Patients’ characteristics
The median age of 300 patients was 58 years (range, 19–90 years). There were 187 males and 113 females (male to female ratio, 1.65:1).(Table 1) Among 300 lymphomas, there were 243 (81.0%) mature B-cell neoplasms, 53 (17.6%) mature T- and NK-cell neoplasms, and 4 (1.3%) precursor lymphoid neoplasms. In mature B-cell neoplasms, diffuse large B-cell lymphoma, not otherwise specified (DLBCL NOS) was the most common with 154 patients, followed by follicular lymphoma in 29 patients, primary diffuse large B-cell lymphoma of the central nervous system (CNS DLBCL) in 17 patients, and mantle cell lymphoma in 11 patients. Among mature T- and NK-cell neoplasms, extranodal NK/T-cell lymphoma, nasal type (ENKTL) was the most common (18 patients), followed by peripheral T-cell lymphoma, not otherwise specified (PTCL NOS) and angioimmunoblastic T-cell lymphoma (AITL) (10 patients each).
Number of SNV/Indel in all cases
When the number of SNV/Indel was counted by dividing VAF by 1%, VAF between 39% and 52% was higher than expected.(Fig. 1) Therefore, this area was considered to be a section with a high probability of including germline mutations. Excluding VAF less than 5% and total read less than 100, the average of the number of SNV/Indel was 22.68 (6804/300). The average number of SNV/Indel was 23.98 in mature B-cell neoplasms and 17.21 in mature T- and NK-cell neoplasms, showing a significant (P < 0.001) difference between the two. When all lymphomas were arranged in the order of median value of the number of SNV/Indel mutations, primary mediastinal large B-cell lymphoma (PMLBL) (median: 32) was the highest, followed by CNS DLBCL (median: 30), DLBCL NOS (median: 23), and anaplastic large cell lymphoma, ALK-negative (ALCL, ALK-) (median: 23).(Fig. 2) Lymphomas with the lowest SNV/Indel number were in order of ALCL, ALK-positive (ALCL, ALK+) (median: 14), follicular T-cell lymphoma (median: 14), and nodal peripheral T-cell lymphoma with TFH phenotype (PTCL TFH) (median: 14.5). The number of variants corresponding to the VAF 39–52% section did not show significant difference according to the type of lymphoma.(P = 0.529) (Fig. 2B)
Number of SNV/Indel in diffuse large B-cell lymphoma variants
Regarding types of DLBCL NOS according to Hans’ classification [30], 93 cases had a post-germinal center B-cell type (activated B-cell type, ABC type) and 53 cases had a germinal center B-cell type (GCB type), showing no significant difference in number of SNV/Indel between these two types of DLBCL NOS.(P = 0.308) (Fig. 3A) Compared with DLBCL NOS, PMLBL (P = 0.030) and CNS DLBCL (P = 0.008) had more SNV/Indel mutations, while EBV-positive diffuse large B-cell lymphoma, not otherwise specified (EBV DLBCL) had significantly (P = 0.048) less SNV/Indel mutations. High grade B-cell lymphoma (HGBCL) (P = 0.287), including double-hit lymphoma and triple-hit lymphoma and DLBCL NOS admixed with extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma), showed no significant (P = 0.199) difference from DLBCL NOS in SNV/indel number. There was no significant difference of SNV/Indel number according to Ann-Arbor stage (Fig. 3B) and therapeutic status (Fig. 3C) in DLBCL variants.
DLBCL, diffuse large B-cell lymphoma; CNS, central nervous system; NOS, not otherwise specified, GCB, germinal center B-cell; ABC, activated B-cell; MALT, mucosa-associated lymphoid tissue, EBV, Epstein-Barr virus; PMLBL, primary mediastinal large B-cell lymphoma, HGBCL, high-grade B-cell lymphoma.
