DNA methylation: The future of crime scene investigation?

Molecular Biology Reports

Volumn 40, Issue 7, 2013, Pages 4349-4360

  Gršković, Branka ^a,b   Zrnec, Dario ^c   Vicković, Sanja ^d   Popović, Maja ^b,e   Mršić, Gordan ^a,b  

^a MINISTRY OF THE INTERIOR   (Croatia)

^b UNIVERSITY OF SPLIT   (Croatia)

^c UNIVERSITY OF ZAGREB   (Croatia)

^d ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^e UNIVERSITY OF ZAGREB   (Croatia)

Author keywords

Body fluid identification; DNA methylation; DNA methylation applications; Epigenetics; Forensic science

Indexed keywords

GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; MESSENGER RNA; METHYL CPG BINDING PROTEIN 2; MICRORNA; RIBONUCLEOPROTEIN; GENETIC MARKER;

AGE DETERMINATION; ALLELE; ANALYTIC METHOD; ANTIGEN DETECTION; APOPTOSIS; BODY FLUID; CANCER PROGNOSIS; CELL CYCLE; CELL INTERACTION; CIRCADIAN RHYTHM; CPG ISLAND; CRIME; DNA DETERMINATION; DNA FINGERPRINTING; DNA MARKER; DNA METHYLATION; DNA MODIFICATION; DNA REPAIR; DNA REPLICATION; DNA SEQUENCE; EPIGENETICS; FORENSIC GENETICS; FORENSIC IDENTIFICATION; FORENSIC SCIENCE; GENE EXPRESSION; GENE LOCUS; GENE MUTATION; GENE SILENCING; GENETIC ANALYSIS; GENETIC IDENTIFICATION; GENETIC VARIABILITY; GENOME IMPRINTING; HUMAN; IMMUNOPRECIPITATION; LEGAL EVIDENCE; MALIGNANT NEOPLASTIC DISEASE; MEIOSIS; MONOZYGOTIC TWINS; NONHUMAN; PARENTAGE ANALYSIS; PROMOTER REGION; REVIEW; RNA ANALYSIS; SALIVA ANALYSIS; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR SUPPRESSOR GENE; X CHROMOSOME INACTIVATION; CHEMISTRY; GENETIC MARKER;

BODY FLUIDS; DNA METHYLATION; EPIGENOMICS; FORENSIC GENETICS; GENETIC MARKERS; HUMANS;

EID: 84879417560     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-013-2525-3     Document Type: Review

References (121)

