GenotypingPortal2

Genotyping Portal

A comprehensive (and freely available) online resource about methods for DNA genotyping, screening and sequencing

Mutation Screening

PCR-SSCP (Single Strand Conformational Polymorphism): Hayashi K. PCR-SSCP: a simple and sensitive method for detection of mutations in the genomic DNA. PCR Methods Appl. 1991 Aug;1(1):34-8.

HRM (High-Resolution Melting): Wittwer CT, Herrmann MG, Moss AA, Rasmussen RP. Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques. 1997 Jan;22(1):130-8.

Capillary SSCP: Larsen LA, Christiansen M, Vuust J, Andersen PS. High-throughput single-strand conformation polymorphism analysis by automated capillary electrophoresis: robust multiplex analysis and pattern-based identification of allelic variants. Hum Mutat. 1999;13(4):318-27.

DHPLC (Denaturing High performance Liquid Chromatography): Liu W, Smith DI, Rechtzigel KJ, Thibodeau SN, James CD. Denaturing high performance liquid chromatography (DHPLC) used in the detection of germline and somatic mutations. Nucleic Acids Res. 1998 Mar 15;26(6):1396-400.

High-resolution melting analysis (HRMA): Willmore C, Holden JA, Zhou L, Tripp S, Wittwer CT, Layfield LJ. Detection of c-kit-activating mutations in gastrointestinal stromal tumors by high-resolution amplicon melting analysis. Am J Clin Pathol. 2004 Aug;122(2):206-16.

Universal digital high-resolution melt: Fraley SI, Hardick J, Jo Masek B, Athamanolap P, Rothman RE, Gaydos CA, Carroll KC, Wakefield T, Wang TH, Yang S. Universal digital high-resolution melt: a novel approach to broad-based profiling of heterogeneous biological samples. Nucleic Acids Res. 2013 Oct;41(18):e175.

PCR-CSGE (PCR-Conformation-sensitive gel electrophoresis): Ganguly A, Rock MJ, Prockop DJ. Conformation-sensitive gel electrophoresis for rapid detection of single-base differences in double-stranded PCR products and DNA fragments: evidence for solvent-induced bends in DNA heteroduplexes. Proc Natl Acad Sci U S A. 1993 Nov 1;90(21):10325-9.

C-CSGE (capillary CSGE): Rozycka M, Collins N, Stratton MR, Wooster R. Rapid detection of DNA sequence variants by conformation-sensitive capillary electrophoresis. Genomics. 2000 Nov 15;70(1):34-40.

M-C-CSGE (multiplex capillary CSGE): Esteban-Cardeñosa E, Duran M, Infante M, Velasco E, Miner C. High-throughput mutation detection method to scan BRCA1 and BRCA2 based on heteroduplex analysis by capillary array electrophoresis. Clin Chem. 2004 Feb;50(2):313-20.

PCR-DGGE (PCR-denaturing gradient gel electrophoresis): Sheffield VC, Cox DR, Lerman LS, Myers RM. Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc Natl Acad Sci U S A. 1989 Jan;86(1):232-6.

TDGS (Two-dimensional gene scanning): Van Orsouw NJ, Li D, van der Vlies P, Scheffer H, Eng C, Buys CH, Li FP, Vijg J. Mutational scanning of large genes by extensive PCR multiplexing and two-dimensional electrophoresis: application to the RB1 gene. Hum Mol Genet. 1996 Jun;5(6):755-61.

F-DOVAM-S (fluorescent-detection of virtually all mutations–SSCP): Mroske C, Muci J, Wang J, Li K, Song W, Yan J, Feng J, Liu Q, Sommer SS. Toward a fluorescent single-strand conformation polymorphism technique that detects all mutations: F-DOVAM-S. Anal Biochem. 2007 Sep 15;368(2):250-7.

EMD (enzymatic mutation detection): Del Tito BJ Jr, Poff HE 3rd, Novotny MA, Cartledge DM, Walker RI 2nd, Earl CD, Bailey AL. Automated fluorescent analysis procedure for enzymatic mutation detection. Clin Chem. 1998 Apr;44(4):731-9.

PTT (Protein truncation test): Hogervorst FB, Cornelis RS, Bout M, v, et al. Rapid detection of BRCA1 mutations by the protein truncation test. Nat Genet. 1995 Jun;10(2):208-12.

