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acronyms.tex
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\newacronym{IARC}{IARC}{International Agency for Research on Cancer}
\newacronym{DNA}{DNA}{Deoxyribonucleic acid}
\newacronym{RNA}{RNA}{Ribonucleic acid}
\newacronym{pre-mRNAs}{pre-mRNAs}{precursor messenger RNA}
\newacronym{TSG}{TSG}{Tumor Suppressor Genes}
\newacronym{lung NENs}{lung NENs}{lung neuroendocrine neoplasms}
\newacronym{LCNEC}{LCNEC}{Large Cell Neuroendocrine Carcinoma}
\newacronym{SCLC}{SCLC}{Small Cell Lung Cancer}
\newacronym{mRNAs}{mRNAs}{messenger RNAs}
\newacronym{miRNAs}{miRNAs}{micro RNAs}
\newacronym{CpG}{CpG}{cytosine–phosphate–guanine }
\newacronym{CML}{CML}{chronic myelogenous leukemia}
\newacronym{SNVs}{SNVs}{Single Nucleotide Variations}
\newacronym{SNP}{SNP}{Single Nucleotide Polymorphism}
\newacronym{LOH}{LOH}{loss of heterozygosity}
\newacronym{UV}{UV}{Ultraviolet}
\newacronym{indels}{indels}{insertions or deletions}
\newacronym{HGP}{HGP}{Human Genome Project}
\newacronym{GWAS}{GWAS}{Genome-Wide Association Studies}
\newacronym{LD}{LD}{linkage disequilibrium}
\newacronym{HapMap}{HapMap}{Haplotype Map project}
\newacronym{cDNA}{cDNA}{complementary DNA}
\newacronym{NGS}{NGS}{Next Generation Sequencing}
\newacronym{PCR}{PCR}{Polymerase Chain Reaction}
\newacronym{WGS}{WGS}{Whole Genome Sequencing}
\newacronym{WES}{WES}{Whole Exome Sequencing}
\newacronym{RNA-Seq}{RNA-Seq}{RNA Sequencing}
\newacronym{ATAC-seq}{ATAC-seq}{Assay of Transposase Accessible Chromatin sequencing}
\newacronym{ChiP-Seq}{ChiP-Seq}{Chromatin immunoprecipitation Sequencing}
\newacronym{TCGA}{TCGA}{The Cancer Genome Atlas}
\newacronym{NIH}{NIH}{National Institutes of Health}
\newacronym{RPPA}{RPPA}{Reverse-Phase Protein Array}
\newacronym{ICGC}{ICGC}{International Cancer Genome Consortium}
\newacronym{ISB-CGC}{ISB-CGC}{ISB Cancer Genomics Cloud}
\newacronym{PCAWG}{PCAWG}{Pan-Cancer Analysis of Whole Genomes}
\newacronym{MRI}{MRI}{Magnetic Resonance Imaging}
\newacronym{dbGAP}{dbGAP}{Database of Genotypes And Phenotypes}
\newacronym{EGA}{EGA}{European-Genome Phenome Archive}
\newacronym{GEO}{GEO}{Gene Expression Omnibus}
\newacronym{GDC}{GDC}{Genomic Data Common}
\newacronym{CGC}{CGC}{Cancer Genomics Cloud}
\newacronym{NCI}{NCI}{National Cancer Institute}
\newacronym{NSCLC}{NSCLC}{Non Small Cell Lung Cancer}
\newacronym{LUAD}{LUAD}{Lung Adenocarcinomas}
\newacronym{LUSC}{LUSC}{Lung Squamous Cell Carcinomas}
\newacronym{WHO}{WHO}{World Health Organization}
\newacronym{COSMIC}{COSMIC}{Catalogue Of Somatic Mutations In Cancer}
\newacronym{ctDNA}{ctDNA}{circulating tumor DNA}
\newacronym{EDA}{EDA}{exploratory data analyses}
\newacronym{ML}{ML}{machine learning}
\newacronym{PCA}{PCA}{Principal Component Analysis}
\newacronym{SVM}{SVM}{Support Vector Machines}
\newacronym{DR}{DR}{dimensionality reduction}
\newacronym{ICA}{ICA}{Independent Component Analysis}
\newacronym{NMF}{NMF}{Non-negative Matrix factorization}
\newacronym{t-SNE}{t-SNE}{t-Distributed Stochastic Neighbor Embedding}
\newacronym{UMAP}{UMAP}{Uniform Manifold Approximation and Projection}
\newacronym{MOFA}{MOFA}{Multi-Omics Factor Analysis}
\newacronym{PLS}{PLS}{Partial Least Squares}
\newacronym{PLS-DA}{PLS-DA}{PLS discriminant analysis}
\newacronym{DIABLO}{DIABLO}{Data Integration Analysis for Biomarker discovery using Latent cOmponents}
\newacronym{NEN}{NEN}{Neuroendocrine neoplasm}
\newacronym{LNEN}{LNEN}{Lung Neuroendocrine Neoplasm}
