Genome Explorations on Genome Explorations

Awards

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News

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Custom Solutions & Advanced Analyses

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We have the SOLUTIONS to meet your BIOINFORMATICS needs

When it comes to developing custom pipelines, implementing the most cutting edge analyses & profiling techniques, we work with our clients to ensure their informatics needs are met. Whether implementing a sofisticated analysis method, designing a custom analysis pipeline, utilizing cutting-edge machine learning techniques for biomarker classification, or simply producing publication-ready figures, our staff combines years of experience with highly qualified personnel to meet your every need.

Below, we have provided a listing of some of our most commonly used tools, software packages, etc. when performing advanced analysis. However, the below tools represent the “tip of the iceberg”. When it comes to our customized solutions, our staff is highly familiar with a variety of statistical programing languages (R, PASW, SAS), general programming languages (Perl, Python, GO, etc.), shell languages (bash, zshell, etc.), and operating system (Windows, MacOs, Linux, etc.). If you would like a custom solution designed to meet your research needs, please direct inquiries to Bioinformatics Scientist Evan Savage, M.S.

GeneMaths XT 2.1

GeneMaths XT 2.1 is perhaps the most complete and professional software for microarray analysis available. Its advanced concept of layers and subsets makes it is possible to work with different layers for different data outputs, for example Cy3 and Cy5, standard deviations, error values, etc., as well as different subsets of genes and/or arrays. Also unique is the full error handling through all analysis, mining, and statistics functions. Further features include: * Active History concept: record and repeat all steps of the analysis through history files and templates * Reliable data normalization for all types of arrays * Interactive querying and pattern matching * Easy plot wizard for all types of plots and graphs * Unsupervised learning through transversal clustering, hierarchical k-means partitioning, PCA, Discriminant Analysis, Self-organizing maps * Supervised learning using neural networks, support-vector machines, k-nearest neighbor * Analysis of variance, multivariate analysis, and a large number of statistical tests * Special analysis tools for time-course experiments * Seamless interaction between all analysis applications * Interactivity with databases on the Internet * Automation and customization through powerful script language

Gene Set Enrichment Analysis (GSEA)

With the explosion of microarray solutions and high-throughput sequencing technologies, RNA expression analysis has become a standard tool in biomedical research. Despite the advancements in genomics technologies, extracting the biological relevance from these applications presents a challenge. The Broad Institute’s GSEA software provides an open-source interface for implementing a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. Using this method, GSEA provides an integrated solution to perform pathway enrichment analysis across a multitude of databases (GO, KEGG, Pathway Commons, etc.), allowing researchers to glean the biological and functional relevance from a priori sets of genes.

Bioconductor Software

The Genome Explorations team always seeks to push the limits of bioinformatics and provide cutting-edge applications and analysis solutions. Oftentimes, this means implementing the latest non-standardized scientific algorithms for data normalization and analysis while exploring the most advanced visualization tools available. Based primarily on the statistical R programming language, Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data. Bioconductor provides access to the most powerful statistical and graphical methods for the analysis of genomic data. Combined with the proficiency of our bioinformatics team, Genome Explorations can provide and implement virtually any analysis or data visualization package for: pre-processing of Affymetrix and cDNA array data, identification of differentially expressed genes, linear and non-linear modeling, prediction, resampling, cluster analysis, time series analysis, supervised classification via support vector machines.

Next-Generation Sequencing Analysis

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Data Acquisition and Basic Analyses: Illumina

Illumina Miseq Reporter Software

The MiSeq system is the first desktop sequencer to offer a fully integrated sequencing ecosystem and provides automated downstream secondary analysis following basecalling by the MiSeq system. After defining a workflow in Illumina’s Experiment Manager, the MiSeq Reporter software launches automatically post-sequencing to perform a variety of anlyses: library QC, demultiplexing, generation of FASTQ files, alignment, variant detection, and VCF generation. Available workflows for the software include:
* Amplicon DS * Assembly * Enrichment * FASTQ Generation * Library QC * Metagenomics * PCR Amplicon * Resequencing * Small RNA * Targeted RNA * TruSeq Amplicon

Illumina Sequencing Analysis Viewer (SAV) Software

Assessing the quality of a sequencing run in real-time is essential to proper maintenance, operation, and evaluation of NGS experiment quality. Illumina’s SAV provides a real-time analysis (RTA) software solution for viewing critical quality metrics on the Illumina sequencing system. Of the multitude of metrics viewable in the software, SAV allows for live identification of flow cell over/under-clustering, monitoring cycle-to-cycle intensities, base-calling quality, read quality, and error rates. In addition to monitoring live run quality, the SAV software allows for quick and easy assessment of post-run quality metrics.

Illumina VariantStudio™ 2.2

The Illumina VariantStudio data analysis software application enables researchers to quickly identify and classify disease-relevant variants, and then communicate significant findings in a structure report. Following secondary analysis and VCF generation in MiSeq Reporter, VariantStudio 2.2 allows for seamless assessment of variant calling, annotation, classification, and reporting. Coupled with BaseSpace, VariantStudio provides virtually instantly accessible reports for collaborative sequencing projects.

Advanced Analyses: Qiagen

Biomedical Genomics Workbench 4

Biomedical Genomics Workbench is a comprehensive and accurate data analysis platform that enables you to find the signal in the noise in your cancer and hereditary disease NGS data. With its broad selection of end-to-end analysis workflows, tools, and visualization modules, it enables easy and accurate discovery, verification, and validation of novel disease biomarkers.
Discover novel insights with greater than 95% sensitivity and unsurpassed accuracy. Biomedical Genomics Workbench guides you through a complete analysis of your genome, exome, targeted amplicon, transcriptome, and epigenetic NGS sequencing data for results you can trust.

