READ ME File For Data generated for PhD thesis "Genetic approaches to improve the diagnosis and management of myeloproliferative neoplasms." Dataset DOI: 10.5258/SOTON/PG/D224 ReadMe Author: MATTHEW SALMON, University of Southampton This dataset supports the thesis entitled "Genetic approaches to improve the diagnosis and management of myeloproliferative neoplasms" AWARDED BY: University of Southampton DATE OF AWARD: 2026 Licence: CC-BY Date of data collection: February 2029 - December 2025 -------------------- DATA & FILE OVERVIEW -------------------- This dataset contains: CUX1_JAK2_data.xlsx: variant calls for CUX1 and JAK2 sequencing for thesis Chapter 2. Ch3.zip: RT-qPCR results from participating laboratories for thesis Chapter 3, containing: │ ├── Lab10_EUTOS5_e13a2_e14a2_results_020918_CLEAN.xlsx │  ├── Lab1_EUTOS5_e13a2_e14a2_results_020918_CLEAN.xlsx │ ├── Lab2_EUTOS5_e13a2_e14a2_results_020918_CLEAN.xlsx │ ├── Lab3_EUTOS5_e13a2_e14a2_results_020918_CLEAN.xlsx │ ├── Lab4_EUTOS5_e13a2_e14a2_results_020918_CLEAN.xlsx │ ├── Lab5_EUTOS5_e13a2_e14a2_results_020918_CLEAN.xlsx │ ├── Lab6_EUTOS5_e13a2_e14a2_results_020918_CLEAN.xlsx │ ├── Lab7_EUTOS5_e13a2_e14a2_results_020918_CLEAN.xlsx │ ├── Lab8_EUTOS5_e13a2_e14a2_results_020918_CLEAN.xlsx │ └── Lab9_EUTOS5_e13a2_e14a2_results_020918_CLEAN.xlsx Ch4.zip Structural variants called from nanopore sequencing for thesis Chapter 4, containing: │   ├── S_10_sniffles.vcf │ ├── S_11_sniffles.vcf │ ├── S_12_sniffles.vcf │ ├── S_13_sniffles.vcf │ ├── S_14_sniffles.vcf │ ├── S_15_sniffles.vcf │ ├── S_16_sniffles.vcf │ ├── S_17_sniffles.vcf │ ├── S_18_sniffles.vcf │ ├── S_19_sniffles.vcf │ ├── S_1_sniffles.vcf │ ├── S_20_sniffles.vcf │ ├── S_2_sniffles.vcf │ ├── S_3_sniffles.vcf │ ├── S_4_sniffles.vcf │ ├── S_5_sniffles.vcf │ ├── S_6_sniffles.vcf │ ├── S_7_sniffles.vcf │ ├── S_8_sniffles.vcf │ └── S_9_sniffles.vcf │ └── README.txt Somatic variant calls for short variants (mutect2), structural variants (manta) and CNVs (controlfreec) for thesis Chapter 5. controlfreec.zip: A_10_vs_B_10.p.value.txt A_11_vs_B_11.p.value.txt A_12_vs_B_12.p.value.txt A_13_vs_B_13.p.value.txt A_14_vs_B_14.p.value.txt A_15_vs_B_15.p.value.txt A_16_vs_B_16.p.value.txt A_17_vs_B_17.p.value.txt A_18_vs_B_18.p.value.txt A_19_vs_B_19.p.value.txt A_1_vs_B_1.p.value.txt A_20_vs_B_20.p.value.txt A_21_vs_B_21.p.value.txt A_22_vs_B_22.p.value.txt A_23_vs_B_23.p.value.txt A_24_vs_B_24.p.value.txt A_25_vs_B_25.p.value.txt A_26_vs_B_26.p.value.txt A_27_vs_B_27.p.value.txt A_28_vs_B_28.p.value.txt