Number of SNV/Indel in mature B-cell lymphomas except DLBCL variants
Results of comparison of the number of SNV/Indel of mature B-cell lymphoma except DLBCL variants are depicted in Fig. 4A. When follicular lymphoma was classified into low grade (grade 1–2, n = 19) and high grade (grade 3A and 3B, n = 10) by histologic grading [27], the number of SNV/indel of high grade follicular lymphoma (median: 20) was significantly (P = 0.013) higher than that of low grade (median: 17). Mantle cell lymphoma, lymphoplasmacytic lymphoma, chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), and nodal marginal zone lymphoma showed no significant difference in the number of SNV/Indel. When compared with DLBCL NOS, low grade follicular lymphoma (P < 0.001) and mantle cell lymphoma (P = 0.026) had significantly less SNV/Indel numbers while high grade follicular lymphoma showed no significant difference (P = 0.973). There was no significant difference of SNV/Indel number according to Ann-Arbor stage (Fig. 4B) and therapeutic status (Fig. 4C) in mature B-cell lymphomas. The remaining small B-cell lymphomas were not suitable for statistical analysis due to small number of cases. However, all of them showed lower SNV/Indel median values than mantle cell lymphoma.
MALT, mucosa-associated lymphoid tissue; CLL/SLL, chronic lymphocytic leukemia/small lymphocytic lymphoma; FL, follicular lymphoma; MALToma, extranodal marginal zone lymphoma of MALT; MCL, mantle cell lymphoma; LPL, lymphoplasmacytic lymphoma; NMZL, nodal marginal zone lymphoma.
Number of SNV/Indel in mature T- and NK-cell neoplasms
PTCL NOS showed no significant difference in SNV/Indel number from ENKTL (P = 0.942) or AITL (P = 0.739).(Fig. 5A) When these three T-cell lymphomas of T follicular helper (TFH) cell origin were compared, the median number of SNV/Indel of AITL was higher than that of follicular T-cell lymphoma (P = 0.133) or PTCL TFH (P = 0.056), although the difference was not statistically significant. In ALCL, the mutational burden was significantly higher in ALK-negative than in ALK-positive (P = 0.049). PTCL NOS showed significantly lower SNV/Indel than DLBCL NOS (P = 0.008). There was no significant difference of SNV/Indel number according to Ann-Arbor stage (Fig. 5B) and therapeutic status (Fig. 5C) in mature T- and NK-cell lymphomas. Tendencies to show more mutations in advanced disease (Ann-Arbor stage III or IV) or post-chemotherapy patients (relapsed/refractory) were observed in ENKTL, but there were not statistical significance.
PTCL, peripheral T-cell lymphoma; NOS, not otherwise specified; TFH, T follicular helper cell; ALCL, anaplastic large cell lymphoma, ALK, anaplastic lymphoma kinase; ENKTL, extranodal NK/T-cell lymphoma, nasal type; AITL, angioimmunoblastic T-cell lymphoma; FTCL, follicular T-cell lymphoma.
Table 1
Clinical characteristics and the number of SNV/Indel by pathologic diagnosis.
Diagnosis
|
Number
of patients
|
Age
|
M:F
|
Ann-Arbor stage
|
Therapeutic status
|
Number of SNV/Indel
|
median (range)
|
I or II
|
III or IV
|
Pre-Tx.
(at diagnosis)
|
Post-Tx.
