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) |