FAQs

This is directly related to the speed of your internet connection. All the data is downloaded/uploaded on the SOPHiA Platform directly from SOPHiA GENETICS Servers and not stored locally. A slow internet connection directly affects performance.

– We recommend a minimum of 10 Mb/s upload speed.

– If you upload large panel files, we recommend a minimum of 20 Mb/s upload speed.

– Please consult your IT department to improve your internet speed limit.

You can use one of the Speed Test links below to confirm your speed connection with our servers based on your location:

Swiss Server

French Server

Australian Server

There could be multiple reasons for a delay.

1) You may have closed your PC before the upload was completed, logged out of your account or removed the files from their original saved location. When a run is uploaded it is associated to a specific, computer, Windows user and a SOPHiA Platform user.

– To resume upload, simply restart the SOPHiA Platform and log in.

– This should be done on the same computer and using the same windows user and the same SOPHiA Platform user credentials that started the run.

– Using other credentials will not work.

2) If you are using a USB key, please make sure not to remove it before the copy is completely finished.

3) If you are using a network folder, make sure the folder is always available during the upload. We recommend making a local copy of the files before starting an upload.

There are two different BRCA1 exon naming conventions.

1) The BRCA1 legacy exon nomenclature is still used by some clinical databases, where exon 4 is missing due to an initial oversight during BRCA1 protein characterization – all following exons have a number increased by one.

2) The standard HGVS/RefSeq/Ensembl nomenclature ranks exons dependent on the specific transcript (NM_*, ENST*) and they are always numbered in increasing order from 1 up to the last exon.

Somatic-FFPE-ctDNA products do not need to follow dual size processing, so less volume of AMpure is needed. Hence all somatic products are composed as:

Box1 in format 48

Box2 in format 32

Variant detection occurs in multiple stages.

1) All the potential variants in the original read alignment are identified, and are subsequently evaluated to remove likely FP while retaining high-confidence variants.

2) A closer investigation considers the reads supporting the variants, including information about other variants in the genomic neighbourhood (e.g. by re-aligning the reads with larger gaps than allowed in the original alignment).

– In some cases, an INDEL can result in FP SNVs (e.g. if the reads do not span the entire INDEL). The SOPHiA Platform identifies these FP artefacts and shifts the supporting reads accordingly (thus moving them from the FP to the real variant). In this situation, a variant can end up having 0% VF as the reads supporting it in the original alignment were shifted to another variant.

– FP artefact variants are kept in the SOPHiA Platform to show you that they were found in the original BAM alignment file, though further analysis showed there is little support for them. Otherwise, you may think they were missed by the SOPHiA Platform, especially if they were detected with a different software. So, in these cases the 0% variant fraction can be interpreted as an FP artefact.

Variants displayed within the SOPHiA Platform are relative to the reference genome (hg19).

There are some cases where the reference genome contains a minor allele. In these cases RefSeq sequences overlapping this region may differ from the reference genome and show the major allele instead. Comparing the sequencing data with the RefSeq sequence, no variant will be identified. However since the SOPHiA Platform uses the reference genome, it will systematically detect a difference and report it.

TIP : The population frequency of the variant is provided within the SOPHiA Platform, making it easy to spot that the variant has a population frequency of almost 100% (and therefore is the major allele) and not clinically relevant.

In the SOPHiA Platform, the Coverage Calculator shows the worst-case minimum coverage among all of the transcripts. If 0 coverage is observed for some transcripts in a gene, the entire gene is listed with 0 coverage. This can be modified by clicking on the “arrow” next to the gene name, to view all transcripts with well covered exons, as well as transcripts with 0-covered exons within the same gene. For detailed instructions please refer to the Operation Manual Section 4.8.

Yes, the Box2 is still usable. The Box2 has to be stocked between +2°C and +8°C but it can travel at room temperature for 5 days. In that case the reagents will not undergo any mutation nor damage. It is just important that the Box2 be stored between +2° and +8°C as soon as possible after reception.

The most common reason is that your Proxy or Firewall is blocking the SOPHiA GENETICS servers. This can be easily fixed by your IT department by updating your firewall rules to allow access to 3 of our servers depending on your location.

