VCYT Q1 2025 Earnings Presentation

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20 © 2025 Veracyte, Inc. All rights reserved. GAAP Gross Profit $ 64,788 $ 62,468 $ 77,913 $ 79,010 $ 78,754 $ 79,508 GAAP Gross Margin 66.0 % 64.5 % 68.1 % 68.2 % 66.4 % 69.5 % Amortization of intangible assets 4,035 2,915 2,909 2,917 2,811 2,585 Stock-based compensation expense 472 487 604 587 641 520 Acquisition related expenses (1) - 60 - - - - Other adjustments (2) - 6 - - - - Non-GAAP Gross Profit $ 69,295 $ 65,936 $ 81,426 $ 82,514 $ 82,206 $ 82,613 Non-GAAP Gross Margin 70.6 % 68.1 % 71.2 % 71.2 % 69.3 % 72.2 % (Unaudited) (In thousands of dollars) Three Months Ended Dec 31, 2023 Mar 31, 2024 Jun 30, 2024 Sep 30, 2024 Dec 31, 2024 Mar 31, 2025 GAAP cost of testing revenue $ 24,105 $ 25,979 $ 27,920 $ 29,029 $ 31,645 $ 28,260 Stock-based compensation expense (392) (390) (497) (524) (562) (446) Acquisition related expenses (1) - (60) - - - - Other adjustments (2) - (6) - - - - Non-GAAP cost of testing revenue $ 23,713 $ 25,523 $ 27,423 $ 28,505 $ 31,083 $ 27,814 GAAP cost of product revenue $ 1,753 $ 2,644 $ 1,874 $ 1,792 $ 2,800 $ 1,422 Stock-based compensation expense - (1) (1) (1) (1) (1) Acquisition related expenses (1) - - - - - - Other adjustments (2) - - - - - - Non-GAAP cost of product revenue $ 1,753 $ 2,643 $ 1,873 $ 1,791 $ 2,799 $ 1,421 GAAP cost of biopharmaceutical and other revenue $ 3,518 $ 2,838 $ 3,812 $ 3,112 $ 2,622 $ 2,698 Stock-based compensation expense (80) (96) (106) (62) (78) (73) Acquisition related expenses (1) - - - - - - Other adjustments (2) - - - - - - Non-GAAP cost of biopharmaceutical and other revenue $ 3,438 $ 2,742 $ 3,706 $ 3,050 $ 2,544 $ 2,625 1. Includes transaction-related expenses as well as post-combination compensation expenses. For the three months ended Mar 31, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics. 2. For the three months ended Mar 31, 2024, adjustments include expense related to restructuring costs associated with portfolio prioritization. 3. Some figures rounded for reporting purposes. Summed quarters may differ slightly from year-to-date figures presented due to rounding.

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21 © 2025 Veracyte, Inc. All rights reserved. (Unaudited) (In thousands of dollars) Three Months Ended Dec 31, 2023 Mar 31, 2024 Jun 30, 2024 Sep 30, 2024 Dec 31, 2024 Mar 31, 2025 GAAP research and development $ 18,673 $ 15,965 $ 16,465 $ 17,574 $ 19,290 $ 17,720 Stock-based compensation expense (1,495) (1,763) (1,895) (1,957) (1,896) (2,066) Acquisition related expenses (1) - (420) 23 459 - - Other adjustments (2) - (278) 2 5 - - Non-GAAP research and development $ 17,178 $ 13,504 $ 14,595 $ 16,081 $ 17,394 $ 15,654 GAAP sales and marketing $ 25,260 $ 23,782 $ 24,216 $ 22,612 $ 24,824 $ 24,454 Stock-based compensation expense (2,498) (1,093) (2,142) (1,790) (1,872) (1,958) Acquisition related expenses (1) - (124) - - - - Other adjustments (2) - (900) (194) 7 - - Non-GAAP sales and marketing $ 22,762 $ 21,665 $ 21,880 $ 20,829 $ 22,952 $ 22,496 GAAP general and administrative $ 23,795 $ 26,210 $ 31,745 $ 25,742 $ 26,913 $ 33,808 Stock-based compensation expense (3,142) (4,676) (5,213) (4,413) (5,220) (6,414) Acquisition related expenses (1) (2,718) (3,469) (1,116) (349) (928) (1,352) Other adjustments (2) - (266) (2,854) (248) (3,196) (3,694) Non-GAAP general and administrative $ 17,935 $ 17,799 $ 22,562 $ 20,732 $ 17,569 $ 22,348 GAAP total operating expenses $ 100,295 $ 67,124 $ 73,307 $ 66,993 $ 74,579 $ 76,604 Amortization of intangible assets (528) (738) (881) (880) (798) (622) Stock-based compensation expense (7,135) (7,532) (9,250) (8,160) (8,988) (10,438) Acquisition related expenses (1) (2,718) (4,442) (1,093) (75) (961) (1,352) Other adjustments (2) (32,039) (1,444) (3,046) (236) (5,917) (3,694) Non-GAAP total operating expenses $ 57,875 $ 52,968 $ 59,037 $ 57,642 $ 57,915 $ 60,498 1. Includes transaction-related expenses as well as post-combination compensation