Analysis of Somatic Mutations in Epigenetic Genes in Major Leukemia Subtypes

Ozkan Bagci

Makale detayları

Analysis of Somatic Mutations in Epigenetic Genes in Major Leukemia Subtypes

Yazarlar:

Ozkan Bagci

Yayıncı:

Selcuk University

Ana Başlıklar:

Tıbbi Genetik (Kanser Genetiği hariç)

Dergi:

Genel Tıp Dergisi Vol.35 Issue 4, pp.746-758

Belge Tipi:

Makale

Yayın Tarihi:

8/2025

Belge Dili:

İngilizce

Document ID (Org No.):

2001356612

pISSN:

2602-3741

Anahtar kelimeler:

Özet:

 Aim: In this study, we aimed to investigate the presence of somatic mutations in DNMT3A, TET1, TET2, IDH1, IDH2, ASXL1 and SETBP1 genes that play a role in epigenetic regulation by NGS analysis of bone marrow samples of 13 ALL, 19 AML, 14 CLL and 15 CML patients.. Material and Method: NA was isolated from bone marrow samples of 13 ALL, 19 AML, 14 CLL and 15 CML patients and Kapa NGS DNA extraction kit was used for sequence analysis. The purity and concentration of the DNA obtained were measured by Qubit fluoremeter, and NadPrep DNA Universal Library Preparation Kit was used for high quality library preparation. Bioinformatic analysis of the data obtained from the study was performed through the portal provided by Roche Diagnostics for NGS solutions. The pathogenicity status of the variants detected in the relevant genes was made according to the ACMG classification. Results: Variations in at least one gene were found in all but one of the 13 patients diagnosed with ALL. Among 7 genes, the most distinct variant was detected in TET3 gene and all of them were VUS variants according to ACMG classification. In 19 patients diagnosed with AML, the gene with the highest number of distinct variants was TET3 and all variants were in the VUS class, followed by TET2 and ASXL1 genes, respectively. Variants were detected in at least one gene in all but 4 AML patients. No variant was detected in 4 of 14 patients diagnosed with CLL. Variants were detected in at least one of the related genes in the remaining patients. One of the 15 patients diagnosed with CML did not have any variant in the relevant genes. In the remaining patients, variants were detected in at least one of the related genes. The genes with the highest number of distinct variants in CML patients were TET3, ASXL1 and SETBP1, respectively. Conclusion: At least one variant of the related genes was detected in all leukaemia subtypes constituting the study sample. In our study, c.856-2AT variant in DNMT3A gene was detected in at least one patient from the patient groups with major leukaemia subtypes. This suggests that this variant may play an important role in haematopoietic stem cell processes.

 Aim: In this study, we aimed to investigate the presence of somatic mutations in DNMT3A, TET1, TET2, IDH1, IDH2, ASXL1 and SETBP1 genes that play a role in epigenetic regulation by NGS analysis of bone marrow samples of 13 ALL, 19 AML, 14 CLL and 15 CML patients.. Material and Method: NA was isolated from bone marrow samples of 13 ALL, 19 AML, 14 CLL and 15 CML patients and Kapa NGS DNA extraction kit was used for sequence analysis. The purity and concentration of the DNA obtained were measured by Qubit fluoremeter, and NadPrep DNA Universal Library Preparation Kit was used for high quality library preparation. Bioinformatic analysis of the data obtained from the study was performed through the portal provided by Roche Diagnostics for NGS solutions. The pathogenicity status of the variants detected in the relevant genes was made according to the ACMG classification. Results: Variations in at least one gene were found in all but one of the 13 patients diagnosed with ALL. Among 7 genes, the most distinct variant was detected in TET3 gene and all of them were VUS variants according to ACMG classification. In 19 patients diagnosed with AML, the gene with the highest number of distinct variants was TET3 and all variants were in the VUS class, followed by TET2 and ASXL1 genes, respectively. Variants were detected in at least one gene in all but 4 AML patients. No variant was detected in 4 of 14 patients diagnosed with CLL. Variants were detected in at least one of the related genes in the remaining patients. One of the 15 patients diagnosed with CML did not have any variant in the relevant genes. In the remaining patients, variants were detected in at least one of the related genes. The genes with the highest number of distinct variants in CML patients were TET3, ASXL1 and SETBP1, respectively. Conclusion: At least one variant of the related genes was detected in all leukaemia subtypes constituting the study sample. In our study, c.856-2AT variant in DNMT3A gene was detected in at least one patient from the patient groups with major leukaemia subtypes. This suggests that this variant may play an important role in haematopoietic stem cell processes.

 Aim: In this study, we aimed to investigate the presence of somatic mutations in DNMT3A, TET1, TET2, IDH1, IDH2, ASXL1 and SETBP1 genes that play a role in epigenetic regulation by NGS analysis of bone marrow samples of 13 ALL, 19 AML, 14 CLL and 15 CML patients.. Material and Method: NA was isolated from bone marrow samples of 13 ALL, 19 AML, 14 CLL and 15 CML patients and Kapa NGS DNA extraction kit was used for sequence analysis. The purity and concentration of the DNA obtained were measured by Qubit fluoremeter, and NadPrep DNA Universal Library Preparation Kit was used for high quality library preparation. Bioinformatic analysis of the data obtained from the study was performed through the portal provided by Roche Diagnostics for NGS solutions. The pathogenicity status of the variants detected in the relevant genes was made according to the ACMG classification. Results: Variations in at least one gene were found in all but one of the 13 patients diagnosed with ALL. Among 7 genes, the most distinct variant was detected in TET3 gene and all of them were VUS variants according to ACMG classification. In 19 patients diagnosed with AML, the gene with the highest number of distinct variants was TET3 and all variants were in the VUS class, followed by TET2 and ASXL1 genes, respectively. Variants were detected in at least one gene in all but 4 AML patients. No variant was detected in 4 of 14 patients diagnosed with CLL. Variants were detected in at least one of the related genes in the remaining patients. One of the 15 patients diagnosed with CML did not have any variant in the relevant genes. In the remaining patients, variants were detected in at least one of the related genes. The genes with the highest number of distinct variants in CML patients were TET3, ASXL1 and SETBP1, respectively. Conclusion: At least one variant of the related genes was detected in all leukaemia subtypes constituting the study sample. In our study, c.856-2AT variant in DNMT3A gene was detected in at least one patient from the patient groups with major leukaemia subtypes. This suggests that this variant may play an important role in haematopoietic stem cell processes.