France or Belgium, open access to (All in secure mode (https) and port 443):

fr.sophiagenetics.com

ddm.sophiagenetics.com

dev.sophiagenetics.com

Australia, open access to (All in secure mode (https) and port 443):

aus.sophiagenetics.com

ddm.sophiagenetics.com

dev.sophiagenetics.com

 United States, open access to (All in secure mode (https) and port 443):

us.sophiagenetics.com

ddm.sophiagenetics.com

dev.sophiagenetics.com

Canada, open access to (All in secure mode (https) and port 443):

ca.sophiagenetics.com

ddm.sophiagenetics.com

dev.sophiagenetics.com

Other countries, open access to (All in secure mode (https) and port 443):

ch.sophiagenetics.com

ddm.sophiagenetics.com

dev.sophiagenetics.com

If the SOPHiA Platform cannot automatically detect your proxy configuration based on the computer’s network settings, you will need to define the proxy configuration and force SOPHiA Platform to use it.

Example: if you need to go through the proxy “”sophiagenetics”” and the port 8000, you can create a file in c:\Users\userfolder\.dg-cache\proxyCfg.txt with the following text:

-Dhttps.proxyHost=sophiagenetics

-Dhttps.proxyPort=8000

-Dhttp.proxyHost=sophiagenetics

-Dhttp.proxyPort=8000

If your proxy also needs authentication, the user will be prompted upon startup to enter the credentials.

The variant fraction of the INDEL is based on all the reads at the start position of the deletion (anchor position), including reads that do not span the entire deletion. If other software only counts reads that span the deletion, the variant fraction could be different.

Some samples may exhibit increased fluctuation in the normalised coverage levels per target region, which is reported in the “result summary” and the per-sample coverage plots in the CNV report. In such cases, it is not possible to distinguish coverage “noise” from real CNVs, and this is why samples may be rejected from CNV calling.

TIPs

– The fluctuation of the normalized coverage depends on many factors like the purity of the DNA sample, stability of the laboratory conditions and preparation steps, and the number of samples analyzed in a run.

– Analyzing more samples together (of the same gene panel) generally improves the accuracy of the CNV detection and reduces the number of rejected cases.

– The reliability of CNV detection depends much more on the library preparation and amplification steps than on the sequencing step, so high base call quality does not guarantee that CNV calling will be successful.

We recommend using D1000, High sensitivity.

You can request this information in the OR-Ticket assigned to your order.

The BDS number can be found at two different locations:

  • On the side sticker of Box 1 of the SOPHiA GENETICS Bundle Solution (-15 °C to -25 °C storage temperature)
  • In the annex of the delivery note

For detailed instructions please refer to the Operation Manual Section 2.3.

BDS FAQ

Figure 1: Location of BDS numbers on SOPHiA GENETICS Bundle Solution kit box 1

Note: each BDS number is related to one lot number and Bundle Solution kit box. If different members of your team conduct library preparation and sample upload, please make sure that they are all informed about this implementation.

Please email technical support at [email protected] and explain the situation. Our experts will take care of your request.

You can request this information in the OR-Ticket assigned to your order.

This means at least one of the uploaded FASTQ files is corrupted.

– Often this can be fixed by copying the files again from the sequencer to your pc followed by a second attempt at uploading to the SOPHiA Platform.

– If you use a USB key, please make sure not to remove it before the copy is completely finished.

– If you are using a network folder, make sure the folder is available during the upload.

– We recommend that you make a local copy before starting the upload.

TIP: Confirm that you are using zipped FASTQ files “*.fastq.gz”

Non-Regression Reports are generated after major SOPHiA Platform updates that could affect variant detection. Such reports are sent at least one week before the Platform update. Most minor SOPHiA Platform updates do not affect the variant detection in commercial panels and are not included in Non-Regression Reports.

Please contact our support by sending an email to this address: [email protected] You can explain the situation and our experts will take care of this request.

Please email technical support at [email protected] and explain the situation. Our experts will take care of your request.

