US 20120208712A1
· Sibille
· 2012
[cited by applicant]
US 20220259646A1
· Li
· 2022
[cited by examiner]
WO 2013173394
· 2013
[cited by applicant]
WO 2016181128
· 2016
[cited by applicant]
Barritt et al., “Mitochondrial DNA point mutation in human oocytes is associated with maternal age,” Jan. 2000, Reproductive BioMedicine Online, vol. 1. No 3., 96-100. (Year: 2000).
[cited by examiner]
Goodwin et al., “1D genome sequencing on the oxford nanopore MinION. Current Protocols in Human Genetics,” 2017, 94, 18.11.1-18.11.14. (Year: 2017).
[cited by examiner]
Kim et al., “Analysis of mixtures using next generation sequencing of mitochondrial DNA hypervariable regions,” Mar. 2015, Croat Med J., 56, 208-17 (Year: 2015).
[cited by examiner]
Adikusuma, et al., “Large deletions induced by Cas9 cleavage”, Nature, 560(7717):E8-E9 (2018).
[cited by applicant]
Ancora, et al., “Complete sequence of human mitochondrial DNA obtained by combining multiple displacement amplification and next30 generation sequencing on a single oocyte”, Mitochondrial DNA Part A, DNA Mapping, Sequen…
[cited by applicant]
Aravanis, et al., “Next-Generation Sequencing of Circulating Tumor DNA for Early Cancer Detection”, Cell, 168(4): 571-574 (2017).
[cited by applicant]
Bi, et al., “Long-read individual-molecule sequencing reveals CRISPR induced genetic heterogeneity in human ESCs”, Genome Biol., 21(1):213, 14 pages (2020a).
[cited by applicant]
Bi, et al., “Single-cell Individual Complete 5 mtDNA Sequencing Uncovers Hidden Mitochondrial Heterogeneity in Human and Mouse Oocytes,” bioRxiv, 64 pages (2020b).
[cited by applicant]
Brierley, et al., “Role of mitochondrial DNA mutations in human aging: implications for the central nervous system and muscle”, Ann. Neurol., 43(2): 217-223, (1998).
[cited by applicant]
Burtner, et al., “Progeria syndromes and ageing: what is the connection?”, Nat. Rev. Mol. Cell Biol., 11:567-578 (2010).
[cited by applicant]
Cao, et al., “New evidence confirms that the mitochondrial bottleneck is generated without reduction of mitochondrial DNA content in early primordial germ cells of mice”, PLoS genetics, 5(12):e1000756, 8 pages (2009).
[cited by applicant]
Cao, et al., “The mitochondrial bottleneck occurs without reduction of mtDNA content in female mouse germ cells”, Nature Genetics, 39(3):386-390 (2007).
[cited by applicant]
Challen, et al., “Mouse Hematopoietic Stem Cell Identification and Analysis”, Cytometry Part A, 75A:14-24 (2009).
[cited by applicant]
Cheng, et al., “Mice with a targeted disruption of the Fanconi anemia homolog Fanca”, Human Molecular Genetics, 9(12):1805-1811 (2000).
[cited by applicant]
Cingolani, et al., “A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w(1118); iso-2; iso-3”, Fly, 6(2): 80-92 (2012).
[cited by applicant]
Coller, et al., “High frequency of homoplasmic mitochondrial DNA mutations in human tumors can be explained without selection”, Nature Genetics, 28: 147-150 (2001).
[cited by applicant]
Corral-Debrinski, et al., “Association of mitochondrial DNA damage with aging and coronary atherosclerotic heart disease”, Mutat. Res., 275(3-6):169-180 (1992).
[cited by applicant]
Cortopassi, et al., “Detection of a specific mitochondrial DNA deletion in tissues of older humans”, Nucleic Acids Research, 18(23):6927-6933 (1990).
[cited by applicant]
Cree, et al., “A reduction of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes”, Nature Genetics, 40(2):249-254 (2008).
[cited by applicant]
Cretu, et al., “Mapping and phasing of structural variation in patient genomes using nanopore sequencing”, Nat. Commun., 8:1326, 13 pages (2017).
[cited by applicant]
D'Erchia, et al., “Tissue-specific mtDNA abundance from exome data and its correlation with mitochondrial transcription, mass and respiratory activity”, Mitochondrion, 20:13-21 (2015).
[cited by applicant]
De Vree, et al., “Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping”, Nat. Biotechnol., 32(10):1019-1025 (2014).
[cited by applicant]
Duan, et al., “Recent Advances in Detecting Mitochondrial DNA Heteroplasmic Variations”, Molecules, 23(2):323, 18 pages (2018).
