EGAGenomicsOtherhttps://ega-archive.org/studies/EGAS00001003387EGAEGA study EGAS00001003387clonealign: 10X genomics chromium single-cell RNA-sequencingEGArestrictedRNA, dTAF[[II]]230, TAF[[II]]250, d230, RNA Sequence Determination, RNA Sequence Determinations, Heterograft, Sequence Determination, RNA Sequence, TAF200, Genome Sequencing, l(3)84Ab, dTAFII250, BG:DS00004.13, TRANSPL HETEROL, TAFII-250, TAF250/230, Transplantations, EfW1, Client, Cell, Determinations, dTAF230, dmTAF[[II]]230, TAFII250, Complete Genome, XENOTRANSPL, heterologous transplantation., dmTAF1, Taf230, p230, TAF[[II]]250/230, TFIID, Analysis, Heterologous Transplantations, TAF250, Taf[[II]]250, Xenograft, Taf200, Complete, Xenotransplantation, dTAF[[II]]250, TAF[[II]]230, Whole Genome, TFIID TAF250, Analyses, Transplantation, cel, Determination, cell, Complete Genome Sequencing, Heterografts, Taf1p, HETEROL TRANSPL, TAF[II]250, patient, Xenografts, CG17603, TAF[[II]], Sequence Determinations, Sequencing, sample population, dTAF250, DmelCG17603, Xenotransplantations, Taf250, RNA Sequence Analyses, Patient, SR3-5, Clients, RNA Sequence Analysis, Whole, sample, xenotransplant, RNA Sequencing, TAF, TAF230, Heterologous, TAF1, Sequence AnalysesPopulation Explosions, triple-receptor negative breast cancer, Ribonucleic, determination, Breast Neoplasms, Heterograft, Gene Expression Profile, Past, Profiles, TRANSPL HETEROL, Tumor, TNBC, dmTAF[[II]]230, triple-negative breast cancer, School-Age, Techniques, relapse, sampling, Method, Associations, triple-negative breast carcinoma, Relapses, Non Polyadenylated, RNA Gene Products, Growth, thymus nucleic acid, Gene Expressions, TFIID TAF250, Genomes, Triple Negative Breast Cancer, cel, Natural, Breast Cancers, Recurrences, procedures, Signatures, Xenotransplantations, Methodological Studies, Expression Signature, malignant neoplasm, scientific observation, Transcriptomes, Double-Stranded DNA, Malignancies, deoxyribonucleic acids, DNAn, Tumors, Relapse, dTAF[[II]]230, Baby Bust, ribose nucleic acid, Expression Profiles, ribonucleic acids, TAF200, Triple-Negative Breast Cancer, RNA-seq, Double-Stranded, TAFII-250, Procedure, TAF250/230, (Deoxyribonucleotide)n+m, High Fertility, Gene Expression, TAFII250, Benign, Recrudescence, School Age, Ribonukleinsaeure, Expression Signatures, pentosenucleic acids, Triple-Negative, Ribonucleic acids, desoxyribose nucleic acid, Expression Profile, Heterologous Transplantations, Transcriptome Profiles, DNA sequencing, Acid, Xenograft, Populations, Past Trend, Triple-Negative Breast Neoplasms, absence, Xenotransplantation, ER Negative PR Negative HER2 Negative Breast Cancer, Transplantation, Zero Population Growth, ER-Negative PR-Negative HER2-Negative Breast Neoplasms, Heterogeneity, Benign Neoplasms, Methodological, whole genome, Xenografts, CG17603, TAF[[II]], Methodological Study, Malignant Neoplasms, Past Trends, Taf250, Patient, SR3-5, ds DNA, Triple-Negative Breast Neoplasm, School-Age Population, DNA, other neoplasm, ER-Negative PR-Negative HER2-Negative Breast Cancer, TAF230, d230, DNS, Procedures, (Deoxyribonucleotide)n, Transcriptome Profile, Neoplasms, Benign Neoplasm, Triple-Negative Breast Cancers, Gene, dTAFII250, RNA-seq., Transplantations, EfW1, Malignant, Deoxyribonucleic acids, heterologous transplantation, Deoxyribonucleic Acid, dmTAF1, Taf230, Genetic heterogeneity, resistance, Studies, Gene Products, Whole Transcriptome Shotgun Sequencing, Technique, TAF250, School-Age Populations, Taf200, dTAF[[II]]250, Malignancy, cell, Recrudescences, Baby Booms, Profile, Natural Increases, absent from organism, Heterografts, Double Stranded, Taf1p, Natural Increase, Deoxyribonucleic acid, Population, Expressions, Trends, Non-Polyadenylated RNA, Study, Neoplasias, dTAF250, Baby Busts, Explosions, Clients, Triple Negative Breast Neoplasm, Population Growth and Natural Resources, Expression, (Deoxyribonucleotide)m, School Age Population, TAF, Heterologous, Cancer, measuring, Baby Boom, RNA, TAF[[II]]250, High Fertility Population, Transcriptome, Malignant Neoplasm, DNAn+1, l(3)84Ab, RNS, BG:DS00004.13, Client, Cell, dTAF230, Population Explosion, Explosion, MT, XENOTRANSPL, Trend, p230, yeast nucleic acid, chemical analysis, Gene Expression Signatures, Neoplasm, TAF[[II]]250/230, TFIID, Gene Expression Signature, techniques, ds-DNA, Taf[[II]]250, Increases, ribonucleic acid, primary cancer, Breast Neoplasm, TAF[[II]]230, Non Polyadenylated RNA, Non-Polyadenylated, HETEROL TRANSPL, TAF[II]250, patient, Ribonucleic Acid, Cancers, malignant tumor, School Age Populations, High Fertility Populations, ER Negative PR Negative HER2 Negative Breast Neoplasms, sample collection, DmelCG17603, Population Size and Growth, Increase, Gene Expression Profiles, Breast Cancer, Desoxyribonukleinsaeure, assay, Signature, Neoplasia, methodology, TAF1falseSingle cell RNA sequencing and Whole Genome Sequencing on different cells from the same sample for a triple negative patient derived xenograft and ovarian cancer cell lines.Measuring gene expression of genomically defined tumour clones at single cell resolution would associate functional consequences to somatic alterations, as a prelude to elucidating pathways driving cell population growth, resistance and relapse. In the absence of scalable methods to simultaneously assay DNA and RNA from the same single cell, independent sampling of cell populations for parallel measurement of single cell DNA and single cell RNA must be computationally mapped for genome-transcriptome association. Here we present clonealign, a robust statistical framework to assign gene expression states to cancer clones using single-cell RNA-seq and DNA-seq independently sampled from an heterogeneous cancer cell population. We apply clonealign to triple-negative breast cancer patient derived xenografts and high-grade serous ovarian cancer cell lines and discover clone-specific dysregulated biological pathways not visible using either DNA-Seq or RNA-Seq alone.2022-11-22 12:10:03EGAS000010033879606EGAD00001004552EGAC00000000011