d3b-center/hope-cohort-analysis

Correlation of gene alterations vs clinical variables

Closed this issue · 2 comments

komalsrathi commented

Correlation between any following gene mutations with age OR sex:

  • NF1
  • TP53
  • IDH1
  • ATM
  • PDGFRA
  • CDKN2A
  • TSC2
  • ASXL1
  • SMARCA4

Additional questions:

  • if there is coexistence correlation ATRX and TP53
  • if the coexistence is correlated with age group or sex ATRX and TP53
  • if there is coexistence correlation H3F3A and TP53
  • if the coexistence is correlated with age group or sex H3F3A and TP53
  • if there is coexistence correlation NF1 and ATRX
  • if the coexistence is correlated with age group or sex

cc: @mkoptyra

komalsrathi commented
  1. Correlation between gene alterations coded as simple Absent or Present (if ANY type of alteration is present in a gene) with Age or Sex. I actually tested all genes used in the oncoprint instead of limiting to the above list and NONE of the genes had Chi-square p-value < 0.05.
komalsrathi commented

ATRX-TP53:

1. Coexistence correlation: 0.00015
2. Age: 0.321
3. Sex: 0.354
4. Adult: 0.007049
5. Pediatric: 0.0298
6. Male: 0.004222
7. Female: 0.06625
8. Pediatric female: 0.4545
9. Pediatric male: 0.1138

H3F3A-TP53:

1. Coexistence correlation: 0.00939
2. Age: 1
3. Sex: 0.747
4. Adult: 0.3691
5. Pediatric: 0.02095
6. Male: 0.5493
7. Female: 0.004127
8. Pediatric female: 0.03131
9. Pediatric male: 0.5029

NF1-ATRX:

1. Coexistence correlation: 0.04196
2. Age: 0.335
3. Sex: 0.561
4. Adult: 1
5. Pediatric: 0.001736
6. Male: 0.4446
7. Female: 0.1127
8. Pediatric female: 0.01519
9. Pediatric male: 0.1138