[cited by applicant]
Elliott, et al., “Pathogenic mitochondrial DNA mutations are common in the general Population”, Am. J. Hum. Genet., 83(2):254-260 (2008).
[cited by applicant]
Filges, et al., “Impact of Polymerase Fidelity on Background Error Rates in Next-Generation Sequencing with Unique Molecular Identifiers/Barcodes”, Scientific Reports, 9(1):3503, 7 pages (2019).
[cited by applicant]
Floros, et al., “Segregation of mitochondrial DNA heteroplasmy through a developmental genetic bottleneck in human embryos”, Nature Cell Biology, 20(2):144-151 (2018).
[cited by applicant]
Gehring, et al., “SomaticSignatures: inferring mutational signatures from single-nucleotide variants”, Bioinformatics, 31(22):3673-3675 (2015).
[cited by applicant]
Ghezzi, et al., “Mitochondrial DNA haplogroup K is associated with a lower risk of Parkinson's disease in Italians”, Eur. J. Hum. Genet., 13:748-752 (2005).
[cited by applicant]
Goodwin, et al., “Coming of age: ten years of next-generation sequencing technologies”, Nature Reviews, 17:333-351 (2016).
[cited by applicant]
Haapaniemi, et al., “CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response”, Nature Medicine, 24:927-930 (2018).
[cited by applicant]
Han, et al., “An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing”, Bioinformatics, 34(17):722-731 (2018).
[cited by applicant]
Hiatt, et al., “Parallel, tag-directed assembly of locally derived short sequence reads”, Nat. Methods, 7(2):119-122 (2010).
[cited by applicant]
Hudson, et al., “Two-stage association study and meta-analysis of mitochondrial DNA variants in Parkinson disease”, Neurology, 80:2042-2048 (2013).
[cited by applicant]
Ihry, et al., “p53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells”, Nature Medicine, 24:939-946 (2018).
[cited by applicant]
Ingman, et al., “Rate variation between mitochondrial domains and adaptive evolution in humans”, Human Molecular Genetics, 16(19): 2281-2287 (2007).
[cited by applicant]
International Search Report for PCT/IB2020/051894 filed Mar. 4, 2020.
[cited by applicant]
Jain, et al., “Nanopore sequencing and assembly of a human genome with ultra-long reads”, Nat. Biotechnol., 36(4):338-345 (2018).
[cited by applicant]
Ju, et al., “Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer”, eLife, 3: e02935, 28 pages (2014).
[cited by applicant]
Kaschutnig, et al., “The Fanconi anemia pathway is required for efficient repair of stress-induced DNA damage in haematopoietic stem cells”, Cell Cycle, 14(17):2734-2742 (2015).
[cited by applicant]
Kauppila, et al., “Base-excision repair deficiency alone or combined with increased oxidative stress does not increase mtDNA point mutations in mice”, Nucleic Acids Res., 46(13):6642-6669 (2018).
[cited by applicant]
Kauppila, et al., “Mammalian Mitochondria and Aging: an Update”, Cell Metab., 25: 57-71 (2017).
[cited by applicant]
Kennedy, et al., “Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage”, PLoS Genetics, 9(9): e1003794, 10 pages (2013).
[cited by applicant]
Kim, et al., “The Role of Mitochondria in Oocyte and Early Embryo Health”, OBM Genetics, 3:1, 29 pages (2019).
[cited by applicant]
Kinde, et al., “Detection and quantification of rare mutations with massively parallel sequencing”, PNAS, 108(23):9530-9535 (2011).
[cited by applicant]
Koike-Yusa, et al., “Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library”, Nature Biotechnology, 32:267-273 (2014).
[cited by applicant]
Koren, et al., “Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation”, Genome Res., 27:722-736 (2017).
[cited by applicant]
Kosicki, et al., “Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements”, Nat. Biotechnol., 36(8):765-771 (2018).
[cited by applicant]
Kukat, et al., “Super-resolution microscopy reveals that mammalian mitochondrial nucleoids have a uniform size and frequently contain a single copy of mtDNA”, PNAS, 108:13534-13539, doi: 10.1073/ pnas. 1109263108 (2011).
[cited by applicant]
Ley, et al., “DNA sequencing of a cytogenetically normal acute myeloid leukemia genome”, Nature, 456:66-72 (2008).
[cited by applicant]
Li, “Minimap2: pairwise alignment for nucleotide sequences”, Bioinformatics, 34(18):3094-3100 (2018).
