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Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow
Ruth N Mackinnon1, Carly Selan, Adrian Zordan
1Victorian Cancer Cytogenetics Service, St Vincent's Hospital (Melbourne), Fitzroy, Vic, Australia. ruth.mackinnon@svhm.org.au.
Molecular Cytogenetics
|February 4, 2012
Summary
Archival cytogenetic specimens and refrigerated bone marrow provide suitable DNA for SNP arrays and array comparative genomic hybridization (CGH). This expands the utility of stored samples for retrospective genetic analysis in hematological malignancies.
Area of Science:
- Molecular Biology
- Genetics
- Biotechnology
Background:
- Nucleic acid analysis is often limited by the availability and quality of archival specimens.
- Archived cytogenetic preparations and diagnostic bone marrow samples are potential sources of genomic DNA.
- Previous studies explored array CGH with fixed cytogenetic preparations, but suitability for SNP arrays remained unclear.
Purpose of the Study:
- To assess the suitability of DNA from archival cytogenetic specimens and long-term refrigerated bone marrow for SNP array and array CGH.
- To determine if DNA extracted from these sources can support advanced genomic analyses.
Main Methods:
- Genomic DNA was extracted from cytogenetic specimens stored in Carnoy's fixative.
- DNA was also extracted from bone marrow stored unfrozen at 4°C for at least 36 days.
- A procedure was developed for extracting DNA from low-cellularity cytogenetic suspensions.
Main Results:
- Both SNP array and array CGH were successfully performed using DNA from fixed cytogenetic specimens.
- Genomic DNA extracted from bone marrow stored refrigerated for 36 days was also suitable for these analyses.
- A method for obtaining usable DNA concentrations from low-cellularity samples was established.
Conclusions:
- Archival cytogenetic preparations and long-term refrigerated bone marrow are valuable sources of DNA for array-based genetic analysis.
- This finding significantly enhances the potential for retrospective genetic analysis of clinical specimens.
- The DNA suitability extends to array karyotyping and potentially broader analytical applications.
