Oracle® Health Sciences Translational Research Center User's Guide Release 3.1.0.3 E66623-05 |
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PDF · Mobi · ePub |
This chapter describes the single patient or subject viewer of TRC. It contains the following topics:
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:
Demographics
Consent Forms Signed
Patient History
Patient Diagnosis
Procedures
Medications Taken
Test or Observation
Specimen Samples Collected
Clinical Encounter (only in patient context)
Specimen with Genomic Results
Derived Files
File Lineage
Variants Found
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.
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.If you have a specified patient or subject count in the single patient or subject screen on the Cohort Query or Cohort List screen, you can navigate through all the selected patients or subjects clinical and genomic history by using the Previous [<] and Next [>] buttons. Under the Patient field, the current Patient's ordinal number (ordinal position of the Patient record within the selection) and the total number of available Patients or Subjects (in the Cohort) will be displayed. For example, in the following figure it is (1 of 8) patients.
If you have navigated from the Cohort Timeline screen into the single patient or subject screen, then the total number of available patient or subject cohort will be the count of patients or subjects selected in the initial pool.
When you log into the application and navigate to the single patient/subject screen, by default, All records source is selected. The Cohort option will be selected when you navigate to single patient or subject screen from any other screen with some patient or subject count. When the Cohort option is selected, you can scan through the patients or subjects selected in the previous screen. When the all record option is selected, you can search through all the patients available in the CDM database.
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
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
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 |
Version Label |
Represents Assembly Version (DNA reference version against which this data was loaded) |
GRCh37(V68) |
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.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 |
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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) |
Alignment Version (DNA Reference Version) |
Represents Assembly Version (DNA reference version against which this data was loaded) |
GRCh37(v68) |
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 |
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 |
Alignment Version (DNA Reference Version) |
Represents Assembly Version (DNA reference version against which this data was loaded) |
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 |
The Assembly Version drop-down is a multi-select component. By default, the last loaded assembly is displayed but this selection can be modified. The Genomic data is filtered out with this assembly version instead of the DNA reference version. One Assembly version can belong to multiple DNA reference versions. A new column Alignment Version (DNA Ref Version) has been added to the genomic data tables as shown in the following figure.
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.
On selecting any of the nodes the details of the variants are displayed in a table as follows:
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 |
Protein Name |
||
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 |
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Site |
||
Specimen Id |
The specimen containing the variant |
HG00096 |
Alignment Version |
Alignment version of a variant |
GRCh37 |
The Dalliance browser is a third party tool that displays a graphical representation of the variant, chromosome or gene range. The variant detail table comprises of hyperlinks for variant reference ID, gene name and chromosome position. Clicking any of these will navigate to the Dalliance browser where you can see the particular VCF tracks around a specific variant, a specific gene, or in an explicitly specified chromosomal range. For example, in the following screenshot, clicking any of the hyperlinks in the Gene column will navigate to the Dalliance browser.
If a file is loaded multiple times for a particular specimen, then the following warning message is displayed. It lists all the multiple files names.
Following are some configurations required to plot the gene track in the Dalliance browser. You can create your own DAS server and the corresponding entries should be added in the TRC.properties file. Following is an example of the required entries, to look up the Authority, University of California Santa Cruz (UCSC) name for the alignment and the public URLs for the Sequence and Genes tracks (reference tracks):
DALLIANCE.AUTHORITY_37=GRCh DALLIANCE.UCSC_NAME_37=hg19 DALLIANCE.SEQ_URL_HG18=http://www.derkholm.net:8080/das/hg18comp/ DALLIANCE.SEQ_URL_HG19=http://www.derkholm.net:8080/das/hg19comp/ DALLIANCE.GENES_URL_HG18=http://www. derkholm.net:8080/das/hsa_54_36p/ DALLIANCE.GENES_URL_HG19=http://www. derkholm.net:8080/das/hsa_59_37d/
While integrating Dalliance with TRC, the server http://www. derkholm.net:8080/das/
has been used. However, this has been shut down.
These can be manually customized in TRC.properties. To add any new alignments, add all the above code to TRC.properties. Make sure that you research the reference for where they can be found. It is possible to use downloaded files instead of public DAS server(s) for reference, but the client should host these files on a web server.
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. If the Patient or Subject ID has been selected in the View Record screen, it will be inherited here. 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.
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.
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.
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), cytobandHG18 (for HG18), or cytobandHG38 (for HG38)
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
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.
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.