GenotypingPortal4

Genotyping Portal

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

Reviews

General Reviews

Bayés M, Gut IG."Overview of genotyping". Molecular analysis and genome discovery: John Wiley & Sons, Ltd (2011): 1-23.

Ragoussis J. Genotyping technologies for genetic research. Annu Rev Genomics Hum Genet. 2009;10:117-33.

Ding C, Jin S. High-throughput methods for SNP genotyping. Methods Mol Biol. 2009;578:245-54

Voisey J, Morris CP. SNP technologies for drug discovery: a current review. Curr Drug Discov Technol. 2008 Sep;5(3):230-5.

Kim S, Misra A. SNP genotyping: technologies and biomedical applications. Annu Rev Biomed Eng. 2007;9:289-320.

Tsongalis GJ, Coleman WB. Clinical genotyping: the need for interrogation of single nucleotide polymorphisms and mutations in the clinical laboratory. Clin Chim Acta. 2006 Jan;363(1-2):127-37.

Sobrino B, Brión M, Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int. 2005 Nov 25;154(2-3):181-94.

Chen X, Sullivan PF. Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenomics J. 2003;3(2):77-96.

Dearlove AM. High throughput genotyping technologies. Brief Funct Genomic Proteomic. 2002 Jul;1(2):139-50.

Shi MM. Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies. Clin Chem. 2001 Feb;47(2):164-72.

Kwok PY. Methods for genotyping single nucleotide polymorphisms. Annu Rev Genomics Hum Genet. 2001;2:235-58.

Syvänen AC. Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet. 2001 Dec;2(12):930-42.

de Paula Careta F, Paneto GG. Recent patents on high-throughput single nucleotide polymorphism (SNP) genotyping methods. Recent Pat DNA Gene Seq. 2012 Aug;6(2):122-6.

How Kit A, Nielsen HM, Tost J. DNA methylation based biomarkers: practical considerations and applications. Biochimie. 2012 Nov;94(11):2314-37.

Gouas L, Goumy C, Véronèse L, Tchirkov A, Vago P. Gene dosage methods as diagnostic tools for the identification of chromosome abnormalities. Pathol Biol (Paris). 2008 Sep;56(6):345-53.

Specific Reviews

LaFramboise T. Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res. 2009 Jul;37 (13):4181-93.

Heather JM, Chain B. The sequence of sequencers: The history of sequencing DNA. Genomics. 2015 Nov 10. pii: S0888-7543(15)30041-0.

Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011 Sep 27;12(11):745-55.

Ke R, Mignardi M, Hauling T, Nilsson M. Fourth Generation of Next-Generation Sequencing Technologies: Promise and Consequences. Hum Mutat. 2016, in press.

Reon BJ, Dutta A. Biological Processes Discovered by High-Throughput Sequencing. Am J Pathol. 2016 Apr;186(4):722-32.

van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. Ten years of next-generation sequencing technology. Trends Genet. 2014 Sep;30(9):418-26.

Mardis ER. Next-generation sequencing platforms. Annu Rev Anal Chem (Palo Alto Calif). 2013;6:287-303.

Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER. The next-generation sequencing revolution and its impact on genomics. Cell. 2013 Sep 26;155(1):27-38.

Boland JF, Chung CC, Roberson D, Mitchell J, Zhang X, Im KM, He J, Chanock SJ, Yeager M, Dean M. The new sequencer on the block: comparison of Life Technology's Proton sequencer to an Illumina HiSeq for whole-exome sequencing. Hum Genet. 2013 Oct;132(10):1153-63.

Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010 Jan;11(1):31-46.

Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet. 2008 Mar;24(3):133-41.

Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 2008;9:387-02.

Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008 Oct;26(10):1135-45.

Stein LD. An introduction to the informatics of "next-generation" sequencing. Curr Protoc Bioinformatics. 2011 Dec;Chapter 11:Unit 11.1.

Spjuth O, Bongcam-Rudloff E, Dahlberg J, Dahlö M, Kallio A, Pireddu L, Vezzi F, Korpelainen E. Recommendations on e-infrastructures for next-generation sequencing. Gigascience. 2016 Jun 7;5:26.

Loose MW. The potential impact of nanopore sequencing on human genetics. Hum Mol Genet. 2017 Oct 1;26(R2):R202-R207.

Jain M, Olsen HE, Paten B, Akeson M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 2016 Nov 25;17(1):239.

