Blood Res 2022; 57(1):
Published online March 31, 2022
https://doi.org/10.5045/br.2022.2021138
© The Korean Society of Hematology
Correspondence to : Jong Gwon Choi
Department of Internal Medicine, Myunggok Medical Research Center, 158 Gwanjeodong-ro, Daejeon 35365, Korea
E-mail: jabuss@naver.com
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
TO THE EDITOR: Translocation of platelet-derived growth factor receptor A (
Patients, occasionally meet the general criteria for classifying their condition as a myeloproliferative neoplasm (MPN) but may not meet all criteria for a particular disease or may exhibit more than one category of diagnostic characteristics. These patients can be diagnosed as MPN unclassifiable (MPN-u). Symptoms are similar to typical MPNs and usually include hepatosplenomegaly and increased numbers of white blood cells (WBCs) and platelets. A bone marrow biopsy reveals megakaryocyte proliferation and hypercellularity in granulocytes or erythrocytes. As the disease progresses, the bone marrow becomes more fibrotic. However, in the current patient,
A 38-year-old man presented to the Konyang University Hospital (Deajeon, South Korea) on March 10, 2017, with abdominal pain that started 2 months before, and thrombocytosis was identified at a local clinic. At the time of admission, the patient had a blood pressure of 130/90 mmHg, heart rate of 78 beats per minute, respiratory rate of 20 breaths per minute, and body temperature of 37°C. There was no significant previous medical history of hypertension, diabetes mellitus, or tuberculosis. On physical examination, we observed organomegaly in the right upper quadrant of the abdomen. However, there was no enlargement of the cervical, axillary, or inguinal lymph nodes. Other examinations were unremarkable. Laboratory tests showed WBCs at 30,300/mL, hemoglobin at 9.4 g/dL, and platelets at 836,000/mL. White blood cells were composed of 24% segmented neutrophils, 17% lymphocytes, 1% monocytes, 3% eosinophils, and 51% basophils. The reticulocyte count was within the normal range. Leukemic blasts were observed in 2% of the cells. Coagulation tests revealed a prothrombin time of 16.4 seconds and an activated partial thromboplastin time of 35.5 seconds. He had a fibrinogen level of 3.13 g/L, D-dimer level of 2.1 mg/mL, and antithrombin activity of 72% (not suggestive of disseminated intravascular coagulation). Peripheral blood showed normocytic and normochromic red blood cells, no polychromasia, a normal WBC count with no toxic granulation or vacuolations, and an increased platelet count. The serum lactate dehydrogenase level was 832 U/L (normal range, 120–240 U/I). The total bilirubin level was 1.04 mg/dL (normal range, 0–0.4 mg/dL). Results for other blood factors, including creatinine and bicarbonate, and liver function tests, were unremarkable. Computed tomography revealed hepatosplenomegaly (16 cm) without an intrasplenic mass. Bone marrow aspiration revealed no particles or peripheral dilution, and immature cells were observed occasionally (Fig. 1). Bone marrow biopsy showed estimated cellularity of approximately 100%, which was hypercellular for the patient’s age. In cellular areas, trilineage hematopoiesis was observed, along with increased numbers of basophils and immature cells. In addition, there were increased numbers of dysplastic megakaryocytes, and diffuse fibrosis was observed in multiple focal areas throughout the bone marrow space (Fig. 2). The
Table 1 Results of next generation gene sequencing before imatinib treatment. PRKG2-PDGFRA translocation with 33.6% variant allele frequency and breakpoints at exon 10 of PRKG2 and exon 12 of PDGFRA.
