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

Genomics

Volumn 97, Issue 4, 2011, Pages 214-222

  Chen, Yi an ^a,b   Choufani, Sanaa ^a   Ferreira, Jose Carlos ^a,b   Grafodatskaya, Daria ^a   Butcher, Darci T ^a   Weksberg, Rosanna ^a,b  

^a HOSPITAL FOR SICK CHILDREN RESEARCH INSTITUTE   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

DNA methylation; Illumina Infinium HumanMethylation 27 BeadChip; Non specific cross reactive probe; Polymorphic CpG; Sex specific DNA methylation; Single nucleotide polymorphism

Indexed keywords

GENOMIC DNA;

ARTICLE; AUTOSOME; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; DNA PROBE; DNA SEQUENCE; FEMALE; GENE DUPLICATION; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; HUMAN; MALE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN TARGETING; SEX CHROMOSOME; SEX LINKAGE; SINGLE NUCLEOTIDE POLYMORPHISM; UNINDEXED SEQUENCE;

CHROMOSOMES, HUMAN; CHROMOSOMES, HUMAN, X; COMPUTATIONAL BIOLOGY; CPG ISLANDS; DATA INTERPRETATION, STATISTICAL; DNA METHYLATION; DNA PROBES; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, GENETIC; SEQUENCE HOMOLOGY;

EID: 79952815844     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2010.12.004     Document Type: Article

References (30)

