Interference of nuclear mitochondrial DNA segments in mitochondrial DNA testing resembles biparental transmission of mitochondrial DNA in humans

Bai, Ru; Cui, Hong; Devaney, Joseph M.; Allis, Katrina; Balog, Amanda; Schnur, Rhonda E.; Shapiro, Faye L.; Brautbar, Ariel; Estrada-Veras, Juvianee; Hochstetler, Laurel; McConkie‐Rosell, Allyn; McDonald, Marie; Solomon, Benjamin D.; Hofherr, Sean E.; Richard, Gabriele; Suchy, Sharon F.

doi:10.1038/s41436-021-01166-1

Cited by 13 publications

(14 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In conclusion, differential centrifugation and alkaline lysis may be used to enrich mitochondrial DNA eliminating the need forPCR amplification or probe hybridization. Avoiding sequence-dependent techniques greatly reduces the effect of NUMT contamination, a problem which has been identified in previous studies 23,24,28,30 . This technique, in addition to a modified bioinformatics pipeline, can be applied to different tissues and achieves ultradeep sequencing coverage.…”

Section: Discussionmentioning

confidence: 96%

Mito-SiPE: A sequence-independent, PCR-free mitochondrial DNA enrichment method for ultra-deep sequencing that minimises amplification and alignment artefacts for the analysis of mitochondrial heteroplasmy/variation

Walsh¹,

Bernard

Pangilinan

et al. 2022

Preprint

View full text Add to dashboard Cite

Background: The analysis of somatic variation in the mitochondrial genome requires deep sequencing of the mitochondrial genome. This is ordinarily achieved by selective enrichment methods, such as PCR amplification or probe hybridization. These methods can introduce bias and are prone to contamination by nuclear-mitochondrial sequences (NUMTs), elements that can introduce artefacts into heteroplasmy analysis. Results: Here, we demonstrate a method to obtain ultra-deep (>80,000X) sequencing coverage of the mitochondrial genome by selectively purifying the organelle with differential centrifugation and alkaline lysis of seven different mouse tissues. This method yields a preparation of highly enriched mtDNA and avoids the pitfalls inherent in the widely employed sequence dependent methods. This methodology avoids false-heteroplasmy calls that occur when long-range PCR amplification is used for mtDNA enrichment. Discussion: Mitochondrial DNA from the un-adapted version of this method did not undergo quantification or short-read sequencing when it was initially reported. Here, we have described a modified version of the protocol and have quantified the increased level of mitochondrial DNA post-enrichment in 7 different mouse tissues. This method will enable researchers to identify changes in low frequency heteroplasmy without introducing PCR biases or NUMT contamination that are falsely identified as heteroplasmy when long-range PCR is used.

show abstract

Section: Discussionmentioning

confidence: 96%

Mito-SiPE: A sequence-independent, PCR-free mitochondrial DNA enrichment method for ultra-deep sequencing that minimises amplification and alignment artefacts for the analysis of mitochondrial heteroplasmy/variation

Walsh¹,

Bernard

Pangilinan

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…First, Salas et al [ 44 ], reanalyzing the data by Luo et al, estimated that the probability of biparental inheritance is below 10 −37 . Second, Bai et al [ 45 ] showed that, in four human families, heteroplasmic fathers transmitted only one mitotype to their progeny. This observation is similar to what we have observed in the present study, which turned out to be consistent with a NUMT transmission.…”

Section: Discussionmentioning

confidence: 99%

NUMTs Can Imitate Biparental Transmission of mtDNA—A Case in Drosophila melanogaster

Parakatselaki

Zhu

Rand

et al. 2022

Genes

View full text Add to dashboard Cite

mtDNA sequences can be incorporated into the nuclear genome and produce nuclear mitochondrial fragments (NUMTs), which resemble mtDNA in their sequence but are transmitted biparentally, like the nuclear genome. NUMTs can be mistaken as real mtDNA and may lead to the erroneous impression that mtDNA is biparentally transmitted. Here, we report a case of mtDNA heteroplasmy in a Drosophila melanogaster DGRP line, in which the one haplotype was biparentally transmitted in an autosomal manner. Given the sequence identity of this haplotype with the mtDNA, the crossing experiments led to uncertainty about whether heteroplasmy was real or an artifact due to a NUMT. More specific experiments revealed that there is a large NUMT insertion in the X chromosome of a specific DGRP line, imitating biparental inheritance of mtDNA. Our result suggests that studies on mtDNA heteroplasmy and on mtDNA inheritance should first exclude the possibility of NUMT interference in their data.

show abstract

“…If the heteroplasmy signature were due to Mega-NUMTs rather than bona fide biparental inheritance, an inverse correlation between the Mega-NUMT haplotype fraction and mtDNA content would be expected. Comparing DNA from buccal cells and muscle, the anticipated dilution effect due to higher mtDNA content in muscle was clearly observed 9,10 . A similar signature was also seen in blood samples, where mtDNA levels reflect the composition of different cell types in whole blood 8 .…”

Section: Inverse Correlation With Mtdna Contentmentioning

confidence: 97%

“…Finally, Bai et al searched for multiHet individuals with ≥5 heteroplasmic mtDNA variants that appeared to have heteroplasmy levels of 10-90%; this study investigated only individuals with no previous blood transfusions or organ transplants, and validated their findings in an independent blood sample 10 . Exome and PCR-amplified mtDNA sequencing identified the multiHet phenomenon in 104 out of 27,388 individuals.…”

Section: Prevalence Of Multihet Individualsmentioning

confidence: 99%

“…Rare variants that arise in a Mega-NUMT will be at very low allelic fractions unless propagated into multiple copies of the 16.6 kb repeat. However, deletions and inversions may be more problematic: tandem repeats are prone to rearrangement and such events were noted in two of the studies 8,10 . In clinical genetics and other disciplines where it is important to clarify whether a multiHet pattern is due to rare Mega-NUMT or genuine mtDNA variants , muscle DNA should be used if possible.…”

Section: Clinical Relevance and Future Perspectivesmentioning

confidence: 99%

See 1 more Smart Citation

Biparental inheritance of mitochondrial DNA revisited

et al. 2021

View full text Add to dashboard Cite

Interference of nuclear mitochondrial DNA segments in mitochondrial DNA testing resembles biparental transmission of mitochondrial DNA in humans

Cited by 13 publications

References 29 publications

Mito-SiPE: A sequence-independent, PCR-free mitochondrial DNA enrichment method for ultra-deep sequencing that minimises amplification and alignment artefacts for the analysis of mitochondrial heteroplasmy/variation

Mito-SiPE: A sequence-independent, PCR-free mitochondrial DNA enrichment method for ultra-deep sequencing that minimises amplification and alignment artefacts for the analysis of mitochondrial heteroplasmy/variation

NUMTs Can Imitate Biparental Transmission of mtDNA—A Case in Drosophila melanogaster

Biparental inheritance of mitochondrial DNA revisited

Contact Info

Product

Resources

About