Dataset of DNA methylation profiles of 189 pediatric central nervous system, soft tissue, and bone tumors

被引：0

作者：

Jugas, Robin ^{[1
,2
]}

Pokorna, Petra ^{[1
,2
,3
]}

Adamcova, Sona ^{[1
,2
]}

Kozelkova, Katerina ^{[1
,2
]}

Knoflickova, Dana ^{[1
,2
,4
]}

Palova, Hana ^{[1
,2
]}

Sterba, Jaroslav ^{[5
,6
]}

Slaby, Ondrej ^{[1
,2
]}

机构：

[1] Masaryk Univ, Fac Med, Dept Biol, Kamenice 753-5, Brno 62500, Czech Republic

[2] Masaryk Univ, Cent European Inst Technol, Kamenice 753-5, Brno, Czech Republic

[3] Masaryk Univ, Fac Sci, Dept Biochem, Kamenice 753-5, Brno 62500, Czech Republic

[4] Masaryk Mem Canc Inst, Dept Oncol Pathol, Zluty Kopec 543-7, Brno 65653, Czech Republic

[5] Masaryk Univ, Univ Hosp Brno, Dept Pediat Oncol, Jihlavska 20, Brno 62500, Czech Republic

[6] Masaryk Univ, Fac Med, Jihlavska 20, Brno 62500, Czech Republic

来源：

DATA IN BRIEF | 2024年 / 55卷

关键词：

Pediatric oncology; Epigenetics; Targeted methylation sequencing; Precision medicine; CLASSIFICATION;

D O I：

10.1016/j.dib.2024.110590

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Alterations in DNA methylation profiles belong to important mechanisms in cancer development, and their assessment can be utilized for rapid and precise diagnostics. Therefore, establishing datasets of methylation profiles can improve and deepen our understanding of the role of epigenetic changes in cancer development as well as improve our diagnostic capabilities. In this dataset, we generated NGS data for 189 samples of pediatric CNS, soft tissue, and bone tumors. The sequencing libraries were prepared using methyl capture bisulfite sequencing, an effective compromise between whole-genome bisulfite sequencing and array-based methods with a more limited scope of target regions. The larger part of the cohort was processed with the Agilent SureSelectXT Human Methyl-Seq kit (149 samples) and the rest with the Illumina TruSeq Methyl Capture EPIC Library Prep Kit (40 samples). The data presented in this article may help other researchers further elucidate the importance of methylation in diagnosing pediatric CNS tumors, soft tissue, and bone tumors.

引用

页数：8

共 10 条

[1]

Andrews S., 2010, FASTQC QUALITY CONTR

[2]

[Anonymous], Dataset of DNA methylation profiles of 189 pediatric central nervous system, soft tissue, and bone tumors-EGA European Genome-Phenome Archive

[3] DNA methylation-based classification of central nervous system tumours [J].

Capper, David ;

Jones, David T. W. ;

Sill, Martin ;

Hovestadt, Volker ;

Schrimpf, Daniel ;

Sturm, Dominik ;

Koelsche, Christian ;

Sahm, Felix ;

Chavez, Lukas ;

Reuss, David E. ;

Kratz, Annekathrin ;

Wefers, Annika K. ;

Huang, Kristin ;

Pajtler, Kristian W. ;

Schweizer, Leonille ;

Stichel, Damian ;

Olar, Adriana ;

Engel, Nils W. ;

Lindenberg, Kerstin ;

Harter, Patrick N. ;

Braczynski, Anne K. ;

Plate, Karl H. ;

Dohmen, Hildegard ;

Garvalov, Boyan K. ;

Coras, Roland ;

Hoelsken, Annett ;

Hewer, Ekkehard ;

Bewerunge-Hudler, Melanie ;

Schick, Matthias ;

Fischer, Roger ;

Beschorner, Rudi ;

Schittenhelm, Jens ;

Staszewski, Ori ;

Wani, Khalida ;

Varlet, Pascale ;

Pages, Melanie ;

Temming, Petra ;

Lohmann, Dietmar ;

Selt, Florian ;

Witt, Hendrik ;

Milde, Till ;

Witt, Olaf ;

Aronica, Eleonora ;

Giangaspero, Felice ;

Rushing, Elisabeth ;

Scheurlen, Wolfram ;

Geisenberger, Christoph ;

Rodriguez, Fausto J. ;

Becker, Albert ;

Preusser, Matthias .