Complete end-to-end and customizable analysis workflows for the comprehensive discovery, verification, and validation of novel biomarkers
Specialized functionalities such as primer and primer-dimer removal for highly accurate targeted amplicon sequencing results
High sensitivity detection of germline and low frequency variants from DNA-seq and RNA-seq data
Unsurpassed accuracy for copy number detection in exome and targeted amplicon sequencing data
Easy viewing of findings such as dynamic protein structures in 3D, and sequencing reads afford faster discovery

Microarray Analysis

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Data Acquisition and Basic Analyses

GeneChip® Command Console® (AGCC)

AGCC is the latest generation of instrument control software for GeneChip systems. The Command Console® software provides an intuitive set of tools for instrument control and data management used in the processing of GeneChip Arrays. Genome Explorations uses the AGCC suite for automated data collection and instrument control with the GeneChip® Fluidics Station 400 and the GeneChip® Scanner 3000. Using the latest in scientific algorithms, the software summarizes probe cell intensity data (CEL file generation) and enables sample/array registration, data management, instrument control, and automatic image gridding for downstream probe-level summarization (CHP file generation) via other Affymetrix software applications or Bioconductor modules. The Command Console® software provides seamless integration with downstream primary analysis applications such as Affymetrix® Expression Console, Axiom Analysis Suite, Genotyping Console, and Transcriptome Analysis Console.

Affymetrix® Expression Console ™ Software

The Expression Console™ provides an intuitive software package allowing for quick and easy intensity normalization, data quality control, and data summarization for any GeneChip array. Using the latest advancements in normalization algorithms, the Expression Console contains convenient, standardized workflows for both gene-level and exon-level analysis. Genome Explorations harnesses the Expression Console to summarize data from thousands of samples, across thousands of genes, hundreds of thousands of exons, and hundreds of thousands of different transcript isoforms. The software provides a convenient, easy-to-use analysis workflow that enables CHP files to be generated from CEL files with minimal effort using standardized approaches tailored by Affymetrix and informed by the latest scientific advancements in genomics. Downstream, the Expression Console provides seamless integration with Affymetrix® Transcription Analysis Console for analysis of Affymetrix transcriptomic microarray solutions.

Affymetrix® Transcriptome Analysis Console (TAC) Software 4.0

TAC 4.0 was developed by Affymetrix to overcome the complexities of identification of differential expression, identification of alternative splicing events, and visualization of complex gene pathway networks, miRNA and target gene interactions, and alternative splicing events. Combined with the comprehensive coverage of Affymetrix high-density microarray solutions, Genome Explorations uses TAC 4.0 software for advancing from raw data to biological results in minutes. Integrating the advanced LIMMA & EventPointer capabilities from Bioconductor, Genome Explorations uses the TAC 4.0 software to provide a basic analysis workflow for performing simple statistical tests for differential expression and splicing events in low-complexity experimental models.

Affymetrix® DMET™ Console

DMET™ Console Analysis Software provides both the flexibility for user-defined reporting as well as comprehensive translation for the most relevant genes. The DMET Plus Solution, which includes arrays, assay, and the DMET Console Analysis Software, provides the broadest coverage, single pharmacogenetic assay. Genome Explorations utilizes the DMET system to enable rapid genetic analysis of the involvement of metabolic pathways in drug metabolism for clinical pharmacogenetic research. Using the DMET system allows us to take one step closer towards the vision of personalized medicine by helping to avoid adverse drug responses, increase treatment efficacy, and provide improved healthcare outcomes.

Chromosome Analysis Suite (ChAS)

Chromosome Analysis Suite is a software offering intuitive and flexible workflow for accurate analysis tailored for cytogenetics. ChAS was developed with input from leading experts and is customized for copy number and cytogenetics research analysis and reporting. ChAS allows for the summarization of chromosomal aberrations across the genome. Chromosomal aberrations may include copy number gain or loss, mosaicism, or loss/absence of heterozygosity (LOH/AOH). Combined with expression data, we can integrate copy number data with Concurrent Molecular Analysis Profiling (CoMAP™). In addition, ChAS utilizes the latest human genome build (Hg38) to provide the most up-to-date ONIM, DGV, Ensembl, ClinVar, and RefSeq annotations.

Patents Genome-Explorations,Inc has Contributed to

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Cloning of cytochrome p450 genes from Nicotiana

Publication Number: US 8658856 B2 Publication Date: Feb 25, 2014 Inventor: Dongmei Xu

Abstract: The present invention relates to p450 enzymes and nucleic acid sequences encoding p450 enzymes in Nicotiana, and methods of using those enzymes and nucleic acid sequences to alter plant phenotypes.
Contribution: Genome Explorations generated data used in support of patent and application. Hybridization experiments were conducted by Genome Explorations, Inc. (Memphis, Tenn.). The RNA samples used in hybridization consisted of six pairs of nonconverter/converter isogenic lines that were induced by ethylene treatments…Twelve sets of hybridizations were successful as evidenced by the Expression Report generated using detection instruments from Genome Explorations…

Tissue-specific differentiation matrices and uses thereof

Publication Number: US 20130195814 A1 Publication Date: Aug 1, 2013 Inventor: Xiao-Dong Chen

Abstract: In some aspects, this invention provides a method of making a bone marrow-derived tissue-specific stem cell proliferation, expansion, isolation and rejuvenation extracellular matrix. In other aspects, this invention provides a method of making a tissue-specific fibroblast-derived stem cell differentiation extracellular matrix. Also provided are methods of using such a cell-derived preservation or differentiation matrices to induce tissue-specific differentiation of pluripotent cells, repair damaged tissue, and treat a subject having a physiologic deficiency using the same.
Contribution: Genome Explorations generated data used in support of patent and application. After pooling, RNA was sent to Genome Explorations (available on the world wide web at qenomeexplorations.com). There, RNA was converted to DNA and the labeled cRNA was prepared, which were hybridized onto Affymetrix Human Genome U133 Plus 2.0 chips. The chips were scanned, and data were pre-analyzed using Affymetrix MAS 5.0. Gene expression levels on “Plastic” chips (Plastic-A, Plastic-B, and Plastic-C) were compared…

Use of emt gene signatures in cancer drug discovery, diagnostics, and treatment

Publication Number: US 20120302572 A1 Publication Date: Nov 29, 2012 Inventor: Julie Kan, Stuart Thomson, Gretchen M. Argast, Matthew E. O’Connor, Murray Robinson, Bin Feng, Joerg Heyer, Maria I. Chiu, Richard Nicoletti

Abstract: The present invention provides diagnostic methods for assessing the EMT status of tumor cells, and for predicting the effectiveness of treatment of a cancer patient with an EGFR or IGF-1R kinase inhibitor, utilizing an EMT gene signature index score. The present invention further provides methods for treating patients with cancer that incorporate these methods.
Contribution: Genome Explorations generated data used in support of patent and application. On experimental day 7, the cells were trypsinized, washed, pelleted, and snap frozen. Cell pellets were sent to Genome Explorations (Memphis, Tenn.) or Expression Analysis (Durham, N.C.) for isolation of RNA. mRNA was then processed to cDNA, amplified and labeled for hybridization to Affymetrix U133 Plus 2.0 mRNA microarrays. After hybridization and washing,..