Mardis ER. A decade's perspective on DNA sequencing technology. Nature. 2011 Feb 10;470(7333):198-203.

Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010 Jan;11(1):31-46.

Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet. 2011 Jun;12(6):443-51.

Shen Y, Wu BL. Designing a simple multiplex ligation-dependent probe amplification (MLPA) assay for rapid detection of copy number variants in the genome. J Genet Genomics. 2009 Apr;36(4):257-65.

Kubista M, Andrade JM, Bengtsson M, ..., Strömbom L, Ståhlberg A, Zoric N. The real-time polymerase chain reaction. Mol Aspects Med. 2006 Apr-Jun;27(2-3):95-125.

Gibson NJ. The use of real-time PCR methods in DNA sequence variation analysis. Clin Chim Acta. 2006 Jan;363(1-2):32-47.

Navarro E, Serrano-Heras G, Castaño MJ, Solera J. Real-time PCR detection chemistry. Clin Chim Acta. 2015 Jan 15;439:231-50.

Markoulatos P, Siafakas N, Moncany M. Multiplex polymerase chain reaction: a practical approach. J Clin Lab Anal. 2002;16(1):47-51.

Edwards MC, Gibbs RA. Multiplex PCR: advantages, development, and applications. PCR Methods Appl. 1994 Feb;3(4):S65-75.

Mauger F, How-Kit A, Tost J. COLD-PCR Technologies in the Area of Personalized Medicine: Methodology and Applications. Mol Diagn Ther. 2017 Jun;21(3):269-283.

Reed GH, Kent JO, Wittwer CT. High-resolution DNA melting analysis for simple and efficient molecular diagnostics.Pharmacogenomics. 2007 Jun;8(6):597-608.

Er TK, Chang JG. High-resolution melting: applications in genetic disorders. Clin Chim Acta. 2012 Dec 24;414:197-201.

Vossen RH, Aten E, Roos A, den Dunnen JT. High-resolution melting analysis (HRMA): more than just sequence variant screening. Hum Mutat. 2009 Jun;30(6):860-6.

Faltin B, Zengerle R, von Stetten F. Current methods for fluorescence-based universal sequence-dependent detection of nucleic acids in homogenous assays and clinical applications. Clin Chem. 2013 Nov;59(11):1567-82.

Dunbar SA. Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection. Clin Chim Acta. 2006 Jan;363(1-2):71-82.

Sham P, Bader JS, Craig I, O'Donovan M, Owen M. DNA Pooling: a tool for large-scale association studies. Nat Rev Genet. 2002 Nov;3(11):862-71.

Lovmar L, Syvänen AC. Multiple displacement amplification to create a long-lasting source of DNA for genetic studies. Hum Mutat. 2006 Jul;27(7):603-14.

Steinberg K, Beck J, Nickerson D, ..., Hannon H, Khoury MJ, Sampson E. DNA banking for epidemiologic studies: a review of current practices. Epidemiology. 2002 May;13(3):246-54.

Steinberg KK, Sanderlin KC, Ou CY, Hannon WH, McQuillan GM, Sampson EJ. DNA banking in epidemiologic studies. Epidemiol Rev. 1997;19(1):156-62.

Hernández HG, Tse MY, Pang SC, Arboleda H, Forero DA. Optimizing methodologies for PCR-based DNA methylation analysis. Biotechniques. 2013 Oct;55(4):181-97.

Kurdyukov S, Bullock M. DNA Methylation Analysis: Choosing the Right Method. Biology (Basel). 2016 Jan 6;5(1).

Bock C. Analysing and interpreting DNA methylation data. Nat Rev Genet. 2012 Oct;13(10):705-19.

Shanmuganathan R, Basheer NB, Amirthalingam L, Muthukumar H, Kaliaperumal R, Shanmugam K. Conventional and nanotechniques for DNA methylation profiling. J Mol Diagn. 2013 Jan;15(1):17-26.

Gupta R, Nagarajan A, Wajapeyee N. Advances in genome-wide DNA methylation analysis. Biotechniques. 2010 Oct;49(4):iii-xi.

Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet. 2010 Mar;11(3):191-203.

Derks S, Lentjes MH, Hellebrekers DM, de Bruïne AP, Herman JG, van Engeland M. Methylation-specific PCR unraveled. Cell Oncol. 2004;26(5-6):291-9.

