Polygenic Risk Score Software
The Polygenic Risk Score (PRS) software - Predict module provides PRS predictions from IDAT files produced by the iScan System™. The analysis includes PRS predictions and imputed genotype results, and the production of quality metrics. Analysis can be started using the Microarray Analysis Setup in BaseSpace™ Sequence Hub.
The Predict module runs using Illumina Connected Analytics (ICA), a hosted environment for managing, processing, and analyzing genomic data. Before sending data to ICA, BeadChip DMAP files must be accessioned with the ICA command-line interface (CLI). To download and install ICA CLI v1.2, refer to the instructions in the ICA online help.
CLI Installation
Use the installation instructions to install the Illumina Connected Analytics CLI.
Mac and Linux Systems
| 1. | Download the CLI from the ICA online help. |
| 2. | Open the Terminal application, and then navigate to the directory containing the CLI file. |
| 3. | Copy the CLI file to a folder included in your $PATH environment variable list of paths, such as usr/local/bin, as follows. |
| • | If you have read/write access, use the following command: |
cp ica /usr/local/bin
| • | If you do not have read/write access to usr/local/bin, use sudo before the cp command: |
sudo cp ica /usr/local/bin
| • | If you do not have sudo access, contact your administrator, or add the CLI file to a different location and update your $PATH. For information on updating the environment variable, refer to the documentation for your shell. |
| 4. | Use the following command to make the CLI executable: |
sudo chmod a+x /usr/local/bin/ica
Windows Systems
| 1. | Download the CLI from the ICA online help. |
| 2. | Open a command prompt and navigate to the directory containing the CLI file. |
| 3. | If you have not previously made a directory, then copy the CLI file to a folder included in your $PATH environment variable list of paths, such as C:\Program Files, using the following command. If you do not have write access to the folder, open the CMD window in Administrative mode. |
mkdir "C:\Program Files\Illumina" copy ica.exe "C:\Program Files\Illumina"
Make sure that C:\Program Files\Illumina directory is included in your %path% list of paths.
| 4. | Run the *.exe file from its folder using the command-line interface. |
Command Index
Use the following usage syntax when using the CLI:
$ ica infinium [command] [required parameters] [optional parameters]
help
Provides help for any command in the application.
Usage:
ica help [command] [flags]
ica config
Sets the configuration specifications in the config.yaml file.
Usage:
ica config [flags]
ica config [command]
|
Command |
Description |
|---|---|
|
get |
Get configuration information. |
|
set |
Set configuration information. |
infinium
The root command for actions that act on Infinium arrays resources.
Usage:
ica infinium [flags]
|
Command |
Description |
|---|---|
|
beadchips |
BeadChip actions. |
|
products |
Product actions. |
|
Flags |
Description |
|---|---|
|
-h --help |
Help for the infinium command. |
infinium beadchips
The root command for actions that act on BeadChips.
Usage:
ica infinium beadchips [flags]
ica infinium beadchips [command]
|
Command |
Description |
|---|---|
|
create |
Accession a BeadChip. |
|
get |
Retrieve an existing BeadChip. |
|
list |
List the existing BeadChip. |
|
Flags |
Description |
|---|---|
|
-h --help |
Help for BeadChips. |
infinium beadchips create
Accession a BeadChip.
Usage:
ica infinium beadchips create [local path to beadchip directory] [local path to success directory] [local path to failure directory] [flags]
|
Flags |
Description |
|---|---|
|
-h --help |
Help for BeadChips. |
|
--log-file string |
Log file. Default is create_beadchips.log. |
Infinium products
The root command for actions that act on products.
Usage:
ica infinium products [flags]
ica infinium products [command]
|
Command |
Description |
|---|---|
|
create |
Create a product in ICA. |
|
get |
Retrieve product information. |
|
list |
List existing products. |
|
Flags |
Description |
|---|---|
|
-h --help |
Help for Infinium manifests upload. |
infinium products create
Creates a product in ICA. Command requires the local path to a product description in XML format.
Usage:
ica infinium products create [local path to product definition file] [flags]
|
Flags |
Description |
|---|---|
|
-h --help |
Help for infinium manifests upload. |
infinium products get
Retrieve information on a product. Command requires product ID provided by products list command as input. Command returns the product name, number of samples, part number, revision number, and time created.
Usage:
ica infinium products get [product id] [flags]
infinium products list
List existing products added to ICA. Command returns the product ID, product name, revision number, part number, and time created.