Methods and Compositions for Tissue Engineering

Publication Number: US 20120148539 A1 Publication Date: Jun 14, 2012 Inventor: Moulay Hicham Alaoui-Ismaili

Abstract: Disclosed herein are methods and compositions for promoting endochondral bone formation. The invention includes methods of promoting endochondral bone formation by down-regulating the expression of the DIO2 gene or the activity of the deiodinase protein. The invention also includes methods of up-regulating the activity of the FGFR3, ADAMTS9, HEY1, HAS3, and/or MFI2 genes and/or the activity of the expression products of those genes to promote endochondral bone formation. The invention also includes compositions of BMP-7 and agonists of FGFR3, ADAMTS9, HEY1, HAS3, and/or MFI2 proteins. Compositions can further include mesenchymal stem cells.
Contribution: Genome Explorations generated data used in support of patent and application. Data analysis was performed by Genome Explorations, Inc. (Memphis, Tenn.). Data were normalized using two different methods, the Affymetrix Statistical Algorithm MAS 5.0 (GCOS v1.4) and RMA (Lockhart et al., (1996), Nat Biotechnol…Each normalized data set was subjected to ANOVA and independent t-tests at each time point (treated versus control) using the Benjamini-Hochberg FDR correction method…

Methods for the identification of agents that inhibit mesenchymal-like tumor cells or their formation

Publication Number: US 7951549 B2 Publication Date: May 31, 2011 Inventor: John D. Haley, Stuart Thomson, Julie Kan, Salam A. Shaaban

Abstract: The present invention provides tumor cell preparations for use as models of the EMT process for use in the identification of anti-cancer agents, wherein said tumor cell preparations comprise cells of the epithelial tumor cell line H358, which are stimulated by receptor ligands to induce EMT, or which have been engineered to inducibly express a protein that stimulates EMT. The present invention also provides methods of identifying potential anti-cancer agents by using such tumor cell preparations to identify agents that inhibit EMT, stimulate MET, or inhibit the growth of mesenchymal-like cells. Such agents should be particularly useful when used in conjunction with other anti-cancer drugs such as EGFR and IGF-1R kinase inhibitors, which appear to be less effective at inhibiting tumor cells that have undergone an EMT.
Contribution: Explorations generated data used in support of patent and application. On experimental day 7, the cells were trypsinized, washed, pelleted, and snap frozen. Cell pellets were sent to Genome Explorations for mRNA isolation and analysis by Affymetrix Human Genome 133 Plus 2.0 Array. On experimental day 7, cells were harvested for protein. For analysis of total protein, nuclear, membrane and cytosol fractions were prepared using PROTEOEXTRACT® reagent (EMD #444810). Proteins were then precipitated using …

Compositions and methods of use of EPB1, and ErbB3 binding protein

Publication Number: US 7838495 B2 Publication Date: Nov 23, 2010 Inventor: Yuexing Zhang, Anne Hamburger

Abstract: Inhibition of the proliferation of hormone refractory prostate cancer cells is achieved by administering EPB1, an ErbB3 binding protein, in combination with another anti-proliferation therapy such as administration of antiandrogens, other anticancer agents, radiation therapy, or surgery. Administration of EPB1 reverses the phenotype of hormone-resistant prostate cancer cells to hormone-sensitive prostate cancer cells.
Contribution: Genome Explorations generated data used in support of patent and application. First and second strand cDNA were synthesized from 5-15 μg of total RNA at Genome Explorations (Memphis, Tenn.) using the SuperScript Double-Stranded cDNA Synthesis Kit…Microarray processing and data analysis was performed at Genome Explorations (Memphis, Tenn.). U133A oligonucleotide arrays (Affymetrix) containing ˜33,000 full length annotated genes together with additional probe sets designed to represent EST sequences were used for the analysis…

Nucleotide sequences coding plant monooxygenase for use in identifying modulators of nornicotine levels in tobacco

Publication Number: US 7812227 B2 Publication Date: Oct 12, 2010 Inventor: Dongmei Xu

ErbB3 binding protein compositions and methods of use

Publication Number: 7,718,626 Publication Date: May 18, 2010 Inventor: Yue-xing Zhang, Anne W. Hamburger

Abstract: A method of repressing a cell-cycle gene, which is regulated by an E2F transcription factor, in a cell, wherein the method comprises contacting the cell with a cell-cycle gene-repressing amount of ErbB3 binding protein (Ebp1); a method of inhibiting prostate cancer in a mammal, wherein the method comprises administering to the mammal a prostate cancer-inhibiting amount of Ebp1; a composition comprising an Ebp1-expressing viral vector that expresses a cell-cycle gene-repressing amount of Ebp1; and a composition comprising polymer-packaged DNA comprising and expressing a cell-cycle gene-repressing amount of Ebp1.
Contribution: Genome Explorations generated data used in support of patent and application. Microarray Analysis: First and second strand cDNA were synthesized from 5-15 μg of total RNA at Genome Explorations (Nashville, Tenn.) using the SuperScript Double-Stranded cDNA Synthesis Kit (Gibco Life Technologies, Gaithersburg, Md.) and an oligo-dT24-T7 (5′-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3′) (SEQ ID NO: 3) primer according to the manufacturer’s instructions…

Nicotiana nucleic acid molecules and uses thereof

Publication Number: US7700834 B2 Publication Date: Apr 20, 2010 Inventor: Dongmei Xu, Mark T. Nielsen

