2022
Postmortem Human Dura Mater Cells Exhibit Phenotypic, Transcriptomic and Genetic Abnormalities that Impact their Use for Disease Modeling
Argouarch A, Schultz N, Yang A, Jang Y, Garcia K, Cosme C, Corrales C, Nana A, Karydas A, Spina S, Grinberg L, Miller B, Wyss-Coray T, Abyzov A, Goodarzi H, Seeley W, Kao A. Postmortem Human Dura Mater Cells Exhibit Phenotypic, Transcriptomic and Genetic Abnormalities that Impact their Use for Disease Modeling. Stem Cell Reviews And Reports 2022, 18: 3050-3065. PMID: 35809166, PMCID: PMC9622518, DOI: 10.1007/s12015-022-10416-x.Peer-Reviewed Original ResearchConceptsDivergent gene expression profilesDefective DNA damage repairDisease modelingDNA damage repairGene expression profilesSpecific cell typesCell linesDura mater cellsDermal fibroblastsSomatic mutation signaturesPatient-derived cellsNormal biologyDamage repairExpression profilesSlow growth rateDifferentiation protocolsCell typesFibroblast-like cellsMutation signaturesProtein markersHuman dermal fibroblastsExhibit phenotypicNeurodegenerative diseasesDura materFibroblasts
2020
SCELLECTOR: ranking amplification bias in single cells using shallow sequencing
Sarangi V, Jourdon A, Bae T, Panda A, Vaccarino F, Abyzov A. SCELLECTOR: ranking amplification bias in single cells using shallow sequencing. BMC Bioinformatics 2020, 21: 521. PMID: 33183232, PMCID: PMC7663899, DOI: 10.1186/s12859-020-03858-y.Peer-Reviewed Original ResearchConceptsMultiple displacement amplificationShallow sequencingSingle-cell platformsSingle-cell sequencingCoverage sequencing dataSingle cellsHuman neuronal cellsMosaic mutationsAmount of DNAAmplification qualityCell sequencingCoverage sequencingHigh-coverage dataSequencing dataHaplotype informationPhi29 polymeraseDNA damageIndividual cellsNeuronal cellsSequencingAmplification biasAllelic imbalancePresence of sitesMutationsFragment lengthCell Lineage Tracing and Cellular Diversity in Humans
Abyzov A, Vaccarino FM. Cell Lineage Tracing and Cellular Diversity in Humans. Annual Review Of Genomics And Human Genetics 2020, 21: 101-116. PMID: 32413272, DOI: 10.1146/annurev-genom-083118-015241.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsCell DifferentiationCell LineageCell NucleusDevelopmental BiologyDNA MethylationDNA, MitochondrialEmbryo, MammalianHumansSingle-Cell AnalysisConceptsLineage tracingLineage mapCell lineage mapCell lineage tracingDNA methylation statusComplex biological processesMultiple cell typesMulticellular organismsCellular diversityMitochondrial DNALineage hierarchyCell lineagesBiological processesNatural variationCell typesMethylation statusLineagesNoncancerous cellsRecent studiesFetal developmentGeneral conceptual designCellsOrganismsHumansDNA
2012
Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells
Abyzov A, Mariani J, Palejev D, Zhang Y, Haney MS, Tomasini L, Ferrandino AF, Rosenberg Belmaker LA, Szekely A, Wilson M, Kocabas A, Calixto NE, Grigorenko EL, Huttner A, Chawarska K, Weissman S, Urban AE, Gerstein M, Vaccarino FM. Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature 2012, 492: 438-442. PMID: 23160490, PMCID: PMC3532053, DOI: 10.1038/nature11629.Peer-Reviewed Original Research