1 Refer to “Note 1—Change in accounting policies—Statement of Cash Flows - Interest Classification” for details on change in accounting policy.

SOPHiA GENETICS SA and its consolidated subsidiaries (NASDAQ: SOPH) (“the Company”) is a cloud-native software company in the healthcare space, incorporated on March 18, 2011, and headquartered in Rolle, Switzerland. The Company is dedicated to establishing the practice of data-driven medicine as the standard of care in health care and for life sciences research. The Company has built a cloud-native software platform capable of analyzing data and generating insights from complex multimodal datasets and different diagnostic modalities. This platform, commercialized as “SOPHiA DDM TM,” standardizes, computes, and analyzes digital health data and is used in decentralized locations to break down data silos. The Company collectively refers to SOPHiA DDM TM Platform and related products and solutions as “SOPHiA DDM Platform.”

As of March 31, 2025, the Company had the following wholly owned subsidiaries:

All intercompany transactions and balances have been eliminated in consolidation.

The Company’s Board of Directors approved the issue of the unaudited interim condensed consolidated financial statements on May 6, 2025.

These unaudited interim condensed consolidated financial statements, as of and for the three months ended March 31, 2025, of the Company have been prepared in accordance with International Accounting Standard (“IAS”) 34, Interim Financial Reporting (“IAS 34”) as issued by the International Accounting Standards Board (“IASB”) and should be read in conjunction with the audited consolidated financial statements as of and for the year ended December 31, 2024.

The material accounting policies adopted in the preparation of these unaudited interim condensed consolidated financial statements are the same as those applied in the Company’s annual consolidated financial statements as of and for the year ended December 31, 2024, other than those described below, and have been consistently applied, unless otherwise stated. Where expense is definitively calculated only on an annual basis, as is the case for income taxes and pension costs, appropriate estimates are made for interim reporting periods.

Borrowings are initially recognized at fair value, net of transaction costs incurred. Transaction costs include any incremental costs directly attributable to the acquisition of the financial liability, that would otherwise have not been incurred if the Company did not acquire the financial instrument. Borrowings are subsequently measured at amortized cost using the effective interest method. The effective interest method recognizes any difference between the loan proceeds, net of transaction costs, and the redemption amount as interest expense through the profit and loss statement for the period. Changes in the effective interest rate (“EIR”) are updated prospectively based on the most recent interest payment rate at the end of each reporting period. Borrowings are removed from the balance sheet when the obligation is discharged, cancelled, or repaid. When the borrowing is removed from the balance sheet, any difference between the carrying amount of the financial liability, and the consideration paid, is recognized in profit or loss as a non-operating income or expense. Borrowings are classified as current liabilities unless the maturity date is greater than 12 months or Company has an unconditional right to defer settlement of the liability for at least 12 months after the reporting period.

Taxes on income in the interim periods are accrued using the tax rates that would be applicable based on the expected annual profit or loss of each of the Company entities.

Post-employment defined benefit plan expense in interim reporting periods is recognized on the basis of the current year cost estimate made by the actuaries in their annual report as of the end of the preceding year. Potential remeasurement gains or losses from the defined benefits plan are estimated based on the relevant indexes at the end of the reporting period and recorded in the Company’s statements of comprehensive loss.

Previously, the Company had designated cash in a separate bank account to be used exclusively to settle potential liabilities arising from claims against Directors and Officers covered under the Company’s Directors and Officers Insurances Policy (“D&O Policy”). Setting up the designated account significantly reduced the premiums associated with the D&O Policy. As of March 31, 2024 the Company had $15 million of designated cash in a separate bank account to be used exclusively to settle potential liabilities arising from claims against Directors and Officers covered under the Company’s D&O Policy. In June 2024, the Company renewed the policy and under the new D&O policy removed the requirement for the Company to maintain a designated cash amount. The new D&O policy and elimination of designated cash went into effect in July 2024.

Effective January 1, 2025, the Company revised its accounting policy regarding the classification of interest paid and interest received in the Statement of Cash Flows. Interest paid was reclassified from Net cash flows used in operating activities to Net cash flows used in financing activities, and interest received was reclassified from Net cash flows used in operating activities to Net cash flows used in investing activities. The Company assessed the change in accounting policy under IAS 8, in accordance with the guidance regarding a voluntary change in accounting policy.

The reclassification of interest paid was elected to provide a more cohesive presentation of payments related to the Company’s borrowings and lease liabilities. Prior to the change in accounting policy, interest paid on borrowings and lease liabilities were classified as operating cash flows, while proceeds from borrowings, net of transaction costs and payments of principal portion of lease liabilities are classified as financing cash flows. The change aligns interest payments with their associated transactions.

In addition, the Company reclassified interest received to investing activities, as the majority of interest received relates to interest earned on cash and cash equivalents and short-term investments. The Company believes this updated classification better reflects the nature and source of these cash inflows and provides more relevant and reliable information.

The Company determined the voluntary change in accounting policy did not have an impact on basic and diluted earnings per share under IAS 33 - Earnings per Share.

The Company applied the change in accounting policy retrospectively and has recast prior period comparative information within the Statement of Cash Flows to ensure consistency and comparability with the current period presentation. As part of the retrospective application, cash flows changed as follows for the three months ended March 31, 2024: Net cash used in operating activities increased by $0.8 million, Net cash flow used in investing activities decreased by $1.0 million, and Net cash flow used in financing activities increased by $0.1 million.

There are no new IFRS standards, amendments, or interpretations that are mandatory as of January 1, 2025 that are relevant to the Company.

In April 2024, IFRS 18, Presentation and Disclosure in Financial Statements, was issued to achieve comparability of the financial performance of similar entities. The standard, which will replace IAS 1 impacts the presentation of primary financial statements and notes, including the statement of earnings where companies will be required to present separate categories of income and expense for operating, investing, and financing activities with prescribed subtotals for each new category. The standard will also require management-defined performance measures to be explained and included in a separate note within the consolidated financial statements. The standard is effective for annual reporting periods beginning on or after January 1, 2027, and requires retrospective application. The Company is currently evaluating the new standard to determine if it will have a material impact on the Company’s financial statements.

There are no other IFRS Accounting Standards or IFRS Interpretations Committee interpretations that are not yet effective and that could have a material impact to the interim condensed consolidated financial statements.

The preparation of the unaudited interim condensed consolidated financial statements in conformity with IAS 34 requires management to make judgments, estimates and assumptions. Information regarding accounting areas where such judgments, estimates and assumptions are of particular significance is set out in the annual financial statements under “Critical estimates and judgments.”

These unaudited interim condensed consolidated financial statements have been prepared on a going concern basis.

Items included in the financial statements of each of the Company’s entities are measured using the currency of the primary economic environment in which the entity operates (“functional currency”). The Company’s reporting currency of the Company’s consolidated financial statements is the United States Dollar (“USD”). Assets and liabilities denominated in foreign currencies are translated at the month-end spot exchange rates, income statement accounts are translated at average rates of exchange for the period presented, and equity is translated at historical exchange rates. Any translation gains or losses are recorded in other comprehensive income (loss). Gains or losses resulting from foreign currency transactions are included in net income.

The financial statements have been prepared on a historical cost basis except for certain assets and liabilities, which are carried at fair value.

As of March 31, 2025, the Company had issued 79,321,220 shares, of which 66,821,501 are outstanding, and 12,499,719 are held by the Company as treasury shares. As of March 31, 2024, the Company had issued 76,898,164 shares, of which 65,375,093 were outstanding, and 11,523,071 were held by the Company as treasury shares.

