Skip to main content

Advertisement

Log in

A novel compound-primed multiplex ARMS-PCR (CPMAP) for simultaneous detection of common PAH gene mutations

  • Original Article
  • Published:
Metabolic Brain Disease Aims and scope Submit manuscript

Abstract

In this study, we introduce a novel compound-primed multiplex ARMS PCR (CPMAP) for simultaneous detection of common PAH gene mutations. This approach was used successfully for simultaneous identification of six most common PAH gene mutations in 137 phenylketonuria patients in the Iranian population. A total of six normal and six mutant allele-specific primers and 4 common primers containing a tag sequence of 12 base pair at the 5ˊ-end were designed and used in two separate optimized multiplex ARMS reactions followed by hot-start PCR. The products were separated and visualized on 3% agarose gel. The CPMAP genotyping data were completely in accordance with the direct sequencing results. The CPMAP suggests a reliable, economical and rapid method for simultaneous detection of PAH point mutations using conventional PCR, which could be applied for diagnosis of other gene mutations.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Ajami N, Kazeminezhad SR, Foroughmand AM, Hasanpour M, Aminzadeh M (2013) A preliminary mutation analysis of phenylketonuria in southwest Iran. Genet Mol Res 12:4958–4966

    Article  PubMed  CAS  Google Scholar 

  • Alibakhshi R, Moradi K, Mohebbi Z, Ghadiri K (2014) Mutation analysis of PAH gene in patients with PKU in western Iran and its association with polymorphisms: identification of four novel mutations. Metab Brain Dis 29:131–138

    Article  PubMed  CAS  Google Scholar 

  • Aulehla-Scholz C, Heilbronner H (2003) Mutational spectrum in German patients with phenylalanine hydroxylase deficiency. Hum Mutat 21:399–400

    Article  PubMed  Google Scholar 

  • Biglari A, Saffari F, Rashvand Z, Alizadeh S, Najafipour R, Sahmani M (2015) Mutations of the phenylalanine hydroxylase gene in Iranian patients with phenylketonuria. SpringerPlus 4:542

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Blievernicht JK, Schaeffeler E, Klein K, Eichelbaum M, Schwab M, Zanger UM (2007) MALDI-TOF mass spectrometry for multiplex genotyping of CYP2B6 single-nucleotide polymorphisms. Clin Chem 53:24–33

    Article  PubMed  CAS  Google Scholar 

  • Bonyadi M, Omrani O, Moghanjoghi SM, Shiva S (2010) Mutations of the phenylalanine hydroxylase gene in Iranian Azeri Turkish patients with phenylketonuria. Genet Test Mol Biomarkers 14:233–235

    Article  PubMed  CAS  Google Scholar 

  • Brownie J, Shawcross S, Theaker J, Whitcombe D, Ferrie R, Newton C, Little S (1997) The elimination of primer-dimer accumulation in PCR. Nucleic Acids Res 25:3235–3241

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Edwards MC, Gibbs RA (1994) Multiplex PCR: advantages, development, and applications. Genome Res 3:S65–S75

    Article  CAS  Google Scholar 

  • Ferrie RM, Schwarz MJ, Robertson NH, Vaudin S, Super M, Malone G, Little S (1992) Development, multiplexing, and application of ARMS tests for common mutations in the CFTR gene. Am J Hum Genet 51:251

    PubMed  PubMed Central  CAS  Google Scholar 

  • Fortina P et al (1992) Non-radioactive detection of the most common mutations in the cystic fibrosis transmembrane conductance regulator gene by multiplex allele-specific polymerase chain reaction. Hum Genet 90:375–378

    Article  PubMed  CAS  Google Scholar 

  • Ghiasvand NM et al (2009) Prevalence of classical phenylketonuria in mentally retarded individuals in Iran. J Inherit Metab Dis 32:283–287

