Blueprint Medicines Reports First Quarter 2019 Financial Results -- Avapritinib NDA for PDGFRA Exon 18 mutant GIST and fourth-line GIST on track for submission to FDA in second quarter -- -- BLU-667 granted Breakthrough

Blueprint Medicines Reports First Quarter 2019 Financial Results

-- Avapritinib NDA for PDGFRA Exon 18 mutant GIST and fourth-line GIST on track for submission to FDA in second quarter --

-- BLU-667 granted Breakthrough Therapy Designation for the treatment of RET fusion-positive NSCLC --

-- Avapritinib data in GIST and BLU-667 data in RET-altered NSCLC and MTC accepted for presentation at ASCO --

-- Avapritinib data in advanced systemic mastocytosis accepted for presentation at EHA --

-- Completed follow-on offering and raised approximately $327.2 million in net proceeds --

CAMBRIDGE, Mass., May 9, 2019 Blueprint Medicines Corporation (NASDAQ:BPMC), a precision therapy company focused on genomically defined cancers, rare diseases and cancer immunotherapy, today reported financial results and provided a business update for the quarter ended March 31, 2019.

Based on significant clinical and regulatory progress in the first quarter, we accelerated multiple programs and advanced our 2020 Blueprint' strategy to transform Blueprint Medicines into a fully-integrated precision therapy company, said Jeff Albers, Chief Executive Officer of Blueprint Medicines. We are especially encouraged that the FDA granted Breakthrough Therapy Designation to BLU-667 for RET-fusion-positive NSCLC, and we look forward to presenting updated data from our Phase 1 ARROW trial at the ASCO Annual Meeting next month. In addition, our follow-on public offering in April further strengthened our financial position, enabling us to continue to build the company ahead of multiple planned marketing applications for avapritinib and BLU-667 in the United States and Europe over the next 18 months.

First Quarter 2019 Highlights and Recent Progress:

Avapritinib: Gastrointestinal stromal tumors (GIST):

Avapritinib: Systemic mastocytosis (SM):

BLU-667: RET-altered solid tumors:

BLU-554: Advanced hepatocellular carcinoma (HCC)

BLU-782: Fibrodysplasia ossificans progressiva (FOP):

Key Upcoming Milestones:

The company expects to achieve the following near-term milestones:

First Quarter 2019 Financial Results:

Based on its current plans, Blueprint Medicines expects that its existing cash, cash equivalents and investments, including the estimated net proceeds of approximately $327.2 million from its April 2019 follow-on public offering but excluding any potential option fees and milestone payments under its existing collaborations with Roche and CStone Pharmaceuticals, will be sufficient to enable it to fund its operating expenses and capital expenditure requirements into the middle of 2021.

Conference Call Information:

Blueprint Medicines will host a live conference call and webcast at 8:30 a.m. ET today to discuss first quarter 2019 financial results and recent business activities. The conference call may be accessed by dialing (855) 728-4793 (domestic) or (503) 343-6666 (international) and referring to conference ID 9671728. A webcast of the conference call will be available in the Investors section of the Blueprint Medicines' website at http://ir.blueprintmedicines.com. The archived webcast will be available on Blueprint Medicines' website approximately two hours after the conference call and will be available for 30 days following the call.

About Blueprint Medicines:

Cautionary Note Regarding Forward-Looking Statements:

This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995, as amended, including, without limitation, statements regarding plans and timelines for the development of avapritinib, BLU-667, BLU-554 and BLU-782; plans and timelines for submitting an NDA to the FDA and an MAA to the EMA for avapritinib for the treatment of GIST; plans and timelines for presenting the registration dataset for avapritinib in PDGFRA Exon 18 mutant GIST and fourth-line GIST; plans and timelines for submitting an NDA to the FDA for avapritinib for the treatment of advanced SM; plans and timelines for presenting updated data from the Phase 1 EXPLORER trial of avapritinib in advanced SM; plans and timelines for submitting NDAs to the FDA for BLU-667 for the treatment of RET-fusion NSCLC and RET-fusion MTC; plans and timelines for presenting updated data from the Phase 1 ARROW trial of BLU-667 in RET-altered cancers; expectations regarding the results from the Phase 1 clinical trial of BLU-782 in patients with FOP; plans and timelines for initiating a Phase 2 clinical trial of BLU-782 in patients with FOP; plans and timelines for patient enrollment in China in the ongoing global Phase 1 trial of BLU-554 in patients with advanced HCC; the potential benefits of Blueprint Medicines' current and future drug candidates in treating patients; expectations regarding Blueprint Medicines' existing cash, cash equivalents and investments; and Blueprint Medicines' strategy, goals and anticipated milestones, business plans and focus. The words may, will, could, would, should, expect, plan, anticipate, intend, believe, estimate, predict, project, potential, continue, target and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. Any forward-looking statements in this press release are based on management's current expectations and beliefs and are subject to a number of risks, uncertainties and important factors that may cause actual events or results to differ materially from those expressed or implied by any forward-looking statements contained in this press release, including, without limitation, risks and uncertainties related to the delay of any current or planned clinical trials or the development of Blueprint Medicines' drug candidates, including avapritinib, BLU-667, BLU-554 and BLU-782; Blueprint Medicines' advancement of multiple early-stage efforts; Blueprint Medicines' ability to successfully demonstrate the safety and efficacy of its drug candidates and gain approval of its drug candidates on a timely basis, if at all; the preclinical and clinical results for Blueprint Medicines' drug candidates, which may not support further development of such drug candidates; actions of regulatory agencies, which may affect the initiation, timing and progress of clinical trials; Blueprint Medicines' ability to develop and commercialize companion diagnostic tests for its current and future drug candidates; and the success of Blueprint Medicines' current and future collaborations, including its cancer

immunotherapy collaboration with F. Hoffmann-La Roche Ltd and Hoffmann-La Roche Inc. and its collaboration with CStone Pharmaceuticals. These and other risks and uncertainties are described in greater detail in the section entitled Risk Factors in Blueprint Medicines' Annual Report on Form 10-K for the year ended December 31, 2018, as filed with the Securities and Exchange Commission (SEC) on February 26, 2019, and any other filings that Blueprint Medicines has made or may make with the SEC in the future. Any forward-looking statements contained in this press release represent Blueprint Medicines' views only as of the date hereof and should not be relied upon as representing its views as of any subsequent date. Except as required by law, Blueprint Medicines explicitly disclaims any obligation to update any forward-looking statements.

Blueprint Medicines Corporation

Selected Condensed Consolidated Balance Sheet Data

(1) Blueprint Medicines defines working capital as current assets less current liabilities.

Blueprint Medicines Corporation

Condensed Consolidated Statements of Operations Data

(in thousands, except per share data)

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