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PTEN Loss Pan-Cancer Dependency Atlas - Phase 1 Classifier Summary
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Total cell lines with lineage annotation: 2119
PTEN-lost:    209
PTEN-intact:  1885
Excluded (missense VUS): 25

Loss mechanism breakdown:
  Deletion only:      34
  Mutation only:      175
  Both (del+mut):     0

Co-alteration frequencies (among PTEN-lost):
  PIK3CA hotspot: 15/209 (7.2%)
  TP53 mutated:   144/209 (68.9%)
  RB1 altered:    44/209 (21.1%)

Expression cross-validation:
  Median expression (lost):   4.40
  Median expression (intact): 5.00
  Mann-Whitney p-value:       9.55e-13
  % lost below intact Q25:    54.6%
  Discordant (lost w/ high expr): 36

Qualifying cancer types (9 of 34):
  (threshold: >= 5 PTEN-lost + >= 10 PTEN-intact with CRISPR)

  Uterus                         lost= 23 intact= 20 freq=53.5% CRISPR: 19/14
  CNS/Brain                      lost= 47 intact= 75 freq=38.5% CRISPR: 34/50
  Skin                           lost= 22 intact=128 freq=14.7% CRISPR: 14/61
  Breast                         lost= 13 intact= 82 freq=13.7% CRISPR: 10/42
  Bowel                          lost= 10 intact= 86 freq=10.4% CRISPR: 8/53
  Ovary/Fallopian Tube           lost=  7 intact= 67 freq=9.5% CRISPR: 6/52
  Lymphoid                       lost= 23 intact=233 freq=9.0% CRISPR: 13/78
  Lung                           lost= 21 intact=237 freq=8.1% CRISPR: 8/117
  Esophagus/Stomach              lost=  7 intact= 97 freq=6.7% CRISPR: 5/64

Non-qualifying types with PTEN loss (14):
  Prostate                       lost=  3 intact= 12 CRISPR: 2/8
  Thyroid                        lost=  4 intact= 21 CRISPR: 2/9
  Bladder/Urinary Tract          lost=  4 intact= 35 CRISPR: 4/30
  Testis                         lost=  1 intact= 11 CRISPR: 1/4
  Liver                          lost=  2 intact= 26 CRISPR: 2/21
  Biliary Tract                  lost=  3 intact= 42 CRISPR: 3/31
  Myeloid                        lost=  5 intact= 82 CRISPR: 4/38
  Pleura                         lost=  2 intact= 34 CRISPR: 1/20
  Kidney                         lost=  4 intact= 70 CRISPR: 4/31
  Cervix                         lost=  1 intact= 25 CRISPR: 1/17
  Peripheral Nervous System      lost=  2 intact= 58 CRISPR: 0/45
  Head and Neck                  lost=  3 intact= 90 CRISPR: 3/73
  Pancreas                       lost=  1 intact= 67 CRISPR: 1/47
  Bone                           lost=  1 intact= 91 CRISPR: 1/48
