UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No.     )*

Progenity, Inc.

(Name of Issuer)

Common Stock, par value $0.001 per share

(Title of Class of Securities)

74319F107

(CUSIP Number)

Andrew C. Hyman, Esq.

Athyrium Capital Management, LP

505 Fifth Avenue, 18th Floor

New York, New York 10017

(212) 402-6925

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

June 23, 2020

(Date of Event Which Requires Filing of This Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§ 240.13d-1(e), 240.13d-l(f) or 240.13d-1(g), check the following box.  ☐

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See § 240.13d-7 for other parties to whom copies are to be sent.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

This statement on Schedule 13D relates to the common stock, par value $0.001 per share (“Common Stock”), of Progenity, Inc., a Delaware corporation (the “Company”). The address of the principal executive offices of the Company is 4330 La Jolla Village Drive, Suite 200, San Diego, California 92122.

(a)-(c) & (f) This Schedule 13D is filed jointly by the following persons pursuant to Rule 13d-1(k) promulgated under the Securities Exchange Act of 1934:

(1) Athyrium Opportunities Fund (A) LP, a Delaware limited partnership (“Fund A”), is an investment partnership engaged in the business of making equity and debt investments;

(2) Athyrium Opportunities Fund (B) LP, a Delaware limited partnership (“Fund B” and, together with Fund A, the “Joint Funds”), is an investment partnership engaged in the business of making equity and debt investments;

(3) Athyrium Opportunities III Co-Invest 1 LP, a Delaware limited partnership (“Co-Invest LP”), is an investment partnership engaged in the business of making equity and debt investments;

(4) Athyrium Opportunities III Acquisition 2 LP, a Delaware limited partnership (“Acquisition 2 LP”), is an investment partnership engaged in the business of making equity and debt investments;

(5) Athyrium Opportunities 2020 LP, a Delaware limited partnership (“2020 LP” and, together with the Joint Funds, Co-Invest LP and Acquisition 2 LP, the “Funds”), is an investment partnership engaged in the business of making equity and debt investments;

(6) Athyrium Opportunities Associates LP, a Delaware limited partnership (“Associates LP”), is engaged in the business of being the general partner of the Joint Funds;

(7) Athyrium Opportunities Associates GP LLC, a Delaware limited liability company (“Associates GP”), is engaged in the business of being the general partner of Associates LP;

(8) Athyrium Capital Management, LP, a Delaware limited partnership (“ACM”), is engaged in the business of being a member of Associates GP and an investment sub-adviser to Opportunities Advisers (as defined below);

(9) Athyrium Capital Holdings, LLC, a Delaware limited liability company (“ACH”), is engaged in the business of being the general partner of ACM;

(10) Jeffrey A. Ferrell is an individual citizen of the United States whose principal occupation is to serve as the Managing Member of ACH and GP Holdings (as defined below) and the President of ACM, Associates GP, Associates III GP (as defined below) and Associates Co-Invest (as defined below);

(11) Athyrium Opportunities Advisers LLC, a Delaware limited liability company (“Opportunities Advisers”), is engaged in the business of being an investment adviser to the Joint Funds;

(12) NB Alternatives Advisers LLC, a Delaware limited liability company (“Alternatives Advisers”), is engaged in the business of being the sole member of Opportunities Advisers;

(13) NB Alternatives GP Holdings LLC, a Delaware limited liability company (“Alternatives GP”), is engaged in the business of being a member of Associates GP;

(14) NB Alternatives Holdings LLC, a Delaware limited liability company (“Alternatives Holdings”), is engaged in the business of being the sole member of Alternatives GP and a member of Alternatives Advisers;

(15) Athyrium Opportunities Associates Co-Invest LLC, a Delaware limited liability company (“Associates Co-Invest”), is engaged in the business of being the general partner of Co-Invest LP;

(16) Athyrium Funds GP Holdings LLC, a Delaware limited liability company (“GP Holdings”), is engaged in the business of being the managing member of Associates Co-Invest and Associates III GP (as defined below);

(17) Athyrium Opportunities Associates III LP, a Delaware limited partnership (“Associates III LP”), is engaged in the business of being the general partner of Acquisition 2 LP and 2020 LP; and

(18) Athyrium Opportunities Associates III GP LLC, a Delaware limited liability company (“Associates III GP”), is engaged in the business of being the general partner of Associates III LP.