On July 5, 2024, the Company issued 2,423,056 registered shares to SOPHiA GENETICS LTD pursuant to a share delivery and repurchase agreement, which were immediately exercised, and repurchased the shares to hold as treasury shares for the purposes of administering the Company's equity incentive programs along other uses. As of March 31, 2025, the Company held 12,499,719 treasury shares. As of March 31, 2024, the Company held 11,523,071 treasury shares.

Treasury shares are recognized at acquisition cost and recorded at the time of the transaction. Upon exercise of share options or vesting of restricted stock units, the treasury shares are subsequently transferred. Any consideration received is included in shareholders’ equity.

As of March 31, 2025, the carrying amount was a reasonable approximation of fair value for the following financial assets and liabilities:

•Cash and cash equivalents

•Accounts receivable

•Other non-current assets—lease deposits

•Accounts payable

•Accrued liabilities

•Lease liabilities

•Borrowings

The following table presents the Company’s fair value hierarchy for its financial assets and financial liabilities that were measured at fair value on a recurring basis (in thousands):

In the three months ended March 31, 2025, there were no significant changes in the business or economic circumstances that affected the fair value of the Company’s financial assets and financial liabilities.

In the course of its business, the Company is exposed to a number of financial risks including credit and counterparty risk, funding and liquidity risk and market risk (i.e. foreign currency risk and interest rate risk). The unaudited interim condensed consolidated financial statements do not include all financial risk management information and disclosures required in the annual financial statements and should be read in conjunction with the Company’s consolidated financial statements as of December 31, 2024. There have been no significant changes in financial risk management since year-end.

The Company operates in a single operating segment. The Company’s financial information is reviewed, and its performance assessed as a single segment by the senior management team led by the Chief Executive Officer (“CEO”), the Company’s Chief Operating Decision Maker (“CODM”).

When disaggregating revenue, the Company considered all of the economic factors that may affect its revenues. The Company assesses its revenues, both SOPHiA DDM Platform and Workflow equipment and services revenues, by four geographic regions Europe, the Middle East, and Africa (“EMEA”); North America (“NORAM”); Latin America (“LATAM”); and Asia-Pacific (“APAC”). Additionally, the Company assesses revenues generated in its domiciled country and any country with significant revenue. The Company determines the country in which the revenue is generated based on the end customer geographic location. The following table disaggregates the Company's revenue from contracts with customers by geographic market (in USD thousands):

The Company’s revenue from contracts with customers has been allocated to the revenue streams indicated in the table below (in USD thousands):

The following table presents the trade receivable and accrued contract revenue less the expected credit loss (in USD thousands):

The Company records increases to, reversals of, and write-offs of the allowance for expected credit losses as “Selling and Marketing” expenses within its interim condensed consolidated statements of loss. The following table provides a rollforward of the allowance for expected credit losses for the three months ended March 31, 2025 and 2024, that is deducted from the amortized cost basis of accounts receivable to present the net amount expected to be collected (in USD thousands):

As of March 31, 2025 and December 31, 2024, the Company’s largest customer’s balance represented 16% and 18% of accounts receivable, respectively. All customer balances that individually exceeded 1% of accounts receivable in aggregate amounted to $7.0 million and $5.0 million as of March 31, 2025 and December 31, 2024, respectively.

The Company’s shares are comprised of ordinary shares. Each share has a nominal value of $0.05 (CHF 0.05). The basic loss per share is calculated by dividing the net loss attributable to shareholders by the weighted average number of shares in issue during the period excluding treasury shares, which are owned by the Company. The table presents the loss for the three months ended March 31, 2025 and 2024, respectively (in USD thousands, except shares and loss per share):

For the three months ended March 31, 2025 and 2024, the potential impact, on the calculation of loss per share, of the existing potential ordinary shares related to the share option plans and warrants are not presented, as the impact would be to dilute a loss, which causes them to be deemed “non-dilutive” for the purposes of the required disclosure.

On June 27, 2024 the Company entered into a 73-month lease for office space in Boston, Massachusetts primarily to support the expansion of the Company’s growth in the United States. The lease in total is for approximately 12,807 square feet. The Company makes fixed payments and additional variable payments depending on the usage of the asset during the contract period. Upon gaining access to the space in September 2024, the Company recorded a right-of-use asset of $2.0 million and a lease liability of $1.9 million. The difference between the ROU and lease liability of less than $0.1 million is driven by initial direct costs to obtain the lease.

On May 2, 2024 (the “closing date”), the Company and its subsidiary SOPHiA GENETICS, Inc. entered into a credit agreement and guaranty (the “Perceptive Credit Agreement”) with Perceptive Credit Holdings IV, LP, as lender and administrative agent, pursuant to which the Company may borrow up to $50.0 million principal amount of term loans, including (i) an initial tranche of $15.0 million principal amount of term loans on the closing date and (ii) up to $35.0 million principal amount of term loans that the Company may draw upon on or prior to March 31, 2026, subject to satisfaction of certain customary conditions. The term loans are scheduled to mature on the fifth anniversary of the closing date and accrue interest at Term SOFR plus 6.25% per annum. The Perceptive Credit Agreement contains customary covenants, including an affirmative covenant to maintain qualified cash of at least $3.0 million, an affirmative last twelve months revenue covenant tested on a quarterly basis beginning June 30, 2024, and negative covenants including limitations on indebtedness, liens, fundamental changes, asset sales, investments, dividends and other restricted payments and other matters customarily restricted in such agreements.

In addition, the Company issued to Perceptive Credit Holdings IV, LP a warrant certificate representing the right to purchase up to 400,000 ordinary shares at $4.9992 per share, with 200,000 ordinary shares available immediately and an additional 200,000 ordinary shares to be available upon the drawdown of the second tranche of the term loans.

The Company calculated the fair value of the warrant obligation on issuance using the Black-Scholes pricing model. The warrant obligation was recorded at an initial fair value of $0.7 million on May 2, 2024. Key inputs for the valuation of the warrant obligation upon issuance were as follows:

The Company remeasures the fair value of the warrant obligation on a quarterly basis. Key inputs for the remeasurement of the warrant obligation as of March 31, 2025 and December 31, 2024 were as follows:

The loan was recorded at an initial amortized cost of $13.3 million on May 2, 2024. This amount represents the residual amount of the $15.0 million draw down after allocating $0.7 million for the fair value of the warrant obligation and the $1.1 million of transaction costs to be amortized as interest expense over the life of the loan.

The following table presents any movements in the liability for the three months ended March 31, 2025 (in USD thousands):

The Company estimated the EIR over the three months from March 31, 2025 to June 30, 2025 as 14.42%.

The Company notes there were no outstanding amounts under this credit agreement for the three months ended March 31, 2024.

On April 23, 2024 the Company terminated its existing credit agreement with Credit Suisse SA for up to CHF 5.0 million ($5.5 million). Additionally, the Company entered into a new credit agreement with Credit Suisse SA for up to CHF 0.1 million ($0.1 million) to be used for cash credits, contingent liabilities, or as margin for OTC derivative transactions. Borrowings under the new credit agreement will bear interest at a rate to be established between the Company and Credit Suisse SA at the time of each draw down. As of March 31, 2025, the Company had no borrowings outstanding under the Credit Facility.

Share-based compensation expense for all stock awards consists of the following (in USD thousands):

Related parties are comprised of the Company’s executive officers and directors, including their affiliates, and any person that directly, or indirectly through one or more intermediaries, controls, is controlled by, or is under common control of, the Company.

Key management personnel are comprised of seven Executive Officers and Directors and six Non-Executive Directors as of March 31, 2025. Key management personnel were comprised of six Executive Officers and Directors and seven Non-Executive Directors as of March 31, 2024.

