DNA fragmentation simulation method (FSM) and fragment size matching improve aCGH performance of FFPE tissues.

DNA Fragment Size Matching Facilitated by the FSM Method is More Critical to Array Quality than Previously Identified Factors Having demonstrated the highly significant contributions of FSM analysis and matched DNA fragment sizes to aCGH quality, we sought to further assess the relative effects of fragment size compared to other previously reported variables such as Proteinase K digestion time, array hybridization time, and concentration and source of DNA in array hybridization reactions.

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