    Article  Google Scholar 

  • Guldberg P et al (1998) A European multicenter study of phenylalanine hydroxylase deficiency: classification of 105 mutations and a general system for genotype-based prediction of metabolic phenotype. Am J Med Genet 63:71–79

    CAS  Google Scholar 

  • Habib A, Fallahzadeh MH, Kazeroni HR, Ganjkarimi AH (2015) Incidence of phenylketonuria in Southern Iran. Iran J Med Sci 35:137–139

    Google Scholar 

  • Hamzehloei T, Hosseini SA, Vakili R, Mojarad M (2012) Mutation spectrum of the PAH gene in the PKU patients from Khorasan Razavi province of Iran. Gene 506:230–232

    Article  PubMed  CAS  Google Scholar 

  • Hanley WB (2004) Adult phenylketonuria. Am J Med 117:590–595

    Article  PubMed  CAS  Google Scholar 

  • Henegariu O, Heerema NA, Dlouhy SR, Vance GH, Vogt PH (1997) Multiplex PCR: critical parameters and step-by-step protocol. Biotechniques 23:504–511

    Article  PubMed  CAS  Google Scholar 

  • Inagaki S et al (2004) A new 39-plex analysis method for SNPs including 15 blood group loci. Forensic Sci Int 144:45–57

    Article  PubMed  CAS  Google Scholar 

  • Kleiman S et al (1994) Origins of hyperphenylalaninemia in Israel. Eur J Hum Genet 2:24–34

    Article  PubMed  CAS  Google Scholar 

  • Koochmeshgi J, Bagheri A, Hosseini-Mazinani SM (2002) Incidence of phenylketonuria in Iran estimated from consanguineous marriages. J Inherit Metab Dis 25:80–81

    Article  PubMed  CAS  Google Scholar 

  • Kostandyan N et al (2011) The spectrum of phenylketonuria genotypes in the Armenian population: identification of three novel mutant PAH alleles. Mol Genet Metab 104:S93–S96

    Article  PubMed  CAS  Google Scholar 

  • Kwok S, Kellogg DE, McKinney N, Spasic D, Goda L, Levenson C, Sninsky JJ (1990) Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Res 18:999–1005

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Little S (2001) Amplification refractory mutation system (ARMS) analysis of point mutations. Curr Protoc Hum Genet:9.8. 1–9.8. 12

  • Loeber JG (2007) Neonatal screening in Europe; the situation in 2004. J Inherit Metab Dis 30:430–438

    Article  PubMed  Google Scholar 

  • Lorenz TC (2012) Polymerase chain reaction: basic protocol plus troubleshooting and optimization strategies. J Vis Exp 63:3998

    Google Scholar 

  • Markoulatos P, Samara V, Siafakas N, Plakokefalos E, Spyrou N, Moncany ML (1999) Development of a quadriplex polymerase chain reaction for human cytomegalovirus detection. J Clin Lab Anal 13:99–105

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Multer GL, Boynton KA (1995) PCR bias in amplification of androgen receptor alleles, a trinucleotide repeat marker used in clonality studies. Nucleic Acids Res 23:1411–1418

    Article  Google Scholar 

  • Old JM (1996) Hemoglobinopathies: community clues to mutation detection. In: Elles R (ed) Methods in Molecular Medicine: Molecular Diagnosis of Genetic Diseases. Humana Press, Totowa, pp 169–183. https://doi.org/10.1385/0-89603-346-5:169

    Chapter  Google Scholar 

  • Özalp I, Coşkun T, Ceyhan M, Tokol S, Oran O, Erdem G, Takinalp G, Durmuş Z, Tarikahya Y (1986) Incidence of phenylketonuria and hyperphenylalaninaemia in a sample of the Turkish newborn population. In: Addison GM, Harkness RA, Isherwood DM, Pollitt RJ (eds) Practical Developments in Inherited Metabolic Disease: DNA Analysis, Phenylketonuria and Screening for Congenital Adrenal Hyperplasia: Proceedings of the 23rd Annual Symposium of the SSIEM, Liverpool, September 1985. Springer Netherlands, Dordrecht, pp 237–239. https://doi.org/10.1007/978-94-009-4131-1_35