The following table provides compensation for key management and non-executive directors (in USD thousands):

During the three months ended March 31, 2025 and 2024 no related party transactions with Executive Officers or Directors occurred.

The Company has evaluated, for potential recognition and disclosure, events that occurred prior to the date at which the unaudited interim condensed consolidated financial statements were approved to be issued. There were no material subsequent events.

You should read the following discussion and analysis of our financial condition and results of operations in conjunction with our interim condensed consolidated financial statements and the related notes included as Exhibit 99.1 to the Report on Form 6-K to which this discussion and analysis is included as Exhibit 99.2 and our audited financial statements and the related notes and the section “Operating and Financial Review and Prospects” in our Annual Report on Form 20-F for the year ended December 31, 2024.

Our interim condensed consolidated financial statements are presented in U.S. dollars and have been prepared in accordance with IFRS Accounting Standards as issued by the International Accounting Standards Board (“IFRS”). None of the consolidated financial statements were prepared in accordance with generally accepted accounting principles in the United States (“U.S. GAAP”). The terms “dollar,” “USD” and “$” refer to U.S. dollars and the terms “Swiss franc” and “CHF” refer to the legal currency of Switzerland, unless otherwise indicated.

Unless otherwise indicated or the context otherwise requires, all references to “SOPHiA GENETICS,” “SOPH,” the “Company,” “we,” “our,” “ours,” “us” or similar terms refer to SOPHiA GENETICS SA and its consolidated subsidiaries.

This discussion and analysis contain statements that constitute forward-looking statements. All statements other than statements of historical facts, including statements regarding our future results of operations and financial position, business strategy, technology, as well as plans and objectives of management for future operations are forward-looking statements. Many forward-looking statements can be identified by the use of forward-looking words such as “anticipate,” “believe,” “could,” “expect,” “should,” “plan,” “intend,” “estimate,” “will” and “potential,” among others. Forward-looking statements are based on our management’s beliefs and assumptions and on information currently available to our management. Such statements are subject to risks and uncertainties, and actual results may differ materially from those expressed or implied in the forward-looking statements due to various factors, including, but not limited to, those identified in the “Risk Factors” section of our Annual Report on Form 20-F for the year ended December 31, 2024 and in our other Securities and Exchange Commission (“SEC”) filings. These forward-looking statements include, among others:

•our expectations regarding our revenue, gross margin, expenses, other operating results and cash usage, including statements relating to the portion of our remaining performance obligation that we expect to recognize as revenue in future periods;

•our plans regarding further development of our SOPHiA DDMTM Platform and related products and solutions, which we collectively refer to as “SOPHiA DDM Platform,” and its expansion into additional features, applications and data modalities;

•future investments in our business, our anticipated capital expenditures and our estimates regarding our capital requirements, future revenues, expenses, reimbursement rates and needs for additional financing;

•our expectations regarding the market size for our platform, applications, products, and services and the market acceptance they will be able to achieve;

•our expectations regarding changes in the healthcare systems in different jurisdictions, in particular with respect to the manner in which electronic health records are collected, distributed and accessed by various stakeholders;

•the timing or outcome of any domestic and international regulatory submissions;

•impact from future regulatory, judicial, and legislative changes or developments in the United States and foreign countries, including with respect to FDA and other regulatory authorities’ staffing and funding;

•changes in tariffs, trade barriers and price and exchange controls;

•our ability to acquire new customers and successfully engage and retain customers;

•the costs and success of our marketing efforts, and our ability to promote our brand;

•our ability to increase demand for our applications, products, and services, obtain favorable coverage and reimbursement determinations from third-party payors and expand geographically;

•our expectations of the reliability, accuracy and performance of our applications, products, and services, as well as expectations of the benefits to patients, medical personnel and providers of our applications, products and services;

•our expectations regarding our ability, and that of our manufacturers, to manufacture our products;

•our efforts to successfully develop and commercialize our applications, products, and services;

•our competitive position and the development of and projections relating to our competitors or our industry;

•our ability to identify and successfully enter into strategic collaborations in the future, and our assumptions regarding any potential revenue that we may generate thereunder;

•our ability to obtain, maintain, protect and enforce intellectual property protection for our technology, applications, products, and services, and the scope of such protection;

•our ability to operate our business without infringing, misappropriating or otherwise violating the intellectual property or proprietary rights of third parties;

•our ability to attract and retain qualified key management and technical personnel; and

•our expectations regarding the time during which we will be an emerging growth company under the Jumpstart our Business Startups Act of 2012 (“JOBS Act”) and a foreign private issuer.

These forward-looking statements speak only as of the date of this discussion and analysis and are subject to a number of risks, uncertainties and assumptions described in the “Risk Factors” section of our Annual Form 20-F for the year ended December 31, 2024, this discussion and analysis and our other SEC filings. Because forward-looking statements are inherently subject to risks and uncertainties, some of which cannot be predicted or quantified and some of which are beyond our control, you should not rely on these forward-looking statements as predictions of future events. The events and circumstances reflected in our forward-looking statements may not be achieved or occur and actual results could differ materially from those projected in the forward-looking statements. Moreover, we operate in an evolving environment. New risk factors and uncertainties may emerge from time to time, and it is not possible for management to predict all risk factors and uncertainties. Except as required by applicable law, we do not plan to publicly update or revise any forward-looking statements contained herein, whether as a result of any new information, future events, changed circumstances or otherwise. You should read this discussion and analysis completely and with the understanding that our actual future results may be materially different from what we expect.

We are a cloud-native software technology company in the healthcare space dedicated to establishing the practice of data-driven medicine as the standard of care and for life sciences research. We purposefully built a cloud-native software platform capable of analyzing data and generating insights from complex multimodal data sets and different diagnostic modalities. Our platform standardizes, computes and analyzes digital health data and is used across decentralized locations to break down data silos. This enables healthcare institutions to share knowledge and experiences and to build a collective intelligence. We envision a future in which all clinical diagnostic test data is channeled through a decentralized analytics platform that will provide insights powered by large real-world data sets and AI. We believe that a decentralized platform is the most powerful and effective solution to create the largest network, leverage data and bring the benefits of data-driven medicine to customers and patients globally. In doing so, we can both support and benefit from growth across the healthcare ecosystem.

In 2014, we launched the first application of our platform to analyze next-generation sequencing (“NGS”) data for cancer diagnosis. We offer a broad range of applications used by healthcare providers, clinical and life sciences research laboratories and biopharmaceutical companies for precision medicine across oncology, rare diseases, infectious diseases, cardiology, neurology, metabolism and other disease areas. In 2019, we launched our solution for radiomics data that enables longitudinal monitoring of cancer patients and tumor progression throughout their disease journey. In 2022, we unveiled SOPHiA CarePath, our multimodal solution that integrates the capabilities of our genomics and radiomics solutions with additional modalities to further enable clinical decision-making. The module will allow healthcare practitioners to visualize data across multiple modalities (including genomic, radiomic, clinical, and biological) for individual patients in a longitudinal manner and derive additional insights through cohort design and comparison. SOPHiA CarePath has already been deployed as part of our Deep-Lung IV multimodal clinical study on non-small cell lung cancer.

We offer a range of platform access models to meet our customers’ needs. Our primary pricing strategy for our clinical customers is a pay-per-use model, in which customers can access our platform free of charge but pay for each analysis performed using our platform. To commercialize our applications and products, we employ our direct sales force, use local distributors and form collaborations with other global product and service providers in the healthcare ecosystem to assemble solutions to address customer needs. For example, we combine our solutions and applications with other products used in the genomic testing process to provide customers integrated products in the testing workflow. As of March 31, 2025, our direct sales team consisted of more than 102 field-based commercial representatives.

