2021
Comprehensive identification of somatic nucleotide variants in human brain tissue
Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino F, Moran J, Urban A, Kidd J, Mills R, Abyzov A. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biology 2021, 22: 92. PMID: 33781308, PMCID: PMC8006362, DOI: 10.1186/s13059-021-02285-3.Peer-Reviewed Original ResearchConceptsSomatic SNVsSomatic single nucleotide variantsWhole-genome sequencing dataSequencing dataBulk DNA samplesCell lineage treesSomatic mosaicismSingle nucleotide variantsLineage treesSomatic nucleotide variantsCellular processesDNA replicationHuman genomeSomatic tissuesDNA repairNucleotide variantsComprehensive identificationDNA samplesMosaic variantsNon-cancerous tissuesDNASingle individualMultiple replicatesHuman brain tissueVariants
2015
The PsychENCODE project
Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N. The PsychENCODE project. Nature Neuroscience 2015, 18: 1707-1712. PMID: 26605881, PMCID: PMC4675669, DOI: 10.1038/nn.4156.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrainChromosome MappingEpigenesis, GeneticGenetic CodeHumansMental DisordersTranscriptome
1999
Identification, Chromosomal Assignment, and Expression Analysis of the Human Homeodomain-Containing Gene Orthopedia (OTP)
Lin X, State M, Vaccarino F, Greally J, Hass M, Leckman J. Identification, Chromosomal Assignment, and Expression Analysis of the Human Homeodomain-Containing Gene Orthopedia (OTP). Genomics 1999, 60: 96-104. PMID: 10458915, DOI: 10.1006/geno.1999.5882.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceBrainChromosome BandingChromosome MappingChromosomes, Human, Pair 5DNA, ComplementaryDrosophila ProteinsExonsGene ExpressionGene Expression Regulation, DevelopmentalGenesHomeodomain ProteinsHumansImmunohistochemistryIn Situ Hybridization, FluorescenceIntronsMolecular Sequence DataNerve Tissue ProteinsRatsRats, Sprague-DawleySequence AlignmentSequence Analysis, DNASequence Homology, Amino AcidConceptsHuman cDNAHuman homologueRadiation hybrid panel mappingDeduced amino acid sequenceHelix transcription factorOpen reading frameAmino acid sequenceHuman HomeodomainChromosomal assignmentHomeodomain genesCell fateGenomic libraryTranscription factorsHuman chromosomesReading frameGene productsAcid sequenceHD geneExpression analysisC-terminusYAC clonesNovel polyclonal antibodyOrthopediaCell migration patternsHuman fetal brain tissue
1996
Characterization and Sequence Analysis of the Human Homeobox-Containing GeneGBX2
Lin X, Swaroop A, Vaccarino F, Murtha M, Haas M, Ji X, Ruddle F, Leckman J. Characterization and Sequence Analysis of the Human Homeobox-Containing GeneGBX2. Genomics 1996, 31: 335-342. PMID: 8838315, DOI: 10.1006/geno.1996.0056.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceBrainCell LineChromosome MappingChromosomes, Human, Pair 2Cloning, MolecularDNA PrimersDNA, ComplementaryFemaleGene ExpressionGenomic LibraryHomeodomain ProteinsHumansMolecular Sequence DataPregnancyRodentiaSequence AnalysisSequence Homology, Amino AcidConceptsFetal brain cDNA libraryBrain cDNA libraryCDNA clonesCDNA librarySomatic cell hybrid analysisHuman fetal brain cDNA libraryCell hybrid analysisHuman genomic cloneAmino-terminal endAmino acid residuesHuman homeoboxesGenomic clonesHomologous genesGBX2 geneHomeobox genesCpG islandsNucleotide sequenceMouse embryosUntranslated regionProline residuesNorthern analysisAcid residuesSequence analysisGenesPolymerase chain reaction