Wednesday, September 19, 2007

Spotted BACs take on In-situ Oligonucleotides in CGH


Having been technical support for our spotting devices for the last 10 years I just love to see spotted microarrays take on the "high density" platforms and perform well. Anyone out there who believes a spotted microarray cannot manufactured reproducibly needs to review the data on the following poster.

www.abrf.org/ResearchGroups/Microarray/Activities/Final2007MARGposter.ppt

RPCI's (Roswell Park Cancer Institute) 19K BAC array performed admirably and reported the best CV when compared to Agilent, Affymetrix and Illumina. The paper is being prepared but the early reported conclusions are as follows:

  • All platforms demonstrated good precision between replicates.
  • Illumina and Affymetrix 500K microarray indentified 100% of the known losses and gains in HL60 DNA.
  • The three platforms with fewer probes, Agilent, Affymetrix U133 and BAC spotted microarrays identified most (89%) but not all of the know losses and gains in HL60 DNA.
  • When CBS Analysis was used to assess resolution, all platforms detected 100% of the known gains and losses in HL60 DNA.
  • Overall, three novel changes were also detected by various platforms and all platforms found changes in chromosome 16.
The current BAC microarrays from RPCI are made at 160 kilobase resolution using the 946 Micro Spotting Pins and a BRSPH64 Printhead. The BAC sample preparation and spotting technology creates a microarray where all 3 billion bases of the human genome are on a single microarray, available for hybridization! A comparison in resolution between traditional methods and different microarray platforms is as follows:



Resolution

Coverage

Traditional Cytogenetics

Karyotyping

>10Mb

Complete


SKY

>2 Mb

Complete


Traditional CGH

> 2 Mb

Complete


FISH (interphase)

> 20 kb

Probe Specific


FISH (Metaphase)

> 20 Kb

Probe Specific

Microarray CGH

BAC

~100 Kb

Complete


cDNA

2 Kb

Genes Only


Oligonucleotide 60mer

0.06 Kb

Complete


Oligonucleotide
25mer

0.025

Complete


The BAC microarray is only platform in the comparison study that did not use oligos on the microarray. However, pre-synthesized oligos can be manufactured into microarray using ex-situ spotting and microarray manufacturing is a service that we provide. If you have an interest in applying microarray CGH, please view the tools, kits and reagents used in CGH microarray at:
http://arrayit.com/CGH_Microarrays/cgh_microarrays.html
get a 5% discount off on the products on this website by mentioning promotional code CGH0100107 when placing the order. This discount is of list price only and not applicable to any other quote or offer. .