Abstract: The present invention features Nicotiana nucleic acid sequences such as sequences encoding constitutive, or ethylene or senescence induced polypeptides, in particular cytochrome p450 enzymes, in Nicotiana plants and methods for using these nucleic acid sequences and plants to alter desirable traits, for example by using breeding protocols.
Contribution: Genome Explorations generated data used in support of patent and application. All 14 sets of hybridizations were successful as evidenced by the Expression Report generated using detection instruments by Genome Explorations, Inc. (Memphis, Tenn.). The main reports included analyses of Noise, Scale factor, background, total probe sets, number and percentage of present and absent probe sets, signal intensity of housekeeping controls…

Method of Regulating Gene Expression

Publication Number: US ²⁰⁰⁹⁄_0099259 A1 Publication Date: Apr 16, 2009 Inventor: Zeina Jouni, Joshua Anthony, Steven C. Rumsey, Deshanie Rai, Kumar Sesha Kothapalli, James T. Brenna Abstract: The present invention is directed to a novel method for modulation the expression of one or more genes in a subject by administering an amount of DHA and ARA to the subject.
Contribution: Genome Explorations generated data used in support of patent and application RNA preparations and array hybridizations were processed at Genome Explorations, Memphis, Tenn. http://www.genome-explorations.com. The completed raw data sets were downloaded from the Genome Explorations secure ftp servers. Data are expressed as mean±SD. Statistical analysis was conducted using analysis of variance (ANOVA) to test the hypothesis of equivalent means for measures taken at 12 weeks…

Use of dha and ara in the preparation of a composition for regulating gene expression

Publication Number: WO2007100566 A2 Publication Date: Sep 7, 2007 Inventor: Zeina Jouni, J Thomas Brenna, Joshua C Anthony, Kumar Sesha Durga Kothapalli, Steven C Rumsey, Deshanie Rai

Abstract: The present invention is directed to a novel method for modulating the expression of one or more genes in a subject by administering an amount of DHA and ARA to the subject.
Contribution: Genome Explorations generated data used in support of patent and application. (One hybridization was performed for each animal (12 chips total). RNA preparations and array hybridizations were processed at GenomeExplorations, Memphis, TN. The completed raw data sets were downloaded from the Genome Explorations secure ftp servers. Statistics ### [00064] Data are expressed as mean±SD. Statistical analysis was conducted using analysis of variance (ANOVA)…

Method for increasing the expression of pulmonary surfactant protein-B

Publication Number: US 20070202052 A1 Publication Date: Aug 30, 2007 Inventor: Thomas Brenna, Kumar Sesha Durga Kothapali, Zeina Jouni, Joshua C. Anthony, Steven C. Rumsey

Abstract: The present invention is directed to a novel method for increasing the expression of pulmonary surfactant protein-B in an infant. The method comprises administration of a therapeutically effective amount of DHA and ARA, alone or in combination with one another, to the infant.
Contribution: Genome Explorations generated data used in support of patent and application. RNA preparations and array hybridizations were processed at Genome Explorations, Memphis, Tenn. http://www.genome-explorations.com. The completed raw data sets were downloaded from the Genome Explorations secure ftp servers…

Mammalian cell modified with genes encoding plant late embryogenesis protein HVA1, trehalose transport protein, or a trehalose synthesis pathway; freezing and/or drying organs for storage prior to use

Publication Number: US 20070202052 A1 Publication Date: Aug 25, 2005 Inventor: Paul Conrad, Lynn Allen-Hoffmann

Abstract: The present invention relates generally to compositions and method for freezing and/or drying organs for storage prior to use. In particular, the present invention relates to the genetic modification of cells used to form organs so that organs formed from the genetically modified cells can be dried. According to the invention, mammalian cells may be modified with genes encoding plant late embryogenesis protein HVA1, trehalose transport protein, or a trehalose synthesis pathway. The invention also provides methods of treating patients with organs that have been preserved by freezing and/or drying.
Contribution: Genome Explorations generated data used in support of patent and application. Gene array analysis is used to monitor global changes in gene expression following recovery from the dried state, RNA from rehydrated and control (not preserved) tissue is submitted to Genome Explorations, Inc., which will perform gene expression array hybridization and data analysis. Biotinylated cDNA probes is generated from the RNA samples and is hybridized to the U133 GeneChips from …

Mammalian cell modified with genes encoding plant late embryogenesis protein HVA1, trehalose transport protein, or a trehalose synthesis pathway; freezing and/or drying organs for storage prior to use

Publication Number: US 20050186185 A1 Publication Date: Aug 25, 2005 Inventor: Paul Conrad, Lynn Allen-Hoffmann

Companion Dx & Biomarker Discovery

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Companion and Complimentary Diagnostics

Companion diagnostics continue to play an ever expanding role in personalized healthcare as physician’s seek to better more accurately forecast patients’ potential responses to various treatment options. Whether you are a pharmaceutical company embarking on a new drug/Companion diagnostic offering or an independent Companion diagnostic manufacturer, our team can provide unparalled support to ensure expedient and successful parallel development of both your companion test and drug/biologic.

Types of Services Available

Cytogenetics

Molecular

Genotyping Analysis (SNP)

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Mutation Analysis: Single Nucleotide Poloymorphism (SNP)

Mutations are genetic alterations either in germ or non-germ (somatic) cells. Mutations can impact the formation of various diseases as well as affect the response of a patient to particular drug treatments. The mutation can be an insertion, deletion, missense or nonsense mutation in the coding or non-coding regions. In some cases, a mutation occurs at the intron-exon boundary and affects the normal splicing of the transcript. Mutation analysis, mutation screening, exon resequencing, and SNP discovery all involve high volumes of PCR amplification and sequencing. Genome Explorations provides extensive expertise to support your SNP and mutation analysis research objectives.