This filter is designed to reduce the number of false positive (FP) variant calls and avoid false negatives (FN) in homopolymer regions on IonTorrent platforms. It works by distinguishing systematic errors from the real biological variant signal. The signal is compared across samples, and if a certain pattern is found in every sample it is regarded as a likely systematic error and not real.

This variant caller handles only variants in homopolymers (i.e., variants that change the length of the homopolymer) or small INDELs like single nucleotide insertions or deletions, as such variants are known to be most affected by errors of the IonTorrent platform. This filter does not affect SNPs or other types of INDELs.

IMPORTANT NOTE: The module requires a minimum of 4 samples (minimum 8 recommended). Fewer than 4 samples will not benefit from the multi-sample variant caller, leading to potential differences in the reported variants.

TIP: only samples processed together should be analysed together, as error profiles can be different between runs.

Both exon numbering systems are available in the SOPHiA Platform.

– On the SNVs/INDELs and Warnings tab, legacy exon names are given in the exon_id column and RefSeq exon numbers are displayed in the exon_rank column (the corresponding RefSeq transcript is in the ReqSeq/Transcript column).

– On the CNV results page, the copy numbers are reported with the legacy exon names. These can be matched to RefSeq exon numbers using the gene structure plot provided in the SOPHiA Platform.

While uploading a run, you may need to manually select the experiment type (Somatic / Germline). Simply double-click the Experiment Type and select the correct value for each sample.

This warning only affects amplicon-based target enrichment.

The presence of a variant in the region where the primer anneals can affect binding affinity, and low binding affinity can affect the PCR amplification. The end result is that for this particular allele, the entire amplicon may not amplify, and hence “”allele dropout” (no longer visible in the data). Only sequences from reads from the allele without the variant would be present in the data. If there are any other variants on the same allele (as the variant causing the allele drop-out) and they are not covered by other amplicons, they will be missed.

Variants that can cause an allele drop-out will only be detected if there are other amplicons overlapping the primer region. The end primer of the last amplicon of a target region or the primers of standalone amplicons will not be covered, so the SOPHiA Platform can not provide a warning for potential drop-outs in such amplicons.

TIP: In such cases, the relative coverage for that amplicon would be lower. If CNV analysis is available for a given panel, it can confirm an allele drop-out in the same region as a deletion / undetermined status. If there is no CNV result, we recommend comparing the relative coverage of this amplicon across several samples. The majority of SNVs will likely not cause an issue, since many enrichment kit providers include common polymorphisms in their primers. In the case of INDELs, an allele drop-out is very probable, and we recommend confirming the region with another method (e.g. Sanger sequencing.)

Using PMS2 and PMS2CL as an example: For both gene and pseudogene, exons 11-15 are very similar and the SOPHiA Platform provides a warning for all variants that are detected in PMS2 exons 11-15 according to one of 3 categories:

Pseudogene_identical

applies to all variants detected in PMS2 exon 15, which are identical to the corresponding exon in PMS2CL. This warning indicates that it is impossible to distinguish a variant listed for PMS2 exon 15 from a variant that may be located in the corresponding exon in pseudogene PMS2CL.

Pseudogene_polymorphism

applies to variants detected in PMS2 exon 13 or exon 14, which are very similar to the corresponding exons in PMS2CL and – importantly – where gene conversion is frequently observed. These PMS2 exons may have replaced the corresponding sequence in the PMS2CL pseudogene locus or vice versa. Despite the fact that PMS2 and PMS2CL sequences can be distinguished in these exons, no high confidence conclusions can be made since the observed PMS2 sequence (and any variants detected in this context) could originate either from the PMS2 gene locus or the PMS2CL pseudogene locus (due to gene conversion).

Pseudogene_distinct

applies to variants detected in PMS2 exon 12 or exon 11, which are very similar to the corresponding exons in PMS2CL but where gene conversion is rare. Here, the PMS2 sequence can be distinguished from the corresponding PMS2CL sequence with reasonable confidence (e.g. the observed PMS2 sequence (and any variants detected in this context) actually originates from PMS2 and not the PMS2CL pseudogene).