expenses. For the three months ended March 31, 2025, adjustments consist primarily of transaction-related expenses associated with the acquisition of C2i Genomics ($1.3 million). For the three months ended December 31, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics ($1.0 million). For the three months ended Sep 30, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics ($0.1 million). For the three months ended Jun 30, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics ($1.0 million) and adjustments relating to the remeasurement of contingent consideration related to our adoption of a multi-platform IVD strategy ($0.1 million). For the three months ended Mar 31, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics. For the three months ended Dec 31, 2023, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics ($2.6 million) and remeasurement of contingent consideration related to our adoption of a multi-platform IVD strategy ($0.1 million). 2. For the three months ended March 31, 2025, adjustments primarily include expense related to Veracyte SAS investment review ($3.8 million), partially offset by adjustments related to restructuring costs ($0.1 million). For the three months ended December 31, 2024, adjustments primarily include expense related to Veracyte SAS site investment review ($3.2 million) and expense related to the impairment charge associated with HalioDx ($2.7 million). For the three months ended Sep 30,2024, adjustments primarily include expense related to restructuring costs ($0.2 million). For the three months ended Jun 30, 2024, adjustments primarily include expense related to restructuring costs associated with a reduction in our Biopharmaceutical and Other segment ($2.9 million) and with portfolio prioritization ($0.2 million). For the three months ended Mar 31, 2024, adjustment includes $1.4 million expense related to restructuring costs associated with portfolio prioritization. For the three months ended Dec 31, 2023, adjustment includes $32.0 million expense related to the impairment charge associated with HalioDx. 3. Some figures rounded for reporting purposes. Summed quarters may differ slightly from year-to-date figures presented due to rounding.

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22 © 2025 Veracyte, Inc. All rights reserved. (Unaudited) (In thousands of dollars) Three Months Ended Dec 31, 2023 Mar 31, 2024 Jun 30, 2024 Sep 30, 2024 Dec 31, 2024 Mar 31, 2025 GAAP Net Income (Loss) $ (28,293) $ (1,864) $ 5,734 $ 15,155 $ 5,113 $ 7,047 GAAP Net Income (Loss) as a % of Revenue (28.8 %) (1.9 %) 5.0 % 13.1 % 4.3 % 6.2 % Amortization of intangible assets 4,563 3,653 3,790 3,797 3,609 3,207 Depreciation expense 1,773 1,937 1,948 2,081 2,643 2,155 Stock-based compensation expense 7,607 8,019 9,854 8,747 9,629 10,958 Acquisition related expenses (1) 2,718 4,502 1,093 75 961 1,352 Other expense (income), net (2) (3,399) (3,262) (3,052) (3,366) (1,967) (2,976) Other adjustments (3) 32,039 1,450 3,046 (853) 7,807 2,591 Income tax expense (benefit) (2,179) (44) 1,627 1,693 (1,670) 381 Adjusted EBITDA $ 14,829 $ 14,391 $ 24,040 $ 27,329 $ 26,125 $ 24,715 Adjusted EBITDA as a % of Revenue 15.1 % 14.9 % 21.0 % 23.6 % 22.0 % 21.6 % 1. Includes transaction-related expenses as well as post-combination compensation expenses. For the three months ended March 31, 2025, adjustments consist primarily of transaction-related expenses associated with the acquisition of C2i Genomics ($1.3 million). For the three months ended December 31, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics ($1.0 million). For the three months ended Sep 30, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics ($0.1 million). For the three months ended June 30, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics ($1.0 million) and adjustments relating to the remeasurement of contingent consideration related to our adoption of a multi-platform IVD strategy ($0.1 million). For the three months ended Mar 31, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics. For the three months ended Dec 31, 2023, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics ($2.6 million) and remeasurement of contingent consideration related to our adoption of a multi-platform IVD strategy ($0.1 million). 