Search results for "SNV"

showing 3 items of 3 documents

A catalog of HLA type, HLA expression, and neo-epitope candidates in human cancer cell lines

2014

Cancer cell lines are a tremendous resource for cancer biology and therapy development. These multipurpose tools are commonly used to examine the genetic origin of cancers, to identify potential novel tumor targets, such as tumor antigens for vaccine devel-opment, and utilized to screen potential therapies in preclinical studies. Mutations, gene expression, and drug sensitivity have been determined for many cell lines using next-generation sequencing (NGS). However, the human leukocyte antigen (HLA) type and HLA expression of tumor cell lines, characterizations necessary for the development of cancer vaccines, have remained largely incomplete and, such information, when available, has been …

HLA typeCCLE Cancer Cell Line Encyclopediamedicine.medical_treatmentCOSMIC Catalog of Somatic Mutations in CancerImmunologyBRENDA BRaunschweig ENzyme DatabaseSNV single nucleotide variationRNA-SeqHuman leukocyte antigenBiologynsSNV non synonymous SNVTranscriptomeLoss of heterozygosityAntigenGenotypemedicineImmunology and AllergyRNA-SeqRNA-Seq RNA SequencingOriginal ResearchGeneticsHLA expressionneoepitopescancer cell linesSRA Sequence Read ArchiveCancerImmunotherapymedicine.diseaseHLA Human Leukocyte AntigenOncologyRPKM reads per kilobase of exon model per million mapped readsIEDB Immune Epitope Databasesomatic mutationsimmunotherapyDLBCL diffuse large B-cell lymphomaNGS Next Generation SequencingOncoImmunology
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SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations

2016

Various approaches to calling single-nucleotide variants (SNVs) or insertion-or-deletion (indel) mutations have been developed based on next-generation sequencing (NGS). However, most of them are dedicated to a particular type of mutation, e.g. germline SNVs in normal cells, somatic SNVs in cancer/tumor cells, or indels only. In the literature, efficient and integrated callers for both germline and somatic SNVs/indels have not yet been extensively investigated. We present SNVSniffer, an efficient and integrated caller identifying both germline and somatic SNVs/indels from NGS data. In this algorithm, we propose the use of Bayesian probabilistic models to identify SNVs and investigate a mult…

0301 basic medicineSomatic cellBayesian probabilityBiologyPolymorphism Single NucleotideGermline03 medical and health sciencesGene FrequencyINDEL MutationStructural BiologyModelling and SimulationIndel callingGenetic variationHumansAlleleIndelMolecular BiologyOvarian NeoplasmsGeneticsResearchApplied MathematicsComputational BiologyHigh-Throughput Nucleotide SequencingSNP callingSomatic SNV callingCystadenocarcinoma SerousComputer Science ApplicationsGerm Cells030104 developmental biologyBayesian modelModeling and SimulationMutation (genetic algorithm)FemaleMultinomial distributionAlgorithmsBMC Systems Biology
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Interim Report on the Research Phase

1993

This is the report of one year of interdisciplinary team research in preparation of the Dassenetch Integrated Development Program (DIDP), SNV (Netherlands Development Organization) – ETHIOPIA

Omo deltaDassenetchSNVEthiopiaSettore M-DEA/01 - Discipline DemoetnoantropologicheOmo Valley
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