6 Single Patient or Subject Viewer

This chapter describes the single patient or subject viewer of TRC. It contains the following topics:

View Records
Circular Genomics Viewer

6.1 View Records

The View Record screen is designed to help you focus on the discreet medical history or genomic history of a particular patient. Even though the Cohort Query functions provide tools for selecting or examining cohorts of patients, it can be difficult to define the appropriate criteria without a closer examination of the data itself. With the Single Patient Viewer, you can drill into the data details of a particular patient, and locate the attribute or data element that is most pivotal as selection criteria for your cohort.

The viewer is designed to display data for one particular patient or subject, based on the unidentified Patient or Subject Identifier within the CDM database. The Patient or Subject Identifiers are displayed when you list patients or subjects from a query (Cohort List tab).

At the top of the screen, there is a search function for locating the particular patient or subject to view. The search is based on the unidentified Patient Identifier, to protect patient identity in patient context and Subject Identifier along with associated study in the Subject Context. After selecting the patient or subject you want to examine, the system displays all the available information about that patient or subject, organized in distinct section as follows:

Clinical Data

Demographics
Consent Forms Signed
Patient History
Patient Diagnosis
Procedures or Treatments Undergone
Medications Taken
Test or Observation
Specimen Samples Collected
Clinical Encounter (only in patient context)

Genomic Data

Specimen with Genomic Results
Derived Files
File Lineage
Variants Found

Figure 6-1 View Record

Description of "Figure 6-1 View Record"

At the bottom of the page, there is a Print button, which prints the current screen.

You select the check box next to the name of any one section to show the display of that section.

Figure 6-2 Hide and Display Options

Description of "Figure 6-2 Hide and Display Options"

Below each section, there is an Export button that enables you to save the displayed data in a discreet file.

A patient or subject may have significant volumes of information, hence the sections are designed to display multiple rows. If you type a value in the blank section above any one particular attribute and press Enter, the system will filter the rows in that section, based on the value you enter. This lets you focus on one particular row of data. In addition, clicking the header of any column with sort the data within the column.

Note:

The attributes that display for the various categories align with the data terms and definitions that are described in the Cohort Query tab, where you select criteria for selecting patients or subjects.

6.1.1 Clinical Data

The attributes displayed for each section are listed below:

Demographics

Gender, Marital Status, Age, Date of Birth, Deceased Date, Ethnicity, Race, City, Zip code, County, State, Country

In case you have a special role (pi-user role) then additional columns will be displayed in the Demographics section Contact Info, Street Address, Related Patients or Subjects
Consent Forms Signed

Consent Type Name, Consent Type Code, Description, Consent Status Name, Status Code, Start Date, End Date, Data Source
Patient History

History or Risk Name, History or Risk Code, Type, Start Date, End Date, Frequency (Units), Amount (Units), Text Value of Code, Applicable To, Data Source
Patient Diagnosis

Diagnosis Name, Code, Age at First Onset (in Years), Onset Date, Date Reported, End Date, Status, Anatomical Site Name, Anatomical Site Code, Data Source
Procedures or Treatments Undergone

Procedure Name, Procedure Code, Procedure Type, Type Code, Start Date, End Date, Outcome, Anatomical Site Name, Anatomical Site Code, Data Source
Medications Taken

Medication Name, Medication Code, Description, Start Date, End Date, Dosage, Dosage Units, Outcome, Data Source
Test or Observation

Test or Observation Name, Test or Observation Code, Type Date, Numeric Result (Units), Result (text), Data Source
Specimen Samples Collected

Specimen Type Name, Specimen Type Code, Date Collected, Anatomical Site Name, Anatomical Site Code, Amount, Units, Data Source
Clinical Encounter

Encounter Id, Encounter Type, Start Data, End Date, Additional Details (clicking this provides more details about the encounter like Event Name, Event Type, Start Date, End Date, Location Name (Location Type)), Data Source

6.1.2 Genomic Data

Genomic data is displayed in four sections as follows:

Table 6-1 Specimens with Genomic Results

Column Heading	Definition	Sample Value or Values
Specimen Id	Specimen belonging to the selected patient or subject	HG00096
Specimen Vendor Id	Specimen Vendor for that specimen	Vcf
DNA Reference Version	Reference Version of the specimen	GrCH37
Sequence Variants Results	Whether the sample has sequence variants results	Yes / No
Copy Number Variation Results	Whether the sample has copy number variants results	Yes / No
Single Channel Microarray Results	Whether the sample has single channel results	Yes / No
Dual Channel Microarray Results	Whether the sample has dual channel results	Yes / No
Rna-Seq Expression Results	Whether the sample has rna sequencing results	Yes / No

Derived Files (Level 3 or 4 results loaded into ODB schema tables for querying) and

File Lineage (Level 1 or 2 files linked to from ODB tables (frequently in binary format and not yet interpreted)

Note:

If you have appropriate permissions, and if files are present in the middle tier accessible location, the path listed in the File Name fields for Genomic data are enabled to allow you to click and download the files directly from CE.

Table 6-2 Derived Files

Column Heading	Definition	Sample Value or Values
Filename	Filename including path of the genomic file stored including path	C:/John_specimen01.vcf
File Size in MB	Size of the File in MB	Numeric, positive integer
File URI	URI of the file	File://trc/abc.maf
Alternate Filepath	The FTP path of the file
File Type, Version	Type of file and Version	Variant Call Format, 4.1
Result Type	Type of result data in the file	Sequencing, Copy Number Variation, Gene Expression (2-channel or single channel)
DNA Reference Version	Reference Version of the specimen	GrCH37
Total Number of Specimen in File	Total number of specimen that the file contains where not all specimen belong to the selected patient	Numeric, positive integer
Last Updated	When record was last updated	19-Mar-2012

Table 6-3 File Lineage

Column Heading	Definition	Sample Value or Values
Parent Filename	Parent Filename including path of the genomic file stored including path	C:/John_specimen01.BAM
File Size in MB	Size of the File in MB	Numeric
File URI	URI of the file	File://trc/abc.maf
Alternate Filepath	The FTP path of the file
File Type, Version	Type of file and Version	Binary Alignment Map, 1.0
DNA Reference Version	Reference Version of the specimen	GrCH37
Last Updated	When record was last updated	19-Mar-2012
Derived Child Files: File - Specimen Id, Vendor Id	Information about Derived Results files that have their lineage based on the particular Low Level file.	C:/John_specimen01.vcf - HG00096_1,HarvardLab1

6.1.2.1 Variants Found

This displays the different variants available for a patient. These variants are grouped and displayed in a hierarchical structure with the count of the variants displayed for each type of variants.

Figure 6-3 Variants Found

Description of "Figure 6-3 Variants Found"

On selecting any of the nodes the details of the variants are displayed in a table as follows:

Table 6-4 Variant Details

Column Heading	Definition	Sample Value or Values
Chromosome	Chromosome location of the variant	1
Position	The position of the variant within the chromosome	Numeric value
Reference Allele	The reference allele of the variant	C
Alternate Allele	The alternate allele of the variant	G
Gene	The gene containing the variant	BID
Transcript	The transcript name	ENSTXXX
Variant Name	The reference id of the variant	rs111
Variant Type	The type of variant	Substitution
Variant Status	Status of the variant	Known
Amino Acid
SIFT Impact	The SIFT impact of the variant	Intolerant
Polyphen Impact	The polyphen Impact of the variant	Damaging
Drug	The related drug	Clofazimine
Associated Disease	The disease associated to the variant	Anaemia
Histology
Site
Specimen Id	The specimen containing the variant	HG00096

6.2 Circular Genomics Viewer

Circular genomic data viewer provides an interface for you to visualize the genomic data which includes variation, micro array expression, copy number variation, dual channel expression and rna sequencing. The system uses the VisQuick tool, which is a Javascript library built specifically for genomic data visualization.

You must select Patient ID or Subject ID (study), which are required fields. Optionally, you can also select Specimen Type and Anatomical Site to add filter criteria. In addition the DNA Reference Version selected is used to filter out the results and determine the cytoband to be used while rendering the circular genomic plot for any of the five data types. Based on the filter criteria the matching specimen in any of the five result types are displayed. You can select specimens of different result types however only one specimen of each result type is allowed. By default, the cytoband of chromosomes is also plotted which is the outer most ring of the circular plot.

