Clinical Validation of Fragile X Syndrome Screening by DNA Methylation Array

Laila C Schenkel; Charles Schwartz; Cindy Skinner; David I Rodenhiser; Peter J Ainsworth; Guillaume Pare; Bekim Sadikovic

doi:10.1016/j.jmoldx.2016.06.005

Clinical Validation of Fragile X Syndrome Screening by DNA Methylation Array

J Mol Diagn. 2016 Nov;18(6):834-841. doi: 10.1016/j.jmoldx.2016.06.005. Epub 2016 Aug 29.

Authors

Laila C Schenkel¹, Charles Schwartz², Cindy Skinner², David I Rodenhiser³, Peter J Ainsworth⁴, Guillaume Pare⁵, Bekim Sadikovic⁶

Affiliations

¹ Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
² Center for Molecular Studies, J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina.
³ Department of Biochemistry, Oncology and Paediatrics, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Center, London, Ontario, Canada; Children's Health Research Institute, London Health Sciences Center, London, Ontario, Canada.
⁴ Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Department of Biochemistry, Oncology and Paediatrics, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Center, London, Ontario, Canada; Children's Health Research Institute, London Health Sciences Center, London, Ontario, Canada; Molecular Genetics Laboratory, London Health Sciences Center, London, Ontario, Canada.
⁵ Departments of Pathology and Molecular Medicine and Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada.
⁶ Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Center, London, Ontario, Canada; Children's Health Research Institute, London Health Sciences Center, London, Ontario, Canada; Molecular Genetics Laboratory, London Health Sciences Center, London, Ontario, Canada. Electronic address: bekim.sadikovic@lhsc.on.ca.

PMID: 27585064
DOI: 10.1016/j.jmoldx.2016.06.005

Abstract

Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability. It is most frequently caused by an abnormal expansion of the CGG trinucleotide repeat (>200 repeats) located in the promoter of the fragile X mental retardation gene (FMR1), resulting in promoter DNA hypermethylation and gene silencing. Current clinical tests for FXS are technically challenging and labor intensive, and may involve use of hazardous chemicals or radioisotopes. We clinically validated the Illumina Infinium HumanMethylation450 DNA methylation array for FXS screening. We assessed genome-wide and FMR1-specific DNA methylation in 32 males previously diagnosed with FXS, including nine with mosaicism, as well as five females with full mutation, and premutation carrier males (n = 11) and females (n = 11), who were compared to 300 normal control DNA samples. Our findings demonstrate 100% sensitivity and specificity for detection of FXS in male patients, as well as the ability to differentiate patients with mosaic methylation defects. Full mutation and premutation carrier females did not show FMR1 methylation changes. We have clinically validated this genome-wide DNA methylation assay as a cost- and labor-effective alternative for sensitive and specific screening for FXS, while ruling out the most common differential diagnoses of FXS, Prader-Willi syndrome, and Sotos syndrome in the same assay.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

CpG Islands
DNA Methylation*
Female
Fragile X Mental Retardation Protein / genetics
Fragile X Syndrome / diagnosis*
Fragile X Syndrome / genetics*
Gene Silencing
Humans
Male
Mutation
Oligonucleotide Array Sequence Analysis / methods*
Oligonucleotide Array Sequence Analysis / standards*
Polymerase Chain Reaction / methods
Promoter Regions, Genetic
Reproducibility of Results
Trinucleotide Repeat Expansion
Trinucleotide Repeats

Substances

Fragile X Mental Retardation Protein