Methods and systems for nucleic acid sequencing validation, calibration and normalization

• US 10,337,058 B2
• Filed: 09/17/2015
• Issued: 07/02/2019
• Est. Priority Date: 02/19/2010
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Shen, Min-Yi, Greiner, Douglas
• Primary Examiner(s): Flinders, Jeremy C
• Application Number:
  US14/856,623
• Publication Number:
  US 20160076096A1
• Time in Patent Office: 1,384 Days
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2533/107 Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2545/101 with an internal standard/control
• CPC Class Codes: C12Q 2563/149 Particles, e.g. beads
• CPC Class Codes: C12Q 2600/166 Oligonucleotides used as internal standards, controls or normalisation probes
• CPC Class Codes: G01N 2201/1242 Validating, e.g. range invalidation, suspending operation
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

A system for performing quality control for nucleic acid sample sequencing is disclosed. The system comprises a set of solid supports, each solid support having attached thereto a plurality of nucleic acid sequences, wherein the set comprises plural groups of solid supports and each group contains solid supports having the same nucleic acid sequences attached thereto. The nucleic acid sequences of each group differ from each other. The nucleic acid sequences are synthetically derived, and the nucleic acids sequences are designed such that the nucleic acid sequences produce a predefined pattern of detectable signals during a sequencing run. A method of preparing a quality control for performing nucleic acid sample sequencing, a method of validating a nucleic acid sequencing instrument during a nucleic acid sequencing experiment, and a method of processing nucleic acid sequencing data during a nucleic acid sequencing experiment are also disclosed.

Claims

1. A method of preparing a quality control for performing nucleic acid sample sequencing, comprising:

generating a set of synthetic nucleic acid sequences, wherein each synthetic nucleic acid sequence in the set of synthetic nucleic acid sequences differs and wherein each of the synthetic nucleic acid sequences in the set of synthetic nucleic acid sequences produces a predefined pattern of detectable signals during sequencing;

attaching one or more synthetic nucleic acid sequences from the set of synthetic nucleic acid sequences to solid supports in plural groups of solid supports, wherein the plural groups of solid supports are divided into a plurality of subsets and wherein the one or more synthetic nucleic acid sequences are attached to the solid supports in the plural groups such that, when nucleic acid sample sequencing is performed, all possible color transitions are observed for consecutive ligation cycles for each subset of the plural groups of solid supports; and

combining each group of solid supports with the synthetic nucleic acid sequences attached to create a control set of solid supports for performing nucleic acid sample sequencing.

2. The method of claim 1, wherein attaching the set of synthetic nucleic acid sequences to solid supports comprises attaching each of the synthetic nucleic acid sequences to beads.

3. The method of claim 1, wherein generating a set of synthetic nucleic acid sequences comprises designing each synthetic nucleic acid sequence of the set such that consecutive ligation cycles during a sequencing-by-ligation process yield a predefined color transition.

4. The method of claim 1, wherein a number of subsets is equal to a total number of unique detectable signals.

5. The method of claim 1, wherein combining each group of solid supports comprises combining at least 1024 groups of solid supports.

6. The method of claim 1, wherein generating a set of synthetic nucleic acid sequences comprises generating each synthetic nucleic acid sequence with a plurality of tag sequences, wherein the plurality of tag sequences comprise the same sequences or different sequences.

7. The method of claim 6, wherein generating a set of synthetic nucleic acid sequences further comprises disposing an internal adapter sequence between each of the plurality of tag sequences.

8. The method of claim 1, wherein generating a set of synthetic nucleic acid sequences comprises designing the synthetic nucleic acid sequences such that a folding free energy of each synthetic nucleic acid sequence is minimized.

9. The method of claim 2, wherein generating a set of synthetic nucleic acid sequences comprises designing each nucleic acid sequence such that for a given range of bases within each nucleic acid sequence, every possible combination of bases is represented.