oncomine focus assay part iii: variant analysis · 4. search by any unique identifier you used to...

For Research Use Only. Not for use in diagnostic procedures.

Oncomine™ Focus AssayPart III: Variant Analysis USER GUIDE

Catalog Numbers A29229Publication Number MAN0015821

Revision A.0

The information in this guide is subject to change without notice.DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL,INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOURUSE OF IT.

Revision history. Pub. No. MAN0015821

Revision Date DescriptionA.0 23 Aug 2016 Oncomine™ Focus Assay, Part III: Variant Analysis User Guide. Provides

instruction for Ion Reporter™ Software analysis of Oncomine™ FocusAssay sequencing results.

Important Licensing Information. These products may be covered by one or more Limited Use Label Licenses. By use of these products, you acceptthe terms and conditions of all applicable Limited Use Label Licenses.Corporate entity. Life Technologies Corporation | Carlsbad, CA 92008 USA | Toll Free in USA 1 800 955 6288

TRADEMARKS. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.

©2016 Thermo Fisher Scientific Inc. All rights reserved.

Contents

■ CHAPTER 1 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Analysis workflows in Ion Reporter™ Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

View results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Export Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8Oncomine™ Focus Assay with Ion Reporter™ software v5.2 . . . . . . . . . . . . . . . . . . . . . . . 8

Manually launch an Oncomine™ analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

■ APPENDIX A CNV Baseline Creation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Use VCIB CNV Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Add Samples to an Existing VCIB CNV Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Copy an Ion Reporter™ Analysis Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Launch an Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

■ APPENDIX B Subset Filter Creation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Create a Gene-level Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Create a Variant-level filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20Create a new VariantDB using the provided file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20Create a new Annotation Set using the new VariantDB and existingOncomine™ annotation sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21Create a new Filter Chain using the new VariantDB . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23Create a copied Workflow using both the new Annotation Set and newFilter Chain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24Use new workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

■ APPENDIX C CNV Somatic Confidence Filter . . . . . . . . . . . . . . . . . . . . . . . . 26

Understanding CNV Somatic Confidence Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

■ APPENDIX D No Template Control workaround . . . . . . . . . . . . . . . . . . . . . 28

Reanalyze analyses with No Template Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Oncomine™ Focus Assay, Part III: Variant Analysis User Guide 3

■ APPENDIX E Documentation and support . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Related documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Obtain information from the Help system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Customer and technical support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Contents

4 Oncomine™ Focus Assay, Part III: Variant Analysis User Guide

Methods

Analysis workflows in Ion Reporter™ Software

If your Planned Runs were set up correctly in Torrent Suite™ Software, automatedanalysis has already been performed and you can view the Oncomine™ analysisresults in Ion Reporter™ Software. For instructions on manually launching an analysis,see “Manually launch an Oncomine™ analysis“ on page 9.

Note:· If you are using Ion Reporter™ Software v5.0, refer to the Oncomine™ Focus Assay,

Part V: Variant Analysis User Guide (Pub. No. MAN0013549) for more information.· Microsoft™ Excel™, or other spreadsheet tool, is required for viewing .vcf, .csv

and .tsv files.

Available workflows in Ion Reporter™ Software v5.2 include:

Analysis Workflow Description

Ion Reporter™ Software v5.2 workflows

Oncomine™ Focus - 520 - w2.1 - DNA andFusions - Single Sample

Detects and annotates low frequencysomatic variants (SNPs, InDels, CNVs) fromtargeted DNA libraries, as well as genefusions from targeted RNA libraries, of theOncomine™ Focus Assay.

Oncomine™ Focus - 520 - w2.1 - DNA -Single Sample

Detects and annotates low frequencysomatic variants (SNPs, InDels, CNVs) fromtargeted DNA libraries of the Oncomine™

Focus Assay.

Oncomine™ Focus - 520 - w2.1 - Fusions -Single Sample

Detects and annotates gene fusions fromtargeted RNA libraries of the Oncomine™

Focus Assay.

Oncomine™ Focus - 520 - w2.1 - AnnotateVariants - Single Sample

Annotates VCF files from the Oncomine™

Focus Assay.

