Page 246 - 2021_09-Haematologica-web

Case Report
Table 2. Tissue-based cancer microarray and next-generation sequencing analysis of sequential grey zone lymphomas. Case #1, 16M, Paired NS-cHL and CNS LBCL Microarray
Cytobands
2p16.3-p12 9p24.3-q34.3 4q21.22-q21.23 6p25.3-p11.2 12p13.33-q24.33 Xp22.33-q28 Yp11.31-q11.23
Size (Mbp)
28.2 140.9 1.1 57.0 133.6 155.0 26.1
Pos (hg19)
chr5:112102044 chr4:126239848 chr19:15272113 chr16:3819314 chr5:112175211 chr12:122064705 chr9:135145055 chr2:39251255 chr6:152651971 chr6:152630998 chr6:152565729 chr6:152464786
Size (Mbp)
243.0 140.9 35.1 3.0 128.0 4.0 49.2 14.6 28.1 117.3 16.9 12.5 52.8 43.7 1.1 38.4 7.7 22.3 88.1 44.5
Pos (hg19)
chr17:7577569 chr4:153249384 chr11:119170426 chr4:187557893 chr12:49423015 chr7:103338388 chr21:39795460 chr16:72830889
Type
Gain Gain Loss CN-LOH Gain Gain Loss
RefSeq RNA
NM_000038.5 NM_024582.4 NM_000435.2 NM_004380.2 NM_000038.5 NM_032790.3 NM_015046.5 NM_005633.3 NM_182961.3 NM_182961.3 NM_182961.3 NM_182961.3
Type
Gain Gain Gain CN-LOH Gain Gain CN-LOH CG-LOH CN-LOH Gain Gain Loss Gain CN-LOH Gain Gain Loss Loss CN-LOH CG-LOH
RefSeqRNA
NM_000546.5 NM_033632.3 NM_005188.3 NM_005245.3 NM_003482.3 NM_005045.3 NM_001136154.1 NM_006885.3
Array Nomenclature
arr[hg19] 2p16.3p12(50,889,958-79,060,207)x3 arr[hg19] 9p24.3q34.3(204,737-141,054,761)x3 arr[hg19] 4q21.22q21.23(83,278,777-84,335,477)x1 arr[hg19] 6p25.3p11.2(204,908-57,160,035)x2 hmz arr[hg19] 12p13.33q24.33(189,399-133,818,115)x3 arr[hg19] Xp22.33q28(177,941-155,219,364)x2 arr[hg19] Yp11.31q11.23(2,660,162-28,799,935)x0 Case #1, 16M, Paired NS-cHL and CNS LBCL NGS
CDS; Protein; VAF (NS-cHL/LBCL)
c.157G>A; p.Gly53Arg; 0.05
c.2282T>G; p.Leu761Trp; 0.37
c.6326G>A; p.Arg2109Gln; 0.48
c.2921C>A; p.Thr974Asn; 0.44/0.47
c.3920T>A; p.Ile1307Lys; 0.56/0.45
c.58G>A; p.Gly20Ser; 0.62/0.29
c.7234A>G; p.Ile2412Val; 0.47/0.28
c.1098T>A; p.Asp366Glu; 0.44/0.48
c.13849A>C; p.Asn4617His; 0.41/0.47
c.17174C>A; p.Thr5725Asn; 0.42/0.51
c.19635G>T; p.Arg6545Ser; 0.44/0.46
c.25091C>T; p.Pro8364Leu; 0.47/0.51
Case #2, 17F, Paired NS-cHL and CNS LBCL Microarray
Array Nomenclature
arr[hg19] 2p25.3q37.3(21,493-243,052,331)x3 arr[hg19] 9p24.3q34.3(204,737-141,054,761)x5 arr[hg19] 16p13.13p11.1(83,886-35,271,725)x3 arr[hg19] 1p36.11p35.3(25,194,298-28,160,199)x2 hmz arr[hg19] 5p15.33q23.3(38,138-128,042,790)x3 arr[hg19] 5q23.3q31.1(128,063,275-132,042,740)x5 arr[hg19] 5q31.1q35.3(131,530,440-180,698,312)x2 hmz arr[hg19] 6p25.3p23(204,908-14,823,522)x3 hmz arr[hg19] 6p23p21.1(14,984,113-43,101,670)x2 hmz arr[hg19] 12p12.3q24.33(16,480,948-133,818,115)x3 arr[hg19] 15q11.1q14(20,161,371-37,079,572)x3 arr[hg19] 15q14q21.2(37,094,935-49,619,400)x1 arr[hg19] 15q21.2q26.3(49,643,377-102,397,317)x3 arr[hg19] 16q11.2q24.3(46,461,308-90,158,005)x2 hmz arr[hg19] 19p13.3(247,231-1,351,916)x3