Comparison of Methods: Eng C, Brody LC, Wagner TM, ..., Nathanson KL, Ostrander E, Frank TS. Interpreting epidemiological research: blinded comparison of methods used to estimate the prevalence of inherited mutations in BRCA1. J Med Genet. 2001 Dec;38(12):824-33.

Prioritization of regions for screening: Braun TA, Shankar SP, Davis S, O'Leary B, Scheetz TE, Clark AF, Sheffield VC, Casavant TL, Stone EM. Prioritizing regions of candidate genes for efficient mutation screening. Hum Mutat. 2006 Feb;27(2):195-200.

DNA Sequencing

DNA sequencing-Sanger: Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7.

Nanopore sequencing: Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O'Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018 Apr;36(4):338-345.

DNA sequencing-454: Margulies M, Egholm M, Altman WE, ..., Yu P, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005 Sep 15;437(7057):376-80.

DNA sequencing-Illumina: Bentley DR, Balasubramanian S, Swerdlow HP, ..., Klenerman D, Durbin R, Smith AJ. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008 Nov 6;456(7218):53-9.

DNA sequencing-SOLiD: McKernan KJ, Peckham HE, Costa GL, ..., Reese MG, De La Vega FM, Blanchard AP. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 2009 Sep;19(9):1527-41.

DNA sequencing-Helicos: Pushkarev D, Neff NF, Quake SR. Single-molecule sequencing of an individual human genome. Nat Biotechnol. 2009 Sep;27(9):847-52.

DNA sequencing-Complete Genomics: Drmanac R, Sparks AB, Callow MJ, ..., Ballinger DG, Church GM, Reid CA. Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays. Science. 2010 Jan 1;327(5961):78-81.

DNA sequencing-Pacific Biosciences: Eid J, Fehr A, Gray J, ..., Zhong F, Korlach J, Turner S. Real-time DNA sequencing from single polymerase molecules. Science. 2009 Jan 2;323(5910):133-8.

DNA sequencing-Ion Torrent: Rothberg JM, Hinz W, Rearick TM, ..., J, Williams A, Roth GT, Bustillo J. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011 Jul 20;475(7356):348-52.

DNA-chip-based capture (NimbleGen): Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkaloğlu A, Ozen S, Sanjad S, Nelson-Williams C, Farhi A, Mane S, Lifton RP. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19096-101.

DNA-probe-based solution hybridization (NimbleGen): Bainbridge MN, Wang M, Burgess DL, Kovar C, Rodesch MJ, D'Ascenzo M, Kitzman J, Wu YQ, Newsham I, Richmond TA, Jeddeloh JA, Muzny D, Albert TJ, Gibbs RA. Whole exome capture in solution with 3 Gbp of data. Genome Biol. 2010;11(6):R62.

RNA-probe-based solution hybridization (Agilent): Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009 Feb;27(2):182-9.

Exome Capture-MIP: Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM, Shendure J. Multiplex amplification of large sets of human exons. Nat Methods. 2007 Nov;4(11):931-6.

AluScan: Mei L, Ding X, Tsang SY, Pun FW, Ng SK, Yang J, Zhao C, Li D, Wan W, Yu CH, Tan TC, Poon WS, Leung GK, Ng HK, Zhang L, Xue H. AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome. BMC Genomics. 2011 Nov 17;12:564.

Hi-Plex: Nguyen-Dumont T, Pope BJ, Hammet F, Southey MC, Park DJ. A high-plex PCR approach for massively parallel sequencing. Biotechniques. 2013 Aug;55(2):69-74.

TLA (Targeted Locus Amplification): de Vree PJ, de Wit E, Yilmaz M, van de Heijning M, Klous P, Verstegen MJ, Wan Y, Teunissen H, Krijger PH, Geeven G, Eijk PP, Sie D, Ylstra B, Hulsman LO, van Dooren MF, van Zutven LJ, van den Ouweland A, Verbeek S, van Dijk KW, Cornelissen M, Das AT, Berkhout B, Sikkema-Raddatz B, van den Berg E, van der Vlies P, Weening D, den Dunnen JT, Matusiak M, Lamkanfi M, Ligtenberg MJ, ter Brugge P, Jonkers J, Foekens JA, Martens JW, van der Luijt R, van Amstel HK, van Min M, Splinter E, de Laat W. Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping. Nat Biotechnol. 2014 Oct;32(10):1019-25

Exome sequencing: Ng SB, Turner EH, Robertson PD, ..., Bamshad M, Nickerson DA, Shendure J. Targeted capture and massively parallel sequencing of 12 human exomes. Nature. 2009 Sep 10;461(7261):272-6.

