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Genomic microarrays: Applications to gene discovery and molecular karyotype. August, 2005. David H. Ledbetter, Ph.D. Department of Human Genetics Emory University firstname.lastname@example.org. (T 2 AG 3 ) n. 3 -20 kb. Subtelomeric Region. 100 - 300 kb. Human Telomere Structure.
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David H. Ledbetter, Ph.D.
Department of Human Genetics
Biesecker, Am. J. Med. Genet. 107:263-266, 2002
Conclusion: G-banding alone is insufficient to identify clinically significant segmental aneusomy. Additional molecular cytogenetic technologies are needed.
Britt Ravnan, James Tepperberg, Christa Martin
Genzyme, LabCorp and U. Chicago
>12,000 cases examined
3.2 % abnormals identified
0.4% polymorphisms, benign variants
2.8% clinically significant
tel – 68F18
Cardoso et al. (2003) Am J Hum Genet,72:918-930
Lese Martin et al. (2002) J Med Genet 39(10):734-740
= clone size
~ 100 kb
Pinkel et al., Nat Genet (1998), 20(2):207-11
Patient DNA (male)
Control DNA (female)
Gain = green
Loss = red
Detected by array
ALL 17 IMBALANCES WERE
IDENTIFIED USING CGH-ARRAYS
Ratio = 0.51
Ratio = 0.52
Phenotype: MR, hypopigmentation
Multiple 1ptel clones from telomere to 4 Mb
Phenotype: MR, obesity
Patient DNA (male), Control DNA (female)
Gain = green, Loss = red
Microcephaly, autism (parents pending)
bilateral colobomas, DD, seizures, left ptosis (Cat Eye)
Targets only clinically relevant loci and clones are not spaced evenly across genome
Range from 1-3 Mb spacing
to complete genome tiling path
consisting of >32,000 clones!
2,500 clones; 1.4 Mb
Array image from UCSF website
~79 kb resolution
BC Cancer Agency
Krzywinski et al., Nucleic Acids Res (2004) 32(12):3651-60.
Chose the two re-array plates that had the highest number of clones in the 15q11-15q13 region. (Plates 2B1 and 3A1)
3A1 was a partially filled plate of 43 clones
135 tiling path clones total
aCGH-15 Pilot Study- Clone Selection
Total clones: 178
Average coverage on chr15: 1 clone ~ 470 kb
Average coverage in q11-q13: 1 clone ~150 kb
Class II deletion
Class I deletion
Pervasive Developmental Delay
Phenotype suggestive of PW
Christa Lese Martin, Ph.D.
Andrew Wong, Ph.D.
Lorraine May, M.S.
David Johnson, B.S.
Devan Pressley, B.S.
Courtney Works, B.S.
March of Dimes