We are continually developing strategic relationships and engaging in strategic transactions across the healthcare ecosystem with companies who also provide products and services to our customers.

In March, 2025, we reached the milestone of surpassing 2 million cumulative genomic profiles analyzed by SOPHiA DDM since inception.

In April 2025, the U.S. District Court for the Eastern District of Texas, Association for Molecular Pathology, et al. v. U.S. Food and Drug Administration, et al., vacated the FDA’s Laboratory Developed Tests (“LDT”) Final Rule, which was scheduled to be phased in over four years and would have redefined LDTs as in vitro diagnostics, thereby requiring FDA clearance for such tests. Under the LDT Final Rule, the FDA would have mandated premarket review for LDTs and required compliance with other FDA regulations in line with the established medical device guidelines. These requirements would have increased both the cost and time required to commercialize an LDT, reducing the financial incentives for laboratories to develop such tests. This, in turn, could have led to decreased demand for our RUO applications and products. We continue to monitor the impact of this decision and any further actions by the FDA on this matter.

There have been no material changes to our risk factors from those described in the “Item 3. Key Information—D. Risk Factors” section of our Annual Report on Form 20-F for the year ended December 31, 2024, except for the the items disclosed below:

In April 2025, the United States government announced significant changes to its trade policy, including the imposition of tariffs. The new tariff system consists of two tiers: a 10% baseline tariff on all imports to the United States and higher reciprocal tariffs on imported goods from approximately 60 countries. While an initial 31% tariff was announced on goods from Switzerland, where our headquarters are located, this has since been revised, and imports from Switzerland are now subject to only the baseline 10% tariff. The situation remains fluid and is evolving rapidly, and the Company is closely monitoring developments.

We operate internationally, with the majority of our bundles assembled at and shipped from our headquarters in Switzerland. While the majority of our revenues are generated from the EMEA region and are not directly impacted by these tariffs, our sale of bundles to the United States will be subject to additional costs due to the tariffs, leading to increases in our cost of revenue and decreases in our gross margin if we are unable to offset such costs by increasing our prices. In addition, tariffs could lead to higher operating expenses. These effects could adversely affect our financial condition and results of operations. Furthermore, the imposition of tariffs by the United States may prompt other countries, including Switzerland, to impose reciprocal tariffs, which could impact the cost of our raw materials purchased from the United States.

We regularly monitor a number of key performance indicators and metrics to evaluate our business, measure our performance, identify key operating trends and formulate financial projections and strategic plans. We believe that the following metrics are representative of our current business, but the metrics we use to measure our performance could change as our business continues to evolve. Our key performance indicators primarily focus on metrics related to our SOPHiA DDM Platform, as platform revenue comprises the majority of our revenues.

Our Core Genomics Customers can access our platform using three different models: dry lab access, bundle access and integrated access. In the dry lab access model, our customers use the testing instruments and solutions of their choice and our SOPHiA DDM Platform and algorithms for variant detection and identification. In the bundle access model, we bundle DNA enrichment solutions with our analytics solution to provide customers the ability to perform end-to-end workflows. In the integrated access model, our customers have their samples processed and sequenced through select SOPHiA DDM Platform collaborators within our clinical network and access their data through our SOPHiA DDM Platform. As used in this section, the term “Core Genomics Customer” refers to any customer who generated revenue through usage of our dry lab, bundle, or integrated access models. We exclude from this definition customers who only use Alamut through our SOPHiA DDM Platform.

We are continually refining our KPIs, as our business continues to evolve and we make revisions to our methodologies to calculate our key performance indicators.

The following table shows platform analysis volume for the three months ended March 31, 2025 and 2024:

*The figures in the table above have been adjusted to exclude analyses conducted during the period but for which chargebacks were issued or other adjustments were made to customers after the period. We do not believe that such adjustments are material to the periods presented.

Platform analysis volume represents a key business metric that reflects our overall business performance, as we generate revenue on a pay-per-analysis basis. Platform analysis volume measures the number of analyses that generated revenue to us and were conducted by our Core Genomics Customers. Analysis volume is a direct function of the number of active customers and usage rates across our customer base during a specified time period. While our platform analysis volume is a major driver of our revenue growth, other factors, including application and product pricing, access model used, and customer size mix, also affect our revenue. Because of that, our revenue may increase in periods in which our analysis volume decreases and vice versa.

Analysis volume increased to 93,008 from 83,833 for the three months ended March 31, 2025, representing year-over-year growth of 11%. This increase was primarily driven by higher usage from existing customers and the onboarding of new customers to our platform, with particularly strong volume growth in NORAM and APAC, but partially offset by a decline in LATAM volumes.

The following table shows the number of Core Genomics Customers as of March 31, 2025 and 2024:

We track the number of our Core Genomics Customers, defined as the number of customers who generated revenue through usage of our bundle access, dry lab, and integrated access models during the specified time period, as a key measure of our ability to generate recurring revenue from our install base. We exclude from this number any customers who do not utilize our SOPHiA DDM Platform through one of the three access modes, such as customers who only use Alamut and our biopharma customers. This number also excludes customers without any usage of our SOPHiA DDM Platform over the past twelve months and customers who have executed agreements with us but have not yet generated any revenue, including customers that are in the process of being onboarded onto our SOPHiA DDM Platform.

Core Genomics Customers increased to 490 as of March 31, 2025 from 463 as of March 31, 2024. The increase was primarily attributable to our continued customer acquisition momentum over the course of the intervening period net of churn.

The following table shows the net dollar retention as of March 31, 2025 and 2024:

We track net dollar retention for our dry lab, bundle access, and integrated access customers as a measure of our ability to grow the revenue generated from our Core Genomics Customers through our “land and expand” strategy net of revenue churn, which we define as the annualized revenues we estimate to have lost from customers who access our platform through our dry lab access, bundle access and integrated access models and have not generated revenue over the past twelve months in that period based on their average quarterly revenue contributions from point of onboarding as a percentage of total recurring platform revenue. To calculate net dollar retention, we first specify a measurement period consisting of the trailing two-year period from our fiscal period end. Next, we define a measurement cohort consisting of Core Genomics Customers who use our dry lab access, bundle access, and integrated access models from whom we have generated revenues during the first month of the measurement period, which we believe is generally representative of our overall dry lab access, bundle access, and integrated customer base. We then calculate our net dollar retention as the ratio between the U.S. dollar amount of revenue generated from this cohort in the second year of the measurement period and the U.S. dollar amount of revenue generated in the first year. Any customer in the cohort that did not use our platform in the second year are included in the calculation as having contributed zero revenue in the second year.

Net dollar retention decreased to 103% as of March 31, 2025 compared to 123% as of March 31, 2024. This decrease was caused by slower revenue growth in LATAM, and an annualized revenue churn rate of 4%, which is in line with our historical averages.

For a discussion of our components of results of operations, see the “Operating and Financial Review and Prospects—Operating Results—Components of Results of Operations” section of our Annual Report on Form 20-F for the year ended December 31, 2024.