Sequencing of difficult templates: Kieleczawa J, Mazaika E. Optimization of protocol for sequencing of difficult templates. J Biomol Tech. 2010 Jul;21(2):97-102.

DNA Sequencing facilities: Needleman D, Adam D, Detwiler M, Escobar H, Kieleczawa J, Pershard R, Schweitzer P, Wiebe G. DNA sequencing research group: 2006 general survey of DNA sequencing facilities. J Biomol Tech. 2007 Apr;18(2):113-9.

Primer design-Sequencing: Li K, Brownley A, Stockwell TB, Beeson K, McIntosh TC, Busam D, Ferriera S, Murphy S, Levy S. Novel computational methods for increasing PCR primer design effectiveness in directed sequencing. BMC Bioinformatics. 2008 Apr 11;9:191.

Comparison of exome sequencing platforms: Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 2011 Sep 25;29(10):908-14.

Comparison of whole-exome capture platforms: Asan, Xu Y, Jiang H, Tyler-Smith C, Xue Y, Jiang T, Wang J, Wu M, Liu X, Tian G, Wang J, Wang J, Yang H, Zhang X. Comprehensive comparison of three commercial human whole-exome capture platforms. Genome Biol. 2011 Sep 28;12(9):R95.

Comparison of target enrichment methods: Bodi K, Perera AG, Adams PS, Bintzler D, Dewar K, Grove DS, Kieleczawa J, Lyons RH, Neubert TA, Noll AC, Singh S, Steen R, Zianni M. Comparison of commercially available target enrichment methods for next-generation sequencing. J Biomol Tech. 2013 Jul;24(2):73-86.

Comparison of whole-exome capture platforms: Chilamakuri CS, Lorenz S, Madoui MA, Vodák D, Sun J, Hovig E, Myklebost O, Meza-Zepeda LA. Performance comparison of four exome capture systems for deep sequencing. BMC Genomics. 2014 Jun 9;15:449.

Comparison of whole-exome capture platforms: Shigemizu D, Momozawa Y, Abe T, Morizono T, Boroevich KA, Takata S, Ashikawa K, Kubo M, Tsunoda T. Performance comparison of four commercial human whole-exome capture platforms. Sci Rep. 2015 Aug 3;5:12742.

Comparison of whole-exome capture platforms: Zhang G, Wang J, Yang J, Li W, Deng Y, Li J, Huang J, Hu S, Zhang B. Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling. BMC Genomics. 2015 Aug 5;16:581.

Comparison of whole-exome capture platforms: Samorodnitsky E, Jewell BM, Hagopian R, Miya J, Wing MR, Lyon E, Damodaran S, Bhatt D, Reeser JW, Datta J, Roychowdhury S. Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing. Hum Mutat. 2015 Sep;36(9):903-14.

Comparison of whole-exome capture platforms: Meienberg J, Zerjavic K, Keller I, Okoniewski M, Patrignani A, Ludin K, Xu Z, Steinmann B, Carrel T, Röthlisberger B, Schlapbach R, Bruggmann R, Matyas G. New insights into the performance of human whole-exome capture platforms. Nucleic Acids Res. 2015 Jun 23;43(11):e76.

Comparison of exome and genome sequencing: Lelieveld SH, Spielmann M, Mundlos S, Veltman JA, Gilissen C. Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein-Coding Regions. Hum Mutat. 2015 Aug;36(8):815-22.

Comparison of whole-exome sequencing methods: Damiati E, Borsani G, Giacopuzzi E. Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies. Hum Genet. 2016 May;135(5):499-511.

Comparison of variant callers: Liu X, Han S, Wang Z, Gelernter J, Yang BZ. Variant callers for next-generation sequencing data: a comparison study. PLoS One. 2013 Sep 27;8(9):e75619.

