Identifying and Correcting An Allelic Ladder Signal For DNA Analysis

• US 20130273529A1
• Filed: 12/30/2010
• Published: 10/17/2013
• Est. Priority Date: 12/30/2010
• Status: Active Grant

• Current Assignee: Analogic Corporation
• Original Assignee: Analogic Corporation
• Inventors: Lai, Ching Ming
• Granted Patent: US 9,920,362 B2
• Time in Patent Office: Days
• US Class Current: 435/6.1
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

A method for determining an allelic ladder signal for DNA analysis includes obtaining a measured allelic ladder signal for an allelic ladder substance, which includes a plurality of fragments, obtaining a reference set of expected fragment sizes of fragments of the ladder substance, and generating a signal identifying whether a peak for a fragment size of the measured ladder signal is a true peak of the ladder substance based on the reference set of expected fragment sizes, wherein the allelic ladder signal for DNA analysis includes the true peaks identified in the signal.

Claims

1. A method for determining an allelic ladder signal for DNA analysis, comprising:

obtaining a measured allelic ladder signal for an allelic ladder substance, which includes a plurality of fragments;

obtaining a reference set of expected fragment sizes of fragments of the ladder substance; and

generating a signal identifying whether a peak for a fragment size of the measured ladder signal is a true peak of the ladder substance based on the reference set of expected fragment sizes, wherein the allelic ladder signal for DNA analysis includes the true peaks identified in the signal.

2. The method of claim 1, further comprising:

generating a plurality of deviations indicative of differences in fragment sizes of peaks in the measured ladder signal and a fragment size of a peak in the reference set of expected fragment sizes, wherein the signal is generated based on the deviation signals.

3. The method of claim 2, further comprising:

identifying a peak of the peaks of the measured ladder signal that has the smallest of the deviations;

comparing the smallest deviation with a predetermined fragment size range about the fragment size of the peak in the reference set of expected fragment sizes; and

determining the peak is a true peak in response to the smallest deviation being within the range about the fragment size of the peak in the reference set of expected fragment sizes.

4. The method of claim 3, further comprising:

identifying the other peaks are false peaks, wherein false peaks are discarded.

5. The method of claim 3, further comprising:

determining a peak is a false peak in response to a corresponding deviation not being the smallest deviation.

6. The method of claim 3, further comprising:

determining the measured ladder signal is missing a peak in response to the smallest deviation being outside of the range about the fragment size of the peak in the reference set of expected fragment sizes.

7. The method of claim 6, further comprising:

generating a peak for the missing peak.

8. The method of claim 7, wherein generating the peak includes interpolating ILS-translated fragment sizes from neighboring peaks to generate the missing peak.

9. The method of claim 8, further comprising:

determining an interpolation coefficient used to interpolate the missing peak based on a corresponding fragment size in the reference set.

10. The method of claim 7, further comprising:

determining an allele number for an ILS translated DNA fragment size based on a corrected ladder signal, which includes the generated missing peaks and does not include the discarded peaks.

11. The method of claim 10, wherein the DNA sample and the ladder substance are concurrently processed in different lanes of a sample carrier.

12. The method of claim 1, wherein the reference set of expected fragment sizes of the fragments in the ladder includes an average of the fragment sizes from a plurality of ladder signals previously successfully verified.

13. The method of claim 12, further comprising:

updating the average based on a newly acquired and successfully verified ladder signal.

14. A system, comprising:

a plurality of processing stations configured to concurrently process one or more DNA samples and an allelic ladder substance carried by different channels of a sample carrier, wherein the an internal lane sizing substance is include with both the DNA samples and the allelic ladder substance;

a reader that detects light emitted from fragments of the one or more DNA samples, the internal lane sizing substance and the allelic ladder substance in response to illuminating the fragments, and that generates one or more DNA signals, an internal lane sizing signal and an allelic ladder signal indicative of the detected light;

a translator that translates the one or more DNA signals from units of migration time to units of fragment size based on the internal lane sizing signal, and translates the ladder signals from units of migration time to units of fragment size based on the internal lane sizing signal; and

a ladder signal corrector that corrects the internal lane sizing translated allelic ladder signal, wherein the corrected internal lane sizing translated ladder signal provides a mapping from allele numbers to internal lane sizing translated DNA fragment sizes in the internal lane sizing translated DNA signal.

15. The system of claim 14, wherein the ladder signal corrector corrects the allelic ladder signal through removing false peaks from the allelic ladder signal.

16. The system of claim 14, wherein the ladder signal corrector corrects the allelic ladder signal through creating missing peaks of the allelic ladder signal.

17. The system of claim 14, wherein the ladder signal corrector identifies true peaks in the allelic ladder.

18. The system of claim 14, the ladder signal corrector, comprising:

a peak comparator that compares fragments sizes of the peaks in the allelic ladder signal with a set of predetermined fragment sizes for the allelic ladder substance and generates deviations there between;

a deviation evaluator that compares the deviations with a predetermined fragment size range about the fragment sizes in the set; and

a peak acceptor that accepts a peak of the allelic ladder signal as a true peak of a fragment size in the ladder substance in response to a corresponding fragment size having a smallest deviation to the fragment size in the set of predetermined fragment sizes and the smallest deviation satisfying the fragment size range.

19. The system of claim 18, wherein the peak acceptor rejects the other peaks with deviations satisfying the fragment size range for the fragment size in the set of predetermined fragment sizes.

20. The system of claim 18, wherein the peak acceptor creates a peak for a fragment size in the set of predetermined fragment sizes in response to no peak in the allelic ladder signal having a deviation satisfying the fragment size range for the fragment size.

21. A method, comprising:

determining allele numbers for ILS translated DNA fragment sizes of an ILS translated DNA signal using on a mapping of ILS fragment size to allele number that is based on a measured ILS translated allelic ladder signal, which is corrected by identifying and discarding false peaks and identifying and creating missing peaks so as to includes only a complete set of true allelic ladder substance peaks.