2023
Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study
Abdi M, Aliyev E, Trost B, Kohailan M, Aamer W, Syed N, Shaath R, Gandhi G, Engchuan W, Howe J, Thiruvahindrapuram B, Geng M, Whitney J, Syed A, Lakshmi J, Hussein S, Albashir N, Hussein A, Poggiolini I, Elhag S, Palaniswamy S, Kambouris M, de Fatima Janjua M, Tahir M, Nazeer A, Shahwar D, Azeem M, Mokrab Y, Aati N, Akil A, Scherer S, Kamal M, Fakhro K. Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study. Genome Medicine 2023, 15: 81. PMID: 37805537, PMCID: PMC10560429, DOI: 10.1186/s13073-023-01228-w.Peer-Reviewed Original ResearchConceptsTandem repeat expansionsSingle nucleotide variantsGenetic architectureNovel ASD candidate genesWhole-genome sequencing dataMitochondrial DNA variantsASD candidate genesMulti-omics researchGenomic architectureRecessive variationMtDNA variantsCandidate genesDNA variantsSequencing dataRepeat expansionNumber variantsSNVs/indelsDe novoNon-consanguineous familyGenesGenetics guidelinesUnique resourcePathogenic variantsFamilyMedical Genetics guidelinesBeyond the Global Brain Differences: Intraindividual Variability Differences in 1q21.1 Distal and 15q11.2 BP1-BP2 Deletion Carriers
Boen R, Kaufmann T, van der Meer D, Frei O, Agartz I, Ames D, Andersson M, Armstrong N, Artiges E, Atkins J, Bauer J, Benedetti F, Boomsma D, Brodaty H, Brosch K, Buckner R, Cairns M, Calhoun V, Caspers S, Cichon S, Corvin A, Crespo-Facorro B, Dannlowski U, David F, de Geus E, de Zubicaray G, Desrivières S, Doherty J, Donohoe G, Ehrlich S, Eising E, Espeseth T, Fisher S, Forstner A, Fortaner-Uyà L, Frouin V, Fukunaga M, Ge T, Glahn D, Goltermann J, Grabe H, Green M, Groenewold N, Grotegerd D, Grøntvedt G, Hahn T, Hashimoto R, Hehir-Kwa J, Henskens F, Holmes A, Håberg A, Haavik J, Jacquemont S, Jansen A, Jockwitz C, Jönsson E, Kikuchi M, Kircher T, Kumar K, Le Hellard S, Leu C, Linden D, Liu J, Loughnan R, Mather K, McMahon K, McRae A, Medland S, Meinert S, Moreau C, Morris D, Mowry B, Mühleisen T, Nenadić I, Nöthen M, Nyberg L, Ophoff R, Owen M, Pantelis C, Paolini M, Paus T, Pausova Z, Persson K, Quidé Y, Marques T, Sachdev P, Sando S, Schall U, Scott R, Selbæk G, Shumskaya E, Silva A, Sisodiya S, Stein F, Stein D, Straube B, Streit F, Strike L, Teumer A, Teutenberg L, Thalamuthu A, Tooney P, Tordesillas-Gutierrez D, Trollor J, van ’t Ent D, van den Bree M, van Haren N, Vázquez-Bourgon J, Völzke H, Wen W, Wittfeld K, Ching C, Westlye L, Thompson P, Bearden C, Selmer K, Alnæs D, Andreassen O, Sønderby I, Group E. Beyond the Global Brain Differences: Intraindividual Variability Differences in 1q21.1 Distal and 15q11.2 BP1-BP2 Deletion Carriers. Biological Psychiatry 2023, 95: 147-160. PMID: 37661008, PMCID: PMC7615370, DOI: 10.1016/j.biopsych.2023.08.018.Peer-Reviewed Original ResearchConceptsMedial visual cortexCortical surface areaBrain differencesCortical thicknessTemporal poleVisual cortexDeletion carriersGlobal brain measuresRegional brain differencesCopy number variantsSuperior temporal cortexSomatosensory cortexBrain valuesAltered neurodevelopmentAuditory cortexGlobal differencesRegional differencesTemporal cortexNumber variantsPosterior cingulateCortexBrain structuresBrain measuresStandardized differenceNoncarriersCopy number variants and fetal structural abnormalities in stillborn fetuses: A secondary analysis of the Stillbirth Collaborative Research Network study