arr[hg19] 21p11.2q22.3(9,648,314-48,097,610)x3 arr[hg19] 22q13.2q13.33(43,487,259-51,213,826)x1 arr[hg19] Xp22.33p22.11(177,941-22,471,996)x1 arr[hg19] Xp22.11q23(22,634,971-110,738,270)x2 hmz arr[hg19] Xq23q28(110,762,820-155,219,364)x3 hmz Case #2, 17F, Paired NS-cHL and CNS LBCL NGS
CDS; Protein; VAF (NS-cHL/LBCL)
c.712T>C; p.Cys238Arg; 0.51 c.1394G>A; p.Arg465His; 0.45 c.2656G>A; p.Glu886Lys; 0.40 c.3818A>T; p.His1273Leu; 0.45 c.14080G>C; p.Glu4694Gln; 0.50/0.30 c.1055A>G; p.Asn352Ser; 0.51/0.49 c.281T>G; p.Val94Gly; 0.46/0.33 c.5692G>C; p.Gly1898Arg; 0.47/0.95
Gene
APC FAT4 NOTCH3 CREBBP APC ORAI1 SETX SOS1 SYNE1 SYNE1 SYNE1 SYNE1
Cytobands
2p25.3-q37.3 9p24.3-q34.3 16p13.13-p11.1 1p36.11-p35.3 5p15.33-q23.3 5q23.3-q31.1 5q31.1-q35.3 6p25.3-p23 6p23-p21.1 12p12.3-q24.33 15q11.1-q14 15q14-q21.2 15q21.2-q26.3 16q11.2-q24.3 19p13.3-p13.3 21p11.2-q22.3 22q13.2-q13.33 Xp22.33-p22.11 Xp22.11-q23 Xq23-q28
Gene
TP53 FBXW7 CBL FAT1 KMT2D RELN ERG ZFHX3
Interpretation
CNS LBCL only, Reported in GZL* CNS LBCL only, Reported in GZL* CNS LBCL only
CNS LBCL only*
CNS LBCL only*
CNS LBCL only
CNS LBCL only
Interpretation
III, CNS LBCL only
III, CNS LBCL only
III, CNS LBCL only
III, Shared, Reported in GZL III, Shared
III, Shared III, Shared III, Shared III, Shared III, Shared III, Shared III, Shared
Interpretation
CNS LBCL only, Reported in GZL* CNS LBCL only, Reported in GZL* CNS LBCL only, Reported in GZL Shared
CNS LBCL only
CNS LBCL only
CNS LBCL only
CNS LBCL only*
CNS LBCL only
CNS LBCL only*
CNS LBCL only
CNS LBCL only
CNS LBCL only
CNS LBCL only
CNS LBCL only
CNS LBCL only
CNS LBCL only
CNS LBCL onl y
CNS LBCL only
CNS LBCL only
Interpretation
I/II, CNS LBCL only, Reported in GZL I/II, CNS LBCL only
III, CNS LBCL only
III, CNS LBCL only
III, Shared, Reported in GZL
III, Shared, Reported in GZL
III, Shared
III, Shared
*Detected in both CNS LBCL cases. NS-cHL: classic Hodgkin lymphoma, nodular-sclerosing subtype; CNS: central nervous system; LBCL: large B-cell lymphoma; NGS: next-generation sequencing;Pos:genomiccoordinate;RefSeq:referencetranscriptID;CDS:codingsequence;VAF:variantallelefrequency; Mbp:megabasepairs;GZL:greyzonelymphoma;CG-LOH: copy-gain loss of heterozygozity; cHL: CN-LOH, copy-neutral loss of heterozygosity.
2534
haematologica | 2021; 106(9)