1. Virkler K, Lednev IK (2009) Analysis of body fluids for forensic purposes: from laboratory testing to non-destructive rapid confirmatory identification at a crime scene. Forensic Sci Int 188(1-3):1-17. doi: 10.1016/j.forsciint.2009.02.013
2. Lee HY, Park MJ, Choi A, An JH, Yang WI, Shin KJ (2011) Potential forensic application of DNA methylation profiling to body fluid identification. Int J Legal Med 126(1):55-62. doi: 10.1007/s00414-011-0569-2
3. Frumkin D, Wasserstrom A, Budowle B, Davidson A (2011) DNA methylation-based forensic tissue identification. Forensic Sci Int Genet 5:517-524. doi: 10.1016/j.fsigen.2010.12.001
4. Fleming R, Harbison S (2010) The development of a mRNA multiplex RT-PCR assay for the definitive identification of body fluids. Forensic Sci Int Genet 4:244-256. doi: 10.1016/j.fsigen.2009.10.006
5. Zubakov D, Boersma AWM, Choi Y, van Kuijk PF, Wiemer EAC, Kayser M (2010) MicroRNA markers for forensic body fluid identification obtained from microarray screening and quantitative RT-PCR confirmation. Int J Legal Med 124(3):217-226. doi: 10.1007/s00414-009-0402-3
6. Bibikova M, Fan JB (2010) Genome-wide DNA methylation profiling. WIREs Syst Biol Med 2:210-223. doi: 10.1002/wsbm.35
7. Bell JT, Tsai PC, Yang TP et al (2012) Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet 8(4):e1002629. doi: 10.1371/journal.pgen. 1002629
8. Zubakov D, Liu F, Choi Y, van Ljcken WFJ, Oostra B, van Duijn CM, Lewin J, Kayser M (2011) mRNA expression and DNA methylation biomarkers for estimating chronological age from blood. In: 24th World Congress of the International Society for Forensic Genetics (ISFG). http://isfg2011.book-of-abstracts.com/ fileadmin/isfg2011/ISFG-BoA-2011-Web.pdf
9. Bocklandt S, Lin W, Sehl ME, Sanchez FJ, Sinsheimer JS, Horvath S, Vilain E (2011) Epigenetic predictor of age. PLoS One 6:e14821. doi: 10.1371/journal.pone.0014821
10. Zhao G, Yang Q, Huang D, Yu C, Yang R, Chen H, Mei K (2005) Study on the application of parent-of-origin specific DNA methylation markers to forensic genetics. Forensic Sci Int 154(2-3):122-127. doi: 10.1016/j.forsciint.2004.09. 123
11. Nakayashiki N, Takamiya M, Shimamoto K, Aoki Y, Hashiyada M (2009) Investigation of the methylation status around parent-of-origin detectable SNPs in imprinted genes. Forensic Sci Int Genet 3(4):227-232
12. Coolen MW, Statham AL, Qu W, Campbell MJ, Henders AK, Montgomery GW, Martin NG, Clark SJ (2011) Impact of the genome on the epigenome is manifested in DNA methylation patterns of imprinted regions in monozygotic and dizygotic twins. PLoS One 6(10):e25590. doi: 10.1371/journal.pone.0025590
13. Coolen MW, Statham AL, Gardiner-Garden M, Clark SJ (2007) Genomic profiling of CpG methylation and allelic specificity using quantitative high throughput mass spectrometry: critical evaluation and improvements. Nucleic Acids Res 35:e119. doi: 10.1093/nar/gkm662
14. Li C, Zhang S, Que T, Li L, Zhao S (2011) Identical but not the same: the value of DNA methylation profiling in forensic discrimination within monozygotic twins. Forensic Sci Int 3(1):e337-e338. doi: 10.1016/j.fsigss.2011. 09.031
15. Frumkin D, Wasserstrom A, Davidson A, Grafit A (2010) Authentication of forensic DNA samples. Forensic Sci Int Genet 4:95-103. doi: 10.1016/j.fsigen. 2009.06.009
16. Nakatome M, Orii M, Hamajima M, Hirata Y, Uemura M, Hirayama S, Isobe I (2011) Methylation analysis of circadian clock gene promoters in forensic autopsy specimens. Leg Med (Tokyo) 13(4):205-209. doi: 10.1016/j.legalmed.2011. 03.001
17. Henikoff S, Matzke MA (1997) Exploring and explaining epigenetic effects. Trends Genet 13:293-295. doi: 10.1016/S0168-9525(97)01219-5