Workalemahu T, Dalton S, Son S, Allshouse A, Carey A, Page J, Blue N, Thorsten V, Goldenberg R, Pinar H, Reddy U, Silver R. Copy number variants and fetal structural abnormalities in stillborn fetuses: A secondary analysis of the Stillbirth Collaborative Research Network study. BJOG An International Journal Of Obstetrics & Gynaecology 2023, 131: 157-162. PMID: 37264725, PMCID: PMC10689565, DOI: 10.1111/1471-0528.17561.Peer-Reviewed Original ResearchConceptsCopy number variantsFetal structural malformationsAbnormal copy number variantsNumber variantsSingle nucleotide polymorphism arrayResearch Network StudyStillbirth casesDNA copy number variantsSpecific copy number variantsCardiac defectsPolymorphism arrayStructural malformationsSecondary analysisCraniofacial defectsGenesSpecific malformation typesFetal structural abnormalitiesWald chi-square testUnknown clinical significanceChi-square testKbSkeletal defectsBenign copy number variantsPathogenic deletionsClinical significanceEstimation on risk of spontaneous abortions by genomic disorders from a meta‐analysis of microarray results on large case series of pregnancy losses
Peng G, Zhou Q, Chai H, Wen J, Zhao H, Taylor H, Jiang Y, Li P. Estimation on risk of spontaneous abortions by genomic disorders from a meta‐analysis of microarray results on large case series of pregnancy losses. Molecular Genetics & Genomic Medicine 2023, 11: e2181. PMID: 37013615, PMCID: PMC10422064, DOI: 10.1002/mgg3.2181.Peer-Reviewed Original ResearchConceptsGenomic disordersChromosome microarray analysisWilliams-Beuren syndromePathogenic copy number variantsPopulation genetic studiesWolf-Hirschhorn syndromeCopy number variantsDiGeorge syndromeMicroarray analysisMicroarray resultsChromosomal abnormalitiesGenetic studiesNumber variantsGenetic counseling
2022
Copy number variants and fetal growth in stillbirths
Dalton S, Workalemahu T, Allshouse A, Page J, Reddy U, Saade G, Pinar H, Goldenberg R, Dudley D, Silver R. Copy number variants and fetal growth in stillbirths. American Journal Of Obstetrics And Gynecology 2022, 228: 579.e1-579.e11. PMID: 36356697, PMCID: PMC10149588, DOI: 10.1016/j.ajog.2022.11.1274.Peer-Reviewed Original ResearchConceptsAbnormal copy number variantsFetal growth abnormalitiesGestational ageOdds ratioStillbirth Collaborative Research NetworkGenetic abnormalitiesChromosomal microarrayGestational age outcomesGestational age infantsGrowth abnormalitiesClinical risk factorsCohort study designAdjusted odds ratioCopy number variantsUnknown clinical significancePathogenic copy number variantsPlacental insufficiencyAge infantsNumber variantsFetal growthMaternal ageRisk factorsClinical significanceHigh incidenceStillbirth
2021
An 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 toolkitIndelsGenesLociVariantsRole of candidate gene variants in modulating the risk and severity of alcoholic hepatitis
Beaudoin JJ, Liang T, Tang Q, Banini BA, Shah VH, Sanyal AJ, Chalasani NP, Gawrieh S. Role of candidate gene variants in modulating the risk and severity of alcoholic hepatitis. Alcohol Clinical And Experimental Research 2021, 45: 709-719. PMID: 33616244, PMCID: PMC8076096, DOI: 10.1111/acer.14581.Peer-Reviewed Original ResearchConceptsPatatin-like phospholipase domain-containing protein 3Effects of variantsCopy number variantsAcyltransferase domainDomain-containing protein 3Genetic basisCandidate genesCandidate gene variantsGenetic variantsNumber variantsHaptoglobin geneIndividual variantsProtein 3Member 2AllelesGenesGene variantsRisk allelesTransmembrane 6Affected individualsVariantsAssociation of structural variation with cardiometabolic traits in Finns