[cited by applicant]
Li, et al., “Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations”, PNAS, 112(8):2491-2496 (2015).
[cited by applicant]
Li, et al., “Generation of Blastocyst-like Structures from Mouse Embryonic and Adult Cell Cultures”, Cell, 179(3): 687-702.e618 (2019).
[cited by applicant]
Li, et al., “The Sequence Alignment/Map format and SAMtools”, Bioinformatics, 25:2078-2079 (2009).
[cited by applicant]
Lin, et al., “Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations”, Nat. Commun., 5:4767, 12 pages (2014).
[cited by applicant]
Loman, et al., “A complete bacterial genome assembled de novo using only nanopore sequencing data”, Nat. Methods, 12:733-751 (2015).
[cited by applicant]
Lott, et al., “mtDNA Variation and Analysis Using Mitomap and Mitomaster”, Curr. Protoc. Bioinformatics, 44(123): 21-26 (2013).
[cited by applicant]
Ludwig, et al., “Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics”, Cell, 176(6):1325-1339.e22 (2019).
[cited by applicant]
Ma, et al., “Inter-homologue repair in fertilized human eggs?”, Nature, 548:413-419 (2017).
[cited by applicant]
Martin, “Cutadapt removes adapter sequences from high-throughput sequencing reads”, 17(1): 10-12 (2011).
[cited by applicant]
Martincorena, et al., “High burden and pervasive positive selection of somatic mutations in normal human skin”, Science, 348(6237):880-886 (2015).
[cited by applicant]
Merkle, et al., “Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations”, Nature, 545(7653):229-233 (2017).
[cited by applicant]
Minoche, et al., “Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems”, Genome Biol., 12:R112, 15 pages (2011).
[cited by applicant]
Moehrle, et al., “Aging of hematopoietic stem cells: DNA damage and mutations?”, Exp. Hematol., 44(10):895-901 (2016).
[cited by applicant]
Monnot, et al., “Segregation of mtDNA throughout human embryofetal development: m.3243A>G as a model system”, Hum. Mutat., 32(1):116-125 (2011).
[cited by applicant]
Morris, et al., “Pervasive within-Mitochondrion Single-Nucleotide Variant Heteroplasmy as Revealed by Single-Mitochondrion Sequencing”, Cell Rep., 21(10): 2706-2713 (2017).
[cited by applicant]
Nei, et al., “Simple Methods for Estimating the Numbers of Synonymous and Nonsynonymous Nucleotide Substitutions”, Mol. Biol. Evol., 3(5):418-426 (1986).
[cited by applicant]
Ni, et al., “MitoRCA-seq reveals unbalanced cytocine to thymine transition in Polg mutant mice”, Scientific Reports, 5:12049, 13 pages (2015).
[cited by applicant]
Nielsen, “Molecular signatures of natural selection”, Annu. Rev. Genet., 39: 197-218 (2005).
[cited by applicant]
Norddahl, et al., “Accumulating mitochondrial DNA mutations drive premature hematopoietic aging phenotypes distinct from physiological stem cell aging”, Cell Stem Cell, 8(5):499-510 (2011).
[cited by applicant]
Okamura, et al., “an alternative pluripotent state confers interspeices chimaeric competency”, Genes Genet. Syst., 90:405-405 (2015).
[cited by applicant]
Palovcak, et al., “Maintenance of genome stability by Fanconi anemia proteins”, Cell Biosci., 7(8) 18 pages (2017).
[cited by applicant]
Parmar, et al., “Mouse models of Fanconi anemia”, Mutat. Res., 668(1-2):133-140 (2009).
[cited by applicant]
Payne, et al., “Deep resequencing of mitochondrial DNA”, Methods in Molecular Biology, Mitochondrial Medicine, 1264:59-66 (2015).
[cited by applicant]
Piko, et al., “Amounts of mitochondrial DNA and abundance of some mitochondrial gene transcripts in early mouse embryos”, Dev. Biol., 123(2):364-374 (1987).
[cited by applicant]
Rebolledo-Jaramillo, et al., “Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA”, PNAS, 111:15474-15479 (2014).
[cited by applicant]
Salk, et al., “Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations”, Nat. Rev. Genet., 19(5):269-285 (2018).
[cited by applicant]
Santibanez-Koref, et al., “Assessing mitochondrial heteroplasmy using next generation sequencing: a note of caution”, Mitochondrion, 46:302-306 (2019).
[cited by applicant]
Schon, et al., “Human mitochondrial DNA: roles of inherited and somatic mutations”, Nature Reviews, 13(12):878-890 (2012).
