Systems and methods for obtaining and managing sequence data

Abstract

Systems and methods for biological sample processing are described. A production line extracts genomic DNA from a biological sample, amplifies target components of the sample and produces sequence data for markers from the amplified components. The markers are associated with tests identified in a requisition received with the sample and some markers may be associated with unrequisitioned tests. A sample information management system (SIMS) controls and monitors the production line and subsequent analysis of the results using information in a quality control (QC) database to validate the results. A repository comprising the QC database and a research database receives and aggregates the results without identifying the source of the sample. A portal may be provided to provide access to the research database to a plurality of external contributors. Contributors can selectively provide additional research data and data can be processed using data mining and curation tools.

1 . A method for analyzing diagnostic information, comprising:
 extracting genomic DNA from a sample,   obtaining sequence data for a plurality of markers, the plurality of markers including a first set of markers which are associated with one or more tests identified in a first requisition corresponding to the sample and a second set of markers which are not associated with the one or more tests identified in the requisition;   generating a response to the requisition, the response being based upon an analysis of sequence data corresponding to the first set of markers and the one or more tests with the generation of the response excluding analysis of the second set of markers with respect to tests other than the one or more tests;   assigning an identifier to the sequence data, the identifier identifying the sample, the requisition and information related to the analysis;   storing the sequence data in a repository of data, the repository providing data for analysis; and   reporting additional results of an analysis of the sequence data associated with one or markers of the second set of markers in response to a second requisition, the second requisition identifying a test different from the one or more tests.   
     
     
         2 . The method of  claim 1 , wherein assigning an identifier includes rendering the source of the sample and the requisition anonymous. 
     
     
         3 . The method of  claim 2 , wherein the second requisition includes the identifier. 
     
     
         4 . The method of  claim 2 , wherein the information related to the analysis identifies the date of the analysis. 
     
     
         5 . The method of  claim 1 , wherein generating a response to the requisition includes performing quality control on the results of an analysis of the sequence data. 
     
     
         6 . The method of  claim 5 , wherein performing quality control includes performing a comparison using quality information derived from the repository. 
     
     
         7 . The method of  claim 6 , wherein performing quality control includes updating the quality information using the results of the analysis of the sequence data. 
     
     
         8 . The method of  claim 1 , wherein the repository is accessible to contributors through a portal. 
     
     
         9 . The method of  claim 8 , further comprising the step of updating the repository based on contributions made by the contributors. 
     
     
         10 . The method of  claim 1  wherein the second requisition is made after receiving the results of the first requisition. 
     
     
         11 . The method of  claim 1  wherein the test identified in the second requisition was not available for identification at the time the first requisition was made. 
     
     
         12 . The method of  claim 11  wherein the second requisition was made at the time of the first requisition and comprised a request for additional results associated with one or more tests not then available for requisition with such results to be delivered after the occurrence of the availability for requisition of at least one of such one or more tests which were not available at the time the first requisition was made. 
     
     
         13 . A method for analyzing diagnostic information, comprising:
 extracting genomic DNA from a sample,   obtaining sequence data for a plurality of markers, the plurality of markers including a first set of markers which are associated with one or more tests identified in a first requisition corresponding to the sample and a second set of markers which are not associated with the one or more tests identified in the requisition, wherein the first requisition includes a request to receive future notifications of health information associated with the sequence data;   generating a response to the requisition, the response being based upon an analysis of sequence data corresponding to the first set of markers and the one or more tests with the generation of the response excluding analysis of the second set of markers with respect to tests other than the one or more tests;   assigning an identifier to the sequence data, the identifier identifying the sample, the requisition and information related to the analysis;   storing the sequence data in a repository of data, the repository providing data for analysis;   after generating the response, generating a notification of health information based upon an analysis of some of the sequence data wherein the health information which is the subject of the notification comprises health information which is different from the health information in the response;   and generating such health information after consent for its generation is received.   
     
     
         14 . The method of  claim 13  wherein the health information which is the subject of the notification concerns a change to a prediction in the response where such change arises due to a change in the content of the repository. 
     
     
         15 . The method of  claim 13  wherein the health information which is the subject of the notification concerns one or more tests which were not available for requisition at the time of the first requisition. 
     
     
         16 . The method of  claim 15  wherein the health information which is the subject of the notification is generated with reference to sequence data corresponding to at least one marker of the second set of markers. 
     
     
         17 . The method of  claim 13  wherein the consent for generating such health information is provided with the first requisition. 
     
     
         18 . A system for analyzing diagnostic information, comprising:
 a sample processing production line including
 a genomic DNA extractor configured to extract DNA from a biological sample, 
 a target amplifier configured to amplify components of the extracted DNA, and 
 a sequencer that produces sequence data for a plurality of markers from the amplified components, the plurality of markers including markers associated with one or more tests identified in a requisition received with the sample; 
   a sample information management system (SIMS) that controls processing of the sample by processing production line and analysis of the results of the processing of the sample;   a quality control (QC) database that provides the SIMS with QC information, the SIMS using the QC information to validate the processing of the sample and the analysis of the results;   a repository comprising one or more databases, the repository aggregating the results generated by processing a plurality of samples, the repository including the quality control database and a research database; and   an analyzer that generates the results using information in the repository.   
     
     
         19 . The system of  claim 18 , wherein information identifying a source of the sample is removed from the sample, the requisition and the results, and wherein the SIMS controls the processing and analysis of the system using a unique identifier assigned to the sample, the requisition and the results. 
     
     
         20 . The system of  claim 18 , wherein a subset of the results are delivered to the source of the sample, the subset of results corresponds to a set of tests identified in the requisition. 
     
     
         21 - 28 . (canceled)