Chen L, Abel HJ, Das I, Larson DE, Ganel L, Kanchi KL, Regier AA, Young EP, Kang CJ, Scott AJ, Chiang C, Wang X, Lu S, Christ R, Service SK, Chiang CWK, Havulinna AS, Kuusisto J, Boehnke M, Laakso M, Palotie A, Ripatti S, Freimer NB, Locke AE, Stitziel NO, Hall IM. Association of structural variation with cardiometabolic traits in Finns. American Journal Of Human Genetics 2021, 108: 583-596. PMID: 33798444, PMCID: PMC8059371, DOI: 10.1016/j.ajhg.2021.03.008.Peer-Reviewed Original ResearchMeSH KeywordsAllelesCardiovascular DiseasesCholesterolDNA Copy Number VariationsFemaleFinlandGenome, HumanGenomic Structural VariationGenotypeHigh-Throughput Nucleotide SequencingHumansMaleMitochondrial ProteinsPromoter Regions, GeneticPyruvate Dehydrogenase (Lipoamide)-PhosphatasePyruvic AcidSerum Albumin, HumanConceptsSingle nucleotide variantsCopy number variantsQuantitative traitsGenome-wide significant associationStructural variationsTrait mapping studiesDeep whole-genome sequencing dataGenome structural variationsWhole-genome sequencing dataStrong phenotypic effectsComplex genomic regionsCardiometabolic traitsLow-frequency structural variationsEvolutionary timeGenomic regionsPhenotypic effectsSequencing dataNucleotide variantsGenotype dataGene deletionNumber variantsTraitsGenetic associationCandidate associationsExome sequencingAn 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
Complex 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 variants
2019
Integrated FISH, Karyotyping and aCGH Analyses for Effective Prenatal Diagnosis of Common Aneuploidies and Other Cytogenomic Abnormalities
Chai H, DiAdamo A, Grommisch B, Boyle J, Amato K, Wang D, Wen J, Li P. Integrated FISH, Karyotyping and aCGH Analyses for Effective Prenatal Diagnosis of Common Aneuploidies and Other Cytogenomic Abnormalities. Medical Sciences 2019, 7: 16. PMID: 30678103, PMCID: PMC6410168, DOI: 10.3390/medsci7020016.Peer-Reviewed Original ResearchArray comparative genomic hybridizationPathogenic copy number variantsMosaic patternStructural chromosomal rearrangementsChromosomal structural rearrangementsCopy number variantsComparative genomic hybridizationChromosomal rearrangementsGenomic imbalancesCommon aneuploidiesNumber variantsCellular proliferationIntegrated fishGenomic hybridizationFishSitu hybridizationStructural rearrangementsReflex FISHStructural chromosomal abnormalitiesSex chromosome aneuploidyACGH analysisChromosome aneuploidyAneuploidyCell culturesHybridization
2018
Genetic Basis for Congenital Heart Disease: Revisited: A Scientific Statement From the American Heart Association
Pierpont ME, Brueckner M, Chung WK, Garg V, Lacro RV, McGuire AL, Mital S, Priest JR, Pu WT, Roberts A, Ware SM, Gelb BD, Russell MW, Medicine O. Genetic Basis for Congenital Heart Disease: Revisited: A Scientific Statement From the American Heart Association. Circulation 2018, 138: 1. PMID: 30571578, PMCID: PMC6555769, DOI: 10.1161/cir.0000000000000606.Peer-Reviewed Original ResearchDe Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis
Wang S, Mandell JD, Kumar Y, Sun N, Morris MT, Arbelaez J, Nasello C, Dong S, Duhn C, Zhao X, Yang Z, Padmanabhuni SS, Yu D, King RA, Dietrich A, Khalifa N, Dahl N, Huang AY, Neale BM, Coppola G, Mathews CA, Scharf JM, Study T, Abdulkadir M, Arbelaez J, Bodmer B, Bromberg Y, Brown L, Cheon K, Coffey B, Deng L, Dietrich A, Dong S, Duhn C, Elzerman L, Fernandez T, Fremer C, Garcia-Delgar B, Gilbert D, Grice D, Hagstrøm J, Hedderly T, Heiman G, Heyman I, Hoekstra P, Hong H, Huyser C, Kim E, Kim Y, Kim Y, King R, Koh Y, Kook S, Kuperman S, Leventhal B, Ludolph A, Madruga-Garrido M, Mandell J, Maras A, Mir P, Morer A, Morris M, Müller-Vahl K, Münchau A, Murphy T, Nasello C, Plessen K, Poisner H, Roessner V, Sanders S, Shin E, Song D, Song J, State M, Sun N, Thackray J, Tischfield J, Tübing J, Visscher F, Wanderer S, Wang S, Willsey A, Woods M, Xing J, Zhang Y, Zhao X, Zinner S, Initiative