Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27407700.fastq.gz | Fastqsanger.gz | |||
| SRR27407701.fastq.gz | Fastqsanger.gz | |||
| SRR27407702.fastq.gz | Fastqsanger.gz | |||
| SRR27407703.fastq.gz | Fastqsanger.gz | |||
| SRR27407704.fastq.gz | Fastqsanger.gz |
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Project description:Genome-wide analysis of single nucleotide polymorphisms in 64 acute myeloid leukemias has revealed that 20% exhibited large regions of homozygosity that could not be accounted for by visible chromosomal abnormalities in the karyotype. Further analysis confirmed that these patterns were due to partial uniparental disomy (UPD). Remission bone marrow was available from five patients showing UPD in their leukemias, and in all cases the homozygosity was found to be restricted to the leukemic clone. Two examples of UPD11p were shown to be of different parental origin as indicated by the methylation pattern of the H19 gene. Furthermore, a previously identified homozygous mutation in the CEBPA gene coincided with a large-scale UPD on chromosome 19. These cryptic chromosomal abnormalities, which seem to be nonrandom, have the characteristics of somatic recombination events and may define an important new subclass of leukemia. Patient No. from Table 1 of Raghavan et al 2005 and Sample name Patient No: 1 = Sample name: AML sample 35 diagnosis Patient No: 1 = Sample name: AML sample 107 remission Patient No: 2 = Sample name: AML sample 37 diagnosis Patient No: 3 = Sample name: AML sample 10 diagnosis Patient No: 3 = Sample name: AML sample 44 remission Patient No: 4 = Sample name: AML sample 20 diagnosis Patient No: 5 = Sample name: AML sample 65 diagnosis Patient No: 6 = Sample name: AML sample 69 diagnosis Patient No: 6 = Sample name: AML sample 94 remission Patient No: 7 = Sample name: AML sample 40 diagnosis Patient No: 7 = Sample name: AML sample 41 remission Patient No: 8 = Sample name: AML sample 64 diagnosis Patient No: 9 = Sample name: AML sample 7 diagnosis Patient No: 10 = Sample name: AML sample 49 diagnosis Patient No: 10 = Sample name: AML sample 106 remission Patient No: 11 = Sample name: AML sample 76 diagnosis Patient No: 12 = Sample name: AML sample 79 diagnosis Keywords: DNA copy number, loss of heterozygosity
2007-04-11 | GSE7490 | GEO
Project description:Each total RNA sample is hybridized to two different arrays: Affymetrix U133A (GPL96) and U133B (GPL97). For most of the normal tissue samples there is a renal clear cell carcinoma sample from the same patient. There is no matching tumor sample for normal sample N1. For most of the renal clear cell carcinoma samples there is a corresponding adjacent normal tissue sample from the same patient. There are no matching normal tissue samples for C011 or C032. Keywords = kidney Keywords = renal Keywords = RCC Keywords = carcinoma Keywords = cancer Keywords: parallel sample
2003-11-25 | GSE781 | GEO
Project description:Comparative genomic hybridization microarrays (array CGH or molecular karyotyping) for the detection of congenital chromosomal aberrations is the application of microarray technology that is coming fastest into routine clinical application. When using a two-channel microarray of genomic DNA probes for array CGH, the basic setup consists in hybridizing a patient sample against a normal reference sample and detecting copy number variations through the deviation of fluorescent signal intensity between patient and normal reference. Two major disadvantages of this setup are (1) the use of half of the resources to measure a (little informative) reference sample and (2) the possibility that deviating signals are caused by benign copy number variation in the “normal” reference instead of a patient aberration. We therefore propose a new experimental loop design that compares three patients in three hybridizations (Patient 1 vs. Patient 3, Patient 3 vs. Patient 2, and Patient 2 vs. Patient 1). We develop and compare two statistical methods (linear models of log ratios and mixed models of absolute measurements). In an analysis of data from 27 patients seen at our genetics center, this new setup together with the linear model analysis significantly overcomes the limitations of the classical setup. Furthermore, we observed that the linear models of the log-ratios had a higher signal-to-noise ratio than the mixed models of the absolute intensities. These improvements are important to guarantee a maximal efficiency of array CGH in a clinical setting and will therefore contribute to its quick adoption as a routine diagnostic tool. The method is implemented as a web application and is available at www.esat.kuleuven.be/loop. Keywords: comparative genomic hybridization
2007-12-01 | GSE6538 | GEO
Project description:Quantitative proteomics analysis was performed on two samples of localized prostate tumors from one patient (R40) and eight samples from metastatic prostate cancer sites. One sample from the right lung, one sample from the peritoneal lymph node, and two samples from the mediastinal lymph node were collected from one patient (R43). One sample from the liver and one sample from kidney were collected from another patient (R45). One sample from the periaortic lymph node and one sample from the dura were collected from another patient (R55).
