Build a cohort query
You can query on any combination of the following data:
Parent topic: Modify criteria for queries using the Cohort Query
Patient Information
In this section;
Parent topic: Build a cohort query
Consent
Note:
To define search criteria for Consent, the criteria must include at least one of the following attributes: Consent Type, Consent Code or Consent Status.Parent topic: Patient Information
Clinical Data
In this section:
- Diagnosis
- Clinical Encounter
- Appointment
- Procedure
- Medication
- Patient History
- Test or Observation
- Specimen
- Study
- Relative Time Events
Parent topic: Build a cohort query
Diagnosis
A criteria defined using the Diagnosis dialog can be linked to criteria for Procedure, Medication, Test or Observation and Specimen to create a single set of linked criteria. Such linked set can be ANDed to any other criteria including another Diagnosis based linked set(s) or standalone criteria defined using any of the clinical or genomic data, for example:
Diagnosis (DA1 or DA2 or DA3…) OR (DB1 or DB2 or DB3…)
- WITH Procedure P1 or P2 or P3…
- WITH Medication M1 or M2 or M3…
- WITH Test or Observation T1 or T2 or T3…
- WITH Specimen S1 or S2 or S3…
AND
Diagnosis (DA2 or DA3 or DA4… ) OR (DB2 or DB3 or DB4…)
- WITH Procedure P3 or P4 or P5…
- WITH Medication M3 or M4 or M5…
- WITH Test or Observation T3 or T4 or T5…
- WITH Specimen S1 or S2 or S3…
AND
Diagnosis D7 or D8 or D9…
AND
Procedure P10 or P11 or P12…
AND
Medication M10 or M11 or M12…
AND
History H1 or H2 or H3…
AND
Specimen S1 or S2 or S3…
...
AND
Criteria defined on Genomic data
Have you checked "Before you begin building your query" yet?
Parent topic: Clinical Data
Clinical Encounter
Back to "Build a cohort query".
Have you checked "Before you begin building your query" yet?
Parent topic: Clinical Data
Appointment
Back to Build a cohort query.
Have you checked Before you begin building your query yet?
Parent topic: Clinical Data
Procedure
Back to Build a cohort query.
Have you checked Before you begin building your query yet?
Parent topic: Clinical Data
Medication
Back to "Build a cohort query".
Have you checked "Before you begin building your query" yet?
Parent topic: Clinical Data
Patient History
Back to "Build a cohort query".
Have you checked "Before you begin building your query" yet?
Parent topic: Clinical Data
Test or Observation
Back to Build a cohort query.
Have you checked Before you begin building your query yet?
Parent topic: Clinical Data
Study
Back to Build a cohort query.
Have you checked Before you begin building your query yet?
Parent topic: Clinical Data
Relative Time Events
You can search for patients who have a particular diagnosis, procedure, or medication combination in a particular chronological order. For example, you can search for patients who:
- Received a diagnosis of X disease any time after starting medication A.
- Had procedure K 30 days or more after receiving a diagnosis of Y.
- Started medication B at the same time as having procedure M.
- In the Cohort Query screen, click the Clinical Data category, then click Relative Time Events.
- Under “Select Patients who have, Step 1" select Diagnosis, Procedure, Medication, Test or Observation, or Genomic Variant.
- Specify how the events in Step 1 and Step 3 are time-related: “at any time while" or specify a condition.
- Under Step 3, specify the related event: having Diagnosis, undergoing Procedure, or taking Medication.
- Under Insert as selec eithert:
- Inclusion to include the criteria in the query.
- Exclusion to exclude the criteria from the query.
- Click Submit.
Back to "Build a cohort query".
Have you checked "Before you begin building your query" yet?
Parent topic: Clinical Data
Genomic Data
Topics in this section:
Parent topic: Build a cohort query
Sequence Variants
-
- In the Cohort Query screen, click the Genomic Data category, then click Sequence Variants.
- You can search on Specimen Type or Anatomical Site.
- To search for a Specimen Type:
-
- Either enter part or all of the value for Specimen Type or click the search icon ().
- In the Select Specimen Type window, select the condition for Specimen Type Name, Specimen Type Code or Code System and enter part of the code.
- Select the specimen code, name and code system that you want to use in your query from the left side and move them into the right side using the arrow ().
- Click Submit.
- To search for an Anatomical Site:
-
- Either enter part or all of a value for Anatomical Site or click the search icon ().
