2025
Plant graph-based pangenomics: techniques, applications, and challenges
Du Z, He J, Jiao W. Plant graph-based pangenomics: techniques, applications, and challenges. ABIOTECH 2025, 1-16. DOI: 10.1007/s42994-025-00206-7.Peer-Reviewed Original ResearchNovo-assembled genomeMolecular breeding of cropsDNA sequencing technologiesInvestigate population diversityAgronomically important genesBreeding of cropsPangenome graphsGenetic mapSmall variantsGenomic regionsGenetic diversityGraph pangenomeSequencing technologiesGenomic analysisPangenomic studiesGenomic studiesGenetic variationImportant genesMolecular breedingStructural variantsPangenomeGenomeCrop breedingPlantsVariantsCFTR 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
2024
Haplotype‐Resolved Genotyping and Association Analysis of 1,020 β‐Thalassemia Patients by Targeted Long‐Read Sequencing
Ye Y, Niu C, Mao A, Qin L, Zhan J, Chen W, Liu Z, Xie T, Zhang Q, Li J, Huang L, Meng W, Liu Y, Liao L, Cai J, Liu R, Zhang X, Zeng L, Li Y, Lin B, Li K, Hua X, Huang B, Qin H, Huang Y, Huang Z, Lao J, Qu X, Chen J, Feng X, Liu Q, Lin W, Zhou X, Liang Y, Long X, Qin J, Yan L, Zhu W, Yu L, Fan C, Tang D, Zhong T, Tan J, Ren Z, Xu X. Haplotype‐Resolved Genotyping and Association Analysis of 1,020 β‐Thalassemia Patients by Targeted Long‐Read Sequencing. Advanced Science 2024, 12: 2410992. PMID: 39737841, PMCID: PMC11884621, DOI: 10.1002/advs.202410992.Peer-Reviewed Original ResearchConceptsLong-read sequencingSingle nucleotide variantsGene clusterGlobin gene clusterT-LRSHomologous regionsStructural variantsB-thalassemia patientsTargeted long-read sequencingRare structural variantsB-thalassemiaErythroid transcription factorsHaplotype phasingNucleotide variantsAssociation analysisTranscription factorsGenetic variantsRare mutationsHaplotypesMutation spectrumExpression of fetal hemoglobinMutationsReduce transfusion dependencePatients to dateGenes/lociAn integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
Li C, Bonder M, Syed S, Jensen M, Consortium H, Group H, Gerstein M, Zody M, Chaisson M, Talkowski M, Marschall T, Korbel J, Eichler E, Lee C, Shi X. An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes. Genome Research 2024, 34: 2304-2318. PMID: 39638559, PMCID: PMC11694747, DOI: 10.1101/gr.279419.124.Peer-Reviewed Original ResearchConceptsTopologically associating domainsTopologically associating domains boundariesImpact of structural variantsLymphoblastoid cell linesStructural variantsHuman genomeGene regulationAdjacent TADsHuman lymphoblastoid cell linesCell linesSub-TADGenomic structureInsulate genesChromatin architectureImpact of deletionChromatin structureGenomeAberrant regulationAnalysis pipelineMammalian speciesGenesCCREsFunctional impactChromatinRegulationGenomic Determinants of Clinical Outcomes in Multiple Myeloma with t(11;14)(CCND1;IGH) Treated with Venetoclax
Kaddoura M, Wiedmeier-Nutor J, Gupta V, Ziccheddu B, Shivaram S, Tang H, Fonseca R, Durante M, Matulis S, Jelinek T, Landgren O, Mitsiades C, Bergsagel P, Braggio E, Boise L, Fonseca R, Kumar S, Maura F, Baughn L. Genomic Determinants of Clinical Outcomes in Multiple Myeloma with t(11;14)(CCND1;IGH) Treated with Venetoclax. Blood 2024, 144: 249. DOI: 10.1182/blood-2024-204071.Peer-Reviewed Original ResearchProgression free survivalSingle nucleotide variantsWhole-genome sequencingMultiple myelomaMM patientsFocal deletionsCopy number variantsMechanisms of resistanceTraining cohortValidation cohortChronic lymphocytic leukemia treated with venetoclaxDisease progressionMAPK pathwayMedian progression free survivalPopulation of MM patientsDeterminants of clinical outcomeAnti-CD38 agentsTreated with venetoclaxComprehensive genomic profilingMAPK pathway mutationsStructural variantsAcute myeloid leukemiaGenomic eventsLoss of NoxaNovel drug combinationsExpanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders
Jurgens J, Barry B, Chan W, MacKinnon S, Whitman M, Ruiz P, Pratt B, England E, Pais L, Lemire G, Groopman E, Glaze C, Russell K, Singer-Berk M, Di Gioia S, Lee A, Andrews C, Shaaban S, Wirth M, Bekele S, Toffoloni M, Bradford V, Foster E, Berube L, Rivera-Quiles C, Mensching F, Sanchis-Juan A, Fu J, Wong I, Zhao X, Wilson M, Weisburd B, Lek M, Consortium O, Abarca-Barriga H, Al-Haddad C, Berman J, Bothun E, Capasso J, Chacon-Camacho O, Chang L, Christiansen S, Ciccarelli M, Cordonnier M, Cox G, Curry C, Dagi L, Dahm T, David K, Davitt B, De Berardinis T, Demer J, Désir J, D’Esposito F, Drack A, Eggenberger E, Elder J, Elliott A, Epley K, Feldman H, Ferreira C, Flaherty M, Fulton A, Gerth-Kahlert C, Gottlob I, Grill S, Halliday D, Hanisch F, Hay E, Heidary G, Holder C, Horton J, Iannaccone A, Isenberg S, Johnston S, Kahana A, Katowitz J, Kazlas M, Kerr N, Kimonis V, Ko M, Koc F, Larsen D, Lay-Son G, Ledoux D, Levin A, Levy R, Lyons C, Mackey D, Magli A, Mantagos I, Marti C, Maystadt I, McKenzie F, Menezes M, Mikail C, Miller D, Miller K, Mills M, Miyana K, Moller H, Mullineaux L, Nishimura J, Noble A, Pandey P, Pavone P, Penzien J, Petersen R, Phalen J, Poduri A, Polo C, Prasov L, Ramos F, Ramos-Caceres M, Robb R, Rossillion B, Sahin M, Singer H, Smith L, Sorkin J, Soul J, Staffieri S, Stalker H, Stasheff S, Strassberg S, Strominger M, Taranath D, Thomas I, Traboulsi E, Ugrin M, VanderVeen D, Vincent A, G M, Wabbels B, Wong A, Woods C, Wu C, Yang E, Yeung A, Young T, Zenteno J, Zubcov-Iwantscheff A, Zwaan J, Brand H, Talkowski M, MacArthur D, O’Donnell-Luria A, Robson C, Hunter D, Engle E. Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders. Genetics In Medicine 2024, 27: 101216. PMID: 39033378, PMCID: PMC11739428, DOI: 10.1016/j.gim.2024.101216.Peer-Reviewed Original ResearchCongenital cranial dysinnervation disordersPrioritized variantsProtein-coding regionsSingle-nucleotide variantsDe novo variantsAnimal model phenotypesGenetically heterogeneous disorderAnalysis of pedigreesGenes associated with syndromesGenome sequenceStructural variantsMendelian conditionsModel phenotypesGenotype/phenotype correlationGenetic etiologyGenotype/phenotype associationsPathogenic variant(sGenesFunctional studiesSyndrome phenotypeSyndrome componentsPhenotypeGeneticsProbandsVariants
2023
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
Rozowsky J, Gao J, Borsari B, Yang Y, Galeev T, Gürsoy G, Epstein C, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun M, Wright J, Chang J, Cameron C, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona G, Chee S, Chhetri S, Cortez Martins G, Danyko C, Davis C, Farid D, Farrell N, Gabdank I, Gofin Y, Gorkin D, Gu M, Hecht V, Hitz B, Issner R, Jiang Y, Kirsche M, Kong X, Lam B, Li S, Li B, Li X, Lin K, Luo R, Mackiewicz M, Meng R, Moore J, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt H, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber J, Sedlazeck F, See L, Sherman R, Shi X, Shi M, Sloan C, Strattan J, Tan Z, Tanaka F, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry J, Mendenhall E, Noble W, Weng Z, Levine M, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers R, Snyder M, Choudhary J, Milosavljevic A, Schatz M, Bernstein B, Guigó R, Gingeras T, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell 2023, 186: 1493-1511.e40. PMID: 37001506, PMCID: PMC10074325, DOI: 10.1016/j.cell.2023.02.018.Peer-Reviewed Original Research