2. Includes interest income and income related to research tax credits. 3. For the three months ended March 31, 2025, adjustments primarily include expense related to Veracyte SAS site investment review ($3.8 million), partially offset by adjustments related to restructuring costs ($0.1 million) and the exclusion of unrealized gains associated with foreign exchange impacts on stock-based compensation and intercompany loans ($1.1 million). For the three months ended December 31, 2024, adjustments primarily include the exclusion of unrealized losses associated with foreign exchange impacts on stock-based compensation and intercompany loans ($1.9 million), expense related to Veracyte SAS site investment review ($3.2 million) and expense related to the impairment charge associated with HalioDx ($2.7 million). For the three months ended Sep 30, 2024, adjustments include the exclusion of unrealized gains associated with foreign exchange impacts on stock-based compensation and intercompany loans ($1.1 million) partially offset by expense related to restructuring costs ($0.2 million). For the three months ended June 30, 2024, adjustments primarily include expense related to restructuring costs associated with a reduction in our Biopharmaceutical and Other segment ($2.9 million) and with portfolio prioritization ($0.2 million). For the three months ended Mar 31, 2024, adjustment includes $1.4 million expense related to restructuring costs associated with portfolio prioritization. For the three months ended Dec 31, 2023, adjustment includes $32.0 million expense related to the impairment charge associated with HalioDx. 4. Some figures rounded for reporting purposes. Summed quarters may differ slightly from year-to-date figures presented due to rounding.

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23 © 2025 Veracyte, Inc. All rights reserved. (Unaudited) (In thousands of dollars) Twelve Months Ended Dec 31, 2024 GAAP Net Income (Loss) $ 24,138 GAAP Net Income (Loss) as a % of Revenue 5.4 % Amortization of intangible assets 14,849 Depreciation expense 8,610 Stock-based compensation expense 36,249 Acquisition related expenses (1) 6,631 Other expense (income), net (2) (11,647) Other adjustments (3) 11,450 Income tax expense (benefit) 1,606 Adjusted EBITDA $ 91,886 Adjusted EBITDA as a % of Revenue 20.6 % 1. Includes transaction-related expenses as well as post-combination compensation expenses. For the twelve months ended December 31, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics. For the twelve months ended December 31, 2023, adjustments consist primarily of remeasurement of contingent consideration related to our adoption of a multi-platform IVD strategy, post-combination compensation expenses associated with the acquisition of HalioDx and transaction related expenses associated with the acquisition of C2i Genomics. 2. Includes interest income and income related to research tax credits. 3. For the twelve months ended December 31, 2024, adjustments primarily include expense related to restructuring costs associated with a reduction in our Biopharmaceutical and Other segment and with portfolio prioritization, expense related to Veracyte SAS site investment review, expense related to the impairment charge associated with HalioDx and the exclusion of unrealized losses associated with foreign exchange impacts on stock-based compensation and intercompany loans. For the twelve months ended December 31, 2023, adjustments primarily include $34.9 million expense related to the impairment charge associated with the nCounter license intangible assets, $32.0 million expense related to the impairment charge associated with HalioDx and $1.3 million related to other impairment charges.

