2024
Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes
Maury E, Jones A, Seplyarskiy V, Nguyen T, Rosenbluh C, Bae T, Wang Y, Abyzov A, Khoshkhoo S, Chahine Y, Zhao S, Venkatesh S, Root E, Voloudakis G, Roussos P, Network B, Park P, Akbarian S, Brennand K, Reilly S, Lee E, Sunyaev S, Walsh C, Chess A. Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes. Science 2024, 386: 217-224. PMID: 39388546, PMCID: PMC11490355, DOI: 10.1126/science.adq1456.Peer-Reviewed Original ResearchConceptsTranscription factor binding sitesWhole-genome sequencingOpen chromatinMutational processesSomatic mutationsFactor binding sitesSchizophrenia casesSchizophrenia risk genesSomatic mosaicismSomatic variantsRisk genesG mutationGene expressionGermline mutationsBinding sitesGenesMutationsIncreased somatic mutationsChromatinMosaic somatic mutationsPrenatal neurogenesisContext of schizophreniaBrain neuronsSchizophrenia brainVariants
2023
Control-independent mosaic single nucleotide variant detection with DeepMosaic
Yang X, Xu X, Breuss M, Antaki D, Ball L, Chung C, Shen J, Li C, George R, Wang Y, Bae T, Cheng Y, Abyzov A, Wei L, Alexandrov L, Sebat J, Gleeson J. Control-independent mosaic single nucleotide variant detection with DeepMosaic. Nature Biotechnology 2023, 41: 870-877. PMID: 36593400, PMCID: PMC10314968, DOI: 10.1038/s41587-022-01559-w.Peer-Reviewed Original Research
2022
Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability
Bae T, Fasching L, Wang Y, Shin JH, Suvakov M, Jang Y, Norton S, Dias C, Mariani J, Jourdon A, Wu F, Panda A, Pattni R, Chahine Y, Yeh R, Roberts RC, Huttner A, Kleinman JE, Hyde TM, Straub RE, Walsh CA, Urban A, Leckman J, Weinberger D, Vaccarino F, Abyzov A, Walsh C, Park P, Sestan N, Weinberger D, Moran J, Gage F, Vaccarino F, Gleeson J, Mathern G, Courchesne E, Roy S, Chess A, Akbarian S, Bizzotto S, Coulter M, Dias C, D’Gama A, Ganz J, Hill R, Huang A, Khoshkhoo S, Kim S, Lee A, Lodato M, Maury E, Miller M, Borges-Monroy R, Rodin R, Zhou Z, Bohrson C, Chu C, Cortes-Ciriano I, Dou Y, Galor A, Gulhan D, Kwon M, Luquette J, Sherman M, Viswanadham V, Jones A, Rosenbluh C, Cho S, Langmead B, Thorpe J, Erwin J, Jaffe A, McConnell M, Narurkar R, Paquola A, Shin J, Straub R, Abyzov A, Bae T, Jang Y, Wang Y, Molitor C, Peters M, Linker S, Reed P, Wang M, Urban A, Zhou B, Zhu X, Pattni R, Serres Amero A, Juan D, Lobon I, Marques-Bonet T, Solis Moruno M, Garcia Perez R, Povolotskaya I, Soriano E, Antaki D, Averbuj D, Ball L, Breuss M, Yang X, Chung C, Emery S, Flasch D, Kidd J, Kopera H, Kwan K, Mills R, Moldovan J, Sun C, Zhao X, Zhou W, Frisbie T, Cherskov A, Fasching L, Jourdon A, Pochareddy S, Scuderi S. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability. Science 2022, 377: 511-517. PMID: 35901164, PMCID: PMC9420557, DOI: 10.1126/science.abm6222.Peer-Reviewed Original ResearchMeSH KeywordsAgingAutistic DisorderBrainEnhancer Elements, GeneticGene Expression RegulationHumansMutagenesisMutationProtein BindingTranscription FactorsWhole Genome SequencingConceptsTranscription factorsSomatic mutationsPutative transcription factorEnhancer-like regionSingle nucleotide mutationsWhole-genome sequencingGene regulationSomatic duplicationGenome sequencingDamaging mutationsBackground mutagenesisMutationsHypermutabilityClonal expansionMotifDiseased brainPotential linkVivo clonal expansionMutagenesisGenesDuplicationSequencingRegulation
2021
CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing
Suvakov M, Panda A, Diesh C, Holmes I, Abyzov A. CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing. GigaScience 2021, 10: giab074. PMID: 34817058, PMCID: PMC8612020, DOI: 10.1093/gigascience/giab074.Peer-Reviewed Original ResearchMeSH KeywordsAllelesDNA Copy Number VariationsGenomicsHigh-Throughput Nucleotide SequencingSequence Analysis, DNASoftwareWhole Genome SequencingLandmarks of human embryonic development inscribed in somatic mutations
Bizzotto S, Dou Y, Ganz J, Doan R, Kwon M, Bohrson C, Kim S, Bae T, Abyzov A, Network† N, Park P, Walsh C. Landmarks of human embryonic development inscribed in somatic mutations. Science 2021, 371: 1249-1253. PMID: 33737485, PMCID: PMC8170505, DOI: 10.1126/science.abe1544.Peer-Reviewed Original ResearchConceptsSomatic single nucleotide variantsHuman embryonic developmentEmbryonic developmentEarly embryonic cell divisionsTransposase-accessible chromatin sequencingSingle cellsSingle-nucleus assayHigh-depth whole-genome sequencingSingle-nucleus RNA sequencingEmbryonic cell divisionCell lineage informationDistinct germ layersOnset of gastrulationSingle nucleotide variantsOrganismal developmentWhole-genome sequencingExtraembryonic tissuesCell divisionRNA sequencingProgenitor poolLineage informationGerm layersEarly progenitorsMultiple tissuesSequencing
2019
Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
Zhou B, Ho S, Greer S, Zhu X, Bell J, Arthur J, Spies N, Zhang X, Byeon S, Pattni R, Ben-Efraim N, Haney M, Haraksingh R, Song G, Ji H, Perrin D, Wong W, Abyzov A, Urban A. Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562. Genome Research 2019, 29: 472-484. PMID: 30737237, PMCID: PMC6396411, DOI: 10.1101/gr.234948.118.Peer-Reviewed Original ResearchConceptsWhole-genome analysisStructural variantsFunctional genomicsEpigenomic dataAllele-specific DNA methylationComprehensive whole-genome analysisWhole-genome bisulfite sequencing dataGenomic structural featuresCopy numberLinked-read sequencingAllele-specific expressionEntire chromosome armsBisulfite sequencing dataAllele-specific deletionsComplex structural variantsTumor suppressor geneEpigenomic characteristicsChromosome armsGenome sequenceChromosome segmentsDNA methylationRNA-seqGenome characteristicsRetrotransposon insertionGenomic variant information