\newacronym{NET}{NET}{Neuroendocrine tumor}
\newacronym{NEC}{NEC}{Neuroendocrine carcinoma}
\newacronym{pan-LNEN}{pan-LNEN}{pan-cancer lung NEN}
\newacronym{GSEA}{GSEA}{Gene Set Enrichment Analyses}
\newacronym{MHC}{MHC}{Major Histocompatibility Complex }
\newacronym{FAIR}{FAIR}{Findable, Accessible, Interoperable, Reusable}
\newacronym{QC}{QC}{quality controls}
\newacronym{SD}{SD}{sequence difference}
\newacronym{PC}{PC}{principal components}
\newacronym{MI}{MI}{Moran index}
\newacronym{FFPE}{FFPE}{Formalin-Fixed Paraffin-Embedded}
\newacronym{TWAS}{TWAS}{transcriptome-wide association study}
\newacronym{eQTL}{eQTL}{expression quantitative trait loci}
\newacronym{PRS}{PRS}{Polygenic Risk Scores }
\newacronym{gw-SNPs}{gw-SNPs}{genome-wide significant SNPs}
\newacronym{GTEx}{GTEx}{Genotype-Tissue Expression}
\newacronym{APT}{APT}{Affymetrix Power Tools}
\newacronym{BRCA}{BRCA}{Breast Invasive Carcinoma}
\newacronym{MAF}{MAF}{Minor Allele Frequency}
\newacronym{maf}{maf}{Mutation Annotation Format}
\newacronym{MC3}{MC3}{Multi-Center Mutation Calling in Multiple Cancers}
\newacronym{AF}{AF}{Alternative frequency}
\newacronym{IGSR}{IGSR}{International Genome Sample Resource}
\newacronym{VCF}{VCF}{Variant Call Format}
\newacronym{BCF}{BCF}{Binary Variant Call Format,}
\newacronym{TRICL-ILCCO}{TRICL-ILCCO}{Transdisciplinary Research of Cancer in Lung of the International Lung Cancer Consortium}
\newacronym{GWAx}{GWAx}{family history GWAS}
\newacronym{GSCAN}{GSCAN}{GWAS & Sequencing Consortium of Alcohol and Nicotine}
\newacronym{NNLS}{NNLS}{non-negative least squares}
\newacronym{GSVA}{GSVA}{Gene Set Variation Analysis}
\newacronym{MR}{MR}{Mendelian Randomization}
\newacronym{RCT}{RCT}{Randomized Control Trials}
\newacronym{CPD}{CPD}{cigarettes per day}
\newacronym{SmkCes}{SmkCes}{smoking cessation}
\newacronym{SmkInit}{SmkInit}{smoking initiation}
\newacronym{AgeInit}{AgeInit}{age of initiation}
\newacronym{MTAG}{MTAG}{Multi-trait Analysis of GWAS}
\newacronym{COPD}{COPD}{chronic obstructive pulmonary disease}
\newacronym{BMI}{BMI}{Body Mass Index}
\newacronym{MSI}{MSI}{Microsatellite Instability}
\newacronym{ELMER}{ELMER}{Enhancer Linking by Methylation/Expression Relationships}
\newacronym{FEV}{FEV}{Forced Expiratory Volume}
\newacronym{TRACERx}{TRACERx}{Tracking Cancer Evolution through Therapy}
\newacronym{ICGC-ARGO}{ICGC-ARGO}{Accelerate Research in Genomic Oncology}
\newacronym{GeCIP}{GeCIP}{Genomics England Clinical Interpretation Partnership}
\newacronym{CGI}{CGI}{Cancer Genome Interpreter }
\newacronym{CVCDAP}{CVCDAP}{Cancer Virtual Cohort Discovery Analysis Platform}
\newacronym{B1MG}{B1MG}{Beyond 1 Million Genomes}
\newacronym{GA4GH}{GA4GH}{Global Alliance for Genomics and Health}
\newacronym{GDPR}{GDPR}{General Data Protection Regulation}
\newacronym{GATK}{GATK}{Genome Analysis Toolkit}
\newacronym{BAM}{BAM}{Binary Alignment Map}
\newacronym{IVW}{IVW}{Inverse Variance Weighted}
\newacronym{IREB2}{IREB2}{Iron Responsive Element Binding Protein 2}
\newacronym{CHRNA5}{CHRNA5}{Cholinergic Receptor Nicotinic Alpha 5 Subunit}
\newacronym{CHRNA3}{CHRNA3}{Cholinergic Receptor Nicotinic Alpha 3 Subunit}
\newacronym{CHRNB4}{CHRNB4}{Cholinergic Receptor Nicotinic Beta 4 Subunit}
\newacronym{EGFR}{EGFR}{Epidermal Growth Factor Receptor}
\newacronym{EGFR}{EGFR}{Epidermal Growth Factor Receptor}
\newacronym{DLL3}{DLL3}{Delta Like Canonical Notch Ligand 3}
\newacronym{OTP}{OTP}{Orthopedia Homeobox}
\newacronym{ALK}{ALK}{ALK Receptor Tyrosine Kinase}