Washington, D.C. 20549
Pursuant to Section 13 or 15(d) of the
Securities Exchange Act of 1934
Date of Report (Date of earliest event reported): November 4, 2021
Bionano Genomics, Inc.
(Exact Name of Registrant as Specified in its Charter)
Delaware 001-3861326-1756290
(State or Other Jurisdiction
of Incorporation)
File Number)
(IRS Employer
Identification No.)
9540 Towne Centre Drive, Suite 100
San Diego, California
(Address of Principal Executive Offices)(Zip Code)
Registrant’s telephone number, including area code: (858888-7600
Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions:
    Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)
    Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)
     Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))
     Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))
Securities registered pursuant to Section 12(b) of the Act:
Title of each classTrading Symbol(s)Name of each exchange on which registered
Common Stock, $0.0001 par value per shareBNGOThe Nasdaq Stock Market, LLC
Warrants to purchase Common StockBNGOWThe Nasdaq Stock Market, LLC
Indicate by check mark whether the registrant is an emerging growth company as defined in Rule 405 of the Securities Act of 1933 (§230.405 of this chapter) or Rule 12b-2 of the Securities Exchange Act of 1934 (§240.12b-2 of this chapter).
Emerging growth company
If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.

Item 2.02 Results of Operations and Financial Condition.
On November 4, 2021, Bionano Genomics, Inc. (the “Company”) issued a press release reporting its financial results for the third quarter ended September 30, 2021.  The full text of the press release is attached as Exhibit 99.1 to this Current Report on Form 8-K.
In accordance with General Instruction B.2. of Form 8-K, the information contained or incorporated herein, including the press release filed as Exhibit 99.1, shall not be deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), or otherwise subject to the liabilities of that section, nor shall it be deemed to be incorporated by reference into any filing under the Securities Act of 1933, as amended, or the Exchange Act, whether made before or after the date hereof, except as expressly set forth by specific reference in such filing to this Current Report on Form 8-K.
Item 8.01 Other Events.
As previously announced, the Company is hosting a conference call on November 4, 2021 at 4:30 PM Eastern Time to review its financial results for its third quarter ended September 30, 2021 and to provide a business update (the “Earnings Call”). A presentation to accompany the Earnings Call (the “Corporate Presentation”) is attached hereto as Exhibit 99.2. Information contained in the Corporate Presentation may also be used by the Company in future meetings regarding the Company.
Item 9.01 Financial Statements and Exhibits.
(d) Exhibits
Exhibit No.  Description
104Inline XBRL for the cover page of this Current Report on Form 8-K

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned hereunto duly authorized.
 Bionano Genomics, Inc.
Date: November 4, 2021
 By: /s/ R. Erik Holmlin, Ph.D.
  R. Erik Holmlin, Ph.D.
  President and Chief Executive Officer
(Principal Executive Officer)

Bionano Genomics Reports Third Quarter 2021 Financial Results and Highlights Recent Business Progress

Acquisition of BioDiscovery transforms Bionano from the structural variation company into a data solutions provider with the potential to offer the most comprehensive variant analysis platform in genomics
Total revenue of $4.7 million, a 112% year-over-year total revenue increase, driven by growth in the Saphyr® installed base
Record number of Saphyr shipments and installations for any quarter to date
Launched protocols for ultra-high molecular weight DNA isolation from amniocentesis and chorionic villus sampling (CVS) for prenatal applications
Remaining 2021 milestones on track
Strong balance sheet with $326.1 million in cash and short term investments as of September 30, 2021
Conference call today, Thursday, November 4, at 4:30 pm ET

SAN DIEGO, November 4, 2021 – Bionano Genomics, Inc. (NASDAQ: BNGO) today reported financial results and business achievements for the quarter ended September 30, 2021 and highlighted recent corporate updates.

“We had the strongest quarter in Bionano’s history with a record number of Saphyr shipments and installations, including adoptions at several notable sites, including leading hospitals, cytogenetics labs and academic medical centers around the world. With the acquisition of BioDiscovery, a leading software company with best-in-class solutions for analysis, visualization, interpretation and reporting of genomics data. for microarray and next-generation sequencing (NGS), we are transitioning Bionano Genomics from being the structural variation company into a data solutions provider. We believe this will enable access to an expanded market opportunity by leveraging the NGS market through software. We are extremely pleased with the progress we are making and the fact that outstanding leaders are joining Bionano to join us in transforming the way the world sees the genome,” commented Erik Holmlin, PhD, Chief Executive Officer of Bionano Genomics.