Please email technical support at [email protected] and explain the situation. Our experts will take care of your request.

This error is related to the use of certain theme configurations in MS Windows and is easily fixed.

View this short video or follow the instructions below.

https://youtu.be/T_o_c_KR8BI

1) Go to Settings in Windows
2) Click on Personalisation
3) Go to Themes
4) Click on Theme Settings
5) From the drop-down, select, for example, “High Contrast White”. Any theme with a high contrast value should be fine.

There are several reasons why the SOPHiA Platform may classify a variant as “low-confidence”.

1. The variant may occur in a low complexity region (e.g. homopolymers or heteropolymers). Such regions adversely affect amplification (polymerase slippage) and hinder reliable variant calling. Variants in these regions are filtered with a “problematic_region” tag.

2. The variant may have a variant fraction lower than expected (germline) or lower than what can be confidently called with a statistical test (somatic). Variants with low variant fractions are filtered as “ow_variant_fraction”.

3. A variant with low coverage is filtered with a “low_coverage” tag. Many germline solutions give warnings for regions covered with less than 50x and any variant detected in a region with less than 30x will be classified as low-confidence. The exact thresholds may vary between solutions.

4. In some somatic solutions, a minimum number of supporting reads (usually at least 50) for the alternate sequence is required for confident variant calling. Variants that were detected but are not supported by at least 50 reads are filtered as “low_alt_coverage”.

5. Variants outside the target region of the solution are filtered as ‘off-target’. For capture-based solutions, many off-target variants may be observed in regions flanking the target region that still have sufficient coverage for reliable variant calling.

6. INDELs in long homopolymers are filtered as ‘homopolymer_region’. Long homopolymers impede reliable variant calling due to experimental artefacts like polymerase slippage leading to elevated sequencing errors. A high error rate in homopolymers is often observed on most sequencing platforms. Therefore, any INDEL identified in homopolymers greater than a certain length (exact length cut-offs are solution-specific) are filtered as “homopolymer_region”.

Variants outside the target region defined by the solution are filtered as “off-target”.

– For capture based enrichment, many off-target variants may be observed in regions flanking the target region that still have sufficient coverage for variant calling.

– For amplicon-based enrichment, if the variant is located in the region covered by a primer and no other amplicons overlap this region, they are classified as “off target”.

Low clustering possible causes (1200 to 1400 K/mm2 expected for Illumina MiSeq v3):

– Imprecise quantification of final libraries

– Inaccurate dilution/mixing of libraries before loading

– Denaturation issues

– Insufficient mixing of the MiSeq reagent cartridge (normally requires 10x inversion once thawed)

High clustering possible causes:

– Imprecise quantification of final libraries

– Inaccurate dilution/mixing of libraries before loading on the MiSeq

The acceptance standard for a Non-Regression Report is that the overall variant detection sensitivity in any validated solution (measured on all confirmed reference variants) must be unchanged or increased. Any changes in the detection of reference variants are analysed in detail and are explained by bioinformatics experts in the report.

Our laboratory organises the shipment (pickup) of both boxes the same day but occasionally the two boxes may continue the journey separately.

The second box should arrive soon.

Our logistics team is constantly tracking all your shipments to make sure you will be delivered as soon as possible.

The logistics team continually tracks all shipments to ensure rapid delivery to you. The laboratory organizes the shipment (pick up) of both boxes on the same day however, depending on the transporter, the boxes might continue the journey separately.

Ensure the following capture protocol recommendations are respected:

Speedvac parameters

Ensure the use of:

– Low bind tubes

– Suitable 1.5 ml tube rotor

– Temperature settings between 45 and 50°C (we recommend 45°C with machine settings on medium).

The DNA pellet should be visible.

Wash buffer preparation

Ensure that all reagents used to prepare buffers are properly mixed (vortex). This is particularly important for “Wash Buffer I” that typically contains precipitates.

Hybridization and washes

Always use a calibrated thermocycler and verify heat block temperature with a calibrated thermometer.

– During the stringent washes follow the exact protocol timing for each step.