- In the Select Anatomical
Site window, select one of the
Search Modes:
- Classic Search. More search conditions are available.
- Hierarchy Drill-in Search. You can drill down to see the patient count for any sub-level.
- Search for an anatomical site either by Anatomical Site Name, Anatomical Site Code, Code System ID, or Code System Name and click Search.
- Select any Anatomical Site codes, names and code systems that you want to use from the left side and move them into the right side using the arrow ().
- Click Submit.
- You can also search for patients by different genomic criteria. In
the Select Patients based on section, select one:
- having Variants in selected Genes: this enables you to search variants in specific genes.
- having selected Genomic Variants enables you to search for variants by their Cosmic or dbSNP identifiers.
- having Variants within specified Genomic Region enables you to search variants in specified genomic location.
- having Zygosity enables you to search variants with specific zygosity: Any, Homozygous, Heterozygous or Hemizygous.
- having Amino Acid enables
to search for specific amino acid changes in selected genes
or caused by specific genomic variant.
- Enter a Hugo Symbol with an optional parameter of amino acid change (such as K483Q,33_34insGA, R603*, 601Kdel, T1738Ifs, K2137delinsRE, K224_D225delinsN) and you can see list of amino acid changes existing in the database.
- Enter a variant identifier like Cosmic dbSNP or HGVS identifier and you can see all associated amino acid changes.
Select the amino acids of interest and submit to search for patients or subjects having these amino acid changes. having Genotypes enables you to search for specific genotypes like AT, or AA, or wildtype (same as reference), and so on.
- After selecting the genomic criteria, expand the Variant
Location section and specify a value for the
selected option.
- Select either at Genomic Variant or at Genomic Position. Add a value.
- Select an Assembly Version.
- Click View Available Genotypes.
- Under Insert as select either:
- Inclusion to include the criteria in the query.
- Exclusion to exclude the criteria from the query.
Tip:
This applies to all of the criteria specified above. - Click Submit.
- (Optional) Step 2 Additional criteria
- To add additional parameters to your query in the Step 2 tab:
- In the Sequence Variants window, click Step 2 (Optional).
- Select any or all of the following parameters:
- Variant Attribute:
-
- Specify Variant Types from the options below: Substitution, Insertion, Deletion, Indel, or Complex.
- Select a Variant Impact: Synonymous, Missense, Nonsense, Unknown.
- Select a Variant Status: Select Any, Known, or Novel.
- Strand: Select Any, + for forward, or - for reverse.
- Nonsynonymous Substitution Scores:
-
- Select either with Polyphen option or the with SIFT option.
- Select a condition for the Version.
- Either enter a Transcript ID or search for one by clicking the search icon .
- Variant Parameters Depending on the Sequencing File Type:
-
- Select either VCF, MAF or CGI master var.
- Select the condition for all active fields according to your choice in Step a.
- Under Insert as select:
- Inclusion to include the criteria in the query.
- Exclusion to exclude the criteria from the query.
- Click Submit.
See "Metadata Filters".
Back to "Build a cohort query".
Have you checked "Before you begin building your query" yet?
Parent topic: Genomic Data
Copy Number Variation
See Metadata Filters.
Back to "Build a cohort query".
Have you checked "Before you begin building your query" yet?
Parent topic: Genomic Data
Microarray Expression
- In the Cohort Query screen, click the Genomic Data category, then click Microarray Expression.
- To select patients with Microarray Expression Results:
- Select the Microarray Attributes: the Array Type, the
conditions and values for Intensity, P-value and/ or Call.
- n the Expression for Genes from select either: Ad-hoc list, Pathway or Gene Set. Then select the Assembly Version and the DNA Reference Version.
- Under Insert as select either:
- Inclusion to include the criteria in the query.
- Exclusion to exclude the criteria from the query.
- Click Submit.
See Metadata Filters.
Back to "Build a cohort query".
Have you checked "Before you begin building your query" yet?
Parent topic: Genomic Data
RNA-seq Expression
See Metadata Filters.
Back to "Build a cohort query".
Have you checked "Before you begin building your query" yet?
Parent topic: Genomic Data
Metadata Filters
This option is available at the bottom of each of the genomic criteria screens.
To add metadata filters:
Back to "Build a cohort query".
Have you checked "Before you begin building your query" yet?
Parent topic: Genomic Data