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Filter Categories

Filter Categories allow users simple or complex options in which to filter the subjects in their project. These categories are found on the Subjects tab of the PHC.

Filter categories and options are available within the Standard tab, as seen in below: Filter Categories

And within the Advanced tab, as seen here: Advanced Filter Categories

Clicking the "+" beside each category will open the options available for further selection and filtering.


Saved Filters

Saved Filters are complex filters created and saved by users with the Layout Admin ABAC privilege to give other users easy access to useful filters to view their subject data. (E.g., An admin may select filtering criteria seen in high risk cancer patients and save it as a filter named High Risk Cancer Patients for other users to access.)

Click here for more information on accessing and creating a Saved Filter.


Subject Identifiers

Many of these filter options are disabled in masked mode .

Masked Mode

Clicking this icon in the top right corner of the screen will put you into unmasked mode where you can view these filter options and the data that corresponds with it.

Unmasked Mode

Name - Search by full name or start of first/last name

Email - Search by with single email or a comma separated email list

Subject ID - Separate multiple identifiers with a comma


Demographics

Birth Sex

  • Male
  • Female
  • Unknown

Living Status

  • Living
  • Deceased

Subject Age

  • Lower
  • Upper Subject

Subject Zip Code (1-5 digits separated with commas)

Subject Race

Subject Ethnicity

Subject Tags - Subject Tags are a special label placed on FHIR data.


Surveys

This clip illustrates some of the options available under Surveys.

Survey Status

Survey Assignment

  • Assigned Survey - Dropdown menu allows you to pick a survey from the project
  • "All versions of the survey?" (If unchecked, you can select what versions of the survey you want to specifically view)

  • Assignment Count - Lower and Upper Value boxes (E.g., filtering subjects who have been assigned 1-3 instances of version 1.0 of survey "X")

Survey Status

  • Survey dropdown menu allows you to pick a survey from the project
  • "All versions of the survey?" checkbox
    • Checked = Filters on all the versions of the assigned survey
    • Unchecked = Opens a Survey versions dropdown menu to let you select the major and minor versions of the survey to filter on

Survey Status checkboxes

  • Not Started
  • In Progress
  • Completed

Filter By Date toggle (Days Ago or Start Date/End Date)

  • After X Days Ago (Relative box checked)/ Start Date (Relative box unchecked)
  • Before X Days Ago (Relative box checked)/ End Date (Relative box unchecked)

Survey Results

Here you can filter your subjects based on how they answered a specific survey question.

  • Survey dropdown - Select a survey from the project
  • Survey Question - Select the survey question of interest from the survey selected in the Survey dropdown
    • Aggregation
      • Average Response
      • Maximum Response
      • Minimum Response
    • Answer - Select the survey answer you want to filter on

Filter your subjects based on the consent and their consent completion status.

Consent Versions

  • Consent Version dropdown menu - Select the major version of the consent
  • Consent Minor Version - After selecting the Major Version, you can select any minor versions you want to filter on

Consent Status checkboxes

  • Pending - User has yet to consent
  • Active - User has consented
  • Rejected - User has rejected or revoked the consent

Filter By Date toggle (Days Ago or Start Date/End Date)

  • After X Days Ago (Relative box checked)/ Start Date (Relative box unchecked)
  • Before X Days Ago (Relative box checked)/ End Date (Relative box unchecked)

LIFE Extend

  • Checkbox to filter subjects who have been invited to a project and have logged data using the LIFE or LIFE Extend apps

Cohorts

  • Filter for subjects in Cohort dropdown menu

Conditions

  • Search box for Subject Conditions

Procedures

  • Search box for Subject Procedures

Medications

  • Search box for Subject Medications

Observations

Observations Exist search box

Filter By Date toggle (Days Ago or Start Date/End Date)

  • After X Days Ago (Relative box checked)/ Start Date (Relative box unchecked)
  • Before X Days Ago (Relative box checked)/ End Date (Relative box unchecked)

Observation Value

This search box allows you to select an observation type, comparison operator (=, !=, >), and input the comparison value.