A. Annotated variants TRANSLOCATION: | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
GeneA | GeneB | cnt_ReadA | cnt_ReadB | Total_read | ChrA | ChrB | Read.posA | Read.posB | Direction | |||||||
PDGFRA | PRKG2 | 154 | 129 | 283 | chr4:55141064 | chr4:82065407 | NM_006206_Exon(12/23)_Frame(0,1) | NM_006259_Exon(10/19)_Frame(2,2) | PRKG2→PDGFRA | |||||||
B. Known variants SNV: | ||||||||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP | ||||||
MKI67 | NM_002417 | exon14 | c.9670C>T | p.R3224W | nonsynonmous SNV | chr10:129899557 | 1746 | 42.55% | COSM916078 | rs754802357 | ||||||
MCU2 | NM_002457 | exon30 | c.5356A>C | p.K1786Q | nonsynonmous SNV | chr11:1093537 | 697 | 8.03% | COSM4145288 | rs80200693 | ||||||
LRRK2 | NM_198578 | exon11 | c.1256C>T | p.A419V | nonsynonmous SNV | chr12:40646786 | 1020 | 44.41% | COSM147473 | rs34594498 | ||||||
BCL7A | NM_020993 | exon4 | c.359A>C | p.N120T | nonsynonmous SNV | chr12:122481879 | 724 | 46.55% | COSM5880386 | rs34821485 | ||||||
WDR90 | NM_145294 | exon16 | c.1804C>T | p.R602W | nonsynonmous SNV | chr16:705658 | 758 | 44.2% | COSM3273238 | rs201699835 | ||||||
PALB2 | NM_024675 | exon4 | c.925A>G | p.I309V | nonsynonmous SNV | chr16:23646942 | 1710 | 45.5% | COSM3957351 | rs3809683 | ||||||
ZNF24 | NM_006965 | exon3 | c.427C>T | p.L143F | nonsynonmous SNV | chr18:32919934 | 1054 | 43.93% | COSM5854150 | rs148053646 | ||||||
INDEL: | ||||||||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP | ||||||
MSH6 | NM_000179 | exon10 | c.4065_4066insTTGA | p.T1355fs | frameshift insertion | chr2:48033981 | 764 | 40.45% | COSM3186044 | NA | ||||||
C. Novel Variants SNV: | ||||||||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP | ||||||
SDHC | NM_003001 | exon2 | c.25G>A | p.V9I | nonsynonmous SNV | chr1:161293408 | 689 | 55.15% | rs774768866 | |||||||
ALK | NM_004304 | exon18 | c.3035C>T | p.T1012M | nonsynonmous SNV | chr2:29449820 | 1332 | 46.1% | rs35073634 | |||||||
ERBB4 | NM_005235 | exon24 | c.2935C>G | p.R979G | nonsynonmous SNV | chr2:212286761 | 1177 | 45.2% | rs574197848 | |||||||
BARD1 | NM_000465 | exon4 | c.722C>G | p.S241C | nonsynonmous SNV | chr2:215645876 | 2397 | 46.06% | rs3738885 | |||||||
HIST1H2BJ | NM_021058 | exon1 | c.215A>G | p.E72G | nonsynonmous SNV | chr6:27100315 | 1660 | 47.89% | NA | |||||||
KDM4C | NM_015061 | exon18 | c.2447G>A | p.R816Q | nonsynonmous SNV | chr9:7103707 | 1055 | 44.36% | rs180710573 | |||||||
ABL1 | NM_007313 | exon10 | c.1601T>C | p.V534A | nonsynonmous SNV | chr9:133755917 | 559 | 40.97% | rs776483252 | |||||||
NUP98 | NM_016320 | exon11 | c.1192A>G | p.S398G | nonsynonmous SNV | chr11:3774621 | 937 | 46.42% | rs144302699 | |||||||
PTPRO | NM_030667 | exon17 | c.2648A>T | p.Y895F | nonsynonmous SNV | chr12:15713183 | 1553 | 49.45% | rs759525747 | |||||||
FANCA | NM_000135 | exon42 | c.4232C>T | p.P1411L | nonsynonmous SNV | chr16:89805318 | 1230 | 45.61% | rs201494304 | |||||||
GTSE1 | NM_016426 | exon9 | c.1688G>C | p.R563T | nonsynonmous SNV | chr22:46722515 | 1135 | 47.84% | rs760482340 | |||||||
PCLO | NM_033026 | exon2 | c.1561C>G | p.P521A | nonsynonmous SNV | chr7:82784396 | 618 | 14.24% | NA |
Table 2 Results of next generation gene sequencing after imatinib treatment. The oncogenic mutation (PRKG2/PDGFRA translocation) has disappeared.