18. Russo VEA, Martienssen RA, Riggs AD (1996) Epigenetic mechanisms of gene regulation. Cold Spring Harbor, New York
19. Gibney ER, Nolan CM (2010) Epigenetics and gene expression. Heredity 105(1):4-13
20. Jirtle RL, Skinner MK (2007) Environmental epigenomics and disease susceptibility. Nat Rev Genet 8:253-262. doi: 10.1038/nrg2045
21. Hamilton JP (2011) Epigenetics: principles and practice. Dig Dis 29:130-135. doi: 10.1159/000323874
22. Bird A, Macleod D (2004) Reading the DNA methylation signal. Cold Spring Harb Symp Quant Biol 69:113-118. doi: 10.1101/sqb.2004.69.113
23. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293(5532):1074-1080. doi: 10.1126/science.1063127
24. Herman JG, Baylin SB (2003) Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med 349:2042-2054
25. Holliday R, Pugh JE (1975) DNA modification mechanisms and gene activity during development. Science 187:226-232
26. Riggs AD (1975) X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet 14(1):9-25
27. El-Maarri O (2003) Methods: DNA methylation. Adv Exp Med Biol 544:197-204
28. Burgers WA, Fuks F, Kouzarides T (2002) DNA methyltransferases get connected to chromatin. Trends Genet 18:275-277. doi: 10.1016/S0168-9525(02) 02667-7
29. Takai D, Jones PA (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 99(6):3740-3745. doi: 10.1073/pnas.052410099
30. Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 196(2):261-268. doi: 10.1016/0022-2836(87)90689-9
31. Lander ES, Linton LM, Birren B et al (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860-921. doi: 10.1038/35057062
32. Venter JC, Adams MD, Myers EW et al (2001) The sequence of the human genome. Science 291(5507):1304-1351. doi: 10.1126/science.1058040
33. Ehrlich M (1982) Amount and distribution of 5-methylcytosine in human DNA from different types of tissues or cells. Nucleic Acids Res 10:2709-2721. doi: 10.1093/nar/10.8.2709
34. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16:6-21. doi: 10.1101/gad.947102
35. Antequera F, Bird A (1993) Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci USA 90:11995-11999
36. Bird AP, Wolffe AP (1999) Methylation-induced repression - belts, braces, and chromatin. Cell 99:451-454. doi: 10.1016/S0092-8674(00)81532-9
37. Jaenisch R, Harbers K, Jahner D, Stewart C, Stuhlmann H (1982) DNA methylation, retroviruses, and embryogenesis. J Cell Biochem 20(4):331-336
38. Christensen BC, Houseman EA, Marsit CJ, Zheng S, Wrensch MR, Wiemels JL, Nelson HH, Karagas MR, Padbury JF, Bueno R, Sugarbaker DJ, Yeh RF, Wiencke JK, Kelsey KT (2009) Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet 5:e1000602. doi: 10.1371/journal.pgen.1000602
39. Schilling E, Rehli M (2007) Global, comparative analysis of tissue-specific promoter CpG methylation. Genomics 90(3):314-323. doi: 10.1016/j.ygeno.2007.04.011
40. Kitamura E, Igarashi J, Morohashi A, Hida N, Oinuma T, Nemoto N, Song F, Ghosh S, Held WA, Yoshida-Noro C, Nagase H (2007) Analysis of tissue-specific differentially methylated regions (TDMs) in humans. Genomics 89(3):326-337. doi: 10.1016/j.ygeno.2006.11.006
41. Igarashi J, Muroi S, Kawashima H, Wang X, Shinojima Y, Kitamura E, Oinuma T, Nemoto N, Song F, Ghosh S, Held WA, Nagase H (2008) Quantitative analysis of human tissue-specific differences in methylation. Biochem Biophys Res Commun 376(4):658-664. doi: 10.1016/j.bbrc.2008.09.044
42. Song F, Mahmood S, Ghosh S, Liang P, Smiraglia DJ, Nagase H, Held WA (2009) Tissue specific differentially methylated regions (TDMR): changes in DNA methylation during development. Genomics 93(2):130-139. doi: 10.1016/j.ygeno.2008.09.003
