Journal: Molecular and Clinical Oncology

Article Title: Analysis of genes encoding epigenetic regulators in myeloproliferative neoplasms: Coexistence of a novel SETBP1 mutation in a patient with a p.V617F JAK2 positive myelofibrosis

doi: 10.3892/mco.2019.1840

Figure Lengend Snippet: Human cancer cell lines tested.

Article Snippet: Informed consent was obtained from all patients and procedures were approved by the Ethical Committee on Clinical Research of University of Navarra. table ft1 table-wrap mode="anchored" t5 Table II. caption a7 Cell line name Repository (number) Origin A-549 DSMZ (ACC-107) Lung carcinoma BK-006 ECACC p.V617F JAK2 positive PV BK-013 ECACC (98100924) p.V617F JAK2 negative ET BK015 ECACC (99092421) p.V617F JAK2 negative ET DAUDI DSMZ (ACC-78) Burkitt lymphoma EOL-1 DSMZ (ACC-386) Acute myeloid eosinophilic leukemia F-36P DSMZ (ACC-543) Acute myeloid leukemia secondary to myelodysplastic syndrome (MDS) HCC-1937 DSMZ (ACC-513) Breast carcinoma HEL DSMZ ACC-11 Erythroleukemia HL60 DSMZ ACC-3 Acute myeloid leukemia (AML) HU3 Dr Morgan, USA Acute megakaryoblastic leukemia K-562 DSMZ ACC-10 BCR-ABL1 positive chronic myeloid leukemia (CML) in blast crisis KARPAS-299 DSMZ ACC-31 T cell lymphoma KARPAS-422 DSMZ ACC-32 B cell lymphoma M-07e DSMZ ACC-104 Acute megakaryoblastic leukemia MG-63 ATCC: CRL-1427 Osteosarcoma MOLM-13 DSMZ ACC-554 Acute myeloid leukemia (AML) MOLT-16 DSMZ ACC-29 T cell acute lymphoid leukemia (T-ALL) MOLT-4 DSMZ ACC-362 Acute lymphoid leukemia (ALL) MV-411 DSMZ ACC-102 Acute monoblastic/monocytic leukemia RAJI DSMZ ACC-319 Burkitt lymphoma REH DSMZ ACC-22 B-ALL (t(12;21) (p13;q22) (fusion ETV6-RUNX1 )) SET2 DSMZ ACC-608 p.V617F JAK2 positive ET TF-1 DSMZ ACC-334 Erythroleukemia UKE-1 Dr W. Fiedelr, Hamburg, Germany p.V617F JAK2 positive ET transformed to AML Open in a separate window ECACC, European Collection of Cell Culture; DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen.

Techniques: Transformation Assay

Journal: Nature Communications

Article Title: Clinical application of tumour-in-normal contamination assessment from whole genome sequencing

doi: 10.1038/s41467-023-44158-2

Figure Lengend Snippet: a Scatter distribution of somatic mutation VAF in tumour and normal samples ( a – f represent case 1). VAF is shown for n=982 mutations detected from WGS data which reside within heterozygous diploid regions in the tumour genome. Two variants of clinical significance are highlighted; a TP53 frameshift deletion (c.594delA) and a JAK2 V617F mutation. Neither mutation would be detected using a standard tumour-normal calling pipeline, due to the tumour contamination in the normal. b , c Histograms of VAF values for tumour and normal samples in ( a ). d Deconvolution analysis with TINC. n = 378 clonal mutations were identified in the tumour using MOBSTER (upper panel) with mean VAF ~45% (cluster C1). Subsequent deconvolution determines one cluster in the normal sample for the corresponding mutations with a VAF peak at about ~8% (lower panel). e Representation of somatic mutation VAF in tumour and normal samples. After deconvolution of somatic mutations ( d ), clonality can be attributed to the mutations in ( a )—clonal mutations with teal dots. f TIT and TIN scores can be determined from the parameters fit by the deconvolution methods, accounting for the copy state of somatic SNVs. In this case, the data indicate an overall tumour purity of 90% (TIT score, high-purity tumour sample) and tumour-in-normal contamination level of ~16% (TIN score). g Representation of somatic mutation VAF in tumour and normal samples ( g – i represent case 2) as in ( a – c ). For this case, a previously identified (by Fluorescence in situ hybridisation) translocation resulting in a PML-RARA fusion was not detected using a standard tumour-normal analysis pipeline. h Deconvolution identifies a cluster of clonal somatic mutations of n = 358 SNVs (cluster C1) with VAF ~30%. i Representation of contamination in tumour and normal samples. TIT and TIN scores determined by TINC, expressed in cellular proportions and adjusted for copy number states, show a tumour purity of ~60% (TIT), and tumour contamination of the normal sample of ~16% (TIN).

