Comparison

Empire Genomics

Empire Genomics

 

Empire Genomics was created in 2006 from research started at the prestigious Roswell Park Cancer Institute in Buffalo, New York. The laboratory has a strong track record in the development of high throughput technologies to enable genome-wide analyses aimed at determining the underlying mechanisms for diseases. Having played a fundamental role in the Human Genome Project and created the foundational Bacterial Artificial Chromosomes which served as the basis for sequencing the genome, Empire Genomics developed significant expertise in genomic research. It is from this strong experiential base that we bring our capabilities, tools and techniques to support the research, clinical and drug discovery global community.

Realizing the possibility of where genomics tools will take medicine is not difficult to see, however for this potential to become reality will take genomic solutions which are robust and permit the high resolution detection of genomic aberrations and their corresponding correlations to underlying phenotypes. Traditionally the field has been plagued with immature technological tools with too much inconsistency, no customization and uncontrollable variability. Empire Genomics is excited to bring its expertise to bear on these challenges.

Empire Genomics is committed to working with the scientific community to bring the best in genomic technologies to bear on the complex systems biology questions that we collectively seek to answer. We will continually work to remove costly variation, inconsistency and the lack of reproducibility that has prevented the field from rapidly moving forward with discoveries.

The Products include:

FISH Probes:

Fluorescence In Situ Hybridization (FISH) is a molecular diagnostic technique utilizing labeled DNA probes to detect or confirm gene or chromosome abnormalities. It is often used in cancer diagnosis. The sample DNA (metaphase chromosomes or interphase nuclei) is first denatured, a fluorescently labeled probe of interest is then added to the denatured sample mixture and hybridizes with the sample DNA at the target site as it re-anneals back into a double stranded DNA. The probe signal can then be seen through a fluorescent microscope and the sample DNA can be scored for the presence or absence of the signal. Unlike most other techniques used to study chromosomes, FISH does not have to be performed on cells that are actively dividing. This makes it a very versatile procedure. Uses encompass a wide range of applications such as the detection of aneuploidy, constitutional microdeletion syndromes as well as rearrangements. These aberrations have clinical implications for numerous genetic diseases such as leukemia, lymphoma, solid tumors, autism and other developmental syndromes. FISH probes are commonly made from BAC clones. Empire Genomics provides access to over one million BAC clones from the Roswell Park Cancer Institute genomic libraries, which are available for purchase as custom-labeled FISH probes. Empire Genomics can provide custom designed FISH probes and also offers a number of premade gene specific probes. Control probes are available as well.

Custom FISH Probe Designs

Empire Genomics specializes in custom development of FISH probes based on customer specifications. Our custom FISH solutions extend beyond single gene, single region analysis. Our FISH probe panels utilize multiple probes that are each labeled with a unique fluorophore. This allows for the simultaneous identification of several possible anomalies in a single sample.

 

Empire Genomics will work with you to design custom FISH probe panel(s) for simultaneous coverage of larger regions of interest, which may require the design a probe panel for full coverage of specific diseases. All Empire Genomics FISH probes are directly labeled using standard Nick Translation protocols and are provided with hybridization buffer solution.

Gene Specific Probes

Empire Genomics manufactures locus-specific probes that are ideal for the rapid identification of a range of chromosomal aberrations across the genome. Specific to regions of interest in oncology and constitutional syndromes, our catalog probes are designed for the purpose of detecting and defining various rearrangements, deletions and trisomies frequently observed in these areas.

 

Chromosome Control Probes

Standard controls are typically utilized in cytogenetic laboratory testing, including FISH studies. For metaphase FISH, it is recommended that FISH tests include control probes to tag the chromosome(s) of interest. Such probes afford a limited level of quality control by providing an internal control of hybridization efficiency. The target sequence on a normal chromosome serves as the best control of technical variables. If a probe is used that does not have an inherent chromosome control signal (ie, an X or Y chromosome probe analysis in a male with clonal loss of the Y chromosome), another sample that is known to have the probe target (a normal 46, XY male for this example) should be run in parallel with the patient sample.

BAC Clones

Empire Genomics is pleased to announce the introduction of custom labeled Fluorescence in situ Hybridization FISH Probes for a range of molecular and cytogenetic applications.