Chris Stewart, Chief Financial Officer of Bionano added: “Q3 was another excellent quarter. We continued to achieve meaningful year-over-year revenue growth and maintained a strong balance sheet with $326 million of cash and marketable securities as of the quarter-end. We also remain on track to achieve the milestones we laid out in the first quarter of 2021.”                
Recent Business Highlight

On October 18, 2021, we closed our acquisition of BioDiscovery, Inc. The transaction is expected to accelerate and broaden Bionano’s market leadership in digital cytogenetics and comprehensive genome analysis. Bionano’s transaction consideration for the acquisition of BioDiscovery was up to $100 million, consisting of a combination of cash and equity. A portion of the equity is subject to vesting based on continued service of key employees and a portion of the cash is contingent on achieving full integration of OGM data into BioDiscovery’s software platform.

Key Business Highlights in Q3

The Company executed on its commercialization strategy, built scientific momentum by presenting data at key scientific meetings and drove utilization of Saphyr at key institutions across the globe, with the following highlights:

Expanded the installed base of Saphyr systems from 121 at the end of Q2 to 141 at the end of Q3. During the quarter ended September 30,2021, we shipped a total of 24 Saphyr systems to the field, compared to 11 systems shipped in the same quarter in 2020.

Sold 3,969 nanochannel array flow cells during the quarter ended September 30, 2021, which is the most flow cells sold in any quarter ever and represents 122% growth over the same quarter in 2020.

Commercial release of solutions for isolation of ultra-high molecular weight DNA for prenatal applications supporting the use of samples derived from amniocentesis and CVS. Bionano Prep SP Amnio and CVS Culture DNA Isolation Protocol supports both fresh cultures and cryopreserved cells, which expands the markets served for OGM.

OGM with Saphyr was adopted at several notable cytogenetics laboratories and academic medical centers in the United States, including Brigham & Woman’s Hospital, which is using OGM to identify structural variations in constitutional and cancer applications. Outside the US, Saphyr was adopted in Australia, Europe and China.

The largest clinical research study to date evaluating OGM was published in The Journal of Molecular Diagnostics for a rare muscle disease, facioscapulohumeral muscular dystrophy, or FSHD, in about 351 patients. The                
results demonstrated that OGM provided data more quickly, accurately, and reproducibly than the current gold standard method of Southern blot analysis. The findings support the rationale for adopting OGM as an alternative to Southern blot analysis as OGM had a greater sizing accuracy as well as a greater than 99% concordance with Southern blot analysis.

NuProbe Global, a global molecular diagnostics leader, adopted Saphyr to be integrated their proprietary tools, Quantitative Amplicon Sequencing (QASeq) and Blocker Displacement Amplification (BDA), for research and development efforts in reproductive health and oncology liquid biopsies.

Saphyr customers and Bionano conducted 10 presentations at the Annual Cancer Genomics Consortium Meeting in mid-August 2021, highlighting the benefits of OGM for clinical research applications in solid tumor analysis, hematological malignancies, products of conception, prenatal and postnatal constitutional genetics. More than 500 participants from around the globe attended virtually, highlighting the strong interest in OGM for cancer genomics.

Bionano customers presented 11 presentations on OGM at the European Society of Human Genetics (ESHG) meeting in late August 2021, demonstrating the clinical utility of OGM across many therapeutic application areas, along with the unique capabilities of Bionano’s Saphyr® system to detect all classes of structural variants, across the genome, at a superior resolution relative to traditional techniques.

Added exceptional talent across commercial leadership functions, including Amanda Lettmann as Vice President of Global Customer Experience, Alex Helm as Vice President Strategic Product Marketing, Stephanie Hoyle as Vice President Corporate Marketing, Amanda Hernandez as Vice President of Global Sales Training and Development, Justin Leighton as Vice President and General Manager, Lineagen, and Bob Hertsenberg as North America Sales Director.

Financial Highlights

Total revenue for the third quarter of 2021 was $4.7 million, up 21% from $3.9 million in the second quarter and up 112% from $2.2 million in the same period of 2020. The sequential increase was driven by increased demand for our Saphyr optical genome mapping solutions, including increased instrument sales and greater demand for our reagent rental program and consumables. The year-over-                
year increase was driven by both higher product sales and by the addition of revenue from Lineagen.