Services Include:

Extraction of genomic DNA from samples (fresh, fixed, and/or paraffin-embedded)

Amplicon selection and primer design to target regions of interest or SNPs

Assay development and optimization

PCR amplification of genomic DNA using optimized conditions

High-throughput PCR purification and bi-directional DNA sequencing per amplicon

Automated and manual sequencing results analysis

Final report identifying mutations

Expression Analysis

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Gene Expression Services

Scientists at Genome Explorations have worked with over 350 scientists worldwide in meeting their gene expression needs. As an industry leader in the microarray field and a certified provider of Affymetrix® microarray services and Life Technologies qPCR services, we have developed a series of SOPs that allow us to reproducibly generate global gene expression data sets of the highest quality. Our validated microarray protocols consistently result in sample-to-sample variability of less than 0.5% (industry standard is 2.0%).

Validation of microarray results or small and intermediate sized gene expression projects can be analyzed by RT-qPCR or digital PCR, utilizing Life Technologies, BioRad, and Fluidigm Biomark platforms.

Applications

Gene Expression Profiling: High through-put gene expression screening

Diagnostics: Disease specific development of diagnostic tools

Biomarkers: Discovery of diagnostics and therapeutics biomarkers

Pharmacogenomics: Target identification and validation

Toxicology: Tox. screening for existing and novel drugs

Chromosomal Abnormality Analysis (FiSH)

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Genotyping and Chromosome Analysis Services

Applications

High-through-put screening of genome wide polymorphisms
Disease specific association studies
Disease specific linkage studies
Pharmacogenomics – target identification and validation
Haplotype testing
Chromosome copy number analysis
Gene copy number analysis
Loss of heterozygosity (LOH) analysis

Genomic Research Services

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DEFINE, DESIGN, DISCOVER

Our experienced scientists work one-on-one with scientists, researchers and clinicians to provide a ‘Complete Solution’ for Genotyping, Gene Expression and miRNA Profiling Services, from experimental design to in-depth data analysis and advanced bioinformatics. Our ‘Complete Solutions’ include state of the art Technologies from Illumina, Thermofisher Scientific and Affymetrix for challenging specimens, such as LCM, FFPE and whole blood samples. With over 40 years of combined experience, our scientists at Genome Explorations have developed detailed standard operating procedures (SOPs) that allow us to consistently generate the highest quality, most reproducible data sets in the industry. Genome Explorations has received global acknowledgements for their achievements, and has been the industry leader in Providing Complete Genomics Solutions since 2001.

Define

With over 40 years of combined experience in molecular research and diagnostics, Genome Explorations partners with our clients to define the core biological and clinical requirements for each individual project. We know that obtaining the right answer is impossible without asking the right questions.

Design

After problem definition and delineation of research goals, Genome Explorations collaborates with our clients to ensure the technology selected for analysis will achieve the most specific and complete result. Whether your research requires expression profiling, genotyping or chromosomal abnormality analysis, Genome Explorations has the appropriate platform.

Discover

As part of our ‘Complete Solution’ the Bioinformatics team at Genome explorations provides advanced bioinformatics and statistical analyses generate meaningful usable data sets that allow our clients fastest path to publication and or submission for clinical trials.

We are a CAP-accredited, CLIA-licensed facility with unequaled access, efficiency, and flexibility. Genome Explorations is a global leader in genomic analyses and next generation sequencing leading to major impact on molecular diagnostics.

Inherited Disease MDx

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Predict, Prepare, Prevent!

As research continues to gain new insight into the role of genes in various diseases, including cancer, we now have the ability to test for certain genes known to increase risks for birth defects, cancers, heart disease, and many other maladies. Identification of predisposition mutations allow a proactive approach to inform the decision making process, proactively assess treament options, and help reduce the risk of developing a deadly disease later in life.

Cancer Predisposition

GenHet Cancer Predisposition Profile (145 Genes)

Genome Explorations cancer predisposition profile provides essential information for patients with a personal or family history of cancer. Identification of potential cancer risk is the first step in determining the best way to possibly delay, or even prevent, the development of certain cancers. Predisposition Targeted Panel is a multiplexed PCR-based assay for targeted enrichment of the coding (exonic) regions of the 145 genes commonly mutated in 88 inherited oncogenic diseases

Cardiomyopathy

GenCardio Cardiomyopathy Panel (58 Genes)

Cardiomyopathy refers to disease of the heart. Cardiomyopathy can have many causes including genetic mutation. Genome Explorations provides an extensive look at the genetic mutations associated with inherited cardiomyopathy including:

Hypertrophic cardiomyopathy(HCM or HOCM)
Dilated cardiomyopathy (DCM)
Arrhythmogenic right ventricular cardiomyopathy (ARVC)

Cystic Fibrosis

GenHet CFTR Panel (1 Gene)

CFTR stands for Cystic Fibrosis Transmembrane Conductance Regulator. The CFTR protein is essential in for salt and water balances on epithelial surfaces such as the lung and pancrease. In cystic fibrosis, mutations affect the the mucus layer lining the epithelial surfaces in the lungs and pancreas. Well over one thousand mutations have been described that affect the CFTR gene in different ways.

Inherited Disease(s)

GenHet Carrier Inherited Diseases Panel (164 Genes)

GenHet Carrier Testing Panel is a collection of multiplexed PCR primer assays for targeted enrichment of the coding (exonic) regions of 164 genes mutated in the most deleterious and most prevalent (at least 5 in one million) recessively (autosomal or X-linked) inherited disorders. Carrier testing checks whether both parents planning to conceive children carry recessive mutations for the same disease(s), which could be inherited by the children. Causal mutations in the disease-associated genes are known for many but not all of these diseases.

Cancer Specific MDx

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Detect, Characterize.

Genomic research continues to identify mutations associated with specific cancers and, in combination with clinical research, to identify their clinical relevance to a specific cancer and the prognosis/treatment for patients. While some mutations may be pathogenic, some are benign. Mutation profiling allows us to identify which mutations are present, determine clinical significance of those mutations, and identify pathogentic mutations with actionable therapies. To this end, mutation profiling using next generation sequencing and targeted cancer-specific panels allows us to detect mutations across multiple genes simultaneously and to screen patient susceptibility to a specific cancer.

