2022
A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation
Yanchus C, Drucker K, Kollmeyer T, Tsai R, Winick-Ng W, Liang M, Malik A, Pawling J, De Lorenzo S, Ali A, Decker P, Kosel M, Panda A, Al-Zahrani K, Jiang L, Browning J, Lowden C, Geuenich M, Hernandez J, Gosio J, Ahmed M, Loganathan S, Berman J, Trcka D, Michealraj K, Fortin J, Carson B, Hollingsworth E, Jacinto S, Mazrooei P, Zhou L, Elia A, Lupien M, He H, Murphy D, Wang L, Abyzov A, Dennis J, Maass P, Campbell K, Wilson M, Lachance D, Wrensch M, Wiencke J, Mak T, Pennacchio L, Dickel D, Visel A, Wrana J, Taylor M, Zadeh G, Dirks P, Eckel-Passow J, Attisano L, Pombo A, Ida C, Kvon E, Jenkins R, Schramek D. A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation. Science 2022, 378: 68-78. PMID: 36201590, PMCID: PMC9926876, DOI: 10.1126/science.abj2890.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrain NeoplasmsChromosomes, Human, Pair 8GliomaHumansIsocitrate DehydrogenaseMiceMutationPolymorphism, Single NucleotideConceptsNoncoding single nucleotide polymorphismSingle nucleotide polymorphismsCausal variantsMolecular pathwaysIsocitrate dehydrogenaseLethal gliomaHeritable predispositionGlioma formationTumor developmentLow-grade gliomasMutant lower grade gliomasPolymorphismMouse modelPromoterLociEnhancerSixfold greater riskRs55705857PathwayMechanisticallyDehydrogenaseDisruptsExpressionPenetranceCancer risk
2020
Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH and FAM20C
Eckel-Passow J, Drucker K, Kollmeyer T, Kosel M, Decker P, Molinaro A, Rice T, Praska C, Clark L, Caron A, Abyzov A, Batzler A, Song J, Pekmezci M, Hansen H, McCoy L, Bracci P, Wiemels J, Wiencke J, Francis S, Burns T, Giannini C, Lachance D, Wrensch M, Jenkins R. Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH and FAM20C. Neuro-Oncology 2020, 22: 1602-1613. PMID: 32386320, PMCID: PMC7690366, DOI: 10.1093/neuonc/noaa117.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesGenome-wide p-value thresholdGlioma genome-wide association studiesElongation helicase 1Germline variantsChromosome 2Helicase 1Identifies variantsChromosome 7Association studiesChromosome 20Molecular subtypesMutationsGlioma molecular subtypesWild-type gliomasFAM20CDehydrogenase mutationsP-value thresholdPromoter mutationsAssociation of variantsIsocitrate dehydrogenase (IDH) mutationD2HGDHTelomerase reverse transcriptase (TERT) promoter mutationsNew regionsVariants
2008
MSB: A mean-shift-based approach for the analysis of structural variation in the genome
Wang LY, Abyzov A, Korbel JO, Snyder M, Gerstein M. MSB: A mean-shift-based approach for the analysis of structural variation in the genome. Genome Research 2008, 19: 106-117. PMID: 19037015, PMCID: PMC2612956, DOI: 10.1101/gr.080069.108.Peer-Reviewed Original ResearchConceptsProbability density functionNumber of segmentsGood parameter initializationLikelihood functionArray CGH experimentsKernel-based approachUnderlying distributionModel parametersParameter initializationParticular assumptionsNonparametric methodsExpectation maximizationComputational methodsConvergenceGlobal criterionLocal gradients