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

• US 10,337,057 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:
  US14/856,614
• Publication Number:
  US 20160076095A1
• 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 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: 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 system for performing quality control for nucleic acid sample sequencing, the system comprising:

a set of solid supports, each solid support having attached thereto one or more nucleic acid sequences comprising a plurality of nucleic acid molecules,

wherein the set comprises plural groups of solid supports and each group contains solid supports having same ones of the one or more nucleic acid sequences attached thereto,

wherein the plural groups of solid supports are divided into a plurality of subsets,

wherein the one or more nucleic acid sequences are attached 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,

wherein the one or more nucleic acid sequences of each group differ from the one or more nucleic acid sequences each other groups,

wherein the one or more nucleic acid sequences are synthetically derived, and

wherein the one or more nucleic acid sequences produce a predefined pattern of detectable signals during a sequencing run.

2. The system of claim 1, wherein the solid supports are beads.

3. The system of claim 1, wherein the one or more nucleic acid sequences are designed such that consecutive ligation cycles during a sequencing-by-ligation process yield a predefined color transition.

4. The system of claim 3, wherein a number of subsets is equal to a total number of unique detectable signals.

5. The system of claim 1, wherein the set comprises at least 1024 groups of solid supports.

6. The system of claim 1, wherein the one or more nucleic acid sequences comprise a plurality of tag sequences, wherein the plurality of tag sequences comprise the same sequence or different sequences.

7. The system of claim 6, wherein an internal adapter sequence is disposed between each of the plurality of tag sequences.

8. The system of claim 1, wherein the one or more nucleic acid sequences are designed such that a folding free energy of each sequence is minimized.

9. The system of claim 1, wherein a number of subsets is equal to a number of unique detectable signals.

10. The system of claim 1, wherein the one or more nucleic acid sequences are designed such that for a given range of bases within each nucleic acid sequence, every possible combination of bases is represented.