NATURE, 2018, 555 (7697) :469-+

[4] Sarcoma classification by DNA methylation profiling [J].

Koelsche, Christian ;

Schrimpf, Daniel ;

Stichel, Damian ;

Sill, Martin ;

Sahm, Felix ;

Reuss, David E. ;

Blattner, Mirjam ;

Worst, Barbara ;

Heilig, Christoph E. ;

Beck, Katja ;

Horak, Peter ;

Kreutzfeldt, Simon ;

Paff, Elke ;

Stark, Sebastian ;

Johann, Pascal ;

Selt, Florian ;

Ecker, Jonas ;

Sturm, Dominik ;

Pajtler, Kristian W. ;

Reinhardt, Annekathrin ;

Wefers, Annika K. ;

Sievers, Philipp ;

Ebrahimi, Azadeh ;

Suwala, Abigail ;

Fernandez-Klett, Francisco ;

Casalini, Belen ;

Korshunov, Andrey ;

Hovestadt, Volker ;

Kommoss, Felix K. F. ;

Kriegsmann, Mark ;

Schick, Matthias ;

Bewerunge-Hudler, Melanie ;

Milde, Till ;

Witt, Olaf ;

Kulozik, Andreas E. ;

Kool, Marcel ;

Romero-Perez, Laura ;

Gruenewald, Thomas G. P. ;

Kirchner, Thomas ;

Wick, Wolfgang ;

Platten, Michael ;

Unterberg, Andreas ;

Uhl, Matthias ;

Abdollahi, Amir ;

Debus, Juergen ;

Lehner, Burkhard ;

Thomas, Christian ;

Hasselblatt, Martin ;

Paulus, Werner ;

Hartmann, Christian .

NATURE COMMUNICATIONS, 2021, 12 (01)

[5]

Krueger F., 2015, Trim Galore: A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files

[6] Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications [J].

Krueger, Felix ;

Andrews, Simon R. .

BIOINFORMATICS, 2011, 27 (11) :1571-1572

[7] The 2021 WHO Classification of Tumors of the Central Nervous System: a summary [J].

Louis, David N. ;

Perry, Arie ;

Wesseling, Pieter ;

Brat, Daniel J. ;

Cree, Ian A. ;

Figarella-Branger, Dominique ;

Hawkins, Cynthia ;

Ng, H. K. ;

Pfister, Stefan M. ;

Reifenberger, Guido ;

Soffietti, Riccardo ;

von Deimling, Andreas ;

Ellison, David W. .

NEURO-ONCOLOGY, 2021, 23 (08) :1231-1251

[8] The growing role of epigenetics in childhood cancers [J].

Panditharatna, Eshini ;

Filbin, Mariella G. .

CURRENT OPINION IN PEDIATRICS, 2020, 32 (01) :67-75

[9] Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [J].

Pidsley, Ruth ;

Zotenko, Elena ;

Peters, Timothy J. ;

Lawrence, Mitchell G. ;

Risbridger, Gail P. ;

Molloy, Peter ;

Van Djik, Susan ;

Muhlhausler, Beverly ;

Stirzaker, Clare ;

Clark, Susan J. .

GENOME BIOLOGY, 2016, 17

[10]

Yuan DS, 2024, medRxiv, DOI [10.1101/2024.01.22.24301523, 10.1101/2024.01.22.24301523v1, DOI 10.1101/2024.01.22.24301523V1, DOI 10.1101/2024.01.22.24301523]

← 1 →