Skip to main content

Advertisement

Table 1 Methods/techniques for detecting/analysis of Differential DNA methylation

From: Crime investigation through DNA methylation analysis: methods and applications in forensics

S. No. Methods/Techniques Quantity of human DNA required Maximum Resolution (bp) Gene Specific Epigenomic Priced in USD References
1. Bisulfite Sequencing (BS-Seq)/BS-Pyrosequencing/Whole Genome Bisulfite Sequencing (WGBS)a 30 ng / 50 pg/2-5 μga respectively 1 $100 + $100-1000 per test, (DNA methylation analysis kit from Thermo Fisher Scientific) (Gu et al., 2010; Bibikova et al., 2011; Antunes et al., 2016; Vidaki et al., 2016)
2. Methyl Specific PCR (MSP)/MethylLight MSP/Mc-MSPa 100 pg / 10 pg/ 1-10 μg respectively 1 $100 + $100-300 per test, (DNA methylation analysis kit from Thermo Fisher Scientific) (Herman et al., 1996; Rand et al., 2002; Kristensen et al., 2008; Lo et al., 2009)
3. COBRA Methylation Assay/ Bio-COBRAb 1 μg/20 ng respectively Not Applicable $100 + $100-200 per test, (DNA methylation analysis kit from Thermo Fisher Scientific) (Xiong and Laird, 1997; Brena et al., 2006; Brena and Plass, 2009; Yang et al., 2010)
4. HELP Methylation Assayb 100 ng - 1 μg Not Applicable $100 + $200 per test, (Thermo Fisher Scientific, New England Biolabs) (Khulan et al., 2006; Oda and Greally, 2009; Shaknovich et al., 2010)
5. Methylation-sensitive Restriction Enzyme based Microarray (MRE-Microarray)b 250 ng - 2 μg 1 $100 + $5,800- 16 tests, EPIC array (Fouse et al., 2010)
6. Illumina Infinium Methylation Assay (Bead Array and NGS Analysis)a 200 ng - 1 μg 1 $3,300 12 tests, EPIC library, $5,800 16 tests, EPIC array (Bibikova et al., 2011; Thompson et al., 2012; Touleimat and Tost, 2012; McCartney et al., 2016; Pidsley et al., 2016)
7. Methyl-CpG Binding Domain Protein Sequencing (MBD-Seq)c 5 ng - 1 μg 150 $550 – 48 tests (diagenode®) (Fraga et al., 2003; Rauch and Pfeifer, 2005; Lan et al., 2011; Aberg et al., 2012)
8. Methylated DNA Immunoprecipitation (MeDIP) PCR/Sequencingc 120 ng - 1.0 μg 100 $390 – 24 tests, $590 – 48 tests (abcam®) (Mohn et al., 2009; Sorensen and Collas, 2009; Borgel et al., 2012; Taiwo et al., 2012; Zhao et al., 2014; Staunstrup et al., 2016)
9. Methylation Analysis through Single Base Extension (SBE)a 0.5 ng to 1.0 ng of gDNA or 1.0-5.0 ng of cloned template DNA 1 $840 – 100 tests,(SNaPshot™ Multiplex Kit from Thermo Fisher Scientific) (Kaminsky and Petronis, 2009; Forat et al., 2016)
  1. aMethods based on PCR/sequencing of bisulfite treated DNA
  2. bMethods based on restriction digestion analysis
  3. cMethods based on methyl-directed antibody or capture protein
  4. dThe prices are approximate obtained from Company websites in November 2017 for the specific kit only, excluding the associated costs such as infrastructure or cost to isolate DNA from the challenging exhibits.