Molecular Cytogenetic

CGX Oligo Arrays

perkinelmer-logo-smallCGX Oligo Arrays are microarrays specifically designed, developed and verified by Signature Genomics for the detection of small genetic aberrations associated with learning disability and dysmorphic features in research applications. The oligonucleotide probes on the CGX™, CGX™-HD and CGX™-SNP arrays distributed throughout the genome with specific focus on over 245 cytogenetically relevant regions, 980 functionally significant genes, pericentromeric regions, and subtelomeres.

CGX™ Onco Arrays

perkinelmer-logo-smallCGX™ Onco Arrays are microarrays specifically designed, developed and verified by Signature Genomics for the detection of small genetic aberrations associate with hematological disorders such as leukemias and lymphomas, as well as genes associated with solid tumors. The arrays offer whole genome coverage with specific oncology relevant regions targeted in higher resolution to permit the detection of clinically relevant findings below the detection resolution of conventional karyotyping or FISH analysis. Furthermore, the combination of CGH and SNP probes on the same array allows the detection of copy-number as well as copy-neutral genomic aberrations in one single experiment.

The PerkinElmer CGX™ Onco Arrays and reagents, together with our Oncoglyphix® software package offer a streamlined and simple analysis workflow for faster and more accurate detection of genomic aberrations in oncology samples.

Array characteristics that will benefit your work

  • Proven design, representing over 2410 cancer relevant regions based on hg19
  • Coverage of genes present in the CCMC (Cancer Cytogenomics Micorarray Consortium) and Cancer Gene Census (http://www.sanger.ac.uk/genetics/CGP/census/) designs, genes cited more recently in the literature, and genes that are family members of known tumor-related factors
  • Combined copy number and LOH detection on the same array
  • Oncoglyphix® for fast and streamlined data interpretation

ScanRI

perkinelmer-logo-smallOne critically important step in the microarray analysis workflow is the generation of high-quality images. Our ScanRI scanner portfolio includes easy to use and reliable benchtop scanners that meet these criteria and offer flexibility for array users. All our scanners use a dual laser confocal system, and provide simultaneous 2-color image acquisition with scanning resolutions ranging from 1 μm to 40 μm.

Combined with their low background noise and high sensitivity, our ScanRI portfolio provides attractive solutions that accommodate different workflow requirements.

CGX™ Hybridization Oven

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The CGX™ Hybridization Oven is designed for optimal hybridization performance to achieve consistent and reliable results. The oven is a compact and flexible instrument designed for an optimal microarray processing workflow.

 

High Throughput

Designed to hold up to 24 CGX™ Hybridization Chambers.

Consistent Data

Reproducible results.

Flexibility

  • Variable temperature control range; from + 5° to 70°C (+/- 0.1°C)
  • Variable rotation speed control from 5 to 20 RPM.

BACs-on-BeadsTM Technology

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Fast and targeted molecular karyotyping with new, revolutionary PerkinElmer technology BACs-on-Beads™

BACs are Bacterial Artificial Chromosomes, large cloned sequences of human DNA, typically 170,000 bases long. BACs have long been used for fluorescent in situ hybridization (FISH). BACs-on-Beads is a technology where DNA probes generated from selected BACs are immobilized onto Luminex® encoded beads. The resulting bead sets are used to assay for chromosomal gains and losses from minute sample amounts with high throughput.

A BACs-on-Beads bead set can contain up to 98 different BACs-on-Beads probes targeted to various regions of the human genome. In addition 2 non-homologous oligonucleotide beads are used for background subtraction.

Sample and reference DNAs are enzymatically labeled with biotin. The enzymatic labeling step provides significant amplification of the sample and therefore small DNA amounts can be used as input. BACs-on-Beads analysis comprises hybridization of the purified biotin labeled DNA to BACs-on-Beads probes representing the specific targeted sequences. Post hybridization a fluorescent streptavidin-phycoerythrin reporter is added and bound to the biotin labels. The relative amount of fluorescent DNA bound to the beads is determined using a Luminex instrument system and BoBsoft™ analysis software.

BoBsoft performs normalization of data measured from each sample with respect to data from the male and female references. All samples are compared to both male and female references, so the sex of the sample does not need to be known prior to the assay. Normal diploid loci generate ratios of 1.0. Single copy gains generate ratios of 1.3 to 1.4, and single-allele deletions generate ratios of 0.6 to 0.8. Reliability in the result is achieved by having carefully selected the probes used as well as by having several probes covering a chromosomal region generally deflecting together if a gain or loss has occurred in this region.

KaryoLite™ BoBs™

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Aneuploidy Detection In Preimplantation Genetic Screening (PGS) Research

KaryoLite BoBs has been developed to detect aneuploidies, gains and losses in all 24 chromosomes in a single assay. This assay is being offered for research use only. The product covers both p and q arms of all chromosomes 1-22, X and Y. It is a bead-based molecular karyotyping assay utilizing probes derived from BAC DNA and coupled to encoded microspheres. It consists of 90 DNA probes immobilized onto polystyrene microspheres distinguishable by the Luminex® instrument system.

For True Rapid Aneuploidy Detection

  • Results in less than 24 hours

Complete procedure from sample to result takes less than 24 hours, allowing your laboratory to obtain results the following day.

