Methods for analysis of DNA fragments

Patent metadata

Field	Value
Publication number	US-11597971-B2
Application number	US-201414528242-A
Country	US
Kind code	B2
Filing date	Oct 30, 2014
Priority date	May 1, 2012
Publication date	Mar 7, 2023
Grant date	Mar 7, 2023

Abstract

A method of genotyping includes applying a sample solution including a plurality of copies of a sample polynucleotide to an array of sensors. The sample polynucleotide includes a region associated with an allele. The method further includes measuring using a plurality of sensors of the array of sensors a characteristic of the region of the plurality of copies of the sample polynucleotide and determining using a computational circuitry and the measured characteristics a statistical value indicative of the allele.

First claim

What is claimed is:

1. A method of genotyping, the method comprising:
fragmenting DNA to form a plurality of fragments, the plurality of fragments including a sample polynucleotide including a variable number tandem repeat region associated with an allele of an individual;
amplifying at least the sample polynucleotide to form a sample solution including a plurality of copies of the sample polynucleotide;
applying the sample solution including a plurality of copies of a sample polynucleotide to an array of sensors having a corresponding well array, the sensors of the array of sensors including ion sensitive field effect transistors, copies of the plurality of copies being secured to polymer matrices in different wells of the well array associated with a plurality of sensors of the array of sensors;
sequencing with each sensor of the plurality of sensors of the array of sensors at least the variable number tandem repeat region of a copy of the plurality of copies of the sample polynucleotide, the ion sensitive field effect transistors providing current or voltage signals in response to sequencing reactions;
for the each sensor of the plurality of the sensors, determining with a computational circuitry, based on the current or voltage signals, a number of tandem repeats with the variable number tandem repeat region for a set of sequenced copies of the plurality of copies;
using the computational circuitry, aggregating from each sensor of the plurality of sensors the number of tandem repeats;
determining with the computational circuitry based at least in part on aggregating the number of tandem repeats an average value of a tandem repeat; and
identifying the individual based in part on the average value of the tandem repeat.

2. The method of claim 1 , wherein the allele is associated with human identification.

3. The method of claim 1 , wherein determining the average value includes determining a mean number of tandem repeats.

4. The method of claim 1 , wherein determining the average value includes determining a mode number of tandem repeats.

5. A method of genotyping, the method comprising:
fragmenting DNA to form a plurality of fragments, the plurality of fragments including a sample polynucleotide, the sample polynucleotide having a variable number tandem repeat region associated with an allele associated with human identification of an individual;
amplifying a sample polynucleotide to provide a sample solution including a plurality of copies of the sample polynucleotide;
applying the sample solution including the plurality of copies of a sample polynucleotide to an array of sensors having a corresponding well array, the sensors of the array of sensors including ion sensitive field effect transistors, copies of the plurality of copies being secured to polymer matrices in different wells of the well array associated with a plurality of sensors of the array of sensors;
sequencing with each sensor of the plurality of sensors of the array of sensors at least the variable number tandem repeat region of a copy of the plurality of copies of the sample polynucleotide;
for each sensor, determining with a computational circuitry a number of tandem repeats with the variable number tandem repeat region for the copy of the plurality of copies;
aggregating from each sensor of the plurality of sensors the number of tandem repeats to form a distribution;
determining with the computational circuitry based at least in part on aggregating the number of tandem repeats an average value of a tandem repeat; and
identifying the individual based in part on the average value of the tandem repeat.

6. The method of claim 5 , wherein determining the average value includes determining a mean number of tandem repeats.

7. The method of claim 5 , wherein determining the average value includes determining a mode number of tandem repeats.

Assignees

• Life Technologies Corp

Inventors

• Merriman Barry
• Mola Paul
• Gardner Mark

Classifications

• C12Q1/6874 Primary

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title