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.
|