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Update FAQ.md (#6385)
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* Update FAQ.md
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jjgao authored Jul 15, 2019
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Expand Up @@ -177,9 +177,9 @@ A “splice site” mutation occurs in an intron, in a splice acceptor or donor
### What do “Amplification”, “Gain”, “Deep Deletion”, “Shallow Deletion” and "-2", "-1", "0", "1", and "2" mean in the copy-number data?
These levels are derived from copy-number analysis algorithms like GISTIC or RAE, and indicate the copy-number level per gene:
* -2 or Deep Deletion indicates a deep loss, possibly a homozygous deletion
* -1 or Shallow Deletion indicates a shallow loss, possible a heterozygous deletion
* -1 or Shallow Deletion indicates a shallow loss, possibley a heterozygous deletion
* 0 is diploid
* 1 or Gain indicates a low-level gain (a few additional copies copies, often broad)
* 1 or Gain indicates a low-level gain (a few additional copies, often broad)
* 2 or Amplification indicate a high-level amplification (more copies, often focal)

Note that these calls are putative. We consider the deep deletions and amplifications as biologically relevant for individual genes by default. Note that these calls are usually not manually reviewed, and due to differences in purity and ploidy between samples, there may be false positives and false negatives.
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