Sequence overlap between autosomal and sex-linked probes on the Illumina HumanMethylation27 microarray

被引：62

作者：

Chen, Yi-an ^{[1
,2
]}

Choufani, Sanaa ^{[1
]}

Ferreira, Jose Carlos ^{[1
,2
]}

Grafodatskaya, Daria ^{[1
]}

Butcher, Darci T. ^{[1
]}

Weksberg, Rosanna ^{[1
,2
]}

机构：

[1] Hosp Sick Children, Div Clin & Metab Genet, Res Inst, Program Genet & Genome Biol, Toronto, ON M5G 2L3, Canada

[2] Univ Toronto, Inst Med Sci, Toronto, ON M5S 1A1, Canada

来源：

GENOMICS | 2011年 / 97卷 / 04期

基金：

加拿大健康研究院;

关键词：

Illumina Infinium HumanMethylation 27 BeadChip; Non-specific cross-reactive probe; Sex-specific DNA methylation; Polymorphic CpG; Single-nucleotide polymorphism; DNA methylation; DNA METHYLATION; TESTICULAR BIOPSIES; EXPRESSION; PATTERNS; GENDER; GENES; BLOOD; LOCI;

D O I：

10.1016/j.ygeno.2010.12.004

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

The Illumina Infinium HumanMethylation27 BeadChip (Illumina 27k) microarray is a high-throughput platform capable of interrogating the human DNA methylome. In a search for autosomal sex-specific DNA methylation using this microarray, we discovered autosomal CpG loci showing significant methylation differences between the sexes. However, we found that the majority of these probes cross-reacted with sequences from sex chromosomes. Moreover, we determined that 6-10% of the microarray probes are nonspecific and map to highly homologous genomic sequences. Using probes targeting different CpGs that are exact duplicates of each other, we investigated the precision of these repeat measurements and concluded that the overall precision of this microarray is excellent. In addition, we identified a small number of probes targeting CpGs that include single-nucleotide polymorphisms. Overall, our findings address several technical issues associated with the Illumina 27k microarray that, once considered, will enhance the analysis and interpretation of data generated from this platform. (C) 2010 Elsevier Inc. All rights reserved.

引用

页码：214 / 222

页数：9

共 30 条

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