Gross margin for the third quarter of 2021 was 24.8%, compared to 37.3% in the prior quarter and 33.4% from the third quarter of 2020. The decrease was primarily due to an increase in laboratory and warranty related expense that are expected to be non-recurring.

Third quarter operating expense was $21.8 million, compared to $17.9 million in the prior quarter and $11.0 million in the third quarter of 2020. The sequential increase was mainly due to a $1.8 million increase in headcount and related expenses and a $1.5 million increase in Research and Development expenses related to expanding our supply chain to produce higher volumes. Third quarter operating expense included $2.8 million of non-cash stock-based compensation. The year-over-year increase was primarily due to increased headcount-related spending as we build out all facets of our organization to support our expected commercial progress and increased research and development costs.

At September 30, 2021, the Company had cash, cash equivalents, and short-term investments of $326.1 million compared to cash and cash equivalents of $38.4 million at December 31, 2020. The increase in cash is primarily due to the equity raises that were completed in the first quarter of 2021.

Remaining Anticipated Milestones for 2021 – Initiatives to Drive Global Adoption of Saphyr

4Q21: Interim publication of results from pediatric clinical study
4Q21: Validation of LDTs by 3 sites in both our prenatal clinical study and our pediatric clinical study
4Q21: Initial prototype of next gen high throughput Saphyr
4Q21: Reach installed base of 150 systems to achieve a 50% increase over year end 2020                
Conference Call & Webcast Details

Date:Thursday, November 4, 2021
Time:4:30 p.m. Eastern Time
Toll Free:
Conference ID:

To access the call, participants should dial the applicable telephone number above at least 5 minutes prior to the start of the call. An archived version of the webcast will be available for replay in the Investors section of the Bionano website.

About Bionano Genomics
Bionano is a provider of genome analysis solutions that can enable researchers and clinicians to reveal answers to challenging questions in biology and medicine. The Company’s mission is to transform the way the world sees the genome through OGM solutions, diagnostic services and software. The Company offers OGM solutions for applications across basic, translational and clinical research. Through its Lineagen business, the Company also provides diagnostic testing for patients with clinical presentations consistent with autism spectrum disorder and other neurodevelopmental disabilities. Through its BioDiscovery business, the Company also offers an industry-leading, platform-agnostic software solution, which integrates next-generation sequencing and microarray data designed to provide analysis, visualization, interpretation and reporting of copy number variants, single-nucleotide variants and absence of heterozygosity across the genome in one consolidated view. For more information, visit, or