Comparison of variant callers: Hwang S, Kim E, Lee I, Marcotte EM. Systematic comparison of variant calling pipelines using gold standard personal exome variants. Sci Rep. 2015 Dec 7;5:17875.

EpiGenetics

BSP (Bisulfite sequencing): Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1827-31.

MSP (Methylation-Specific PCR): Herman JG, Graff JR, Myöhänen S, Nelkin BD, Baylin SB. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9821-6.

MS-HRM (Methylation-Sensitive High Resolution Melting): Wojdacz TK, Dobrovic A. Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res. 2007;35(6):e41.

dMS-HRM (digital MS-HRM): Candiloro IL, Mikeska T, Hokland P, Dobrovic A. Rapid analysis of heterogeneously methylated DNA using digital methylation-sensitive high resolution melting: application to the CDKN2B (p15) gene. Epigenetics Chromatin. 2008 Nov 3;1(1):7.

MethyLight: Eads CA, Danenberg KD, Kawakami K, Saltz LB, Blake C, Shibata D, Danenberg PV, Laird PW. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res. 2000 Apr 15;28(8):E32.

Pyrosequencing/Methylation: Colella S, Shen L, Baggerly KA, Issa JP, Krahe R. Sensitive and quantitative universal Pyrosequencing methylation analysis of CpG sites. Biotechniques. 2003 Jul;35(1):146-50.

Sequenom/Methylation: Ehrich M, Nelson MR, Stanssens P, Zabeau M, Liloglou T, Xinarianos G, Cantor CR, Field JK, van den Boom D. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15785-90.

Digital BSP: Chhibber A, Schroeder BG. Single-molecule polymerase chain reaction reduces bias: application to DNA methylation analysis by bisulfite sequencing. Anal Biochem. 2008 Jun 1;377(1):46-54.

Digital MS-HRM: Candiloro IL, Mikeska T, Hokland P, Dobrovic A. Rapid analysis of heterogeneously methylated DNA using digital methylation-sensitive high resolution melting: application to the CDKN2B (p15) gene. Epigenetics Chromatin. 2008 Nov 3;1(1):7.

Digital MethyLight: Weisenberger DJ, Trinh BN, Campan M, Sharma S, Long TI, Ananthnarayan S, Liang G, Esteva FJ, Hortobagyi GN, McCormick F, Jones PA, Laird PW. DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Res. 2008 Aug;36(14):4689-98.

MethylQuant: Thomassin H, Kress C, Grange T. MethylQuant: a sensitive method for quantifying methylation of specific cytosines within the genome. Nucleic Acids Res. 2004 Dec 2;32(21):e168.

MS-MLPA (Methylation-Specific MLPA): Nygren AO, Ameziane N, Duarte HM, Vijzelaar RN, Waisfisz Q, Hess CJ, Schouten JP, Errami A. Methylation-specific MLPA (MS-MLPA): simultaneous detection of CpG methylation and copy number changes of up to 40 sequences. Nucleic Acids Res. 2005 Aug 16;33(14):e128.

SMART-MSP (Sensitive Melting Analysis after Real Time- MSP): Kristensen LS, Mikeska T, Krypuy M, Dobrovic A. Sensitive Melting Analysis after Real Time- Methylation Specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection. Nucleic Acids Res. 2008 Apr;36(7):e42.

M-MethyLight (Multiplex MethyLight): He Q, Chen HY, Bai EQ, Luo YX, Fu RJ, He YS, Jiang J, Wang HQ. Development of a multiplex MethyLight assay for the detection of multigene methylation in human colorectal cancer. Cancer Genet Cytogenet. 2010 Oct 1;202(1):1-10.

Q-MSP (real-time Quantitative MSP): Lo YM, Wong IH, Zhang J, Tein MS, Ng MH, Hjelm NM. Quantitative analysis of aberrant p16 methylation using real-time quantitative methylation-specific polymerase chain reaction. Cancer Res. 1999 Aug 15;59(16):3899-903.