1. Brunner A.L., Johnson D.S., Kim S.W. Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E, Oyolu CB, Schroth GP, Absher DM, Baker JC, Myers RM, Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 2009, 19:1044-1056.
2. Deneberg S., Grövdal M., Karimi M., Jansson M., Nahi H., Corbacioglu A., Gaidzik V., Döhner K., Paul C., Ekström T.J., Hellström-Lindberg E., Lehmann S. Gene-specific and global methylation patterns predict outcome in patients with acute myeloid leukemia. Leukemia 2010, 24:932-941.
3. Baker M. Epigenome: mapping in motion. Nat. Meth. 2010, 7:181-186.
4. Bibikova M., Le J., Barnes B., Saedinia-Melnyk S., Zhou L., Shen R., Gunderson K.L., Genome-wide D.N.A. methylation profiling using Infinium assay. Epigenomics 2010, 1:177-200.
5. Liu J., Morgan M., Hutchison K., Calhoun V.D. A study of the influence of sex on genome wide methylation. PLoS ONE 2010, 5:e10028.
6. Fraga M.F. Berdasco M, Ballestar E, Ropero S, Lopez-Nieva P, Lopez-Serra L, Martín-Subero JI, Calasanz MJ, Lopez de Silanes I, Setien F, Casado S, Fernandez AF, Siebert R, Stifani S, Esteller M, Epigenetic inactivation of the Groucho homologue gene TLE1 in hematologic malignancies. Cancer Res. 2008, 68:4116-4122.
7. Chelala C., Khan A., Lemoine N.R. SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. Bioinformatics 2009, 25:655-661.
8. Hu T., Gerace L. cDNA cloning and analysis of the expression of nucleoporin p45. Gene 1998, 221:245-253.
9. Fox M.S., Ares V.X., Turek P.J. Haqq C, Reijo Pera RA, Feasibility of global gene expression analysis in testicular biopsies from infertile men. Mol. Reprod. Dev. 2003, 66:403-421.
10. Hammoud S.S., Purwar J., Pflueger C., Cairns B.R., Carrell D.T. Alterations in sperm DNA methylation patterns at imprinted loci in two classes of infertility. Fertil Steril. 2010, 94:1728-1733.
11. Tunc O., Tremellen K. Oxidative DNA damage impairs global sperm DNA methylation in infertile men. J. Assist. Reprod. Genet. 2009, 26:37-44. 5.
12. Khazamipour N., Noruzinia M., Fatehmanesh P., Keyhanee M., Pujol P. MTHFR promoter hypermethylation in testicular biopsies of patients with non-obstructive azoospermia: the role of epigenetics in male infertility. Hum. Reprod. 2009, 24:2361-2364.
13. Wiencke J.K. Zheng S, Lafuente A, Lafuente MJ, Grudzen C, Wrensch MR, Miike R, Ballesta A, Trias M, Aberrant methylation of p16INK4a in anatomic and gender-specific subtypes of sporadic colorectal cancer. Cancer Epidemiol. Biomark. Prev. 1999, 8:501-506.
14. Sarter B., Long T.I., Tsong W.H., Koh W.P., Yu M.C., Laird P.W. Sex differential in methylation patterns of selected genes in Singapore Chinese. Hum. Genet. 2005, 117:402-403.
15. El-Maarri O., Becker T., Junen J., Manzoor S.S., Diaz-Lacava A., Schwaab R., Wienker T., Oldenburg J. Gender specific differences in levels of DNA methylation at selected loci from human total blood: a tendency toward higher methylation levels in males. Hum. Genet. 2007, 122:505-514.
16. Wu J.Y. Wang J, Lai JC, Cheng YW, Yeh KT, Wu TC, Chen CY, Lee H, Association of O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation with p53 mutation occurrence in non-small cell lung cancer with different histology, gender, and smoking status. Ann. Surg. Oncol. 2008, 15:3272-3277.
17. Boks M.P., Derks E.M., Weisenberger D.J., Strengman E., Janson E., Sommer I.E., Kahn R.S., Ophoff R.A. The relationship of DNA methylation with age, gender and genotype in twins and healthy controls. PLoS ONE 2009, 4:e6767.
18. Bibikova M., Lin Z., Zhou L., Chudin E., Garcia E.W., Wu B., Doucet D., Thomas N.J., Wang Y., Vollmer E., High-throughput D.N.A. methylation profiling using universal bead arrays. Genome Res. 2006, 16:383-393.
19. Kane M.D., Jatkoe T.A., Stumpf C.R. Lu J, Thomas JD, Madore SJ, Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res. 2000, 28:4552-4557.
20. Evertsz E.M., Au-Young J., Ruvolo M.V., Lim A.C., Reynolds M.A. Hybridization cross-reactivity within homologous gene families on glass cDNA microarrays. Biotechniques 2001, 31:1182-1192.
21. Hughes T.R. Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS, Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 2001, 19:342-347.
22. Lyne R., Burns G., Mata J., Penkett C.J., Rustici G., Chen D., Langford C., Vetrie D., Bähler J. Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data. BMC Genomics 2003, 4:27-41.
23. Cortese R., Krispin M., Weiss G., Berlin K., Eckhardt F. DNA methylation profiling of pseudogene-parental gene pairs and two gene families. Genomics 2008, 91:492-502.
24. Kelkar A., Deobagkar D. Methylation profile of genes on the human X chromosome. Epigenetics 2010, 5:612-618.
25. Goto Y., Kimura H., Inactive X. chromosome-specific histone H3 modifications and CpG hypomethylation flank a chromatin boundary between an X-inactivated and an escape gene. Nucleic Acids Res. 2009, 37:7416-7428.
26. Zeschnigk M., Martin M., Betzl G., Kalbe A., Sirsch C., Buiting K., Gross S., Fritzilas E., Frey B., Rahmann S., Horsthemke B. Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete. Hum. Mol. Genet. 2009, 18:1439-1448.
27. Kanduri M., Cahill N., Göransson H., Enström C., Ryan F., Isaksson A., Rosenquist R. Differential genome-wide array-based methylation profiles in prognostic subsets of chronic lymphocytic leukemia. Blood 2010, 115:296-305.
28. Zhang D., Cheng L., Badner J.A., Chen C., Chen Q., Luo W., Craig D.W., Redman M., Gershon E.S., Liu C. Genetic control of individual differences in gene-specific methylation in human brain. Am. J. Hum. Genet. 2010, 86:411-419.
29. Grafodatskaya D., Choufani S., Ferreira J.C., Butcher D.T., Lou Y., Zhao C., Scherer S.W., Weksberg R. EBV transformation and cell culturing destabilizes DNA methylation in human lymphoblastoid cell lines. Genomics 2010, 95:73-83.
30. Kent W.J. BLAT-the BLAST-like alignment tool. Genome Res. 2002, 12:656-664.