DNA Copy Number Variations

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  Subject Areas on Research

  • A 32 kb critical region excluding Y402H in CFH mediates risk for age-related macular degeneration. 
  • A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. 
  • A genome-wide association study of resistance to HIV infection in highly exposed uninfected individuals with hemophilia A. 
  • A genome-wide scan for common alleles affecting risk for autism. 
  • A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. 
  • A nCounter CNV Assay to Detect HER2 Amplification: A Correlation Study with Immunohistochemistry and In Situ Hybridization in Advanced Gastric Cancer. 
  • A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder. 
  • A pilot genome-wide association study shows genomic variants enriched in the non-tumor cells of patients with well-differentiated neuroendocrine tumors of the ileum. 
  • A statistical framework for determination of minimal plasmid copy number required for transgene expression in mammalian cells. 
  • APOE4 Copy Number-Dependent Proteomic Changes in the Cerebrospinal Fluid. 
  • ASTN2 modulates synaptic strength by trafficking and degradation of surface proteins. 
  • An evaluation of copy number variation detection tools from whole-exome sequencing data. 
  • An integrative approach identified genes associated with drug response in gastric cancer. 
  • Antiepileptic Drug Teratogenicity and De Novo Genetic Variation Load. 
  • Association between reduced copy-number at T-cell receptor gamma (TCRgamma) and childhood allergic asthma: A possible role for somatic mosaicism. 
  • Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis. 
  • Attenuation of the retinoblastoma pathway in pancreatic neuroendocrine tumors due to increased cdk4/cdk6. 
  • Bayesian joint analysis of heterogeneous genomics data. 
  • CODAS syndrome is associated with mutations of LONP1, encoding mitochondrial AAA+ Lon protease. 
  • Chromosomal microarray analysis in clinical evaluation of neurodevelopmental disorders-reporting a novel deletion of SETDB1 and illustration of counseling challenge. 
  • Circulating tumor DNA alterations in patients with metastatic castration-resistant prostate cancer. 
  • Comparative Genomic Analysis of the Pheromone Receptor Class 1 Family (V1R) Reveals Extreme Complexity in Mouse Lemurs (Genus, Microcebus) and a Chromosomal Hotspot across Mammals. 
  • Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays. 
  • Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. 
  • Comprehensive molecular portraits of human breast tumours. 
  • Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. 
  • Contributions of Mamu-A*01 status and TRIM5 allele expression, but not CCL3L copy number variation, to the control of SIVmac251 replication in Indian-origin rhesus monkeys. 
  • Convergence of genes and cellular pathways dysregulated in autism spectrum disorders. 
  • Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer. 
  • Copy Number Variants of Undetermined Significance Are Not Associated with Worse Clinical Outcomes in Hypoplastic Left Heart Syndrome. 
  • Copy number variation at chromosome 5q21.2 is associated with intraocular pressure. 
  • Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest. 
  • Copy number variation in the dosage-sensitive 16p11.2 interval accounts for only a small proportion of autism incidence: a systematic review and meta-analysis. 
  • Copy number variation is associated with gene expression change in archaea. 
  • Copy number variation of KIR genes influences HIV-1 control. 
  • Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer. 
  • DNA copy number variants of known glaucoma genes in relation to primary open-angle glaucoma. 
  • Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries. 
  • Detectable clonal mosaicism from birth to old age and its relationship to cancer. 
  • Detecting differential copy number variation between groups of samples. 
  • Differential copy number aberrations in novel candidate genes associated with progression from in situ to invasive ductal carcinoma of the breast. 
  • Discordant and heterogeneous clinically relevant genomic alterations in circulating tumor cells vs plasma DNA from men with metastatic castration resistant prostate cancer. 
  • Dual Molecular Effects of Dominant RORA Mutations Cause Two Variants of Syndromic Intellectual Disability with Either Autism or Cerebellar Ataxia. 
  • Effects of early life exposure to ultraviolet C radiation on mitochondrial DNA content, transcription, ATP production, and oxygen consumption in developing Caenorhabditis elegans. 
