Introduction 1 14 15 ® 1 1 Table 1 Spectrophotometric result of total DNA yield, DNA purity, and labeling efficiency, for fresh, formalin-fixed and UMFIX-exposed samples Sample Total DNA (μg) A260/A280 A260/A230 Sample-cy5 labeling efficiency (pmol/μg) Control-cy3 labeling efficiency (pmol/μg) Fresh 1 3.89 1.77 1.43 70.8 111 Fresh 2 2.94 1.86 1.79 42.8 89.6 Fresh 3 2.93 1.9 2 52.8 97 Mean ± SD 3.25 ± 0.55 1.84 ± 0.07 1.74 ± 0.29 55.47 ± 14.19 99.20 ± 10.87 UMFIX 1 6.416 1.85 2 78.6 110 UMFIX 2 2.7138 1.86 1.84 49.6 88 UMFIX 3 4.012 1.86 1.8 48.2 81.8 Mean ± SD 4.38 ± 1.88 1.86 ± 0.01 1.88 ± 0.11 58.80 ± 17.16 93.27 ± 14.82 Formalin 1 5.366 1.58 0.84 59.8 142.4 Formalin 2 4.0424 1.67 1.11 41.2 73.4 Formalin 3 4.427 1.93 2.08 36.2 77.4 Mean ± SD 4.61 ± 0.68 1.73 ± 0.18 1.34 ± 0.65 45.73 ± 12.44 97.73 ± 38.73 1  2  3  Fig. 1 a b c L  numbers  S  U  F  P  N   Genomic DNA from the skin samples and the control female DNA (Promega, Madison, WI) were then subjected to amplification according to Agilent’s (Palo Alto, CA) protocol for oligonucleotide array-based CGH for genomic DNA (version 2.0 August 2005). Amplification, of both male genomic DNA and female control DNA, 100 ng each, was performed using Qiagen REPLI-g Amplification Kit. Amplified DNA was digested during a 2 h incubation at 37°C, with Alu I and Rsa I (10 U/μl; 5μl/reaction) restriction enzymes (Promega, Madison, WI). Purification of digested DNA was performed with QIAprep Spin Miniprep Kit (Qiagen, Valencia, CA). Digested DNA was subjected to electrophoresis to evaluate quality of amplified DNA by visual inspection of its uniformity and range. 1 1 9 1 2 Table 2 Representative data of microarray scan quality measurement Sample Non-uniform feature Reproducibility: non-control replicated probes median %CV Saturated feature Red Green Red Green Red Green Fresh 1 113 379 7 8 0 1 Fresh 2 51 139 4 4 0 0 Fresh 3 38 135 5 6 0 0 Mean ± SD 67 ± 40 218 ± 140 5 ± 1 6 ± 2 0 0 UMFIX 1 352 560 13 13 0 0 UMFIX 2 85 179 7 8 0 0 UMFIX 3 36 136 6 7 0 0 Mean ± SD 158 ± 170 292 ± 233 8 ± 4 9 ± 3 0 0 Formalin 1 1,402 302 77 6 285 1 Formalin 2 1,987 157 37 12 361 0 Formalin 3 3,135 170 94 8 326 0 Mean ± SD 2,175 ± 882 210 ± 80 69 ± 30 9 ± 3 324 ± 38 0 Red  green  1  2  3  These findings may be attributed to erratic and random fragmentation of DNA in formalin-fixed samples. The fragmentation itself results in increase background noise and aberrant signal intensity due to random hybridization. 2 Fig. 2 x y Green  Red  X  Y   6 11 12 20 Samples used in nearly all a-CGH studies have been fresh or fresh-frozen tissue. Such material, although useful in research settings, is impractical and cumbersome to use in clinical practice. Furthermore, because diagnostic biopsy samples are relatively small, the amount of residual tissue for additional ancillary testing may be inadequate. Hence there is a great need to develop test strategies that require minimal amounts of tissue and are robust enough to withstand pre-analytical sample preparation. Simplified schemes for sample preservation that allow reliable histomorphology along with preservation of high quality macromolecules are desirable. 19 18 10 21 4 4 5 7 10 3 13 2 9 16 17 18 8 11 In summary, we show that by using a new molecular fixative it is possible to preserve skin tissue DNA that is suitable for array CGH studies; identical to fresh tissue. This can be achieved using same methods and protocols used for fresh samples.