Affymetrix, Inc.

Eric B Schell

Alan J Williams

John E Blume

Charles Garrett Miyada

Christopher Allen Davies

Yanxiang Cao

Shivani Nautiyal

Gangwu Mei

John F Palma

Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.

Analysis of methylation using nucleic acid arrays

Arrays for genome-wide analysis of methylation are disclosed. IN a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within cpG islands in samples from human, mouse and rat genomes.

The invention provides arrays for analysis of compromised nucleic acid samples, for example, nucleic acids obtained from formalin fixed paraffin embedded samples and methods to analyzed these compromised samples. Arrays are disclosed in which the probe selection region used to select probes for the array is the 300 bases of the target MRNA that are immediately upstream of the start of the poly(A) tail of the mRNA. The probes selected for the array are more biased toward the 3' end of the mRNA than other arrays that are currently available.

Methods of analysis of degraded nucleic acid samples

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Mountain View, CA, United States of America

Eric B Schell