Download Case study I: DNA copy number changes

Array-CGH and SNP-analysis
Helle Lybæk
Introduction to Microarray technology
September 2009
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DNA copy number changes
Background
• The underlying cause of the developmental delay remains unidentified
in approx. 50% of these individuals
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• Children and adults with mental retardation (IQ<70) represent a
large group of the general population, approx. 1–3%
• Chromosomal abnormalities are a known cause of mental retardation
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Chromosomal analysis by G-banding
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Chromosomal analysis by G-banding
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Chromosomal analysis by G-banding
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Resolution: 5-10 Mb
Chromosomal analysis by G-banding
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?
Detection rate in MR-patients: 10-16%; The majority have normal findings
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Background
• Need of more knowledge about which chromosomal abnormalities
-and disrupted genes- that cause developmental impairment
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• Need of development -and application- of improved chromosomal
screening methods for better detection of chromosomal abnormalities
in MR-patients
From chromosomes to arrays
2x
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2x
NMC-produced array with BAC-DNA from 3500 clones; Resolution: ~1 Mb
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Chromosomal analysis by array-CGH
Patient DNA
Normal DNA
Cot-1 DNA
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Normal DNA-spots
Duplication
Normal
Deletion
1 Mb array-CGH analysis
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1 Mb array-CGH analysis
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1 Mb array-CGH analysis
del: 41,2Mb – 45,3Mb
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del(3)(p21.3p22.1)
The MR-patient had normal findings on G-banding
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dup(7)(q35q36.1)
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dup: 144Mb – 152Mb
del(7)(q36.2qter)
del: 154Mb – 158,5Mb
Array-CGH analysis
1 Mb array-CGH (NMC BAC-array with 18.000 DNA spots)
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6 Kb array-CGH (Agilent oligo-array with 244.000 DNA spots)
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Array-CGH analysis
-4
-2 -1
0 +1 +2 +4
6 Kb oligo array-CGH
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-0.6 -0.4 0.0 0.4 0.6
1 Mb BAC array-CGH
Lybæk et al., Eur J Hum Genet 2009, 904-10
Genotype-phenotype mapping
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Disease genes can be identified by overlapping phenotypes
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Array-CGH mapping of MR-patients
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Mapping of 96 MR-patients for improved genotype-phenotype information
Lybæk et al., Eur J Hum Genet 2008, 1318-28
Array-CGH mapping of MR-patients
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Detection rate: 27% in MR-patients with normal findings on G-banding
Lybæk et al., Eur J Hum Genet 2008, 1318-28
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SNP-based DNA copy number analysis
• Normal occurring single base variants
• More than 6 millions SNP´s in the
human genome
• Approx 1 SNP per 1.000 bp
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SNP: Single Nucleotide Polymorphism
• 90% of the genes are covered by
at least one SNP
SNP-based DNA copy number analysis
• Resolution: ~1,4 kb
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• 900.000 SNPs
• 900.000 oligos
Affymetrix SNP-array 6.0
Comparison of the DNA copy number of the detected SNPs and oligos
in the patient sample versus in a control group (database)
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SNP-based DNA copy number analysis
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Detection of a 17,4 kb sized deletion; Easier to pinpoint candidate genes
Result from the microarray-group at Center for Medical Genetics and Molecular Medicine, HUH
Copy number variations (CNVs)
Approx. 12% of the human genome consists of copy number variations
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i.e. DNA-variants in the genome which are frequent
occurring in the normal population and that does not
(themselves) give rise to a phenotype/disease even
though genes are localised in these areas!
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SNP-based DNA copy number analysis
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The higher analysis resolution the more detection of CNVs
Result from the microarray-group at Center for Medical Genetics and Molecular Medicine, HUH
DNA copy number analysis –
New possibilities and challenges
- Before the time-consuming challenge was to find the areas with
chromosome- or gene abnormalities
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The microarray-technology has given us new possibilities and new
challenges:
- Today the time-consuming challenge is to interpret the findings you
surely will make!
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