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Mouse Genome CGH Microarray 44A

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Mouse Genome CGH Microarray Kit 44ADesigned for CGH, Validated with samples of known aberrations

Designed for genome-wide profiling of genomic aberrations on a single chip. Genome-wide coverage with average resolution ~35kb Based on UCSC Genome Browser mm5 (NCBI Build 33) All probes and annotations mapped to mm6 (NCBI Build 34) Probe selection biased toward genes (73% intragenic vs. 27% intergenic) Optimized probe design for aCGH application Similar probe design and validation process as used in Human CGH array Include CGH eQC grid Compatible with current Agilent microarray platform and CGH protocols

Part number: G4414A List price: $3750/Kit with volume break Discount: EDU (20%) and VEU Standard catalog array packaging

Only commercially available Mouse CGH Microarray !

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Mouse Genome CGH Microarray Kit 44ADesigned for CGH, Validated with samples of known aberrations

Consisting of ~43,000 60-mer oligonucleotide probes on 1”x3” slide Genome-wide coverage with average resolution ~35kb* Content source: UCSC Genome Browser mm5 (NCBI Build 33) All probes and annotations mapped to latest NCBI Build 34 Probe selection biased toward genes 1 probe per well-characterized gene

2 or more probes for each of ~1100 cancer genes

Intragenic probes (73%); intergenic probes (27%) Optimized probe design for CGH application Ability to detect single copy and homozygous deletions as well as low and high level amplifications Compatible with current Agilent microarray platform and protocols

* Calculated by using the total size of the non-repeated genome divided by the total # of features

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• Tiled candidate probes across non-repeat masked regions across the genome in 30 bp steps between cut sites for restriction enzymes (RsaI and AluI) – sourced from UCSC Genome Browser mm5 (NCBI Build 33)

• Performed homology search and retained highly specific probes

• Filtered homology-searched probe set on the same in silico parameters as used in designing Human CGH array

• Selected the best set of ~ 80,000 semifinal probes biasing toward genes & exons

• Performed empirical validation using normal M/F cell-line samples and outliers were eliminated

• Remove any probes that do not map to NCBI Build 34

• Final probe set within a narrow Tm range

Probe Design Methodology

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Genomic Coverage and Probe Distribution

Total # of Features44,290 # of Biological Probes43,020 # of Unique Biological Probes42,404 # of Replicated Biological Probes

308 x 3 Total # of Control probes1,270___________________________________________

Intragenic probes 31,552 (73%)

Exonic probes 17,344 (55%)

Intronic probes 14,208 (45%) Intergenic probes 11,468 (27%)

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Mouse CGH Array Processing

Oligo aCGH v2.0 protocol (Supplement with following material changes)

Mouse Cot-1 DNA (1.0mg/ml) Invitrogen p/n 18440-016

C57BL/6J Genomic DNA: Male Jackson Labs p/n 000664

C57BL/6J Genomic DNA: Female Jackson Labs p/n 000664

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Mouse Genomic DNA

Digested

Phi29 amplified

Un-cut

DigestedUn-cut

Un-amplified

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Separation Histogram

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Log2 Ratio

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3ug gDNA into Direct Labeling

X probes

autosome probes

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Ts65Dn Mouse

Ts65Dn mice are trisomic for the genes carried in the small translocation chromosome, symbolized Ts(1716)65Dn, that are normally located on Chr16.

Learn more from www.jax.org

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Ts(1716)65Dn Chromosome 16

Polarity=1 Polarity=-1 Combined

3ug gDNA into Direct Labeling

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Ts(1716)65Dn Chromosome 16 Breakpoint

T65Dn translocation breaks mouse Chr 16 just proximal to the amyloid precursor protein (App) gene and contains the HSA21-homologous genes from App to the telomere.

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Aberrations in Lymphoma Cell Line 1(Combined dye-swaps; 10pt. Moving average)

Collaboration Data from Lynda Chin, DFCI

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Aberrations in Lymphoma Cell Line 2(Combined dye-swaps; 10pt. Moving average)

Collaboration Data from Lynda Chin, DFCI