GenotypingPortal1

Genotyping Portal

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

SNP Genotyping

SNP Arrays-Affymetrix: Kennedy GC, Matsuzaki H, Dong S, Liu WM, Huang J, Liu G, Su X, Cao M, Chen W, Zhang J, Liu W, Yang G, Di X, Ryder T, He Z, Surti U, Phillips MS, Boyce-Jacino MT, Fodor SP, Jones KW. Large-scale genotyping of complex DNA. Nat Biotechnol. 2003 Oct;21(10):1233-7.

SNP Arrays-Illumina: Gunderson KL, Steemers FJ, Lee G, Mendoza LG, Chee MS. A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet. 2005 May;37(5):549-54.

Sequenom: Tang K, Fu DJ, Julien D, Braun A, Cantor CR, Köster H. Chip-based genotyping by mass spectrometry. Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10016-20.

TaqMan: Livak KJ, Marmaro J, Todd JA. Towards fully automated genome-wide polymorphism screening. Nat Genet. 1995 Apr;9(4):341-2.

HRM (High-Resolution Melting): Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ. High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem. 2003 Jun;49(6 Pt 1):853-60.

M-HRM (Multiplex HRM): Seipp MT, Pattison D, Durtschi JD, Jama M, Voelkerding KV, Wittwer CT. Quadruplex genotyping of F5, F2, and MTHFR variants in a single closed tube by high-resolution amplicon melting. Clin Chem. 2008 Jan;54(1):108-15.

PCR-RFLP (Restriction Fragment Lenght Polymorphism): Deng GR. A sensitive non-radioactive PCR-RFLP analysis for detecting point mutations at 12th codon of oncogene c-Ha-ras in DNAs of gastric cancer. Nucleic Acids Res. 1988 Jul 11;16(13):6231.

PCR-ASO (Allele-Specific Oligonucleotide): Farr CJ, Saiki RK, Erlich HA, McCormick F, Marshall CJ. Analysis of RAS gene mutations in acute myeloid leukemia by polymerase chain reaction and oligonucleotide probes. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1629-33.

PCR-OLA (Oligonucleotide Ligation Assay): Nickerson DA, Kaiser R, Lappin S, Stewart J, Hood L, Landegren U. Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay. Proc Natl Acad Sci U S A. 1990 Nov;87(22):8923-7.

PCR-PIRA (Primer Introduced Restriction Analysis): Jacobson DR, Moskovits T. Rapid, nonradioactive screening for activating ras oncogene mutations using PCR-primer introduced restriction analysis (PCR-PIRA). PCR Methods Appl. 1991 Nov;1(2):146-8.

ARMS-PCR (Amplification Refractory Mutation System): Newton CR, Graham A, Heptinstall LE, Powell SJ, Summers C, Kalsheker N, Smith JC, Markham AF. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 1989 Apr 11;17(7):2503-16.

Fluorescence-labelled multiplex ARMS-PCR: Lubin IM, Yamada NA, Stansel RM, Pace RG, Rohlfs EM, Silverman LM. HFE genotyping using multiplex allele-specific polymerase chain reaction and capillary electrophoresis. Arch Pathol Lab Med. 1999 Dec;123(12):1177-81.

ARMS-qPCR: Bai RK, Wong LJ. Detection and quantification of heteroplasmic mutant mitochondrial DNA by real-time amplification refractory mutation system quantitative PCR analysis: a single-step approach. Clin Chem. 2004 Jun;50(6):996-1001.

TD-ARMS-qPCR (Touchdown ARMS-qPCR): Wu WM, Tsai HJ, Pang JH, Wang HS, Hong HS, Lee YS. Touchdown thermocycling program enables a robust single nucleotide polymorphism typing method based on allele-specific real-time polymerase chain reaction. Anal Biochem. 2005 Apr 15;339(2):290-6.

Tetra-primer ARMS-PCR: Ye S, Dhillon S, Ke X, Collins AR, Day IN. An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Res. 2001 Sep 1;29(17):E88-8.