– Pipet gently.

– Never vortex.

PCR

Always use a completely thawed polymerase mix and ensure homogenization before use.

– Prepare small aliquots if numerous freeze/thaw cycles are required.

– Make sure to properly mix the PCR reaction on the beads.

DNA Clean up

AMPure beads must be equilibrated at room temperature.

– Do not over-dry the beads (no visible cracks) as this reduces the yield of recovered DNA.

Yes, the custom filter builder can be used to find variants with low variant fractions. For detailed instructions please refer to the Operation Manual Section 5. Alternatively follow these simplified instructions:

1) New filters use only retained variants by default. Low confidence variants can be added by dragging the built-in rule “Low confidence” onto the left bar with the initial variants count. This ensures your new filter contains both retained and the low-confidence variants.

2) Create a filter for the low-confidence variants based on the filter value. Select “Filter” from the drop down box on the top right corner and drag it onto the “”low confidence variants”” box. By selecting this feature the filter value should be “low_variant_fraction”, and as a result, only low-confidence variants that were previously rejected for low variant fraction will now be kept.

3) This filter may be further adapted to include other parameters such as applicability to only variants in certain genes, of certain coding consequences, etc..

No. It is not possible to perform captures with only 1 sample.

The SOPHiA capture protocols have been optimized to work in general with 4, 8 and 12 samples per capture*.

– These formats are designed to optimize multiplexing for each solution.

– Performing captures with only 1 sample would require a higher amount of starting DNA to obtain good results.

– Efficient captures require a minimum amount of DNA (between 1.2 µg and 1.8 µg for our protocols) and an appropriate number of probes.

* The Whole Exome Solution by SOPHiA GENETICS is the only kit where a capture with 3 samples is possible due to the large amount of probes.

No, it is not possible to over dry the pellet. However, care should be taken when proceeding to the hybridization step

– Always ensure that the pellet is well re-suspended when transferring the full volume to a PCR tube

The SOPHiA Platform does not use paired-end information to detect structural rearrangements: genomic rearrangements cannot be detected. If a genomic rearrangement occurs in or adjacent to some amplicons, they will likely not amplify correctly. Thus, there would be no useable data.

It may be possible to multiplex samples in the same run if the following conditions are met:

1) Using an index length of 8bp

2) Using standard Illumina sequencing primers

3) Using a MiSeq™, NextSeq™ or HiSeq®

For the MiniSeq™ platform, simultaneous analysis on both kits is not possible. In this case, samples can still be sequenced together but will require separate analysis. This can be accomplished by analysing the samples from the other commercial kit first and then re-importing the run into a new analysis once the first has completed.

The Variant Filter Builder is a cross functional tool that allows you to create and apply custom filters to variants based on different operators / variables and built-in rules, including the ability to set custom thresholds.

For example, when setting a custom threshold for the pathogenic community value:

– Add “level:count”. Here, the “level” refers to the pathogenicity flag, while the “count” refers to the number of times that this variant has been flagged as such.

If you already know the number of times that a specific pathogenicity flag has been used, you can use a definitive number with the setting of “MATCHES WITH”.

– Example: a variant that has been flagged as pathogenicity level 4, three times by the community. You will then add the following to the value field 4:3

If you do not know the number of times that a specific pathogenicity flag has been used, you can make use the wildcard symbol “*” which represents “anything”

– Example: a variant that has been flagged as pathogenicity level 5, multiple times by the community. You will then add the following to the value field 5:*

If you would like to add multiple values, these can be added and separated by a comma.

– Example: a variant that has been flagged as pathogenicity level 4, three times by the community OR a variant that has been flagged as pathogenicity level 5, multiple times by the community 4:3, 5:*

For detailed instructions please refer to the Operation Manual Section 5.

See screenshots to illustrate this filter.

csm screenshot 1
csm screenshot 2

SOPHiA Platform updates are not released until all known issues are addressed. The Non-Regression Reports that are sent reflect the final optimized status of variant detection.

For detailed instructions please refer to the Operation Manual Section 2.2.