Forward-Looking Statements
This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Words such as “may,” “will,” “expect,” “plan,” “anticipate,” “estimate,” “intend” and similar expressions (as well as other words or expressions referencing future events, conditions or circumstances) convey uncertainty of future events or outcomes and are intended to identify these forward-looking statements. Forward-looking statements include statements regarding our intentions, beliefs,                
projections, outlook, analyses or current expectations concerning, among other things: the expected benefits of our acquisition of BioDiscovery, including with respect to its impact on our market leadership; our anticipated milestones for the remainder of 2021, including that we remain on track to achieve these milestones; and the advancement of our business strategy. Each of these forward-looking statements involves risks and uncertainties. Actual results or developments may differ materially from those projected or implied in these forward-looking statements. Factors that may cause such a difference include the risks and uncertainties associated with: the impact of the COVID-19 pandemic on our business and the global economy; general market conditions; changes in the competitive landscape and the introduction of competitive products; changes in our strategic and commercial plans; our ability to obtain sufficient financing to fund our strategic plans and commercialization efforts; the ability of medical and research institutions to obtain funding to support adoption or continued use of our technologies; the loss of key members of management and our commercial team; our inability to achieve the anticipated benefits from our acquisitions of Lineagen and BioDiscovery; and the risks and uncertainties associated with our business and financial condition in general, including the risks and uncertainties described in our filings with the Securities and Exchange Commission, including, without limitation, our Annual Report on Form 10-K for the year ended December 31, 2021 and in other filings subsequently made by us with the Securities and Exchange Commission. All forward-looking statements contained in this press release speak only as of the date on which they were made and are based on management's assumptions and estimates as of such date. We do not undertake any obligation to publicly update any forward-looking statements, whether as a result of the receipt of new information, the occurrence of future events or otherwise.                
Company Contact:
Erik Holmlin, CEO
Bionano Genomics, Inc.
+1 (858) 888-7610
Investor Relations and
Media Contact:
Amy Conrad
Juniper Point
+1 (858) 366-3243                
Bionano Genomics, Inc.
Condensed Consolidated Balance Sheet
September 30, 2021
December 31, 2020
Current assets:  
Cash and cash equivalents$140,736,000 $38,449,000 
Investments $185,333,000 $— 
Accounts receivable, net2,996,000 2,775,000 
Inventory9,020,000 3,316,000 
Prepaid expenses and other current assets3,962,000 2,250,000 
Total current assets342,047,000 46,790,000 
Property and equipment, net8,554,000 4,910,000 
Intangible Assets1,238,000 1,475,000 
Goodwill7,173,000 7,173,000 
Other Long Term Assets$645,000 $103,000 
Total assets$359,657,000 $60,451,000 
Liabilities and stockholders’ equity
Current liabilities:
Accounts payable$7,875,000 $2,930,000 
Accrued expenses9,416,000 5,599,000 
Contract liabilities411,000 416,000 
Total current liabilities17,702,000 8,945,000 
Long-term debt— 16,326,000 
Long-term contract liabilities158,000 98,000 
Other non-current liabilities232,000 — 
Total liabilities18,092,000 25,369,000 
Stockholders’ equity:
Common stock28,000 19,000 
Additional paid-in capital534,823,000 178,747,000 
Accumulated deficit(193,170,000)(143,684,000)
Accumulated Other Comprehensive Loss(116,000)— 
Total stockholders’ equity341,565,000 35,082,000 
Total liabilities and stockholders’ equity$359,657,000 $60,451,000                
Bionano Genomics, Inc.
Condensed Consolidated Statement of Operations (Unaudited)
Three Months Ended September 30,Nine Months Ended
September 30,
Product revenue$3,300,000 $1,580,000 $7,845,000 $3,503,000 
Service and other revenue1,355,000 616,000 3,834,000 1,010,000 
Total revenue4,655,000 2,196,000 11,679,000 4,513,000 
Cost of revenue:
Cost of product revenue2,340,000 1,136,000 5,723,000 2,426,000 
Cost of service and other revenue1,161,000 324,000 2,321,000 493,000 
Total cost of revenue3,501,000 1,460,000 8,044,000 2,919,000 
Operating expenses:
Research and development6,505,000 2,304,000 13,270,000 7,379,000 
Selling, general and administrative15,327,000 8,659,000 38,683,000 21,640,000 
Total operating expenses21,832,000 10,963,000 51,953,000 29,019,000 
Loss from operations(20,678,000)(10,227,000)(48,318,000)(27,425,000)
Other income (expenses):
Interest income (expense)27,000 (589,000)(721,000)(1,911,000)
Gain on forgiveness of PPP Loan— — 1,775,000 — 
Loss on debt extinguishment— — (2,076,000)— 
Other income (expense)(67,000)54,000 (96,000)— 
Total other income (expense)(40,000)(535,000)(1,118,000)(1,911,000)
Loss before income taxes(20,718,000)(10,762,000)(49,436,000)(29,336,000)
Provision for income taxes(35,000)(30,000)(50,000)(40,000)
Net loss$(20,753,000)$(10,792,000)$(49,486,000)$(29,376,000)

