
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


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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

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
	
	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
	
	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

--------------------------
METHODOLOGICAL INFORMATION
--------------------------
See Methods sections of thesis for methodological information. Thesis DOI: 10.5258/SOTON/PG/T224


May 2026