A. Annotated variants B. Known variants SNV: | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP |
MKI67 | NM_002417 | exon14 | c.9670C>T | p.R3224W | nonsynonmous SNV | chr10:129899557 | 2254 | 41.33% | COSM916078 | rs754802357 |
ZNF24 | NM_006965 | exon3 | c.427C>T | p.L143F | nonsynonmous SNV | chr18:32919934 | 1447 | 44.3% | COSM5854150 | rs148053646 |
INDEL: | ||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP |
MKI67 | NM_002417 | exon13 | c.4991_4992del | p.T1664fs | frameshift insertion | chr10:129905112 | 3486 | 2.35% | COSM916119 | rs145960091 |
C. Novel variants SNV: | ||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP |
SDHC | NM_003001 | exon2 | c.25G>A | p.V9I | nonsynonmous SNV | chr1:161293408 | 633 | 52.45% | rs774768866 | |
ERBB4 | NM_005235 | exon24 | c.2935C>G | p.R979G | nonsynonmous SNV | chr2:212286761 | 1620 | 44.88% | rs574197848 | |
BARD1 | NM_000465 | exon4 | c.722C>G | p.S241C | nonsynonmous SNV | chr2:215645876 | 2889 | 46.49% | rs3738885 | |
FGFR4 | NM_002011 | exon13 | c.1817G>A | p.R606Q | nonsynonmous SNV | chr5:176522720 | 243 | 48.56% | rs757092386 | |
HIST1H2BJ | NM_021058 | exon1 | c.215A>G | p.E72G | nonsynonmous SNV | chr6:27100315 | 2154 | 50.0% | NA | |
ABL1 | NM_007313 | exon10 | c.1601T>C | p.V534A | nonsynonmous SNV | chr9:133755917 | 718 | 42.9% | rs776483252 | |
NUP98 | NM_016320 | exon11 | c.1192A>G | p.S398G | nonsynonmous SNV | chr11:3774621 | 1283 | 45.91% | rs144302699 | |
PTPRO | NM_030667 | exon17 | c.2648A>T | p.Y895F | nonsynonmous SNV | chr12:15713183 | 1521 | 48.06% | rs759525747 | |
FANCA | NM_000135 | exon42 | c.4232C>T | p.P1411L | nonsynonmous SNV | chr16:89805318 | 1747 | 46.48% | rs201494304 | |
GTSE1 | NM_016426 | exon9 | c.1688G>C | p.R563T | nonsynonmous SNV | chr22:46722515 | 1415 | 46.08% | rs760482340 | |
RUNX1 | NM_001754 | exon9 | c.1270T>G | p.S424A | nonsynonmous SNV | chr21:36164605 | 225 | 25.33% | NA |
Translocation of
CDK5 regulatory subunit-related protein 2 (
The
No potential conflicts of interest relevant to this article were reported.
Blood Res 2022; 57(1): 69-74
Published online March 31, 2022 https://doi.org/10.5045/br.2022.2021138
Copyright © The Korean Society of Hematology.
Jong Gwon Choi1,2, Do Yeun Cho1
1Department of Oncology-Hematology, Konyang University Hospital, 2Department of Internal Medicine, Myunggok Medical Research Center, Deajeon, Korea
Correspondence to:Jong Gwon Choi
Department of Internal Medicine, Myunggok Medical Research Center, 158 Gwanjeodong-ro, Daejeon 35365, Korea
E-mail: jabuss@naver.com
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
TO THE EDITOR: Translocation of platelet-derived growth factor receptor A (
Patients, occasionally meet the general criteria for classifying their condition as a myeloproliferative neoplasm (MPN) but may not meet all criteria for a particular disease or may exhibit more than one category of diagnostic characteristics. These patients can be diagnosed as MPN unclassifiable (MPN-u). Symptoms are similar to typical MPNs and usually include hepatosplenomegaly and increased numbers of white blood cells (WBCs) and platelets. A bone marrow biopsy reveals megakaryocyte proliferation and hypercellularity in granulocytes or erythrocytes. As the disease progresses, the bone marrow becomes more fibrotic. However, in the current patient,
