Method and apparatus for allele peak fitting and attribute extraction from DNA sample data

67 Pages·2014·3.79 MB·English

US008645073B2
(12) United States Patent (10) Patent N0.: US 8,645,073 B2
Gilbert et al. (45) Date of Patent: Feb. 4, 2014
(54) METHOD AND APPARATUS FOR ALLELE Robert C. Holte, Very Simple Classi?cation Rules Perform Well On
PEAK FITTING AND ATTRIBUTE Most Commonly Used Datasets (Kluwer Academic Publishers, Bos
ton) 1993, pp. 63-90.
EXTRACTION FROM DNA SAMPLE DATA
Computer Software Reviews, J. Am. Chem. Soc., vol. 114, No. 20,
(75) Inventors: Kenneth H. Gilbert, Knoxville, TN 1992, pp. 7961-7962.
Baeza-Baeza, J. J. et al., Prediction of Peak Shape as a Function of
(US); John Douglas BirdWell, Oak
Retention in Reversed-Phase Liquid Chromatography, Journal of
Ridge, TN (US); Tse-Wei Wang, Oak
Chromatography A, 1022, (2004) pp. 17-24.
Ridge, TN (US); Dale V. Stransberry, Caballero, R. D. et al., Parabolic-Lorentzian Modi?ed Gaussian
Knoxville, TN (US) Model for Describing and Deconvolving Chromatographic Peaks,
Journal of Chromatography A, 954, (2002), pp. 59-76.
(73) Assignee: University of Tennessee Research
Di Marco, Valerio B. et al., Mathematical Functions for the Repre
Foundation, Knoxville, TN (US) sentation of Chromatographic Peaks, Journal of Chromatography A,
931, (2001), pp. 1-30.
( * ) Notice: Subject to any disclaimer, the term of this
Eanes, Ritchie C. et al., Peak?tteriAn Integrated Excel-based
patent is extended or adjusted under 35 Visual Basic Program for Processing Multiple Skewed and Shifting
U.S.C. 154(b) by 1555 days. Gaussian-like Soectral Peaks Simultaneously: Application to Radio
Frequency Glow Discharge Ion Trap Mass Spectrometry,
(21) Appl. No.: 11/913,098
Spectrochimica Acta Part B, 55, (2000), pp. 403-428.
(22) PCT Filed: Jul. 28, 2006 Erny, Guillaume L. et al., Electromigration Dispersion in Capillary
Zone Electrophoresis Experimental Validation of Use of the Haaroff
(86) PCT No.: PCT/US2006/029434 Van der Linde Function, Journal of Chromatography A, 959, (2002)
pp. 229-239.
§ 371 (0X1)’
Lan, Kevin et al., A Hybrid of Exponential and Gaussian Functions as
(2), (4) Date: Oct. 30, 2007 a Simple Model of Asymmetric Chromatographic Peaks, Journal of
(87) PCT Pub. No.: WO2007/024408 Chromatography A, 915, (2001), pp. 1-13.
Li, Jianwei, Comparison of the Capability of Peak Functions in
PCT Pub. Date: Mar. 1, 2007 Describing Real Chromatographic Peaks, Journal of Chromatogra
phy A, 952, (2002), pp. 63-70.
(65) Prior Publication Data Marquardt, Donald W., An Algorithm for Least-Squares Estimation
of Nonlinear Parameters, Journal of the Society for Industrial and
US 2009/0228245 A1 Sep. 10, 2009
Applied Mathematics, vol. 11, No. 2 (Jun. 1963), pp. 431-441.
Nikitas, P. et al., On the Equations Describing Chromatographic
Peaks and the Problem of the Deconvolution of Overlapped Peaks,
Related US. Application Data Journal of Chromatography A, 912, (2001), pp. 13-29.
Pai, Su-Cheng, Temporally Covolued Gaussian Equations for Chro
(60) Provisional application No. 60/709,424, ?led on Aug. matographic Peaks, Journal of Chromatography A, 1028, (2004), pp.
19, 2005. 89-103.
Steffen, B. et al., A New Mathematical Procedure to Evaluate Peaks
in Complex Chromatograms, Journal of Chromatography A, 1071,
(51) Int. Cl.
(2005), pp. 239-246.
G01N 33/48 (2006.01)
Walsh, S. et al., Non-Linear Curve Fitting Using Microsoft Excel
C12Q 1/68 (2006.01) Solver, Talanta, vol. 42, No. 4, 1995, Great Britain, pp. 561-572.
(52) US. Cl. Levenberg, Kenneth, “A Method for the Solution of Certain Non
Linear Problems in Least Squares,” Quarterly of Applied Mathemat
USPC ............................................... .. 702/19; 435/6
ics, 2:164-168, 1944.
