SecProbe.io

Mail Stop 3030

June 5 , 2018

Via E -mail
R. Erik Holmlin, Ph.D.
President and Chief Executive Officer
Bionano Genomics, Inc.
9640 Towne Centre Drive, Suite 100
San Diego, California 92121

Re: Bionano Genomics, Inc.
Draft Registration Statement on Form S -1
Submitted May 14, 2018
  CIK No. 0001411690

Dear Dr. Holmlin:

We have reviewed your draft registration statement and have the following comments.  In
some of our comments, we may ask you to provide us with information so we may better
underst and your disclosure.

Please respond to this letter by providing any requested information and by publicly
filing your registration statement and non -public draft submission on EDGAR.  If you do not
believe our comments apply to your facts and circumstance s or do not believe revisions in
response to these comments are appropriate, please tell us why in your response.

After reviewing the information you provide in response to these comments and your
filed registration statement, we may have additional comments.

Cover Page

1. Please supplementally provide us with copies of all written communications, as defined
in Rule  405 under the Securities Act, that you , or anyone authorized to do so on your
behalf , present to potential investors in reliance on Section 5(d) of the Securities Act,
whether or not they retain copies of the communications.

2. We note your disclosure that  the closing of the offering is contingent on Nasdaq listing of
your common stock.  This contingency appears to create an offering that is other than a
firm commitment.  It is unclear whether the underwriters will be collecting funds prior to
the contingen cy being satisfied.  If so, please tell us whether the underwriters  will comply
with Rule 15c2 -4.

R. Erik Holmlin, Ph.D.
Bionano Genomics, Inc.
June 5, 2018
Page 2

 Overview, page 1

3. Please provide the basis for your beliefs regarding your product, including but not limited
to your belief that your product is cost -effec tive.  Also, given your extensive disclosure
regarding the attributes and functionality of your product relative to competing products,
please explain the reasons for your current level of sales and share of the market in which
you compete.

4. Please tell us the criteria you used to determine that the customers you highlight are
objectively representative of your business.  Include in your response whether any
unnamed customers also satisfy those criteria.

5. Please revise to disclose clearly and prominently the research use only designation of
your system and consumables.  Also revise to disclose how this designation impacts you r
addressable market.

Market Opportunity, page 2

6. Please tell us your basis for the addressable market calculations, given its res earch use
only designation, and provide a more detailed discussion of underlying assumptions used
in your calculations.  Please also provide your basis for the 15% figure on page 67.

Our Focus Areas, page 4

7. Please revise to clarify how you are addressin g these focus areas, including that you are
providing a system for research use only rather than the diagnosis or treatment of an y of
the diseases you mention.

Risk Factors, page 11

8. Please add risk factor disclosure for the exclusive forum provision disclosed on page 113.
Include as a separate risk factor a discussion of the risks associated with the provision
designating the U.S. federal district courts as the exclusive forum for re solving any
complaint asserting a cause of action arising under the Securities Act.

Provisions of our secured term loan facility…, page 14

9. Please expand your risk factor to include a brief description of the financial covenants
contained in your loan a greement.  Also, if the potential risk you discuss has actually
occurred, please revise to state so directly.  For example, please revise to address your
default and subsequent forbearance agreement from Western Alliance Bank for failing to
raise additiona l capital as of December 31, 2017 as described on page 58.

R. Erik Holmlin, Ph.D.
Bionano Genomics, Inc.
June 5, 2018
Page 3

 Use of Proceeds, page 46

10. Please disclose the amount of proceeds that you currently intend to use for each of the
purposes mentioned in the penultimate paragraph of this section.  Also, provide more
detail regarding your plan to expand your commercial capabilities and what research and
development activities you intend to fund.

Capitalization, page 48

11. Please explain to us how you calculated total capitalization in the table.

Comparison of th e Years Ended December 31, 2016 and 2017, page 56

12. Please quantify the amount of the increase in revenues attributable to changes in price
and increases in volume.  Also, provide the relative growth rate in revenue from sales of
instruments versus consumab les.