Article Snippet: In this case, the analysis performed during the 100,000 Genomes Project (Genomics England pipeline 1.0, Online Methods) failed to detect a driver somatic hotspot variant in the JAK2 gene (ENST00000381652:p.V617F) due to TIN contamination (variant supported by 50 out of 110 paired reads in the tumour, and 4 out of 34 in the normal; Fig. ).

Techniques: Mutagenesis, Fluorescence, In Situ, Hybridization, Translocation Assay

Journal: Molecular and Clinical Oncology

Article Title: Analysis of genes encoding epigenetic regulators in myeloproliferative neoplasms: Coexistence of a novel SETBP1 mutation in a patient with a p.V617F JAK2 positive myelofibrosis

doi: 10.3892/mco.2019.1840

Figure Lengend Snippet: Human cancer cell lines tested.

Article Snippet: Informed consent was obtained from all patients and procedures were approved by the Ethical Committee on Clinical Research of University of Navarra. table ft1 table-wrap mode="anchored" t5 Table II. caption a7 Cell line name Repository (number) Origin A-549 DSMZ (ACC-107) Lung carcinoma BK-006 ECACC p.V617F JAK2 positive PV BK-013 ECACC (98100924) p.V617F JAK2 negative ET BK015 ECACC (99092421) p.V617F JAK2 negative ET DAUDI DSMZ (ACC-78) Burkitt lymphoma EOL-1 DSMZ (ACC-386) Acute myeloid eosinophilic leukemia F-36P DSMZ (ACC-543) Acute myeloid leukemia secondary to myelodysplastic syndrome (MDS) HCC-1937 DSMZ (ACC-513) Breast carcinoma HEL DSMZ ACC-11 Erythroleukemia HL60 DSMZ ACC-3 Acute myeloid leukemia (AML) HU3 Dr Morgan, USA Acute megakaryoblastic leukemia K-562 DSMZ ACC-10 BCR-ABL1 positive chronic myeloid leukemia (CML) in blast crisis KARPAS-299 DSMZ ACC-31 T cell lymphoma KARPAS-422 DSMZ ACC-32 B cell lymphoma M-07e DSMZ ACC-104 Acute megakaryoblastic leukemia MG-63 ATCC: CRL-1427 Osteosarcoma MOLM-13 DSMZ ACC-554 Acute myeloid leukemia (AML) MOLT-16 DSMZ ACC-29 T cell acute lymphoid leukemia (T-ALL) MOLT-4 DSMZ ACC-362 Acute lymphoid leukemia (ALL) MV-411 DSMZ ACC-102 Acute monoblastic/monocytic leukemia RAJI DSMZ ACC-319 Burkitt lymphoma REH DSMZ ACC-22 B-ALL (t(12;21) (p13;q22) (fusion ETV6-RUNX1 )) SET2 DSMZ ACC-608 p.V617F JAK2 positive ET TF-1 DSMZ ACC-334 Erythroleukemia UKE-1 Dr W. Fiedelr, Hamburg, Germany p.V617F JAK2 positive ET transformed to AML Open in a separate window ECACC, European Collection of Cell Culture; DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen.