Hussmann D, Hansen LL. Methylation-Sensitive High Resolution Melting (MS-HRM). Methods Mol Biol. 2018;1708:551-571.

Moelans CB, Atanesyan L, Savola SP, van Diest PJ. Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA). Methods Mol Biol. 2018;1708:537-549.

Michels KB, Binder AM. Considerations for Design and Analysis of DNA Methylation Studies. Methods Mol Biol. 2018;1708:31-46.

Beikircher G, Pulverer W, Hofner M, Noehammer C, Weinhaeusel A. Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes "MSRE-qPCR". Methods Mol Biol. 2018;1708:407-424.

Busato F, Dejeux E, El Abdalaoui H, Gut IG, Tost J. Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing®. Methods Mol Biol. 2018;1708:427-445.

Ramalho-Carvalho J, Henrique R, Jerónimo C. Methylation-Specific PCR. Methods Mol Biol. 2018;1708:447-472.

Fackler MJ, Sukumar S. Quantitation of DNA Methylation by Quantitative Multiplex Methylation-Specific PCR (QM-MSP) Assay. Methods Mol Biol. 2018;1708:473-496.

Mitchell SM, Rand KN, Xu ZZ, Ho T, Brown GS, Ross JP, Molloy PL. Helper-Dependent Chain Reaction (HDCR) for Selective Amplification of Methylated DNA Sequences. Methods Mol Biol. 2018;1708:587-601.

Campan M, Weisenberger DJ, Trinh B, Laird PW. MethyLight and Digital MethyLight. Methods Mol Biol. 2018;1708:497-513.

Kunze S. Quantitative Region-Specific DNA Methylation Analysis by the EpiTYPER™ Technology. Methods Mol Biol. 2018;1708:515-535.

Schrey AW, Alvarez M, Foust CM, Kilvitis HJ, Lee JD, Liebl AL, Martin LB, Richards CL, Robertson M. Ecological Epigenetics: Beyond MS-AFLP. Integr Comp Biol. 2013 Aug;53(2):340-50.

Moelans CB, Atanesyan L, Savola SP, van Diest PJ. Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA). Methods Mol Biol. 2018;1708:537-549.

Montpetit AJ, Alhareeri AA, Montpetit M, Starkweather AR, Elmore LW, Filler K, Mohanraj L, Burton CW, Menzies VS, Lyon DE, Jackson-Cook CK. Telomere length: a review of methods for measurement. Nurs Res. 2014 Jul-Aug;63(4):289-99.

Lustig AJ. Potential Risks in the Paradigm of Basic to Translational Research: A Critical Evaluation of qPCR Telomere Size Techniques. J Cancer Epidemiol Treat. 2015;1(1):28-37.

Hendling M, Barišić I. In-silico Design of DNA Oligonucleotides: Challenges and Approaches. Comput Struct Biotechnol J. 2019 Jul 29;17:1056-1065.

Bartlett J, Stirling D (Eds.) (2003). PCR protocols (Vol. 226). Totowa NJ USA: Humana Press.

Chuang LY, Cheng YH, Yang CH. Specific primer design for the polymerase chain reaction. Biotechnol Lett. 2013 Oct;35(10):1541-9.

Dieffenbach CW, Lowe TM, Dveksler GS. General concepts for PCR primer design. PCR Methods Appl. 1993 Dec;3(3):S30-7.

Singh, V. K., & Kumar, A. (2001). PCR primer design. Mol. Biol. Today, 2, 27-32.

Abd-Elsalam KA. Bioinformatic tools and guideline for PCR primer design. Afr J Biotechnol 2003; 2(5): 91-95.

Bustin SA. How to speed up the polymerase chain reaction. Biomol Detect Quantif. 2017 Jun 20;12:10-14.

Morley AA. Digital PCR: A brief history. Biomol Detect Quantif. 2014 Aug 15;1(1):1-2.

Cao L, Cui X, Hu J, Li Z, Choi JR, Yang Q, Lin M, Ying Hui L, Xu F. Advances in digital polymerase chain reaction (dPCR) and its emerging biomedical applications. Biosens Bioelectron. 2017 Apr 15;90:459-474.

Miller JR, Andre R. Quantitative polymerase chain reaction. Br J Hosp Med (Lond). 2014 Dec;75(12):C188-92.