2022
The Human Pangenome Project: a global resource to map genomic diversity
Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, Garrison N, Graves-Lindsay TA, Ji H, Kenny EE, Koenig BA, Li D, Marschall T, McMichael JF, Novak AM, Purushotham D, Schneider VA, Schultz BI, Smith MW, Sofia HJ, Weissman T, Flicek P, Li H, Miga KH, Paten B, Jarvis ED, Hall IM, Eichler EE, Haussler D. The Human Pangenome Project: a global resource to map genomic diversity. Nature 2022, 604: 437-446. PMID: 35444317, PMCID: PMC9402379, DOI: 10.1038/s41586-022-04601-8.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsHuman reference genomeReference genomeGenomic diversityGenomic variationHuman genomic variationGlobal genomic diversitySingle nucleotide variantsGene-disease associationsDiploid genomeGenetic resourcesGenomeGenomic researchFuture biomedical researchHigh-quality referenceStructural variantsHuman geneticsRoutine assemblyCommon variantsFunctional elementsPolymorphic regionDiversityBiomedical researchVariantsMajor updateGenetics
2021
Integrated genomic analyses of cutaneous T-cell lymphomas reveal the molecular bases for disease heterogeneity
Park J, Daniels J, Wartewig T, Ringbloom KG, Martinez-Escala ME, Choi S, Thomas JJ, Doukas PG, Yang J, Snowden C, Law C, Lee Y, Lee K, Zhang Y, Conran C, Tegtmeyer K, Mo SH, Pease DR, Jothishankar B, Kwok PY, Abdulla FR, Pro B, Louissaint A, Boggon T, Sosman J, Guitart J, Rao D, Ruland J, Choi J. Integrated genomic analyses of cutaneous T-cell lymphomas reveal the molecular bases for disease heterogeneity. Blood 2021, 138: 1225-1236. PMID: 34115827, PMCID: PMC8499046, DOI: 10.1182/blood.2020009655.Peer-Reviewed Original ResearchConceptsPutative driver genesDriver genesCutaneous T-cell lymphomaDisease phenotypePutative tumor suppressorT-cell lymphomaMycosis fungoidesDiverse disease phenotypesPutative genetic causesSezary syndromeDNA/RNA sequencingGenomic analysisRNA sequencingMolecular basisTumor suppressorDisease stageStructural variantsGenetic relationshipsTranscriptional signatureGenesDisease heterogeneityFunctional assaysNovel insightsSkin-homing T cellsLeukemic diseaseStructural variants are a major source of gene expression differences in humans and often affect multiple nearby genes
Scott AJ, Chiang C, Hall IM. Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes. Genome Research 2021, 31: gr.275488.121. PMID: 34544830, PMCID: PMC8647827, DOI: 10.1101/gr.275488.121.Peer-Reviewed Original ResearchRare structural variantsGene expression differencesStructural variantsNearby genesExpression differencesGene expressionMultiple nearby genesIndividual structural variantsHuman genome diversityMobile element insertionsGene expression changesGene expression outliersCommon structural variantsCurrent annotationGenome diversityPhenotypic variationGTEx projectRegulatory elementsElement insertionsExpression outliersMultiple genesDifferent genesExpression changesMultitissue analysesGenesAn open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
MalariaGEN, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare G, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NP, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Research 2021, 6: 42. PMID: 33824913, PMCID: PMC8008441, DOI: 10.12688/wellcomeopenres.16168.2.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsStrong geographic differentiationGenome variation dataHigh-quality genotypesGeographic differentiationGenome variationGenetic evidenceShort indelsEvolutionary processesStructural variantsMosquito stagesNumber variantsData-sharing networksNucleotide polymorphismsVariation dataWorldwide sampleAnalysis pipelineGenomic epidemiologyMarker of resistanceDrug resistanceSurveillance toolkitIndelsGenesLociVariantsFunctional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element
