|
Services - SNP Genotyping
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.
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.
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 covered under 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 reprenting the alleles of interest in the sample are covalently immobilized in distinct locations on 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 manufacaturing of oligonucleotide microarrays for traditional SNP, and CGH microarray applicatons. 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 simultanious genotyping from 1 to 360,000 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
Shipping and Receiving, Suite 5
524 East Weddell Drive
Sunnyvale, CA 94089
USA
Phone: 408-744-1331
Ordering Information
|
Product
|
Description
|
Catalog ID
|
Price (US dollars)*
|
|
Oligonucleotide Microarray Capture Sequence Design
|
Arrayit Oligonucleotide Microarray capture sequence design service for genotyping microarrays. Oligonucleotide capture sequences hybridize to labeled patient samples in solution with the SNP sequence located in center position. Customers provide 100 bp of DNA sequence with the SNP in the center position. Two designed primers are required to genotype each allele. Pricing is per oligonucleotide pair (2 oligos). Quantity pricing is available for large projects.
|
OMC
|
$32
|
|
Oligonucleotide Microarray Fluorescent Probe Design
|
Arrayit Oligonucleotide Microarray fluorescent probe design service for genotyping microarrays. Fluorescent probes hybridize to capture sequence oligonucleotides on the microarray surface to control for hybridization affinity and specificity, with the SNP located in center position. Customers provide 100 bp of DNA with the SNP in the center position. Two designed fluorescent probes are required to quality control eacj bi-allelic SNP. QC fluorescent probes are not essential but are highly recommended prior to testing patient samples. Pricing is per fluorescent pair (2 oligos), with wild type probes labeled with cyanine 3 (green) and mutant probes labeled with cyanine 5 (red). Quantity pricing is available for large projects.
|
OMP
|
$42
|
|
Oligonucleotide Microarray Sequence Validation
|
Arrayit Oligonucleotide Microarray sequence validation for capture oligonucleotides and fluorescent probes including complete bioinformatic analysis to determine accuracy to database sequences and 100% complementarity to wild type and mutant alleles. Pricing is per four oligonucleotides (two capture sequences and two fluorescent probes per bi-allelic marker). Quantity pricing is available for large projects.
|
OMV
|
$56
|
|
Oligonucleotide Microarray Oligonucleotide Synthesis
|
Arrayit Oligonucleotide Microarray modified primer and two-color fluorescent probe oligonucleotide synthesis including 200 nmole synthesis scale sufficient to genotype 10,000 samples and quality control by mass spectroscopy. Each synthesis includes two primers and two probes (4 oligonucleotides total). Quantity pricing is available for large projects.
|
OMS
|
$195
|
|
Oligonucleotide Microarray DNA Preparation
|
Arrayit Oligonucleotide Microarray genomic DNA preparation from blood, biopses, siliva, cultured cells, and other biological preparations. Preparation includes cell lysis, RNA degradation, purification, quantification and QC. Quantity pricing is available for large projects.
|
OMD
|
$12
|
|
Oligonucleotide Microarray Manufacturing
|
Arrayit Oligonucleotide Microarray manufacturing to print capture agent oligonucleotides into microarrays for oligonucleotide microarray genotyping. Pricing will depend on the number of capture agents per microarray, the number of microarrays per substrate slide, and the total number of microarrays printed. Quantity pricing is available for large projects.
|
OMM
|
$39
|
|
Oligonucleotide Microarray Genotyping
|
Arrayit Oligonucleotide Microarray genotyping including patient sample labeling and purification, hybridization, scanning, quantification and data analysis, and a guaranteed genotyping accuracy of >99.9%. Pricing will depend on the number of SNPs and patient samples. Quantity pricing is available for large projects.
|
OMG
|
$268
|
|
VIP Primer Design
|
Arrayit VIP genotyping primer design service to amplify any SNP of interest using customer provided DNA sequences (100 bp of sequence information required with the SNP in the center position). Two designed primers are required to amplify each allele. Pricing is per primer pair (2 primers). Quantity pricing is available for large projects.
|
VIPP
|
$32
|
|
VIP Probe Design
|
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.
|
VIPR
|
$42
|
|
VIP Sequence Validation
|
Arrayit VIP genotyping primer and probe sequence validation service to ensure efficient amplification of each locus and efficient hybrdization during genotyping. Each bi-allice locus requires sequence validation of two primers and two probes. Pricing is per primer and probe pair (4 sequences total). Quantity pricing is available for large projects.
|
VIPV
|
$59
|
|
VIP Primer and Probe Synthesis
|
Arrayit VIP genotyping modified primer and two-color fluorescent probe oligonucleotide synthesis including 200 nmole synthesis scale sufficient to genotype 10,000 samples and quality control by mass spectroscopy. Each synthesis includes two primers and two probes (4 oligonucleotides total). Quantity pricing is available for large projects.
|
VIPS
|
$200
|
|
VIP Genomic DNA Preparation
|
Arrayit VIP genotyping genomic DNA preparation from blood, biopses, siliva, cultured cells, and other biological preparations. Preparation includes cell lysis, RNA degradation, purification, quantification and QC. Quantity pricing is available for large projects.
|
VIPD
|
$11
|
|
VIP DNA Amplification and Purification
|
Arrayit VIP genotyping amplification and purification of SNP amplicons. Preparation includes PCR amplification, amplicon purification, quantification, QC and sample preparation. Yield of 2-10 µg is sufficient to print 500 VIP microarrays. Pricing is per 100 µl PCR reaction. Quantity pricing is available for large projects.
|
VIPA
|
$11
|
|
VIP Genotyping
|
Arrayit VIP genotyping of SNPs using VIP microarrays including microarray printing, hybridization, processsing, scanning, quantification, data analysis and reporting. Reports include definitive genotyping information for wild type, carrier and mutant genoytypes at 99.9% guaranteed accuracy. Pricing is per SNP per patient sample. Quantity pricing is available for large projects.
|
VIPG
|
$26
|
To order Arrayit genotyping SNP genotyping services call 408-744-1331, fax 408-744-1711, email arrayit@arrayit.com or click on the purchase button to proceed directly to the shop site.
*International pricing may vary as much as 30% (or more depending on country) due to import duties, stocking fees and technical support.
*Add shipping and handling to all orders.
Copyright 1993-2013 Arrayit Corporation. All rights reserved.
|