Usage:
ica infinium products list [flags]
|
Flags |
Description |
|---|---|
|
-h --help |
Help for the infinium analysisfiles get command. |
|
--maxitems int |
Maximum number of items to return. Use 0 for no limit. Default is 50. |
|
--page-size int32 |
Optimizes listing operations by limiting the number of items retrieved with each API call. Default is 1000. |
|
--page-token string |
Page token used for retrieving paged list results. |
|
--part-number string |
Product part number. |
|
--revision string |
Product revision. |
|
--sort-by string |
Specifies the order to list items. Default is timeCreated Desc. |
login
Logs user into CLI and starts session.
Usage:
ica login [username] [flags]
|
Flags |
Description |
|---|---|
|
--api-key string |
API key for authentication |
|
--auth-url string |
Single sign-on authentication server address. Default is login.illumina.com. |
|
-d, --domain string |
Optionally pass the domain name that you are logging into. |
|
-h --help |
Help for the login command. |
|
--local-port int |
Local port for single sign-on authentication flow. Default is 8282. |
|
--session-token string |
Session token for authentication. |
|
--sso |
Use single sign-on. |
|
--workgroup-id string |
Workgroup ID to set current workgroup context. |
|
--workgroup-name string |
Workgroup name to set current workgroup context. |
version
Get version of ICA.
Usage:
ica version [flags]
|
Flags |
Description |
|---|---|
|
-h --help |
Help for the logout command. |
Before Scanning BeadChips
Accession BeadChips before scanning and starting analysis. Accept all necessary End User License Agreements in BaseSpace Sequence Hub before scanning begins.
Login
| 1. | Open the command window (Windows) or the terminal window (Mac or Linux). |
| 2. | If you know your workgroup name, log in with your user name, password, and workgroup name using the following command: |
$ ica login user@mydomain.com --workgroup-name [workgroup-name]
| 3. | If you do not know your workgroup name, log in and get the available workgroup names first using the following commands: |
$ ica login user@mydomain.com
$ ica workgroups list
| 4. | Make a note of your workgroup name, and then log in with the workgroup name. |
Workgroups must be created before login. Using a workgroup allows all members of the workgroup to share access to resources, analyses, and data. For instructions on how to create a workgroup, refer to Create a Workgroup and Assign Admins from the BaseSpace Sequence Hub Help Center.
Create Product
New products must be created so that they can be selected when you create a configuration in the Microarray Analysis Setup in BaseSpace Sequence Hub and are available to BeadChip accessioning. Commonly used commercial Infinium products are already set up in the system. These products are identified in BaseSpace Sequence Hub under Add Custom Configuration or in the latest product release notes.
Use the products create command to create products in ICA. The command requires a file path to a location that contains the product file in the XML format. Refer to the following example:
$ ica infinium products create /user/productfiles/product.xml
This file is available at support.illumina.com.
Accession BeadChips
BeadChips must be accessioned so that the IDAT files produced by scanning are associated with the correct analysis. DMAP files for the specific array product used are parsed to accession BeadChips. It is possible to automate BeadChip accessioning using a batch file (*.bat). For more information on automating this step, contact Illumina Technical Support.
Use the beadchips create command to accession BeadChips into ICA. The command parses the DMAPs and moves them to one of two locations you set. The command requires the following information:
| • | File path to the locally saved DMAP files. |
| • | File path to a folder where successfully accessioned DMAPs can be moved. |
| • | File path to a folder where DMAPs that were not successfully accessioned can be moved. |
The folders for the parsed DMAPs must be created before running the command.
Example:
$ ica infinium beadchips create [local path to beadchip directory] [local path to success directory] [local path to failure directory] [flags]
BeadChips must be accessioned in the workgroup context. Make sure to log in with a --workgroup name before you accession the BeadChips.
It is recommended that you create a log file to provide additional information on accessioning failures using the --log-file flag.
After accessioning, BeadChips can be scanned.
Scan BeadChips and Check Data Quality
To send data to ICA during scanning, refer to Use Illumina Connected Analytics (ICA) with the iScan System in the Starting the System section of the iScan System Product Documentation. A valid workgroup must be selected during the scan setup so that data can be sent to ICA for analysis with the Predict module.
After BeadChips have been scanned and IDATs have been produced, it is best practice to use GenomeStudio and make sure that the data quality meets Illumina product specifications before you submit samples to the Predict module.
The samples submitted to the Predict module are charged for analysis on a per sample basis. As part of the analysis, the module checks sample QC. Call rates of greater than 98.3% per sample and an average call rate across the batch of greater than 97% are required to output results from the module successfully.