A 38-year-old man presented to the Konyang University Hospital (Deajeon, South Korea) on March 10, 2017, with abdominal pain that started 2 months before, and thrombocytosis was identified at a local clinic. At the time of admission, the patient had a blood pressure of 130/90 mmHg, heart rate of 78 beats per minute, respiratory rate of 20 breaths per minute, and body temperature of 37°C. There was no significant previous medical history of hypertension, diabetes mellitus, or tuberculosis. On physical examination, we observed organomegaly in the right upper quadrant of the abdomen. However, there was no enlargement of the cervical, axillary, or inguinal lymph nodes. Other examinations were unremarkable. Laboratory tests showed WBCs at 30,300/mL, hemoglobin at 9.4 g/dL, and platelets at 836,000/mL. White blood cells were composed of 24% segmented neutrophils, 17% lymphocytes, 1% monocytes, 3% eosinophils, and 51% basophils. The reticulocyte count was within the normal range. Leukemic blasts were observed in 2% of the cells. Coagulation tests revealed a prothrombin time of 16.4 seconds and an activated partial thromboplastin time of 35.5 seconds. He had a fibrinogen level of 3.13 g/L, D-dimer level of 2.1 mg/mL, and antithrombin activity of 72% (not suggestive of disseminated intravascular coagulation). Peripheral blood showed normocytic and normochromic red blood cells, no polychromasia, a normal WBC count with no toxic granulation or vacuolations, and an increased platelet count. The serum lactate dehydrogenase level was 832 U/L (normal range, 120–240 U/I). The total bilirubin level was 1.04 mg/dL (normal range, 0–0.4 mg/dL). Results for other blood factors, including creatinine and bicarbonate, and liver function tests, were unremarkable. Computed tomography revealed hepatosplenomegaly (16 cm) without an intrasplenic mass. Bone marrow aspiration revealed no particles or peripheral dilution, and immature cells were observed occasionally (Fig. 1). Bone marrow biopsy showed estimated cellularity of approximately 100%, which was hypercellular for the patient’s age. In cellular areas, trilineage hematopoiesis was observed, along with increased numbers of basophils and immature cells. In addition, there were increased numbers of dysplastic megakaryocytes, and diffuse fibrosis was observed in multiple focal areas throughout the bone marrow space (Fig. 2). The
Table 1 . Results of next generation gene sequencing before imatinib treatment. PRKG2-PDGFRA translocation with 33.6% variant allele frequency and breakpoints at exon 10 of PRKG2 and exon 12 of PDGFRA..
A. Annotated variants TRANSLOCATION: | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
GeneA | GeneB | cnt_ReadA | cnt_ReadB | Total_read | ChrA | ChrB | Read.posA | Read.posB | Direction | |||||||
PDGFRA | PRKG2 | 154 | 129 | 283 | chr4:55141064 | chr4:82065407 | NM_006206_Exon(12/23)_Frame(0,1) | NM_006259_Exon(10/19)_Frame(2,2) | PRKG2→PDGFRA | |||||||
B. Known variants SNV: | ||||||||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP | ||||||
MKI67 | NM_002417 | exon14 | c.9670C>T | p.R3224W | nonsynonmous SNV | chr10:129899557 | 1746 | 42.55% | COSM916078 | rs754802357 | ||||||
MCU2 | NM_002457 | exon30 | c.5356A>C | p.K1786Q | nonsynonmous SNV | chr11:1093537 | 697 | 8.03% | COSM4145288 | rs80200693 | ||||||
LRRK2 | NM_198578 | exon11 | c.1256C>T | p.A419V | nonsynonmous SNV | chr12:40646786 | 1020 | 44.41% | COSM147473 | rs34594498 | ||||||
BCL7A | NM_020993 | exon4 | c.359A>C | p.N120T | nonsynonmous SNV | chr12:122481879 | 724 | 46.55% | COSM5880386 | rs34821485 | ||||||
WDR90 | NM_145294 | exon16 | c.1804C>T | p.R602W | nonsynonmous SNV | chr16:705658 | 758 | 44.2% | COSM3273238 | rs201699835 | ||||||
PALB2 | NM_024675 | exon4 | c.925A>G | p.I309V | nonsynonmous SNV | chr16:23646942 | 1710 | 45.5% | COSM3957351 | rs3809683 | ||||||
ZNF24 | NM_006965 | exon3 | c.427C>T | p.L143F | nonsynonmous SNV | chr18:32919934 | 1054 | 43.93% | COSM5854150 | rs148053646 | ||||||
INDEL: | ||||||||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP | ||||||
MSH6 | NM_000179 | exon10 | c.4065_4066insTTGA | p.T1355fs | frameshift insertion | chr2:48033981 | 764 | 40.45% | COSM3186044 | NA | ||||||