(relapsed/
refractory)
|
Mean
|
Median
|
Range
|
Mature B-cell neoplasms
|
243
|
|
|
|
|
|
|
|
|
|
Diffuse large B-cell lymphoma, NOS
|
154
|
61 (26–86)
|
93:61
|
71
|
83
|
125
|
29
|
24.84
|
23
|
11–87
|
Primary diffuse large B-cell lymphoma of the CNS
|
17
|
62 (34–86)
|
10:7
|
17
|
0
|
16
|
1
|
31.53
|
30
|
17–51
|
Primary mediastinal large B-cell lymphoma
|
5
|
36 (25–62)
|
3:2
|
1
|
4
|
5
|
0
|
31.80
|
32
|
26–41
|
EBV-positive diffuse large B-cell lymphoma, NOS
|
6
|
62 (19–90)
|
4:2
|
2
|
4
|
5
|
1
|
17.00
|
18
|
5–28
|
High-grade B-cell lymphoma
|
6
|
50.5 (37–63)
|
5:1
|
1
|
5
|
4
|
2
|
20.83
|
21.5
|
15–27
|
Burkitt lymphoma
|
1
|
69
|
0:1
|
0
|
1
|
0
|
1
|
22.00
|
22
|
|
Plasmablastic lymphoma
|
2
|
58 (52–64)
|
2:0
|
1
|
1
|
1
|
1
|
19.50
|
19.5
|
17–22
|
Follicular lymphoma
|
29
|
50 (28–79)
|
18:11
|
5
|
24
|
27
|
2
|
19.62
|
18
|
8–35
|
Mantle cell lymphoma
|
11
|
63 (47–80)
|
8:3
|
2
|
9
|
7
|
4
|
19.09
|
20
|
11–27
|
Nodal marginal zone lymphoma
|
3
|
59 (58–63)
|
1:2
|
2
|
1
|
2
|
1
|
23.33
|
16
|
12–42
|
Extranodal marginal zone lymphoma of MALT
|
4
|
55.5 (44–68)
|
2:2
|
3
|
1
|
3
|
1
|
19.25
|
20.5
|
13–23
|
Lymphoplasmacytic lymphoma
|
2
|
59.5 (53–66)
|
2:0
|
0
|
2
|
0
|
2
|
17.00
|
17
|
14–20
|
Chronic lymphocytic leukemia/Small lymphocytic lymphoma
|
3
|
56 (53–61)
|
1:2
|
0
|
3
|
3
|
0
|
15.33
|
16
|
10–20
|
Mature T- and NK-cell neoplasms
|
53
|
|
|
|
|
|
|
|
|
|
Peripheral T-cell lymphoma, NOS
|
10
|
48 (25–71)
|
7:3
|
3
|
7
|
5
|
5
|
17.60
|
18
|
11–23
|
Angioimmunoblastaic T-cell lymphoma
|
10
|
66.5 (43–81)
|
5:5
|
0
|
10
|
7
|
3
|
18.70
|
19.5
|
10–24
|
Follicular T-cell lymphoma
|
2
|
50 (48–52)
|
2:0
|
0
|
2
|
1
|
1
|
14.00
|
14
|
13–15
|
Nodal peripheral T-cell lymphoma with TFH phenotype
|
4
|
68.5 (64–75)
|
3:1
|
0
|
4
|
3
|
1
|
14.25
|
14.5
|
13–15
|
Extranodal NK/T-cell lymphoma, nasal type
|
18
|
56 (32–79)
|
11:7
|
11
|
7
|
12
|
6
|
17.44
|
17
|
9–25
|
Anaplastaic large cell lymphoms, ALK-positive
|
5
|
35 (20–58)
|
4:1
|
1
|
4
|
4
|
1
|
12.20
|
14
|
6–16
|
Anaplastaic large cell lymphoms, ALK-neative
|
4
|
40 (29–56)
|
3:1
|
1
|
3
|
4
|
0
|
22.25
|
23
|
15–28
|
Precursor lymphoid neoplasms
|
4
|
|
|
|
|
|
|
|
|
|
Lymphoblastic leukemia/lymphoma
|
4
|
44.5 (34–70)
|
3:1
|
1
|
3
|
4
|
0
|
19.00
|
19.5
|
15–22
|
Total
|
300
|
58 (19–90)
|
187:113
|
122
|
178
|
238
|
62
|
22.68
|
21
|
5–87
|
SNV, single nucleotide variant; NOS, not otherwise specified. |