View results

Ion Reporter™ Software analyses are performed automatically upon uploading of thedata files from the Torrent Suite™ Software. To view the results:

1. Log in to the Ion Reporter™ Software.

2. Click the Analyses tab.

1


3. In the Application dropdown list, select the Oncomine-specific analyses (DNA,Fusions, DNA and Fusions, or Annotate Variants) to view.

4. In the Analyses screen you can:

To… Action

Open an Analysis Results screen Click the sample's hyperlink (in the Analysiscolumn).

View details Click in the blank space of the analysis' row.

Sort chronologically Click in the Created On column header.

1 2 3

1 Open Analysis Results screen2 View details3 Sort chronologically

Chapter 1 MethodsView results1


5. In the Analysis Results screen sort or filter the data using the Oncomine™-specificannotations. See the software's help menu for more options.

a. In the Filter Options pane select the desired Filter Chain (the default isOncomine Variants, 5% CI CNV ploidy ≥ gain of 2 over normal (5.2)).

b. In the Oncomine tab, click the column headers to sort the list of variants byOncomine Variant Class or Oncomine Gene Class.

c. In the Ontologies tab, click the column headers to sort the list by variantType or Genes.

Chapter 1 MethodsView results 1


Export Results

To export a report:

1. Click Download, then select All Variants, Filtered Variants or Current ResultsTSV.

2. Click Home4Notifications to open the Notifications screen, then click todownload your results.The software generates a .zip file with four folders: QC, Variants,Workflow_Settings, and CNV Baseline. Within the Variants folder, you’ll find theOncomine™ annotated .vcf file, which is used by the Oncomine™ KnowledgebaseReporter. For more information on the CNV output files, see “Copy an IonReporter™ Analysis Workflow“ on page 13.

3. Open the annotated .vcf file, then scroll to the Oncomine™ annotations.

The following annotations may be added:

Oncomine™

Gene ClassOncomine™

Variant Class Variant Type Annotation Criteria

Gain-of-Function

Amplification Copy NumberAmplification

• Variant occurs in one of the19 Oncomine™ Focus copy-gain genes

• SVTYPE = “CNV”

• Copy Number 5% CI foldchange over normal is ≥2(e.g., Copy Number 5% CIvalue is ≥4 when 2 copies areexpected)

Fusion Gene Fusion • Positive fusion call (SVTYPE =“Fusion” and FILTER =“PASS”) in one the 271Oncomine™ Focus fusionvariants

Oncomine™ FocusAssay with IonReporter™

software v5.2

Chapter 1 MethodsExport Results1


Oncomine™

Gene ClassOncomine™

Variant Class Variant Type Annotation Criteria

Gain-of-Function

Hotspot Gain of FunctionMissenseHotspotMutation

• Variant's functional impact ismissense

• Variant occurs in one of 35hotspot genes on the assay

• Variant's transcript and codonposition occur in pre-definedmissense hotspot list

• Allele Frequency (AF) ≥0.05,Alternate Allele ObservationCount (FAO) ≥10

Gain of FunctionIn FrameHotspotMutation


• Variant's function, transcriptand coding syntax occur inpre-defined in-frame hotspotlist


Gain of FunctionSplice SiteHotspotMutation


• Variant's transcript, location,and exon occur in pre-definedsplice site hotspot list


Manually launch an Oncomine™ analysis

To launch an analysis manually:

1. In the Workflows screen, select DNA and Fusions from the Applicationdropdown list.

2. Type Oncomine in the search field, then click Search (or press Enter).

3. In the Workflow Name column, click Oncomine Focus - 520 - w2.1 - DNA andFusions - Single Sample, then select Launch Analysis from the Actionsdropdown list.

4. Search by any unique identifier you used to label your samples during setup,ensure the sample's Cellularity % and Sample Type are defined.

5. Click the checkbox to select a DNA sample and a Fusions sample.

Chapter 1 MethodsManually launch an Oncomine™ analysis 1


6. In the Sample Groups pane, click Add Samples to add to a sample group.

7. Enter a Group Name, click Add to Analysis, then click Next.

8. Ensure that the Oncomine Variant Annotator v2.1 plugin is selected, then clickNext.

9. (Optional) Enter an Analysis Name and Description, then click Launch Analysis.