  • Ozgüç M, Ozalp I, Coşkun T, Yilmaz E, Erdem H, Ayter S (1993) Mutation analysis in Turkish phenylketonuria patients. J Med Genet 30:129–130

    Article  PubMed  PubMed Central  Google Scholar 

  • Rithidech KN, Dunn JJ, Gordon CR (1997) Combining multiplex and touchdown PCR to screen murine microsatellite polymorphisms. Biotechniques 23:36, 40, 42, 44

  • Ruano G, Fenton W, Kidd KK (1989) Biphasic amplification of very dilute DNA samples via'booster'PCR. Nucleic Acids Res 17:5407

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Scriver CR, Kaufman S (2001) Hyperphenylalaninemia: phenylalanine hydroxylase deficiency. The Metabolic and Molecular Bases of Inherited Diseases:1667-1724

  • Senemar S, Ganjekarimi H, Fathzadeh M, Tarami B, Bazrgar M (2009) Epidemiological and clinical study of Phenylketonuria (PKU) disease in the National Screening Program of Neonates, Fars province, Southern Iran. Iran J Public Health 38:58–64

    Google Scholar 

  • Shi MM (2001) Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies. Clin Chem 47:164–172

    PubMed  CAS  Google Scholar 

  • Shi X, Tang C, Zhou D, Sun J, Lu Z (2009) PCR product microarray based on polyacrylic acid-modified surface for SNP genotyping. Electrophoresis 30:1286–1296

    Article  PubMed  CAS  Google Scholar 

  • Shuber AP, Grondin VJ, Klinger KW (1995) A simplified procedure for developing multiplex PCRs. Genome Res 5:488–493

    Article  PubMed  CAS  Google Scholar 

  • Toubanaki DK, Christopoulos TK, Ioannou PC, Flordellis CS (2008) Identification of single-nucleotide polymorphisms by the oligonucleotide ligation reaction: a DNA biosensor for simultaneous visual detection of both alleles. Anal Chem 81:218–224

    Article  CAS  Google Scholar 

  • Vallian S, Barahimi E, Moeini H (2003) Phenylketonuria in Iranian population: a study in institutions for mentally retarded in Isfahan. Mutat Res 526:45–52

    Article  PubMed  CAS  Google Scholar 

  • Walter JΗ, White FJ (2004) Blood phenylalanine control in adolescents with phenylketonuria. Int J Adolesc Med Health 16:41–45

    Article  PubMed  Google Scholar 

  • Yanagawa T, Koga H (2009) Modified multiple primer extension method. Single Nucleotide Polymorphisms: Methods and Protocols 425–435

  • Zare-Karizi S, Hosseini-Mazinani SM, Khazaei-Koohpar Z, Seifati S, Shahsavan-Behboodi B, Akbari MT, Koochmeshgi J (2011) Mutation spectrum of phenylketonuria in Iranian population. Mol Genet Metab 102:29–32

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

This study was supported by University of Isfahan institutional review board (IRB) for research and ethics approval (Approval Ref No. 790205). We are immensely grateful to Dr. Austin J Carlson for constructive and thorough proofreading and English language editing of our manuscript.

Funding

This study was supported by University of Isfahan institutional review board (IRB) for research and ethics approval (Approval Ref No. 790205).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Sadeq Vallian.

Ethics declarations

Conflicts of interest

The authors declare that they have no conflicts of interest.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shaykholeslam Esfahani, M., Shaykholeslam Esfahani, E. & Vallian, S. A novel compound-primed multiplex ARMS-PCR (CPMAP) for simultaneous detection of common PAH gene mutations. Metab Brain Dis 33, 1165–1173 (2018). https://doi.org/10.1007/s11011-018-0210-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11011-018-0210-x

Keywords

Navigation