A statistical method for single sample analysis of HumanMethylation450 array data: genome-wide methylation analysis of patients with imprinting disorders.
BACKGROUND
The Illumina Infinium HumanMethylation450 BeadChip is an array-based technology for analysing DNA methylation at approximately 475,000 differentially methylated cytosines across the human genome. Hitherto, the array has been used for case-control studies, where sample numbers can be sufficient to yield statistically robust data on a genome-wide basis. We recently reported an informatic pipeline capable of yielding statistically and biologically significant results using only five cases, which expanded the use of this technology to rare disease studies. However, the clinical application of these technologies requires the ability to perform robust analysis of individual patients.


RESULTS
Here we report a novel informatic approach for methylation array analysis of single samples, using the Crawford-Howell t-test. We tested our approach on patients with ultra-rare imprinting disorders with aberrant DNA methylation at multiple locations across the genome, which was previously detected by targeted testing. However, array analysis outperformed targeted assays in three ways: it detected loci not normally analysed by targeted testing, detected methylation changes too subtle to detect by the targeted testing and reported broad and consistent methylation changes across genetic loci not captured by point testing.


CONCLUSIONS
This method has potential clinical utility for human disorders where DNA methylation change may be a biomarker of disease.
Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK.
Faisal I
FI
Rezwan
Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK ; Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, Wilts SO2 8BJ UK.
Louise E
LE
Docherty
Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK ; Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, Wilts SO2 8BJ UK.
Rebecca L
RL
Poole
Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK.
Gabrielle A
GA
Lockett
The David Hide Asthma and Allergy Research Centre, St Mary's Hospital, Newport, Isle of Wight PO30 5TG UK ; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK.
S Hasan
SH
Arshad
Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK.
John W
JW
Holloway
Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK ; Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Southampton, UK.
I Karen
IK
Temple
Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK ; Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, Wilts SO2 8BJ UK.
Deborah Jg
DJ
Mackay
Crawford-Howell t-test; Illumina HumanMethylation450 array; Methylation; Single case-control analysis