2019
DOI: 10.1038/s41436-018-0350-8
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eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data

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Cited by 39 publications
(28 citation statements)
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“…The functional effect of the variants were predicted using open-source algorithms including PolyPhen-2 131 , PANTHER 132 , Envision 133 , MutationAssessor 134 , MutPred2 135 and SNPs&GO 136 . The mtDNA deletion was also determined via MitoDel 137 and eKLIPse 138 . MitoDel is a tool for detecting and quantifying mtDNA deletions even at low heteroplasmy levels via the BLAT split read mapping method.…”
Section: Methodsmentioning
confidence: 99%
“…The functional effect of the variants were predicted using open-source algorithms including PolyPhen-2 131 , PANTHER 132 , Envision 133 , MutationAssessor 134 , MutPred2 135 and SNPs&GO 136 . The mtDNA deletion was also determined via MitoDel 137 and eKLIPse 138 . MitoDel is a tool for detecting and quantifying mtDNA deletions even at low heteroplasmy levels via the BLAT split read mapping method.…”
Section: Methodsmentioning
confidence: 99%
“…Although, statistical analyzes never reached a significant P value, a trend toward a difference was found for each heteroplasmy level category in blood samples between controls and patients, while not in urine (Supplemental Figures 4 and 5). We then searched for differences between the frequency of mtDNA deletions in blood and urine samplings using eKLIPSE software (18), but without evidence of significant differences. Long-range PCR revealed the absence of mtDNA deletion in the skin biopsies (Supplemental Figure 6).…”
Section: Resultsmentioning
confidence: 99%
“…Another manual curation, including coverage, being away from indels, and MNPs, as well as the Ts/Tv ratio, was used in the filtering process. Long-range structural variation was run using eKLIPse [ 59 ].…”
Section: Methodsmentioning
confidence: 99%