View records

To view a patient record:

1. On the Home page, on the left, click the Single Patient Viewer icon ().
2. Enter the patient ID.
3. Select the Source:
   • All records is the default option. This allows you to search through all available patients in the CDM database.
   • Cohort
4. Select the clinical and genomic data you want to view for the patient.
5. Click Submit.

To sort patient or subject data, either click the phenotype column to reorder them, or enter a value in the blank field, at the top of any column, then hit Enter.

In the Diagnosis table, the column Additional Diagnosis Details displays hyperlinked text for coded values of Grade, Stage, Staging System, Primary Tumor, Node Extension and Metastasis associated with the Diagnosis. The tool tip on the text displays the corresponding code names. To see detailed values of these attributes click the hyperlink to display the Diagnosis Details window.

In the Procedure, Test or Observation, Medication and Specimen tables the column Diagnosis Details displays the Diagnosis that is associated with these records.

In the Medications Taken table the column Procedure Data displays the Procedure in context of which the Medication was prescribed.

In the Test or Observation table, use the drop down list 'Additional data to be displayed' to select the columns that should be displayed in the table. Irrespective of the columns selected for display, data from all of the Test or Observation columns is included in the exported data.

In the Diagnosis, Procedure, Medication and Test or Observation tables, the columns Visit ID, Encounter Type Name and Encounter Type Code display the information about the Encounter with which the above clinical events are associated.

To save patient or subject data in an Excel file, click the Export button () next to the category title. You can export either all data or just the selected criteria.

Variants can only be exported separately. To do so, follow these steps below:

1. In the Single Patient Viewer screen, on the left, select the Variants checkbox.
2. Click Submit. The Variants hierarchy graph is displayed on the right side of the screen.
3. Click on any nodes in the graph to display the tables with Variants data and select it. These tables show 500 records only.
4. Along the top, click Export to export the variants. Variants are exported in an XLS file for the selected node.

For more information, see:

• Display Variant Found
  
• Export Variant Found
  
• Navigate through selected patients or subjects
  
• View genomic data
  
• Select the Assembly Version
  

Display Variant Found

When the user clicks on one of the top 2 level nodes (Variants, Coding, Non-Coding , Unknown)

• If the count of variants is less than a threshold value, then the variant table is displayed.
• If the count is greater, then a message is displayed to select any lower-level node.

Click on the text on the individual nodes to display the table with the variants for the node.

Note:

If there are child nodes, clicking on the + sign will expand the node and display child nodes. However, if there are no child nodes, the graphs will disappear. The user must refresh the page to display the graphs again.

Export Variant Found

While exporting the variants found, if the count of variants is higher than threshold value, user will be to choose a chromosome from drop down list to narrow down the variants.

Note:

If the number of variants that you want to export exceeds the limit of 50000, contact your database administrator. The limit can be modified within the database. For more details, see the Oracle Healthcare Translational Research Administrator's Guide on the Oracle Help Center.

Navigate through selected patients or subjects

To navigate through patients' or subjects' data in the Single Patient Viewer, keep in mind three things:

1. If the selected patient ID generates a patient or subject count larger than 1, you can navigate through patients' or subjects' history using the Previous and Next buttons found next to the Patient ID field, on the left. This is also available for patient or subject counts generated in the Cohort Query or Cohort Viewer screens.
2. Every patient has an ordinal number (his position within the selection) listed under the Patient field. If the selected source is a cohort, then the total number of available patients or subjects from that cohort is also displayed.
3. If you went from the Cohort Timeline screen to the Single Patient Viewer screen, then the total number of available patients or subjects in the cohort is the count of patients or subjects selected in the initial pool, in the cohort timeline.

View genomic data

Genomic data is displayed in four sections as follows:

• Specimen with Genomic Results
  
• Derived Files
  
• File Lineage
  
• Variants Found
  

Specimen with Genomic Results

Table 4-1 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
Genotyping Results	Whether the sample has genotyping results	Yes/No

Derived Files

Table 4-2 Derived Files

Column Heading	Definition	Sample Value or Values
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)
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

File Lineage

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 let you click and download the files directly from Oracle Healthcare Translational Research.

Table 4-3 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
Alternate Filepath	The FTP path of the file	--
Alignment Version (DNA Reference Version)	Represents Assembly Version (DNA reference version against which this data was loaded)	GrCH37
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

Variants Found

Selecting this option displays 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.

Note:

Variants can only be exported after they've been submitted.

Variant details are displayed in a table as follows:

Table 4-4 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
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
Primary Histology	Histology information from COSMIC database	Carcinoma
Histology Subtypes	Histology subtypes from COSMIC database	Adenocarcinoma
Primary Site	Primary site from COSMIC database	Large_Intestine
Site Subtypes	Site Subtypes from COSMIC database	colon:NS:NS,NS:NS:NS
Specimen Id	The specimen containing the variant	HG00096
Alignment Version	Alignment version of a variant	GRCh37

Select the Assembly Version

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.