Multiplex Tetra-Primer ARMS-PCR: Piccioli P, Serra M, Gismondi V, Pedemonte S, Loiacono F, Lastraioli S, Bertario L, De Angioletti M, Varesco L, Notaro R. Multiplex tetra-primer amplification refractory mutation system PCR to detect 6 common germline mutations of the MUTYH gene associated with polyposis and colorectal cancer. Clin Chem. 2006 Apr;52(4):739-43.

M-T-ARMS-PCR-CE: Zhang C, Liu Y, Ring BZ, Nie K, Yang M, Wang M, Shen H, Wu X, Ma X. A novel multiplex tetra-primer ARMS-PCR for the simultaneous genotyping of six single nucleotide polymorphisms associated with female cancers. PLoS One. 2013 Apr 17;8(4):e62126.

Bi-PASA (Bidirectional PCR Amplification of Specific Alleles): Liu Q, Thorland EC, Heit JA, Sommer SS. Overlapping PCR for bidirectional PCR amplification of specific alleles: a rapid one-tube method for simultaneously differentiating homozygotes and heterozygotes. Genome Res. 1997 Apr;7(4):389-98.

PCR-DASH (Dynamic Allele-Specific Hybridization): Prince JA, Feuk L, Howell WM, Jobs M, Emahazion T, Blennow K, Brookes AJ. Robust and accurate single nucleotide polymorphism genotyping by dynamic allele-specific hybridization (DASH): design criteria and assay validation. Genome Res. 2001 Jan;11(1):152-62.

Pyrosequencing: Ronaghi M, Karamohamed S, Pettersson B, Uhlén M, Nyrén P. Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem. 1996 Nov 1;242(1):84-9.

Molecular Beacons: Marras SA, Kramer FR, Tyagi S. Multiplex detection of single-nucleotide variations using molecular beacons. Genet Anal. 1999 Feb;14(5-6):151-6.

FP-TDI (fluorescence polarization-template directed dye terminator incorporation): Chen X, Levine L, Kwok PY. Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res. 1999 May;9(5):492-8.

Invader Assay: Mein CA, Barratt BJ, Dunn MG, Siegmund T, Smith AN, Esposito L, Nutland S, Stevens HE, Wilson AJ, Phillips MS, Jarvis N, Law S, de Arruda M, Todd JA. Evaluation of single nucleotide polymorphism typing with invader on PCR amplicons and its automation. Genome Res. 2000 Mar;10(3):330-43.

xMAP: Ye F, Li MS, Taylor JD, Nguyen Q, Colton HM, Casey WM, Wagner M, Weiner MP, Chen J. Fluorescent microsphere-based readout technology for multiplexed human single nucleotide polymorphism analysis and bacterial identification. Hum Mutat. 2001 Apr;17(4):305-16.

SNaPshot: Pati N, Schowinsky V, Kokanovic O, Magnuson V, Ghosh S. A comparison between SNaPshot, pyrosequencing, and biplex invader SNP genotyping methods: accuracy, cost, and throughput. J Biochem Biophys Methods. 2004 Jul 30;60(1):1-12.

SNPlex: Tobler AR, Short S, Andersen MR, Paner TM, Briggs JC, Lambert SM, Wu PP, Wang Y, Spoonde AY, Koehler RT, Peyret N, Chen C, Broomer AJ, Ridzon DA, Zhou H, Hoo BS, Hayashibara KC, Leong LN, Ma CN, Rosenblum BB, Day JP, Ziegle JS, De La Vega FM, Rhodes MD, Hennessy KM, Wenz HM. The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping. J Biomol Tech. 2005 Dec;16(4):398-406.

GOOD Assay: Sauer S, Lechner D, Berlin K, Lehrach H, Escary JL, Fox N, Gut IG. A novel procedure for efficient genotyping of single nucleotide polymorphisms. Nucleic Acids Res. 2000 Mar 1;28(5):E13.

