Allele quantification using molecular inversion probes (MIP)

Wang, Yuker; Moorhead, Martin; Karlin-Neumann, George; Falkowski, Matthew; Chen, Chunnuan; Siddiqui, Farhan Asif; Davis, Ronald W.; Willis, T. D.; Faham, Malek

doi:10.1093/nar/gni177

Cited by 83 publications

(63 citation statements)

References 25 publications

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“…Inclusion of universal tails at the ends of 5C primers allows subsequent amplification of ligated primers. LMA-based approaches are quantitative and can be performed at high levels of multiplexing using thousands of primers in a single reaction (Fan et al 2004;Bibikova et al 2005;Hardenbol et al 2005;Wang et al 2005).…”

Section: Outline Of the 5c Technologymentioning

confidence: 99%

“…For example, the methylation status of 1534 CpG sites was assessed using a mixture of ∼6000 primers (Bibikova et al 2005). Another example is the use of highly multiplexed LMA with up to 20,000 Molecular Inversion Probes in a single reaction to detect single nucleotide polymorphisms (SNPs) (Hardenbol et al 2005;Wang et al 2005). When 5C is performed at a similar level of multiplexing, e.g., using 10,000 5C primers in a single experi- Table 7.…”

Section: C Applicationsmentioning

confidence: 99%

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Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Dostie¹,

et al. 2006

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Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology. 3C converts physical chromatin interactions into specific ligation products, which are quantified individually by PCR. Here we present a high-throughput 3C approach, 3C-Carbon Copy (5C), that employs microarrays or quantitative DNA sequencing using 454-technology as detection methods. We applied 5C to analyze a 400-kb region containing the human ␤-globin locus and a 100-kb conserved gene desert region. We validated 5C by detection of several previously identified looping interactions in the ␤-globin locus. We also identified a new looping interaction in K562 cells between the ␤-globin Locus Control Region and the ␥-␦-globin intergenic region. Interestingly, this region has been implicated in the control of developmental globin gene switching. 5C should be widely applicable for large-scale mapping of cis-and trans-interaction networks of genomic elements and for the study of higher-order chromosome structure.

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Section: Outline Of the 5c Technologymentioning

confidence: 99%

Section: C Applicationsmentioning

confidence: 99%

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Dostie¹,

et al. 2006

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“…The design and performance of the molecular inversion probe GMA has been described extensively by other authors. [11][12][13] Formalin-fixed, paraffin-embedded particle clots from normal bone marrow aspirates without disease (individuals unrelated to this study cohort) were used to generate control probe signal values.…”

Section: Hybridization and Data Analysismentioning

confidence: 99%

Differentiation of Malignant Melanoma From Benign Nevus Using a Novel Genomic Microarray With Low Specimen Requirements

Chandler¹,

Rowe²,

Florell³

et al. 2012

Archives of Pathology &Amp; Laboratory Medicine

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N Context.-Histologic examination of clinically suspicious melanocytic lesions is very sensitive and specific for the detection of malignant melanoma. Yet, the malignant potential of a small percentage of melanocytic lesions remains histologically uncertain. Molecular testing offers the potential to detect the genetic alterations that lead to malignant behavior without overt histologic evidence of malignancy.Objective.-To differentiate benign melanocytic nevi from malignant melanoma and to predict the clinical course of melanocytic lesions with ambiguous histology using a novel genomic microarray.Design.-We applied a newly developed single-nucleotide polymorphism genomic microarray to formalin-fixed, paraffin-embedded melanocytic lesions to differentiate benign nevi (n = 23) from malignant melanoma (n = 30) and to predict the clinical course of a set of histologically ambiguous melanocytic lesions (n = 11).Results.-For cases with unambiguous histology, there was excellent sensitivity and specificity for identifying malignant melanoma with this genomic microarray (89% sensitivity, 100% specificity). For cases with ambiguous histology, the performance of this genomic microarray was less impressive.Conclusions.-Without microdissection and with quantities of DNA one-tenth what is required for more commonly used microarrays, this microarray can differentiate between malignant melanoma and benign melanocytic nevi. For histologically ambiguous lesions, longer clinical follow-up is needed to confidently determine the sensitivity and specificity of this microarray. Some of the previous technical hurdles to the clinical application of genomic microarray technology are being overcome, and the advantages over A pproximately 2% of the United States population (6 195 000 individuals) will be diagnosed with malignant melanoma during their lifetime.1 Rendering the diagnosis of malignant melanoma is currently a 2-tiered process beginning with a history and visual inspection and ending with a microscopic examination. This screening and confirmatory testing algorithm results in good sensitivity and specificity; however, several studies have demonstrated room for improvement.2-5 The seminal works by Bastian et al, 6,7 Dalton et al, 8 and Gerami et al 9 provided hope that adding a molecular test as a third tier for diagnostically challenging melanocytic lesions could increase both sensitivity and specificity and improve the accuracy of clinical prognostication. We analyzed archived formalin-fixed, paraffin-embedded (FFPE) skin biopsies of 64 melanocytic lesions (23 benign nevi, 27 primary malignant melanomas, 3 metastatic melanomas, and 11 melanocytic lesions of uncertain malignant potential [MLUMPs]) with a 330 000-probe single-nucleotide polymorphism (SNP) genomic microarray (GMA) to determine if gains and losses of chromosomal material could predict benign or malignant clinical behavior. Our results indicate that SNP-GMA is a sensitive and specific method for identifying malignant melanoma when the histology is unambiguous. For s...

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“…The aCGH consists of CNV probes, while SNP-arrays have mainly SNP probes. While the CNV probes provide only CNV information, SNP-arrays generate both SNP genotype and CNV information using the signal intensity to generate CNV information [5,6]. The combined use of CNV and SNP probes is ideal for maximal coverage and high resolution in detection of these variants [5].…”

Section: Introductionmentioning

confidence: 99%

Utilization of the oncoscan microarray assay in cancer diagnostics

2017

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Current strategies for cancer patient management include the use of genomic and proteomic test results to help guide therapeutic selection. The need for multi-target variant analysis is highlighted by the growing number of novel therapies to treat tumors with specific profiles and the increasing recognition that cancer is an extremely heterogeneous syndrome. Microarray analysis is a powerful genomic tool that provides genome-wide genetic information that is critical for guiding cancer treatments. Unlike constitutional applications of microarray analysis which are performed on whole blood samples, microarray analysis of solid tumors is challenging because tumor tissues are typically formalin fixed and paraffin embedded (FFPE). Genomic DNA extracted from FFPE tissues can also be fragmented into small pieces and yield much lower concentrations of DNA. We validated and implemented the Affymetrix OncoScan® FFPE assay to enable genome-wide analysis from these types of samples. The Affymetrix OncoScan® assay utilizes molecular inversion probes that generate multiplexed array hybridization targets from as short as 40 base-pairs of sequence and as low as approximately 80 ng of genomic DNA. OncoScan microarray analysis provides genomic information that includes structural variations, copy number variations and SNPs in a timely and a cost-effective manner from FFPE tumor tissues.

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Allele quantification using molecular inversion probes (MIP)

Cited by 83 publications

References 25 publications

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Differentiation of Malignant Melanoma From Benign Nevus Using a Novel Genomic Microarray With Low Specimen Requirements

Utilization of the oncoscan microarray assay in cancer diagnostics

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