Limits...
Universal heteroplasmy of human mitochondrial DNA.

Payne BA, Wilson IJ, Yu-Wai-Man P, Coxhead J, Deehan D, Horvath R, Taylor RW, Samuels DC, Santibanez-Koref M, Chinnery PF - Hum. Mol. Genet. (2012)

Bottom Line: In contrast, we show that OPA1 mutations, which indirectly affect mtDNA maintenance, do not increase point mutation load.The demonstration of universal mtDNA heteroplasmy has fundamental implications for our understanding of mtDNA inheritance and evolution.Ostensibly de novo somatic mtDNA mutations, seen in mtDNA maintenance disorders and neurodegenerative disease and aging, will partly be due to the clonal expansion of low-level inherited variants.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastleupon-Tyne NE1 3BZ, UK.

ABSTRACT
Mammalian cells contain thousands of copies of mitochondrial DNA (mtDNA). At birth, these are thought to be identical in most humans. Here, we use long read length ultra-deep resequencing-by-synthesis to interrogate regions of the mtDNA genome from related and unrelated individuals at unprecedented resolution. We show that very low-level heteroplasmic variance is present in all tested healthy individuals, and is likely to be due to both inherited and somatic single base substitutions. Using this approach, we demonstrate an increase in mtDNA mutations in the skeletal muscle of patients with a proofreading-deficient mtDNA polymerase γ due to POLG mutations. In contrast, we show that OPA1 mutations, which indirectly affect mtDNA maintenance, do not increase point mutation load. The demonstration of universal mtDNA heteroplasmy has fundamental implications for our understanding of mtDNA inheritance and evolution. Ostensibly de novo somatic mtDNA mutations, seen in mtDNA maintenance disorders and neurodegenerative disease and aging, will partly be due to the clonal expansion of low-level inherited variants.

Show MeSH

Related in: MedlinePlus

Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An amplicon was produced from cloned DNA for each mtDNA amplicon (MT-HV2, MT-CO3) along with an autosomal amplicon (BRCA2) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at >0.2% heteroplasmy level, with no inherent differences between the different DNA templates.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC3526165&req=5

DDS435F1: Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An amplicon was produced from cloned DNA for each mtDNA amplicon (MT-HV2, MT-CO3) along with an autosomal amplicon (BRCA2) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at >0.2% heteroplasmy level, with no inherent differences between the different DNA templates.

Mentions: Using this highly stringent approach, there were no variants present at >0.2% heteroplasmy in any of the cloned or genomic DNA templates (Fig. 1). This demonstrated the low background noise level using the 454 UDS approach and indicated that variants detected at >0.2% heteroplasmy are highly likely to be generated in vivo and to be of biological origin.Figure 1.


Universal heteroplasmy of human mitochondrial DNA.

Payne BA, Wilson IJ, Yu-Wai-Man P, Coxhead J, Deehan D, Horvath R, Taylor RW, Samuels DC, Santibanez-Koref M, Chinnery PF - Hum. Mol. Genet. (2012)

Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An amplicon was produced from cloned DNA for each mtDNA amplicon (MT-HV2, MT-CO3) along with an autosomal amplicon (BRCA2) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at >0.2% heteroplasmy level, with no inherent differences between the different DNA templates.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3526165&req=5

DDS435F1: Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An amplicon was produced from cloned DNA for each mtDNA amplicon (MT-HV2, MT-CO3) along with an autosomal amplicon (BRCA2) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at >0.2% heteroplasmy level, with no inherent differences between the different DNA templates.
Mentions: Using this highly stringent approach, there were no variants present at >0.2% heteroplasmy in any of the cloned or genomic DNA templates (Fig. 1). This demonstrated the low background noise level using the 454 UDS approach and indicated that variants detected at >0.2% heteroplasmy are highly likely to be generated in vivo and to be of biological origin.Figure 1.

Bottom Line: In contrast, we show that OPA1 mutations, which indirectly affect mtDNA maintenance, do not increase point mutation load.The demonstration of universal mtDNA heteroplasmy has fundamental implications for our understanding of mtDNA inheritance and evolution.Ostensibly de novo somatic mtDNA mutations, seen in mtDNA maintenance disorders and neurodegenerative disease and aging, will partly be due to the clonal expansion of low-level inherited variants.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastleupon-Tyne NE1 3BZ, UK.

ABSTRACT
Mammalian cells contain thousands of copies of mitochondrial DNA (mtDNA). At birth, these are thought to be identical in most humans. Here, we use long read length ultra-deep resequencing-by-synthesis to interrogate regions of the mtDNA genome from related and unrelated individuals at unprecedented resolution. We show that very low-level heteroplasmic variance is present in all tested healthy individuals, and is likely to be due to both inherited and somatic single base substitutions. Using this approach, we demonstrate an increase in mtDNA mutations in the skeletal muscle of patients with a proofreading-deficient mtDNA polymerase γ due to POLG mutations. In contrast, we show that OPA1 mutations, which indirectly affect mtDNA maintenance, do not increase point mutation load. The demonstration of universal mtDNA heteroplasmy has fundamental implications for our understanding of mtDNA inheritance and evolution. Ostensibly de novo somatic mtDNA mutations, seen in mtDNA maintenance disorders and neurodegenerative disease and aging, will partly be due to the clonal expansion of low-level inherited variants.

Show MeSH
Related in: MedlinePlus