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

Nicholas C.L. Wong, Gavin D. Meredith, George Marnellos, Miroslav Dudas, Mandy Parkinson-Bates, Minhee S. Halemba, Zac Chatterton, Jovana Maksimovic, David M. Ashley, Francoise Mechinaud, Jeffrey Mark Craig, Richard Saffery

Research output: Contribution to journalArticleResearchpeer-review

Abstract

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.

Original languageEnglish
Article number11
Number of pages6
JournalGigaScience
Volume4
Issue number1
DOIs
Publication statusPublished - 18 Mar 2015
Externally publishedYes

Keywords

  • Childhood leukaemia
  • DNA methylation
  • Epigenetics
  • NGS
  • SOLiD MBD-Seq

Cite this

Wong, Nicholas C.L. ; Meredith, Gavin D. ; Marnellos, George ; Dudas, Miroslav ; Parkinson-Bates, Mandy ; Halemba, Minhee S. ; Chatterton, Zac ; Maksimovic, Jovana ; Ashley, David M. ; Mechinaud, Francoise ; Craig, Jeffrey Mark ; Saffery, Richard. / Paediatric leukaemia DNA methylation profiling using MBD enrichment and SOLiD sequencing on archival bone marrow smears. In: GigaScience. 2015 ; Vol. 4, No. 1.
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title = "Paediatric leukaemia DNA methylation profiling using MBD enrichment and SOLiD sequencing on archival bone marrow smears",
abstract = "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.",
keywords = "Childhood leukaemia, DNA methylation, Epigenetics, NGS, SOLiD MBD-Seq",
author = "Wong, {Nicholas C.L.} and Meredith, {Gavin D.} and George Marnellos and Miroslav Dudas and Mandy Parkinson-Bates and Halemba, {Minhee S.} and Zac Chatterton and Jovana Maksimovic and Ashley, {David M.} and Francoise Mechinaud and Craig, {Jeffrey Mark} and Richard Saffery",
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Wong, NCL, Meredith, GD, Marnellos, G, Dudas, M, Parkinson-Bates, M, Halemba, MS, Chatterton, Z, Maksimovic, J, Ashley, DM, Mechinaud, F, Craig, JM & Saffery, R 2015, 'Paediatric leukaemia DNA methylation profiling using MBD enrichment and SOLiD sequencing on archival bone marrow smears' GigaScience, vol. 4, no. 1, 11. https://doi.org/10.1186/s13742-015-0050-0

Paediatric leukaemia DNA methylation profiling using MBD enrichment and SOLiD sequencing on archival bone marrow smears. / Wong, Nicholas C.L.; Meredith, Gavin D.; Marnellos, George; Dudas, Miroslav; Parkinson-Bates, Mandy; Halemba, Minhee S.; Chatterton, Zac; Maksimovic, Jovana; Ashley, David M.; Mechinaud, Francoise; Craig, Jeffrey Mark; Saffery, Richard.

In: GigaScience, Vol. 4, No. 1, 11, 18.03.2015.

Research output: Contribution to journalArticleResearchpeer-review

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T1 - Paediatric leukaemia DNA methylation profiling using MBD enrichment and SOLiD sequencing on archival bone marrow smears

AU - Wong, Nicholas C.L.

AU - Meredith, Gavin D.

AU - Marnellos, George

AU - Dudas, Miroslav

AU - Parkinson-Bates, Mandy

AU - Halemba, Minhee S.

AU - Chatterton, Zac

AU - Maksimovic, Jovana

AU - Ashley, David M.

AU - Mechinaud, Francoise

AU - Craig, Jeffrey Mark

AU - Saffery, Richard

PY - 2015/3/18

Y1 - 2015/3/18

N2 - 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.

AB - 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.

KW - Childhood leukaemia

KW - DNA methylation

KW - Epigenetics

KW - NGS

KW - SOLiD MBD-Seq

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DO - 10.1186/s13742-015-0050-0

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