43. Jones PA, Laird PW (1999) Cancer-epigenetics comes of age. Nat Genet 21(2):163-167. doi: 10.1038/5947
44. Baylin SB, Herman JG (2000) DNA hypermethylation in tumorigenesis: epigenetics joins genetics. Trends Genet 16:168-174. doi: 10.1016/S0168-9525(99) 01971-X
45. Baylin SB, Esteller M, Rountree MR, Backman KE, Schuebel K, Herman JG (2001) Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Hum Mol Genet 10:687-692. doi: 10.1093/hmg/10.7.687
46. Watanabe Y, Maekawa M (2010) Methylation of DNA in cancer. Adv Clin Chem 52:145-167. doi: 10.1016/S0065-2423(10)52006-7
47. Park YJ, Claus R, Weichenhan D, Plass C (2011) Genome-wide epigenetic modifications in cancer. Prog Drug Res 67:25-49
48. Hochedlinger K, Jaenisch R (2006) Nuclear reprogramming and pluripotency. Nature 441:1061-1067. doi: 10.1038/nature04955
49. Huang K, Fan G (2010) DNA methylation in cell differentiation and reprogramming: an emerging systematic view. Regen Med 5(4):531-544. doi: 10.2217/rme.10.35
50. Straussman R, Nejman D, Roberts D, Steinfeld I, Blum B, Benvenisty N, Simon I, Yakhini Z, Cedar H (2009) Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol 16:564-571. doi: 10.1038/nsmb.1594
51. De Carvalho DD, You JS, Jones PA (2010) DNA methylation and cellular reprogramming. Trends Cell Biol 20:609-617. doi: 10.1016/j.tcb.2010.08.003
52. Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128(4):683-692. doi: 10.1016/j.cell.2007.01.029
53. Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9:465-476. doi: 10.1038/nrg2341
54. Gartler SM, Riggs AD (1983) Mammalian X-chromosome inactivation. Annu Rev Genet 17:155-190
55. Jones PA, Baylin SB (2002) The fundamental role of epigenetic events in cancer. Nat Rev Genet 3(6):415-428. doi: 10.1038/nrg816
56. Miranda BA, Jones PA (2007) DNA methylation: the nuts and bolts of repression. J Cell Physiol 213(2):384-390. doi: 10.1002/JCP
57. Futscher BW, Oshiro MM, Wozniak RJ, Holtan N, Hanigan CL, Duan H, Domann FE (2002) Role for DNA methylation in the control of cell type specific maspin expression. Nat Genet 31:175-179. doi: 10.1038/ng886
58. Hattori N, Nishino K, Ko YG, Ohgane J, Tanaka S, Shiota K (2004) Epigenetic control of mouse Oct-4 gene expression in embryonic stem cells and trophoblast stem cells. J Biol Chem 279:17063-17069. doi: 10.1074/jbc.M309002200
59. Blelloch R, Wang Z, Meissner A, Pollard S, Smith A, Jaenisch R (2006) Reprogramming efficiency following somatic cell nuclear transfer is influenced by the differentiation and methylation state of the donor nucleus. Stem Cells 24:2007-2013. doi: 10.1634/stemcells.2006-0050
60. Feinberg AP, Vogelstein B (1983) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301:89-92. doi: 10.1038/301089a0
61. Sakai T, Toguchida J, Ohtani N, Yandell DW, Rapaport JM, Dryja TP (1991) Allele-specific hypermethylation of the retinoblastoma tumor-suppressor gene. Am J Hum Genet 48(5):880-888
62. Herman JG, Merlo A, Mao L, Lapidus RG, Issa JP, Davidson NE, Sidransky D, Baylin SB (1995) Inactivation of the CDKN2/p16/MTS1 gene is frequently associated with aberrant DNA methylation in all common human cancers. Cancer Res 55:4525-4530
63. Muller HM, Widschwendter A, Fiegl H, Ivarsson L, Goebel G, Perkmann E, Marth C, Widschwendter M (2003) DNA methylation in serum of breast cancer patients. Cancer Res 63:7641-7645
64. Kim E, Kim Y, Jeong P, Ha Y, Bae S, Kim W (2008) Methylation of the RUNX3 promoter as a potential prognostic marker for bladder tumor. J Urol 180(3):1141-1145. doi: 10.1016/j.juro.2008.05.002