C. Novel Variants SNV: | ||||||||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP | ||||||
SDHC | NM_003001 | exon2 | c.25G>A | p.V9I | nonsynonmous SNV | chr1:161293408 | 689 | 55.15% | rs774768866 | |||||||
ALK | NM_004304 | exon18 | c.3035C>T | p.T1012M | nonsynonmous SNV | chr2:29449820 | 1332 | 46.1% | rs35073634 | |||||||
ERBB4 | NM_005235 | exon24 | c.2935C>G | p.R979G | nonsynonmous SNV | chr2:212286761 | 1177 | 45.2% | rs574197848 | |||||||
BARD1 | NM_000465 | exon4 | c.722C>G | p.S241C | nonsynonmous SNV | chr2:215645876 | 2397 | 46.06% | rs3738885 | |||||||
HIST1H2BJ | NM_021058 | exon1 | c.215A>G | p.E72G | nonsynonmous SNV | chr6:27100315 | 1660 | 47.89% | NA | |||||||
KDM4C | NM_015061 | exon18 | c.2447G>A | p.R816Q | nonsynonmous SNV | chr9:7103707 | 1055 | 44.36% | rs180710573 | |||||||
ABL1 | NM_007313 | exon10 | c.1601T>C | p.V534A | nonsynonmous SNV | chr9:133755917 | 559 | 40.97% | rs776483252 | |||||||
NUP98 | NM_016320 | exon11 | c.1192A>G | p.S398G | nonsynonmous SNV | chr11:3774621 | 937 | 46.42% | rs144302699 | |||||||
PTPRO | NM_030667 | exon17 | c.2648A>T | p.Y895F | nonsynonmous SNV | chr12:15713183 | 1553 | 49.45% | rs759525747 | |||||||
FANCA | NM_000135 | exon42 | c.4232C>T | p.P1411L | nonsynonmous SNV | chr16:89805318 | 1230 | 45.61% | rs201494304 | |||||||
GTSE1 | NM_016426 | exon9 | c.1688G>C | p.R563T | nonsynonmous SNV | chr22:46722515 | 1135 | 47.84% | rs760482340 | |||||||
PCLO | NM_033026 | exon2 | c.1561C>G | p.P521A | nonsynonmous SNV | chr7:82784396 | 618 | 14.24% | NA |
Table 2 . Results of next generation gene sequencing after imatinib treatment. The oncogenic mutation (PRKG2/PDGFRA translocation) has disappeared..
A. Annotated variants B. Known variants SNV: | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP |
MKI67 | NM_002417 | exon14 | c.9670C>T | p.R3224W | nonsynonmous SNV | chr10:129899557 | 2254 | 41.33% | COSM916078 | rs754802357 |
ZNF24 | NM_006965 | exon3 | c.427C>T | p.L143F | nonsynonmous SNV | chr18:32919934 | 1447 | 44.3% | COSM5854150 | rs148053646 |
INDEL: | ||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP |
MKI67 | NM_002417 | exon13 | c.4991_4992del | p.T1664fs | frameshift insertion | chr10:129905112 | 3486 | 2.35% | COSM916119 | rs145960091 |
C. Novel variants SNV: | ||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP |
SDHC | NM_003001 | exon2 | c.25G>A | p.V9I | nonsynonmous SNV | chr1:161293408 | 633 | 52.45% | rs774768866 | |
ERBB4 | NM_005235 | exon24 | c.2935C>G | p.R979G | nonsynonmous SNV | chr2:212286761 | 1620 | 44.88% | rs574197848 | |
BARD1 | NM_000465 | exon4 | c.722C>G | p.S241C | nonsynonmous SNV | chr2:215645876 | 2889 | 46.49% | rs3738885 | |
FGFR4 | NM_002011 | exon13 | c.1817G>A | p.R606Q | nonsynonmous SNV | chr5:176522720 | 243 | 48.56% | rs757092386 | |
HIST1H2BJ | NM_021058 | exon1 | c.215A>G | p.E72G | nonsynonmous SNV | chr6:27100315 | 2154 | 50.0% | NA | |
ABL1 | NM_007313 | exon10 | c.1601T>C | p.V534A | nonsynonmous SNV | chr9:133755917 | 718 | 42.9% | rs776483252 | |
NUP98 | NM_016320 | exon11 | c.1192A>G | p.S398G | nonsynonmous SNV | chr11:3774621 | 1283 | 45.91% | rs144302699 | |
PTPRO | NM_030667 | exon17 | c.2648A>T | p.Y895F | nonsynonmous SNV | chr12:15713183 | 1521 | 48.06% | rs759525747 | |
FANCA | NM_000135 | exon42 | c.4232C>T | p.P1411L | nonsynonmous SNV | chr16:89805318 | 1747 | 46.48% | rs201494304 | |
GTSE1 | NM_016426 | exon9 | c.1688G>C | p.R563T | nonsynonmous SNV | chr22:46722515 | 1415 | 46.08% | rs760482340 | |
RUNX1 | NM_001754 | exon9 | c.1270T>G | p.S424A | nonsynonmous SNV | chr21:36164605 | 225 | 25.33% | NA |
Translocation of
CDK5 regulatory subunit-related protein 2 (
The
No potential conflicts of interest relevant to this article were reported.
