Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA217001 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Array-based comparative genomic hybridization (aCGH) was used to evaluate DNA copy number alterations related and non related to HPV infection status aiming to identify potential molecular markers in penile cancer (PC).
2015-02-20 | GSE50134 | GEO
Project description:<p>Cervical cancer is responsible for 10-15% of cancer related deaths in women worldwide. The etiological role of infection with high-risk human papilloma viruses (HPV) in carcinomas of the cervix is well established. In general, the development of cervical carcinomas follows a progression from persistent HPV infection through precancerous lesions to invasive cancer. Previous studies have implicated somatic mutations in PIK3CA, PTEN, TP53, STK11 and KRAS as well as chromosome-arm level copy number alterations in the pathogenesis of cervical carcinomas. Here, we report whole exome sequencing analysis of 118 cervical carcinoma-normal paired samples from patients in Norway and Mexico, as well as transcriptome sequencing of 80 cases and whole genome sequencing of 13 tumor-normal pairs. Novel somatic mutations include recurrent E322K substitutions in the MAPK1 gene encoding the ERK2 kinase and inactivating mutations in the HLA-B gene. In addition, recurrent somatic mutations in FBXW7, EP300, and NFE2L2 are novel in the context of primary cervical carcinomas. Analysis of HPV integration sites revealed recurrent integration into the RAD51B locus as well as co-occurrence of HPV genome integration and copy number gains within several genomic loci. These findings shed new light on the pathogenesis of cervical carcinomas and suggest potential novel therapeutic targets.</p>
| phs000600 | dbGaP
Project description:Gene expression microarray was used to evaluate altered genes related and non related to HPV infection status in order to identify potential molecular markers in penile cancer (PC). RNA was extracted from thirty-nine fresh frozen PC samples and submitted to gene expression microarray. The normal penile pool consisted of total RNA from five autopsy glands. Specific gene expression alterations were investigated by RT-qPCR. DNA was also extracted from penile samples and submitted to HPV genotyping.
2015-02-27 | E-GEOD-57955 | biostudies-arrayexpress
Project description:<p>Head and neck squamous cell carcinoma (HNSCC) is the sixth leading cancer by incidence worldwide(1). Various chemical carcinogens (tobacco, alcohol and betel nut), human papillomavirus (HPV) infection, and genetic predisposition contribute to the etiology of HNSCC, and to the complex genetic alterations in tumor subsets that differ in prognosis and response to therapies (2).</p> <p>Recently, a comprehensive landscape of genomic and transcriptomic alterations in HNSCC tumors has emerged from The Cancer Genome Atlas (TCGA) Network (3). TCGA revealed novel and previously recognized gene and chromosomal region copy number alterations (CNAs), mutations, and expression clusters, and defined their frequency, co-occurrence, and relationship to common and rare subtypes of HPV(-) and (+) tumors that vary in prognosis. To identify cell line models for determining the functional role and therapeutic importance of these alterations, we are performing whole exome and RNA sequencing and bioinformatic analysis of an expanded panel of 15 HPV(-) and 11 HPV(+) HNSCC cell lines and primary oral keratinocytes.</p> <p>We find that the recurrent genomic alterations in cell lines are remarkably consistent with those found in more aggressive tumors, from which cell lines have traditionally been most readily adapted to culture (4). Genome-wide correlation of CN (copy number) with expression identified a suite of potential drivers or modifier genes that differ by HPV status, and are of potential biologic and therapeutic relevance. Further, our findings elucidate and validate genomic alterations underpinning numerous discoveries made with these widely-used and recently derived HNSCC lines, and provide a roadmap for their potential use as models for future studies of tumor subtypes with worse prognosis.</p> <p>References</p> <p> <ol> <li>Torre LA, Bray F, Siegel RL, Ferlay J, Lortet-Tieulent J, Jemal A. Global cancer statistics, 2012. CA Cancer J Clin. 2015;65(2):87-108.</li> <li>Van Waes C, Musbahi O. Genomics and advances towards precision medicine for head and neck squamous cell carcinoma. Laryngoscope Investig Otolaryngol. 2017;2(5):310-9.</li> <li>Cancer Genome Atlas N. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015;517(7536):576-82.</li> <li>White JS, Weissfeld JL, Ragin CC, Rossie KM, Martin CL, Shuster M, et al. The influence of clinical and demographic risk factors on the establishment of head and neck squamous cell carcinoma cell lines. Oral Oncol. 2007;43(7):701-12.</li> </ol> </p>
| phs001581 | dbGaP
Project description:SNP array data from 45 adrenocortical carcinomas were used to detect recurrent copy number alterations.
2014-04-29 | GSE49276 | GEO
Project description:SNP array data from 125 hepatocellular carcinomas were used to detect recurrent copy number alterations.
2012-02-27 | GSE32649 | GEO
Project description:SNP array data from 76 adrenocortical carcinomas were used to detect recurrent copy number alterations.
2014-04-07 | GSE52296 | GEO
Project description:SNP array data from 127 hepatocellular adenomas and carcinomas were used to detect recurrent copy number alterations.
2013-12-18 | GSE43092 | GEO
Project description:HPV-positive oral squamous cell carcinomas (OSCCs) are specific biological and clinical entities, characterized by a more favorable prognosis compared to HPV-negative OSCCs and occurring generally in non-smoking and non-drinking younger individuals. However, poor information is available on the molecular and the clinical behavior of HPV-positive oral cancers occurring in smoking/drinking subjects. Thus, this study was designed to compare, at molecular level, two OSCC cell lines, both derived from drinking and smoking individuals and differing for presence/absence of HPV infection.
2019-12-01 | E-MTAB-6152 | biostudies-arrayexpress
Project description:Identification of copy number alterations of HPV-positive and HPV-negative vulvar squamous cell carcinomas (VSCC) and vulvar intraepithelial neoplasias (VIN), with special focus on VIN with and without VSCC, the latter group being defined as VIN with no VSCC development during >10 year follow-up.
2018-07-01 | E-MTAB-6113 | biostudies-arrayexpress