Baxter J, Johnson N, Tomczyk K, Gillespie A, Maguire S, Brough R, Fachal L, Michailidou K, Bolla M, Wang Q, Dennis J, Ahearn T, Andrulis I, Anton-Culver H, Antonenkova N, Arndt V, Aronson K, Augustinsson A, Becher H, Beckmann M, Behrens S, Benitez J, Bermisheva M, Bogdanova N, Bojesen S, Brenner H, Brucker S, Cai Q, Campa D, Canzian F, Castelao J, Chan T, Chang-Claude J, Chanock S, Chenevix-Trench G, Choi J, Clarke C, Collaborators N, Colonna S, Conroy D, Couch F, Cox A, Cross S, Czene K, Daly M, Devilee P, Dörk T, Dossus L, Dwek M, Eccles D, Ekici A, Eliassen A, Engel C, Fasching P, Figueroa J, Flyger H, Gago-Dominguez M, Gao C, García-Closas M, García-Sáenz J, Ghoussaini M, Giles G, Goldberg M, González-Neira A, Guénel P, Gündert M, Haeberle L, Hahnen E, Haiman C, Hall P, Hamann U, Hartman M, Hatse S, Hauke J, Hollestelle A, Hoppe R, Hopper J, Hou M, Investigators K, Investigators A, Ito H, Iwasaki M, Jager A, Jakubowska A, Janni W, John E, Joseph V, Jung A, Kaaks R, Kang D, Keeman R, Khusnutdinova E, Kim S, Kosma V, Kraft P, Kristensen V, Kubelka-Sabit K, Kurian A, Kwong A, Lacey J, Lambrechts D, Larson N, Larsson S, Le Marchand L, Lejbkowicz F, Li J, Long J, Lophatananon A, Lubiński J, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Matsuo K, Mavroudis D, Mayes R, Menon U, Milne R, Taib N, Muir K, Muranen T, Murphy R, Nevanlinna H, O’Brien K, Offit K, Olson J, Olsson H, Park S, Park-Simon T, Patel A, Peterlongo P, Peto J, Plaseska-Karanfilska D, Presneau N, Pylkäs K, Rack B, Rennert G, Romero A, Ruebner M, Rüdiger T, Saloustros E, Sandler D, Sawyer E, Schmidt M, Schmutzler R, Schneeweiss A, Schoemaker M, Shah M, Shen C, Shu X, Simard J, Southey M, Stone J, Surowy H, Swerdlow A, Tamimi R, Tapper W, Taylor J, Teo S, Teras L, Terry M, Toland A, Tomlinson I, Truong T, Tseng C, Untch M, Vachon C, van den Ouweland A, Wang S, Weinberg C, Wendt C, Winham S, Winqvist R, Wolk A, Wu A, Yamaji T, Zheng W, Ziogas A, Pharoah P, Dunning A, Easton D, Pettitt S, Lord C, Haider S, Orr N, Fletcher O. Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element. American Journal Of Human Genetics 2021, 108: 1190-1203. PMID: 34146516, PMCID: PMC8322933, DOI: 10.1016/j.ajhg.2021.05.013.Peer-Reviewed Original ResearchConceptsBreast cancer risk lociCredible causal variantsCancer risk lociRegulatory elementsCausal variantsRisk lociCell type-specific transcriptionDeletion alleleTranscription factor binding regionsIdentified putative regulatory elementsChIP-seq dataPutative regulatory elementsCell type-specific expressionSignal 2ChIP-seqFunctional annotationStructural variantsDNase IBinding regionCRISPR assayIGFBP5 promoterEstrogen receptor-positive breast cancerReceptor-positive breast cancerRisk of estrogen receptor-positive breast cancerLociAn open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson T, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley E, Auburn S, Awandare G, Ba H, Baraka V, Barry A, Bejon P, Bertin G, Boni M, Borrmann S, Bousema T, Branch O, Bull P, Busby G, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day N, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp A, Drakeley C, Drury E, Duffy P, Echeverry D, Egwang T, Erko B, Fairhurst R, Faiz A, Fanello C, Fukuda M, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton W, Harrison G, Hart L, Henrichs C, Hien T, Hill C, Hodgson A, Hubbart C, Imwong M, Ishengoma D, Jackson S, Jacob C, Jeffery B, Jeffreys A, Johnson K, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski D, Kyaw M, Lim P, Lon C, Loua K, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu O, Montgomery J, Mueller I, Newton P, Nguyen T, Nguyen T, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier L, Ocholla H, Oduro A, Omedo I, Onyamboko M, Ouedraogo J, Oyebola K, Pearson R, Peshu N, Phyo A, Plowe C, Price R, Pukrittayakamee S, Randrianarivelojosia M, Rayner J, Ringwald P, Rockett K, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson V, Stalker J, Su X, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems T, Wendler J, White N, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Research 2021, 6: 42. DOI: 10.12688/wellcomeopenres.16168.1.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsStrong geographic differentiationGenome variation dataHigh-quality genotypesGeographic differentiationGenome variationGenetic evidenceShort indelsEvolutionary processesStructural variantsMosquito stagesNumber variantsData-sharing networksNucleotide polymorphismsVariation dataWorldwide sampleAnalysis pipelineGenomic epidemiologyMarker of resistanceDrug resistanceSurveillance toolkitIndelsGenesLociVariants
2020
Chromosome-scale, haplotype-resolved assembly of human genomes
Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook J, Moemke T, Marschall T, Sedlazeck F, Aach J, Chin C, Church G, Li H. Chromosome-scale, haplotype-resolved assembly of human genomes. Nature Biotechnology 2020, 39: 309-312. PMID: 33288905, PMCID: PMC7954703, DOI: 10.1038/s41587-020-0711-0.Peer-Reviewed Original ResearchConceptsHaplotype-resolved assembliesHuman genomeStructural variantsAssembly of human genomesDiscovery of structural variantsChromosome-scale phasingComplex genetic variationKiller cell immunoglobulin-like receptorsChromosome-scaleDiploid assemblyHaplotype-resolvedContig lengthGenome assemblyHeterozygous sitesTransposon insertionHaplotype variationGenetic variationPedigree informationGenomePhase assemblyPrecision medicineHuman leukocyte antigenImmunoglobulin-like receptorsAssemblyImportant regionsComplex mosaic structural variations in human fetal brains
Sekar S, Tomasini L, Proukakis C, Bae T, Manlove L, Jang Y, Scuderi S, Zhou B, Kalyva M, Amiri A, Mariani J, Sedlazeck F, Urban AE, Vaccarino F, Abyzov A. Complex mosaic structural variations in human fetal brains. Genome Research 2020, 30: gr.262667.120. PMID: 33122304, PMCID: PMC7706730, DOI: 10.1101/gr.262667.120.Peer-Reviewed Original ResearchConceptsSingle nucleotide variantsCopy number variantsStructural variantsMegabase-scale copy number variantsHuman fetal brainFunctional consequencesMobile element insertionsSimilar functional consequencesFetal brainMosaic single-nucleotide variantsAdult brain neuronsStructural variationsPotential functional consequencesKilobase scaleDNA eventsGenomic fragmentDifferent chromosomesElement insertionsClonal approachHuman brain cellsFetal human brainNucleotide variantsReplication errorsHuman brainNumber variantsFunctional annotation of rare structural variation in the human brain
Han L, Zhao X, Benton ML, Perumal T, Collins RL, Hoffman GE, Johnson JS, Sloofman L, Wang HZ, Stone MR, Brennand K, Brand H, Sieberts S, Marenco S, Peters M, Lipska B, Roussos P, Capra J, Talkowski M, Ruderfer D. Functional annotation of rare structural variation in the human brain. Nature Communications 2020, 11: 2990. PMID: 32533064, PMCID: PMC7293301, DOI: 10.1038/s41467-020-16736-1.Peer-Reviewed Original ResearchMapping and characterization of structural variation in 17,795 human genomes