The following table summarizes our results of operations:

The following table presents revenue by stream:

Revenue was $17.8 million for the three months ended March 31, 2025 as compared to $15.8 million for the three months ended March 31, 2024. This increase was primarily attributable to an increase in SOPHiA DDM Platform revenue, partially offset by a foreign exchange headwind of $0.4 million, related to unfavorable movements in exchange rates between key transactional currencies, particularly the euro, and our presentation currency, the U.S. dollar. SOPHiA DDM Platform revenue was $17.3 million for the three months ended March 31, 2025 as compared to $15.4 million for the three months ended March 31, 2024. This increase was primarily attributable to new customers onboarded onto our platform and increased usage across our existing customers primarily in the US, partially offset by a slight decrease of $0.3 million in biopharma revenue driven by customer budget constraints and other macro environment impacts. Alamut was relatively constant with an increase of $0.1 million. Workflow equipment and services revenue was $0.4 million for both the three months ended March 31, 2025 and 2024.

The following table presents cost of revenue, gross profit, and gross margin:

Cost of revenue was $5.6 million for the three months ended March 31, 2025 as compared to $5.4 million for the three months ended March 31, 2024. The increase was primarily driven by a $0.5 million increase in amortization of capitalized development costs as newly developed products were commercialized, a $0.1 million increase in computational and storage-related expenses due to increased analysis volume; partially offset by a $0.5 million decrease in biopharma costs due to the decline in biopharma revenue. The increase in gross profit margin to 69% for the three months ended March 31, 2025 as compared to 66% for the three months ended March 31, 2024 was primarily driven by a favorable mix from DDM platform revenue and by our efforts in the cost of revenue cost management and economies of scale.

The following table presents research and development costs, selling and marketing costs, general and administrative costs, and other operating income, net:

Research and development costs were $9.1 million for the three months ended March 31, 2025 as compared to $9.4 million for the three months ended March 31, 2024. The decrease was primarily driven by a $0.2 million decrease in lab supplies and office expenses as a result of our ongoing cost-saving measures, as well as a $0.1 million decrease in professional fees as we reduce our reliance on outsourced development services.

Selling and marketing costs were $7.5 million for the three months ended March 31, 2025 as compared to $7.0 million for the three months ended March 31, 2024. The increase was primarily attributable to a $0.3 million increase in employee-related expenses, including share-based compensation, as we expanded sales force; and a $0.2 million increase in shipping costs due to higher sales volumes.

General and administrative costs were $11.6 million for three months ended March 31, 2025 as compared to $12.8 million for the three months ended March 31, 2024. This decrease was primarily attributable to a $1.0 million decrease in employee-related expenses, including share-based compensation, reflective of changes in our workforce composition as we continue to scale and align with market conditions; and a $0.2 million decrease in license costs as a result of ongoing efforts to consolidate and streamline our software platforms.

Other operating income, net was less than $0.1 million for both the three months ended March 31, 2025 and 2024.

The following table presents interest income:

Interest income was $0.5 million for the three months ended March 31, 2025, compared to $0.9 million for the three months ended March 31, 2024. The decrease was primarily driven by lower average cash balances held in interest-earning bank accounts and short-term deposits, as well as a decline in interest rates.

The following table presents interest expense:

Interest expense was $0.7 million for the three months ended March 31, 2025, compared to $0.1 million for the three months ended March 31, 2024. The increase was primarily driven by a $0.5 million increase in interest expense related to borrowings under the Perceptive Credit Agreement, which was not entered into until May 2024.

The following table presents fair value adjustments on warrant obligations:

Fair value adjustments on warrant obligations had a loss of less than $0.1 million for the three months ended March 31, 2025. We did not have any fair value adjustments on warrant obligations for the three months ended March 31, 2024 as the warrant certificate was issued on May 2, 2024 in connection with the Perceptive Credit Agreement.

The following table presents foreign exchange gains (losses), net:

Foreign exchange losses, net were $0.6 million for the three months ended March 31, 2025, compared to foreign exchange gains, net of $4.6 million for the three months ended March 31, 2024. This increase in foreign exchange losses was primarily driven by a $5.5 million decrease in unrealized foreign exchange gains, net, largely resulting from the revaluation of intercompany foreign currency receivable balances into SOPHiA GENETICS SA’s functional currency, the Swiss franc; partially offset by a $0.2 million increase in realized foreign exchange losses, net. Unrealized gains and losses do not constitute a cash impact until the related transactions are settled.

The following table presents income tax expense:

Income tax expense was $0.5 million for the three months ended March 31, 2025 as compared to $0.3 million for the three months ended March 31, 2024. The increase in tax expense was primarily attributable to an estimated increase in tax liability in France.

Our principal sources of liquidity were cash and cash equivalents totaling $68.5 million and $80.2 million as of March 31, 2025 and December 31, 2024, respectively, which were held for a variety of growth initiatives and investments in our SOPHiA DDM Platform and related solutions, applications, products, and services as well as working capital purposes. Our cash and cash equivalents are comprised of cash on hand, bank deposits, money market funds, and bank and other short-term highly liquid investments with original maturities of three months or less.

On May 2, 2024 (the “closing date”), SOPHiA GENETICS SA and our subsidiary SOPHiA GENETICS, Inc. entered into a credit agreement and guaranty (the “Perceptive Credit Agreement”) with Perceptive Credit Holdings IV, LP, as lender and administrative agent, pursuant to which we may borrow up to $50.0 million principal amount of term loans, including (i) an initial tranche of $15.0 million principal amount of term loans on the closing date and (ii) up to $35.0 million principal amount of term loans that we may draw upon on or prior to March 31, 2026, subject to satisfaction of certain customary conditions. The term loans are scheduled to mature on the fifth anniversary of the closing date and accrue interest at Term Secured Overnight Financing Rate (“SOFR”) plus 6.25% per annum; provided that upon the occurrence and during the continuation of any event of default, the term loans will accrue interest at Term SOFR plus 9.25% per annum. The obligations under the Perceptive Credit Agreement are secured by substantially all of our and certain of our subsidiaries’ assets. The Perceptive Credit Agreement contains customary covenants, including an affirmative covenant to maintain qualified cash of at least $3.0 million, an affirmative last twelve months revenue covenant tested on a quarterly basis beginning June 30, 2024, and negative covenants including limitations on indebtedness, liens, fundamental changes, asset sales, investments, dividends and other restricted payments and other matters customarily restricted in such agreements. We remain in full compliance with all covenants contained in the Perceptive Credit Agreement as of March 31, 2025.

In addition, we issued to Perceptive Credit Holdings IV, LP a warrant certificate representing the right to purchase up to 400,000 ordinary shares at $4.9992 per share, with 200,000 ordinary shares available immediately and an additional 200,000 ordinary shares to be available upon the drawdown of the second tranche of the term loans. The purchase rights represented by the warrant certificate is exercisable, on a cash basis, at any time prior to the tenth anniversary of the applicable date of availability.

On April 23, 2024, we entered into a credit agreement (the “Credit Facility”) with Credit Suisse SA for up to CHF0.1 million ($0.1 million) to be used for cash credits, contingent liabilities, or as margin for OTC derivative transactions. Borrowings under the Credit Facility will bear interest at a rate to be established between us and Credit Suisse SA at the time of each draw down. As of March 31, 2025, we had no borrowings outstanding under the Credit Facility.

In August 2022, we filed a shelf registration statement for total gross amount of $200 million, which allows us to offer and sell, in one or more offerings, any combination of ordinary shares, debt securities, warrants, subscription rights, purchase contracts, and units (collectively, the “securities”). For the three months ended March 31, 2025, we did not utilize the shelf registration and executed no offerings of securities .

In August 2023, we established an at-the-market offering program pursuant to which we may sell, from time to time, ordinary shares having an aggregate offering price of $50.0 million. For the three months ended March 31, 2025, we did not sell any ordinary shares under this program.