Kalle E, Kubista M, Rensing C. Multi-template polymerase chain reaction. Biomol Detect Quantif. 2014 Dec 4;2:11-29.

Gadkar Vy, Filion M. New Developments in Quantitative Real-time Polymerase Chain Reaction Technology. Curr Issues Mol Biol. 2014;16:1-6.

Nagy B. Application of real-time polymerase chain reaction in the clinical genetic practice. J Pediatr Genet. 2013 Mar;2(1):1-8.

Garcia JG, Ma SF. Polymerase chain reaction: a landmark in the history of gene technology. Crit Care Med. 2005 Dec;33(12 Suppl):S429-32.

McDowell D. The polymerase chain reaction patents: going, going,... still going. J R Soc Med. 2006 Feb;99(2):62-4.

Powledge TM. The polymerase chain reaction. Adv Physiol Educ. 2004 Dec;28(1-4):44-50.

Wilhelm J, Pingoud A. Real-time polymerase chain reaction. Chembiochem. 2003 Nov 7;4(11):1120-8.

Arya M, Shergill IS, Williamson M, Gommersall L, Arya N, Patel HR. Basic principles of real-time quantitative PCR. Expert Rev Mol Diagn. 2005 Mar;5(2):209-19.

Bustin S, Huggett J. qPCR primer design revisited. Biomol Detect Quantif. 2017 Nov 22;14:19-28.

Wang X, Spandidos A, Wang H, Seed B. PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update. Nucleic Acids Res. 2012 Jan;40(Database issue):D1144-9.

Lefever S, Vandesompele J, Speleman F, Pattyn F. RTPrimerDB: the portal for real-time PCR primers and probes. Nucleic Acids Res. 2009 Jan;37(Database issue):D942-5.

Pabinger S, Rödiger S, Kriegner A, Vierlinger K, Weinhäusel A. A survey of tools for the analysis of quantitative PCR (qPCR) data. Biomol Detect Quantif. 2014 Sep 6;1(1):23-33.

Medrano RF, de Oliveira CA. Guidelines for the tetra-primer ARMS-PCR technique development. Mol Biotechnol. 2014 Jul;56(7):599-608.

Kumar A, Chordia N. In silico PCR primer designing and validation. Methods Mol Biol. 2015;1275:143-51.

Chavali S, Mahajan A, Tabassum R, Maiti S, Bharadwaj D. Oligonucleotide properties determination and primer designing: a critical examination of predictions. Bioinformatics. 2005 Oct 15;21(20):3918-25.

Schrader C, Schielke A, Ellerbroek L, Johne R. PCR inhibitors - occurrence, properties and removal. J Appl Microbiol. 2012 Nov;113(5):1014-26.

Terpe K. Overview of thermostable DNA polymerases for classical PCR applications: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol. 2013 Dec;97(24):10243-54.

Fore J Jr, Wiechers IR, Cook-Deegan R. The effects of business practices, licensing, and intellectual property on development and dissemination of the polymerase chain reaction: case study. J Biomed Discov Collab. 2006 Jul 3;1:7.

Almassian DR, Cockrell LM, Nelson WM. Portable nucleic acid thermocyclers. Chem Soc Rev. 2013 Nov 21;42(22):8769-98.

Ahmad F, Hashsham SA. Miniaturized nucleic acid amplification systems for rapid and point-of-care diagnostics: a review. Anal Chim Acta. 2012 Jul 6;733:1-15.

Rajendran VK, Bakthavathsalam P, Bergquist PL, Sunna A. Smartphone technology facilitates point-of-care nucleic acid diagnosis: a beginner's guide. Crit Rev Clin Lab Sci. 2020, in press.

Miao G, Zhang L, Zhang J, Ge S, Xia N, Qian S, Yu D, Qiu X. Free convective PCR: From principle study to commercial applications-A critical review. Anal Chim Acta. 2020 Apr 29;1108:177-197

Mifflin TE. Setting up a PCR laboratory. CSH Protoc. 2007 Jul 1;2007:pdb.top14.

Dieffenbach CW, Dveksler GS. Setting up a PCR laboratory. PCR Methods Appl. 1993 Oct;3(2):S2-7.

Lo YM, Chan KC. Setting up a polymerase chain reaction laboratory. Methods Mol Biol. 2006;336:11-8.