The persons described in (1) through (18) above are referred to herein as the “Reporting Persons.” A list of the directors, executive officers, managers, members and partners, as applicable, of each Reporting Person (collectively, the “Covered Persons”) is attached hereto as Annex A and is incorporated by reference herein. To the knowledge of the Reporting Persons, each of the Covered Persons that is a natural person is a United States citizen, except for Elin Strong, who is a citizen of Norway.

The principal business address of each of the Reporting Persons listed as (1)-(2), (6)-(7), (11)-(12) and (14), and each Covered Person associated with the foregoing Reporting Persons, is c/o NB Alternatives Advisers LLC, 1290 Avenue of the Americas, New York, New York 10104.

The principal business address of the Reporting Person listed as (13) and each associated Covered Person is 325 N. Saint Paul Street, Suite 4900, Dallas, TX 75201.

The principal business address of each of the Reporting Persons listed as (3)-(5), (8)-(10) and (15)-(18) and each associated Covered Person is c/o Athyrium Capital Management, LP, 505 Fifth Avenue, Floor 18, New York, New York 10017.

(d) During the last five years, none of the Reporting Persons or, to their knowledge, none of the Covered Persons, has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors).

(e) On December 17, 2018, the Securities and Exchange Commission (the “SEC”) announced that Alternatives Advisers, without admitting or denying any wrongdoing, consented to the entry of an order (the “Order”) by the SEC focused solely on certain expense allocations relating to Dyal Capital Partner’s (“Dyal”) Business Services Platform (the “BSP”), a team within Dyal focused on providing client development, talent management, operational advisory and other services to the partner managers in which certain Dyal funds invest. No other businesses of Alternatives Advisers utilize the BSP (or a similar model) nor allocate the expense associated with the BSP to Alternatives Advisers-advised funds. The Order had no finding of intentional wrongdoing or fraud, and found that the issues relating to the BSP expenses ceased in 2017. Alternatives Advisers agreed as part of the settlement to pay a disgorgement amount to certain Dyal funds covering 2012—2016, and to pay a civil monetary penalty to the SEC.

Other than as disclosed in the foregoing paragraph, during the last five years, none of the Reporting Persons or, to their knowledge, none of the Covered Persons, has been a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and, as a result of such proceeding, was or is subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

On October 27, 2017, the Company and Co-Invest LP entered into a Series B Preferred Stock Purchase Agreement (the “2017 Series B Stock Purchase Agreement”), which provided for the sale of shares of Series B Preferred Stock at a purchase price of $3.53 per share for an aggregate purchase price of $50.0 million. Also on October 27, 2017, the Company issued the Warrant to Co-Invest LP providing the right to purchase additional shares of Series B Preferred Stock.

On August 27, 2019, the Company and Athyrium Opportunities III Acquisition LP (“Acquisition LP”) entered into a Series B Preferred Stock Purchase Agreement pursuant to which Acquisition LP purchased shares of Series B Preferred Stock at $2.75 per share for an aggregate purchase price of $25.0 million. Also on August 27, 2019, the Company exchanged shares of its Series B Preferred Stock for the shares of its Series A-1 Preferred Stock held by the Joint Funds, which were acquired on June 12, 2013 for an aggregate purchase price of$11.2 million.