We have funded our operations primarily through equity financing and through revenue generated from the sale of access to our SOPHiA DDM Platform and related licenses and services. Invoices for our products and services are a substantial source of revenue for our business, which are included on our condensed consolidated balance sheet as trade receivables prior to collection. Accordingly, collections from our customers have a material impact on our cash flows from operating activities. As we expect our revenue to grow, we also expect our accounts receivable and inventory balances to increase, which could result in greater working capital requirements.

We expect to continue to incur net losses for the foreseeable future as we continue to devote substantial resources to research and development, in particular, to further expand the applications and modalities of our SOPHiA DDM Platform in order to accommodate multimodal data analytics capabilities across a wide range of disease areas; selling and marketing efforts for our SOPHiA DDM Platform to establish and maintain relationships with our collaborators and customers; and obtaining regulatory clearances or approvals for our SOPHiA DDM Platform and our applications, products, and services. We believe that our existing cash and cash equivalents will be sufficient to meet our working capital and capital expenditure needs for at least the next twelve months. We have based this estimate on assumptions that may prove to be wrong, and we could use our capital resources sooner than we currently expect. Our future capital requirements will depend on many factors, which are outlined in our Annual Report on Form 20-F for the year ended December 31, 2024 and our subsequent filings with the SEC.

The following table summarizes our cash flows for three months ended March 31, 2025 and 2024:

1Refer to “Note 1—Change in accounting policies—Statement of Cash Flows - Interest Classification”, included as Exhibit 99.1 to the Report on Form 6-K to which this discussion and analysis is included as Exhibit 99.2, for details on change in accounting policy.

Net cash used in operating activities was $10.8 million for the three months ended March 31, 2025, compared to $14.6 million for the three months ended March 31, 2024. The increase was primarily driven by a $6.0 million change in net non-cash finance income (expense) from $5.0 million of non-cash finance income to $0.9 million of non-cash finance expense as we incurred less foreign exchange gain on intercompany loans; and a $0.9 million improvement in working capital driven by an increase in invoices issued at the end of the reporting period as compared to 2024; partially offset by a $3.5 million increase in loss before tax, primarily reflecting a $5.2 million increase in foreign exchange losses driven by unrealized foreign exchange losses on our intercompany loan.

Net cash used in investing activities was $1.0 million for the three months ended March 31, 2025, compared to $1.0 million for the three months ended March 31, 2024. The decrease was primarily driven by a $0.4 million decrease in capitalized development costs; partially offset by a $0.5 million decrease in interest received due to lower average cash balances held in interest-earning bank accounts and short-term deposits, as well as a decline in interest rates.

Net cash used in financing activities was $1.0 million for the three months ended March 31, 2025, compared to cash used of $0.7 million for the three months ended March 31, 2024. The decrease was primarily driven by a $0.4 million increase in interest paid, arising from our Perceptive Credit Agreement.

As of March 31, 2025, there have been no material changes to our contractual obligations and commitments from those described in the “Operating and Financial Review and Prospects” section of our Annual Report on Form 20-F for the year ended December 31, 2024.

There were no changes to our internal control over financial reporting during the three months ended March 31, 2025 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

We have a minimum purchase agreement with a vendor related to computational and hosting-related costs. As part of the agreement, we have a total minimum commitment of approximately $72.5 million from the period beginning November 1, 2022 through October 31, 2027 and an additional one-year grace period to meet the minimum commitment by October 31, 2028. As of March 31, 2025 and December 31, 2024, our remaining commitments are $56.6 million and $58.8 million, respectively.

Other than the above agreement, we did not have, during the periods presented, and we do not currently have, any off-balance sheet arrangements or commitments that may have a material current or future effect on financial condition, changes in financial condition, results of operations, liquidity, capital expenditures, capital resources, or significant components of revenues or expenses.

We had cash and cash equivalents totaling $68.5 million as of March 31, 2025, which are comprised of cash on hand, bank deposits, money market funds, and bank and other short-term highly liquid investments with original maturities of three months or less. Our cash equivalents are subject to market risk due to changes in interest rates. Fixed rate securities may have their market value adversely affected due to a rise in interest rates. Due in part to these factors, our future investment income may fall short of expectation due to changes in interest rates or we may suffer losses in principal if we are forced to sell securities that decline in market value due to changes in interest rates.

As of March 31, 2025, we currently have $15.0 million of debt outstanding under the Perceptive Credit Agreement. Based on the terms of the Perceptive Credit Agreement, the monthly interest expense fluctuates based on the SOFR reference rate that is two business days prior to the first day of the preceding calendar month. Given our outstanding debt under this agreement, we are subject to interest rate risk related to debt obligations if the SOFR were to move significantly.

We do not believe that a hypothetical 100 basis points change in interest rates would have a material effect on our business, financial condition, or results of operations. We do not enter into investments for trading or speculative purposes. We do not use any financial instruments to manage our interest rate risk exposure.

We operate internationally and a portion of our revenue, expenses, assets, liabilities, and cash flows are denominated in currencies other than our presentation currency. As a result, we are exposed to fluctuations in foreign exchange rates.

We do not believe that there have been material changes in our foreign exchange risk exposure from the disclosure included in the “Item 11. Quantitative and Qualitative Disclosures About Market Risk” section of our Annual Report on Form 20-F for the year ended December 31, 2024.

We are exposed to credit risk from our operating activities, primarily trade receivables. Credit risk is the risk that a counterparty will be unable to meet its obligations under a financial instrument or customer contract.

Allowance is made for lifetime expected credit losses as invoices are issued. The amount of allowance initially recognized is based on historical experience, tempered by expected changes in future cash collections, due to, for example, expected improved customer liquidity or more active credit management.

We do not believe that credit risk had a material effect on our business, financial condition, or results of operations. The largest customer balance represented 16% of accounts receivable as of March 31, 2025, which is attributable to one of our largest distributors. This distributor has a strong payment history and is in good standing with us. Our cash and cash equivalents are deposited with reputable financial institutions. If customers representing a significant percentage of our trade receivables are unable to meet their payment obligations to us, we may suffer harm to our business, financial condition, or results of operations.

We believe our business is able to pass along increases in the costs of providing our applications, products, and services caused by inflation by increasing the prices of our applications, products, and services. For multi-year contracts, our general terms and conditions allow us to increase prices, at minimum on an annual basis. However, we do not believe that inflation had a material effect on our business, financial condition, or results of operations. If our costs were to become subject to significant inflationary pressures, we may not be able to fully offset such higher costs through price increases. Our inability or failure to do so could harm our business, financial condition, or results of operations.

The preparation of financial statements in conformity with IFRS Accounting Standards requires the use of accounting estimates. It also requires management to exercise judgment in applying our accounting policies. Disclosed below are the areas which require a high degree of judgment, significant assumptions and/or estimates. The most significant assumptions used in the financial statements are the underlying assumptions used in revenue recognition, capitalized internal development costs, share-based compensation, goodwill impairment testing, defined benefit pension liabilities, expected credit loss, income taxes, term loans, and warrant obligations. We base estimates and assumptions on historical experience when available and on various factors that we determined to be reasonable under the circumstances. We evaluate our estimates and assumptions on an ongoing basis. Our actual results may differ from these estimates under different assumptions or conditions.

Our material accounting policies and critical estimates that involve a higher degree of judgment and complexity are described in the “Item 5. Operating and Financial Review and Prospects—E. Critical Accounting Estimates” section of our Annual Report on Form 20-F for the year ended December 31, 2024. There have been no material changes to our material accounting policies and critical estimates as disclosed therein, with the exception of our adoption of recent accounting pronouncements, as discussed below.

