Project description:We collected blood samples of two non-obstructive azoospermia patients, and performed whole exome sequencing to explore the causal mutations for male infertility.

2021-06-22 | E-MTAB-9287 | biostudies-arrayexpress

Whole exome sequencing of TSCC (tongue squamous cell carcinoma)

Project description:Of the multiple anatomical sites represented in oral cancer, squamous cell carcinoma of the tongue (TSCC) shows the highest incidence among younger age group. Chewing betel leaf, areca nut & slaked lime and smoking tobacco are common practises in India which have direct clinical implication in TSCC carcinogenesis. Here, for the first time we define the landscape of genomic alterations in TSCC from the Indian diaspora which would help to identify novel therapeutic targets for clinical intervention and define the genetic basis for TSCC. We performed high throughput sequencing of fifty four tongue samples using whole exome sequencing (n=47, 23 paired normal tumor and 1 unpaired) and transcriptome sequencing (n=17, 10 tumor and 5 normal). Mutation, copy number analysis were carried out using exome sequencing data and transcriptome analysis provided expressed genes and transcript fusions in tongue cancer patients. Further, integrated analysis were performed to identify biologically relevant alterations. Our preliminary analysis revealed presence of most frequently altered mutations in TSCC which includes mutations in TP53, NOTCH1, CDKN2A, USP6, KMT2D etc, consistent with literature. We observed high frequency of CG/T(GC/A) transversions in non-CpG islands, a signature associated with tobacco exposure. Somatic copy number analysis revealed copy number gain in known hallmarks such as CCND1, MYC, ORAOV1 genes along with copy number alteration in novel genes. Significant positive correlation was observed in the genes harbouring copy number gains and showing increased expression.

2018-05-31 | E-MTAB-4653 | biostudies-arrayexpress

Whole exome sequencing of human primary uveal melanomas

Project description:Primary uveal melanomas show multiple genetic alterations. To determine mutational status of six human primary uveal melanomas, we performed whole exome sequencing (WES) and called Single Nucleotide Polimorphism (SNPs) to identify somatic mutations in these human primary uveal melanomas.

2021-01-25 | GSE138664 | GEO

Cervical Adenocarcinoma Whole Exome sequencing

Project description:Raw data of exome sequencing of 17 paired samples and 1 orphan tumor sample, total 18 samples

2022-02-12 | E-MTAB-9766 | biostudies-arrayexpress

ID8 whole exome sequence

Project description:The data in this submission relate to whole exome sequencing from murine ovarian cancer cell line ID8. All sequencing was performed by Beckman Coulter Genomics, Grenoble, France in February 2013.

2018-03-31 | E-MTAB-4663 | biostudies-arrayexpress

Cancer Survivor Study (CCSS) Original Cohort (diagnosed 1970-1986) Whole Exome Sequencing

Project description:Cancer Survivor Study (CCSS) Original Cohort (diagnosed 1970-1986) Whole Exome Sequencing

| PRJNA655262 | ENA