SNPWave: van Eijk MJ, Broekhof JL, van der Poel HJ, Hogers RC, Schneiders H, Kamerbeek J, Verstege E, van Aart JW, Geerlings H, Buntjer JB, van Oeveren AJ, Vos P. SNPWave: a flexible multiplexed SNP genotyping technology. Nucleic Acids Res. 2004 Mar 5;32(4):e47.

ALM-ASA (Adapter Ligation-Mediated Allele-specific Amplification): Wang WP, Ni KY, Zhou GH. Multiplex single nucleotide polymorphism genotyping by adapter ligation-mediated allele-specific amplification. Anal Biochem. 2006 Aug 15;355(2):240-8.

PCR-CTPP (PCR with Confronting Two-Pair Primers): Hamajima N, Saito T, Matsuo K, Tajima K. Competitive amplification and unspecific amplification in polymerase chain reaction with confronting two-pair primers. J Mol Diagn. 2002 May;4(2):103-7.

Melt-MAMA (Melt analysis of Mismatch Amplification Mutation Assays): Germer S, Higuchi R. Single-tube genotyping without oligonucleotide probes. Genome Res. 1999 Jan;9(1):72-8.

McSNP (Melting curve SNP): Ye J, Parra EJ, Sosnoski DM, Hiester K, Underhill PA, Shriver MD. Melting curve SNP (McSNP) genotyping: a useful approach for diallelic genotyping in forensic science. J Forensic Sci. 2002 May;47(3):593-600.

Tetra-Primer PCR (TP-PCR): Ye S, Humphries S, Green F. Allele specific amplification by tetra-primer PCR. Nucleic Acids Res. 1992 Mar 11;20(5):1152.

SNP-SCALE (SNP Scoring by Colour And Length Exclusion): Hinten GN, Hale MC, Gratten J, Mossman JA, Lowder GN, Mann MK, Slate J. SNP SCALE: SNP scoring by colour and length exclusion. Mol Ecol Notes 2007;7:377-88.

Multiplex SNP-SCALE: Kenta T, Gratten J, Haigh NS, Hinten GN, Slate J, Butlin RK, Burke T. Multiplex SNP-SCALE: a cost-effective medium-throughput single nucleotide polymorphism genotyping method. Mol Ecol Resour. 2008 Nov;8(6):1230-8.

TSP (Temperature Switch PCR ): Tabone T, Mather DE, Hayden MJ. Temperature switch PCR (TSP): Robust assay design for reliable amplification and genotyping of SNPs. BMC Genomics. 2009 Dec 3;10:580.

Bi-ASA (BiDirectional Allele-Specific Amplification): Waterfall CM, Cobb BD. Single tube genotyping of sickle cell anaemia using PCR-based SNP analysis. Nucleic Acids Res. 2001 Dec 1;29(23):E119.

ASB-PCR (Allele-Specific Blocker PCR): Morlan J, Baker J, Sinicropi D. Mutation detection by real-time PCR: a simple, robust and highly selective method. PLoS One. 2009;4(2):e4584.

D-PCR-A (Divergent PCR Assay): Gentilini F, Turba ME. Two novel real-time PCR methods for genotyping the von Willebrand disease type I mutation in Doberman Pinscher dogs. Vet J. 2013 Aug 1. doi:pii: S1090-0233(13)00085-3.

BAMPER (Bioluminometric Assay coupled with Modified Primer Extension Reactions): Zhou GH, Shirakura H, Kamahori M, Okano K, Nagai K, Kambara H. A gel-free SNP genotyping method: bioluminometric assay coupled with modified primer extension reactions (BAMPER) directly from double-stranded PCR products. Hum Mutat. 2004 Aug;24(2):155-63.