Table 1 . Results of next generation gene sequencing before imatinib treatment. PRKG2-PDGFRA translocation with 33.6% variant allele frequency and breakpoints at exon 10 of PRKG2 and exon 12 of PDGFRA..
A. Annotated variants TRANSLOCATION: | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
GeneA | GeneB | cnt_ReadA | cnt_ReadB | Total_read | ChrA | ChrB | Read.posA | Read.posB | Direction | |||||||
PDGFRA | PRKG2 | 154 | 129 | 283 | chr4:55141064 | chr4:82065407 | NM_006206_Exon(12/23)_Frame(0,1) | NM_006259_Exon(10/19)_Frame(2,2) | PRKG2→PDGFRA | |||||||
B. Known variants SNV: | ||||||||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP | ||||||
MKI67 | NM_002417 | exon14 | c.9670C>T | p.R3224W | nonsynonmous SNV | chr10:129899557 | 1746 | 42.55% | COSM916078 | rs754802357 | ||||||
MCU2 | NM_002457 | exon30 | c.5356A>C | p.K1786Q | nonsynonmous SNV | chr11:1093537 | 697 | 8.03% | COSM4145288 | rs80200693 | ||||||
LRRK2 | NM_198578 | exon11 | c.1256C>T | p.A419V | nonsynonmous SNV | chr12:40646786 | 1020 | 44.41% | COSM147473 | rs34594498 | ||||||
BCL7A | NM_020993 | exon4 | c.359A>C | p.N120T | nonsynonmous SNV | chr12:122481879 | 724 | 46.55% | COSM5880386 | rs34821485 | ||||||
WDR90 | NM_145294 | exon16 | c.1804C>T | p.R602W | nonsynonmous SNV | chr16:705658 | 758 | 44.2% | COSM3273238 | rs201699835 | ||||||
PALB2 | NM_024675 | exon4 | c.925A>G | p.I309V | nonsynonmous SNV | chr16:23646942 | 1710 | 45.5% | COSM3957351 | rs3809683 | ||||||
ZNF24 | NM_006965 | exon3 | c.427C>T | p.L143F | nonsynonmous SNV | chr18:32919934 | 1054 | 43.93% | COSM5854150 | rs148053646 | ||||||
INDEL: | ||||||||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP | ||||||
MSH6 | NM_000179 | exon10 | c.4065_4066insTTGA | p.T1355fs | frameshift insertion | chr2:48033981 | 764 | 40.45% | COSM3186044 | NA | ||||||
C. Novel Variants SNV: | ||||||||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP | ||||||
SDHC | NM_003001 | exon2 | c.25G>A | p.V9I | nonsynonmous SNV | chr1:161293408 | 689 | 55.15% | rs774768866 | |||||||
ALK | NM_004304 | exon18 | c.3035C>T | p.T1012M | nonsynonmous SNV | chr2:29449820 | 1332 | 46.1% | rs35073634 | |||||||
ERBB4 | NM_005235 | exon24 | c.2935C>G | p.R979G | nonsynonmous SNV | chr2:212286761 | 1177 | 45.2% | rs574197848 | |||||||
BARD1 | NM_000465 | exon4 | c.722C>G | p.S241C | nonsynonmous SNV | chr2:215645876 | 2397 | 46.06% | rs3738885 | |||||||
HIST1H2BJ | NM_021058 | exon1 | c.215A>G | p.E72G | nonsynonmous SNV | chr6:27100315 | 1660 | 47.89% | NA | |||||||
KDM4C | NM_015061 | exon18 | c.2447G>A | p.R816Q | nonsynonmous SNV | chr9:7103707 | 1055 | 44.36% | rs180710573 | |||||||
ABL1 | NM_007313 | exon10 | c.1601T>C | p.V534A | nonsynonmous SNV | chr9:133755917 | 559 | 40.97% | rs776483252 | |||||||