Chapter 1 MethodsManually launch an Oncomine™ analysis1


CNV Baseline Creation

The following instructions walk you through using the new Variability CorrectionInformation Baseline (VCIB) CNV baseline, creating a new VCIB CNV baseline, oraugmenting an existing VCIB CNV baseline for Oncomine™ Focus Assay panels.

Use VCIB CNV Baseline

If you want to use the VCIB CNV baseline included in Ion Reporter™ Software v5.0,simply select it when creating your workflow.

Note: The VCIB baseline is currently noncompatible with the Ion GRCh38 humanreference.

Add Samples to an Existing VCIB CNV Baseline

Ion Reporter™ Software provides a wizard to guide you through Copy NumberVariation (CNV) Baseline creation. This example describes how to add additionalsamples to an existing CNV baseline.

1. Click the Workflows tab, then click the Presets sub-tab.

2. In the Create Preset menu, select Copy Number Baseline.

3. Select AmpliSeq.

4. Select Oncomine Focus DNA Regions v1.1 as your Targets Region file. ClickNext.

5. In the Algorithm Type page, verify CNV VCIB 1.0 is selected.

A


6. Select Start with an existing CNV Baseline. Select a baseline. For our example,we selected Oncomine™ Focus Assay Baseline v2.0.

Note: By default, the software will prompt you to add another 48 samples,however, you can set the number to 1 or more. Add non-Normal samples.Marking samples as "Normal" in the augmentation workflow has no effect; onlythe original Normals in the initial baseline creation are treated as normals in theaugmented baseline.

7. Click the Configure Parameters link.

8. Go to Cnv Baseline Creation4Advanced. Set the Minimum number of samplesrequired to add to an existing baseline to the number you are adding. ClickDone. Click Next.

Appendix A CNV Baseline CreationAdd Samples to an Existing VCIB CNV BaselineA


9. Select additional samples and click Next.

10. Enter a name for your baseline and then click Create Baseline to save it.

Copy an Ion Reporter™ Analysis Workflow

You can create a new Analysis workflow from the Ion Reporter™ Home tab byselecting Create workflow and using the workflow wizard to enter settings, but asimpler way is to copy an existing Oncomine™ workflow and edit it by adding yourbaseline of choice. Perform the following steps:

1. On the Workflows4Overview tab, scroll to find an appropriate Oncomine™

Focus workflow and select it. For our example, we chose Oncomine™ Focus - 520- w2.1 - DNA and Fusions - Single Sample.

2. On the Actions menu to the right of the list, click Copy. The workflow wizardlaunches.

3. On the Reference tab, select the Oncomine™ Focus DNA Regions v1.1 file fromTarget Regions dropdown.

4. Select Oncomine™ Focus DNA Hotspots v1.1 regions file from Hotspot Regionsdrop-down menu.

5. If you are analyzing fusion samples, select Oncomine™ Focus RNA Fusions v1.1.Click Next.

Appendix A CNV Baseline CreationCopy an Ion Reporter™ Analysis Workflow A


6. Click the Copy Number chevron. Select the baseline you want to use from theBaseline pull-down menu, then click Next.

7. On the Plugins tab, select Oncomine Variant Annotator v2.1 plugin.

8. On the Parameters tab, review default settings.

Note: Although Read Mapping parameters are exposed in the workflowcreation, it is not necessary to change any settings.

9. On the Confirm tab, enter a new name for your workflow in the Workflow Namefield, then click Save Workflow.

Appendix A CNV Baseline CreationCopy an Ion Reporter™ Analysis WorkflowA


Launch an Analysis

1. In the Home tab, click Launch Analysis.

2. In the Workflow tab, select your custom workflow and click Next. For ourexample, we chose Copy of Oncomine™ Focus Panel v2.0 - DNA - SingleSample.

Appendix A CNV Baseline CreationLaunch an Analysis A


3. Select the sample(s) you wish to run in your analysis and click Next twice toadvance through Plugins tab to Confirm and Launch.

Note: The Percentage Cellularity sample attribute is required for DNA onlysamples, and Percentage Cellularity and Cancer Type sample attributes arerequired for DNA and Fusions samples.

