Search results for "Hla expression"

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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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In Silico HLA Typing Using Standard RNA-Seq Sequence Reads

2015

Next-generation sequencing (NGS) enables high-throughput transcriptome profi ling using the RNA-Seq assay, resulting in billions of short sequence reads. Worldwide adoption has been rapid: many laboratories worldwide generate transcriptome sequence reads daily. Here, we describe methods for obtaining a sample’s human leukocyte antigen (HLA) class I and II types and HLA expression using standard NGS RNA- Seq sequence reads. We demonstrate the application using our algorithm, seq2HLA, and a publicly available RNA-Seq dataset from the Burkitt lymphoma cell line Raji.

TranscriptomeGeneticsIn silicoRNARNA-SeqHuman leukocyte antigenHla expressionBiologySequence (medicine)
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