Techniques: Transformation Assay

Journal: The Pan African Medical Journal

Article Title: JAK2 p.(V617F) mutation in Tunisian myeloproliferative neoplasms and its genotype-phenotype correlation

doi: 10.11604/pamj.2021.39.194.28307

Figure Lengend Snippet: basic clinical and hematological characteristics in negative and positive JAK2 p.(V617F) mutation in all tested Tunisian patients

Article Snippet: We performed an Allele specific real-time quantitative fluorescence PCR (AS-qPCR) using ipsogen JAK2 MutaSearch Kit, designed for the specific and quantitative determination of DNA copy number of JAK2 p.(V617F) mutation and JAK2 wild type with respective primers [ ]. p.(V617F) positive control (PC-V617F JAK2 ), negative control (NC-V617F JAK2 ), cut-off sample (COS-V617F JAK2 ) were provided by the kit.

Techniques: Mutagenesis, Cell Counting

Journal: The Pan African Medical Journal

Article Title: JAK2 p.(V617F) mutation in Tunisian myeloproliferative neoplasms and its genotype-phenotype correlation

doi: 10.11604/pamj.2021.39.194.28307

Figure Lengend Snippet: genotype-phenotype correlation in the different subgroups of myeloproliferative neoplasms in Tunisia

Article Snippet: We performed an Allele specific real-time quantitative fluorescence PCR (AS-qPCR) using ipsogen JAK2 MutaSearch Kit, designed for the specific and quantitative determination of DNA copy number of JAK2 p.(V617F) mutation and JAK2 wild type with respective primers [ ]. p.(V617F) positive control (PC-V617F JAK2 ), negative control (NC-V617F JAK2 ), cut-off sample (COS-V617F JAK2 ) were provided by the kit.

Techniques: Cell Counting

Journal: The Pan African Medical Journal

Article Title: JAK2 p.(V617F) mutation in Tunisian myeloproliferative neoplasms and its genotype-phenotype correlation

doi: 10.11604/pamj.2021.39.194.28307

Figure Lengend Snippet: age distribution in wild type and mutant JAK2 subgroups (ET: essential thrombocythemia; MPNs: myeloproliferative neoplasms; PMF: Primary myelofibrosis; PV: polycythemia vera; WT: wildtype)

Article Snippet: We performed an Allele specific real-time quantitative fluorescence PCR (AS-qPCR) using ipsogen JAK2 MutaSearch Kit, designed for the specific and quantitative determination of DNA copy number of JAK2 p.(V617F) mutation and JAK2 wild type with respective primers [ ]. p.(V617F) positive control (PC-V617F JAK2 ), negative control (NC-V617F JAK2 ), cut-off sample (COS-V617F JAK2 ) were provided by the kit.

Techniques: Mutagenesis

Journal: The Pan African Medical Journal

Article Title: JAK2 p.(V617F) mutation in Tunisian myeloproliferative neoplasms and its genotype-phenotype correlation

doi: 10.11604/pamj.2021.39.194.28307

Figure Lengend Snippet: sex-specific differences in Tunisian cohort and wild type or mutant JAK2 subgroups (ET: essential thrombocythemia; PMF: primary myelofibrosis; PV: polycythemia vera)

Article Snippet: We performed an Allele specific real-time quantitative fluorescence PCR (AS-qPCR) using ipsogen JAK2 MutaSearch Kit, designed for the specific and quantitative determination of DNA copy number of JAK2 p.(V617F) mutation and JAK2 wild type with respective primers [ ]. p.(V617F) positive control (PC-V617F JAK2 ), negative control (NC-V617F JAK2 ), cut-off sample (COS-V617F JAK2 ) were provided by the kit.

Techniques: Mutagenesis

Journal: The Pan African Medical Journal

Article Title: JAK2 p.(V617F) mutation in Tunisian myeloproliferative neoplasms and its genotype-phenotype correlation

doi: 10.11604/pamj.2021.39.194.28307

Figure Lengend Snippet: associations of JAK2 p.(V617F) mutation with hemogram variations in different subgroups of myeloproliferative neoplasms in some reported studies and Tunisian patients

Article Snippet: We performed an Allele specific real-time quantitative fluorescence PCR (AS-qPCR) using ipsogen JAK2 MutaSearch Kit, designed for the specific and quantitative determination of DNA copy number of JAK2 p.(V617F) mutation and JAK2 wild type with respective primers [ ]. p.(V617F) positive control (PC-V617F JAK2 ), negative control (NC-V617F JAK2 ), cut-off sample (COS-V617F JAK2 ) were provided by the kit.

