAs, localized in different regions of the mtDNA sequence. This method was compared with quantification of radioactive signals from Southern-blot analysis. We also determined the mitochondrial-to-nuclear DNA ratio in muscle, liver, and cultured fibroblasts from a patient with mtDNA depletion and in liver from two patients with mtDNA overreplication. Results: Both methods quantified 5–76% of deleted mtDNA in muscle, 59–97% of mtDNA depletion in the tissues, and 1.7- to 4.1-fold mtDNA overreplication in liver. The data obtained were concordant, with a linear correlation coefficient (r2) between the two methods of 0.94, and indicated that quantitative PCR has a higher sensitivity than Southern-blot analysis. Conclusions: Real-time quantitative PCR can determine the copy number of either deleted or full-length mtDNA in patients with mitochondrial diseases and has advantages over classic Southern-blot analysis.


2000 ◽  
Vol 10 (1) ◽  
pp. 56-58 ◽  
Author(s):  
Yolanda Campos ◽  
Miguel A Martı́n ◽  
Cristina Caballero ◽  
Juan C Rubio ◽  
Francisco de la Cruz ◽  
...  

2018 ◽  
Vol 481 ◽  
pp. 156-160 ◽  
Author(s):  
Michela Semeraro ◽  
Sara Boenzi ◽  
Rosalba Carrozzo ◽  
Daria Diodato ◽  
Diego Martinelli ◽  
...  

2003 ◽  
Vol 88 (12) ◽  
pp. 5893-5897 ◽  
Author(s):  
T. Tukel ◽  
O. Uyguner ◽  
J. Q. Wei ◽  
M. Yuksel-Apak ◽  
N. Saka ◽  
...  

Abstract 21-Hydroxylase deficiency is a recessively inherited disorder resulting from mutations in the CYP21 gene. The CYP21 gene is located along with the CYP21P pseudogene in the human leukocyte antigen major histocompatibility complex region on chromosome 6. Molecular diagnosis is difficult due to the 98% similarity of CYP21 and CYP21P genes and the fact that almost all frequently reported mutations reside on the pseudogene. Allele-specific PCR for the 8 most frequently reported point mutations was performed in 31 Turkish families with at least a single 21-hydroxylase-deficient individual. The allele frequencies of the point mutations were as follows: P30L, 0%; IVS2 (AS,A/C-G,-13), 22.5%; G110Δ8nt, 3.2%; I172N, 11.4%; exon 6 cluster (I236N, V237E, M239K), 3.2%; V281L, 0%; Q318X, 8%; and R356W, 9.6%. Large deletions and gene conversions were detected by Southern blot analysis, and the allele frequencies were 9.6% and 22.5%, respectively. Sequence analysis of the gene, performed on patients with only 1 mutated allele, revealed 2 missense mutations (R339H and P435S). A novel semiquantitative PCR/enzyme digestion-based method for the detection of large scale deletions/conversions of the gene was developed for routine diagnostic purposes, and its accuracy was shown by comparison with the results of Southern blot analysis.


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