NUP98 | NM_016320 | exon11 | c.1192A>G | p.S398G | nonsynonmous SNV | chr11:3774621 | 937 | 46.42% | rs144302699 | |||||||
PTPRO | NM_030667 | exon17 | c.2648A>T | p.Y895F | nonsynonmous SNV | chr12:15713183 | 1553 | 49.45% | rs759525747 | |||||||
FANCA | NM_000135 | exon42 | c.4232C>T | p.P1411L | nonsynonmous SNV | chr16:89805318 | 1230 | 45.61% | rs201494304 | |||||||
GTSE1 | NM_016426 | exon9 | c.1688G>C | p.R563T | nonsynonmous SNV | chr22:46722515 | 1135 | 47.84% | rs760482340 | |||||||
PCLO | NM_033026 | exon2 | c.1561C>G | p.P521A | nonsynonmous SNV | chr7:82784396 | 618 | 14.24% | NA |
Table 2 . Results of next generation gene sequencing after imatinib treatment. The oncogenic mutation (PRKG2/PDGFRA translocation) has disappeared..
A. Annotated variants B. Known variants SNV: | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP |
MKI67 | NM_002417 | exon14 | c.9670C>T | p.R3224W | nonsynonmous SNV | chr10:129899557 | 2254 | 41.33% | COSM916078 | rs754802357 |
ZNF24 | NM_006965 | exon3 | c.427C>T | p.L143F | nonsynonmous SNV | chr18:32919934 | 1447 | 44.3% | COSM5854150 | rs148053646 |
INDEL: | ||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP |
MKI67 | NM_002417 | exon13 | c.4991_4992del | p.T1664fs | frameshift insertion | chr10:129905112 | 3486 | 2.35% | COSM916119 | rs145960091 |
C. Novel variants SNV: | ||||||||||
Gene | RefseqID | Exon | DNAchange | AAchange | Func | ChrPos | Read depth | VAF | COSMIC | dbSNP |
SDHC | NM_003001 | exon2 | c.25G>A | p.V9I | nonsynonmous SNV | chr1:161293408 | 633 | 52.45% | rs774768866 | |
ERBB4 | NM_005235 | exon24 | c.2935C>G | p.R979G | nonsynonmous SNV | chr2:212286761 | 1620 | 44.88% | rs574197848 | |
BARD1 | NM_000465 | exon4 | c.722C>G | p.S241C | nonsynonmous SNV | chr2:215645876 | 2889 | 46.49% | rs3738885 | |
FGFR4 | NM_002011 | exon13 | c.1817G>A | p.R606Q | nonsynonmous SNV | chr5:176522720 | 243 | 48.56% | rs757092386 | |
HIST1H2BJ | NM_021058 | exon1 | c.215A>G | p.E72G | nonsynonmous SNV | chr6:27100315 | 2154 | 50.0% | NA | |
ABL1 | NM_007313 | exon10 | c.1601T>C | p.V534A | nonsynonmous SNV | chr9:133755917 | 718 | 42.9% | rs776483252 | |
NUP98 | NM_016320 | exon11 | c.1192A>G | p.S398G | nonsynonmous SNV | chr11:3774621 | 1283 | 45.91% | rs144302699 | |
PTPRO | NM_030667 | exon17 | c.2648A>T | p.Y895F | nonsynonmous SNV | chr12:15713183 | 1521 | 48.06% | rs759525747 | |
FANCA | NM_000135 | exon42 | c.4232C>T | p.P1411L | nonsynonmous SNV | chr16:89805318 | 1747 | 46.48% | rs201494304 | |
GTSE1 | NM_016426 | exon9 | c.1688G>C | p.R563T | nonsynonmous SNV | chr22:46722515 | 1415 | 46.08% | rs760482340 | |
RUNX1 | NM_001754 | exon9 | c.1270T>G | p.S424A | nonsynonmous SNV | chr21:36164605 | 225 | 25.33% | NA |