All GenOnc Cancer-Specific Gene Panels

Breast Cancer

GenOnc BRCA1 & 2 Gene Panel (2 Genes, 174 amplicons; CPT codes: 81211, 81213)

GenOnc Germline and somatic mutations of BRCA genes have been shown, in clinical trials of advanced ovarian cancer, to induce favorable responses to a class of drugs known as PARP inhibitors. BRCA genes are now important biomarkers for the management of ovarian cancer. The BRCA1 and BRCA2 GeneRead DNAseq Targeted Panel has been designed to enable comprehensive and efficient analysis of the two genes from blood and FFPE samples. The panel is part of a sample-to-insight workflow that enables you to go from DNA sample to interpreted variants in 3 days.

GenOnc Comprehensive Breast Cancer Panel (93 Genes)

GenOnc Breast Cancer Targeted Panel is a collection of multiplexed PCR primer assays for targeted enrichment of the coding (exonic) regions of the 44 genes most commonly mutated in human breast cancer samples. Mutations in these oncogenes and tumor suppressor genes are often relevant for tumor classification, and warrant extensive investigation to enhance the understanding of carcinogenesis. Breast cancer is a heterogeneous disease, and each tumor subtype has a specific prognosis and molecular mechanism. These molecular mechanisms include point mutations, potentially rendering the gene of interest inactive or hyperactive. For example, PIK3CA (p110α), a PI3K catalytic subunit, is commonly mutated in a variety of breast cancer subtypes. One common activating mutation for PIK3CA is H1047R. This mutation can cause an increase in PI3K/PTEN/AKT signaling, a common carcinogenic mechanism. There are hundreds of additional identified PIK3CA mutations, and many have functional consequences. In addition, there are clearly many other genes that are highly mutated in breast cancer. Therefore, sequencing analysis is an efficient method to examine a tumor sample for multiple potentially mutated genes. This panel narrows the focus to the most relevant mutated genes in breast cancer, using a variety of resources such as recent whole genome/exome sequencing studies from scientific networks including the Cancer Genome Atlas. Curated databases such as the Cancer Gene Census and COSMIC (Catalogue of Somatic Mutations in Cancer) are also used.

Colorectal Cancer

GenOnc Colorectal Cancer Panel (71 Genes)

GenOnc Colorectal Cancer Panel is a collection of multiplexed PCR primer assays for targeted enrichment of the coding (exonic) regions of the 38 genes most commonly mutated in human colorectal cancer samples. Mutations in these oncogenes and tumor suppressor genes are often relevant for tumor classification, and warrant extensive investigation to enhance the understanding of carcinogenesis. Colorectal cancer has an increased incidence in older patients, and is easily treated if detected at an early stage. There are 2 major mechanisms of colorectal cancer progression: microsatellite instability and chromosomal instability. Due to these mechanisms, multiple genes are commonly mutated in a colorectal tumor. For example, the tumor suppressor gene adenomatosis polyposis coli (APC) is commonly mutated in colorectal cancer, dysregulating Wnt signaling. Each patient’s tumor is different, and few present with identical APC mutations. In addition, Wnt signaling can also be dysregulated in colorectal cancer due to β-catenin (CTNNB1) mutation or mutations of genes further upstream in the signaling pathway. Therefore, a panel of key genes commonly mutated in colorectal cancer is an efficient way to research a tumor sample’s potential carcinogenic mechanisms. This panel narrows the focus to the most relevant mutated genes in colorectal cancer, using a variety of resources such as recent whole genome/exome sequencing studies from scientific networks including the Cancer Genome Atlas. Curated databases such as the Cancer Gene Census and COSMIC (Catalogue of Somatic Mutations in Cancer) are also used.

Myeloid Leukemia

GenOnc Myeloid Neoplasm Panel (141 Genes)

GenOnc Myeloid Neoplasms Panel is a collection of multiplexed PCR primer assays for targeted enrichment of thecoding (exonic) regions of the 50 genes most commonly mutated in human myeloid leukemia samples. Mutationsin these oncogenes and tumor suppressor genes are often relevant for cancer classification, and warrant extensiveinvestigation to enhance the understanding of carcinogenesis. The term myeloid leukemia covers a spectrum ofdiseases called hematological neoplasms, but mostly refers to cancer of the blood or bone marrow characterized by an abnormal increase in immature myeloid white blood cells. Common initiating events for leukemia carcinogenesis are upregulation of survival genes and dysregulation of cell growth. Genes commonly mutated during these events include the receptor tyrosine kinases FLT3 or KIT for acute myeloid leukemia, and TP53 or RB1 for chronic myeloid leukemia. Each of these genes can acquire a variety of different mutations, and each myeloid neoplasm itself can acquire mutations in multiple genes. Therefore, a panel of key genes commonly mutated in myeloid leukemia is an efficient way to research a tumor sample’s potential carcinogenic mechanisms. This panel narrows the focus to the most relevant mutated genes in myeloid leukemia, using a variety of resources such as recent whole genome/exome sequencing studies from scientific networks including the Cancer Genome Atlas. Curated databases such as the Cancer Gene Census and COSMIC (Catalogue of Somatic Mutations in Cancer) are also used.

Liver Cancer

GenOnc Liver Cancer Panel (33 Genes)

GenOnc Liver Cancer Panel is a collection of multiplexed PCR primer assays for targeted enrichment of the coding (exonic) regions of the 33 genes most commonly mutated in human liver cancer samples. Mutations in these oncogenes and tumor suppressor genes are often relevant for tumor classification, and warrant extensive investigation to enhance the understanding of carcinogenesis. Hepatocellular carcinoma (HCC), the most common form of liver cancer, has a poor prognosis and low survival rate. The second most common form of liver cancer is cholangiocarcinoma, a cancer of the bile ducts. Although these 2 forms of liver cancer have different molecular mechanisms and prognoses, there are some similarities. For example, TP53 and ß-catenin are the most common mutated genes in HCC, whereas TP53 and KRAS are the most common mutated genes in cholangiocarcinoma. There are multiple potential mutation sites in each of these genes. Therefore, sequencing analysis is an efficient method to examine a tumor sample. This panel narrows the focus to the most relevant mutated genes in liver cancer, using a variety of resources such as recent whole genome/exome sequencing studies from scientific networks including the Cancer Genome Atlas. Curated databases such as the Cancer Gene Census and COSMIC (Catalogue of Somatic Mutations in Cancer) are also used.