Abel HJ, Larson DE, Regier AA, Chiang C, Das I, Kanchi KL, Layer RM, Neale BM, Salerno WJ, Reeves C, Buyske S, Matise T, Muzny D, Zody M, Lander E, Dutcher S, Stitziel N, Hall I. Mapping and characterization of structural variation in 17,795 human genomes. Nature 2020, 583: 83-89. PMID: 32460305, PMCID: PMC7547914, DOI: 10.1038/s41586-020-2371-0.Peer-Reviewed Original ResearchConceptsStructural variantsWhole-genome sequencingHuman genomeUltra-rare structural variantsRare structural variantsSuch structural variantsSingle nucleotide variantsNoncoding elementsDosage sensitivityGenomeHuman geneticsSmall insertionsComplex rearrangementsDeletion variantsSmall variantsStructural variationsGenesSequencingAllelesForm of variationVariantsElement classesSite frequency dataDeleterious effectsGeneticsAnalyses of non-coding somatic drivers in 2,658 cancer whole genomes
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen J, Getz G. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 2020, 578: 102-111. PMID: 32025015, PMCID: PMC7054214, DOI: 10.1038/s41586-020-1965-x.Peer-Reviewed Original ResearchConceptsInternational Cancer Genome ConsortiumStructural variantsPoint mutationsDriver discoveryProtein-coding genesNon-coding genesNon-coding regionsPan-cancer analysisDriver point mutationsSomatic driversCancer Genome AtlasRegulatory sequencesCancer genomesUntranslated regionGenome ConsortiumFocal deletionsGenesGenome AtlasGenomeNovel candidatesMutationsRecurrent breakpointsRegion of TP53DiscoveryVariantsPan-cancer analysis of whole genomes
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Pan-cancer analysis of whole genomes. Nature 2020, 578: 82-93. PMID: 32025007, PMCID: PMC7025898, DOI: 10.1038/s41586-020-1969-6.Peer-Reviewed Original ResearchMeSH KeywordsCell ProliferationCellular SenescenceChromothripsisCloud ComputingDNA Mutational AnalysisEvolution, MolecularFemaleGenome, HumanGenomicsGerm-Line MutationHigh-Throughput Nucleotide SequencingHumansInformation DisseminationMaleMutagenesisMutationNeoplasmsOncogenesPromoter Regions, GeneticReproducibility of ResultsRNA SplicingTelomeraseTelomereConceptsPan-Cancer Analysis of Whole GenomesInternational Cancer Genome ConsortiumPan-cancer analysisPan-Cancer Analysis of Whole Genomes ConsortiumStructural variantsNon-coding genomic elementsPoint mutationsAnalysis of Whole GenomesSomatic mutationsNon-coding mutationsRare germline variantsAbnormal telomere maintenanceConsequences of somatic mutationsPattern of somatic mutationsSignatures of mutational processesCancer driver discoveryCancer-associated genesSomatic point mutationsGenomic elementsWhole genomeLow replicative activitySmall insertionsCancer Genome ConsortiumBase substitutionsCancer genomes
2019
Somatic mutations and clonal dynamics in healthy and cirrhotic human liver
Brunner S, Roberts N, Wylie L, Moore L, Aitken S, Davies S, Sanders M, Ellis P, Alder C, Hooks Y, Abascal F, Stratton M, Martincorena I, Hoare M, Campbell P. Somatic mutations and clonal dynamics in healthy and cirrhotic human liver. Nature 2019, 574: 538-542. PMID: 31645727, PMCID: PMC6837891, DOI: 10.1038/s41586-019-1670-9.Peer-Reviewed Original ResearchConceptsChronic liver diseaseHepatocellular carcinomaLiver diseaseCirrhotic liverMutational burdenSomatic mutationsMutational signaturesProgression to chronic liver diseaseSynchronous hepatocellular carcinomaNon-malignant hepatocytesExcessive alcohol intakeComplexity of hepatocellular carcinomaBands of fibrosisNon-alcoholic fatty liver diseaseStructural variantsFatty liver diseaseGenome of hepatocellular carcinomaClinical spectrumAlcohol intakeLiver failureViral hepatitisClonal expansionMalignant transformationHealth to diseaseRegenerative nodules
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