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Table 2 Overview of temporal genomic heterogeneity

From: Characterizing temporal genomic heterogeneity in pediatric low-grade gliomas

  BRAF fusion BRAF V600E CDKN2A deletion H3K27M mut. IDH1 mut. FGFR1 fusion NTRK2 fusion MYB fusion MYBL1 fusion ATRX loss
Entire Cohort (all diagnoses, n = 45)
Patients with paired tumor samples tested 34 44 26 21 28 28 17 16 12 18
Conserved
  Remained positive
(S, I)
17
(S = 9, I = 1)
2
(S = 0, I = 0)
4
(S = 1, I = 0)
0 2*
(S = 0, I = 1)
0 0 0 0 1#
(S = 0, I = 1)
  Remained negative
(S, I)
17
(S = 4, I = 3)
41
(S = 17, I = 5)
11
(S = 4, I = 1)
21
(S = 9, I = 3)
26
(S = 10, I = 2)
27
(S = 10, I = 4)
17
(S = 5, I = 3)
16
(S = 5, I = 3)
12
(S = 4, I = 2)
17
(S = 7,
I = 3)
Changed
 Acquired
(S, I)
0 0 7
(S = 3, I = 1)
0 0 1
(S = 0,
I = 0)
0 0 0 0
 Lost
(S, I)
0 1
(S = 0, I = 0)
4a
(S = 1, I = 2)
0 0 0 0 0 0 0
By Histolopathologic diagnosis:
Pilocytic or Pilomyxoid Astroyctoma (n = 28)
Patients with paired tumor samples tested 23 28 19 13 15 19 9 10 7 10
Conserved
  Remained positive
(S, I)
15
(S = 9, I = 1)
0 4
(S = 2, I = 0)
0 0 0 0 0 0 0
  Remained negative
(S, I)
8
(S = 2, I = 1)
27
(S = 14, I = 2)
6
(S = 2, I = 0)
13
(S = 6, I = 1)
15
(S = 7, I = 1)
18
(S = 8, I = 2)
9
(S = 3, I = 1)
10
(S = 3, I = 1)
7
(S = 2, I = 1)
10
(S = 5,
I = 1)
Changed
 Acquired
(S, I)
0 0 6
(S = 2, I = 1)
0 0 1
(S = 0,
I = 0)
0 0 0 0
 Lost
(S, I)
0 1
(S = 0, I = 0)
3a
(S = 1, I = 1)
0 0 0 0 0 0 0
Diffuse Astrocytoma (n = 7)
Patients with paired tumor samples tested 3 6 2 5 7 5 4 2 1 2
Conserved
  Remained positive
(S, I)
0 0 0 0 2*
(S = 0, I = 1)
0 0 0 0 1#
(S = 0, I = 0
  Remained negative
(S, I)
3
(S = 0, I = 1)
6
(S = 1, I = 1)
0
(S = 0, I = 0)
5
(S = 1, I = 0)
5
(S = 1, I = 0)
5
(S = 1, I = 1)
4
(S = 0, I = 1)
2
(S = 0, I = 1)
1
(S = 0, I = 0)
1
(S = 0,
I = 1)
Changed
 Acquired
(S, I)
0 0 0 0 0 0 0 0 0 0
 Lost
(S, I)
0 0 1
(S = 0, I = 1)
0 0 0 0 0 0 0
Ganglioglioma (n = 5)
Patients with paired tumor samples tested 4 5 1 0 2 1 1 1 1 2
Conserved
  Remained positive
(S, I)
2
(S = 1, I = 0)
2
(S = 0, I = 0)
0 0 0 0 0 0 0 0
  Remained negative
(S, I)
2
(S = 0, I = 0)
3
(S = 1, I = 0)
1
(S = 0, I = 0)
0 2
(S = 0, I = 0)
1
(S = 0, I = 0)
1
(S = 0, I = 0)
1
(S = 0, I = 0)
1
(S = 0, I = 0)
2
(S = 0, I = 0)
Changed
 Acquired
(S, I)
0 0 0 0 0 0 0 0 0 0
 Lost
(S, I)
0 0 0 0 0 0 0 0 0 0
 Other LGGs (n = 5)
Patients with paired tumor samples tested 4 5 4 3 4 3 3 3 3 4
Conserved
  Remained positive
(S, I)
0 0 0 0 0 0 0 0 0 0
  Remained negative
(S, I)
4
(S = 2, I = 1)
5
(S = 2, I = 1)
3
(S = 2, I = 0)
3
(S = 2, I = 1)
4
(S = 2, I = 1)
3
(S = 2, I = 1)
3
(S = 2, I = 1)
3
(S = 2, I = 1)
3
(S = 2, I = 1)
4
(S = 2, I = 1)
Changed
 Acquired
(S, I)
0 0 1
(S = 2, I = 1)
0 0 0 0 0 0 0
 Lost
(S, I)
0 0 0 0 0 0 0 0 0 0
  1. Results for the entire cohort (all histologic diagnoses) are shown together at the top, followed by results for each histologic diagnosis subgroup individually. The number of patients who had testing for a given genetic alteration performed on paired tumor specimens is shown in the top row of each category. Subsequent rows illustrate the number of patients with conversed or changed (acquired or lost) status for given genetic alterations, specifying the number of patients who received systemic therapy (“S”) or irradiation (“I”) between surgeries
  2. * One of these patients had conserved IDH1 R132H mutations (Patient #33) and the other had conserved IDH1 R132G mutations (Patient #32)
  3. #Although this patient had conserved ATRX loss demonstrated on IHC, sequencing revealed different ATRX mutations in the diagnostic and recurrent tumor samples, as described in the text
  4. aOne of these patients had CDKN2A testing performed on three tumor specimens, with CDKN2A deletions identified (conserved) on the first two tumor samples, and subsequently lost on the third (post-mortem) tumor sample