2024-11-21 | PXD056300 | Pride
Project description:Infantile neuroaxonal dystrophy (INAD) is an ultra-rare early-onset autosomal recessive neurodegenerative disorder due to PLA2G6 variants. Copy number analysis of SNP arrays was performed on one INAD patient sample.
2023-05-31 | GSE233748 | GEO
Project description:CNV and LOH analysis of patient sample PN11-0204
| PRJNA173884 | ENA
Project description:Genome-wide analysis of single nucleotide polymorphisms in 64 acute myeloid leukemias has revealed that 20% exhibited large regions of homozygosity that could not be accounted for by visible chromosomal abnormalities in the karyotype. Further analysis confirmed that these patterns were due to partial uniparental disomy (UPD). Remission bone marrow was available from five patients showing UPD in their leukemias, and in all cases the homozygosity was found to be restricted to the leukemic clone. Two examples of UPD11p were shown to be of different parental origin as indicated by the methylation pattern of the H19 gene. Furthermore, a previously identified homozygous mutation in the CEBPA gene coincided with a large-scale UPD on chromosome 19. These cryptic chromosomal abnormalities, which seem to be nonrandom, have the characteristics of somatic recombination events and may define an important new subclass of leukemia. Patient No. from Table 1 of Raghavan et al 2005 and Sample name; Patient No: 1 = Sample name: AML sample 35 diagnosis; Patient No: 1 = Sample name: AML sample 107 remission; Patient No: 2 = Sample name: AML sample 37 diagnosis; Patient No: 3 = Sample name: AML sample 10 diagnosis; Patient No: 3 = Sample name: AML sample 44 remission; Patient No: 4 = Sample name: AML sample 20 diagnosis; Patient No: 5 = Sample name: AML sample 65 diagnosis; Patient No: 6 = Sample name: AML sample 69 diagnosis; Patient No: 6 = Sample name: AML sample 94 remission; Patient No: 7 = Sample name: AML sample 40 diagnosis; Patient No: 7 = Sample name: AML sample 41 remission; Patient No: 8 = Sample name: AML sample 64 diagnosis; Patient No: 9 = Sample name: AML sample 7 diagnosis; Patient No: 10 = Sample name: AML sample 49 diagnosis; Patient No: 10 = Sample name: AML sample 106 remission; Patient No: 11 = Sample name: AML sample 76 diagnosis; Patient No: 12 = Sample name: AML sample 79 diagnosis Experiment Overall Design: DNA from 64 diagnostic AML samples were analysed using Affymetrix 10K SNP arrays. Large regions of homozygosity were identified and compared with remission bone marrow where available.
2008-06-15 | E-GEOD-7490 | biostudies-arrayexpress
Project description:The purpose of this study was to assess the global transcriptional changes in a pediatric AML primary sample treated with Tamibarotene. This patient sample has a retinoic acid receptor alpha (RARA) super-enhancer, which is correlated with higher RARA mRNA levels and increased sensitivity to Tamibarotene in vitro and in vivo (Patient-derived xenograft mouse model).
2021-08-01 | GSE155559 | GEO
Project description:Three sample types are available: Primary patient samples after surgery that were flash-frozen and after short-term culture and after subsequent xenotransplantation into Nude rats or Nod/Scid, NSG or Nude mice. As well as longterm cell cultures derived from the xenotransplanted human tumors. Patient samples end with _B, mouse xenotransplanted tumors with_X and cell lines with_C. The preceeding numbers always indicate the patient association, whereas the following number inidcates mouse generation (X), passage number(C) or number of surgical samples (B) taken.
2020-10-01 | GSE137959 | GEO
Project description:Aiming to develop novel biomarker for cancer prediction after successful treatment of interferon therapy SVR-HCC is HCC appearance after IFN treatment. Each sample was collected 3 times; before IFN treatment, after IFN treatment, and appearance of HCC in SVR-HCC group. HCV-CHC is not HCC appearance after interferon treatment. Each sample was collected three times, before IFN treatment, after IFN treatment, and observation period after IFN treatment. For example, the sample which is SVR-HCC002-1 is the patient who suffered from HCC after IFN treatment, was collected before IFN treatment. SVR-HCC001-3 is missing.
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