[cited by applicant]
Sedlazeck, et al., “Accurate detection of complex structural variations using single-molecule sequencing”, Nat. Methods, 15(6):461-468 (2018).
[cited by applicant]
Shendure, et al., “Next-generation DNA sequencing”, Nature Biotechnology, 26(10):1135-1145 (2008).
[cited by applicant]
Simpson, et al., “Detecting DNA cytosine methylation using nanopore sequencing”, Nat. Methods, 14(4):407-410 (2017).
[cited by applicant]
Smith, et al., “UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy”, Genome Res., 27: 491-499 (2017).
[cited by applicant]
Sovic, et al., “Fast and sensitive mapping of nanopore sequencing reads with GraphMap”, Nat. Commun., 7:11307, 11 pages (2016).
[cited by applicant]
Sperling, et al., “The genetics of myelodysplastic syndrome: from clonal hematopoiesis to secondary leukemia”, Nat. Rev. Cancer, 17(1):5-19 (2017).
[cited by applicant]
Stewart, et al., The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease, Nature Reviews, 16(9):530-542 (2015).
[cited by applicant]
Tajima, et al., “The development of novel quantification assay for mitochondrial DNA heteroplasmy aimed at preimplantation genetic diagnosis of Leigh encephalopathy”, J. Assist Reprod. Genet., 24(6):227-232 (2007).
[cited by applicant]
Tanaka, et al., “Strand asymmetry in human mitochondrial DNA mutations”, Genomics, 22(2):327-335 (1994).
[cited by applicant]
Thorburn, et al., “Healthy Baby Girl Born Following Pre-Implantation Genetic Diagnosis for Mitochondrial DNA 25 M.8993t > G Mutation”, Molecular Genetics and Metabolism, 98(1-2):5-6 (2009).
[cited by applicant]
Treff, et al., “Blastocyst preimplantation genetic diagnosis (PGD) of a mitochondrial DNA disorder”, Fertil. Steril., 98(5):1236-1240 (2012).
[cited by applicant]
Underhill, et al., “Use of Y chromosome and mitochondrial DNA population structure in tracing human migrations”, Annu. Rev. Genet., 41:539-564 (2007).
[cited by applicant]
Van Overbeek, et al., “DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks”, Molecular Cell, 63(4):633-646 (2016).
[cited by applicant]
Wai, et al., “The mitochondrial DNA genetic bottleneck results from replication of a subpopulation of genomes”, Nature Genetics, 40(12):1484-1488 (2008).
[cited by applicant]
Wallace, et al., “Mitochondrial DNA genetics and the heteroplasmy conundrum in evolution and disease”, Cold Spring Harbor Perspectives in Biology, 5(11): a021220 (2013).
[cited by applicant]
Walter, et al., “Exit from dormancy provokes DNA-damage-induced attrition in haematopoietic stem cells”, Nature, 520(7548):549-552 (2015).
[cited by applicant]
Weirather, et al., “Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis”, F1000Res 6:100, 32 pages (2017).
[cited by applicant]
Wenger, et al., “Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome”, Nature Biotechnology, 37(10):1155-1162 (2019).
[cited by applicant]
Yang, et al., 'Derivation of Pluripotent Stem Cells with in Vivo Embryonic and Extraembryonic Potency, Cell, 169(2):243-257, e225 (2017).
[cited by applicant]
Yao, et al., “Age-dependent accumulation of mtDNA mutations in murine hematopoietic stem cells is modulated by the nuclear genetic background”, Hum. Mol. Genet., 16(3):286-294 (2007).
[cited by applicant]
Yu, et al., “Effects of combined epidermal growth factor, brain-derived neurotrophic factor and insulin-like growth factor-1 on human oocyte maturation and early fertilized and cloned embryo development”, Hum. Reprod., …
[cited by applicant]
Yuan, et al., “Comprehensive molecular characterization of mitochondrial genomes in human cancers”, Nature Genetics, 52(3):342-352 (2020).
[cited by applicant]
Zagordi, et al., “Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies”, Nucleic Acids Res., 38(21):7400-7409 (2010).
[cited by applicant]
Zaidi, et al., “Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees”, PNAS, 116(50):25172-25178 (2019).
[cited by applicant]
Zhang, et al., “The mitochondrial DNA genetic bottleneck: inheritance and beyond”, Essays Biochem., 62(3):225-234 (2018).
[cited by applicant]
Zhou, et al., “Evaluating nanopore sequencing data processing pipelines for structural variation identification”, Genome Biol., 20(1):237, 13 pages (2019).
[cited by applicant]