Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving virus or bacteriophage
Patent
1995-06-30
1998-12-29
Horlick, Kenneth R.
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving virus or bacteriophage
435 6, 435 911, 436 94, 204461, 382129, C12Q 170, C12Q 168, G01N 3348, G06K 900
Patent
active
058539794
ABSTRACT:
Normalization of experimental fragment patterns for nucleic acid polymers having putatively known sequences starts with obtaining at least one raw fragment pattern for the experimental sample. The raw fragment pattern represents the positions of a selected nucleic acid base within the polymer as a function of migration time or distance. This raw fragment pattern is conditioned using conventional baseline correction and noise reduction technique to yield a clean fragment pattern. The clean fragment pattern is then evaluated to determine one or more "normalization coefficients." These normalization coefficients reflect the displacement, stretching or shrinking, and rate of stretching or shrinking of the clean fragment, or segments thereof, which are necessary to obtain a suitably high degree of correlation between the clean fragment pattern and a standard fragment pattern which represents the positions of the selected nucleic acid base within a standard polymer actually having the known sequence as a function of migration time or distance. The normalization coefficients are then applied to the clean fragment pattern to produce a normalized fragment pattern which is used for base-calling in a conventional manner. This method may be implemented in an apparatus comprising a computer processor programmed to determine normalization coefficients for an experimental fragment pattern. This computer may be separate from the electrophoresis apparatus, or part of an integrated unit.
REFERENCES:
patent: 3742202 (1973-06-01), Spreitzhofer
patent: 4720786 (1988-01-01), Hara
patent: 4811218 (1989-03-01), Hunkapiller et al.
patent: 4941092 (1990-07-01), Hara et al.
patent: 4960999 (1990-10-01), McKean et al.
patent: 4982326 (1991-01-01), Kaneko
patent: 5108179 (1992-04-01), Myers
patent: 5119316 (1992-06-01), Dam et al.
patent: 5190632 (1993-03-01), Fujimiya et al.
patent: 5213673 (1993-05-01), Fujimiya et al.
patent: 5246866 (1993-09-01), Nasu et al.
patent: 5273632 (1993-12-01), Stockham et al.
patent: 5365455 (1994-11-01), Tibbetts et al.
patent: 5419825 (1995-05-01), Fujii
patent: 5502773 (1996-03-01), Tibbetts et al.
Bowling et al., "Neighboring Nucleotide Interactions During DNA Sequencing Electrophoresis", Nucleic Acids Res. 19: 3089-3097 (1991).
Giddings et al., "An Adaptive, Object Oriented Strategy for Base calling in DNA Sequences", Nucleic Acids Res. 21: 4530-4540 (1993).
Golden II, et al., "Pattern Recognition for Automated DNA Sequencing: I. On-Line Signal Conditioning and Feature Extraction for Basecalling".
Tibbetts et al., "Neural Networks for Automated Basecalling of gel-Based Sequencing Ladders".
Smith et al., "Fluoresence detection of automated DNA sequence analysis", Nature 321: 674-679 (1986).
Mayrand et al., "The use of fluorescence detection and internal lane standards to size PCR products".
Koutny et al., "Automated Image Analysis for Distortion Compensation in Sequencing Gel Electrophoresis" Applied Spectroscopy 46: 136-141 (1992).
Chi Vrijmoed
Dee Gregory
Gilchrist Rodney D.
Green Ronald J.
Stevens John K.
Horlick Kenneth R.
Visible Genetics Inc.
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