4. In the Confirm and Launch tab, enter a name for your analysis and click LaunchAnalysis.

Appendix A CNV Baseline CreationLaunch an AnalysisA


5. Review your results on the Analysis tab. In the Details pane on the right, you canconfirm the CNV workflow and baseline used.

6. Optionally, you can download the Analysis Results and view them visually withthe cn_results.png file in the CNVBaseline folder.

Interpretation example: This plot shows log2 ratios across the genome andhighlights panel CNV IDs. The alternating blue and green color is used todistinguish between adjacent CNV IDs. The outliers are the small pink circles.The numbers at the bottom of the plot on the X axis are the chromosomes. Abovethis are the CNV ID names and the mean CN call for each CNV ID. You can seecopy number gains on chromosome 7 and chromosome 11. The MAPD numberat the top of the plot is a QC metric measuring the noisiness of the sample. AMAPD greater than 0.5 is considered to fail QC. Below the MAPD is the BAM filename. Log2 ratios of 0 are equivalent to a copy number call of 2, which is theexpected normal. If the sample was from a male, you would expect to see a copynumber of 1 for chromosome X.

Note: If using IGV Light to view Oncomine™ analyses, somatic VCIB CNV callsare listed as "passed" in the confidence column. Since Oncomine™ DNA used theVCIB CNV calling algorithm, the data fro VCIB somatic CNV calls hasConfidence Intervals, but it doesn't have the Confidence Score all other IonReporter™ CNV detection algorithms deliver. So, since that filter doesn't exist tofilter out any of the data, all of the somatic VCIB CNV calls get listed as "passed"since the Confidence filter doesn't apply to them and weeds them out.

Appendix A CNV Baseline CreationLaunch an Analysis A


Subset Filter Creation

If you do not want to generate information on all the Oncomine™ variants, you cancreate subset filters to look at only certain genes and variants. This appendix providesexamples for creating subset filters.

Create a Gene-level Filter

If you just want to filter for a set of genes in your Oncomine™ analyses, applying theGene Symbol filter is the easiest approach.

1. Go to Analyses4Overview and select an Oncomine™ analysis' hyperlink.

2. Click the New icon on the Filter Chains panel at the right of your screen.

3. On the Create Filter Chain window, enter a name for your gene-level filter. Forour example, we've named it My Oncomine Genes.

4. In the Choose Filter drop-down menu, select Gene Symbol.

B


5. Type gene symbols of interest one-by-one in the Search text box. For each genesymbol, search, select and Set. For our example, we searched for: MTOR, ALK,and EGFR.

a. Next, go back to the filter drop-down menu and select Oncomine, and setFilter Value to In. Click Set to add it to the filter chain. Click Apply.

b. Click Save Filter Chain in the Details column.

Your new filter is now available for use.

6. Next, copy a relevant workflow and select this new filter chain as the default.

Appendix B Subset Filter CreationCreate a Gene-level Filter B


Create a Variant-level filter

If you only want to review a subset of variants from theoncomine_focus_variantDB.vcf file provided by field support, you first must create avariantDB using that file, then an Annotation Set using the new VariantDB, then afilter chain, and finally a workflow using both the new Annotation Set and FilterChain.

1. Go to Workflows4Presets and click the Create Preset button. Then selectAnnotation Set.

2. On the Create Annotation Set screen, enter a name. For our example, we havenamed it My Onco Variants.

3. In the Choose Type drop-down box, select VariantDB (Custom).

4. Select the Create New tab.

5. Enter a name and version for the new variantDB. In our example, we named itMyoncovariants and set the version to 1.0.

Create a newVariantDB usingthe provided file

Appendix B Subset Filter CreationCreate a Variant-level filterB


6. Scroll down and click Select File. Browse to the oncomine_focus_variantDB.vcffile and click Open. Then click Upload on the Create Annotation Set window.

7. Click Save and My Onco Variants database appears on the Workflow Presetsscreen.

Next, create another Annotation Set that includes the variant DB annotation set youcreated in the previous section.

