PROBER: oligonucleotide FISH probe design software

Navin, Nicholas; Grubor, Vladimir; Hicks, Jim; Leibu, Evan; Thomas, Elizabeth; Troge, Jennifer; Riggs, Michael; Lundin, Per; Månér, Susanne; Sebat, Jonathan; Zetterberg, Anders; Wigler, Michael

doi:10.1093/bioinformatics/btl273

Cited by 32 publications

(24 citation statements)

References 6 publications

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“…For the interdigitation analysis, probes were created from bacterial artificial chromosomes (BAC) selected using the UCSD Genome Browser. For the determination of copy number in the deletions and amplifications of the aneuploid tumors, probes were made with PCR amplification of primers identified through the PROBER algorithm designed in this laboratory (Navin et al 2006). Genomic sequences of 100 kb containing target amplifications were tiled with 50 probes (800-1400 bp).…”

Section: Probe Design For Fishmentioning

confidence: 99%

Novel patterns of genome rearrangement and their association with survival in breast cancer

Hicks¹,

Krasnitz²,

Lakshmi³

et al. 2006

Genome Res.

297

341

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Representational Oligonucleotide Microarray Analysis (ROMA) detects genomic amplifications and deletions with boundaries defined at a resolution of ∼50 kb. We have used this technique to examine 243 breast tumors from two separate studies for which detailed clinical data were available. The very high resolution of this technology has enabled us to identify three characteristic patterns of genomic copy number variation in diploid tumors and to measure correlations with patient survival. One of these patterns is characterized by multiple closely spaced amplicons, or “firestorms,” limited to single chromosome arms. These multiple amplifications are highly correlated with aggressive disease and poor survival even when the rest of the genome is relatively quiet. Analysis of a selected subset of clinical material suggests that a simple genomic calculation, based on the number and proximity of genomic alterations, correlates with life-table estimates of the probability of overall survival in patients with primary breast cancer. Based on this sample, we generate the working hypothesis that copy number profiling might provide information useful in making clinical decisions, especially regarding the use or not of systemic therapies (hormonal therapy, chemotherapy), in the management of operable primary breast cancer with ostensibly good prognosis, for example, small, node-negative, hormone-receptor-positive diploid cases.

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Section: Probe Design For Fishmentioning

confidence: 99%

Novel patterns of genome rearrangement and their association with survival in breast cancer

Hicks¹,

Krasnitz²,

Lakshmi³

et al. 2006

Genome Res.

297

341

View full text Add to dashboard Cite

show abstract

“…Oligo probes have allowed the visualization of single-copy viral DNA as well as individual mRNA molecules using branched DNA signal amplification (27) or a handful to a few dozen short oligo probes (26,28), and, by targeting blocks of repetitive sequences as a strategy to amplify signal, enabled the first FISHbased genome-wide RNAi screen (29). Oligo probes have also been generated directly from genomic DNA using parallel PCR reactions (30,31). However, the high cost of synthesizing oligo probes has limited their use.…”

mentioning

confidence: 99%

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

Beliveau

Joyce

Apostolopoulos

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

398

472

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A host of observations demonstrating the relationship between nuclear architecture and processes such as gene expression have led to a number of new technologies for interrogating chromosome positioning. Whereas some of these technologies reconstruct intermolecular interactions, others have enhanced our ability to visualize chromosomes in situ. Here, we describe an oligonucleotide-and PCR-based strategy for fluorescence in situ hybridization (FISH) and a bioinformatic platform that enables this technology to be extended to any organism whose genome has been sequenced. The oligonucleotide probes are renewable, highly efficient, and able to robustly label chromosomes in cell culture, fixed tissues, and metaphase spreads. Our method gives researchers precise control over the sequences they target and allows for single and multicolor imaging of regions ranging from tens of kilobases to megabases with the same basic protocol. We anticipate this technology will lead to an enhanced ability to visualize interphase and metaphase chromosomes.T he role of chromosome positioning in gene regulation and chromosome stability is fueling a growing interest in technologies that reveal the in situ organization of the genome. Among these technologies are chromosome conformation capture (3C) (1) and its several iterations, such as Hi-C (2), which are applied to populations of nuclei to identify chromosomal regions that are in close proximity to each other (3, 4). Another technology is fluorescence in situ hybridization (FISH), wherein nucleic acids are targeted by fluorescently labeled probes and then visualized via microscopy; this technology is an extension of methods that once used radioactive probes and autoradiography but have since been adapted to use nonradioactive labels (5-11). FISH is a single-cell assay, making it especially powerful for the detection of rare events that might otherwise be lost in mixed or asynchronous populations of cells. In addition, because FISH is applied to fixed cells, it can reveal the positioning of chromosomes relative to nuclear, cytoplasmic, and even tissue structures. FISH can also be used to visualize RNA, permitting the simultaneous assessment of gene expression, chromosome position, and protein localization.FISH probes are typically derived from cloned genomic regions or flow-sorted chromosomes, which are labeled directly via nick translation or PCR in the presence of fluorophore-conjugated nucleotides or labeled indirectly with nucleotide-conjugated haptens, such as biotin and digoxigenin, and then visualized with secondary detection reagents. Probe DNA is often fragmented into ∼150-to 250-bp pieces to facilitate its penetration into fixed cells (12) and, as many genomic clones contain repetitive sequences that occur abundantly in the genome, hybridization is typically performed in the presence of unlabeled repetitive DNA (13). Another limitation to clone-based probes is that the genomic regions that can be visualized with them are restricted by the availability of clones and the size of ...

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“…Therefore, the utility of each candidate probe needs to be verified before combining sequences. Software that combines identification of repetitive elements and selection of primers for FISH probe synthesis from genomic regions of the human genome has been written (Navin et al 2006). This software does not rely on previously characterized repeat libraries.…”

Section: Discussionmentioning

confidence: 99%

“…This software does not rely on previously characterized repeat libraries. Instead, it assigns sequences a repetitiveness score on the basis of the number of times they are present in a sequence database (Navin et al 2006). Similar software could aid in the development of additional probes for maize.…”

Section: Discussionmentioning

confidence: 99%

Single-Gene Detection and Karyotyping Using Small-Target Fluorescence in Situ Hybridization on Maize Somatic Chromosomes

et al. 2007

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Combined with a system for identifying each of the chromosomes in a genome, visualizing the location of individual genetic loci by fluorescence in situ hybridization (FISH) would aid in assembling physical and genetic maps. Previously, large genomic clones have been successfully used as FISH probes onto somatic chromosomes but this approach is complicated in species with abundant repetitive elements. In this study, repeat-free portions of sequences that were anchored to particular chromosomes including genes, gene clusters, large cDNAs, and portions of BACs obtained from public databases were used to label the corresponding physical location using FISH. A collection of probes that includes at least one marker on each chromosome in the maize complement was assembled, allowing a small-target karyotyping system to be developed. This set provides the foundation onto which additional loci could be added to strengthen further the ability to perform chromosomal identification in maize and its relatives. The probes were demonstrated to produce signals in several wild relatives of maize, including Zea luxurians, Z. diploperennis, and Tripsacum dactyloides.

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PROBER: oligonucleotide FISH probe design software

Abstract: http://prober.cshl.edu

Cited by 32 publications

References 6 publications

Novel patterns of genome rearrangement and their association with survival in breast cancer

Novel patterns of genome rearrangement and their association with survival in breast cancer

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

Single-Gene Detection and Karyotyping Using Small-Target Fluorescence in Situ Hybridization on Maize Somatic Chromosomes

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