Agilent SurePrint G3 CGH SNP Microarray Platform
Contents
1. Superior copy number change detection Added LOH UPD detection increases efficiency and reduces cost Complete workflow from a single supplier Easily customizable to design your own array Agilent s surePrint G3 CGH SNP Microarray Platform Product Note Search for more types of chromosomal aberrations on a single array The power of the Agilent SurePrint G3 Human Comparative Genomic Hybridization CGH Platform has been extended to allow simultaneous detection of copy number and copy neutral changes on the same array increasing efficiency without sacrificing quality Identification of copy neutral changes such as loss of heterozygosity LOH and uniparental disomy UPD is enabled by the addition of a set of SNP probes to Agilent s widely used CGH array followed by data analysis using a novel algorithm implemented within Agilent s Genomic Workbench software Available in a variety of formats using catalog content or customized probe sets Agilent s SurePrint G3 CGH SNP Microarray Platform moves your research quickly to answers you can trust More effective high resolution detection of chromosomal variation Accurate detection of chromosomal variation is the key to understanding the cytogenetic basis underlying a number of developmental disorders Comparative genomic hybridization CGH analysis has revolutionized the field of cytogenetics by providing accurate identification of copy number variations at greater than 10002. 2 Application Note Simultaneous detection of copy number and copy neutral LOH using a single microarray 5990 6274EN Part Number 5190 4240 5190 3393 5188 5220 or 5188 5380 5188 5226 G2534A Varies by array format and quantity G2545A G2530 60029 G4900DA G1662AA G1667AA For a more comprehensive list of peer reviewed publications and research reviews please visit www agilent com genomics This item is not approved for use in diagnostic procedures User is responsible for obtaining regulatory approval or clearance from the appropriate authorities prior to diagnostic use Agilent Technologies shall not be liable for errors contained herein or for incidental or consequential damages in connection with the furnishing performance or use of this material Agilent Technologies Inc 2011 Published in USA December 16 2011 5990 6422EN Agilent Technologies
3. fold resolution compared to traditional karyotyping Until recently however detection of copy neutral chromosomal changes such as LOH or UPD required additional experimentation The Agilent SurePrint G3 Human CGH SNP Platform adds SNP detection to Agilent s robust and highly regarded CGH platform allowing you to rapidly and reliably identify both copy number variations and copy neutral aberrations in a single microarray assay Using the identical high throughput workflow as the SurePrint G3 CGH only microarrays the CGH SNP arrays can be quickly incorporated into your cytogenetics research Available in catalog or custom formats Figure 1 the array offers maximum flexibility while the Agilent 60 mer probes enable high confidence characterization of copy number and copy neutral chromosomal aberrations Agg Agilent Technologies AUE VINANI NOM INANI AUE VINAN UNNI A Agilent Agilent Figure 1 Agilent s SurePrint G3 CGH SNP catalog and custom microarrays are available in multiple formats and feature amounts A customizable platform for simultaneous detection of copy number and copy neutral variation Expanding the current SurePrint G3 selection Agilent s SurePrint G3 CGH SNP arrays are available in both catalog Table 1 and custom design formats The catalog 2x400K SurePrint G3 CGH SNP array contains approximately 300 000 CGH probes and 120 000 SNP probes Genotypes are measured using two SNP probes per SNP providing the highe
4. G3 CGH SNP Microarrays Regions of copy neutral LOH or UPD are then located by identifying of heterozygous SNP calls The Agilent Genomic Workbench software side QC metrics allowing you to evaluate your data with confidence Description SurePrint G3 Human CGH SNP Microarray 2x400K SurePrint G3 Human CGH SNP Microarray 4x180K SurePrint G3 Custom CGH SNP Microarray 1x1M SurePrint G3 Custom CGH SNP Microarray 2x400K SurePrint G3 Custom CGH SNP Microarray 4x180K SurePrint G3 Custom CGH SNP Microarray 8x60K Number of Arrays Slides Number of Slides Kits Part Number 2 D G4842A 4 3 G4890A 1 1 G4882A 2 1 G4883A 4 1 G4884A 8 1 G4885A Note Microarrays are shipped with foil seal After breaking the foil store microarrays at room temperature in the dark under a vacuum desiccator or in a nitrogen purge box Do not expose microarrays to open air during storage Requires Agilent CGH Processing Components Description Surelag Complete DNA Labeling Kit Human Cot 1 DNA Agilent Oligo aCGH Hybridization Kit 25 or 100 Agilent Oligo aCGH Wash Buffer 1 and 2 Set Hybridization Chamber Stainless Hybridization Chamber Gasket Slides Hybridization Oven Hybridization Oven Rotator Rack SureScan Microarray Scanner Agilent Cytogenomics References 1 Manual Agilent Oligonucleotide Array Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood Cells or Tissues with a High Throughput Option manual version 6 3 G4410 90010
