Sample A: Cover Page of Thesis, Project, or Dissertation Proposal

have specific attributes which can be detrimental to the interpretation of the signal intensity
including cross-hybridization, loss of target sequence, SNP presence, and structural accessibility.
These filters affect all samples similarly. Conversely, the measurement reliability filter affects
each sample individually.
I. Unidentifiable Target. The CDF base table for the U95Av2 arrays (Affymetrix
NetAffx; http://www.affymetrix.com/products/arrays/specific/hgu95.affx) was queried
all 409,600 probes for which the probe sequence annotation was known. There
remained 11,432 probes, representing 174 genes, which we eliminated from further
consideration. Affymetrix reports the origin/source of these sequences as unknown
(personal communication, Affymetrix Technical Support to H. Deshmukh) [13].
II. Cross-Hybridization and Loss of Target Sequence. Probe cross hybridization is the
major confounding factor affecting the interpretation of probe responses [9, 10, 20, 21,
25, 50]. We have chosen to follow the Ensembl definitions of cross hybridizations,
where 23/25 nucleotides must be in alignment, and we have queried ENSEMBL
Biomart
(http://www.ensembl.org/biomart/martview/3ee2b94e6eb250f709ffdf9474635fdf) to
acquire the list used to perform this filtering step. This process identifies probes that
align to a single human genome region, and eliminates those which align to more than
one region of the human genome and also those that don’t align at all. We note that
this comparison is available only for perfect match (PM) probes and therefore if
Mismatch (MM) probes are included in the analysis an equivalent list must be acquired
and applied, or the level of filtering is not the same in the two categories of probes.
Without such a step, incorporation of any mismatch probes (MM) information, as
background for PM probes for example, results in a discrepancy in the reliability of the
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