 Amaç: Bu çalışmada, 13 ALL, 19 AML, 14 KLL ve 15 KML hastasının kemik iliği örneklerinin NGS analizi ile epigenetik düzenlemede rol oynayan DNMT3A, TET1, TET2, IDH1, IDH2, ASXL1 ve SETBP1 genlerinde somatik mutasyonların varlığının araştırılması amaçlanmıştır. Gereç ve Yöntem:13 ALL, 19 AML, 14 KLL ve 15 KML hastasının kemik iliği örneklerinden DNA izolasyonu gerçekleştirilmiş ve dizi analizi için Kapa NGS DNA ekstraksiyon kiti kullanılmıştır. Elde edilen DNAnın saflığı ve konsantrasyonu Qubit floremetre ile ölçülmüş, yüksek kalitede kütüphane hazırlanması için NadPrep DNA Universal Library Preparation Kit kullanılmıştır. Çalışmadan elde edilen verilerin biyoinformatik analizi, Roche Diagnostics tarafından NGS çözümleri için sağlanan portal aracılığıyla gerçekleştirilmiştir. İlgili genlerde tespit edilen varyantların patojenite durumu ACMG sınıflandırmasına göre yapılmıştır. Bulgular: ALL tanısı alan 13 hastanın bir hasta hariç, kalan hastaların tamamında en az bir gende varyasyon saptandı. 7 gen arasından en fazla distinct varyant TET3 geninde saptanmış olup tamamı ACMG klasifikasyonuna göre VUS varyantıydı. AML tanısı alan 19 hastada ilgili genler arasında en fazla distinct varyantın saptandığı gen TET3 olup tüm varyantları VUS sınıfındaydı, sonrasında sırasıyla TET2 ve ASXL1 genleri gelmekteydi. AML hastalarının 4ü hariç diğer hastalarda en az bir gende varyant saptanmıştı. KLL tanısı alan 14 hastanın 4ünde herhangi bir varyant saptanmadı. Kalan hastalarda ilgili genlerden en az birisinde varyant saptandı. KML tanısı alan 15 hastadan birisinde ilgili genlerde herhangi bir varyant saptanmadı. Kalan hastalarda ise ilgili genlerin en az birisinde varyant saptandı. KML hastalarında en fazla distinct varyant saptanan genler sırasıyla TET3, ASXL1 ve SETBP1 genleriydi Sonuç: Çalışma örneklemini oluşturan tüm lösemi alt tiplerinde ilgili genlerden en az bir varyant saptanmıştır. Çalışmamızda başlıca lösemi alt tiplerinde olan hasta gruplarından en az bir hastada DNMT3A geninde c.856-2AT varyantı saptanmıştır. Bu durum ilgili varyantın hematopoietik kök hücre süreçlerinde bu genin önemli bir rol oynayabileceğini düşündürmektedir.

Makale detayları

Analysis of Somatic Mutations in Epigenetic Genes in Major Leukemia Subtypes

Yazarlar:

Ozkan Bagci

Yayıncı:

Selcuk University

Ana Başlıklar:

Tıbbi Genetik (Kanser Genetiği hariç)

Dergi:

Genel Tıp Dergisi Vol.35 Issue 4, pp.746-758

Belge Tipi:

Makale

Yayın Tarihi:

8/2025

Belge Dili:

İngilizce

Document ID (Org No.):

2001356612

pISSN:

2602-3741

Chronic myeloid leukaemia

Chronic lymphocytic leukaemia

Acute lymphoblastic leukaemia

Acute myeloid leukaemia

EpigeneticsKronik miyeloid lösemi

Kronik lenfositik lösemi

Akut lenfoblastik lösemi

Akut miyeloid lösemi

Epigenetik

Sayı

Makale detayları

Yazarlar: Ozkan Bagci

Yayıncı: Selcuk University

Ana Başlıklar: Tıbbi Genetik (Kanser Genetiği hariç)

Dergi: Genel Tıp Dergisi Vol.35 Issue 4, pp.746-758

Belge Tipi: Makale

Yayın Tarihi: 8/2025

Belge Dili: İngilizce

Document ID (Org No.): 2001356612

pISSN: 2602-3741

Sayı

Yazarlar:

Ozkan Bagci

Yayıncı:

Selcuk University

Ana Başlıklar:

Tıbbi Genetik (Kanser Genetiği hariç)

Dergi:

Genel Tıp Dergisi Vol.35 Issue 4, pp.746-758

Belge Tipi:

Makale

Yayın Tarihi:

8/2025

Belge Dili:

İngilizce

Document ID (Org No.):

2001356612

pISSN:

2602-3741