5. NP microarrays use the same Agilent CGH identification of copy neutral aberrations as small as 3 Mb workflow as the SurePrint CGH only arrays Restriction digestion of genomic The new SurePrint G3 CGH SNP array enables efficient DNA allows genotyping of SNPs located in the enzymes recognition sites high quality discovery of chromosomal aberrations that cannot be detected in a single assay using any other method 1 Catalog 4x180K CGH SNP Microarray DLR Spread 013 D Se oi 1 Q oo 9 N Q bar ro So No uncut alleles Figure 3 Agilent Genomic Workbench view of SNP data number of uncut alleles bottom panel and CGH data log ratios top panel from a CGH SNP array shows UPD of the entire chromosome 15 Settings for CGH aberration calling ADM 2 threshold 5 minimum of 3 probes 2 0 25 log ratio Powerful data analysis capabilities for both CGH and SNP detection Agilent s Genomic Workbench software for CGH SNP array analysis employs a novel algorithm to measure the total copy number of CGH probes and allele specific copy numbers of SNP probes Copy number aberration calls are determined entirely by non SNP oligonucleotides maximizing signal to noise ratio A SNP call is made from the log ratio of the signal of the sample to the signal of a genotyped internal reference genomic regions with a statistically significant scarcity enables concurrent analysis of CGH and SNP data along Agilent SurePrint
6. romosomal variation Table 1 Comparison of SurePrint CGH SNP 2x400K and 4x180K catalog microarrays Catalog 2x400K CGH SNP Catalog 4x180K CGH SNP Number of CGH probes 300 000 120 000 Median CGH probe spacing 7 Kb 25 Kb ISCA content none ISCA 8x60K version Exon biased yes no Number of SNP probes 120 000 60 000 Number of SNP probes per SNP 2 1 Copy neutral LOH resolution 5 10 Mb 5 10 Mb Easy workflow designed for high quality CGH SNP detection AGIC vn A simple efficient sample preparation process starts from Restriction Digestion Labeling as little as 500 ng DNA and uses enzymatic restriction digestion followed by Klenow based enzymatic labeling Figure 2 The new CGH SNP microarrays are still printed eH cotre a on 1 in x 3 in glass slides and are compatible with Agilent s standard hybridization gaskets and chambers Microarrays Hybridization are scanned at 3 microns using the Agilent SureScan Microarray Scanner G4900DA Novel and powerful algorithmic analysis detects regions A cete of copy neutral LOH or UPD Figure 3 With high quality DNA samples the SNP call rate is greater than 95 with a e greater than 99 accuracy The number and quality of copy ce Microarray number aberrations detected on the SurePrint G3 CGH SNP Probes microarrays is comparable to detection using G3 CGH only microarrays with the added benefit of simultaneous Soh we Figure 2 The SurePrint G3 CGH S
7. st call rate and accuracy per SNP and resulting in 5 10 Mb resolution for LOH UPD detection across the entire genome The CGH probes are gene and exon biased focusing coverage to the most important regions of the genome The catalog 4x180K SurePrint G3 CGH SNP array contains approximately 120 000 CGH probes and 60 000 SNP probes Genotypes on this array are measured using one SNP probe per SNP providing 5 10 Mb resolution for LOH UPD detection across the entire genome The CGH probes consist of the entire ISCA International Standards for Cytogenomic Arrays Consortium http isca genetics emory edu 8x60K version probe set and an additional 60 000 backbone probes The ISCA 8x60K probe set has an even backbone probe coverage of 60 Kb and high density coverage of 500 targeted regions with the spacing of 5 Kb per probe or at least 20 probes per gene region These targeted regions include telomere and unique centromere FISH clone regions microdeletion duplication regions genes of known haploinsufficiency and regions associated with X linked mental disorders Custom SurePrint G3 CGH SNP microarrays can also be readily designed in eArray a free web based application or eArray XD the desktop version of eArray The eArray database houses more than 28 million CGH probes and approximately 65 000 probes for SNPs Multiple microarray formats allow for maximum flexibility while 60 mer probes enable high confidence characterization of ch
Download Pdf Manuals
Related Search
Agilent SurePrint G3 CGH SNP Microarray Platform