A_29_vs_B_29.p.value.txt A_2_vs_B_2.p.value.txt A_30_vs_B_30.p.value.txt A_31_vs_B_31.p.value.txt A_32_vs_B_32.p.value.txt A_33_vs_B_33.p.value.txt A_34_vs_B_34.p.value.txt A_35_vs_B_35.p.value.txt A_36_vs_B_36.p.value.txt A_37_vs_B_37.p.value.txt A_38_vs_B_38.p.value.txt A_39_vs_B_39.p.value.txt A_3_vs_B_3.p.value.txt A_40_vs_B_40.p.value.txt A_41_vs_B_41.p.value.txt A_42_vs_B_42.p.value.txt A_43_vs_B_43.p.value.txt A_44_vs_B_44.p.value.txt A_45_vs_B_45.p.value.txt A_46_vs_B_46.p.value.txt A_47_vs_B_47.p.value.txt A_48_vs_B_48.p.value.txt A_49_vs_B_49.p.value.txt A_4_vs_B_4.p.value.txt A_50_vs_B_50.p.value.txt A_51_vs_B_51.p.value.txt A_52_vs_B_52.p.value.txt A_54_vs_B_54.p.value.txt A_56_vs_B_56.p.value.txt A_58_vs_B_58.p.value.txt A_59_vs_B_59.p.value.txt A_5_vs_B_5.p.value.txt A_62_vs_B_62.p.value.txt A_63_vs_B_63.p.value.txt A_64_vs_B_64.p.value.txt A_65_vs_B_65.p.value.txt A_66_vs_B_66.p.value.txt A_67_vs_B_67.p.value.txt A_68_vs_B_68.p.value.txt A_6_vs_B_6.p.value.txt A_71_vs_B_71.p.value.txt A_73_vs_B_73.p.value.txt A_74_vs_B_74.p.value.txt A_76_vs_B_76.p.value.txt A_77_vs_B_77.p.value.txt A_78_vs_B_78.p.value.txt A_79_vs_B_79.p.value.txt A_7_vs_B_7.p.value.txt A_9_vs_B_9.p.value.txt README.txt manta.zip: A_10_vs_B_10.manta.somatic_sv_VEP.ann.vcf.gz A_11_vs_B_11.manta.somatic_sv_VEP.ann.vcf.gz A_12_vs_B_12.manta.somatic_sv_VEP.ann.vcf.gz A_13_vs_B_13.manta.somatic_sv_VEP.ann.vcf.gz A_14_vs_B_14.manta.somatic_sv_VEP.ann.vcf.gz A_15_vs_B_15.manta.somatic_sv_VEP.ann.vcf.gz A_16_vs_B_16.manta.somatic_sv_VEP.ann.vcf.gz A_17_vs_B_17.manta.somatic_sv_VEP.ann.vcf.gz A_18_vs_B_18.manta.somatic_sv_VEP.ann.vcf.gz A_19_vs_B_19.manta.somatic_sv_VEP.ann.vcf.gz A_1_vs_B_1.manta.somatic_sv_VEP.ann.vcf.gz A_20_vs_B_20.manta.somatic_sv_VEP.ann.vcf.gz A_21_vs_B_21.manta.somatic_sv_VEP.ann.vcf.gz A_22_vs_B_22.manta.somatic_sv_VEP.ann.vcf.gz A_23_vs_B_23.manta.somatic_sv_VEP.ann.vcf.gz A_24_vs_B_24.manta.somatic_sv_VEP.ann.vcf.gz A_25_vs_B_25.manta.somatic_sv_VEP.ann.vcf.gz A_26_vs_B_26.manta.somatic_sv_VEP.ann.vcf.gz A_27_vs_B_27.manta.somatic_sv_VEP.ann.vcf.gz A_28_vs_B_28.manta.somatic_sv_VEP.ann.vcf.gz A_29_vs_B_29.manta.somatic_sv_VEP.ann.vcf.gz A_2_vs_B_2.manta.somatic_sv_VEP.ann.vcf.gz A_30_vs_B_30.manta.somatic_sv_VEP.ann.vcf.gz A_31_vs_B_31.manta.somatic_sv_VEP.ann.vcf.gz A_32_vs_B_32.manta.somatic_sv_VEP.ann.vcf.gz A_33_vs_B_33.manta.somatic_sv_VEP.ann.vcf.gz A_34_vs_B_34.manta.somatic_sv_VEP.ann.vcf.gz A_35_vs_B_35.manta.somatic_sv_VEP.ann.vcf.gz A_36_vs_B_36.manta.somatic_sv_VEP.ann.vcf.gz