SNParray_Illumina_610K - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010000811 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:To identify chromosomal alterations in ATL, SNP array analyses were performed in 19 leukemia cell samples from ATL patients and 9 ATL-related cell lines. ATL displayed complex chromosomal abnormalities, but it contained recurrent chromosomal amplification and deletion, including 14q11 and 14q32, which may be associated with the development of ATL. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved peripheral blood samples and from cell line samples.
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Project description:ATL tumor samples using Affymetrix 250K SNP array
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Project description:SNP array analysis was performed using 168 ATL specimens. To obtain genotypes and intensities for each SNP, Affymetrix 250K SNP arrays were performed for 168 ATL samples.
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Project description:We recently mapped 605 chromosomal breakpoints in 61 ATL cases by spectral karyotyping and identified chromosome 14q11 as one of the most common chromosomal breakpoint regions. To map the precise location of chromosomal breakpoints at 14q11, we performed single-nucleotide polymorphism (SNP)-based comparative genomic hybridization on leukemia cells from acute-type ATL patients. Copy number analysis of Affymetrix 50K SNP arrays was performed for leukemic cell samples from10 acute-type ATL patients.
2014-01-31 | E-GEOD-54509 | biostudies-arrayexpress
Project description:In the study of tumor genetics, formalin-fixed paraffin-embedded (FFPE) tumors are the most readily available tissue samples. While DNA derived from FFPE tissue has been validated for array comparative genomic hybridization (aCGH) application, the suitability of such fragmented DNA for single-nucleotide polymorphism (SNP) array analysis has not been well examined. Furthermore, whole-genome amplification (WGA) has been used in the study of small precursor lesions to produce sufficient amount of DNA for aCGH analysis. It is unclear whether the same approach can be extended to SNP analysis. In this study, we examined the utility and limitations of genotyping platform performed on whole-genome amplified DNA from FFPE tumor samples for both copy number and SNP analyses. We analyzed the results obtained using DNA derived from matched FFPE and frozen tissue samples on Affymetrix 250K Nsp SNP array. Two widely used WGA methods, Qiagen (isothermal protocol) and Sigma (thermocycling protocol), were used to determine how WGA methods affect the results. We found that the use of DNA derived from FFPE tumors (without or with WGA) for high-resolution SNP array application can produce a significant amount of false positive and false negative findings. While some of these misinterpretations appear to cluster in genomic regions with high or low GC contents, the majority appears to occur randomly. Only large-scale chromosome LOH (>10Mb) can be reliably detected from FFPE tumor DNA samples (without or with WGA) but not smaller LOH or copy number alterations. Our findings here indicate a need for caution in SNP array data interpretation when using FFPE tumor-derived DNA, particularly with WGA.
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Project description:Primary central nervous system lymphomas (PCNSL) are extranodal non-Hodgkin lymphomas arising within brain, spine cord or eyes and represent approximately 3% of all primary brain tumors in adults. PCNSL are histologically homogeneous- more than 90% are diffuse large B cell lymphomas - but clinically heterogeneous. Molecular basis which could explain PCNSL agressiveness are unknown due to paucity of biological material (i.e. stereotaxic biopsies). In order to identify recurrent genomic abnormalities in PCNSL, SNP arrays and CGH arrays were analyzed for 27 and 6 PCNSL cases, respectively. Fresh frozen samples were generally investigated by SNP array (Illumina 370K or 610K microarrays) and formalin-fixed paraffin-embedded tissues by CGH array (Nimblegen and Agilent microarrays) except for 3 frozen samples analyzed by CGHa.
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Project description:We recently mapped 605 chromosomal breakpoints in 61 ATL cases by spectral karyotyping and identified chromosome 14q11 as one of the most common chromosomal breakpoint regions. To map the precise location of chromosomal breakpoints at 14q11, we performed single-nucleotide polymorphism (SNP)-based comparative genomic hybridization on leukemia cells from acute-type ATL patients.
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Project description:Affymetrix SNP array data for chicken samples
| PRJNA525994 | ENA