MIP (Molecular Inversion Probe): Hardenbol P, Yu F, Belmont J, Mackenzie J, Bruckner C, Brundage T, Boudreau A, Chow S, Eberle J, Erbilgin A, Falkowski M, Fitzgerald R, Ghose S, Iartchouk O, Jain M, Karlin-Neumann G, Lu X, Miao X, Moore B, Moorhead M, Namsaraev E, Pasternak S, Prakash E, Tran K, Wang Z, Jones HB, Davis RW, Willis TD, Gibbs RA. Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res. 2005 Feb;15(2):269-75.

MIP (Molecular Inversion Probe): Hardenbol P, Banér J, Jain M, Nilsson M, Namsaraev EA, Karlin-Neumann GA, Fakhrai-Rad H, Ronaghi M, Willis TD, Landegren U, Davis RW. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol. 2003 Jun;21(6):673-8.

PrASE (Protease-mediated Allele-Specific Extension): Käller M, Hultin E, Holmberg K, Persson ML, Odeberg J, Lundeberg J, Ahmadian A. Comparison of PrASE and Pyrosequencing for SNP Genotyping. BMC Genomics. 2006 Nov 16;7:291.

ADLAPH (Allele-Discriminating Long and Accurate PCR Haplotyping): Yu CE, Devlin B, Galloway N, Loomis E, Schellenberg GD. ADLAPH: A molecular haplotyping method based on allele-discriminating long-range PCR. Genomics. 2004 Sep;84(3):600-12.

T-Plex RT PCR assay: Baris I, Etlik O, Koksal V, Ocak Z, Baris ST. SYBR green dye-based probe-free SNP genotyping: Introduction of T-Plex real-time PCR assay. Anal Biochem. 2013 Jul 16;441(2):225-231.

BEAMing: Dressman D, Yan H, Traverso G, Kinzler KW, Vogelstein B. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):8817-22.

Multiplex-FRET-Melt: Nicklas JA, Buel E. A real-time multiplex SNP melting assay to discriminate individuals. J Forensic Sci. 2008 Nov;53(6):1316-24.

Multiplex Tetra-Primer ARMS-PCR-CE: Zhang C, Liu Y, Ring BZ, Nie K, Yang M, Wang M, Shen H, Wu X, Ma X. A novel multiplex tetra-primer ARMS-PCR for the simultaneous genotyping of six single nucleotide polymorphisms associated with female cancers. PLoS One. 2013 Apr 17;8(4):e62126.

KASPar (allele-specific PCR amplification of target sequences and endpoint fluorescence genotyping): Smith SM, Maughan PJ. SNP genotyping using KASPar assays. Methods Mol Biol. 2015;1245:243-56.

MARA (Multiplexed Anchored Runoff Amplification): Shapero MH, Zhang J, Loraine A, Liu W, Di X, Liu G, Jones KW. MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays. Nucleic Acids Res. 2004 Dec 15;32(22):e181.

PCR/LDR (multiplex polymerase chain reaction/ligase detection reaction): Khanna M, Park P, Zirvi M, Cao W, Picon A, Day J, Paty P, Barany F. Multiplex PCR/LDR for detection of K-ras mutations in primary colon tumors. Oncogene. 1999 Jan 7;18(1):27-38.

PCR/LDR/capillary electrophoresis: Yi P, Chen Z, Yu L, Zheng Y, Liu G, Xie H, Zhou Y, Zheng X, Han J, Li L. Development of a PCR/LDR/capillary electrophoresis assay with potential for the detection of a beta-thalassemia fetal mutation in maternal plasma. J Matern Fetal Neonatal Med. 2010 Aug;23(8):920-7.

ASQ (allele-specific qPCR): Lee HB, Schwab TL, Koleilat A, Ata H, Daby CL, Cervera RL, McNulty MS, Bostwick HS, Clark KJ. Allele-Specific Quantitative PCR for Accurate, Rapid, and Cost-Effective Genotyping. Hum Gene Ther. 2016 Jun;27(6):425-35.

dF-ARMS (Double fluorescent-amplification refractory mutation detection): Maher C, Crowley D, Cullen C, Wall C, Royston D, Fanning S. Double fluorescent-amplification refractory mutation detection (dF-ARMS) of the factor V Leiden and prothrombin mutations. Thromb Haemost. 1999 Jan;81(1):76-80.

