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Home > Projects > 60mer oligo array
Customised design and printing of a 60mer oligo array in a 4 x 44 K format
 Project leader: Dr John Crolla

Using Agilent’s eArray (v4.5) on line array-cgh design facility (http://earray.chem.agilent.com/earray/login.do) we have produced a “constitutional” oligo array-cgh format which (a) has been designed to provide the maximum genome wide resolution with the probes available and (b) focuses specifically on the known micro-deletion and duplication syndromes.

We have used the following principles for the design:

  • Based on the 1x 44 K Agilent array content (44B)
  • Using 4 x 44 K format to increase productivity and reduce costs
  • Reduce coverage of cancer genes and re-distribute probes more evenly across the genome
  • Select higher density of probes for known micro-deletion/duplication regions (an ongoing and collaborative process see http://www.ngrl.org.uk/Wessex/microdel_collection.htm)

We have used the following design strategies:

  • Check the probe distribution of the newly designed array using UCSC Genome Browser.
  • Reduce all genomic gaps to a maximum of ~ 250 Kb although average coverage is at a considerably greater density in most regions.
  • Collaborating with Agilent’s probe designers to provide coverage for PAR1 which is not currently provided.

The first design has been submitted and slides printed:

All UK NHS Laboratories are encouraged to comment on the current design specification of the NGRL (Wessex) 4x44 K oligo-array. Please contact Dr John Crolla (john.crolla@salisbury.nhs.uk), who will be able to set you up as a collaborator on the eArray facility and will provide information on how to view the customised design in the UCSC genome browser.

The principle identification features of the customised array are as follows:

  • Array Design Name = NGRL WESSEX CONSTITUTIONAL ARRAY CGH V1
  • NGRL (Wessex) design number 015543
  • Slide Format = 4 X 44 K
  • Application = CGH
  • Customer Design ID = NeAT_design
  • Company Number = 7654321
  • Slide Layout = IS-45220-4-V1
  • Submission Date = 29-Nov-2006 16:24
  • Two print runs have been compteted (24th Jan and 27th of Feb, 2007)


Validation of the first 40 array-cgh using the 4x44 K format

DNA from 17 cases with previously diagnosed conventionally karyotyped chromosome abnormalities together with 23 cases with normal karyotypes (most with normal targeted FISH and sub-telomere screens) were run on the arrays. We obtained interpretable results in 38/40 (95%) of the cases and the two failures were due to poor quality test DNA. Full details of the array-cgh results are currently being written up for publication.

Validation cases run on the customised 4x44 K array

Ascertainment Total arrays Informative
results
Failed
Supernumeraray Marker Chromosomes 10* 9 1
DD/MR/DF
(Normal karyotypes)
23 22* 1
Complex visible abnormalities 7 7 0
Totals 40 38 2

Abnormalities observed: * 2 de novo deletions; 2 duplications awaiting parental origin studies.


Last Updated: 8 August, 2008 by G. Watkins.
 
2006 National Genetics Reference Laboratory (Wessex), Salisbury District Hospital, Salisbury SP2 8BJ; Tel: +44 (0)1722 429080; E-mail:ncpc@soton.ac.uk