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丁香实验推荐阅读
Use of SNP-Arrays for ChIP Assays: Computational Aspects

The simultaneous genotyping of thousands of single nucleotide polymorphisms (SNPs) in a genome using SNP-Arrays is a very important tool that is revolutionizing genetics and molecular biology. We expanded the utility of this technique by using it following chromatin immunoprecip ...

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The State-of-the-Art of Chromatin Immunoprecipitation

The biological significance of interactions of nuclear proteins with DNA in the context of gene expression, cell differentiation, or disease has immensely been enhanced by the advent of chromatin immunoprecipitation (ChIP). ChIP is a technique whereby a protein of interest is selecti ...

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Mycosis Fungoides and Szary Syndrome

The development of array comparative genomic hybridization (aCGH) techniques has allowed to characterize more precisely several human neoplasms with the aim of providing prognostic markers and targets for directed therapeutic intervention. Recently, several studies app ...

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Array CGH Reveals Clonal Evolution of Adult T-Cell Leukemia/Lymphoma

Adult T-cell leukemia/lymphoma (ATLL) is the neoplasm caused by human T-cell leukemia virus type 1 (HTLV-1). We performed oligoarray comparative genomic hybridization (CGH) against paired samples comprising peripheral blood (PB) and lymph node (LN) samples from patients with acute ...

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Analysis of Acquired Genomic Copy Number Aberrations and Regions of Loss of Heterozygosity in Acute Myelogenous Leukemia Genomes Using Affymetrix SNP

The application of SNP array technology to the analysis of cancer genomes has greatly advanced our knowledge of the incidence and functional consequences of acquired genomic copy number aberrations (aCNA) and LOH in various malignancies. The major challenges of using SNP arrays are accu ...

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CGH Protocols: Chronic Lymphocytic Leukemia

Array-based comparative genomic hybridization (aCGH) is a powerful assay to identify copy number abnormalities underlying the pathogenesis of cancer. aCGH has become the gold standard for whole genome copy number analysis in medium and large cohorts in clinical and research labora ...

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The Use of Cytogenetic Microarrays in Myelodysplastic Syndrome Characterization

Various microarray platforms, including BAC, oligonucleotide, and SNP arrays, have been shown to �provide clinically useful diagnostic and prognostic information for patients with myelodysplastic syndromes (MDS). Clinically useful arrays are designed with specific purp ...

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Application of Array Comparative Genomic Hybridization in Chronic Myeloid Leukemia

Chromosomal alteration is one of the hallmarks of chronic myeloid leukemia (CML), and the Philadelphia chromosome is the most important and key example of the chromosomal changes in this disease. Indeed, the BCR–ABL1 fusion product is a target against which many tyrosine kinase inhibitors ...

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Epigenomics: Sequencing the Methylome

DNA methylation patterns are increasingly surveyed through methods that utilize massively parallel sequencing. Sequence-based assays developed to detect DNA methylation can be broadly divided into those that depend on affinity enrichment, chemical conversion, or enzymat ...

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Ultradense Array CGH and Discovery of Micro-Copy Number Alterations and Gene Fusions in the Cancer Genome

The characterization of molecular alterations specific to cancer facilitates the discovery of predictive and prognostic biomarkers important to targeted therapeutics. Alterations critical to cancer therapeutics include copy number alterations (CNAs) such as gene ampl ...

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Distinguishing Somatic and Germline Copy Number Events in Cancer Patient DNA Hybridized to Whole-Genome SNP Genotyping Arrays

Chromosomal aneuploidy and segmental copy number changes are common genomic aberrations in �cancer. Copy number alterations (CNAs) arise from deletions, insertions, or duplications resulting in �chromosomal aberrations and aneuploidy. Genomes of normal cells also exhibit ...

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Finding Common Regions of Alteration in Copy Number Data

In this chapter, we review some recent methods designed for detecting recurrent copy number regions, that is, genomic regions that show evidence of being altered in a set of samples. We analyze Affymetrix SNP6 data from 87 Her2-type breast tumors from a recent study using three different methods, s ...

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Array CGH in Brain Tumors

Alterations in the copy number of the cancer genome are frequently observed in brain tumors especially gliomas. Some pertinent examples include amplification of the EGFR locus in chromosome 7p and loss of the PTEN locus in 10q in glioblastoma. Meningiomas are often associated with loss of the N ...

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Array Comparative Genomic Hybridization: An Overview of Protocols, Applications, and Technology Trends

From the earliest observations of human chromosomes in the late 1800s to modern day next generation sequencing technologies, much has been learned about human cancers by the vigorous application of the techniques of the day. In general, resolution has improved tremendously, and corresp ...

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Applications of Array-CGH for Lung Cancer

This chapter summarizes the current knowledge on gene copy number changes found in lung tumors, and their application in the diagnosis, prognostication, and prediction of response to chemotherapy. Examples of the identification of specific “driver” oncogenes within amplified DNA ...

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Nonfamilial Breast Cancer Subtypes

Over the last decade, our knowledge in somatic genetic events related to breast cancer has increased �enormously. Through usage of various genome-wide molecular approaches, it has become increasingly clear that breast cancer is a vastly heterogeneous disease. Microarray-based ge ...

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Array-CGH in Childhood MDS

To study genomic imbalances potentially involved in disease development and/or progression of childhood MDS, array-based comparative genomic hybridization (aCGH) is a helpful tool. Copy number alterations (CNA) of subtle chromosomal regions containing potential candida ...

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Comparative Genomic Hybridization of Wilms tumor

Cytogenetic analysis of solid tumors including Wilms’ tumor is challenging due to poor chromosome morphology, complexity of abnormalities, and to the possibility of stromal cell overgrowth in tissue culture. Molecular cytogenetic techniques such as chromosomal comparative g ...

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Array Comparative Genomic Hybridization in Osteosarcoma

Osteosarcoma, the most frequent primary bone tumor, is a malignant mesenchymal sarcoma with a peak incidence in young children and adolescents. Left untreated, it progresses relentlessly to local and systemic disease, ultimately leading to death within months. Genomically, osteo ...

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Genome-Wide DNA Profiling of HIV-Related B-Cell Lymphomas

Non-Hodgkin lymphomas represent a frequent complication of human immunodeficiency virus (HIV) infection, occurring at higher frequency than in immunocompetent individuals, and causing morbidity and mortality. Here, we present the method we have followed to analyze the genomic ...

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