A_37_vs_B_37.manta.somatic_sv_VEP.ann.vcf.gz A_38_vs_B_38.manta.somatic_sv_VEP.ann.vcf.gz A_39_vs_B_39.manta.somatic_sv_VEP.ann.vcf.gz A_3_vs_B_3.manta.somatic_sv_VEP.ann.vcf.gz A_40_vs_B_40.manta.somatic_sv_VEP.ann.vcf.gz A_41_vs_B_41.manta.somatic_sv_VEP.ann.vcf.gz A_42_vs_B_42.manta.somatic_sv_VEP.ann.vcf.gz A_43_vs_B_43.manta.somatic_sv_VEP.ann.vcf.gz A_44_vs_B_44.manta.somatic_sv_VEP.ann.vcf.gz A_45_vs_B_45.manta.somatic_sv_VEP.ann.vcf.gz A_46_vs_B_46.manta.somatic_sv_VEP.ann.vcf.gz A_47_vs_B_47.manta.somatic_sv_VEP.ann.vcf.gz A_48_vs_B_48.manta.somatic_sv_VEP.ann.vcf.gz A_49_vs_B_49.manta.somatic_sv_VEP.ann.vcf.gz A_4_vs_B_4.manta.somatic_sv_VEP.ann.vcf.gz A_50_vs_B_50.manta.somatic_sv_VEP.ann.vcf.gz A_51_vs_B_51.manta.somatic_sv_VEP.ann.vcf.gz A_52_vs_B_52.manta.somatic_sv_VEP.ann.vcf.gz A_54_vs_B_54.manta.somatic_sv_VEP.ann.vcf.gz A_56_vs_B_56.manta.somatic_sv_VEP.ann.vcf.gz A_58_vs_B_58.manta.somatic_sv_VEP.ann.vcf.gz A_59_vs_B_59.manta.somatic_sv_VEP.ann.vcf.gz A_5_vs_B_5.manta.somatic_sv_VEP.ann.vcf.gz A_62_vs_B_62.manta.somatic_sv_VEP.ann.vcf.gz A_63_vs_B_63.manta.somatic_sv_VEP.ann.vcf.gz A_64_vs_B_64.manta.somatic_sv_VEP.ann.vcf.gz A_65_vs_B_65.manta.somatic_sv_VEP.ann.vcf.gz A_66_vs_B_66.manta.somatic_sv_VEP.ann.vcf.gz A_67_vs_B_67.manta.somatic_sv_VEP.ann.vcf.gz A_68_vs_B_68.manta.somatic_sv_VEP.ann.vcf.gz A_6_vs_B_6.manta.somatic_sv_VEP.ann.vcf.gz A_71_vs_B_71.manta.somatic_sv_VEP.ann.vcf.gz A_73_vs_B_73.manta.somatic_sv_VEP.ann.vcf.gz A_74_vs_B_74.manta.somatic_sv_VEP.ann.vcf.gz A_76_vs_B_76.manta.somatic_sv_VEP.ann.vcf.gz A_77_vs_B_77.manta.somatic_sv_VEP.ann.vcf.gz A_78_vs_B_78.manta.somatic_sv_VEP.ann.vcf.gz A_79_vs_B_79.manta.somatic_sv_VEP.ann.vcf.gz A_7_vs_B_7.manta.somatic_sv_VEP.ann.vcf.gz A_9_vs_B_9.manta.somatic_sv_VEP.ann.vcf.gz README.txt mutect2.zip: A_10_vs_B_10.mutect2.filtered_VEP.ann.vcf.gz A_11_vs_B_11.mutect2.filtered_VEP.ann.vcf.gz A_12_vs_B_12.mutect2.filtered_VEP.ann.vcf.gz A_13_vs_B_13.mutect2.filtered_VEP.ann.vcf.gz A_14_vs_B_14.mutect2.filtered_VEP.ann.vcf.gz A_15_vs_B_15.mutect2.filtered_VEP.ann.vcf.gz A_16_vs_B_16.mutect2.filtered_VEP.ann.vcf.gz A_17_vs_B_17.mutect2.filtered_VEP.ann.vcf.gz A_18_vs_B_18.mutect2.filtered_VEP.ann.vcf.gz A_19_vs_B_19.mutect2.filtered_VEP.ann.vcf.gz A_1_vs_B_1.mutect2.filtered_VEP.ann.vcf.gz A_20_vs_B_20.mutect2.filtered_VEP.ann.vcf.gz A_21_vs_B_21.mutect2.filtered_VEP.ann.vcf.gz A_22_vs_B_22.mutect2.filtered_VEP.ann.vcf.gz A_23_vs_B_23.mutect2.filtered_VEP.ann.vcf.gz A_24_vs_B_24.mutect2.filtered_VEP.ann.vcf.gz A_25_vs_B_25.mutect2.filtered_VEP.ann.vcf.gz