  • Enteropathy-associated T cell lymphoma subtypes are characterized by loss of function of SETD2. 
  • Epigenome-wide association study of mitochondrial genome copy number. 
  • Erythropoietin receptor contributes to melanoma cell survival in vivo. 
  • Evidence for involvement of GNB1L in autism. 
  • Evolutionary and biomedical insights from a marmoset diploid genome assembly. 
  • Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas. 
  • Exome-wide Sequencing Shows Low Mutation Rates and Identifies Novel Mutated Genes in Seminomas. 
  • From the Cover: Arsenite Uncouples Mitochondrial Respiration and Induces a Warburg-like Effect in Caenorhabditis elegans. 
  • Functional impact of global rare copy number variation in autism spectrum disorders. 
  • Gene copy-number variation in haploid and diploid strains of the yeast Saccharomyces cerevisiae. 
  • General olfactory sensitivity database (GOSdb): candidate genes and their genomic variations. 
  • Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition. 
  • Genome-wide Analysis of Common Copy Number Variation and Epithelial Ovarian Cancer Risk. 
  • Genome-wide association identifies diverse causes of common variable immunodeficiency. 
  • Genome-wide association study identifies a maternal copy-number deletion in PSG11 enriched among preeclampsia patients. 
  • Genome-wide scan of copy number variation in late-onset Alzheimer's disease. 
  • Genomic Amplifications and Distal 6q Loss: Novel Markers for Poor Survival in High-risk Neuroblastoma Patients. 
  • Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. 
  • Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing. 
  • Genomic characterization of HER2-positive breast cancer and response to neoadjuvant trastuzumab and chemotherapy-results from the ACOSOG Z1041 (Alliance) trial. 
  • Genomic profiles specific to patient ethnicity in lung adenocarcinoma. 
  • Global analysis of genomic instability caused by DNA replication stress in Saccharomyces cerevisiae. 
  • Heterogeneity within the PF-EPN-B ependymoma subgroup. 
  • Identification of numerous novel disease-causing variants in patients with inherited retinal diseases, combining careful clinical-functional phenotyping with systematic, broad NGS panel-based genotyping. 
  • Identifying human disease genes through cross-species gene mapping of evolutionary conserved processes. 
  • Integrated Analysis of RNA and DNA from the Phase III Trial CALGB 40601 Identifies Predictors of Response to Trastuzumab-Based Neoadjuvant Chemotherapy in HER2-Positive Breast Cancer. 
  • Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer. 
  • Integrated genomic analyses identify ERRFI1 and TACC3 as glioblastoma-targeted genes. 
  • Integrated genomic characterization of endometrial carcinoma. 
  • Integrating common and rare genetic variation in diverse human populations. 
  • Integrative molecular profiling of routine clinical prostate cancer specimens. 
  • LCCC 1025: a phase II study of everolimus, trastuzumab, and vinorelbine to treat progressive HER2-positive breast cancer brain metastases. 
  • LINC00467, Driven by Copy Number Amplification and DNA Demethylation, Is Associated with Oxidative Lipid Metabolism and Immune Infiltration in Breast Cancer. 
  • Latent factor analysis to discover pathway-associated putative segmental aneuploidies in human cancers. 
  • Loss of PTPRM associates with the pathogenic development of colorectal adenoma-carcinoma sequence. 
  • MYC or BCL2 copy number aberration is a strong predictor of outcome in patients with diffuse large B-cell lymphoma. 
  • MYCN amplification drives an aggressive form of spinal ependymoma. 
  • Molecular and clonal evolution in recurrent metastatic gliosarcoma. 
  • Molecular profile and copy number analysis of sporadic colorectal cancer in Taiwan. 
  • Morphologic correlates of molecular alterations in extrauterine Müllerian carcinomas. 
  • Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes. 
  • Nested Inversion Polymorphisms Predispose Chromosome 22q11.2 to Meiotic Rearrangements. 