Figure 6-4 Selection Criteria

Description of "Figure 6-4 Selection Criteria"

Figure 6-5 Specimen for Result Types

Description of "Figure 6-5 Specimen for Result Types"

6.2.1 Selecting Data to Plot

6.2.1.1 Microarray Expression

The microarray expression panel displays all the specimens of the result type expression. You can select only one specimen at a time.

For the selected specimen from the panel, you can view the list of hybridizations available for that specimen. You can select maximum of two hybridizations from the multiple choice box, for which the plot is rendered.

The color delimiter value is used to render color to the data points in the plot based on the intensity value. If the intensity value is above the value defined in color delimiter then the data points have green color Otherwise, the points have red color.

6.2.1.2 Sequencing-Variant Density

This option enables you to plot the density of variants for every 100-kb region for a specimen. The sequence variant density panel displays all the specimens of the result type sequence variants. You can select only one specimen at a time.

6.2.1.3 RNA-Seq Expression

This panel displays all the specimens of result type RNA Sequencing.You can select only one specimen at a time.

The color delimiter value is used to render color to the data points in the plot based on the RPKM value. If the RPKM value is above the value defined in color delimiter then the data points have green color. Otherwise, the points have red color.

You can use the check boxes provided next to each of the result types to determine if the specimen selected will be plotted or not. You can select one or all of the result types for plotting of the graph. Once the specimens are selected, the circular genomic plot is displayed. The outermost circle in the plot is the Cytoband. The supported Cytoband versions are: hg-18 and hg-19.

Note:

To display the cytoband in the Circular Genomic plot we need an entry mapping each DNA Reference Version to the Cytoband in the TRC_LOOKUP_CODE table in the APP_schema.

For each reference version we must insert a row with the following values:

CODE_TYPE : TRC_REFVERSION_CYTOBAND
CODE:cytobandHG19 (for HG19) or cytobandHG18 (for HG18)
CODE_NAME :Name of the loaded DNA reference version (for example, V69)

You can hover over the plot to get details such as:

Microarray Expression: Chromosome, Start Position, End Position, Value and Gene
Copy Number Variation: Chromosome, Start Position, End Position and Value
Sequence Variants: Chromosome, start position, end position, and value. The density value is calculated by: Total number of variants for 100kb region / 100000
Dual Channel Microarray Expression: Chromosome, Start Position, End Position, Value and Gene
Rna Seq Expression: Chromosome, Start Position, End Position, Value and Gene

6.2.1.4 Copy Number Variation

The panel displays all the specimens of the result type copy number variation. You can select only one specimen at a time.

The value for copy number variation depends on the CNV result type selected. If the selected specimen contains data from Genome_Wide_SNP_6 array, then the value for CNV is taken from segment mean stored in the database. If the selected specimen has data from complete genomics, then the value is calculated based on the calledPloidy value stored in the database. The value to be plotted is calculated using the following formula for CNV data from complete genomics:

log2(called_ploidy/expected_ploidy)

where,

expected_ploidy is 2 for chr1-22

expected_ploidy is 2 for chrX for females.

expected_ploidy is 1 for chrX outside the psuedo-autosomal region in males

expected_ploidy is 2 for chrX inside pseudo-autosomal region in males

The pseudoautosomal regions on chrX for 'NCBI build 37' as reported by Complete Genomic are 60000 - 2,699,519 and 154,931,043 - 155,260,559.

The pseudoautosomal regions on chrX for 'NCBI build 36' as reported by Complete Genomic are 0 -2,709,519 and 154,584,237 - 154,913,753.

For called_ploidy zero, there the log2 will be infinity, in such cases the final value is taken as -2.

6.2.1.5 Dual Channel Microarray Expression

This panel displays all the specimens of result type Dual Channel Microarray expression. You can select only one specimen at a time.

The color delimiter value is used to render color to the data points in the plot based on the Log2Ratio value. If the Log2Ratio value is above the value defined in color delimiter then the data points have green color. Otherwise, the points have red color.

6.2.2 Circular Representation

Figure 6-6 Circular Genomic Plot

Description of "Figure 6-6 Circular Genomic Plot"

Note:

In Internet Explorer 9, the compatibility mode should be turned off for Circular Viewer to run properly.