For more information on creating a GenomeStudio project and confirming the genotyping call rates meet the thresholds, refer to GenomeStudio Support Resources at support.illumina.com.
Run Analysis
Run the Microarray Analysis Setup using BaseSpace Sequence Hub as follows.
| 1. | Select the Runs tab. |
| 2. | Select New Run. |
| 3. | Select Microarray Analysis Setup. |
| 4. | For users with ICA v1 run data, make sure Version 2 is selected for ICA to run this analysis type. |
| 5. | Enter the analysis name. |
| 6. | Select the Polygenic Risk Score - Predict module. |
| 7. | Use the Select Project link to choose the project for your output files. |
You can also create a project by selecting the New button in the project selection window.
| 8. | Select your preferred option in the Configuration Settings drop-down menu. |
| 9. | To create a configuration, upload and save the following items: |
| • | Product (available based on accessioned products) |
| • | Manifests (in the CSV and BPM file formats) |
| • | Cluster file (in the EGT file format) |
| • | PRS ID file (in the CSV file format) |
You can also select existing items that have already been uploaded or created.
The PRS ID template is available at support.illumina.com and through the BaseSpace Sequence Hub interface. Users can download the template and enter PRS IDs (1–24) that they would like to calculate. For more information on supported PRS IDs, refer to the release notes.
| 10. | Select Next. |
| 11. | Select either Import Sample Sheet or Select BeadChips. |
| • | If you choose to import a sample sheet, use the displayed Import Sample Sheet link to upload your sample sheet. You can download a template sample sheet by selecting the Download Template link. |
| • | If you choose to select BeadChips, select them from the displayed list of available BeadChips. |
| 12. | Select Launch Analysis. |
View Outputs
| 1. | On the Analyses tab, view the analysis status (eg, initializing or complete). |
| 2. | After the analysis is complete, select the analysis and select the Files tab. |
| 3. | From the Files tab, select the Output folder. |
Outputs
The following information describes the outputs produced by the Predict module.
Per Sample
The per sample outputs include the following files:
| • | PRS PDF file |
| • | SNV VCF file |
PRS PDF File
The PRS PDF file is a per sample output. For an example, refer to Example PRS PDF Output.
SNV VCF File
The software also produces a genotyping variant call file (*.snv.vcf) per sample that contains single nucleotide variants (SNVs) and indels for that sample. This file is referred to as an SNV VCF file. A CSI format index is produced to help retrieve data lines from the SNV VCF file.
Certain SNV and indel calls can be skipped when reported in the VCF. These skipped calls can include the following information:
| • | Unmapped loci |
| • | Intensity-only probes used for CNV identification |
| • | Indels that do not map back to the genome |
The following example shows the content of a typical SNV VCF output file. The last three rows are an example of a variant call output.
##fileformat=VCFv4.1
##source=array-analysis-cli 1.0.1
##genomeBuild=37
##reference=file:///resources/human_g1k_v37.fa
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="GenCall score encoded as a phred quality integer. For merged multi-locus entries, min(GenCall) score is reported.">
##FORMAT=<ID=BAF,Number=1,Type=Float,Description="B Allele Frequency">
##FORMAT=<ID=LRR,Number=1,Type=Float,Description="Log R Ratio">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 205581050157_R06C02
1 567667 rs9651229 C T . PASS . GT:GQ:BAF:LRR 0/0:2:0.007182181:-0.292386
1 568208 rs9701872 T C . PASS . GT:GQ:BAF:LRR 0/0:3:0.004276336:-0.3471435
1 568527 rs11497407 G A . PASS . GT:GQ:BAF:LRR 0/0:1:0:-0.2038793
Per Analysis Batch
The per analysis batch includes the following outputs:
| • | PRS CSV file (results.csv) |
| • | Imputed VCF file (imputed_data.vcf.gz) |
| • | The following PRS log files: |
| – | prs_summary.log |
| – | stderr.log |
| – | stdout.log |
| • | Genotype summary files (gt_sample_summary.csv and gt_sample_summary.json) |
PRS CSV File
The PRS CSV file is provided per analysis batch and is in a format that is ready to incorporate into additional PRS research. The file includes the following information:
| • | Sample ID (in the id column) |
| • | The BeadChip barcode and position (in the code column) |
| • | PRS percentile information |
The following table shows an example of the content in the PRS CSV file.
|
|
id |
code |
prs_title |
title_abbr |
gender |
ancestry_string |
percentile_prs |
risk |
level |
|---|---|---|---|---|---|---|---|---|---|
|
0 |
62 |
205581050157_R05C01 |
hypertension |
HT |
f |
European: 100% |
96 |
57 |
High |
|
1 |
3 |
205581050157_R05C01 |
kidney cancer |
KC |
f |
European: 100% |
48 |
0.7 |
Average |
|
2 |
2 |
205581050157_R05C01 |
breast cancer |
BC |
f |
European: 100% |
45 |
9 |
Average |
Imputed VCF File
The software produces an imputed Variant Call File (VCF) per analysis batch. This file provides information markers that are genotyped. It also shows markers that are inferred through imputation, with imputed markers indicated by the imputed flag.