Pooled DNA-SNP chips: Macgregor S, Zhao ZZ, Henders A, Nicholas MG, Montgomery GW, Visscher PM. Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays. Nucleic Acids Res. 2008 Apr;36(6):e35.

SNaPshot-Issues: Hansen LL, Madsen BE, Pedersen K, Wiuf C. Conflicting results in SNP genotype assessment. Biotechniques. 2007 Dec;43(6):756-60.

Implementation of T-ARMS-PCR: Etlik O, Koksal V, Arican-Baris ST, Baris I. Development and validation of a cost-effective in-house method, tetra-primer ARMS PCR assay, in genotyping of seven clinically important point mutations. Mol Cell Probes. 2011 Aug;25(4):177-81.

Cell Line Controls: Kimbacher C, Paar C, Freystetter A, Berg J. Cell Line Controls for the Genotyping of a Spectrum of Human Single Nucleotide Polymorphisms in the Clinical Laboratory. Clin Lab. 2018 May 1;64(5):823-834.

Comparison of Methods: Etlik O, Koksal V, Arican-Baris ST, Baris I. Development and validation of a cost-effective in-house method, tetra-primer ARMS PCR assay, in genotyping of seven clinically important point mutations. Mol Cell Probes. 2011 Aug;25(4):177-81.

Comparison of Methods: De la Vega FM, Lazaruk KD, Rhodes MD, Wenz MH. Assessment of two flexible and compatible SNP genotyping platforms: TaqMan SNP Genotyping Assays and the SNPlex Genotyping System. Mutat Res. 2005 Jun 3;573(1-2):111-35.

Comparison of Methods: Martino A, Mancuso T, Rossi AM. Application of high-resolution melting to large-scale, high-throughput SNP genotyping: a comparison with the TaqMan method. J Biomol Screen. 2010 Jul;15(6):623-9.

Comparison of Methods: Martino A, Mancuso T, Rossi AM. Application of high-resolution melting to large-scale, high-throughput SNP genotyping: a comparison with the TaqMan method. J Biomol Screen. 2010 Jul;15(6):623-9.

CNV Genotyping

Arrays-CNVs: Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998 Oct;20(2):207-11.

MLPA (Multiplex Ligation-dependent Probe Amplification): Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 2002 Jun 15;30(12):e57.

Southern Blot: Southern E. Southern blotting. Nat Protoc. 2006;1(2):518-25.

qPCR with SYBR-Green: Ponchel F, Toomes C, Bransfield K, ..., Inglehearn CF, Isaacs JD, Markham AF. Real-time PCR based on SYBR-Green I fluorescence: an alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions. BMC Biotechnol. 2003 Oct 13;3:18.

qPCR with TaqMan probes: Heid CA, Stevens J, Livak KJ, Williams PM. Real time quantitative PCR. Genome Res. 1996 Oct;6(10):986-94.

MAQ (multiplex amplicon quantification): Kumps C, Van Roy N, Heyrman L, Goossens D, Del-Favero J, Noguera R, Vandesompele J, Speleman F, De Preter K. Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma. BMC Genomics. 2010 May 12;11:298.

MAPH (Multiplex Amplifiable Probe Hybridisation): Armour JA, Sismani C, Patsalis PC, Cross G. Measurement of locus copy number by hybridisation with amplifiable probes. Nucleic Acids Res. 2000 Jan 15;28(2):605-9.

QuadMAPH: Tyson J, Majerus TM, Walker S, Armour JA. Quadruplex MAPH: improvement of throughput in high-resolution copy number screening. BMC Genomics. 2009 Sep 28;10:453.

