Arrayit offers the finest genotyping platform on the market for single nucleotide polymorphism (SNP) genotyping. Our technology empowers the use of both single sample traditional oligonucleotide microarrays as well as multi-patient VIP microarrays. We offer custom design services for any disease panel for humans, livestock, plants, fungi, bacteria, viruses and other organisms. Arrayit microarrays allow genotyping of a small number to millions of samples quickly, affordably and with 99.9% accuracy. Arrayit VIP genotyping fluorescent probe design service to hybridize any SNP of interest using customer provided DNA sequences (100 bp of sequence information is required for each SNP, with the wild type and mutant alleles in the center position). Two designed fluorescent probes are required to genotype each bi-allelic locus. Pricing is per probe pair (2 probes). Quantity pricing is available for large projects.
Services - Single Nucleotide Polymorphism (SNP) Genotyping for Research, Life Sciences, Microarray Testing and Pharmacogenomic Applications
Arrayit offers the finest genotyping services on the market for single nucleotide polymorphism (SNP) analysis of humans, plants, animals and microorganisms. Our versatile technology platform empowers traditional low-, medium- and high-density oligonucleotide microarrays as well as multi-patient VIP microarrays, which enable the simultaneous genotyping of >80,000 specimens in a single reaction. Customers benefit from our fully custom as well as our catalog microarrays containing up to 2,600,000 SNPs. Arrayit microarrays allow genotyping of dozens to millions of samples quickly, affordably and with 99.9% accuracy for biobanking, cancer genomics, precision medicine and translational research applications. Arrayit genotyping services are provided for research use only.
Oligonucleotide Microarray Genotyping
Arrayit offers fully customized design services for single sample oligonucleotide microarray genotyping. Customer-provided SNP and sequence information is used to design capture agents and fluorescent probes for each allele. Capture agents are printed into microarrays as 1-48 microarrays per 25 x 76 mm glass substrate slide. The capture agents are then qualified by hybridization with synthetic probes to optimize hybridization and wash conditions for the genotyping panel. An amplification and labeling kit as well as all of the instruments, tools, reagents and buffers are provided to allow microarray-based genotyping at the customer location. We also offer the market-leading Affymetrix platform, which enables the simultaneous analysis of 2,600,000 SNPs per microarray.
VIP Genotyping
Arrayit Variation Identification Platform™ genotyping technology empowers the detection of sequence variants such as SNPs for many samples at once. Our platform is universal for nucleic acid-based genetic screening, testing, diagnostics, genotyping and single nucleotide polymorphism (SNP) analysis. It is a hybridization-based analysis of SNPs, mutations, deletions, insertion-deletion mutations (indels), and other minor sequence variations from any organism of interest. It can also be used to detect bacterial and viral sequences required for the diagnosis of infectious diseases caused by agents such as mycobacterium tuberculosis, cytomegalovirus (CMV), human immunodeficiency virus (HIV), bacillus anthracis, and other pathogens. Our technology platform is amenable to cost-effective screening of large populations of samples for genetic variations and is described in U.S. patent 6,913,879.
In one VIP approach, specific genetic loci are amplified by the polymerase chain reaction (PCR), printed into microarrays, and hybridized with fluorescent synthetic oligonucleotides. The hybridized microarrays are then scanned for fluorescence emission to derive genotyping information (Figure 1). Normal, carrier and disease genotypes are distinguished easily by reading green, yellow and red signals in composite microarray images (Figure 2). It is altered hybridization efficiency for each genotype call that leads to different fluorescent intensities in scanned microarray images (Figure 3). Two-color strategies are deployed to increase the precision of the assays (Figure 4). When performed correctly the process is 100% accurate.
Our approach is a dramatic improvement over traditional microarray assays that use oligonucleotides to analyze one or two patient samples at a time (microarray types we also manufacture). With our patented approach, amplicons representing the alleles of interest in the sample are covalently immobilized in distinct locations on a microarray. Computer tracking and 2 color microarray scanning platform enables massively parallel analysis of many samples for many genetic variations in a single assay. Current platform can test from 1 to 100,000 samples for many SNPs in a single round of hybridization affordably.
Arrayit also excels in the manufacturing of oligonucleotide microarrays for traditional SNP, and CGH microarray applications. Contact us at arrayit@arrayit.com with your requirements.
Figure 1. Variation Identification Platform™ methods. Arrayit methods provide universal microarray-based platforms for SNP genotyping. In one VIP approach, specific chromosomal loci are amplified by use of the polymerase chain reaction (PCR), printed into microarrays, and hybridized with fluorescent oligonucleotides. The fluorescent microarrays are then scanned for fluorescence emission and signal strengths provide genotyping information.
Figure 2. Arrayit VIP™ technology allows detection of single nucleotide changes. Amplified DNA from patients with normal (G/G), carrier (G/A) and disease (A/A) genotypes are hybridized with complementary fluorescent oligonucleotides labeled with a green tag to detect the normal sequence and a red tag to detect the disease sequence. Genotypes for the normal, carrier and disease patients are easily identified by reading green, yellow and red signals in composite microarray images.
Figure 3. Arrayit VIP™ technology can utilize two-color fluorescence to expedite the genotyping process. Fluorescent oligonucleotides with cyanine 5 labels (red channel) and cyanine 3 labels (green channel) were co-hybridized to a microarray, scanned for cyanine 3 and cyanine 5 emission, and the fluorescent images were superimposed to produce a composite (bottom panel). The 3 different genotypes are distinguished easily by scoring the red, yellow and green colors.
Figure 4. Arrayit VIP™ technology enables the manufacture of high density microarrays allowing affordable and simultaneous genotyping from 1 to 100,000 different samples for many SNPs of interest. Experimental design is completely flexible.
Customer Information and Samples
Customers should provide the following information and samples with each genotyping order:
- 100 bases of sequence information for each locus, with the SNP at position 50
- wild type and mutant allele sequences for each SNP
- 1.0 µg of genomic DNA or biological material for each sample
Sequence information should be sent by electronic mail to arrayit@arrayit.com.
Genomic DNA and biological samples should be sent by overnight mail on dry ice to Arrayit Corporation.
Figure 5. Arrayit microarray containing 25,000 individual printed elements. VIP microarrays of this density would allow genotyping of 25,000 patient research specimens simultaneously.