1. Go to Workflows4Presets and click the Create Preset button. Then selectAnnotation Set.

2. On the Create Annotation Set screen, enter a name. For our example, we havenamed it My Oncomine Variants Subset.

3. In the Choose Type drop-down box, select VariantDB (Custom).

Create a newAnnotation Setusing the newVariantDB andexistingOncomine™

annotationsources

Appendix B Subset Filter CreationCreate a Variant-level filter B


4. On the Choose Existing tab, find Myoncovariants 1.0 and click Use.

5. Next, go back up to the Type drop-down box add the standard Oncomine™

annotation sets. These include: 5000Exomes, ClinVar, dbSNP, DGV, DrugBank,Gene Ontology, Pfam, PhyloP Scores, RefGene Functional Canonical TranscriptsScores, RefSeq GeneModel, and Oncomine™ Canonical Transcripts. Click Useafter selecting each.

Note: Some annotation sets are under existing selections in the pull-down;including RefGene Functional Canonical Transcripts Scores are underSIFT/PolyPhen, RefSeq Gene Model is under Gene Model, and OncomineCanonical Transcripts are under Transcript Set (Custom).

6. Click Save. A new annotation set named My Oncomine Variants Subset has beencreated.



Next, you create a filter chain that incorporates the Myoncovariants DB.

1. Click Create Preset4Filter Chain.

2. On the Create Filter Chain screen, enter a name for your subset filter chain. Wechose My Oncomine Variants Subset Filter.

3. In the Choose Filter drop-down, select the variantDB you created. Per ourexample, we chose Myoncovariants. Select the variant you want to filter in. ClickSet.

4. Select the variants you want to filter in. Click Set.

Create a newFilter Chain usingthe new VariantDB



5. Click Save.Your new variant subset filter can now be applied to analyses.

Now you need to create a new workflow to use the annotation set and filter chain thatyou created.

1. Go to Workflows4Overview. Click the "New Workflow", and clickActions4Copy.

2. On the Annotation tab, add the new annotation set.

Create a copiedWorkflow usingboth the newAnnotation Setand new FilterChain



3. On the Filters tab, add the new filter chain.

4. Name the workflow.

5. Click Save Workflow.Your new workflow is now available for use on the Workflows tab.

Your variants subset workflow is now ready for use.

Select the Oncomine Focus Panel v2 - specific annotations - DNA and RNA Sampleworkflow and launch an analysis.

Use new workflow



CNV Somatic Confidence Filter

Understanding CNV Somatic Confidence Range

The somatic CNV algorithms in Ion Reporter™ Software deliver not only a ploidyestimate call, but also a pair of 90% confidence values. The 5% lower confidencebound value is the ploidy estimate where there is a 5% chance the true ploidy is belowthat value. The 95% upper confidence bound is the ploidy estimate where it is 95%certain that the true ploidy is below that value. For calling focal amplification thelower bound is important and not the upper bound.

Default filtering for the Oncomine™ Focus Assay looks for Gains whose 5%Confidence interval (5% CI) is at least a ploidy of 2 extra copies over the expectednormal ploidy value (expected ploidy is 2 for autosomes, and X in females and 1 in Xin males). The filter will look for Oncomine™ Annotated variants, and for Oncomine™

Annotated CNVs, in most cases gains of 2 + 2 (gain + expected normal)= 4. Currentlythe Oncomine™ Variant Annotator plugin annotates somatic CNVs on allchromosomes for the known copy gain genes on the Oncomine™ Focus Assay resultswhose 5% CI is >= 4.

How do I look for other gains than the default?

To create a custom somatic CNV filter, choose "CNV Somatic Confidence Range"filter, which has OR selected, and uncheck the "Enabled" checkbox for the "MinimumPloidy Loss (95% CI) user expected" filter. Double check that the the "MinimumPloidy Gain (5% CI) over expected" Enabled checkbox is checked. The new valueshould be the ploidy of gain (over expected normal) you wish to threshold on whenlooking at the 5% CI value. So if looking for gains whose 5% CI value is anything overexpected normal of autosomes (2), leave the value set at 0.0.

The default of 0.0 will find all gains whose 5% CI value is of 2 or greater. Setting thevalue to 1.0 will cause the filter look for all gains whose 5% CI value is of ploidy 3 orgreater, for example.

Please Note that the OVAT annotation will be added to known copy gain genes oneach assay's CNVs by looking at the 5%CI value of >=4.

How do I set the filter to look for gains and for losses?

This is relevant especially for the Oncomine™ Comprehensive Assay CNVs whereTumor Suppressor genes are involved and deletion may have a biological impact.