Aslanzadeh J. Preventing PCR amplification carryover contamination in a clinical laboratory. Ann Clin Lab Sci. 2004 Autumn;34(4):389-96.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015 May;17(5):405-24.

Bruford EA, Braschi B, Denny P, Jones TEM, Seal RL, Tweedie S. Guidelines for human gene nomenclature. Nat Genet. 2020 Aug;52(8):754-758.

Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. EMBO J. 2020 Mar 16;39(6):e103777.

den Dunnen JT, Antonarakis SE. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat. 2000;15(1):7-12.

Protocols

Bustin SA, Mueller R, Nolan T. Parameters for Successful PCR Primer Design. Methods Mol Biol. 2020;2065:5-22.

Rodríguez A, Rodríguez M, Córdoba JJ, Andrade MJ. Design of primers and probes for quantitative real-time PCR methods. Methods Mol Biol. 2015;1275:31-56.

Singh A, Pandey GK. Primer design using Primer Express® for SYBR Green-based quantitative PCR. Methods Mol Biol. 2015;1275:153-64.

Thornton B, Basu C. Rapid and simple method of qPCR primer design. Methods Mol Biol. 2015;1275:173-9.

Thornton B, Basu C. Real-time PCR (qPCR) primer design using free online software. Biochem Mol Biol Educ. 2011 Mar-Apr;39(2):145-54.

Henegariu O, Heerema NA, Dlouhy SR, Vance GH, Vogt PH. Multiplex PCR: critical parameters and step-by-step protocol. Biotechniques. 1997 Sep;23(3):504-11.

Velasco E, Infante M, Durán M, Pérez-Cabornero L, Sanz DJ, Esteban-Cardeñosa E, Miner C. Heteroduplex analysis by capillary array electrophoresis for rapid mutation detection in large multiexon genes. Nat Protoc. 2007;2(1):237-46.

Chen R, Im H, Snyder M. Whole-Exome Enrichment with the Roche NimbleGen SeqCap EZ Exome Library SR Platform. Cold Spring Harb Protoc. 2015 Mar 11;2015(7):634-41.

Ellis JA, Ong B. The MassARRAY(®) System for Targeted SNP Genotyping. Methods Mol Biol. 2017;1492:77-94.

Hui L, DelMonte T, Ranade K. Genotyping using the TaqMan assay. Curr Protoc Hum Genet. 2008 Jan;Chapter 2:Unit 2.10.

Shen GQ, Abdullah KG, Wang QK. The TaqMan method for SNP genotyping. Methods Mol Biol. 2009;578:293-306.

Mayo P, Hartshorne T, Li K, McMunn-Gibson C, Spencer K, Schnetz-Boutaud N. CNV analysis using TaqMan copy number assays. Curr Protoc Hum Genet. 2010 Oct;Chapter 2:Unit2.13.

Gasser RB, Hu M, Chilton NB, Campbell BE, Jex AJ, Otranto D, Cafarchia C, Beveridge I, Zhu X. Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation. Nat Protoc. 2006;1(6):3121-8.

Larsen LA, Jespersgaard C, Andersen PS. Single-strand conformation polymorphism analysis using capillary array electrophoresis for large-scale mutation detection. Nat Protoc. 2007;2(6):1458-66.

Royo JL, Hidalgo M, Ruiz A. Pyrosequencing protocol using a universal biotinylated primer for mutation detection and SNP genotyping. Nat Protoc. 2007;2(7):1734-9.

Lavebratt C, Sengul S. Single nucleotide polymorphism (SNP) allele frequency estimation in DNA pools using Pyrosequencing. Nat Protoc. 2006;1(6):2573-82.

Montgomery J, Wittwer CT, Palais R, Zhou L. Simultaneous mutation scanning and genotyping by high-resolution DNA melting analysis. Nat Protoc. 2007;2(1):59-66.

Erali M, Wittwer CT. High resolution melting analysis for gene scanning. Methods. 2010 Apr;50(4):250-61.

Mori Y, Kanda H, Notomi T. Loop-mediated isothermal amplification (LAMP): recent progress in research and development. J Infect Chemother. 2013 Jun;19(3):404-11.

Barany F. The ligase chain reaction in a PCR world. PCR Methods Appl. 1991 Aug;1(1):5-16.

Fakruddin M, Mannan KS, Chowdhury A, Mazumdar RM, Hossain MN, Islam S, Chowdhury MA. Nucleic acid amplification: Alternative methods of polymerase chain reaction. J Pharm Bioallied Sci. 2013 Oct;5(4):245-52.