13. Please clarify your disclosure that you incurred higher manufacturing costs of your
instruments due to “the purchase quantities at lower volumes on a per -batch basis” given
you sold more instruments in the year ended December 31, 2017 compared to 20 16.

Loan facility, page 58

14. Please disclose the financing milestone that must be achieved in order to extend the
interest -only payments.

Note purchase agreement, page 58

15. Please file the note purchase agreement as an exhibit to your registration statement or
advise.

Business, page 65

Overview, page 65

16. Refer to the fourth paragraph.  Please revise to clarify your disclosure that your product is
being adopted as a “comple ment” to sequencers.  For example, do sequencers detect
variations that your product cannot detect?  Does your product function effectively only
when used with sequencers?

The Saphyr System’s Industry -Leading Sensitivity and Specificity, page 76

17. Please  tell us whether you commissioned any of the publications or studies cited in your
prospectus.

R. Erik Holmlin, Ph.D.
Bionano Genomics, Inc.
June 5, 2018
Page 4

Certain Relationships and Related Party Transactions, page 105

18. Please disclose the conversion or net exercise rate for the securities identified in this
section, such as the February 2018 notes discussed on page F -26 and the number of
securities to be received upon conversion in connection with this transaction.

Principal Stockholders, page 108

19. Please revise your disclosure to identity the natural person or  persons who share voting
and investment control of the shares held by Praise Alliance International Limited and
Full Succeed International Limited.  Also, identify the natural person or persons with
whom Mr. Wang shares voting or investment control of the  shares held by LC Fund VI,
L.P. or advise.

Shares Eligible for Future Sale, page 114

20. We note you are not registering the shares issuable upon exercise of the underwriters’
warrants.  Please revise the disclosure in the second paragraph of this section regarding
the shares underlying the underwriters’ warrants accordingly or advise.

Financial Statements, page F -1

Note 2. Summary of Significant Accounting Policies, page F -8

Revenue Recognition, page F -10

21. We note your  discussion that the timing of revenue recognition on instrument sales is
based upon when delivery has occurred, the price is fixed or determinable, and
collectability is reasonably assured.  Please revise to disclose your accounting for
installation in di rect sales with customers.

22. We note your disclosure on page 79 that you designed the Saphyr system to
accommodate performance upgrades without the need for replacement of the entire
instrument and that performance enhancements will be delivered on a regul ar basis
through software and hardware upgrades.  Please revise to disclose your accounting for
these upgrades.

Note 8. Convertible Preferred Stock and Stockholders’ Deficit, page F -18

Common Stock, page F -21

23. We note the issuances of convertible preferr ed stock at prices significantly higher than
the exercise price of stock options granted.  Please explain to us how you considered the

R. Erik Holmlin, Ph.D.
Bionano Genomics, Inc.
June 5, 2018
Page 5

 convertible preferred stock issuances in the valuation of stock options granted in fiscal
2017.

We remind you that the  company and its management are responsible for the accuracy
and adequacy of their disclosures, notwithstanding any review, comments, action or absence of
action by the staff.

We also remind you that your registration statement must be on file no later than 48 hours
prior to the requested effective date and time.  Refer to Rules 460 and 461 regarding requests for
acceleration.  Please allow adequate time for us to review any ame ndment prior to the requested
effective date of the registration statement.

You may contact Julie Sherman at (202) 551 -3640 or Brian Cascio , Accounting Branch
Chief , at (202) 551 -3676 if you have questions regarding comments on the financial statemen ts
and related matters.  Please contact Heather Percival at (202) 551 -3498 or Geoff Kruczek, Senior
Attorney, at (202) 551 -3641 with any other questions.

Sincerely,

 /s/ Geoff Kruczek for

Amanda Ravitz
Assistant Director
Office of Electronics and Machi nery

cc: James C. Pennington, Esq.
Cooley LLP