In connection with our adoption of IFRS Accounting Standards for the preparation of our financial statements, certain new accounting standards and interpretations have been published that are not mandatory for the December 31, 2024 reporting periods and have not been adopted early by us. These standards are not expected to have a material impact on the entity in the current or future reporting periods and on foreseeable future transactions. See Note 2 to the audited consolidated financial statements included in our Annual Report on Form 20-F for the year ended December 31, 2024 and Note 1 of our unaudited interim condensed consolidated financial statements included as Exhibit 99.1 to the Report on Form 6-K to which this discussion and analysis is included as Exhibit 99.2.

In April 2012, the JOBS Act was enacted. Section 107 of the JOBS Act provides that an emerging growth company can take advantage of an extended transition period for complying with new or revised accounting standards applicable to public companies. This provision allows an emerging growth company to delay the adoption of certain accounting standards until those standards would otherwise apply to private companies. This transition period is only applicable under U.S. GAAP. As a result, we will adopt new or revised accounting standards on the relevant dates on which adoption of such standards is required or permitted by the International Accounting Standards Board.

Subject to certain conditions, as an emerging growth company, we intend to rely on certain of these exemptions, including without limitation, (i) providing an auditor’s attestation report on our system of internal controls over financial reporting pursuant to Section 404(b) of the Sarbanes-Oxley Act and (ii) complying with any requirement that may be adopted by the Public Company Accounting Oversight Board, regarding mandatory audit firm rotation or a supplement to the auditor’s report providing additional information about the audit and the financial statements, known as the critical audit matters.

We will remain an emerging growth company until the earliest of (i) the last day of the fiscal year in which we have total annual gross revenues of $1.235 billion or more; (ii) December 31, 2026; (iii) the date on which we have issued more than $1.0 billion in non-convertible debt during the previous three years; and (iv) the date on which we are deemed to be a large accelerated filer under the rules of the SEC, which means the market value of our ordinary shares that are held by non-affiliates equals or exceeds $700.0 million as of the prior June 30th.

BOSTON, United States and ROLLE, Switzerland, May 6, 2025 — SOPHiA GENETICS (Nasdaq: SOPH), a cloud-native software company and leader in data-driven medicine, today reported financial results for the first quarter ended March 31, 2025.

•Revenue was $17.8 million, up 13% year-over-year or 15% on a constant currency basis

•Gross margin was 68.7% on a reported basis and 75.7% on an adjusted basis, up from 65.9% and 70.5% in the prior year period, respectively

•IFRS net loss increased 27% year-over-year to $17.4 million (including a net foreign exchange P&L impact of $5.2 million), and adjusted EBITDA loss improved 24% year-over-year to $9.8 million

•The company reiterates full-year guidance of revenue between $72 million and $76 million and adjusted EBITDA loss between $35 million and $39 million

"We started the year strong with year-over-year revenue growth of 13%, or 15% on a constant currency basis, as the large amount of new business signed in 2024 begins to ramp,” said Jurgi Camblong, PhD., Chief Executive Officer and Co-founder. “In addition to reaccelerating topline growth, we also continued to optimize SOPHiA DDMTM’s data processing capabilities and delivered a record adjusted gross margin of 75.7%, up 520bps year-over-year. Prudent cost management across all spending categories resulted in a 24% year-over-year improvement to adjusted EBITDA loss during the period, demonstrating steady progress on our path to profitability.”

Camblong added, “Looking ahead, we remain confident in our long-term growth and in the growth prospects of our end markets. New business momentum remains strong, driven by notable catalysts such as the new Liquid Biopsy application MSK-ACCESS® powered with SOPHiA DDMTM, a relatively underpenetrated U.S. market where revenue from core genomics customers grew over 30%, and a large base of new customers to onboard and expand over the remainder of 2025.”

Expanding usage of SOPHiA DDMTM worldwide

•Performed 93,000 analyses on SOPHiA DDMTM, representing 11% year-over-year volume growth

•Reached 490 core genomics customers as of March 31, 2025, up from 463 customers at the end of Q1 2024

•Completed implementation for 33 new core genomics customers during Q1 2025, up from an average of 23 customers implemented per quarter in 2024

•Delivered strong analysis volume growth in NORAM and APAC with 32% and 40% year-over-year growth, respectively

•Hit a major Platform milestone during Q1, passing 2 million cumulative genomic profiles analyzed by SOPHiA DDMTM since inception

•Landed 28 new core genomics customers in Q1 2025 who will implement SOPHiA DDMTM and begin generating revenue over the next twelve months, up from 20 new customers signed in Q1 2024

•Signed major new customers across geographies including Jessa Ziekenhuis in Belgium who is adopting SOPHiA DDMTM for Solid Tumor, Liquid Biopsy, and HemOnc testing; LifeLabs, a central reference lab in Canada, who is adopting Solid Tumor applications; and Premier Integrated Labs in Malaysia who is adopting numerous applications in Hereditary Cancer, HemOnc, and Inherited Disorders, in addition to MSK-ACCESS® powered with SOPHiA DDMTM

•Expanded the October 2024 collaboration with AstraZeneca to accelerate the deployment of MSK-ACCESS® powered with SOPHiA DDMTM globally, extending the scope to 30 total sponsored institutions worldwide

•Recently signed new customers to the Liquid Biopsy application MSK-ACCESS® powered with SOPHiA DDMTM, including Kuwait Cancer Control Center; Centre Hospitalier Régional Universitaire de Nancy in Nancy, France; and Hospital de Amor in Barretos, Brazil

•Continued to drive significant demand for MSK-ACCESS® and MSK-IMPACT® powered with SOPHiA DDMTM, with a healthy and growing pipeline of more than 60 identified opportunities

•Delivered over 30% year-over-year revenue growth from U.S. core genomics customers in Q1

•Expanded our partnerships with two top-ranked U.S. hospitals, including Henry Ford Hospital who is adopting additional Solid Tumor and HemOnc applications on SOPHiA DDMTM and the Mayo Clinic who is adopting HemOnc applications

•Signed Mount Sinai during Q1, one of the leading hospital systems in the world based in New York City, who is adopting HemOnc and Solid Tumor applications

•Achieved a record 75.7% adjusted gross margin, up 520bps year-over-year, by continuing to optimize compute costs and leverage the scale of the cloud-native SOPHiA DDMTM platform

•Remained laser-focused on operational excellence and cost containment and improved adjusted EBITDA loss by 24% year-over-year to $9.8 million

•The Company reaffirms commitment to profitable growth and expects to be approaching adjusted EBITDA breakeven by the end of 2026 and crossing over to positive adjusted EBITDA in the second half of 2027

Based on information as of today, SOPHiA GENETICS is reaffirming the previously provided guidance of:

•Full-year revenue between $72 million and $76 million, representing growth of approximately 10% to 17% compared to FY 2024

•Adjusted EBITDA loss between $35 million and $39 million, compared to $40.2 million in FY 2024

Other than with respect to revenue, the Company only provides guidance on a non-IFRS basis. The Company does not provide a reconciliation of forward-looking adjusted gross margin (non-IFRS measure) to gross margin (the most comparable IFRS financial measure), due to the inherent difficulty in forecasting and quantifying amortization of capitalized research & development expenses that are necessary for such reconciliation. In addition, the Company does not provide a reconciliation of forward-looking adjusted operating loss (non-IFRS measure) to operating loss (the most comparable IFRS financial measure), due to the inherent difficulty in forecasting and quantifying amortization of capitalized research & development expenses and intangible assets, share-based compensation expenses, and non-cash portion of pensions paid in excess of actual contributions, that are necessary for such reconciliation.

