DNA methylome profiling of maternal peripheral blood and placentas reveal potential fetal DNA markers for non-invasive prenatal testing

Molecular Human Reproduction

Volumn 20, Issue 9, 2014, Pages 875-884

  Xiang, Yuqian ^a   Zhang, Junyu ^a   Li, Qiaoli ^a   Zhou, Xinyao ^a   Wang, Teng ^a   Xu, Mingqing ^b   Xia, Shihui ^a   Xing, Qinghe ^a   Wang, Lei ^a   He, Lin ^a,b   Zhao, Xinzhi ^a  

^a FUDAN UNIVERSITY   (China)

^b SHANGHAI JIAO TONG UNIVERSITY   (China)

Author keywords

Comparative methylome analysis; Fetal DNA marker; Non invasive prenatal testing

Indexed keywords

BIOLOGICAL MARKER; DNA;

ASIAN CONTINENTAL ANCESTRY GROUP; BLOOD; CHINA; COMPARATIVE STUDY; DNA METHYLATION; DNA MICROARRAY; FEMALE; FETAL DISEASES; FIRST TRIMESTER PREGNANCY; GENETIC ASSOCIATION; GENETIC EPIGENESIS; HUMAN; IMMUNOPRECIPITATION; MATERNAL SERUM SCREENING TEST; METABOLISM; PLACENTA; PREGNANCY; PREGNANCY COMPLICATIONS; PROCEDURES; VALIDATION STUDY;

ASIAN CONTINENTAL ANCESTRY GROUP; BIOLOGICAL MARKERS; CHINA; DNA; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; FETAL DISEASES; GENOME-WIDE ASSOCIATION STUDY; HUMANS; IMMUNOPRECIPITATION; MATERNAL SERUM SCREENING TESTS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLACENTA; PREGNANCY; PREGNANCY COMPLICATIONS; PREGNANCY TRIMESTER, FIRST;

EID: 84906061035     PISSN: 13609947     EISSN: 14602407     Source Type: Journal    
DOI: 10.1093/molehr/gau048     Document Type: Article

References (40)

1. Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL et al. High density DNA methylation array with single CpG site resolution. Genomics 2011;98:288-295.
2. Cahill N, Bergh AC, Kanduri M, Goransson-Kultima H, Mansouri L, Isaksson A, Ryan F, Smedby KE, Juliusson G, Sundstrom C et al. 450K-array analysis of chronic lymphocytic leukemia cells reveals global DNA methylation to be relatively stable over time and similar in resting and proliferative compartments. Leukemia 2013;27:150-158.
3. Carlson C, Sirotkin H, Pandita R, Goldberg R, McKie J, Wadey R, Patanjali SR, Weissman SM, Anyane-Yeboa K, Warburton Det al. Molecular definition of 22q11 deletions in 151 velo-cardio-facial syndrome patients. Am J Hum Genet 1997;61:620-629.
4. Chan KC, Ding C, Gerovassili A, Yeung SW, Chiu RW, Leung TN, Lau TK, Chim SS, Chung GT, Nicolaides KH et al. Hypermethylated RASSF1A in maternal plasma: a universal fetal DNA marker that improves the reliability of noninvasive prenatal diagnosis. Clin Chem 2006;52:2211-2218.
5. Chim SS, Tong YK, Chiu RW, Lau TK, Leung TN, Chan LY, Oudejans CB, Ding C, Lo YM. Detection of the placental epigenetic signature of the maspin gene in maternal plasma. Proc Natl Acad Sci USA 2005;102: 14753-14758.
6. Chim SS, Jin S, Lee TY, Lun FM, Lee WS, Chan LY, Jin Y, Yang N, Tong YK, Leung TY et al. Systematic search for placental DNA-methylation markers on chromosome 21: toward a maternal plasma-based epigenetic test for fetal trisomy 21. Clin Chem 2008;54:500-511.
7. Chiu RW, Chan KC, Gao Y, Lau VY, Zheng W, Leung TY, Foo CH, Xie B, Tsui NB, Lun FM et al. Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNAin maternal plasma. Proc Natl Acad Sci USA 2008;105:20458-20463.
8. Costa JM, Benachi A, Gautier E, Jouannic JM, Ernault P, Dumez Y. First-trimester fetal sex determination in maternal serum using real-time PCR. Prenat Diagn 2001;21:1070-1074.
9. Dedeurwaerder S, Defrance M, Calonne E, Denis H, Sotiriou C, Fuks F. Evaluation of the Infinium Methylation 450 K technology. Epigenomics 2011;3:771-784.
10. Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 2006;38:1378-1385.
11. Flori E, Doray B, Gautier E, Kohler M, Ernault P, Flori J, Costa JM. Circulating cell-free fetal DNA in maternal serum appears to originate from cyto- and syncytio-trophoblastic cells. Case report. Hum Reprod 2004;19:723-724.
12. Heyn H, Carmona FJ, Gomez A, Ferreira HJ, Bell JT, Sayols S, Ward K, Stefansson OA, Moran S, Sandoval J et al. DNA methylation profiling in breast cancer discordant identical twins identifies DOK7 as novel epigenetic biomarker. Carcinogenesis 2013;34:102-108.
13. Honda H, Miharu N, Ohashi Y, Samura O, Kinutani M, Hara T, Ohama K. Fetal gender determination in early pregnancy through qualitative and quantitative analysis of fetal DNA in maternal serum. Hum Genet 2002; 110:75-79.
14. Illanes S, Parra M, SerraR, Pino K, Figueroa-Diesel H, RomeroC, Arraztoa JA, Michea L, Soothill PW. Increased free fetal DNA levels in early pregnancy plasma of women who subsequently develop preeclampsia and intrauterine growth restriction. Prenat Diagn 2009;29:1118-1122.
15. Kerkel K, Schupf N, Hatta K, Pang D, Salas M, Kratz A, Minden M, Murty V, ZigmanWB, Mayeux RPet al. Altered DNA methylation in leukocytes with trisomy 21. PLoS Genet 2010;6:e1001212.
16. Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 2010;11:191-203.
17. Li N, Ye M, Li Y, Yan Z, Butcher LM, Sun J, Han X, Chen Q, Zhang X, Wang J. Whole genome DNA methylation analysis based on high throughput sequencing technology. Methods 2010;52:203-212.
18. Lo YM, Corbetta N, Chamberlain PF, Rai V, Sargent IL, Redman CW, Wainscoat JS. Presence of fetal DNA in maternal plasma and serum. Lancet 1997;350:485-487.
19. Lo YM, Hjelm NM, Fidler C, Sargent IL, Murphy MF, Chamberlain PF, Poon PM, Redman CW, Wainscoat JS. Prenatal diagnosis of fetal RhD status by molecular analysis of maternal plasma. New Engl J Med 1998; 339:1734-1738.
20. LoYM, Zhang J, Leung TN, Lau TK, ChangAM, HjelmNM. Rapid clearance of fetal DNA from maternal plasma. Am J Hum Genet 1999;64:218-224.
