AFFYMETRIX


AFFYMETRIX  MICROARRAY SERVICES

    We have Affymetrix GeneChip microarray platform which performs the below wide applications:

     1.Diagnostics and Research applications:

     1.Cytogenetics (Copy Number variations)
     2.Prenatal Diagnostics
     3.Post natal Diagnostics
     4.Human Gene expression
     5.miRNA expression
     6.SNP genotyping
     7.Cancer CNV analysis
     8.Drug Metabolism marker assay
     9.Animal and Plant expression
 
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            2.Diagnostic Services:     

        Genetic  Diagnostic test offered:
        Whole genome Chromosomal Array for diagnosing pre-natal, Post-natal disorders and diagnosing IVF failures.
      Applications of Whole Genome Chromosomal Array:
         Prenatal Domain: 
         1.Miscarriages
         2.Repeated miscarriages
         3.IVF failures – To detect genetic abnormalities in partners
         4.Genetic testing on Amniocentic fluid or CVS sample.
         5.Product of conception genetic testing
         6.Pre-implantation genetic Diagnosis / Screening (PGD/PGS) – Coming Soon.

         Postnatal Domain:
         1.Developmental disorders in Children
         2.Intellectual disorders
         3.Mental Retardation
         4.Any genetic syndrome associated with DNA copy number variations.

         What is Reported?
         We detect abnormal copy number variations such as deletions, duplications, Loss of heterozygosity (LOH) 
         and copy neutral loss of heterozygosity(CnLOH or Uniparental Disomy) which are frequent causes for the above conditions.

         Who interprets the data?                                                                                                                                                                                                                                                                                      
         Our Senior and experienced Medical geneticist interprets the data and correlate with clinical features of the patient. 
         Additionally our experienced and certified genetic counselor provides actionable suggestions (therapeutic/diagnostic) to the clinician. 
         We will also provide free genetic counselling to the patients.

        Logistics:
        We have our sales team/logistic person in all major cities that will collect samples from your door step.

      Reporting turn-around-time:
        We provide results within 2-3 weeks. However, for the amniocentesis cases we will provide results within 7-8 days.

      Pricing information: 
        Please write to us for the best possible pricing for your organization. We can discuss / 
        negotiate or consider special pricing based on a long-term agreement.

      Research Applications:
      We undertake research applications services for the below studies to meet your research needs

        1.Human Gene expression
        2.miRNA expression
        3.SNP genotyping
        4.Cancer CNV analysis
        5.Drug Metabolism marker assay
        6.Animal and Plant expression        

      Human Gene Expression Services:
      1. PrimeView Gene Expression array: 

        1.Measure gene expression of more than 36,000 transcripts and variants per sample
        2.Get accurate and reproducible gene expression data by using multiple independent measurements for each transcript.
        3.Produces reliable results with multiple independent measurements per transcript—11
          probes per set for well-annotated sequences 9 probes per set for the remainder.
        4.The PrimeView Human Gene Expression Array is comprised of more than 530,000 probes covering more than 36,000
          transcripts and variants,which represent more than 20,000 genes mapped through RefSeq or via UniGene annotation.
      2.  Clariom D assay:
        The novel Clariom D assay design provides the most intricate transcriptome-wide gene- and exon-level expression profiles, 
        including the ability to detect alternative splicing events of coding and long non-coding (lnc)RNA, in a single three-day experiment.
        1.Generate robust expression profiles from as little as 100 pg of total RNA—as few as 10 cells.
        2.Utilize RNA from various sample types including blood, cells, and fresh/fresh-frozen or FFPE tissues.
        3.Preserve sample integrity and reduce data variability with an assay that does not require a globin or rRNA removal step.

Sample type

Fresh/frozen tissue
Whole blood

FFPE

 Input

50-500 ng

0.1-10 ng

0.5-50 ng

     
     3. Human Transcriptome Array (HTA):
             H  HTA 2.0 maximizes the amount of unique and valuable information possible by minimizing the conserved sequence synthesized on the array. 
             This high-resolution array design contains an unprecedented >6.0 million probes covering coding transcripts and non-coding transcripts.
             70% of the probes on this array cover exons for coding transcripts, and the remaining 30% of probes on the array cover exon-exon splice junctions and non-coding transcripts. 
             The unparalleled coverage of this array provides the deepest insight into all coding and non-coding transcripts available.