Alternatively, please refer to this short educational video:

https://youtu.be/z0lJU-SHl1E

The usage information is displayed*:

– In the “Create Request Form”, next to the BDS number in the drop-down list.

– On the SOPHiA Platform dashboard.

For detailed instructions please refer to the Operation Manual Section 2.3.

BDS FAQ 4

New “BDS Numbers” field available in the Dashboard of SOPHiA DDM. * Not available for kits received through distributors

Exception:

BDS implementation does not concern applications using:

  • Swift Biosciences kits 
  • Devyser kits
  • Illumina Inc. kits
  • Archer Dx FusionPlex® kits
  • Agilent Technologies Inc. MASTR™ kits

The Variant Database Browser (VDB) can be filtered according to various pre-set parameters such as:

– Chromosome number

– Genomic position

– Gene name

– Specific position of cDNA or protein annotations

Once information has been added to the filters, the VDB displays the instances of this variant in all samples in all runs within your account.

For detailed instructions please refer to the Operation Manual Section 10.

Please email technical support at [email protected] and explain the situation. Our experts will take care of your request.

For detailed instructions please refer to the Operation Manual Section 1.1.

Or alternatively, please watch this short educational video:

https://youtu.be/aM_SFRVp2BE

The SOPHiA Platform normalizes the scores provided by the different databases to enable comparisons among the difference sources. For all predictive scores, a value of 1 means likely pathogenic and 0 likely benign irrespective of the database. The scores are transformed as:

SIFT 

“1 – SIFT” score (the original SIFT score is opposite, with 0 being predicted pathogenic and 1 benign)

PolyPhen2 

No transformation (there are two different PolyPhen2 scores, HVAR and HDIV, based on different training sets)

MutationTaster 

Combination of prediction and score (1 – confident, 0 not confident). The SOPHiA Platform displays the score if the prediction is pathogenic or “1 – score” if the prediction is benign

LRT score (not in spider plot but can be selected in the variant table) 

Contains the score and a value omega. The SOPHiA Platform displays “1 – LRT score x 0.5” if omega < 1 or “LRT score x 0.5” if omega ? 1

More detail of such transformations can be found in the dbNSFP database publication:

HTTPS://DOI.ORG/10.1002/HUMU.21517

The document is included inside both packages. If you need an additional copy please send an email to [email protected] and specify the purchase order number in your email.

BDS numbers should be entered when you create a “New Batch Request”.

On the second page of the “Create Request Form”, the BDS column is shaded in gray.

  • Right click in the grey area corresponding to your samples, select the BDS number from the drop-down list.
  • For multiple samples, you can set the BDS number by pressing and holding the CTRL key (or CTRL+SHIFT). Simultaneously click on the relevant samples. Then select the BDS number from the drop-down list.

For detailed instructions please refer to the Operation Manual Section 2.3.

bds faq 2
Figure 2: Second page of the Create Request Form. A dropdown menu allows selection of the BDS numbers available in the account and for a specific test.

Library pool(s) can be diluted in water to reach the recommended final concentration for sequencing: 100pM for the One Touch 2 System, or 75pM for the Ion Chef System.

When stored in low bind tubes, DNA being very stable, libraries may stay at –20°C for months/years prior to usage.

After a long-term storage, it is preferable to repeat quantification by a fluorometric quantitation (e.g. Qubit®, Thermo Fisher Scientific) before usage.

Hotspots can be SNVs or INDELs defined at a genomic, cDNA or protein level.

The SOPHiA Platform has the capability to screen for known hotspot mutations during variant analysis, where the presence or absence of known hotspots is determined (or if they cannot be determined with confidence). If hotspot screening is enabled, it is still possible to switch the Platform view to see all detected variants in all genes of the corresponding solution.

Diseases can easily be added when a new interpretation project is created.

1) After selecting “Add interpretation”, a new window will appear.

2) In the pop-up window, a new link “select” is available.

3) Once clicked, the Disease Ontology tree opens to select a disease.

This disease tree can be searched or alternatively, you can start typing the respective disease name. The list of matching disorders are then immediately highlighted in the list.