(58) Field of Classi?cation Search
Pap, T. L. et al., “Application of a New Mathematical Function for
None Describing Chromatographic Peaks,” Journal of Chromatography A,
See application ?le for complete search history. Elsevier, 930, pp. 53-60, 2001.
Coleman, Thomas et al., “Optimization Toolbox for Use with
(56) References Cited MATLAB,” User’s Guide, v. 2, The MathWorks, Inc., Natick, MA,
selected portions re Least-Squares (Curve Fitting): 1-3 to 1-5, 1-37 to
U.S. PATENT DOCUMENTS 1-39, 1-50 to 1-51, 2-17 to 2-22 and 3-11 to 3-13, Jan. 1999.
(Continued)
5,121,443 A 6/1992 Tomlinson
6,438,499 B1 8/2002 Hayashi
6,741,983 B1 5/2004 Birdwellet a1. Primary Examiner * Anna Skibinsky
7,162,372 B2 1/2007 Wang et al. (74) Attorney, Agent, or Firm * Cameron LLP
2002/0116135 A1 8/2002 Pasika et al.
2005/0059046 A1 3/2005 LaBrenz et al. (57) ABSTRACT
Analysis of DNA is critical to many applications including
FOREIGN PATENT DOCUMENTS
identifying perpetrators of crimes based on genetic evidence
WO 9953423 10/1999 left at crime scenes. An initial step to analyzing DNA data is
W0 WO 99/53423 10/1999 detection, identi?cation, and quantization of allele peaks in
the DNA data. The invention provides a method and appara
OTHER PUBLICATIONS
tus for accurately and expeditiously performing this initial
step by sequentially checking un?tted peaks against various
International Preliminary Examination Report dated Jan. 11, 2008
(PCT/US06/029434). models including a default model, a hybrid peak model, a dual
Frank Alsmeyer et al., “Automatic Generation of Peak-Shaped Mod ?t model and, in special situations, a narrow ?t function and
els,” Applied Spectroscopy, vol. 58, No. 8, 2004, pp. 986-994. a saturated ?t function.
International Search Report (PCT/US2006/029434) dated Dec. 28,
2006, 16 pages. 25 Claims, 42 Drawing Sheets
US 8,645,073 B2
Page 2
(56) References Cited Butler, John M., Forensic DNA TYPING, Biology & Technology
behind STR Markers, Second Edition, Academic Press, Chapter 15,
OTHER PUBLICATIONS STR Genotyping Issues, 2005.
PoZo, Roldan, “Template Numerical Toolkit,” obtained using the BudoWle, Bruce, et al., Population Data on the Thirteen CODIS Core
WayBackMachine from math.nist.gov/tnt/indexhtml, National Short Tandem Repeat Loci in African Americans, US. Caucasians,
Institute of Standards and Technology, pp. 1-2, Last Modifed Mar. 31, Hispanics, Bahamians, Jamaicans, and Trinidadians, Journal of
2004. Forensic Science, 44(6), pp. 1277-1286, 1999.
UnkoWn Author, “The MathWorks-MATLAB and Simulink for BudoWle, Bruce, et al., CODIS STR Loci Data from 41 Sample
Technical Computing,” obtained from Web.archive.org, The Populations, Journal of Forensic Science, 46(3), pp. 453-489, 2001.
MathWorks, Inc., 2005. Gomez, Claude et al., Engineering and Scienti?c Computing With
Unknown Author, “solver.com,” Frontline Systems, Inc., obtained Scilab, Birkhauser, Sectons 8.4-8.4.3, pp. 280-292, 1999.
using the WayBackMAchine from WWW.solver.com, 2005. “An Expert System for Scoring DNA Database Pro?les”; Mark W.
Bertsekas, Dimitri P, Nonlinear Programming, 2nd Ed., Athena Sci Perlin, Ph.D., MD; Cybergenetics, Pittsburgh, PA.; Eleventh Inter
enti?c, Chapter 1, Unconstrained Optimization (including Optimal national Symposium on Human Identi?cation, BiloXi, MS; Oct. 29,
ity Conditions 1.1 and Gradient Methods4Convergence 1.2), 1999. 2000.
Butler, John M., Forensic DNA Typing, Biology & Technology “Using Quality Measures to Facilitate Allele Calling in High
behind STR Markers, Academic Press, Chapter 13, STR Genotyping Throughput Genotyping”; Genome Research; Birgir Palsson, Frosti
Issues, 2001. Palsson, Mark Perlin et al.; 1999 9: 1002-1012.
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US. Patent Feb. 4, 2014 Sheet 4 0f 42 US 8,645,073 B2
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