SYSTEMS AND METHODS FOR RUN-TIME SEQUENCING RUN QUALITY MONITORING

• US 20130331992A1
• Filed: 12/06/2011
• Published: 12/12/2013
• Est. Priority Date: 12/14/2010
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Suri, Puneet, Yang, Chengyong, Subramaniam, Yerramalli, Chang, Sylvia
• Granted Patent: US 9,727,032 B2
• Time in Patent Office: Days
• US Class Current: 700/266
• CPC Class Codes: B24B 41/062 between centres; Dogs
• CPC Class Codes: B24B 41/065 Steady rests
• CPC Class Codes: B24B 5/04 for grinding cylindrical surfaces externally grinding combined cylindrical and conical surfaces B24B5/14
• CPC Class Codes: G05B 11/01 electric
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

Systems and methods of providing run-time quality control and monitoring of a single or multiple sequencing runs are provided herein. In some embodiments, the run-time system includes or is in communication with a processor capable of determining various types of run-time information relating to the quality, progress, etc. of various sequencing runs. In some embodiments, the system can also be in communication with a user interface, for example, a GUI, capable of representing and communicating various types of information to a user regarding the quality of the individual or multiple runs, the functioning of the instrument, an error event, etc. Additionally, the system can capable of receiving actionable information from a user via the GUI thereby allowing the user to terminate or repeat various sequencing steps in a particular run, terminate a entire run, terminate all runs, allow a run to proceed, etc.

Claims

1. A system for sequencing nucleic acid samples, the system comprising:

a sequencing instrument for interrogating a control set and a nucleic acid sample for producing control data for the control set and sample data for the nucleic acid sample; and

a processor in communication with the sequencing instrument configured to;

receive the control data and the sample data from the sequencing instrument;

compare the control data to the sample data; and

perform an event handling routine based on the comparison of the control data to the sample data.

2. The system of claim 1, wherein the processor is further configured to determine a control quality value for the control data and a sample quality value for the sample data.

3. The system of claim 2, wherein the processor is further configured to generate a graphical representation of the sample quality value.

4. The system of claim 1, wherein the event handling routine includes providing an event notification, instructing the sequencing instrument to suspend interrogating the nucleic acid sample, generating a log entry, or any combination thereof.

5. The system of claim 4, wherein providing an event notification includes sending an electronic message, displaying an alert, or any combination thereof.

6. The system of claim 4, wherein providing an event notification includes providing an explanation of the probable cause of an event condition based on comparing the control quality value, the sample quality value, and the threshold.

7. The system of claim 1, wherein the processor is further configured to:

determine a required amount of a reagent needed by a sequencing instrument to sequence a nucleic acid sample;

determine an available amount of the reagent;

identify a time when the sequencing instrument will need an additional amount of the reagent if the required amount exceeds the available amount;

notify an operator of the time when the sequencing instrument will need an additional amount of the reagent; and

instruct the sequencing instrument to suspend interrogating the nucleic acid sample prior to the time when the sequencing instrument will need the additional amount of the reagent;

instruct the sequencing instrument to resume interrogating the nucleic acid sample when the additional amount of the reagent has been added.

8. A computer-implemented method comprising:

receiving control data and sample data from a sequencing instrument,

determining a control quality value for the control data and a sample quality value for the sample data;

comparing the control quality value for the control data to an expected control quality value; and

the sample quality value for the sample data to an expected sample quality value;

determining an event condition based on the comparison.

9. The computer-implemented method of claim 8, further comprising displaying a graphical representation of the sample quality value.

10. The computer-implemented method of claim 8, further comprising performing an event handling routine based on the event condition, wherein the event handling routine includes providing an event notification, instructing the sequencing instrument to suspend interrogating the nucleic acid sample, generating a log entry, or any combination thereof.

11. The computer-implemented method of claim 10, wherein providing an event notification includes sending an electronic message, displaying an alert, or any combination thereof.

12. The computer-implemented method of claim 10, wherein providing an event notification includes providing an explanation of the probable cause of the event condition based on comparing the control quality value, the sample quality value, and the threshold.

13. The computer-implemented method of claim 8, further comprising:

determining a required amount of a reagent needed by a sequencing instrument to sequence a nucleic acid sample;

determining an available amount of the reagent;

identifying a time when the sequencing instrument will need an additional amount of the reagent if the required amount exceeds the available amount;

notifying an operator of the time when the sequencing instrument will need an additional amount of the reagent; and

instructing the sequencing instrument to suspend interrogating the nucleic acid sample prior to the time when the sequencing instrument will need the additional amount of the reagent;

instructing the sequencing instrument to resume interrogating the nucleic acid sample when the additional amount of the reagent has been added.

14. A computer program product, comprising a non-transitory computer-readable storage medium whose contents include a program with instructions being executed on a processor, the instructions comprising:

instructions to obtain control data and sample data from a sequencing instrument,

instructions to determine a control quality value for the control data and a sample quality value for the sample data;

instructions to compare the control quality value and the sample quality value;

instructions to perform an event handling routine when the control quality value or the sample quality value is below a threshold.

15. The computer program product of claim 14, further comprising instructions to generate a graphical representation of the sample quality value.

16. The computer program product of claim 14, wherein instructions to perform the event handling routine include instructions to provide an event notification, instruction to notify the sequencing instrument to suspend interrogating the nucleic acid sample, instructions to generate a log entry, or any combination thereof.

17. The computer program product of claim 15, wherein instructions to provide an event notification includes instructions to send an electronic message, instructions to display an alert, or any combination thereof.

18. The computer program product of claim 15, wherein the instructions to provide an event notification include instructions to provide an explanation of the probable cause of the event condition based on comparing the control quality value, the sample quality value, and the threshold.

19. The computer program product of claim 14, further comprising:

instructions to determine a required amount of a reagent needed by a sequencing instrument to sequence a nucleic acid sample;

instructions to determine an available amount of the reagent;

instructions to identify a time when the sequencing instrument will need an additional amount of the reagent if the required amount exceeds the available amount;

instructions to notify an operator of the time when the sequencing instrument will need an additional amount of the reagent; and

instructions to notify the sequencing instrument to suspend interrogating the nucleic acid sample prior to the time when the sequencing instrument will need the additional amount of the reagent;

instructions to notify the sequencing instrument to resume interrogating the nucleic acid sample when the additional amount of the reagent has been added.

20-32. -32. (canceled)