65. Schneider E, Pliushch G, El Hajj N, Galetzka D, Puhl A, Schorsch M, Frauenknecht K, Riepert T, Tresch A, Müller AM, Coerdt W, Zechner U, Haaf T (2010) Spatial, temporal and interindividual epigenetic variation of functionally important DNA methylation patterns. Nucleic Acids Res 38(12):3880-3890. doi: 10.1093/nar/gkq126
66. Zubakov D, Hanekamp E, Kokshoorn M, van Ijcken W, Kayser M (2008) Stable RNA markers for identification of blood and saliva stains revealed from whole genome expression analysis of time-wise degraded samples. Int J Legal Med 122:135-142. doi: 10.1007/s00414-007-0182-6
67. Dilbeck L (2006) Use of bluestar forensic in lieu of luminol at crime scenes. J Forensic Identif 56(5):706-720
68. Mozayani A, Nozigila C (2006) The forensic laboratory handbook: procedures and practice. Humana Press Inc., Totowa
69. Pang BCM, Cheung BKK (2008) Applicability of two commercially available kits for forensic identification of saliva stains. J Forensic Sci 53(5):1117-1122. doi: 10.1111/j.1556-4029.2008.00814.x
70. Simich JP, Morris SL, Klick RL, Rittenhouse-Diakun K (1999) Validation of the use of a commercially available kit for the identification of prostate specific antigen (PSA) in semen stains. J Forensic Sci 44:1229-1231
71. Allery JP, Telmon N, Mieusset R, Blanc A, Rouge D (2001) Cytological detection of spermatozoa: comparison of three staining methods. J Forensic Sci 46:349-351
72. Heintzman ND, Ren B (2007) The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome. Cell Mol Life Sci 64:386-400. doi: 10.1007/s00018-006-6295-0
73. Visser M, Zubakov D, Ballantyne KN, Kayser M (2011) mRNA-based skin identification for forensic applications. Int J Legal Med 125(2):253-263. doi: 10.1007/s00414-010-0545-2
74. Zubakov D, Kokshooorn M, Kloosterman A, Kayser M (2009) New markers for old stains: stable mRNA markers for blood and saliva identification from up to 16-year-old stains. Int J Legal Med 123:71-74. doi: 10.1007/s00414-008-0249-z
75. Vennemann M, Koppelkamm A (2010) mRNA profiling in forensic genetics I: possibilities and limitations. Forensic Sci Int 203(1-3):71-75. doi: 10.1016/j.forsciint.2010.07.006
76. Lindenbergh A, de Pagter M, Ramdayal G, Visser M, Zubakov D, Kayser M, Sijen T (2012) A multiplex (m)RNA-profiling system for the forensic identification of body fluids and contact traces. Forensic Sci Int 6:565-577. doi: 10.1016/j.fsigen.2012.01.009
77. Phang TW, Shi CY, Chia JN, Ong CN (1994) Amplification of cDNA via RT-PCR using RNA extracted from post-mortem tissue. J Forensic Sci 39(5):1275-1279
78. Meyer S, Temme C, Wahle E (2004) Messenger RNA turnover in eukaryotes: pathways and enzymes. Crit Rev Biochem Mol Biol 39(4):197-216. doi: 10.1080/10409230490513991
79. Brewer G (2002) Messenger RNA decays during aging and development. Age Res Rev 1:607-625. doi: 10.1016/S1568-1637(02)00023-5
80. Hanson EK, Lubenow H, Ballantyne J (2009) Identification of forensically relevant body fluids using a panel of differentially expressed microRNAs. Anal Biochem 387:303-314. doi: 10.1016/j.ab.2009.01.037
81. Wang Z, Luo H, Pan X, Liao M, Hou Y (2011) A model for data analysis of microRNA expression in forensic body fluid identification. Forensic Sci Int Genet 6(3):419-423. doi: 10.1016/j.fsigen.2011.08.008
82. Chen X, Ba Y, Ma L, Cai X, Yin Y, Wang K, Guo J, Zhang Y, Chen J, Guo X, Li Q, Li X, Wang W, Zhang Y, Wang J, Jiang X, Xiang Y, Xu C, Zheng P, Zhang J, Li R, Zhang H, Shang X, Gong T, Ning G, Wang J, Zen K, Zhang J, Zhang CY (2008) Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18:997-1006. doi: 10.1038/cr.2008.282
83. Rossi J (2005) Mammalian Dicer finds a partner. EMBO Rep 6(10):927-929. doi: 10.1038/sj.embor.7400531
