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

GigaScience
Nicholas C WongR Saffery

Abstract

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. 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. Our d...Continue Reading

References

Jul 9, 1999·American Journal of Medical Genetics·L VoullaireK H Choo
Sep 20, 2005·Genome Research·Belinda GiardineAnton Nekrutenko
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Aug 24, 2011·Genome Biology·Tao LiuX Shirley Liu
Apr 26, 2012·Epigenetics : Official Journal of the DNA Methylation Society·Nicholas C WongRichard Saffery
Sep 28, 2013·Nature Genetics·UNKNOWN Cancer Genome Atlas Research NetworkJoshua M Stuart
Jan 8, 2014·Epigenetics : Official Journal of the DNA Methylation Society·Zac ChattertonNicholas C Wong

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJNA272864

Methods Mentioned

BETA
methylation profiling
Fluorescent Activated Cell Sorting
FACS

Software Mentioned

SOLiD
HOMER ( Hypergeometric Optimization of Motif EnRichment )
TARGET
Galaxy
Infinium
Cistrome
[UNK] Genomic Analysis Suite
HOMER
UCSC Genome Browser
Genome Browser

Related Concepts

Related Feeds

Cancer Genomics (Keystone)

Cancer genomics approaches employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Discover the latest research using such technologies in this feed.

Cancer -Omics

A variety of different high-throughput technologies can be used to identify the complete catalog of changes that characterize the molecular profile of cohorts of tumor samples. Discover the latest insights gained from cancer 'omics' in this feed.

Blood And Marrow Transplantation

The use of hematopoietic stem cell transplantation or blood and marrow transplantation (bmt) is on the increase worldwide. BMT is used to replace damaged or destroyed bone marrow with healthy bone marrow stem cells. Here is the latest research on bone and marrow transplantation.