  • New clues to the molecular pathogenesis of Burkitt lymphoma revealed through next-generation sequencing. 
  • Next-Generation Sequencing Concordance Analysis of Comprehensive Solid Tumor Profiling between a Centralized Specialty Laboratory and the Decentralized Personal Genome Diagnostics elio Tissue Complete Kitted Solution. 
  • Novel enriched pathways in superficial malignant peripheral nerve sheath tumours and spindle/desmoplastic melanomas. 
  • PCR-Based Analysis of Mitochondrial DNA Copy Number, Mitochondrial DNA Damage, and Nuclear DNA Damage. 
  • PCR-Based Determination of Mitochondrial DNA Copy Number in Multiple Species. 
  • Pan-cancer Convergence to a Small-Cell Neuroendocrine Phenotype that Shares Susceptibilities with Hematological Malignancies. 
  • Pathogenic Germline Variants in 10,389 Adult Cancers. 
  • Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients. 
  • Predictors of mitochondrial DNA copy number and damage in a mercury-exposed rural Peruvian population near artisanal and small-scale gold mining: An exploratory study. 
  • Quantitative PCR-based measurement of nuclear and mitochondrial DNA damage and repair in mammalian cells. 
  • Risk factors for autism: translating genomic discoveries into diagnostics. 
  • Robust regression analysis of copy number variation data based on a univariate score. 
  • SgD-CNV, a database for common and rare copy number variants in three Asian populations. 
  • Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. 
  • Social affiliation predicts mitochondrial DNA copy number in female rhesus macaques. 
  • Subgroup-specific structural variation across 1,000 medulloblastoma genomes. 
  • Systematic interrogation of 3q26 identifies TLOC1 and SKIL as cancer drivers. 
  • Targeted long-read sequencing identifies missing disease-causing variation. 
  • The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity. 
  • The LINK-A lncRNA interacts with PtdIns(3,4,5)P3 to hyperactivate AKT and confer resistance to AKT inhibitors. 
  • The characterization of twenty sequenced human genomes. 
  • The correlation of copy number variations with longevity in a genome-wide association study of Han Chinese. 
  • The genetic landscape of the childhood cancer medulloblastoma. 
  • The genomic relationship between primary breast carcinomas and their nodal metastases. 
  • The impact of the metabotropic glutamate receptor and other gene family interaction networks on autism. 
  • The oncogenic properties of EWS/WT1 of desmoplastic small round cell tumors are unmasked by loss of p53 in murine embryonic fibroblasts. 
  • The role of lysyl oxidase-like 1 DNA copy number variants in exfoliation glaucoma. 
  • Urinary Anomalies in 22q11.2 Deletion (DiGeorge syndrome): From Copy Number Variations to Single-Gene Determinants of Phenotype. 
  • Using ERDS to infer copy-number variants in high-coverage genomes. 
  • Validation of an oligo-gene signature for the prognostic stratification of ductal carcinoma in situ (DCIS). 
  • Variation in chromosome copy number influences the virulence of Cryptococcus neoformans and occurs in isolates from AIDS patients. 
  • Whole Genomic Copy Number Alterations in Circulating Tumor Cells from Men with Abiraterone or Enzalutamide-Resistant Metastatic Castration-Resistant Prostate Cancer. 
  • Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum. 
  • Whole-exome sequencing of breast cancer, malignant peripheral nerve sheath tumor and neurofibroma from a patient with neurofibromatosis type 1. 
  • cnvCapSeq: detecting copy number variation in long-range targeted resequencing data. 
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  Keywords of People

  • Berchuck, Andrew, James M. Ingram Distinguished Professor of Gynecologic Oncology, Obstetrics and Gynecology, Gynecologic Oncology
  • Liu, Yutao, Adjunct Assistant Professor in the Department of Medicine, Medicine, Medical Genetics
  • McLendon, Roger Edwin, Professor of Pathology, Pathology
  • Yan, Hai, Adjunct Professor of Pathology, Pathology