Array content

Protein coding content

Non-protein coding content

Whole-transcript resolution

Genes (transcript clusters)

44,699

22,829

Transcripts

245,349

40,914

Exons

560,472

109,930

Exon clusters

296,058

82,444

Splice junctions (probe sets)

339,146

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     4. Clariom S expression array:
       Obtain a gene-level view of the transcriptome with Clariom S assays, the next-generation of transcriptome-wide gene-levelexpression
       profiling tools for human, mouse, and rat studies. Clariom S assays provide the fastest, simplest, 
       and most scalable path to generating actionable results. Based on industry-leading microarray technology,
       the novel Clariom S assay design provides extensive coverage of all known well-annotated genes, compatibility with clinical sample types,  
       scalable formats, and flexible data analysis software. Clariom S assays are the tools of choice to find expression biomarkers with known 
       function as quickly, easily, and cost-effectively as possible.
       1.Accurately measure gene-level expression from >20,000 well-annotated genes to get to answers quickly.
       2.Choose a format that suits your throughput needs, processing from 1 to 192 samples a day.
       3.Generate robust expression profiles from as little as 100 pg of total RNA—as few as 10  cells.
       4.Utilize RNA from various sample types including blood, cells, and fresh/fresh-frozen or FFPE tissues.

      Cancer CNV and hot Spot mutation analysis:
      Oncoscan
       Obtaining genome-wide copy number and loss-of-heterozygosity (LOH) profiles from solid tumor samples is a significant challenge 
       due to the difficulty of working with limited amounts of DNA from highly degraded FFPE samples.
       A simple whole-genome scanning approach avoids the traditional single locus, low-resolution bottleneck of FISH and PCR. 
       For next-generation sequencing technologies the requirement for target enrichment and high-depth coverage in order to obtain 
       copy number information from heterogeneous FFPE samples remains a significant challenge.

      Why is genome-wide copy number important in the analysis of solid tumors?
       1.The significance of copy number aberrations is established in an ever increasing number of genes
       2.The number and the type of aberration have been shown to be prognostic as well as diagnostic
       3.Increasing evidence of the occurrence of chromothripsis in multiple solid tumors with potential prognostic and predictive significance
       4.Treatment response may be monitored by detecting aberrations in sub-clones and assessing clonal evolution
       5.Combining whole-genome copy number and LOH data enables a deeper understanding of the disease
      The new OncoScan® CNV FFPE Assay Kit delivers an entirely new perspective on the cancer genome from even the most challenging solid tumor samples.
       1.Low sample input, fast results – from only 80 ng of FFPE-derived DNA to results in 48 hours
       2.One assay, multiple views – whole-genome copy number and loss of heterozygosity (LOH)
       3.High-resolution copy number detection in ~900 cancer genes
       4.Rapid analysis – from data to copy number calls for hundreds of samples in minutes using Nexus Express Software for OncoScan® FFPE Assay Kit
      Model and Applied Research Organisms – Expression arrays
       Model and applied research organisms are valuable for comparative genomics research, evolutionary biology,
       and continue to play a critical role in deciphering the molecular mechanisms underlying human disease,
       and agricultural crop improvement. GeneChip Gene 1.0 ST Arrays have been developed for the analysis of a wide range of model 
       and applied research organisms. These organisms are the latest additions to the growing family of Affymetrix® Gene Expression Microarrays offering whole-transcript coverage.
   Key benefits
       1.Highest transcript coverage – get confident expression measurements of well-annotated content with up to 26 probes per transcript
       2.Whole-transcriptome analysis – capture the transcript isoforms you may miss with 3'-biased expression designs
       3.High data correlation – achieve high inter- and intra-array strip signal correlation (R >0.99)

  • Sensitivity- ≥1:100,000 (≥1.5 pM)                · Dynamic range- ~3 logs
  • Signal correlation coefficient- >0.99            · Total RNA input required- 50–500ng 

  • Probe feature size- 5 μm                          · Background probes- Antigenomic Set
  •  Poly-A controls- dap, lys, phe, thr              · Hybridization controls- bioB, bioC, bioD, creX