QMPSF (quantitative multiplex PCR of short fluorescent fragments): Casilli F, Di Rocco ZC, Gad S, Tournier I, Stoppa-Lyonnet D, Frebourg T, Tosi M. Rapid detection of novel BRCA1 rearrangements in high-risk breast-ovarian cancer families using multiplex PCR of short fluorescent fragments. Hum Mutat. 2002 Sep;20(3):218-26.

QF-PCR (quantitative fluorescent PCR): Pannetier C, Delassus S, Darche S, Saucier C, Kourilsky P. Quantitative titration of nucleic acids by enzymatic amplification reactions run to saturation. Nucleic Acids Res. 1993 Feb 11;21(3):577-83.

CGP (Competitive Genomic PCR): Iwao-Koizumi K, Maekawa K, Nakamura Y, Saito S, Kawamoto S, Nakagawara A, Kato K. A novel technique for measuring variations in DNA copy-number: competitive genomic polymerase chain reaction. BMC Genomics. 2007 Jul 2;8:206.

UPQFM (Universal Primer Quantitative Fluorescent Multiplex PCR): Heath KE, Day IN, Humphries SE. Universal primer quantitative fluorescent multiplex (UPQFM) PCR: a method to detect major and minor rearrangements of the low density lipoprotein receptor gene. J Med Genet. 2000 Apr;37(4):272-80.

RD-PCR (Robust Dosage-PCR): Nguyen VQ, Shi J, Liu Q, Sommer SS. Robust dosage (RD)-PCR protocol for the detection of heterozygous deletions. Biotechniques. 2004 Sep;37(3):360-4.

MLGA (Multiplex Ligation dependent Genome Amplification): Isaksson M, Stenberg J, Dahl F, Thuresson AC, Bondeson ML, Nilsson M. MLGA--a rapid and cost-efficient assay for gene copy-number analysis. Nucleic Acids Res. 2007;35(17):e115.

QF-PCR (Quantitative Fluorescent Multiplex PCR): Pertl B, Yau SC, Sherlock J, Davies AF, Mathew CG, Adinolfi M. Rapid molecular method for prenatal detection of Down's syndrome. Lancet. 1994 May 14;343(8907):1197-8.

CFMSA (Competitive Fluorescent Multiplex STR polymorphism Assay): Yang C, Shen L, Xu Z, Wu X, Mo X, Zhang J, Wang D, Wang Y, Peng Y, Cao L, Jiang Y, Gu H, Chen S, Bian X, Liu J, Qiao D, Yi L. A novel competitive fluorescent multiplex STR polymorphism assay for rapid, reliable and single-tube screening of 22q11.2 copy-number aberrations. Electrophoresis. 2009 Feb;30(3):465-71.

ARCS (Amplification Ratio Control System): Guthrie PA, Gaunt TR, Abdollahi MR, Rodriguez S, Lawlor DA, Smith GD, Day IN. Amplification ratio control system for copy number variation genotyping. Nucleic Acids Res. 2011 Apr;39(8):e54.

Fluorescent Dosage Analysis (FDA): Yau SC, Bobrow M, Mathew CG, Abbs SJ. Accurate diagnosis of carriers of deletions and duplications in Duchenne/Becker muscular dystrophy by fluorescent dosage analysis. J Med Genet. 1996 Jul;33(7):550-8.

SYBR-based duplex qPCR: Torrezan GT, da Silva FC, Krepischi AC, dos Santos EM, Rossi BM, Carraro DM. A novel SYBR-based duplex qPCR for the detection of gene dosage: detection of an APC large deletion in a familial adenomatous polyposis patient with an unusual phenotype. BMC Med Genet. 2012 Jul 16;13:55.

PCR-AGE/indels: Rigat B, Hubert C, Corvol P, Soubrier F. PCR detection of the insertion/deletion polymorphism of the human angiotensin converting enzyme gene (DCP1) (dipeptidyl carboxypeptidase 1). Nucleic Acids Res. 1992 Mar 25;20(6):1433.

