Auto-validation of fluorescent primer extension genotyping assay using signal clustering and neural networks

BMC Bioinformatics

Volumn 5, Issue , 2004, Pages

  Huang, Ching Yu Austin ^a   Studebaker, Joel ^b   Yuryev, Anton ^c   Huang, Jianping ^d   Scott, Kathryn E ^e   Kuebler, Jennifer ^f   Varde, Shobha ^g   Alfisi, Steven ^h   Gelfand, Craig A ⁱ   Pohl, Mark ^j   Boyce Jacino, Michael T ^f  

^a Ctr Pharmacogen/Complex Dis Res   (United States)

^b Care Advantage ^*  (United States)

^c Ariadne Genomics Inc   (United States)

^d NEW JERSEY DEPARTMENT OF HEALTH AND SENIOR SERVICES   (United States)

^e Center for Translational Medicine   (United States)

^f Beckman Coulter Inc   (United States)

^g JOHNSON AND JOHNSON   (United States)

^h Vonage Inc   (United States)

ⁱ BD Technologies   (United States)

^j UNIVERSITY OF MARYLAND   (United States)

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Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL ASSAY; GENOTYPING ASSAYS; HIGH-THROUGHPUT; MULTIPLE SAMPLES; PARAMETRIC VECTORS; PRIMER EXTENSION; SIGNAL CLUSTERS; SIGNAL DISTRIBUTION;

ASSAYS; FLUORESCENCE;

NEURAL NETWORKS;

ARTIFICIAL NEURAL NETWORK; AUTOMATION; BIOASSAY; BIOINFORMATICS; CLUSTER ANALYSIS; COMPUTER PROGRAM; FLUORESCENCE ANALYSIS; GENOTYPE; QUALITY CONTROL; REVIEW; SCORING SYSTEM; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS; ARTIFICIAL INTELLIGENCE; COMPARATIVE STUDY; GENETICS; HUMAN; METABOLISM; POLYMERASE CHAIN REACTION; PREDICTIVE VALUE; PROCEDURES; REPRODUCIBILITY; STATISTICS AND NUMERICAL DATA;

FLUORESCENT DYE; PRIMER DNA;

ARTIFICIAL INTELLIGENCE; AUTOMATION; CLUSTER ANALYSIS; DNA PRIMERS; FLUORESCENT DYES; GENOTYPE; HUMANS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; PREDICTIVE VALUE OF TESTS; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 2942580895     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-36     Document Type: Article

References (10)

1. Yuryev A, Huang J, Pohl M, Patch R, Watson F, Bell P, Donaldson M, Phillips MS, Boyce-Jacino MT: Predicting success of primer extension genotyping assay using statistical modeling. Nucleic Acids Res 2002, 30(23):e131.
2. Altshuler D, Pollara VJ, Cowles CR, Van Etten WJ, Baldwin J, Linton L, Lander ES: An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 2000, 407(6803):513-516.
3. The International SNP Map Working Group. Nature 2001, 409:928-933.
4. SNP database Home Page [http://www.ncbi.nlm.nih.gov/SNP/]
5. Bell PA, Chaturvedi S, Gelfand CA, Huang CY, Kochersperger M, Kopla R, Modica F, Pohl M, Varde S, Zhao R, Zhao X, Boyce-Jacino MT: GenomeLab SNPstream: ultra-high throughput SNP genotyping for pharmacogenomics and drug discovery. Biotechniques 2002, Suppl:70-77.
6. Nikiforov TT, Rendle RB, Goelet P, Rogers YH, Kotewicz ML, Anderson S, Trainor GL, Knapp MR: Genetic Bit Analysis: a solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Res 1994, 22:4167-4175.
7. Weir BS: Genetic data analysis II Sunderland, MA: Sinauer Associates; 1996.
8. Weisman O, Pollack Z: NNUGA - Neural Network Using Genetic Algorithms. [http://www.cs.bgu.ac.il/~omri/NNUGA/.].
9. Fan JB, Chen X, Halushka MK, Berno A, Huang X, Ryder T, Lipshutz RJ, Lockhart DJ, Chakravarti A: Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res 2000, 10(6):853-860.
10. SAS Institute Inc. SAS/STAT User's Guide, Version 8 Cary, NC; 1999.