A_26_vs_B_26.mutect2.filtered_VEP.ann.vcf.gz A_27_vs_B_27.mutect2.filtered_VEP.ann.vcf.gz A_28_vs_B_28.mutect2.filtered_VEP.ann.vcf.gz A_29_vs_B_29.mutect2.filtered_VEP.ann.vcf.gz A_2_vs_B_2.mutect2.filtered_VEP.ann.vcf.gz A_30_vs_B_30.mutect2.filtered_VEP.ann.vcf.gz A_31_vs_B_31.mutect2.filtered_VEP.ann.vcf.gz A_32_vs_B_32.mutect2.filtered_VEP.ann.vcf.gz A_33_vs_B_33.mutect2.filtered_VEP.ann.vcf.gz A_34_vs_B_34.mutect2.filtered_VEP.ann.vcf.gz A_35_vs_B_35.mutect2.filtered_VEP.ann.vcf.gz A_36_vs_B_36.mutect2.filtered_VEP.ann.vcf.gz A_37_vs_B_37.mutect2.filtered_VEP.ann.vcf.gz A_38_vs_B_38.mutect2.filtered_VEP.ann.vcf.gz A_39_vs_B_39.mutect2.filtered_VEP.ann.vcf.gz A_3_vs_B_3.mutect2.filtered_VEP.ann.vcf.gz A_40_vs_B_40.mutect2.filtered_VEP.ann.vcf.gz A_41_vs_B_41.mutect2.filtered_VEP.ann.vcf.gz A_42_vs_B_42.mutect2.filtered_VEP.ann.vcf.gz A_43_vs_B_43.mutect2.filtered_VEP.ann.vcf.gz A_44_vs_B_44.mutect2.filtered_VEP.ann.vcf.gz A_45_vs_B_45.mutect2.filtered_VEP.ann.vcf.gz A_46_vs_B_46.mutect2.filtered_VEP.ann.vcf.gz A_47_vs_B_47.mutect2.filtered_VEP.ann.vcf.gz A_48_vs_B_48.mutect2.filtered_VEP.ann.vcf.gz A_49_vs_B_49.mutect2.filtered_VEP.ann.vcf.gz A_4_vs_B_4.mutect2.filtered_VEP.ann.vcf.gz A_50_vs_B_50.mutect2.filtered_VEP.ann.vcf.gz A_51_vs_B_51.mutect2.filtered_VEP.ann.vcf.gz A_52_vs_B_52.mutect2.filtered_VEP.ann.vcf.gz A_54_vs_B_54.mutect2.filtered_VEP.ann.vcf.gz A_56_vs_B_56.mutect2.filtered_VEP.ann.vcf.gz A_58_vs_B_58.mutect2.filtered_VEP.ann.vcf.gz A_59_vs_B_59.mutect2.filtered_VEP.ann.vcf.gz A_5_vs_B_5.mutect2.filtered_VEP.ann.vcf.gz A_62_vs_B_62.mutect2.filtered_VEP.ann.vcf.gz A_63_vs_B_63.mutect2.filtered_VEP.ann.vcf.gz A_64_vs_B_64.mutect2.filtered_VEP.ann.vcf.gz A_65_vs_B_65.mutect2.filtered_VEP.ann.vcf.gz A_66_vs_B_66.mutect2.filtered_VEP.ann.vcf.gz A_67_vs_B_67.mutect2.filtered_VEP.ann.vcf.gz A_68_vs_B_68.mutect2.filtered_VEP.ann.vcf.gz A_6_vs_B_6.mutect2.filtered_VEP.ann.vcf.gz A_71_vs_B_71.mutect2.filtered_VEP.ann.vcf.gz A_73_vs_B_73.mutect2.filtered_VEP.ann.vcf.gz A_74_vs_B_74.mutect2.filtered_VEP.ann.vcf.gz A_76_vs_B_76.mutect2.filtered_VEP.ann.vcf.gz A_77_vs_B_77.mutect2.filtered_VEP.ann.vcf.gz A_78_vs_B_78.mutect2.filtered_VEP.ann.vcf.gz A_79_vs_B_79.mutect2.filtered_VEP.ann.vcf.gz A_7_vs_B_7.mutect2.filtered_VEP.ann.vcf.gz A_9_vs_B_9.mutect2.filtered_VEP.ann.vcf.gz README.txt -------------------------- METHODOLOGICAL INFORMATION -------------------------- See Methods sections of thesis for methodological information. Thesis DOI: 10.5258/SOTON/PG/T224 May 2026