Lung Cancer

GenOnc Lung Cancer Panel (72 Genes)

GenOnc Lung Cancer Panel is a collection of multiplexed PCR primer assays for targeted enrichment of the coding (exonic) regions of the 45 genes most commonly mutated in human lung cancer samples. Mutations in these oncogenes and tumor suppressor genes are often relevant for tumor classification, and warrant extensive investigation to enhance the understanding of carcinogenesis. The two major forms of lung cancer are small-cell lung carcinoma (SCLC) and non-small-cell lung carcinoma (NSCLC), although these classifications are no longer always used. One gene commonly mutated in both forms of lung cancer is the retinoic acid receptor RARβ (RARB). Mutations in this gene can cause a loss of activity, upregulating oncogenic processes. There are multiple potential mutation sites in RARB. Therefore, sequencing analysis is an efficient method to examine a tumor sample. There are additional genes commonly mutated in lung cancer as well. This panel narrows the focus to the most relevant mutated genes in lung cancer, using a variety of resources such as recent whole genome/exome sequencing studies from scientific networks including the Cancer Genome Atlas. Curated databases such as the Cancer Gene Census and COSMIC (Catalogue of Somatic Mutations in Cancer) are also used.

Ovarian Cancer

GenOnc Ovarian Cancer Panel (32 Genes)

GenOnc Ovarian Cancer Panel is a collection of multiplexed PCR primer assays for targeted enrichment of the coding (exonic) regions of the 32 genes most commonly mutated in human ovarian cancer samples. Mutations in these oncogenes and tumor suppressor genes are often relevant for tumor classification, and warrant extensive investigation to enhance the understanding of carcinogenesis. Ovarian cancer has the highest mortality rate of all gynecological cancers, partly because it is often discovered at a late stage of progression. There are many subsets of ovarian cancer; however they can all be divided into type I (low-grade) tumors or type II (high-grade) tumors. Type I tumors typically have mutations in BRAF and KRAS, whereas type II tumors commonly have mutations in TP53, BRCA1, and BRCA2, increasing genomic instability. A panel of key genes commonly mutated in ovarian cancer is an efficient way to research a tumor sample’s potential carcinogenic mechanisms. This panel narrows the focus to the most relevant mutated genes in ovarian cancer, using a variety of resources such as recent whole genome/exome sequencing studies from scientific networks including the Cancer Genome Atlas. Curated databases such as the Cancer Gene Census and COSMIC (Catalogue of Somatic Mutations in Cancer) are also used.

Prostate Cancer

GenOnc Prostate Cancer Panel (32 Genes)

GenOnc Prostate Cancer Panel is a collection of multiplexed PCR primer assays for targeted enrichment of the coding (exonic) regions of the 32 genes most commonly mutated in human prostate cancer samples. Mutations in these oncogenes and tumor suppressor genes are often relevant for tumor classification, and warrant extensive investigation to enhance the understanding of carcinogenesis. Prostate cancer is a neoplasm of the male reproductive gland with a high mortality rate. There are many mutations that can cause the oncogenic progression of a prostate tumor. For example, NKX3-1 is a tumor suppressor involved in prostate development. Losses of heterozygosity or mutations leading to decreased NKX3-1 expression both promote prostate cancer progression. However, mutations in other genes are typically required for prostate cancer to progress and become invasive. Therefore, sequencing analysis is an efficient method to examine a prostate tumor sample for multiple potential mutations in multiple genes. This panel narrows the focus to the most relevant mutated genes in prostate cancer, using a variety of resources such as recent whole genome/exome sequencing studies from scientific networks including the Cancer Genome Atlas. Curated databases such as the Cancer Gene Census and COSMIC (Catalogue of Somatic Mutations in Cancer) are also used.

Gastric Cancer

GenOnc Gastric Cancer Panel (29 Genes)

GenOnc Gastric Cancer Panel is a collection of multiplexed PCR primer assays for targeted enrichment of the coding (exonic) regions of the 29 genes most commonly mutated in human gastric cancer samples. Mutations in these oncogenes and tumor suppressor genes are often relevant for tumor classification, and warrant extensive investigation to enhance the understanding of carcinogenesis. Gastric cancer, or stomach cancer, originates in any part of the stomach, but can spread to other organs such as the esophagus, liver, lungs, and lymph nodes. Gastric cancer is not as well-defined molecularly as other cancer types, and the key driver mutations have not yet been identified. However, many genes commonly mutated in gastric cancer have been identified, such as PIK3CA. Therefore, a panel of genes commonly mutated in gastric cancer is an efficient way to research a tumor sample’s potential carcinogenic mechanisms. This panel narrows the focus to the most relevant mutated genes in gastric cancer, using a variety of resources such as recent whole genome/exome sequencing studies from scientific networks including the Cancer Genome Atlas. Curated databases such as the Cancer Gene Census and COSMIC (Catalogue of Somatic Mutations in Cancer) are also used.

Targeted Cancer MDx

Wed, 02 May 2018 14:04:58 -0500

Targeted Cancer, Targeted SOLUTIONS.

Through genomic research, we continue to learn more about the complexity of cancer. While cancer continues to be identified by its location in the body (lung, breast, blood, etc.), we have learned that a more accurate way to evaluate cancer treatment is through examination of the underlying changes or mutations which drive cancer development and progression. Those mutations are not limited to location and, in many instances, have very little correlation with the location. Understanding the core genetic mutations which drive cancer progression allows clinicians to replace more traditional treatments with newer, less toxic, therapies that target those specific mutations.

GenOnc Panel 1 - ACTIONABLE Solid Tumor (23 Genes)

Targets key regions of 23 genes identified by the National Comprehensive Cancer Network (NCCN), College of American Pathologists (CAP), and American Society of Clinical Oncology (ASCO) to be clinically actionable somatic mutations in solid tumors

Exons
BRAF, PDGFRA, EGFR (ERBB1), KRAS, NRAS, KIT (CD117).

Hotspots
AKT1, ALK, CTNNB1, ERBB3, ESR1 (ERα), FOXL2, GNA11, GNAQ, IDH1, IDH2, MET, RAF1, RET.