Q3 Webcast and Call November 4, 2021

2 Legal Disclaimer This presentation contains forward-looking statements. Forward-looking statements describe future expectations, plans, results or strategies and are generally preceded by terms such as “may,” “will,” “should,” “could,” “would,” “expects,” “plans,” “anticipates,” “believes,” “estimates,” “projects,” “predicts,” “potential” and similar expressions (including the negative thereof). Forward-looking statements in this presentation include, but are not limited to, statements regarding: (i) growth drivers and expected levels of our organic growth; (ii) improvements to our manufacturing cost efficiency; (iii) the impact of our investment in R&D and commercial initiatives; (iv) our ability to stay in front of competitors’ improvements in technologies; (v) anticipated milestones; (vi) integration of BioDiscovery into our business; and (vii) other statements that are not historical facts. Actual results or developments may differ materially from those projected or implied in these forward-looking statements. Forward-looking statements are based only on current information, assumptions and expectations, and involve a number of risks and uncertainties relating to (i) challenges inherent in developing, manufacturing and commercializing products; (ii) the timing and mix of customer orders among our products; (iii) our ability to further deploy new products and applications and expand the markets for our technology platforms; (iv) third parties’ abilities to manufacture our instruments and consumables; (v) the success of products competitive with our own; (vi) our expectations and beliefs regarding future growth of the business and the markets in which we operate; (vii) the accuracy of our estimates ; (viii) our expectations and beliefs regarding the combined business following the acquisition of BioDiscovery, (ix) our ability to fund our operations; and (x) the application of generally accepted accounting principles which are highly complex and involve many subjective assumptions. We are under no duty to update any of these forward- looking statements after the date of this presentation to conform these statements to actual results or revised expectations, except as required by law. You should, therefore, not rely on these forward-looking statements as representing our views as of any date subsequent to the date of this presentation. Moreover, except as required by law, neither we nor any other person assumes responsibility for the accuracy and completeness of the forward-looking statements contained in this presentation. More information about these and other statements, risks and uncertainties is contained in our filings with the U.S. Securities and Exchange Commission. All forward- looking statements contained in this presentation speak only as of the date on which they were made. We disclaim any intention or obligation to update or revise any forward-looking statements, whether as a result of new information, occurrence of future events or otherwise except as required by applicable law.

+ Creating the Leading Variant Analysis Platform in Genomics

4 Acquisition Expected to Accelerate and Broaden Bionano’s Market Leadership in Cytogenomics and Comprehensive Genome Analysis • Our vision is to make OGM ubiquitous, this vision requires exceptional software • Delivering seamless integration with as many data types as possible, OGM can be used more broadly • Enables Bionano to offer the most comprehensive genome analysis by combining NGS with OGM data in one integrated workflow • We would have the only proprietary data type (OGM) within this software ecosystem • Transforms Bionano into a genomics data solutions provider Data Integration

5 Integration Plan & Operational Structure • Dr. Soheil Shams becomes Chief Informatics Officer (CIO) of Bionano • Location in El Segundo, CA, preserved as Bionano software hub • CIO integrated into Bionano software/informatics programs – Drive integration of SV analysis pipelines into NxClinical software – Streamline consolidation of Access/Solve and NxClinical software – Integrate NGS and microarray data with OGM data to create potentially the most comprehensive genomics software in one seamless workflow • World class team of software engineers, computational biologists, algorithm developers, and an experienced commercial team with expertise supporting genome analysis

6 Summary of Q3 Results R. Erik Holmlin CEO

7 Q3 2021: Creating Momentum Heading into YE Q2 New Applications in Prenatal Testing, Cancer Research & Development Presented 24 10 New Publications in Q3 Talks and Posters Saphyr Systems Shipped 141 total installed Advancing Go to Market – Bionano Data Centric Services, Reagent Rentals & Capital Purchase Total Revenue: $4.7M Global Adoption of Saphyr Strong adoption throughout target geographies, including the US, and new markets for prenatal analysis, cancer research and drug development 11 Presentations on OGM ADDED EXPERIENCED TALENT TO SALES, MARKETING, AND CUSTOMER SUPPORT TEAMS NEW GLOBAL REGIONS & ADOPTIONS 30 Alex Helm Vice President Strategic Product Marketing Amanda Hernandez Vice President Global Sales Training & Development Bob Hertsenberg Director North America Sales Amanda Lettmann Vice President Global Customer Experience Stephanie Hoyle Vice President Global Corporate Marketing