QM-MSP (Quantitative Multiplex-Methylation-Specific PCR): Fackler MJ, McVeigh M, Mehrotra J, Blum MA, Lange J, Lapides A, Garrett E, Argani P, Sukumar S. Quantitative multiplex methylation-specific PCR assay for the detection of promoter hypermethylation in multiple genes in breast cancer. Cancer Res. 2004 Jul 1;64(13):4442-52.

fast-COLD-MS-PCR: Castellanos-Rizaldos E, Milbury CA, Karatza E, Chen CC, Makrigiorgos GM, Merewood A. COLD-PCR Amplification of Bisulfite-Converted DNA Allows the Enrichment and Sequencing of Rare Un-Methylated Genomic Regions. PLoS One. 2014 Apr 11;9(4):e94103

COBRA (COmbined Bisulfite Restriction Analysis): Xiong Z, Laird PW. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res. 1997 Jun 15;25(12):2532-4.

N-MSP (Nested MSP): Palmisano WA, Divine KK, Saccomanno G, Gilliland FD, Baylin SB, Herman JG, Belinsky SA. Predicting lung cancer by detecting aberrant promoter methylation in sputum. Cancer Res. 2000 Nov 1;60(21):5954-8.

RSMA (Restriction enzyme-based Single-cell Methylation Assay): Kantlehner M, Kirchner R, Hartmann P, Ellwart JW, Alunni-Fabbroni M, Schumacher A. A high-throughput DNA methylation analysis of a single cell. Nucleic Acids Res. 2011 Apr;39(7):e44.

ASMM RTQ-PCR (Allele-Specific Methylated Multiplex Real-Time Quantitative PCR): Azzi S, Steunou V, Rousseau A, Rossignol S, Thibaud N, Danton F, Le Jule M, Gicquel C, Le Bouc Y, Netchine I. Allele-specific methylated multiplex real-time quantitative PCR (ASMM RTQ-PCR), a powerful method for diagnosing loss of imprinting of the 11p15 region in Russell Silver and Beckwith Wiedemann syndromes. Hum Mutat. 2011 Feb;32(2):249-58.

ConLight-MSP: Rand K, Qu W, Ho T, Clark SJ, Molloy P. Conversion-specific detection of DNA methylation using real-time polymerase chain reaction (ConLight-MSP) to avoid false positives. Methods. 2002 Jun;27(2):114-20.

MS-AP-PCR (Methylation-Sensitive AP-PCR): Gonzalgo ML, Liang G, Spruck CH 3rd, Zingg JM, Rideout WM 3rd, Jones PA. Identification and characterization of differentially methylated regions of genomic DNA by methylation-sensitive arbitrarily primed PCR. Cancer Res. 1997 Feb 15;57(4):594-9.

qMS-HRM: Migheli F, Stoccoro A, Coppedè F, Wan Omar WA, Failli A, Consolini R, Seccia M, Spisni R, Miccoli P, Mathers JC, Migliore L. Comparison study of MS-HRM and pyrosequencing techniques for quantification of APC and CDKN2A gene methylation. PLoS One. 2013;8(1):e52501.

LoMA-B (lab-on-a-chip system for DNA methylation analysis based on bisulfite conversion): Yoon J, Park MK, Lee TY, Yoon YJ, Shin Y. LoMA-B: a simple and versatile lab-on-a-chip system based on single-channel bisulfite conversion for DNA methylation analysis. Lab Chip. 2015 Sep 7;15(17):3530-9.

QuantiGene-Luminex: Kibriya MG, Jasmine F, Roy S, Ahsan H, Pierce B. Measurement of telomere length: a new assay using QuantiGene chemistry on a Luminex platform. Cancer Epidemiol Biomarkers Prev. 2014 Dec;23(12):2667-72.

QAMA (Quantitative Analysis of Methylated Alleles): Zeschnigk M, Böhringer S, Price EA, Onadim Z, Masshöfer L, Lohmann DR. A novel real-time PCR assay for quantitative analysis of methylated alleles (QAMA): analysis of the retinoblastoma locus. Nucleic Acids Res. 2004 Sep 7;32(16):e125.

MS-LAMP (Methylation-specific loop-mediated isothermal amplification): Zerilli F, Bonanno C, Shehi E, Amicarelli G, Adlerstein D, Makrigiorgos GM. Methylation-specific loop-mediated isothermal amplification for detecting hypermethylated DNA in simplex and multiplex formats. Clin Chem. 2010 Aug;56(8):1287-96.