TIPs:

– You can bookmark regularly selected diseases by clicking the “star” icon next to the disease.

– In cases where several diseases should be selected simultaneously, hold CTRL (MAC: ?cmd) while selecting several diseases.

For detailed instructions please refer to the Operation Manual Section 3.11.3.

add disease fig 1
Figure 1: Select a disease from any level of the ontology tree.

SEARCH FOR A DISEASE

The disease tree can be easily searched. Start typing the respective disease name, the list of terms containing the substring is instantly updated and resulting disorders are highlighted in the list.

BOOKMARK A DISEASE

Users can bookmark often selected diseases by clicking the “star” icon next to the disease. Alternatively, users can click Shift + B (Fig. 2). In both cases, the disease then appears and is saved in the list of bookmarks above the tree.

add disease fig 2
Figure 2: Bookmark a disease by clicking the “star” icon or pressing Shift + B.

MULTI-SELECT DISEASES

Several diseases can be selected and added to an interpretation project by clicking CTRL (Mac: ?cmd) while selecting them (Fig. 3).

add disease fig 3
Figure 3: Multi-select several diseases. Click to select a disease, hold CTRL pressed, select one or more other diseases. Click OK to confirm. All diseases are added to the interpretation project.

The SOPHiA Platform evaluates the impact of each variant using all RefSeq (NM) transcripts of the gene. For each variant, the platform displays the transcript for which it is most deleterious. The variant annotation (coding consequence, cDNA HGVS nomenclature, protein effect) is then provided relative to this transcript. This method is used to minimise the probability of missing a potentially pathogenic mutation.

Upon request, Non-Regression Reports for validated solutions are provided by SOPHiA GENETICS and are sent by email by Subject Matter Experts (SME) or sales representatives.

To create a sample sheet for a MiSeqTM, we recommend using the “”Illumina experiment manager”” software (see details below). The list of index sequences can be found in the annex part of the Bundle Solution by SOPHiA GENETICS protocol.

Follow these instructions in the “”Illumina experiment manager”” software:

– Open the software and click on “Create Sample Sheet”

– Choose “MiSeq”, then “Other”, followed by “FASTQ Only”

– Enter the Reagent Cartridge Barcode (for example MS5903244-300V2 found on the front of the cartridge)

– For the Library Prep Kit, select “TruSeq HT” (Note: if TruSeqHT indices do not appear (new version of Illumina software) select “TruSeq DNA PCR-Free” as the Library Prep Workflow. Followed by “TruSeq DNA CD Indexes” (96 indexes) as the Index Adapters.)

– For Index reads select “2”

– Enter the experiment name

– Enter the investigator name

– Enter a brief description of the experiment

– The date should be automatically entered as the current date; if not, enter the date in the MM/DD/YYYY format.

– Select “Paired End” for read type

– For “Cycles Read 1” choose the number of cycles (for example 151 for a V2 300 cartridge or 301 for a V3 600 cartridge)

– For “Cycles Read 2” choose the same number of cycles as above

– Select “Use Adapter Trimming” and “Use Adapter Trimming Read 2”

– Click on “Next”

– Click on “Add Blank Row” as many times as correlates to the number of samples you have.

– Enter the “Sample ID”, “Index 1 (I7)” and “Index 2 (i5)”” for all your samples according to the table found in the Annex of the Bundle Solution by SOPHiA GENETICS protocol

– Select “Finish” and save the file in “csv” format

You can request this information in the OR-Ticket assigned to your order.

To confirm, please contact support ([email protected]) to find out if an application already exists for your sequencer.

– If the application already exists, it could be activated for immediate use.

– If it does not exist, more time will be needed to develop the application (via our Set-Up Programs).

All SOPHiA GENETICS applications are optimized using real clinical data for a specific combination of sequencer, sample type, gene panel and amplification technology (capture, amplicon, others).

No. Please email technical support at [email protected] and explain the situation. Our experts will help you.

Any generic vacuum pump can be used.

– The only requirement is that the vacuum pump must be compatible with 1.5 ml (low bind) tubes.