T, Androutsos C, Barta C, Farkas L, Fichna J, Georgitsi M, Janik P, Karagiannidis I, Koumoula A, Nagy P, Paschou P, Puchala J, Rizzo R, Szejko N, Szymanska U, Tarnok Z, Tsironi V, Wolanczyk T, Zekanowski C, Genetics T, Barr C, Batterson J, Berlin C, Bruun R, Budman C, Cath D, Chouinard S, Coppola G, Cox N, Darrow S, Davis L, Dion Y, Freimer N, Grados M, Hirschtritt M, Huang A, Illmann C, Kurlan R, Leckman J, Lyon G, Malaty I, Mathews C, MacMahon W, Neale B, Okun M, Osiecki L, Pauls D, Posthuma D, Ramensky V, Robertson M, Rouleau G, Sandor P, Scharf J, Singer H, Smit J, Sul J, Yu D, Fernandez T, Buxbaum J, De Rubeis S, Grice D, Xing J, Heiman G, Tischfield J, Paschou P, Willsey A, State M. De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis. Cell Reports 2018, 24: 3441-3454.e12. PMID: 30257206, PMCID: PMC6475626, DOI: 10.1016/j.celrep.2018.08.082.Peer-Reviewed Original ResearchConceptsCell polarityNumber variantsSequence variantsDe novo damaging variantsDe novoDe novo sequencesCopy number variantsNovo sequencesWhole-exome sequencingDamaging variantsRisk genesGenesCommon pathwayNovoSignificant overlapVariantsTriosGenetic riskSequencingCELSR3PathwayPolaritySequenceSignificant excessFamily17p12 Influences Hematoma Volume and Outcome in Spontaneous Intracerebral Hemorrhage
Marini S, Devan WJ, Radmanesh F, Miyares L, Poterba T, Hansen BM, Norrving B, Jimenez-Conde J, Giralt-Steinhauer E, Elosua R, Cuadrado-Godia E, Soriano C, Roquer J, Kourkoulis CE, Ayres AM, Schwab K, Tirschwell DL, Selim M, Brown DL, Silliman SL, Worrall BB, Meschia JF, Kidwell CS, Montaner J, Fernandez-Cadenas I, Delgado P, Greenberg SM, Lindgren A, Matouk C, Sheth KN, Woo D, Anderson CD, Rosand J, Falcone GJ. 17p12 Influences Hematoma Volume and Outcome in Spontaneous Intracerebral Hemorrhage. Stroke 2018, 49: 1618-1625. PMID: 29915124, PMCID: PMC6085089, DOI: 10.1161/strokeaha.117.020091.Peer-Reviewed Original ResearchConceptsAssociation studiesGenome-wide association studiesNumerous copy number variantsSusceptibility risk lociWide association studyNovel biological pathwaysGenomic regionsIntergenic regionCopy number variantsRisk lociBiological pathwaysSusceptibility lociAssociation testingGenetic variantsNumber variantsEuropean ancestryLociReplicationDiscovery phaseVariantsAncestryImportant determinantPathwayTranslational studiesQuality control
2017
Dissecting Pathway Disturbances Using Network Topology and Multi-platform Genomics Data
Zhang Y, Linder M, Shojaie A, Ouyang Z, Shen R, Baggerly K, Baladandayuthapani V, Zhao H. Dissecting Pathway Disturbances Using Network Topology and Multi-platform Genomics Data. Statistics In Biosciences 2017, 10: 86-106. PMID: 37388623, PMCID: PMC10309155, DOI: 10.1007/s12561-017-9193-0.Peer-Reviewed Original ResearchMolecular regulatory elementsCopy number variantsRegulatory elementsMRNA moleculesPathway-based analysisBRAF pathwayCancer Genome Atlas (TCGA) projectMultiple tumor lineagesTumor-specific aberrationsRegulatory topologyRelevant copy number variantsDiverse cancer typesMultiple omicsGenomic dataMajor geneCancer typesGene expressionSingle-platform analysisOncogenic pathwaysNumber variantsMethylationComplex diseasesTumor lineageAtlas projectPathway
2016
Patterns of genic intolerance of rare copy number variation in 59,898 human exomes