DREAMing (Discrimination of Rare EpiAlleles by Melt): Pisanic TR 2nd, Athamanolap P, Poh W, Chen C, Hulbert A, Brock MV, Herman JG, Wang TH. DREAMing: a simple and ultrasensitive method for assessing intratumor epigenetic heterogeneity directly from liquid biopsies. Nucleic Acids Res. 2015 Dec 15;43(22):e154.

NBSP (normalized-BSP): Brisotto G, di Gennaro A, Damiano V, Armellin M, Perin T, Maestro R, Santarosa M. An improved sequencing-based strategy to estimate locus-specific DNA methylation. BMC Cancer. 2015 Sep 21;15:639.

MBRidge (MB-seq combined with ridge regression): Cai W, Mao F, Teng H, Cai T, Zhao F, Wu J, Sun ZS. MBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolution. J Mol Cell Biol. 2015 Aug;7(4):299-313.

MS-NaME (Methylation Specific Nuclease-assisted Minor-allele Enrichment): Liu Y, Song C, Ladas I, Fitarelli-Kiehl M, Makrigiorgos GM. Methylation-sensitive enrichment of minor DNA alleles using a double-strand DNA-specific nuclease. Nucleic Acids Res. 2017 Apr 7;45(6):e39.

DREAM (Digital Restriction Enzyme Analysis of Methylation): Jelinek J, Liang S, Lu Y, He R, Ramagli LS, Shpall EJ, Estecio MR, Issa JP. Conserved DNA methylation patterns in healthy blood cells and extensive changes in leukemia measured by a new quantitative technique. Epigenetics. 2012 Dec 1;7(12):1368-78.

ddPCR (Droplet digital PCR)-Methylation: Van Wesenbeeck L, Janssens L, Meeuws H, Lagatie O, Stuyver L. Droplet digital PCR is an accurate method to assess methylation status on FFPE samples. Epigenetics. 2018, in press.

ESPCR (end-specific PCR): Rand KN, Molloy PL. Sensitive measurement of unmethylated repeat DNA sequences by end-specific PCR. Biotechniques. 2010 Oct;49(4):xiii-xvii.

MS-D-HRMA (differential-high resolution melting analysis): Malentacchi F, Forni G, Vinci S, Orlando C. Quantitative evaluation of DNA methylation by optimization of a differential-high resolution melt analysis protocol. Nucleic Acids Res. 2009 Jul;37(12):e86.

MS-HDCR (helper-dependent chain reaction): Rand KN, Young GP, Ho T, Molloy PL. Sensitive and selective amplification of methylated DNA sequences using helper-dependent chain reaction in combination with a methylation-dependent restriction enzymes. Nucleic Acids Res. 2013 Jan 7;41(1):e15.

Two-step qMSP: Bianchessi V, Lauri A, Vigorelli V, Toia M, Vinci MC. Evaluating the methylation status of CXCR4 promoter: A cost-effective and sensitive two-step PCR method. Anal Biochem. 2017 Feb 15;519:84-91.

EpiHRMAssay: Cirilli M, Delfino I, Caboni E, Muleo R. EpiHRMAssay, in tube and in silico combined approach for the scanning and epityping of heterogeneous DNA methylation. Biol Meth and Protoc 2017; 2 (1): bpw008.

HELP assay (HpaII tiny fragment Enrichment by Ligation-mediated PCR): Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C, Hatchwell E, Selzer RR, Richmond TA, Green RD, Melnick A, Greally JM. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 2006 Aug;16(8):1046-55.

OBBPA-ddPCR (optimized bias based pre-amplification-digital droplet PCR): Menschikowski M, Jandeck C, Friedemann M, Nacke B, Hantsche S, Tiebel O, Sukocheva O, Hagelgans A. Identification of rare levels of methylated tumor DNA fragments using an optimized bias based pre-amplification-digital droplet PCR (OBBPA-ddPCR). Oncotarget. 2018 Nov 16;9(90):36137-36150.

COBRA-Seq: Varinli H, Statham AL, Clark SJ, Molloy PL, Ross JP. COBRA-Seq: Sensitive and Quantitative Methylome Profiling. Genes (Basel). 2015 Oct 23;6(4):1140-63.

