Method for determining a size of biomolecules

Patent metadata

Field	Value
Publication number	US-11237130-B2
Application number	US-201615738361-A
Country	US
Kind code	B2
Filing date	Jun 30, 2016
Priority date	Jul 1, 2015
Publication date	Feb 1, 2022
Grant date	Feb 1, 2022

Abstract

The present invention relates to a method for determining size of biomolecules separated in a medium by an electric field using marker molecules of known size, comprising —(101) detecting a plurality of bands and forming a detected marker sequence and a detected unknown sequence based on a separation criterion, —(102) determining band properties for each detected band, —(103) comparing the band properties of the detected bands of the detected marker sequence with known band properties for a plurality of marker molecules forming a known marker sequence and assigning a score to each comparison, said score being based on at least one of relative distance, relative intensity, expected distance and expected intensity between bands, —(104) selecting the comparison with the highest score and associating all or a subset of the detected bands of the detected marker sequence with said plurality of marker molecules of the known marker sequence in accordance with said comparison to determine size of the all or a subset of the detected marker sequence, and —(105) comparing the bands of the detected marker sequence with the bands of the detected unknown sequence to determine a size of biomolecules for each identified band of the detected unknown sequence based on the known sizes of the marker molecules. The invention also relates to software configured to perform the method and to a computer readable medium for storing said software.

First claim

The invention claimed is:

1. Method for determining a size of unknown biomolecules separated in a medium by an electric field using marker molecules of known size, comprising
detecting a plurality of data points from a lane and creating a detected lane profile,
creating a previous lane profile based on theoretical data or previously detected data comprising a plurality of marker molecules,
aligning the detected lane profile to the previous lane profile based on a profile alignment calculation to find a best alignment, wherein the profile alignment calculation is based on at least one of expansions and compressions, wherein the profile alignment calculation is further based on dynamic programming that introduces a penalty for adjusting one or more gaps between at least two peaks of the detected lane profile,
determining size of a plurality of marker molecules in the detected lane profile based on the best alignment of the detected lane profile to the previous lane profile,
detecting a plurality of data points corresponding to the unknown biomolecules, and
determining the size of the unknown biomolecules by correlating the data points corresponding to said unknown biomolecules to the determined size of the plurality of marker molecules.

2. Method according to claim 1 , wherein said plurality of data points comprise information of at least one of an intensity and a distance.

3. Method according to claim 1 , wherein the best alignment is determined through a comparison using correlation, preferably Pearson correlation.

4. Software configured to perform the method according to claim 1 .

5. Computer readable medium configured to store the software according to claim 4 .

Assignees

• Cytiva Sweden Ab

Inventors

• Bjorkesten Lennart
• Stafstrom Nils

Classifications

• G01N27/44717 Primary

  Arrangements for investigating the separated zones, e.g. localising zones · CPC title

• G01N27/44721 Primary

  by optical means · CPC title

• C12Q2600/166

  Oligonucleotides used as internal standards, controls or normalisation probes · CPC title

• G01N21/6428

  Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" (in vivo A61B5/00; immunoassay G01N33/53) · CPC title

• G01N30/8693

  Models, e.g. prediction of retention times, method development and validation · CPC title