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An alteration was defined as recurrent, if it was present in at least 25% of the samples [ 10].
A copy number alteration was defined as exceeding the significance threshold of 1 × 10−6 in a minimum of 5 consecutive probes and in more than 30% of the samples.
We have also annotated variants as "reported pathogenic" or "benign" when a gene alteration was defined as such in a published article or as a "variant of unknown clinical significance" otherwise.
A segmental chromosomal alteration was defined as either the presence of an aberration of the respective chromosome arm, as determined by FISH, or in the case of deletion or imbalance, as determined by LOH.
For the purposes of this analysis, a single base pair somatic alteration was defined on the basis that it was observed in a tumor specimen but not in the constitutional DNA of 102 controls from the SNP500 Cancer set, or matched blood DNA of 36 of the Norwegian breast cancer cases.
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Alterations were defined by log2 ratio thresholds of 0.25 for copy number gain.
Copy number alterations were defined as <1.3 (loss) or >2.3 (gains).
The reported CDH1 constitutional alterations are defined as truncating, deletion, insertion, splice site, non-sense, and missense mutations (Table 1); we grouped these mutations as non-missense (truncating, deletion, insertion, splice site and non sense) or missense mutations.
Mood alterations were defined as all AE belonging to one of the following MedDRA high-level group terms: mood disorders and disturbances, not elsewhere classified, and psychiatric and behavioral symptoms, not elsewhere classified.
Cognitive change being defined as an alteration of one or more standard deviation in two or more cognitive domains, the analysis as to how many patients changed with regard to their cognitive function classified 8 patients as having significantly profited from intervention.
An alteration in consciousness was defined as having any of the following: looking or feeling dazed, confusion, difficulty thinking clearly, difficulty responding to mental status questions, inability to describe events immediately before or after the traumatic event, disorientation, or a decreased level of consciousness.
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