QASM (quantitative analysis of single-base methylation): Yu H, Bai L, Tang G, Wang X, Huang M, Cao G, Wang J, Luo Y. Novel Assay for Quantitative Analysis of DNA Methylation at Single-Base Resolution. Clin Chem. 2019 May;65(5):664-673.

MethylationEPIC BeadChip: Pidsley R, Zotenko E, Peters TJ, Lawrence MG, Risbridger GP, Molloy P, Van Djik S, Muhlhausler B, Stirzaker C, Clark SJ. Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. Genome Biol. 2016 Oct 7;17(1):208.

Reduced Representation Bisulfite Sequencing (RRBS): Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005 Oct 13;33(18):5868-77.

Whole-genome bisulfite sequencing: Lister R, Pelizzola M, Dowen RH, ... , Thomson JA, Ren B, Ecker JR. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009 Nov 19;462(7271):315-22.

Illumina/Methylation: Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, Shen R, Gunderson KL. Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics. 2009 Oct;1(1):177-200.

Affymetrix/Methylation: Schumacher A, Kapranov P, Kaminsky Z, Flanagan J, Assadzadeh A, Yau P, Virtanen C, Winegarden N, Cheng J, Gingeras T, Petronis A. Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res. 2006 Jan 20;34(2):528-42.

MS-AFLP: Reyna-López GE, Simpson J, Ruiz-Herrera J. Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Mol Gen Genet. 1997 Feb 27;253(6):703-10.

mRRBS (multiplexed reduced representation bisulfite sequencing): Boyle P, Clement K, Gu H, Smith ZD, Ziller M, Fostel JL, Holmes L, Meldrim J, Kelley F, Gnirke A, Meissner A. Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome Biol. 2012 Oct 3;13(10):R92.

MeDIP-Seq and Ion Torrent: Corley MJ, Zhang W, Zheng X, Lum-Jones A, Maunakea AK. Semiconductor-based sequencing of genome-wide DNA methylation states. Epigenetics. 2015;10(2):153-66.

MLM (Methylation Ligation-dependent Macroarray): Guilleret I, Losi L, Chelbi ST, Fonda S, Bougel S, Saponaro S, Gozzi G, Alberti L, Braunschweig R, Benhattar J. DNA methylation profiling of esophageal adenocarcinoma using Methylation Ligation-dependent Macroarray (MLM). Biochem Biophys Res Commun. 2016 Oct 14;479(2):231-237.

Ion Torrent-Methylation: Pabinger S, Ernst K, Pulverer W, Kallmeyer R, Valdes AM, Metrustry S, Katic D, Nuzzo A, Kriegner A, Vierlinger K, Weinhaeusel A. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers. PLoS One. 2016 Jul 28;11(7):e0160227.

Reversal of PCR bias: Wojdacz TK, Hansen LL. Reversal of PCR bias for improved sensitivity of the DNA methylation melting curve assay. Biotechniques. 2006 Sep;41(3):274, 276, 278.

DNA methylation/visual detection: Li M, Zhang L, Chen G, Zhou J, Yuan Y, Zou J, Yuan M, Chen R, Du F, Cui X, Huang X, Dong J, Tang Z. DNAzyme based visual detection of DNA methylation. Chem Commun (Camb). 2018 Feb 13;54(14):1710-1713.

DNA methylation/Primer design: Fuso A, Ferraguti G, Scarpa S, Ferrer I, Lucarelli M. Disclosing bias in bisulfite assay: MethPrimers underestimate high DNA methylation. PLoS One. 2015 Feb 18;10(2):e0118318.

qPCR-Telomere length: Cawthon RM. Telomere measurement by quantitative PCR. Nucleic Acids Res. 2002 May 15;30(10):e47.

MMQPCR (Monochrome Multiplex Quantitative PCR)-Telomere length: Cawthon RM. Telomere length measurement by a novel monochrome multiplex quantitative PCR method. Nucleic Acids Res. 2009 Feb;37(3):e21.

Optimized protocol for Measuring Relative Telomere Length: Joglekar MV, Satoor SN, Wong WKM, Cheng F, Ma RCW, Hardikar AA. An Optimised Step-by-Step Protocol for . Methods Protoc. 2020 Apr 3;3(2):27.

