Elevated 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 formationDeletionA uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals
Chen J, Rozowsky J, Galeev TR, Harmanci A, Kitchen R, Bedford J, Abyzov A, Kong Y, Regan L, Gerstein M. A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals. Nature Communications 2016, 7: 11101. PMID: 27089393, PMCID: PMC4837449, DOI: 10.1038/ncomms11101.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBinding SitesChromosome MappingComputational BiologyDatabases, GeneticGene ExpressionGene FrequencyGenome, HumanGenomicsGenotypeHigh-Throughput Nucleotide SequencingHuman Genome ProjectHumansInternetMolecular Sequence AnnotationPolymorphism, Single NucleotidePrecision MedicineConceptsSingle nucleotide variantsAllele-specific bindingFunctional genomics data setsAllele-specific behaviorLarge-scale sequencingGenomic data setsAllelic imbalanceNumber of readsChIP-seqRNA-seqGenome ProjectMaternal chromosomesNucleotide variantsPersonal genomesMapping biasAllelic variantsVariant catalogMultiple individualsFunctional effectsProject individualsBindingExpressionVariantsGenomeChromosomesTesting of candidate single nucleotide variants associated with paclitaxel neuropathy in the trial NCCTG N08C1 (Alliance)
Boora G, Kanwar R, Kulkarni A, Abyzov A, Sloan J, Ruddy K, Banck M, Loprinzi C, Beutler A. Testing of candidate single nucleotide variants associated with paclitaxel neuropathy in the trial NCCTG N08C1 (Alliance). Cancer Medicine 2016, 5: 631-639. PMID: 26763541, PMCID: PMC4831281, DOI: 10.1002/cam4.625.Peer-Reviewed Original ResearchConceptsPaclitaxel-induced peripheral neuropathyProtective effectAdditional clinical cohortsSingle nucleotide variantsPrevious reportsGene CYP2C8Pharmacogenomic basisPeripheral neuropathyClinical parametersOdds ratioClinical cohortNucleotide variantsCandidate single nucleotide variantsMultiple studiesHigher likelihoodTaqMan PCRCYP2C8AssociationSequencing analysisRisk effectsSubset of findingsReportNeuropathyPrevious studiesPatients