Use of Paraifin Embedded Material for SNP Array Analysis

DNA fragments extracted from FFPE tissues are usually degraded or small. However, aberrations in copy numbers have been reported using FFPE-derived DNA with the firstgeneration SNP arrays—GeneChip HuSNP (40,45,54) or GeneChip mapping 10 K array (55). The assay for the HuSNP array uses 24 multiplex polymer chain reactions (PCRs) to generate labeled targets for hybridizing with 1494 SNP probe sets.

Multiplex PCR amplification can apparently tolerate degraded DNA because the size of PCR products generated for subsequent hybridization is 100-450 base pairs. However, the 10 K mapping array and the 100 K and 500 K arrays use a specific restriction enzyme to digest the genomic DNA for subsequent ligation with a specific DNA linker. The DNA linkers then act as binding sites for the specific primer to initiate PCR amplification

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rS

A

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B M

B M

B M

Fig. 3. The use of microdissected material increased the sensitivity of the SNP array to LOH in tumor tissues. Regions with LOH are highlighted in black color. B, DNA extracted from bulk tumor tissue without microdissection; M, DNA was extracted from microdissected tumor cells and amplified by the multiple displacement amplification method (52).

and labeling. Most DNA fragments extracted from FFPE samples are less than 0.5 kb and will thus lack two XbaI (for the 10 K array) or Hindffl (for the 50 K Hindffl SNP array) restriction sites. As a result, many SNP loci will not be amplified as labeled targets, thus tremendously decreasing the genotype call rate and the level of hybridization signals.

From our experience, we can obtain a call rate as high as 85%, but most of the time is around 50% when using DNA extracted from most FFPE samples (unpublished data). Further improvements to the SNP array analysis of FFPE samples are still needed.

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