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• NCI's Collection of Studies for General Cancer Research

  This collection contains all of NCIs authorized individual-level genomic datasets currently in dbGaP that are approved for Cancer Research (DS-CA) use only and limitations outlined in the model Data Use Certification Agreement. Access to this study will include any additional authorized individual-level DS-CA datasets that become available. Renewal of this study is required annually. To request access to this study collection, select phs003967.v1.p1 in the dbGaP Authorized Access System.

  Study phs003967

• Comparison Across Multiple Types of Sleep Deprivation

  This study is designed to assess neurobehavioral performance, as well as molecular and physiological changes associated with variations in timing and quantity of sleep. Gene expression changes associated with neurobehavioral (cognitive) performance were assessed in a time-series among individuals randomly assigned to four separate sleep conditions during a 10-day inpatient study: a well-rested control, sleep restriction with nighttime sleep, sleep restriction with daytime sleep to roughly simulate shiftwork schedules, and total (acute) sleep deprivation.

  Study phs003924

• Genomic profiling of fragile X syndrome unmethylated full mutation carriers

  Whole genome sequencing of two unrelated FMR1 unmethylated full mutation carriers. The existence of rare, unmethylated full mutation carriers who carry the mutation that causes fragile X syndrome but do not gain methylation at the locus offers a rare opportunity to study the mechanisms underlying fragile X syndrome. This study aims to investigate the genomic variants in these individuals alongside transcriptomic data to elucidate underlying genomic variants behind transcriptomic differences observed in UFM individuals.

  Study EGAS50000000648

• ResolveCRPS study - RNA-fragment sequencing from snap-frozen skin biopsies

  Complex Regional Pain Syndrome (CRPS) is a disabling pain disorder with unclear cutaneous molecular mechanisms. To identify gene-expression signatures linked to pain intensity and disease progression, we profiled the local transcriptome of CRPS-affected skin. 42 patients agreed to skin biopsies from the CRPS-affected area, which underwent low-input total RNA-seq. Full experimental and bioinformatics protocols are provided in the associated publication and its supplementary material.

  Study EGAS50000001061

• OTOF mutation analysis with massively parallel DNA sequencing in 2,265 Japanese sensorineural hearing loss patients.

  The OTOF gene, encoding otoferlin, is reported to be one of the major causes of non-syndromic recessive sensorineural hearing loss, and is also reported to be the most common cause of non-syndromic recessive auditory neuropathy spectrum disorder (ANSD). In the present study, we performed OTOF mutation analysis using massively parallel DNA sequencing (MPS) to reveal the frequency and clinical characteristics of OTOF-related hearing loss in a large hearing loss population.

  Study JGAS000166

• Analytical study of protein function and RNA expression involved in predicting treatment efficacy and adverse event development in lung cancer radiotherapy.

  The purpose of this study is to elucidate the functions of DNA repair proteins and RNA expression that are involved in the therapeutic efficacy and adverse events of radiotherapy for lung cancer at our hospital. In particular, this is an exploratory study to identify proteins and RNAs involved in the expression of proteins that are likely to be involved in the prediction of radiotherapy response and adverse events.

  Study JGAS000545

• Discovery of genetic factors associated with thiopurine-induced severe adverse events

  Despite NUDT15 variants showing significant association with thiopurine-induced adverse events (AEs) in Asians, it remains unclear whether additional genetic variants should be tested to predict AEs. To clarify it, we performed a genome-wide association study to discover additional variants associated with thiopurine-induced severe AEs, alopecia and leukopenia. GWASs of these AEs were performed with 1221 Japanese patients with inflammatory bowel disease using population-optimized genotyping array and imputation.

  Study JGAS000661

• PTEN homozygous deletion is a negative prognostic factor in Tumor Treating Fields-treated glioblastoma, IDH wildtype patients

  This study investigates genomic determinants of outcome in glioblastoma, IDH-wildtype patients treated with Tumor Treating Fields (TTFields) in addition to standard radiochemotherapy. Tumor tissue from primary glioblastoma at initial diagnosis was profiled using the Illumina TruSight Oncology 500 (TSO500) targeted sequencing panel to characterise somatic alterations. The overarching goal is to provide exploration of genomic determinants of survival and treatment response in TTFields-treated glioblastoma, IDH-wildtype.

  Study EGAS50000001469

• Effect of inflammation on human hematopoietic stem cells in a xenograft model

  Transcriptional heterogeneity in cord blood HSCs was investigated by 10X single-cell Multiome (RNA+ATAC). To investigate the effect of inflammatory stress on human HSC, 10X single-cell Multiome profiling of cells from xenografted mice recovered from repeated inflammatory challenge was performed. To investigate transmission of inflammatory stress-related molecular programs from HSC to their progeny, 10X single-cell RNA sequencing was performed on committed progenitor and myeloid cells from the same mice.

  Study EGAS50000001624

• Genomic landscape of aplastic anemia

  This study investigates the genomic landscape of aplastic anemia using complementary sequencing approaches. Single-cell DNA and protein profiling were performed using the Mission Bio Tapestri platform to characterize clonal structure and immunophenotypic features. Long-read whole-genome sequencing (PacBio) and single-cell whole-genome sequencing (BioSkryb) were also generated to capture structural variants and genome-wide clonal architecture. Together, these datasets aim to elucidate mutational processes and clonal evolution underlying aplastic anemia.

  Study EGAS50000001516