To set a custom filter to look for gains and losses using the CI values, choose the filter"CNV Somatic Confidence Range", and Enable both the "Minimum Ploidy Gain (5%CI) over expected" and the "Minimum Ploidy Loss (95% CI) under expected" filter.

We are now asking the 5% CI value and filter to threshold for Gains, and the 95% CIvalue and filter to threshold Losses.

C


If we set the "Minimum Ploidy Gain (5% CI) over expected greater_than" to 2.0, (2+2=4ploidy for gains, so anything 4 and above will be filtered in as a gain), and the"Minimum Ploidy Loss (95% CI) under expected to be greater_than" value to 0.0(2-0=2 ploidy for losses, so nothing exceeding expected normal of 2 will be filtered inas a loss), we can expect the following example CNV call CI data to cause the CNVdata to be filtered in or out of the results:

A gene with suspected gain with 5% CI = 4.1 and 95% CI = 10.3 will be filtered in

A gene with suspected loss with 5% CI = 0 and 95% CI = 1.0 will be filtered in

A gene with suspected gain with 5% CI = 2.2 and 95% CI = 3.6 will be filtered out (2.2is less than 4)

A gene with suspected gain with 5% CI = 2.1 And 95% CI = 5.2 Will be filtered out (2.1is less than 4)

A gene with 5% CI = 0.8 and 95% CI = 2.1 will be filtered out (0.8 is less than 4 and 2.1is greater than 2)

Appendix C CNV Somatic Confidence FilterUnderstanding CNV Somatic Confidence Range C


No Template Control workaround

Reanalyze analyses with No Template Controls

No Template Controls (NTCs) were not fully supported in Torrent Suite™ Softwarev5.2, but will be supported in Torrent Suite™ Software v5.2.1. If you included NTCs inyour Torrent Suite™ Software v5.2/Ion Reporter™ analysis the "Not enough reads"error may occur. To reanalyze the sample successfully:

1. Locate each NTC sample in the Samples4Overview page in Ion Reporter™

Software.

2. Click the sample's link to open the Define Samples page.

3. In the Attributes screen, select DNA NTC or RNA NTC from the Sample Typedropdown list.

4. Reanalyze the NTC samples with the Oncomine™ Focus - 520 - w2.1 - DNA andFusions - Single Sample workflow.

D


Documentation and support

Related documentation

Document Description

Oncomine™ Focus Assay, Part I: LibraryPreparation User Guide(Pub. No. MAN0015819)

Describes the preparation of Oncomine™

Focus Assay libraries.

Oncomine™ Focus Assay, Part II: Plan aRun, Template Preparation, andSequencing User Guide(Pub. No. MAN0015820)

Describes the automated templatepreparation of Oncomine™ Focus Assaylibraries using the Ion Chef™ System forsequencing on the Ion S5™ System.

Oncomine™ Focus Assay, Part III: VariantAnalysis User Guide(Pub. No. MAN0015821)

Describes how to perform variant analysison Oncomine™ Focus Assay sequence data,and how to view, sort, and filter results.

Note: For additional documentation, see “Customer and technical support“ onpage 29.

Obtain information from the Help system

The Torrent Suite™ Software has a Help system that describes how to use each featureof the user interface.

In the toolbar of the Torrent Suite™ Software window, click Help4Software Help.

You can use the Help system to find topics of interest by:• Reviewing the table of contents• Searching for a specific topic

Customer and technical support

Visit thermofisher.com/support for the latest in services and support, including:• Worldwide contact telephone numbers• Product support, including:

– Product FAQs– Software, patches, and updates

• Order and web support

E


http://thermofisher.com/support

• Product documentation, including:– User guides, manuals, and protocols– Certificates of Analysis– Safety Data Sheets (SDSs; also known as MSDSs)

Note: For SDSs for reagents and chemicals from other manufacturers,contact the manufacturer.

Appendix E Documentation and supportCustomer and technical supportE


For support visit thermofisher.com/support or email [email protected]

thermofisher.com

23 August 2016

http://thermofisher.com/support

mailto:[email protected]

http://thermofisher.com

oncomine focus assay part iii: variant analysis · 4. search by any unique identifier you used to...

Documents