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24 © 2025 Veracyte, Inc. All rights reserved. Diluted EPS, GAAP $ (0.39) $ (0.02) $ 0.07 $ 0.19 $ 0.06 $ 0.09 Amortization of intangible assets 0.06 0.05 0.05 0.05 0.05 0.04 Stock-based compensation expense 0.10 0.11 0.13 0.11 0.12 0.14 Acquisition related expenses (1) 0.04 0.06 0.01 - 0.01 0.02 Other adjustments (2) 0.44 0.02 0.04 (0.01) 0.10 0.03 Tax adjustments (3) (0.05) (0.02) - (0.01) 0.02 (0.01) Rounding and impact of dilutive shares 0.01 (0.01) - - - - Diluted EPS, non-GAAP $ 0.21 $ 0.19 $ 0.30 $ 0.33 $ 0.36 $ 0.31 Diluted WASO, GAAP 73,107,059 74,759,789 77,163,149 78,464,654 79,905,412 80,056,024 Dilutive effect of equity awards (4) 1,117,195 1,117,286 - - - - Diluted WASO, non-GAAP 74,224,254 75,877,075 77,163,149 78,464,654 79,905,412 80,056,024 (Unaudited) (In thousands of dollars) Three Months Ended Dec 31, 2023 Mar 31, 2024 Jun 30, 2024 Sep 30, 2024 Dec 31, 2024 Mar 31, 2025 GAAP Net Income (Loss) $ (28,293) $ (1,864) $ 5,734 $ 15,155 $ 5,113 $ 7,047 Amortization of intangible assets 4,563 3,653 3,790 3,797 3,609 3,207 Stock-based compensation expense 7,607 8,019 9,854 8,747 9,629 10,958 Acquisition related expenses (1) 2,718 4,502 1,093 75 961 1,352 Other adjustments (2) 32,039 1,450 3,046 (853) 7,807 2,591 Tax adjustments (3) (3,387) (1,132) (114) (933) 1,830 (679) Non-GAAP Net Income $ 15,247 $ 14,628 $ 23,403 $ 25,988 $ 28,949 $ 24,476 1. Includes transaction-related expenses as well as post-combination compensation expenses. For the three months ended March 31, 2025, adjustments consist primarily of transaction-related expenses associated with the acquisition of C2i Genomics ($1.3 million). For the three months ended December 31, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics ($1.0 million). For the three months ended Sep 30, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics ($0.1 million). For the three months ended June 30, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics ($1.0 million) and adjustments relating to the remeasurement of contingent consideration related to our adoption of a multi-platform IVD strategy ($0.1 million). For the three months ended Mar 31, 2024, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics. For the three months ended Dec 31, 2023, adjustments consist primarily of transaction related expenses associated with the acquisition of C2i Genomics ($2.6 million) and remeasurement of contingent consideration related to our adoption of a multi-platform IVD strategy ($0.1 million). 2. For the three months ended March 31, 2025, adjustments primarily include expense related to Veracyte SAS site investment review ($3.8 million), partially offset by adjustments related to restructuring costs ($0.1 million) and the exclusion of unrealized gains associated with foreign exchange impacts on stock-based compensation and intercompany loans ($1.1 million). For the three months ended December 31, 2024, adjustments primarily include the exclusion of unrealized losses associated with foreign exchange impacts on stock-based compensation and intercompany loans ($1.9 million), expense related to Veracyte SAS site investment review ($3.2 million) and expense related to the impairment charge associated with HalioDx ($2.7 million). For the three months ended Sep 30, 2024, adjustments include the exclusion of unrealized gains associated with foreign exchange impacts on stock-based compensation and intercompany loans ($1.1 million) partially offset by expense related to restructuring costs ($0.2 million). For the three months ended June 30, 2024, adjustments primarily include expense related to restructuring costs associated with a reduction in our Biopharmaceutical and Other segment ($2.9 million) and with portfolio prioritization ($0.2 million). For the three months ended Mar 31, 2024, adjustment includes $1.4 million expense related to restructuring costs associated with portfolio prioritization. For the three months ended Dec 31, 2023, adjustment includes $32.0 million expense related to the impairment charge associated with HalioDx. 3. Incremental non-GAAP tax expense reflects the tax impact of the non-GAAP adjustments listed. 4. In those periods in which GAAP net (loss) income is negative and non-GAAP net (loss) income is positive, non-GAAP diluted weighted average shares outstanding includes potentially dilutive common shares from equity awards as determined using the treasury stock method. 5. Some figures rounded for reporting purposes. Summed quarters may differ slightly from year-to-date figures presented due to rounding or use of weighted-averages when calculating earnings per share.

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