title: Allele-specific polymerase chain reaction for the detection of Alzheimer's disease-related single nucleotide polymorphisms.
abstract: BACKGROUND
  The incidence of Alzheimer's disease, particularly in developing countries, is expected to increase exponentially as the population ages. Continuing research in this area is essential in order to better understand this disease and develop strategies for treatment and prevention. Genome-wide association studies have identified several loci as genetic risk factors of AD aside from apolipoprotein E such as bridging integrator (BIN1), clusterin (CLU), ATP-binding cassette sub-family A member 7 (ABCA7), complement receptor 1 (CR1) and phosphatidylinositol binding clathrin assembly protein (PICALM). However genetic research in developing countries is often limited by lack of funding and expertise. This study therefore developed and validated a simple, cost effective polymerase chain reaction based technique to determine these single nucleotide polymorphisms.
  
  
  METHODS
  An allele-specific PCR method was developed to detect single nucleotide polymorphisms of BIN1 rs744373, CLU rs11136000, ABCA7 rs3764650, CR1 rs3818361 and PICALM rs3851179 in human DNA samples. Allele-specific primers were designed by using appropriate software to permit the PCR amplification only if the nucleotide at the 3'-end of the primer complemented the base at the wild-type or variant-type DNA sample. The primers were then searched for uniqueness using the Basic Local Alignment Search Tool search engine.
  
  
  RESULTS
  The assay was tested on a hundred samples and accurately detected the homozygous wild-type, homozygous variant-type and heterozygous of each SNP. Validation was by direct DNA sequencing.
  
  
  CONCLUSIONS
  This method will enable researchers to carry out genetic polymorphism studies for genetic risk factors associated with late-onset Alzheimer's disease (BIN1, CLU, ABCA7, CR1 and PICALM) without the use of expensive instrumentation and reagents.
authors: Brain Science Research Laboratory, Faculty of Pharmacy, Universiti Teknologi MARA, Puncak Alam, Selangor, 42300, Malaysia. nuzoif@yahoo.com
authors: Mohd Nazif
authors: MN
authors: Darawi
authors: Chin
authors: C
authors: Ai-Vyrn
authors: Kalavathy
authors: K
authors: Ramasamy
authors: Philip Poi Jun
authors: PP
authors: Hua
authors: Tan Maw
authors: TM
authors: Pin
authors: Shahrul Bahyah
authors: SB
authors: Kamaruzzaman
authors: Abu Bakar Abdul
authors: AB
authors: Majeed
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics; D000368:Aged; D000369:Aged, 80 and over; D000483:Alleles; D000544:Alzheimer Disease / Q000175:diagnosis* / Q000235:genetics; D051152:Clusterin / Q000235:genetics; D005260:Female; D005828:Genetics, Population / Q000379:methods; D015894:Genome, Human; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods; D006801:Humans; D008297:Male; D034041:Monomeric Clathrin Assembly Proteins / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D017463:Receptors, Complement 3b / Q000235:genetics; D015203:Reproducibility of Results; D012307:Risk Factors; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D025521:Tumor Suppressor Proteins / Q000235:genetics
chemical_list: D048868:Adaptor Proteins, Signal Transducing; C101410:BIN1 protein, human; C495242:CLU protein, human; C509991:CR1 protein, human; D051152:Clusterin; D034041:Monomeric Clathrin Assembly Proteins; D009687:Nuclear Proteins; C439003:PICALM protein, human; D017463:Receptors, Complement 3b; D025521:Tumor Suppressor Proteins