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

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.

What is claimed is: 
     
         1 . A method of validating a nucleic acid sequencing instrument during a nucleic acid sequencing experiment, comprising:
 placing a set of solid supports each having a plurality of synthetic nucleic acid sequences attached thereto in a detection area of a nucleic acid sequencing instrument, wherein the set of solid supports comprises plural groups of solid supports that each have the same synthetic nucleic acid sequences attached thereto and wherein the synthetic nucleic acid sequences are designed such that the nucleic acid sequences produce a predefined pattern of observable signals during the nucleic acid sequencing experiment;   placing a nucleic acid sample to be sequenced in a detection area of the nucleic acid sequencing instrument;   performing a ligation cycle to attach dye-labeled probe sequences to the nucleic acid sequences attached to the solid supports and to the nucleic acid sample;   detecting the dye-labeled probes attached to each of the nucleic acid sequences and the nucleic acid sample; and   comparing the detected dye-labeled probe attached to the nucleic acid sequences with the predefined pattern of detectable signals to determine if the instrument is functioning within predefined parameters.   
     
     
         2 . The method of  claim 1 , further comprising repeating the steps of performing a ligation cycle, detecting the dye-labeled probes, and comparing the detected dye-labeled probe. 
     
     
         3 . The method of  claim 1 , further comprising identifying the synthetic nucleic acid sequences based on a presence of a control identification sequence. 
     
     
         4 . The method of  claim 3 , further comprising excluding the synthetic nucleic acid sequences from data corresponding to the nucleic acid sample. 
     
     
         5 . A method comprising:
 placing a solid support having a plurality of synthetic nucleic acid sequences attached thereto in a detection area of a nucleic acid sequencing instrument, wherein the plurality of nucleic acid sequences are arranged in a set of distinct locations, wherein the set of distinct locations comprises plural groups of locations that each have the same synthetic nucleic acid sequences attached thereto and wherein the synthetic nucleic acid sequences are designed such that the nucleic acid sequences produce a predefined pattern of observable signals during the nucleic acid sequencing experiment;   performing a sequencing cycle to attach dye-labeled probes to the nucleic acid sequences;   detecting the dye-labeled probes attached to each of the nucleic acid sequences; and   comparing the detected dye-labeled probe attached to the nucleic acid sequences with the predefined pattern of detectable signals to determine if the instrument is functioning within predefined parameters.   
     
     
         6 . The method of  claim 5 , further comprising modifying the performance of the nucleic acid sequencing instrument in response to comparing. 
     
     
         7 . The method of  claim 6 , wherein modifying the performance includes adjusting data to account for decreased signal-to-noise ratio. 
     
     
         8 . The method of  claim 5 , further comprising placing a nucleic acid sample to be sequenced in a detection area of the nucleic acid sequencing instrument. 
     
     
         9 . The method of  claim 8 , further comprising identifying the synthetic nucleic acid sequences based on a presence of a control identification sequence. 
     
     
         10 . The method of  claim 9 , further comprising excluding the synthetic nucleic acid sequences from data corresponding to the nucleic acid sample.