Genotyping

The human genome is a three-billion letter string of the DNA bases A, T, C and G (the genetic code). Most of that sequence is the same in everyone. But there are many places in the genome where a single letter of the sequence sometimes differs from one person to the next. The analysis of these DNA differences between individuals has become increasingly important in medical research and diagnostics. SNP genotyping is a measurement of genetic variations of single nucleotide polymorphisms (SNPs) between individuals or cells. It is the most common form of genotyping, which is the measurement of DNA sequence variation. A SNP is a single base pair mutation at a specific locus. SNPs are involved in the etiology of many human diseases and are becoming of particular interest in pharmacogenomics or personalized medicine. Empire Genomics offers SNP analysis services utilizing either the Sequenom or Illumina Infinium platforms. Sequenom methodology is one of the cheapest and most error free technologies for high throughput SNP typing. It uses samples arrayed in 384 well plates and allows custom genotyping of SNPs within candidate genes or genomic intervals. The technology involves PCR amplification of the region containing the SNP of interest, an optimized primer extension reaction to generate allele-specific DNA products, and chip-based mass spectrometry for separation and analysis of the DNA analytes. A single post-PCR primer extension reaction generates diagnostic products that, based on their unique mass values, allow discriminating between two alleles. The entire process has been designed for complete automation including assay development, PCR setup, post-PCR treatment, nanoliter transfer of diagnostic products onto silicon chips, serial reading of chip positions in the mass spectrometer, and final analytical interpretation. The Infinium platform from Illumina is an extremely high throughput SNP genotyping system that allows the identification and scoring of up to 2.5 million SNPs per single DNA sample. The Infinium assay relies on direct hybridization of genomic targets to array-bound sequences. Single base extension is followed by fluorescent staining, signal amplification, scanning, and analysis using the Genome Studio software. Due to the high number of SNPs that can be analyzed on infinium chips, simplicity of sample preparation, and relative ease of data analysis, this platform has been widely exploited for dozens of major studies in human genetics. These include whole genome association studies, population genetic analyses, and copy number variation investigations.

Circulating Tumor Cells

Gene Expression Services

The ability to monitor changes in gene expression has been critical in identifying the causes or development of many diseases, especially cancer. Gene expression profiling or microarray analysis has enabled the measurement of thousands of genes in a single RNA sample. There are a variety of microarray platforms that have been developed to accomplish this and the basic idea for each is the same: a glass slide or membrane is spotted or "arrayed" with DNA fragments or oligonucleotides that represent specific gene coding regions. Purified RNA is then fluorescently labeled and hybridized to the slide/membrane. In some cases, hybridization is done simultaneously with reference RNA to facilitate comparison of data across multiple experiments. After thorough washing, the raw data is obtained by laser scanning. The data may then be entered into a database and analyzed by a number of statistical methods. Typically, researchers utilize expression arrays to investigate global gene expression patterns and use quantitative PCR to confirm and individually monitor the gene or genes associated with the particular condition or disease. Empire Genomics can assist in determining global patterns of gene expression alterations through expression arrays from several instrument platforms, or precisely monitor expression of several genes known to be involved in a disease via quantitative PCR. Illumina and Agilent expression arrays are available. Agilent microarrays are manufactured using a proprietary non-contact industrial inkjet printing process, in which oligo monomers are deposited uniformly onto specially-prepared glass slides. This in situ synthesis process prints 60-mer length oligonucleotide probes, base-by-base, from digital sequence files. The Illumina Expression BeadChip provides genome-wide transcriptional coverage of well-characterized genes, gene candidates, and splice variants, delivering high-throughput processing of 12 samples per BeadChip without the need for expensive, specialized automation. Illumina has whole-genome expression arrays for intact RNA samples and DASL arrays for partially degraded or difficult to obtain samples. Real time PCR analysis is available to quantitatively analyze gene expression of one to five genes of interest. Platforms available include ABI Taqman and BioRad MyIQ. Individual samples or 96 or 384 well plates can be analyzed. Predesigned or custom designed probes can be utilized. Differences among Real-Time PCR kits are largely restricted to the DNA polymerases and the detection methods used. Linear sequence-specific oligo probes, commonly known as TaqMan probes, bear a fluorescent reporter dye at the 5’-end and a quencher molecule at the 3’-end. Usually, they are designed to anneal at a sequence slightly downstream of one of the PCR primers. Since fluorescence dye and quencher are in close proximity, the fluorescence is quenched and not detectable. As soon as the Taq polymerase reaches the 5’-end of the probe it cuts-off the fluorescence dye utilising it’s 5’-3’ nuclease activity, thereby releasing the fluorescent reporter into solution. The resulting increase in fluorescence can be measured to monitor the amplification of the target DNA. These probes are very specific, however, they are rather expensive and a new probe has to be designed for every new target DNA. If extra specificity is not necessary, one may circumvent these drawbacks by switching to Real-Time PCR assays based on fluorescent DNA-binding dyes such as SYBR Green I (BioRad). The latter intercalates non-specifically into double-stranded DNA which leads to a thousand-fold increase of the fluorescence signal. Since the amount of DNA is boosted with every new cycle, the fluorescence increases proportionally and can be monitored to measure the amplification of the target DNA. Empire can assist in selection of the array and expression analysis platform that is best for your needs as well as sample quality and quantity analysis and labeling.

Search for products by Empire Genomics

Empire Genomics products by Product Category

Any other questions?

If you have any questions, we are always at your disposal.
If you have not found a product, just send us a request and we'll take care of the rest.
Feel free to use our online services for your request.

 

Our Online-Service

 

Product Request
Recall Request
Easy Ordering
Bulk Request