Whole Coding Region
ERBB2 (HER-2, NEU), PIK3CA (p110-alpha), TP53 (p53).

GenOnc Panel 2 - CLINICALLY-Relevant

GenOnc Cancer Panel 2 - Clinically Relevant Tumor Targeted Panel is a collection of multiplexed PCR primer assays for targeted enrichment of the key regions of 24 genes identified by medical groups and peer-reviewed research to be functionally relevant in the treatment of solid tumors. Clinically relevant mutations in these genes have been identified by guidelines and published opinions from groups such as the National Comprehensive Cancer Network (NCCN), College of American Pathologists (CAP), and American Society of Clinical Oncology (ASCO).

Genes
AKT1, ALK, AR, BRAF, CTNNB1, DDR2, EGFR, ERBB2, FGFR3, GNA11, GNAQ, IDH1, IDH2, KIT, KRAS, MAP2K1, MET, NRAS, PDGFRA, PIK3CA, PTEN, RET, STK11, & TP53.

GenOnc Panel 3 - HOTSPOTS

GenOnc Cancer Panel 3 expands the cancer gene repertoire covered in GenOnc Cancer Panels 1 and 2 by targeting genomic “hot spot” regions in 50 human oncogenes and tumor suppressor genes, detecting 2,800 COSMIC mutations frequently found in a variety of human cancers.

Genes ABL1, EZH2, JAK3, PTEN, AKT1, FBXW7, IDH2, PTPN11, ALK, FGFR1, KDR, RB1, APC, FGFR2, KIT, RET, ATM, FGFR3, KRAS, SMAD4, BRAF, FLT3, MET, SMARCB1, CDH1, GNA11, MLH1, SMO, CDKN2A, GNAS, MPL, SRC, CSF1R, GNAQ, NOTCH1, STK11, CTNNB1, HNF1A, NPM1, TP53, EGFR, HRAS, NRAS, VHL, ERBB2, IDH1, PDGFRA, ERBB4, JAK2, & PIK3CA.

GenOnc Panel 4 – COMPREHENSIVE (275 genes)

The GenOnc Comprehensive Cancer Panel is one of the most comprehensive cancer gene panels available. Encompassing over 50% of the Welcome Trust Sanger Institute Cancer Gene Census, this 409 gene panel targets key tumor suppressor genes and oncogenes that are the most frequently cited and most frequently mutated in cancer. The panel includes genes that function in growth factor and cytokine responses, signaling cascades, apoptosis, DNA repair, cell cycle regulation, transcription regulation, and inflammatory response pathways

GenOnc Panel 5 - PREDISPOSITION (145 genes)

Predisposition Targeted Panel is a multiplexed PCR-based assay for targeted enrichment of the coding (exonic) regions of the 145 genes commonly mutated in 88 inherited oncogenic diseases

Cancer Predisposition
Cancers: AKT1, APC, ATR, BLM, BRCA2, BRIP1, BUB1B, CHEK2 (RAD53), EPCAM, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, HRAS, LIG4, MLH1, MSH2, MSH6, PALB2, PIK3CA (p110-alpha), PMS2, PRKAR1A, PTEN, SLX4 (BTBD12), TP53 (p53), VHL.
Bone: EXT1, EXT2, MTAP, RECQL4, TP53 (p53).
Hereditary Breast-Ovarian: BARD1, BRCA1, BRCA2, CHEK2 (RAD53), RAD51B (RAD51L1), RAD51C, RAD51D (RAD51L3).
Colorectal: APC, AXIN2, GALNT12, MLH3, MUTYH, POLD1, POLE.
Endocrine: AIP, CDC73, CDKN1B (P27KIP1), CYP21A2, GLI3, MAX, MEN1, NDUFA13, NTRK1, PDE11A, PRKAR1A, RET, TMEM127, TP53 (p53), VHL.
Gastrointestinal Tract: ASCC1, BMPR1A (ALK3), CDH1 (E-Cadherin), KIT (CD117), MSR1, PDGFRA, PTEN, RHBDF2, SDHC, SMAD4 (MADH4), STK11 (LKB1).
Head & Neck: CYLD, DKC1, RTEL1, TERC, TERT, TINF2, TSC1, TSC2.
Hematopoietic: ATM, CEBPA, GATA2, KLHDC8B, LYST, MRE11A, NBN (NBS1), RAD50, RUNX1(AML1), SBDS, TERT, WAS.
Kidney: DIS3L2, FH, FLCN, MET, MITF, POU6F2, WT1.
Liver: FAH, HFE, UROD.
Nervous System: ALK, GPC3, KIF1B, NF1, NF2, PRKAR1A, RB1, PHOX2B, SDHA, SDHAF2, SDHB, SDHD, SMARCA4, SMARCB1, SUFU.
Skin: BAP1, CDK4, CDKN2A (p16INK4a), CYLD, DDB2, ERCC2 (XPD), ERCC3 (XPB), ERCC4, ERCC5, ERCC6, FH, FLCN, GLMN, MC1R, MITF, MSH2, POLH, PTCH1, PTCH2, RSPO1, TGFBR1(ALK5), TMC6, TMC8, XPA, XPC, XRCC3.
Soft Tissue: ANTXR1, ANTXR2, CD96, ESCO2, KDR (VEGFR3), PTEN, WRN.
Other Cancers: BRCA2, CHEK1, DICER1, EHBP1, EPHB2, MSMB, MSR1, PALB2, PALLD, RNASEL.

[GenOnc Panel 4 - ]

Clinical Molecular Diagnostics (MDx)

Wed, 02 May 2018 14:04:41 -0500

ESSENTIAL Diagnostics. ACTIONABLE Results.

Today, we know more about the impact of genomic variation upon onset and progression of disease than ever before. Years of research and strategic collaboration have allowed Genome Explorations to develop profiles designed to aid clinicians in their effort to harness information provided by the genetics of individual patients.

Our profiles allow clinicians to evaluate key “trigger” genetic abnormalities, genetic considerations pertaining to certain locations within the body, or genes typically associated with family history of disease. Genome Explorations enables clinicians to look at the entirety of the patient picture and provide answers that are essential to improving patient outcomes.