Ruderfer DM, Hamamsy T, Lek M, Karczewski KJ, Kavanagh D, Samocha KE, Daly M, MacArthur D, Fromer M, Purcell S. Patterns of genic intolerance of rare copy number variation in 59,898 human exomes. Nature Genetics 2016, 48: 1107-1111. PMID: 27533299, PMCID: PMC5042837, DOI: 10.1038/ng.3638.Peer-Reviewed Original ResearchConceptsGenic copy number variantsHuman genetic variationExome Aggregation ConsortiumRare copy number variationsCopy number variationsCopy number variantsExome sequencing dataGenetic variationGenic intoleranceHuman exomeSequencing dataPersonal genomesNumber variationsNumber variantsGenomeIntegrated databaseExomeVariationVariantsConsortiumElevated variant density around SV breakpoints in germline lineage lends support to error-prone replication hypothesis
Dhokarh D, Abyzov A. Elevated variant density around SV breakpoints in germline lineage lends support to error-prone replication hypothesis. Genome Research 2016, 26: 874-881. PMID: 27216746, PMCID: PMC4937565, DOI: 10.1101/gr.205484.116.Peer-Reviewed Original ResearchConceptsSNPs/indelsComplex genomic rearrangementsHundreds of lociComplex human traitsAllele frequency spectrumReplication-based mechanismsBreakpoints of deletionsGermline lineageParental genomesSV breakpointsGenomic rearrangementsGenome ProjectMutational mechanismsDeletion eventsGenomic disordersHeterozygous SNPsStructural variantsVariant densityHuman traitsIndelsNumber variantsFold changeGermline deletionCNV formationDeletionRecurrent genetic defects in classical Hodgkin lymphoma cell lines
Hudnall SD, Meng H, Lozovatsky L, Li P, Strout M, Kleinstein SH. Recurrent genetic defects in classical Hodgkin lymphoma cell lines. Leukemia & Lymphoma 2016, 57: 2890-2900. PMID: 27121023, DOI: 10.1080/10428194.2016.1177179.Peer-Reviewed Original ResearchConceptsMitosis-related genesSingle nucleotide variantsCHL cell linesCell linesRecurrent genetic defectsPathogenic single nucleotide variantsHL cell linesMitotic genesChromosome duplicationClassical Hodgkin lymphoma cell linesGenomic instabilityGenetic analysisWhole-exome sequencingNucleotide variantsGenesHodgkin's lymphoma cell linesLymphoma cell linesNumber variantsKaryotypic analysisGenetic defectsWealth of informationPoor growthVariantsDuplicationLinesSpectrum of Cytogenomic Abnormalities Revealed by Array Comparative Genomic Hybridization on Products of Conception Culture Failure and Normal Karyotype Samples
Zhou Q, Wu SY, Amato K, DiAdamo A, Li P. Spectrum of Cytogenomic Abnormalities Revealed by Array Comparative Genomic Hybridization on Products of Conception Culture Failure and Normal Karyotype Samples. Journal Of Genetics And Genomics 2016, 43: 121-131. PMID: 27020032, DOI: 10.1016/j.jgg.2016.02.002.Peer-Reviewed Original ResearchConceptsCopy number variantsIngenuity Pathway AnalysisPathogenic copy number variantsDosage-sensitive genesCell proliferation pathwaysGenomic copy number variantsArray comparative genomic hybridizationGene networksComparative genomic hybridization analysisComparative genomic hybridizationPathway analysisGenomic hybridization analysisChromosomal abnormalitiesHybridization analysisProliferation pathwaysArray comparative genomic hybridization analysisNumber variantsGenomic hybridizationSitu hybridizationGenesHybridizationCytogenomic abnormalitiesCulture successPolyploidySensitive mechanism
2015
Introduction to statistical methods in genome-wide association studies
Yang C, Li C, Chung D, Chen M, Gelernter J, Zhao H. Introduction to statistical methods in genome-wide association studies. 2015, 26-52. DOI: 10.1017/cbo9781107337459.005.Peer-Reviewed Original ResearchGenome-wide association studiesAssociation studiesPopulation genomic studiesQuantitative trait lociComplex diseasesTrait lociGenomic studiesSingle nucleotide polymorphismsGenetic basisNumber variantsNucleotide polymorphismsPharmaceutical potentialUnique resourceGenomicsLociBroad impactHaplotypesStatistical methodsPolymorphismVariantsPharmacogenomics
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