21. Lo YM, Lun FM, Chan KC, Tsui NB, Chong KC, Lau TK, Leung TY, Zee BC, Cantor CR, Chiu RW. Digital PCR for the molecular detection of fetal chromosomal aneuploidy. Proc Natl Acad Sci USA 2007;104:13116-13121.
22. Lun FM, Chiu RW, Allen Chan KC, Yeung Leung T, Kin Lau T, Dennis Lo YM. Microfluidics digital PCR reveals a higher than expected fraction of fetal DNA in maternal plasma. Clin Chem 2008a;54:1664-1672.
23. Lun FM, Tsui NB, Chan KC, Leung TY, Lau TK, Charoenkwan P, Chow KC, Lo WY, Wanapirak C, Sanguansermsri T et al. Noninvasive prenatal diagnosis of monogenic diseases by digital size selection and relative mutation dosage on DNA in maternal plasma. Proc Natl Acad Sci USA 2008b;105:19920-19925.
24. Masuzaki H, Miura K, Yoshiura KI, Yoshimura S, Niikawa N, Ishimaru T. Detection of cell free placental DNA in maternal plasma: direct evidence from three cases of confined placental mosaicism. J Med Genet 2004;41:289-292.
25. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 2008;40:1166-1174.
26. Old RW, Crea F, Puszy kW, Hulten MA. Candidate epigenetic biomarkers for non-invasive prenatal diagnosis of Down syndrome. Reprod Biomed Online 2007;15:227-235.
27. Papageorgiou EA, Fiegler H, Rakyan V, Beck S, Hulten M, Lamnissou K, Carter NP, Patsalis PC. Sites of differential DNA methylation between placenta and peripheral blood: molecular markers for noninvasive prenatal diagnosis of aneuploidies. Am J Pathol 2009;174:1609-1618.
28. Papageorgiou EA, Karagrigoriou A, Tsaliki E, Velissariou V, Carter NP, Patsalis PC. Fetal-specific DNA methylation ratio permits noninvasive prenatal diagnosis of trisomy 21. Nat Med 2011;17:510-513.
29. Pomraning KR, Smith KM, Freitag M. Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 2009;47:142-150.
30. Rijnders RJ, van der Schoot CE, Bossers B, de Vroede MA, Christiaens GC. Fetal sex determination from maternal plasma in pregnancies at risk for congenital adrenal hyperplasia. Obstet Gynecol 2001;98:374-378.
31. Saito H, Sekizawa A, Morimoto T, Suzuki M, Yanaihara T. Prenatal DNA diagnosis of a single-gene disorder from maternal plasma. Lancet 2000; 356:1170.
32. Sedrak M, Hashad D, Adel H, Azzam A, Elbeltagy N. Use of free fetal DNA in prenatal noninvasive detection of fetal RhD status and fetal gender by molecular analysis of maternal plasma. Genet Test Mol Biomarkers 2011; 15:627-631.
33. Sehnert AJ, Rhees B, Comstock D, de Feo E, Heilek G, Burke J, Rava RP. Optimal detection of fetal chromosomal abnormalities by massively parallel DNA sequencing of cell-free fetal DNA from maternal blood. Clin Chem 2011;57:1042-1049.
34. Shimada K, Murakami K, Shozu M, Segawa T, Sumitani H, Inoue M. Sex-determining region Y levels in maternal plasma: evaluation in abnormal pregnancy. J Obstet Gynaecol Res 2004;30:148-154.
35. Slieker RC, Bos SD, Goeman JJ, Bovee JV, Talens RP, van der Breggen R, Suchiman HE, Lameijer EW, Putter H, van den Akker EB et al. Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array. Epigenetics Chromatin 2013;6:26.
36. Xiang Y, Zhang X, Li Q, Xu J, Zhou X, Wang T, Xing Q, Liu Y, Wang L, He L et al. Promoter hypomethylation of TIMP3 is associated with pre-eclampsia in a Chinese population. Mol Hum Reprod 2013; 19:153-159.
37. Yuen RK, Penaherrera MS, von Dadelszen P, McFadden DE, Robinson WP. DNA methylation profiling of human placentas reveals promoter hypomethylation of multiple genes in early-onset preeclampsia. Eur J Hum Genet 2010;18:1006-1012.
38. Zhang X, Snijders A, Segraves R, Zhang X, Niebuhr A, Albertson D, Yang H, Gray J, Niebuhr E, Bolund L et al. High-resolution mapping of genotype-phenotype relationships in cri du chat syndrome using array comparative genomic hybridization. Am J Hum Genet 2005; 76:312-326.
39. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008;9:R137.
40. Zhao A, Cheng Y, Li X, Li Q, Wang L, Xu J, Xiang Y, Xing Q, He L, Zhao X. Promoter hypomethylation of COMTin human placenta is not associated with the development of pre-eclampsia. Mol Hum Reprod 2011; 17:199-206.