8 Clinically Focused Publications in Q3, 2021 Clinical area of focus Authors Institution Database/Journal Key findings OGM as a tool in clinical cytogenetics/genomics Khan, W.A. and Toledo, D.M. Dartmouth Adv. in Mol. Path. Review OGM in the clinic Solid tumor: Medulloblastoma Chapman, O., et al UCSD bioRxiv Presence of extrachromosomal DNA in MD is associated with relapse Constitutional case study: Choroideremia Fadaie, Z., et al Radboud NL HGG Advances OGM identifies an inverted duplication as pathogenic cause of disease Benchmarking: GIAB Wagner, J., et al NIST bioRxiv Improvements in calling variants in medically relevant genes Constitutional: Postnatal Shieh, J.T., et al UCSF NPJ Genomic Med. 40% Improved diagnostic yield in a cohort of neurodevelopmental disorders by OGM + NGS Basic science: Genome characterization Wong, J., et al Drexel Genomics Method for identification of mobile elements using OGM Solid tumor: Non-small cell lung carcinoma Xia, L., et al West China Hospital Cell Rep. Combining OGM + NGS finds new biomarkers in NSCLC Constitutional: FSHD1 Stence, A.A., et al U. Iowa J. of Mol. Diagnostics Largest clinical cohort (351 pts) on OGM – FSHD1 Constitutional: Risk for Atypical teratoid rhabdoid tumors Sabatella, M., et al Utrecht NL Journal of Pathology OGM identifies a pathogenic insertion missed by short and long read WGS Hematological malignancies: Multiple myeloma Kriegova, E., et al Palacky U.,Czech Scientific Reports OGM analysis of multiple myeloma cohort provides new biomarkers Basic science: Optical replication mapping Wang, W., et al FSU,Curie,U.Mass Molecular Cell First publication of optical replication mapping for studying DNA replication Constitutional: Cytogenetics Mantere, T., et al Radboud NL AJHG 100% concordance with SOC for 85 pts with constitutional disorders Heme malignancies: Cytogenetics Neveling, K., et al Radboud NL AJHG 100% concordance with SOC for 52 pts with hematologic malignancies Constitutional: Hemophilia Fahiminiya, S., et al U. Montreal Hemophilia Detection of recurrent pathogenic inversion causing hemophilia

9 Clinical Affairs Summary

10 Four Large Clinical Studies Getting Underway to Support Penetration of our Target Markets & Support Potential Third-Party Reimbursement Constitutional - Prenatal - Constitutional - Pediatric - Oncology - Heme Malignancies - Oncology - Solid Tumor - Amnio & CVS Illustrate HOW Saphyr can help with NIPT + cases and no-calls • IRB approval  Site recruitment  Site training started  New assay launched  Already enrolled 100+ Goal to become SOC* & detect balanced SVs Peripheral blood, expand into others • IRB approval  1000 subjects  500 enrolled  +200 from Q2 • Data generation Goal to become SOC* w/ detection of all classes of SVs by OGM Peripheral blood, BMA (leukemia/lymphoma)  Site recruitment • Site contracts • Expected study initiation: Q1, 2022 Goal to become SOC* Fresh/frozen tumor tissue, expand into others indicated for breast, colon, GBM melanoma, lung, etc. • Expected study initiation: Q4, 2022 Goal to become SOC* *SOC = Standard of Care  = Update from Q2

11 Financial Overview Chris Stewart CFO

12 Q3 2021 – Financial Results and Key Highlights • Total revenue was $4.7M, up 112% from Q3 2020 • Year-on-year revenue was up in all geographies and across both product and service revenue • Post quarter-end, BioDiscovery acquisition is expected to be moderately accretive Strong cash and short-term investments position with $326M to end Q3 2021 3Q21 $M, except EPS Actual Revenue $4.7 Cost of Revenue 3.5 Gross Profit 1.2 Gross Margin % 24.8% Operating Expense 21.8 Operating Income (Loss) (20.7) Other Expense (Income) (0.1) Net Income (Loss) $ (20.8) Weighted avg shares (M) 280 EPS $ (0.07) Cash $326

13 Summary R. Erik Holmlin CEO

14  Commercial release of prenatal assays for Saphyr and expansion of Saphyr’s menu of pediatric assays Key Anticipated Milestones Expected to Drive Value for BNGO 3Q  Accreditation of Saphyr based LDTs for ALL & FSHD in certain EU markets 2Q 4Q • Interim publication of results from pediatric clinical study  Validation of 3 LDTs total by sites in our prenatal and pediatric clinical studies • Prototype of next-gen high throughput Saphyr • Targeted installed base of 150 systems, potentially a 50% increase over year end 2020 2021

Questions & Answers Contact: R. Erik Holmlin CEO Chris Stewart CFO

16 To continuously innovate to bring new capabilities that accelerate throughput Bionano Genomics: 3 Key Areas of Focus In clinical research and discovery research markets where OGM complements any type of sequencing Through Bionano pivotal clinical studies and third- party support and advocacy Building momentum to drive adoption of OGM GROW the installed base EXPAND the utility of OGM VALIDATE OGM with critical mass of clinical data