84. Bail S, Swerdel M, Liu H, Jiao X, Goff LA, Hart RP, Kiledjian M (2010) Differential regulation of microRNA stability. RNA 16:1032-1039. doi: 10.1261/rna.1851510
85. Chang S, Wen S, Chen D, Jin P (2009) Small regulatory RNAs in neurodevelopmental disorders. Hum Mol Genet 18(R1):R18-R26. doi: 10.1093/hmg/ddp072
86. Vasudevan S, Tong Y, Steitz JA (2007) Switching from repression to activation: microRNAs can up-regulate translation. Science 318(5858):1931-1934. doi: 10.1126/science.1149460
87. Sato F, Tsuchiya S, Terasawa K, Tsujimoto G (2009) Intra-platform repeatability and inter-platform comparability of microRNA microarray technology. PLoS One 5:e5540. doi: 10.1371/journal.pone.0005540
88. Laird PW (2010) Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 11(3):191-203. doi: 10.1038/nrg2732
89. Keshet I, Schlesinger Y, Farkash S, Rand E, Hecht M, Segal E, Pikarski E, Young RA, Niveleau A, Cedar H, Simon I (2006) Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet 38:149-153. doi: 10.1038/ng1719
90. Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Graf S, Tomazou EM, Backdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ, Carter NP, Tavare S, Beck S (2008) An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res 18:1518-1529
91. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schübeler D (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37:853-862. doi: 10.1038/ng1598
92. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39:457-466. doi: 10.1038/ng1990
93. Illingworth R, Kerr A, Desousa D, Jorgensen H, Ellis P, Stalker J, Jackson D, Clee C, Plumb R, Rogers J, Humphray S, Cox T, Langford C, Bird A (2008) A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol 6:e22. doi: 10.1371/journal.pbio.0060022
94. Rauch T, Pfeifer GP (2005) Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab Invest 85(9):1172-1180. doi: 10.1038/labinvest.3700311
95. Lewis JD, Meehan RR, Henzel WJ, Maurer-Fogy I, Jeppesen P, Klein F, Bird A (1992) Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 69(6):905-914. doi: 10.1016/0092-8674(92)90610-O
96. Nan X, Meehan RR, Bird A (1993) Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res 21(21):4886-4892
97. Mill J, Petronis A (2009) Profiling DNA methylation from small amounts of genomic DNA starting material: efficient sodium bisulfite conversion and subsequent whole-genome amplification methods. Mol Biol 507:371-381. doi: 10.1007/978-1-59745-522-027
98. Clark S, Harrison J, Paul CL, Frommer M (1994) High sensitivity mapping of methylated cytosines. Nucleic Acids Res 22:2990-2997
99. Frommer M, McDonald L, Millar D, Collis C, Watt F, Grigg G, Molloy P, Paul C (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89:1827-1831
100. Grunau C, Clark SJ, Rosenthal A (2001) Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res 29:e65. doi: 10.1093/nar/29.13.e65
101. Genereux DP, Johnson WC, Burden AF, Stoger R, Laird CD (2008) Errors in the bisulfite conversion of DNA: modulating inappropriate and failed conversion frequencies. Nucleic Acids Res 36:e150. doi: 10.1093/nar/gkn691
102. Xu H, Zhao Y, Liu Z, Zhu W, Zhou Y, Zhao Z (2011) Bisulfite genomic sequencing of DNA from dried blood spot microvolume samples. Forensic Sci Int Genet 6(3):306-309. doi: 10.1016/j.fsigen.2011.06.007
103. Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, Haefliger C, Horton R, Howe K, Jackson DK, Kunde J, Koenig C, Liddle J, Niblett D, Otto T, Pettett R, Seemann S, Thompson C, West T, Rogers J, Olek A, Berlin K, Beck S (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38:1378-1385. doi: 10.1038/ng1909
104. Zhang Y, Jeltsch A (2010) The application of next generation sequencing in DNA methylation analysis. Genes 1(1):85-101. doi: 10.3390/genes1010085