A Method for measuring the shortest telomeres: Lai TP, Zhang N, Noh J, Mender I, Tedone E, Huang E, Wright WE, Danuser G, Shay JW. A method for measuring the distribution of the shortest telomeres in cells and tissues. Nat Commun. 2017 Nov 7;8(1):1356.

MMQPCR-Master mixes: Jiménez KM, Forero DA. Effect of master mixes on the measurement of telomere length by qPCR. Mol Biol Rep, in press.

ALT-qPCR (Alternative lengthening of telomeres-qPCR): Lau LM, Dagg RA, Henson JD, Au AY, Royds JA, Reddel RR. Detection of alternative lengthening of telomeres by telomere quantitative PCR. Nucleic Acids Res. 2013 Jan;41(2):e34.

PCR Assay for the Measurement of Mitochondrial DNA Content: Hsieh AYY, Budd M, Deng D, Gadawska I, Côté HCF. A Monochrome Multiplex Real-Time Quantitative PCR Assay for the Measurement of Mitochondrial DNA Content. J Mol Diagn. 2018 Sep;20(5):612-620.

Comparison of Methods: Quillien V, Lavenu A, Karayan-Tapon L, Carpentier C, Labussière M, Lesimple T, Chinot O, Wager M, Honnorat J, Saikali S, Fina F, Sanson M, Figarella-Branger D. Comparative assessment of 5 methods (methylation-specific polymerase chain reaction, MethyLight, pyrosequencing, methylation-sensitive high-resolution melting, and immunohistochemistry) to analyze O6-methylguanine-DNA-methyltranferase in a series of 100 glioblastoma patients. Cancer. 2012 Sep 1;118(17):4201-11.

Comparison of Methods: Akika R, Awada Z, Mogharbil N, Zgheib NK. Region of interest methylation analysis: a comparison of MSP with MS-HRM and direct BSP. Mol Biol Rep. 2017 Jul;44(3):295-305.

Comparison of Methods: Kacmarczyk TJ, Fall MP, Zhang X, Xin Y, Li Y, Alonso A, Betel D. "Same difference": comprehensive evaluation of four DNA methylation measurement platforms. Epigenetics Chromatin. 2018 May 25;11(1):21.

Comparison of Methods: Leontiou CA, Hadjidaniel MD, Mina P, Antoniou P, Ioannides M, Patsalis PC. Bisulfite Conversion of DNA: Performance Comparison of Different Kits and Methylation Quantitation of Epigenetic Biomarkers that Have the Potential to Be Used in Non-Invasive Prenatal Testing. PLoS One. 2015 Aug 6;10(8):e0135058.

Comparison of Methods: Holmes EE, Jung M, Meller S, Leisse A, Sailer V, Zech J, Mengdehl M, Garbe LA, Uhl B, Kristiansen G, Dietrich D. Performance evaluation of kits for bisulfite-conversion of DNA from tissues, cell lines, FFPE tissues, aspirates, lavages, effusions, plasma, serum, and urine. PLoS One. 2014 Apr 3;9(4):e93933.

Comparison of Methods: Cunningham JM, Johnson RA, Litzelman K, Skinner HG, Seo S, Engelman CD, Vanderboom RJ, Kimmel GW, Gangnon RE, Riegert-Johnson DL, Baron JA, Potter JD, Haile R, Buchanan DD, Jenkins MA, Rider DN, Thibodeau SN, Petersen GM, Boardman LA. Telomere length varies by DNA extraction method: implications for epidemiologic research. Cancer Epidemiol Biomarkers Prev. 2013 Nov;22(11):2047-54.

Comparison of Methods: Tolios A, Teupser D, Holdt LM. Preanalytical Conditions and DNA Isolation Methods Affect Telomere Length Quantification in Whole Blood. PLoS One. 2015 Dec 4;10(12):e0143889.

Comparison of Methods: Zanet DL, Saberi S, Oliveira L, Sattha B, Gadawski I, Côté HC. Blood and dried blood spot telomere length measurement by qPCR: assay considerations. PLoS One. 2013;8(2):e57787.

Comparison of Methods: Lai TP, Wright WE, Shay JW. Comparison of telomere length measurement methods. Philos Trans R Soc Lond B Biol Sci. 2018 Mar 5;373(1741):20160451.

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