Paediatric leukaemia DNA methylation profiling using MBD enrichment and SOLiD sequencing on archival bone marrow smears

GigaScience

Richard Saffery⁵  Jeffrey M Craig¹  Francoise Mechinaud⁴  David M Ashley⁷  Jovana Maksimovic³  Zac Chatterton²  Minhee Suh Halemba²  Mandy Parkinson-Bates²  Miroslav Dudas⁶  George Marnellos⁶  Gavin D Meredith⁶  Nicholas CL Wong⁸ 

[1] Early Life Epigenetics Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Flemington Road, Parkville 3052, Victoria, Australia;Cancer and Disease Epigenetics Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Flemington Road, Parkville 3052, Victoria, Australia;Bioinformatics Group, Quantitative Sciences Core, Murdoch Childrens Research Institute, Royal Children’s Hospital, Flemington Road, 92008, Parkville 3052, Victoria, Australia;Children’s Cancer Centre, Royal Children’s Hospital, Flemington Road, Parkville 3052, Victoria, Australia;Department of Paediatrics, The University of Melbourne, Children’s Hospital, Flemington Road, Parkville 3052, Victoria, Australia;Life Technologies, Carlsbad 92008, CA, USA;Andrew Love Cancer Centre, Deakin Universit, Swanston Street, Geelong 3220, Victoria, Australia;Pacific Edge Limted, 84 St David Street, Dunedin 9016, New Zealand

关键词: Epigenetics;    NGS;    SOLiD MBD-Seq;    DNA methylation;    Childhood leukaemia;   

Others  :  1149287
DOI  :  10.1186/s13742-015-0050-0

 received in 2014-01-26, accepted in 2015-02-05,  发布年份 2015

【 摘 要 】

Background

Acute Lymphoblastic Leukaemia (ALL) is the most common cancer in children. Over the past four decades, research has advanced the treatment of this cancer from a less than 60% chance of survival to over 85% today. The causal molecular mechanisms remain unclear. Here, we performed sequencing-based genomic DNA methylation profiling of eight paediatric ALL patients using archived bone marrow smear microscope slides.

Findings

SOLiD™ sequencing data was collected from Methyl-Binding Domain (MBD) enriched fractions of genomic DNA. The primary tumour and remission bone marrow sample was analysed from eight patients. Four patients relapsed and the relapsed tumour was analysed. Input and MBD-enriched DNA from each sample was sequenced, aligned to the hg19 reference genome and analysed for enrichment peaks using MACS (Model-based Analysis for ChIP-Seq) and HOMER (Hypergeometric Optimization of Motif EnRichment). In total, 3.67 gigabases (Gb) were sequenced, 2.74 Gb were aligned to the reference genome (average 74.66% alignment efficiency). This dataset enables the interrogation of differential DNA methylation associated with paediatric ALL. Preliminary results reveal concordant regions of enrichment indicative of a DNA methylation signature.

Conclusion

Our dataset represents one of the first SOLiD™MBD-Seq studies performed on paediatric ALL and is the first to utilise archival bone marrow smears. Differential DNA methylation between cancer and equivalent disease-free tissue can be identified and correlated with existing and published genomic studies. Given the rarity of paediatric haematopoietic malignancies, relative to adult counterparts, our demonstration of the utility of archived bone marrow smear samples to high-throughput methylation sequencing approaches offers tremendous potential to explore the role of DNA methylation in the aetiology of cancer.

【 授权许可】

   
2015 Wong et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

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