Techniques: Mutagenesis

Journal: Nature Communications

Article Title: Genetic variation at MECOM , TERT , JAK2 and HBS1L-MYB predisposes to myeloproliferative neoplasms

doi: 10.1038/ncomms7691

Figure Lengend Snippet: This Manhattan plot shows the results of the stage 1 GWAS for all autosomes. Results are plotted as –log10 of the allelic χ 2 P value. At this stage, no SNPs met the stringent genome-wide significance level of P value ≤10 −8 . The three SNPs that attained genome-wide significance and two additional SNPs with moderate association following meta-analysis are highlighted in green, on chromosome 3 (rs2201862 and rs4858647), chromosome 5 (rs2736100), chromosome 6 (rs9376092) and chromosome 9 (rs12339666). This plot was produced using the qqman R package.

Article Snippet: Using a three-stage genome-wide association study of 3,437 MPN cases and 10,083 controls, we identify two SNPs with genome-wide significance in JAK2 V617F -negative MPN: rs12339666 ( JAK2; meta-analysis P =1.27 × 10 −10 ) and rs2201862 ( MECOM ; meta-analysis P =1.96 × 10 −9 ).

Techniques: Genome Wide, Produced

Journal: Nature Communications

Article Title: Genetic variation at MECOM , TERT , JAK2 and HBS1L-MYB predisposes to myeloproliferative neoplasms

doi: 10.1038/ncomms7691

Figure Lengend Snippet: Summary of the top SNPs showing or approaching genome-wide significant association ( P <5 × 10 −8 ) in meta-analysis.

Article Snippet: Using a three-stage genome-wide association study of 3,437 MPN cases and 10,083 controls, we identify two SNPs with genome-wide significance in JAK2 V617F -negative MPN: rs12339666 ( JAK2; meta-analysis P =1.27 × 10 −10 ) and rs2201862 ( MECOM ; meta-analysis P =1.96 × 10 −9 ).

Techniques: Genome Wide

Journal: Nature Communications

Article Title: Genetic variation at MECOM , TERT , JAK2 and HBS1L-MYB predisposes to myeloproliferative neoplasms

doi: 10.1038/ncomms7691

Figure Lengend Snippet: This plot shows the stage 1 results ( n =524 JAK2 V617F -negative cases versus n =2674 controls) in a 400-kb region, which flanks the most significant SNP identified by meta-analysis (rs2201862). SNPs are plotted as the −log10 of the allelic χ 2 P value. The amount of LD between rs220186 and all other SNPs is indicated by the colour of the data points. The two SNPs with red borders (rs16853092 and rs4955627) were also genotyped and replicate at stage 2 but were not taken forward to stage 3 because rs2201862 was more significant at stage 2. The plot was produced using LocusZoom.

Article Snippet: Using a three-stage genome-wide association study of 3,437 MPN cases and 10,083 controls, we identify two SNPs with genome-wide significance in JAK2 V617F -negative MPN: rs12339666 ( JAK2; meta-analysis P =1.27 × 10 −10 ) and rs2201862 ( MECOM ; meta-analysis P =1.96 × 10 −9 ).

Techniques: Produced

Journal: Nature Communications

Article Title: Genetic variation at MECOM , TERT , JAK2 and HBS1L-MYB predisposes to myeloproliferative neoplasms

doi: 10.1038/ncomms7691

Figure Lengend Snippet: Comparison between ET and PV subtype in JAK2 V617F positive cases.

Article Snippet: Using a three-stage genome-wide association study of 3,437 MPN cases and 10,083 controls, we identify two SNPs with genome-wide significance in JAK2 V617F -negative MPN: rs12339666 ( JAK2; meta-analysis P =1.27 × 10 −10 ) and rs2201862 ( MECOM ; meta-analysis P =1.96 × 10 −9 ).

Techniques: Comparison