title: Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies.
abstract: BACKGROUND
  Infinium HumanMethylation 450 BeadChip Arrays by Illumina (Illumina HM450K) are among the most popular CpG microarray platforms widely used in biological and medical research. Several recent studies highlighted the potentially confounding impact of the genomic variation on the results of methylation studies performed using Illumina's Infinium methylation probes. However, the complexity of SNPs impact on the methylation level measurements (β values) has not been comprehensively described.
  
  
  RESULTS
  In our comparative study of European and Asian populations performed using Illumina HM450K, we found that the majority of Infinium probes, which differentiated two examined groups, had SNPs in their target sequence. Characteristic tri-modal or bi-modal patterns of β values distribution among individual samples were observed for CpGs with SNPs in the first and second position, respectively. To better understand how SNPs affect methylation readouts, we investigated their impact in the context of SNP position and type, and of the Illumina probe type (Infinium I or II).
  
  
  CONCLUSIONS
  Our study clearly demonstrates that SNP variation existing in the genome, if not accounted for, may lead to false interpretation of the methylation signal differences suggested by some of the Illumina Infinium probes. In addition, it provides important practical clues for discriminating between differences due to the methylation status and to the genomic polymorphisms, based on the inspection of methylation readouts in individual samples. This approach is of special importance when Illumina Infinium assay is used for any comparative population studies, whether related to cancer, disease, ethnicity where SNP frequencies differentiate the studied groups.
authors.affiliation: Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland. patrycja-daca@wp.pl.
authors.forename: Patrycja
authors.initials: P
authors.lastname: Daca-Roszak
authors.affiliation: Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland. apfeifer@io.gliwice.pl.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Pfeifer
authors.affiliation: Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland. jzebracka@io.gliwice.pl.
authors.forename: Jadwiga
authors.initials: J
authors.lastname: Żebracka-Gala
authors.affiliation: Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland. drusinek@io.gliwice.pl.
authors.forename: Dagmara
authors.initials: D
authors.lastname: Rusinek
authors.affiliation: International Institute of Molecular and Cell Biology, Warsaw, Poland. ola@iimcb.gov.pl.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Szybińska
authors.affiliation: Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland. bjarzab@io.gliwice.pl.
authors.forename: Barbara
authors.initials: B
authors.lastname: Jarząb
authors.affiliation: Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland. wittmich@man.poznan.pl.|International Institute of Molecular and Cell Biology, Warsaw, Poland. wittmich@man.poznan.pl.
authors.forename: Michał
authors.initials: M
authors.lastname: Witt
authors.affiliation: Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland. zietkiee@man.poznan.pl.
authors.forename: Ewa
authors.initials: E
authors.lastname: Ziętkiewicz
mesh_terms: D000483:Alleles; D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods; D005787:Gene Frequency; D005828:Genetics, Population; D023281:Genomics / Q000379:methods; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D020641:Polymorphism, Single Nucleotide