To provide investors with additional information regarding the company’s financial results, SOPHiA GENETICS has disclosed here and elsewhere in this earnings release the following non-IFRS measures:

•Adjusted gross profit, which the company calculates as revenue minus cost of revenue adjusted to exclude amortization of capitalized research and development expenses;

•Adjusted gross profit margin, which the company calculates as adjusted gross profit as a percentage of revenue;

•Adjusted operating loss, which the company calculates as operating loss adjusted to exclude amortization of capitalized research and development expenses, amortization of intangible assets, share-based compensation expense, and non-cash portion of pensions expense paid in excess of actual contributions to match the actuarial expense.

•EBITDA, which the company calculates as loss for the year before depreciation, amortization, interest income, interest expense, fair value adjustments on warrant obligations, foreign exchange (losses) gains, net, and income tax (expense) benefit; and

•Adjusted EBITDA, which the company calculates as EBITDA adjusted to exclude share-based compensation expense, non-cash pension expenses, and costs associated with restructuring.

These non-IFRS measures are key measures used by SOPHiA GENETICS management and board of directors to evaluate its operating performance and generate future operating plans. The exclusion of certain expenses facilitates operating performance comparability across reporting periods by removing the effect of non-cash expenses and certain variable charges. Accordingly, the company believes that these non-IFRS measures provide useful information to investors and others in understanding and evaluating its operating results in the same manner as its management and board of directors.

These non-IFRS measures have limitations as financial measures, and you should not consider them in isolation or as a substitute for analysis of SOPHiA GENETICS’ results as reported under IFRS. Some of these limitations are:

•These non-IFRS measures exclude the impact of depreciation. Although depreciation is a non-cash charge, the assets being depreciated may need to be replaced in the future and these non-IFRS measures do not reflect capital expenditure requirements for such replacements or for new capital expenditures;

•These non-IFRS measures exclude the impact of interest expense. Interest expense will continue to be for the foreseeable future a recurring expense based on the company’s financial liabilities;

•These non-IFRS measures exclude the impact of interest income. Interest income will continue to be for the foreseeable future recurring income based on the company’s financial assets;

•These non-IFRS measures exclude the impact of income taxes. Income taxes will continue to be for the foreseeable future a recurring expense incurred in the various jurisdictions in which the company operates;

•These non-IFRS measures exclude the impact of foreign exchange gains (losses),net. Foreign exchange gains and losses will continue to be for the foreseeable future a recurring expense incurred as the company participates in transactions outside of the company’s functional currency;

•These non-IFRS measures exclude the impact of fair value adjustments of warrant obligations. Fair value adjustments on warrant obligations will continue to be for the foreseeable future a recurring expense incurred as the company has outstanding warrant obligations;

•These non-IFRS measures exclude the impact of amortization of capitalized research and development expenses and intangible assets. Although amortization is a non-cash charge, the assets being amortized may need to be replaced in the future and these non-IFRS measures do not reflect capital expenditure requirements for such replacements or for new capital expenditures;

•These non-IFRS measures exclude the impact of share-based compensation expenses. Share-based compensation has been, and will continue to be for the foreseeable future, a recurring expense in the company’s business and an important part of its compensation strategy;

•These non-IFRS measures exclude the impact of the non-cash portion of pensions paid in excess of actual contributions to match actuarial expenses. Pension expenses have been, and will continue to be for the foreseeable future, a recurring expense in the business; and

•Other companies, including companies in the company’s industry, may calculate these non-IFRS measures differently, which reduces their usefulness as comparative measures.

Because of these limitations, you should consider these non-IFRS measures alongside other financial performance measures, including various cash flow metrics, net income and other IFRS results.

The tables below provide the reconciliation of the most comparable IFRS measures to the non-IFRS measures for the periods presented.

SOPHiA GENETICS operates internationally, and its revenues are generated primarily in the U.S. dollar, the euro and Swiss franc and, to a lesser extent, British pound, Australian dollar, Brazilian real, Turkish lira and Canadian dollar depending on the company’s customers’ geographic locations. Changes in revenue include the impact of changes in foreign currency exchange rates. We present the non-IFRS financial measure “constant currency revenue” (or similar terms such as constant currency revenue growth) to show changes in revenue without giving effect to period-to-period currency fluctuations. Under IFRS, revenues received in local (non-U.S. dollar) currencies are translated into U.S. dollars at the average monthly exchange rate for the month in which the transaction occurred. When the company uses the term “constant currency”, it means that it has translated local currency revenues for the current reporting period into U.S. dollars using the same average foreign currency exchange rates for the conversion of revenues into U.S. dollars that we used to translate local currency revenues for the comparable reporting period of the prior year.

The company then calculates the difference between the IFRS revenue and the constant currency revenue to yield the “constant currency impact” for the current period.

The company’s management and board of directors use constant currency revenue growth to evaluate growth and generate future operating plans. The exclusion of the impact of exchange rate fluctuations provides comparability across reporting periods and reflects the effects of customer acquisition efforts and land-and-expand strategy. Accordingly, it believes that this non-IFRS measure provides useful information to investors and others in understanding and evaluating revenue growth in the same manner as the management and board of directors. However, this non-IFRS measure has limitations, particularly as the exchange rate effects that are eliminated could constitute a significant element of its revenue and could significantly impact performance and prospects. Because of these limitations, you should consider this non-IFRS measure alongside other financial performance measures, including revenue and revenue growth presented in accordance with IFRS and other IFRS results.

The table below provides the reconciliation of the most comparable IFRS growth measures to the non-IFRS growth measures for the current period.

SOPHiA GENETICS will host a conference call and live webcast to discuss the first quarter 2025 results on Tuesday, May 6, 2025, at 8:00 a.m. (08:00) Eastern Time / 2:00 p.m. (14:00) Central European Time. The call will be webcast live on the SOPHiA GENETICS Investor Relations website, ir.sophiagenetics.com. Additionally, an audio replay of the conference call will be available on the SOPHiA GENETICS website after its completion.

SOPHiA GENETICS (Nasdaq: SOPH) is a cloud-native healthcare technology company on a mission to expand access to data-driven medicine by using AI to deliver world-class care to patients with cancer and rare disorders across the globe. It is the creator of SOPHiA DDM™, a platform that analyzes complex genomic and multimodal data and generates real-time, actionable insights for a broad global network of hospital, laboratory, and biopharma institutions. For more information, visit SOPHiAGENETICS.COM and connect with us on LinkedIn.

This press release contains statements that constitute forward-looking statements. All statements other than statements of historical facts contained in this press release, including statements regarding SOPHiA GENETICS future results of operations and financial position, business strategy, products and technology, partnerships and collaborations, as well as plans and objectives of management for future operations, are forward-looking statements. Forward-looking statements are based on SOPHiA GENETICS’ management’s beliefs and assumptions and on information currently available to the company’s management. Such statements are subject to risks and uncertainties, and actual results may differ materially from those expressed or implied in the forward-looking statements due to various factors, including those described in the company’s filings with the U.S. Securities and Exchange Commission. No assurance can be given that such future results will be achieved. Such forward-looking statements contained in this press release speak only as of its date. We expressly disclaim any obligation or undertaking to update these forward-looking statements contained in this press release to reflect any change in the company’s expectations or any change in events, conditions, or circumstances on which such statements are based, unless required to do so by applicable law. No representations or warranties (expressed or implied) are made about the accuracy of any such forward-looking statements.

Kellen Sanger

IR@sophiagenetics.com

media@sophiagenetics.com

1 Refer to “Note 1—Change in accounting policies—Statement of Cash Flows - Interest Classification” for details on change in accounting policy of exhibit 99.1 within of the Form 6-K filed on May 6,2025 .