The following example shows the content of a typical VCF output file. The last three rows are an example of an imputed variant call output.
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##filedate=20221018
##source="beagle.28Jun21.220.jar"
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated ALT Allele Frequencies">
##INFO=<ID=DR2,Number=A,Type=Float,Description="Dosage R-Squared: estimated squared correlation between estimated REF dose [P(RA) + 2*P(RR)] and true REF dose">
##INFO=<ID=IMP,Number=0,Type=Flag,Description="Imputed marker">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=A,Type=Float,Description="estimated ALT dose [P(RA) + 2*P(AA)]">
##FORMAT=<ID=GP,Number=G,Type=Float,Description="Estimated Genotype Probability">
##contig=<ID=1>
##contig=<ID=10>
##contig=<ID=11>
##contig=<ID=12>
##contig=<ID=13>
##contig=<ID=14>
##contig=<ID=15>
##contig=<ID=16>
##contig=<ID=17>
##contig=<ID=18>
##contig=<ID=19>
##contig=<ID=2>
##contig=<ID=20>
##contig=<ID=21>
##contig=<ID=22>
##contig=<ID=3>
##contig=<ID=4>
##contig=<ID=5>
##contig=<ID=6>
##contig=<ID=7>
##contig=<ID=8>
##contig=<ID=9>
##bcftools_concatVersion=1.9-116-g31c9309+htslib-1.10.2-45-gb22e03d-dirty
##bcftools_concatCommand=concat -f /tmp/merge_imputed -Oz -o /tmp/nxf.hkOiv5IJiE/out//imputed_data.vcf.gz; Date=Tue Oct 18 11:12:03 2022
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 205581050157_R10C01 205581050157_R10C02 205581050157_R11C01 205581050157_R11C02 205581050157_R12C01
1 10177 rs367896724 A AC . PASS DR2=0.01;AF=0.3839;IMP GT:DS:GP 0|0:0.72:0.41,0.46,0.13 0|0:0.67:0.44,0.45,0.11 0|0:0.8:0.35,0.49,0.16 0|0:0.8:0.36,0.49,0.15 0|0:0.85:0.33,0.49,0.18
1 10235 rs540431307 T TA . PASS DR2=0.00;AF=0.0007;IMP GT:DS:GP 0|0:0:1,0,0 0|0:0:1,0,0 0|0:0:1,0,0 0|0:0:1,0,0 0|0:0:1,0,0
1 10352 rs555500075 T TA . PASS DR2=0.02;AF=0.4022;IMP GT:DS:GP 0|0:0.81:0.35,0.48,0.16 0|0:0.78:0.37,0.49,0.14 0|0:0.84:0.33,0.5,0.17 0|1:0.85:0.32,0.5,0.18 0|0:0.74:0.39,0.47,0.14
PRS Log File
The PRS log file is a text file that is available per analysis batch. This file provides information on the PRS quality. It includes the following information:
| • | Total markers (called and uncalled) |
| • | Metrics after imputation |
| • | PRS variants used |
Genotype Summary Files
The software produces genotype summary files (gt_sample_summary.csv and gt_sample_summary.json) that contains the following details per sample:
| • | Sample ID |
| • | Sample name |
| • | Sample folder |
| • | Call rate |
| • | LogR Ratio Std Dev |
| • | Gender estimate |
Resources and References
The PRS support pages on the Illumina website provide additional resources. These resources include software, training, compatible products, and documentation. Always check support pages for the latest versions.
|
Resource |
Description |
|---|---|
|
Lab setup and maintenance information for Infinium™ assays. |
|
|
List of consumables and equipment used in Infinium assays, including the PRS software. |
|
|
Instructions for operating and maintaining the iScan System. |
|
|
Instructions for operating and maintaining the Infinium LCG Assay. |
|
|
Instructions for using the hosted environment Illumina Connected Analytics. |
Revision History
|
Document |
Date |
Description of Change |
|
200028099 v00 |
December 2022 |
Initial release. |