HRM/indels: Lin MH, Tseng CH, Tseng CC, Huang CH, Chong CK, Tseng CP. Real-time PCR for rapid genotyping of angiotensin-converting enzyme insertion/deletion polymorphism. Clin Biochem. 2001 Nov;34(8):661-6.

Universal fluorescent PCR/indels: Oka K, Asari M, Omura T, Yoshida M, Maseda C, Yajima D, Matsubara K, Shiono H, Matsuda M, Shimizu K. Genotyping of 38 insertion/deletion polymorphisms for human identification using universal fluorescent PCR. Mol Cell Probes. 2014 Feb;28(1):13-8.

MLGA/indels: Mathot L, Falk-Sörqvist E, Moens L, Allen M, Sjöblom T, Nilsson M. Automated genotyping of biobank samples by multiplex amplification of insertion/deletion polymorphisms. PLoS One. 2012;7(12):e52750.

MALDI/indels: Sasayama T, Kato M, Aburatani H, Kuzuya A, Komiyama M. Simultaneous genotyping of indels and SNPs by mass spectroscopy. J Am Soc Mass Spectrom. 2006 Jan;17(1):3-8.

Sequencing/Indels: Bhangale TR, Stephens M, Nickerson DA. Automating resequencing-based detection of insertion-deletion polymorphisms. Nat Genet. 2006 Dec;38(12):1457-62.

DHPLC/InDels: Koyama RG, Castro RM, De Mello MT, Tufik S, Pedrazzoli M. Simple detection of large InDeLS by DHPLC: the ACE gene as a model. J Biomed Biotechnol. 2008;2008:562183.

TaqMan/Indels: Robledo R, Beggs W, Bender P. A simple and cost-effective method for rapid genotyping of insertion/deletion polymorphisms. Genomics. 2003 Nov;82(5):580-2.

DASH/Indels: Sawyer SL, Howell WM, Brookes AJ. Scoring insertion-deletion polymorphisms by dynamic allele-specific hybridization. Biotechniques. 2003 Aug;35(2):292-8.

HRM/STRs: Nicklas JA, Noreault-Conti T, Buel E. Development of a fast, simple profiling method for sample screening using high resolution melting (HRM) of STRs. J Forensic Sci. 2012 Mar;57(2):478-88.

InDels-Issues: Shanmugam V, Sell KW, Saha BK. Mistyping ACE heterozygotes. PCR Methods Appl. 1993 Oct;3(2):120-1.

VNTRs-Issues: Kaiser R, Tremblay PB, Roots I, Brockmöller J. Validity of PCR with emphasis on variable number of tandem repeat analysis. Clin Biochem. 2002 Feb;35(1):49-56.

CNV Arrays-Comparison: Halper-Stromberg E, Frelin L, Ruczinski I, Scharpf R, Jie C, Carvalho B, Hao H, Hetrick K, Jedlicka A, Dziedzic A, Doheny K, Scott AF, Baylin S, Pevsner J, Spencer F, Irizarry RA. Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinformatics. 2011 Apr 15;27(8):1052-60.

CNV Arrays-Comparison: Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, Hadfield J, Chin SF, Brenton JD, Tavaré S, Caldas C. The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics. 2009 Dec 8;10:588.

Comparison of Methods: Yang C, Zhu X, Yi L, Shi Z, Wang H, Hu Y, Wang Y. Comparative study of three PCR-based copy number variant approaches, CFMSA, M-PCR, and MLPA, in 22q11.2 deletion syndrome. Genet Test Mol Biomarkers. 2009 Dec;13(6):803-8.

Comparison of Methods: Goh SK, Musafer A, Witkowski T, Muralidharan V, Christophi C, Do H, Dobrovic A. Comparison of 3 Methodologies for Genotyping of Small Deletion and Insertion Polymorphisms. Clin Chem. 2016 Jul;62(7):1012-9.

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