105. An JH, Choi A, Shin KJ, Yang WI, Lee HY (2013) DNA methylation-specific multiplex assays for body fluid identification. Int J Legal Med 127(1):35-43. doi: 10.1007/s00414-012-0719-1
106. Madi T, Balamurugan K, Bombardi R, Duncan G, McCord B (2012) The determination of tissue-specific DNA methylation patterns in forensic biofluids using bisulfate modification and pyrosequencing. Electrophoresis 33:1736-1745. doi: 10.1002/elps.201100711
107. Wasserstrom A, Frumkin D, Davidson A, Shpitzen M, Herman Y, Gafny R (2013) Demonstration of DSI-semen - a novel DNA methylation-based forensic semen identification assay. Forensic Sci Int Genet 7(1):136-142. doi: 10.1016/j.fsigen.2012.08.009
108. Naito E, Dewa K, Fukuda M, Sumi H, Wakabayashi Y, Umetsu K, Yuasa I, Yamanouchi H (2003) Novel paternity testing by distinguishing parental alleles at a VNTR locus in the differentially methylated region upstream of the human H19 gene. J Forensic 48(6):1275-1279
109. Xu HD, Naito E, Dewa K, Fukuda M, Sumi H, Yuasa I, Yamanouchi H (2006) Parentally imprinted allele typing at a short tandem repeat locus in intron 1a of imprinted gene KCNQ1. Leg Med (Tokyo) 8(3):139-143
110. Huang D, Lin X, Chen H, Yang Q, Jie Y, Zhai X, Yin H (2008) Parentally imprinted allele (PIA) typing in the differentially methylated region upstream of the human H19 gene. Forensic Sci Int Genet 2(4):286-291. doi: 10.1016/j.fsigen.2008.03.008
111. Koch CM, Wagner W (2011) Epigenetic-aging-signature to determine age in different tissues. Aging (Albany NY) 3(10):1-10
112. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, Heine-Suñer D, Cigudosa JC, Urioste M, Benitez J, Boix-Chornet M, Sanchez-Aguilera A, Ling C, Carlsson E, Poulsen P, Vaag A, Stephan Z, Spector TD, Wu YZ, Plass C, Esteller M (2005) Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 102(30):10604-10609. doi: 10.1073/pnas.0500398102
113. Zheng YM, Wang N, Lei LI, Fan JIN (2011) Whole genome amplification in preimplantation genetic diagnosis. J Zhejiang Univ Sci B 12(1):1-11. doi: 10.1631/jzus.B1000196
114. Liu H-C, Hu C-J, Tang Y-C, Chang J-G (2008) A pilot study for circadian gene disturbance in dementia patients. Neurosci Lett 435:229-233. doi: 10.1016/j.neulet.2008.02.041
115. Ordovás JM, Smith CE (2010) Epigenetics and cardiovascular disease. Nat Rev Cardiol 7:510-519. doi: 10.1038/nrcardio.2010.104
116. Taniguchi H, Fernándes AF, Setién F, Ropero S, Ballestar E, Villanueva A, Yamamoto H, Imai K, Shinomura Y, Esteller M (2009) Epigenetic inactivation of the circadian clock gene BMAL1 in hematologic malignancies. Cancer Res 69:8447-8454. doi: 10.1158/0008-5472.CAN-09-0551
117. Kim HC, Kim JC, Roh SA, Yu CS, Yook JH, Oh ST, Kim BS, Park KC, Chang R (2005) Aberrant CpG island methylation in early-onset sporadic gastric carcinoma. J Cancer Res Clin Oncol 131:733-740. doi: 10.1007/s00432-005-0017-0
118. Kuo SJ, Chen ST, Yeh KT, Hou MF, Chang YS, Hsu NC, Chang JG (2009) Disturbance of circadian gene expression in breast cancer. Virchows Arch 454:467-474. doi: 10.1007/s00428-009-0761-7
119. Chen ST, Choo KB, Hou MF, Yeh KT, Kuo SJ, Chang JG (2005) Deregulated expression of the PER1, PER2, and PER3 genes in breast cancers. Carcinogenesis 26:1241-1246. doi: 10.1093/carcin/bgi075
120. Lin YM, Chang JH, Yeh KT, Yang MY, Liu TC, Lin SF, Su WW, Chang JG (2008) Disturbance of circadian gene expression in hepatocellular carcinoma. Mol Carcinog 47:925-933. doi: 10.1002/mc.20446
121. An JH, Shin KJ, Yang WI, Lee HY (2012) Body fluid identification in forensics. BMB Rep 45(10):545-553. doi: 10.5483/BMBRep.2012.45.10.206