Asiello PJ, Baeumner AJ. Miniaturized isothermal nucleic acid amplification, a review. Lab Chip. 2011 Apr 21;11(8):1420-30.

Craw P, Balachandran W. Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review. Lab Chip. 2012 Jul 21;12(14):2469-86.

Clark SJ, Statham A, Stirzaker C, Molloy PL, Frommer M. DNA methylation: bisulphite modification and analysis. Nat Protoc. 2006;1(5):2353-64.

Wojdacz TK, Dobrovic A, Hansen LL. Methylation-sensitive high-resolution melting. Nat Protoc. 2008;3(12):1903-8.

Patterson K, Molloy L, Qu W, Clark S. DNA methylation: bisulphite modification and analysis. J Vis Exp. 2011 Oct 21;(56). pii: 3170.

Wu MC, Kuan PF. A Guide to Illumina BeadChip Data Analysis. Methods Mol Biol. 2018;1708:303-330.

Sigalotti L, Covre A, Colizzi F, Fratta E. Quantitative Methylation-Specific PCR: A Simple Method for Studying Epigenetic Modifications of Cell-Free DNA. Methods Mol Biol. 2019;1909:137-162.

Wani K, Aldape KD. PCR Techniques in Characterizing DNA Methylation. Methods Mol Biol. 2016;1392:177-86.

Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3(6):1101-8.

Bagasra O. Protocols for the in situ PCR-amplification and detection of mRNA and DNA sequences. Nat Protoc. 2007;2(11):2782-95.

Korbie DJ, Mattick JS. Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nat Protoc. 2008;3(9):1452-6.

Kimura M, Stone RC, Hunt SC, Skurnick J, Lu X, Cao X, Harley CB, Aviv A. Measurement of telomere length by the Southern blot analysis of terminal restriction fragment lengths. Nat Protoc. 2010 Sep;5(9):1596-607.

Axelrad MD, Budagov T, Atzmon G. Telomere length and telomerase activity; a Yin and Yang of cell senescence. J Vis Exp. 2013 May 22;(75):e50246.

Canela A, Klatt P, Blasco MA. Telomere length analysis. Methods Mol Biol. 2007;371:45-72.

Ota M, Fukushima H, Kulski JK, Inoko H. Single nucleotide polymorphism detection by polymerase chain reaction-restriction fragment length polymorphism. Nat Protoc. 2007;2(11):2857-64.

Tomita N, Mori Y, Kanda H, Notomi T. Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nat Protoc. 2008;3(5):877-82.

Frey UH, Bachmann HS, Peters J, Siffert W. PCR-amplification of GC-rich regions: 'slowdown PCR'. Nat Protoc. 2008;3(8):1312-7.

Lang BF, Burger G. Purification of mitochondrial and plastid DNA. Nat Protoc. 2007;2(3):652-60.

Pikor LA, Enfield KS, Cameron H, Lam WL. DNA extraction from paraffin embedded material for genetic and epigenetic analyses. J Vis Exp. 2011 Mar 26;(49).

O'Grady A, Cummins R. Somatic DNA Mutation Analysis. Methods Mol Biol. 2017;1606:219-233.

Sauer S, Reinhardt R, Lehrach H, Gut IG. Single-nucleotide polymorphisms: analysis by mass spectrometry. Nat Protoc. 2006;1(4):1761-71.

Raymaekers M, Smets R, Maes B, Cartuyvels R. Checklist for optimization and validation of real-time PCR assays. J Clin Lab Anal. 2009;23(3):145-51.

Little J, Higgins JP, Ioannidis JP, ..., Infante-Rivard C, Stewart A, Birkett N. Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE Statement. Hum Genet. 2009 Mar;125(2):131-51.

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009 Apr;55(4):611-22.

dMIQE Group, Huggett JF. The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020. Clin Chem. 2020 Aug 1;66(8):1012-1029.

Huang J, Mirel D, Pugh E, Xing C, Robinson PN, Pertsemlidis A, Ding L, Kozlitina J, Maher J, Rios J, Story M, Marthandan N, Scheuermann RH. Minimum Information about a Genotyping Experiment (MIGEN). Stand Genomic Sci. 2011 Nov 30;5(2):224-9.

References tagged in citeulike