2024
Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints
Zhou B, Purmann C, Guo H, Shin G, Huang Y, Pattni R, Meng Q, Greer S, Roychowdhury T, Wood R, Ho M, Dohna H, Abyzov A, Hallmayer J, Wong W, Ji H, Urban A. Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2322834121. PMID: 39042694, PMCID: PMC11295037, DOI: 10.1073/pnas.2322834121.Peer-Reviewed Original ResearchConceptsLong-read sequencingPulse-field gel electrophoresisBase-pair resolutionDNA methylation patternsCell-type specific analysisCell type-specificChromosomal interactionsSequence assemblySegmental duplicationsGenome sequenceGenomic rearrangementsGenomic regionsChromosomal breakpointsHuman genomeGenomic recombinationMethylation patternsSequence analysisHaplotype-specificDeletion haplotypesGel electrophoresisGenomeAmplification-freeBreakpoint locationsMicrodeletion disorderType-specific
2019
Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation
Maldonado MBC, de Rezende Neto NB, Nagamatsu ST, Carazzolle MF, Hoff JL, Whitacre LK, Schnabel RD, Behura SK, McKay SD, Taylor JF, Lopes FL. Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation. PLOS ONE 2019, 14: e0222329. PMID: 31513639, PMCID: PMC6742455, DOI: 10.1371/journal.pone.0222329.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsCpG islandsDNA methylationReference genome sequence assemblyDatabase of SNPsCpG sitesBull Genomes ProjectGenome sequence assemblyDivergent feed efficiencyBovine phenotypesEpigenetic polymorphismEpigenetic controlEpigenetic regulationIntergenic regionNearby genesMethylation targetsGenomic sequencesMethylation patternsSequence assemblyGenome ProjectMethylation profilesMethylation sitesSNP databaseDifferential expressionVariant annotation
2015
Targeted single molecule sequencing methodology for ovarian hyperstimulation syndrome
Orkunoglu-Suer F, Harralson A, Frankfurter D, Gindoff P, O’Brien T. Targeted single molecule sequencing methodology for ovarian hyperstimulation syndrome. BMC Genomics 2015, 16: 264. PMID: 25888426, PMCID: PMC4397691, DOI: 10.1186/s12864-015-1451-2.Peer-Reviewed Original ResearchConceptsSingle molecule sequencingSequence assemblyMolecule sequencingDNA sequencesFunctional analysis of variantsReal-time DNA sequencingGenome Analysis ToolkitTargeted capture enrichmentBase-calling accuracyGC-rich regionEmulsion PCRHuman DNA samplesConventional Sanger sequencingNext generation sequencingMultiplex polymerase chain reactionDepth of coveragePolymerase chain reactionAnalysis of variantsLong readsRead lengthSequencing methodologiesFunctional variantsGeneration sequencingSanger sequencingYield amplicons
2013
The zebrafish reference genome sequence and its relationship to the human genome
Howe K, Clark M, Torroja C, Torrance J, Berthelot C, Muffato M, Collins J, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett J, Koch R, Rauch G, White S, Chow W, Kilian B, Quintais L, Guerra-Assunção J, Zhou Y, Gu Y, Yen J, Vogel J, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire S, Laird G, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliott D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper J, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley C, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster S, Carter N, Harrow J, Ning Z, Herrero J, Searle S, Enright A, Geisler R, Plasterk R, Lee C, Westerfield M, de Jong P, Zon L, Postlethwait J, Nüsslein-Volhard C, Hubbard T, Crollius H, Rogers J, Stemple D. The zebrafish reference genome sequence and its relationship to the human genome. Nature 2013, 496: 498-503. PMID: 23594743, PMCID: PMC3703927, DOI: 10.1038/nature12111.Peer-Reviewed Original ResearchConceptsHigh-quality sequence assembliesHuman protein-coding genesProtein-coding genesReference genome sequenceKey genomic featuresHuman reference genomeZebrafish genomeZebrafish orthologueReference genomeGenome sequenceHuman genomeSequence assemblyGenomic featuresLarge genesGenomeGenesOrthologuesVertebratesSequenceAssembly
2001
Integration of cytogenetic landmarks into the draft sequence of the human genome
BAC Resource Consortium T, Cheung V, Nowak N, Jang W, Kirsch I, Zhao S, Chen X, Furey T, Kim U, Kuo W, Olivier M, Conroy J, Kasprzyk A, Massa H, Yonescu R, Sait S, Thoreen C, Snijders A, Lemyre E, Bailey J, Bruzel A, Burrill W, Clegg S, Collins S, Dhami P, Friedman C, Han C, Herrick S, Lee J, Ligon A, Lowry S, Morley M, Narasimhan S, Osoegawa K, Peng Z, Plajzer-Frick I, Quade B, Scott D, Sirotkin K, Thorpe A, Gray J, Hudson J, Pinkel D, Ried T, Rowen L, Shen-Ong G, Strausberg R, Birney E, Callen D, Cheng J, Cox D, Doggett N, Carter N, Eichler E, Haussler D, Korenberg J, Morton C, Albertson D, Schuler G, de Jong P, Trask B. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 2001, 409: 953-958. PMID: 11237021, PMCID: PMC7845515, DOI: 10.1038/35057192.Peer-Reviewed Original ResearchConceptsHuman genomeDraft sequenceLarge-scale chromatin structureHuman diseasesGenome-wide setLarge-scale duplicationsEvolution of chromosomesCharacterization of genesFirst comprehensive integrationLarge-insert clonesGross chromosomal aberrationsChromatin structureCytogenetic landmarksGene familyRadiation hybridsSequence tagsGenomic sequencesSequence assemblyMolecular basisGenomeSequence differencesFunctional analysisSequence mapsSitu hybridizationChromosomes
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