  • Quick and easy implementation

The KaryoLite BoBs reagents are provided in a single kit.

  • Cost-efficiency

Tens of samples can be run simultaneously reducing the hands-on time required.

  • Easy interpretation

Intuitive BoBsoft™ analysis software presents results that are clear and easy to interpret.

  • More information

Aneuploidies, gains and losses in all 24 chromosomes in one assay.

Constitutional BoBs

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Constitutional BoBs™*, is a BACs-on-Beads™ based assay designed to detect the 5 most common aneuploidies plus gains and losses in 9 well characterized target regions. Constitutional BoBs is a simple, robust assay that offers significant benefits in terms of ease of handling, minute sample volumes, reduced time-to-result and improved pick-up rates.

 

  • Detection of chromosomal gains and losses in 9 microdeletion regions in addition to the most common aneuploidies
  • Results in less than 24 hours from only 100-200 ng of DNA

• More than 80 targets in one assay, up to 96 reactions in a run

Luminex® xMAP® Technology

Luminex® xMAP® Technology is an established multiplexing technology utilizing approximately 5 μm diameter polystyrene beads coded with two different fluorescent dyes.

By using ten different concentrations of each of the two dyes it is possible to generate up to 100 bead types with distinct fluorescent signatures that can be identified through excitation of the coded dyes by the Luminex 100/200™ instrument.

xmap

This allows for a high-throughput, cost-effective multiplexing technology to be implemented in cytogenetic laboratories.

BoBsoft

BoBsoft 2.0 provides data presentation of panel multiplex genomic gain/loss assays. The new features for the application are highlighted below.

 

New BoBsoft 2.0 Features:

 

New Calculation Algorithm and Computed Reference options

  • Users can now choose between the Ratio or Principle Component algorithms, as well as new reference choices (computed and accumulated computed). These options help provide better results when dealing with ‘noisy’ data sets.

Summary Database

  • Historical QC data is now stored to allow monitoring of assay performance and trends
  • Accumulated computed references can also be stored
  • Database Management allows for archiving of the current database to allow accumulation of new data points.

Workflow and User Experience Improvements

  • Automatic BoBs assay panel detection is available when importing results
  • The summary pages and report formats are improved
  • User logins are now available as well as extra security and privileges for admins.

Fragil X product

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FragilEaseTM

Fragile X Syndrome is one of the most commonly inherited forms of intellectual disability and is caused by trinucleotide repeat expansions in the promoter region of the FMR1 gene on chromosome X. When the CGG motif expands above 200 repeats, the FMR1 gene is silenced by methylation causing Fragile X Syndrome with its typical characteristics including elongated face, large or protruding ears and intellectual disability.

Traditionally, Fragile X testing is performed by use of a laboratory developed FMR1-specific PCR often followed by capillary electrophoresis. However, amplifying the entire CGGrich template beyond about 100 – 130 repeats is challenging. In addition, differentiating full mutations from homozygous normal female samples has historically required a Southern blot reflex test.

PerkinElmer’s FragilEaseTM PCR assay is designed to amplify the entire CGG repeat sequence in the FMR1 promoter region. By use of proprietary PCR reagents that allow an accurate amplification of the trinucleotide repeats, FragilEaseTM can reliably detect full mutations with over 900 repeats hence significantly reducing the amount of Southern blot reflexing. In addition, together with the LabChip MultiDX electrophoresis instrument and FraXsoftTM for data analysis and interpretation, PerkinElmer offers a streamlined workflow solution for quick and easy sample analysis with a reporting time of less than a day.

Whole Genome Amplification

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PicoPLEX™ WGA Kit

With PicoPLEX™ WGA (Whole Genome Amplification) kit you can use just one cell to provide the amount of genomic data that has previously required as many as 10,000 cells. Researchers using PicoPLEX WGA reagents can have confidence in the DNA amplification of all 24 chromosomes, for example, prior to KaryoLite BoBs or CGX oligoarray analysis. Single cell samples can be taken from polar bodies, blastomeres or blastocysts for preimplantation genetic diagnosis (PGD) and preimplantation genetic screening (PGS) research applications.

Main benefits include

  • High reproducibility BoBs or aCGH results
  • Low background
  • Simple workflow
  • Results obtained rapidly

The PicoPLEX WGA kit produces amplified DNA suitable for:

  • CNV (Copy Number Variant) analysis using BoBs or CGX oligoarrays
  • SNP genotyping using arrays
  • Mutation detection using arrays and PCR

KRAS and NRAS mutation detection

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Colorectal Cancer (CRC) is the 3rd most common diagnosed cancer with an estimated ~1,000,000 new cases per year worldwide. 50%–60% of patients diagnosed with colorectal cancer will develop metastases during the course of their disease.

One common therapy choice for metastatic CRC (mCRC) patients is the use of EGFR inhibitors such as cetuximab and panitumumab. Efficiency of treatment with both these biologic agents has, up until now, been attributed to the mutation status of KRAS exon 2. Recent studies however have identified additional, previously unreported mutations in the KRAS and NRAS genes (collectively referred to as “RAS mutations”) that are highly relevant when considering administration of anti-EGFR therapies. These additional mutations were found to increase the mutation detection from 40% to 57%, thus identifying an additional 17% of patients potentially not responding to panitumumab therapy.