2024
Syndrome-informed phenotyping identifies a polygenic background for achondroplasia-like facial variation in the general population
Vanneste M, Hoskens H, Goovaerts S, Matthews H, Devine J, Aponte J, Cole J, Shriver M, Marazita M, Weinberg S, Walsh S, Richmond S, Klein O, Spritz R, Peeters H, Hallgrímsson B, Claes P. Syndrome-informed phenotyping identifies a polygenic background for achondroplasia-like facial variation in the general population. Nature Communications 2024, 15: 10458. PMID: 39622794, PMCID: PMC11612227, DOI: 10.1038/s41467-024-54839-1.Peer-Reviewed Original ResearchMeSH KeywordsAchondroplasiaAdolescentAdultAnimalsCase-Control StudiesChildFaceFemaleGenome-Wide Association StudyHumansMaleMiceMultifactorial InheritancePhenotypePolymorphism, Single NucleotideConceptsMultivariate GWASMendelian phenotypesComplex traitsPolygenic backgroundMendelian disordersPolygenic basisGenetic variationGenetic variantsGenetic intersectionAchondroplasia phenotypePhenotypic spectrumPhenotypeGenesSkeletal developmentShape axesCraniofacial shapeGWASFacial variationsThree-dimensional facial scansGeneral populationTraitsControl scoresVariationControl samplesVariantsA common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PKDCC during chondrogenesis
Mohammed J, Arora N, Matthews H, Hansen K, Bader M, Walsh S, Shaffer J, Weinberg S, Swigut T, Claes P, Selleri L, Wysocka J. A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PKDCC during chondrogenesis. ELife 2024, 13: e82564. PMID: 38483448, PMCID: PMC10939500, DOI: 10.7554/elife.82564.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle nucleotide polymorphismsGenome-wide association study studiesDisease predispositionComplex morphological traitsEmbryonic cell typesSkull elementsCognate enhancersAssociation studiesAssociated with quantitative changesPhenotypic traitsPhenotypic variationMorphological traitsJaw shapeNucleotide polymorphismsGenetic variantsMorphological variationTyrosine kinaseCell typesNormal rangeRisk of non-syndromic orofacial cleftsFacial morphogenesisNon-syndromic orofacial cleftsHuman populationSkeletal development
2023
Joint multi-ancestry and admixed GWAS reveals the complex genetics behind human cranial vault shape
Goovaerts S, Hoskens H, Eller R, Herrick N, Musolf A, Justice C, Yuan M, Naqvi S, Lee M, Vandermeulen D, Szabo-Rogers H, Romitti P, Boyadjiev S, Marazita M, Shaffer J, Shriver M, Wysocka J, Walsh S, Weinberg S, Claes P. Joint multi-ancestry and admixed GWAS reveals the complex genetics behind human cranial vault shape. Nature Communications 2023, 14: 7436. PMID: 37973980, PMCID: PMC10654897, DOI: 10.1038/s41467-023-43237-8.Peer-Reviewed Original ResearchILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications
Herrick N, Walsh S. ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications. BMC Bioinformatics 2023, 24: 424. PMID: 37940870, PMCID: PMC10633908, DOI: 10.1186/s12859-023-05548-x.Peer-Reviewed Original ResearchConceptsRaw genomic dataSoftware toolsHigh-performance computing clusterOwn big dataRaw data typesVariant call format filesOpen-source suiteBioinformatics software toolsDownstream applicationsDocker containersGenomic dataLocal machineComputing clusterBig dataConfiguration filesJob executionWindows platformData workflowIntermediate filesSingle commandFormat fileReproducible workflowsVCF filesData typesStorage limitations