2025
CFTR haplotype phasing using long-read genome sequencing from ultralow input DNA
Gandotra N, Tyagi A, Tikhonova I, Storer C, Scharfe C. CFTR haplotype phasing using long-read genome sequencing from ultralow input DNA. Genetics In Medicine Open 2025, 3: 101962. PMID: 40027236, PMCID: PMC11869909, DOI: 10.1016/j.gimo.2025.101962.Peer-Reviewed Original ResearchLong-read genome sequencingSingle-nucleotide variantsHaplotype phasingGenome sequencePathogenic variantsSmall indelsShort-read genome sequencing dataDNA inputShort-read sequencingGenome sequence dataPoly-T tractRare pathogenic variantsGenetic disease screeningIdentified compound heterozygosityGenomic distanceLibrary preparationGenomic variantsAllelic phaseCystic fibrosis patientsSequence dataInput DNAGenotype concordanceGenomic DNAStructural variantsSingle-nucleotide
2020
To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq
Xu J, Kudron MM, Victorsen A, Gao J, Ammouri HN, Navarro FCP, Gevirtzman L, Waterston RH, White KP, Reinke V, Gerstein M. To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq. Nucleic Acids Research 2020, 49: e17-e17. PMID: 33347581, PMCID: PMC7897498, DOI: 10.1093/nar/gkaa1155.Peer-Reviewed Original ResearchConceptsMock immunoprecipitationsSpurious sitesDNA inputCell linesMultiple cell typesOpen chromatinChIP-seqChromatin immunoprecipitationGenomic activityWhole organismNonspecific interactionsIP experimentsImmunoprecipitationCell typesIP antibodyTechnical noiseAbundanceComplex samplesChromatinGenomeSitesGenesOrganismsLinesInteraction
2018
Detection and Quantification of Mosaic Genomic DNA Variation in Primary Somatic Tissues Using ddPCR: Analysis of Mosaic Transposable-Element Insertions, Copy-Number Variants, and Single-Nucleotide Variants
Zhou B, Haney MS, Zhu X, Pattni R, Abyzov A, Urban AE. Detection and Quantification of Mosaic Genomic DNA Variation in Primary Somatic Tissues Using ddPCR: Analysis of Mosaic Transposable-Element Insertions, Copy-Number Variants, and Single-Nucleotide Variants. Methods In Molecular Biology 2018, 1768: 173-190. PMID: 29717444, DOI: 10.1007/978-1-4939-7778-9_11.Peer-Reviewed Original Research
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