Specimen Samples

  • Specimen Availability checkbox - filters subjects with at least one specimen, regardless of specimen type

  • Specimen Types search box


Documents/Media

  • Subject Document References search box (search by a single file extension)

  • Subject Media search box (search by the content type of the media)


Omics Availability

This searches for subjects with sequencing data matching the specifications. This filter is independent of the variant filters, which have their own germline/somatic specification options. - Sequence Availability - Somatic - Germline - Omics Test Availability - Omics Test dropdown menu


Short Genetic Variants

  • Gene Sets dropdown menu - allows you to make multiple selections
  • Genes search box allowing you to input multiple values separated by a comma
  • Sequence Type dropdown menu - you can make multiple selections
    • Germline
    • Somatic
  • Zygosity dropdown menu - allows you to make multiple selections
    • Heterozygous
    • Homozygous
    • Reference
  • Variant Allele Frequency (Min and Max input boxes)
  • Protein Change search box - list of gene variant pairs
  • Coding Effect dropdown menu - allows you to make multiple selections

    • Frameshift
    • Splice site
    • Stop lost
    • Start lost
    • Nonsense
    • Inframe
    • Missense
    • Synonymous
    • UTR3
    • UTR5
    • Other
  • dbSNP rs ID search box - allows you to list multiple values when separated with a comma

  • COSMIC ID search box - allows you to list multiple values when separated with a comma
  • COSMIC Minimum Count search box - allows you to list multiple values when separated with a comma
  • ClinVar Significance dropdown menu - allows you to make multiple selections
    • Pathogenic
    • Pathogenic/Likely Pathogenic
    • Likely Pathogenic
    • Uncertain Significance
    • Likely Benign
    • Benign/Likely Benign
    • Benign
    • Conflicting Interpretations
    • Association
    • Risk Factor
    • Drug Response
    • Not Provided
  • Pop Freq (gnomAD) (Min/Max values)
  • Maximum Across Populations (Min/Max values)

Logic

(Logic is only available in the Subjects Advanced tab)

Logic lets you add another Logical Operator to your filter tree.

To add another Logical Operator:

Add Logical Operator

  1. Click on a Logical Operator card

  2. In the window that opens, be sure you are on the Add tab

  3. Select Logic

  4. Click the "+" button beside Logical Operator

  5. Close the window by clicking the "x"

Settings for the Logical Operator card can be adjusted in the Advanced tab of Subjects. Logical Operators can be set to filter users meeting ALL criteria, ANY criteria, or NO criteria by:

  1. Clicking on the Logical Operator card
  2. In the window that opens, click on the settings tab
  3. Select the button for the filtering setting you desire for all filters attached to that card. Choices include:
    • Subjects in EVERY sub-filter
    • Subjects in ANY sub-filter
    • Subjects in NOT IN ANY sub-filter

Logical Operator cards can be relocated within a filter tree and thus altering its filtering outcome. This is done by grabbing the card handle and dragging it to the new desired location (as seen below).

Move Logical Operator


Copy Number Variants

  • Gene Sets dropdown menu - you can make multiple selections
  • Genes search box - you can input multiple values, separating them with a comma
  • Sequence Type dropdown menu - you can make multiple selections
    • Germline
    • Somatic
  • Copy Number dropdown menu - you can make multiple selections
    • Amplification
    • Gain
    • Neutral
    • Partial Loss
    • Loss

Structural Variants

  • Gene Sets dropdown menu - you can make multiple selections
  • Genes search box - you can input multiple values with a comma
  • Sequence Type dropdown menu - you can make multiple selections
    • Germline
    • Somatic
  • Effect - you can make multiple selections
    • Fusion
    • Rearrangement
    • Truncation
    • Deletion
    • Duplication
  • In Frame - you can make multiple selections
    • Yes
    • No
    • Unknown
  • Lab Reported Significance - you can make multiple selections
    • Pathogenic
    • Likely pathogenic
    • Uncertain significance
    • Other

Gene Expression

  • Gene Sets dropdown menu - you can make multiple selections
  • Genes - you can input multiple values when separating with a comma
  • Sequence Type - you can make multiple selections
    • Germline
    • Somatic
  • Expression Level - Min/Max value boxes
  • Outliers

    • Project Samples dropdown menu

      • TCGA Tumor Samples
      • TCGA Normal Samples
      • GTEx Normal Broad Tissues
      • GTEx Normal Specific Tissues
      • TreeHouse Tumor Samples
    • Not applicable/diseases/tissues - If nothing is selected in the above Project Samples drop down, this dropdown will say "not applicable", but if you select a Project sample, this dropdown menu will show more options for further filtering based on the listed diseases and tissues

    • No. of std deviations textbox
    • Above the mean/Below the mean/Above the median/Below the median dropdown menu

Last update: 2020-08-10