On November 12, 2019, the Company and Acquisition LP entered into a Series B Stock Preferred Stock Purchase Agreement (the “2019 Series B Stock Purchase Agreement”) pursuant to which Acquisition LP purchased additional shares of Series B Preferred Stock at $2.25 per share for an aggregate purchase price of $25.0 million. The conversion price of the Series B Preferred Stock and exercise price of the Warrant were lowered from $2.75 to $2.25 per share (or $13.90 per share as a result of the reverse stock split effected on June 10, 2020). Also on November 12, 2019, Acquisition 2 LP acquired all of the securities of the Company previously held by Acquisition LP and Acquisition LP ceased to own any equity interest in the Company.

On December 19, 2019 and February 28, 2020, Acquisition 2 LP purchased additional shares of Series B Preferred Stock pursuant to the 2019 Series B Stock Purchase Agreement for an aggregate purchase price of $25.0 million and $10.0 million, respectively, at a purchase price of $2.25 per share.

On March 31, 2020, Co-Invest LP and the Company entered into the First Amendment to the Credit Agreement (the “Credit Agreement Amendment”) providing for the payment in shares of the Company’s Series B Preferred Stock of the interest on the amount outstanding under the applicable credit agreement.

On April 3, 2020, the Company and Acquisition 2 LP entered into a Series B Preferred Stock Purchase Agreement pursuant to which Acquisition 2 LP purchased additional shares of Series B Preferred Stock at $2.25 per share for an aggregate purchase price of $10.0 million.

On May 8, 2020, the Company and 2020 LP entered into a Note Purchase Agreement pursuant to which 2020 LP purchased an unsecured convertible promissory note (the “Convertible Note”) with an annual interest rate of 8.0% and in an aggregate principal amount of $15.0 million.

In connection with the consummation of the Company’s initial public offering of its Common Stock, the Series B Preferred Stock and the Convertible Note converted, automatically and without any additional consideration, into 18,319,853 and 1,250,000 shares, respectively, of Common Stock. Further, on June 23, 2020, in connection with the initial public offering of the Company’s Common Stock, 2020 LP purchased 3,333,333 shares of Common Stock at a price of $15.00 per share. The funds used to purchase such shares were composed of the investment capital of 2020 LP.

The Reporting Persons acquired the securities reported herein for investment purposes and intend to review their investments in the Company on a continuing basis. Depending on various factors, including but not limited to the Company’s financial position and strategic direction, price levels of the Common Stock, conditions in the securities markets, various laws and regulations applicable to the Company and companies in its industry and the Reporting Persons’ ownership in the Company, and general economic and industry conditions, the Reporting Persons may in the future take actions with respect to their investment in the Company as they deem appropriate, including changing their current intentions, with respect to any or all matters required to be disclosed herein. Without limiting the foregoing, and subject to any applicable limitations described in Item 6 below under the caption “Lock-Up Agreement,” the Reporting Persons may, from time to time, acquire or cause affiliates to acquire additional shares of Common Stock or other securities of the Company (including any combination or derivative thereof), dispose, or cause affiliates to dispose, of some or all of their Common Stock or other securities of the Company or continue to hold, or cause affiliates to hold, Common Stock or other securities of the Company.

Except as set forth herein, or as would occur upon completion of any of the matters discussed herein, the Reporting Persons have no present plans, proposals or intentions which would result in or relate to any of the transactions described in subparagraphs (a) through (j) of Item 4 of Schedule 13D. Although the foregoing reflects activities presently contemplated by the Reporting Persons and each other individuals named in Item 2 with respect to the Company, the foregoing is subject to change at any time.

The information set forth under Items 3 and 6 is incorporated by reference herein.

(a)-(b) The information contained on the cover pages of this Schedule 13D is incorporated herein by reference.

The Reporting Persons beneficially own in the aggregate 23,303,346 shares of Common Stock, which represents approximately 49.8% of the outstanding shares of Common Stock. All calculations of percentage ownership in this Schedule 13D are based on 45,163,795 shares outstanding after the consummation of the Company’s initial public offering of its Common Stock, as reported in the Company’s final prospectus filed with the SEC on June 22, 2020, plus the 1,250,000 shares of Common Stock issued upon conversion of the Convertible Note and the 400,160 shares of Common Stock issuable upon exercise of the Warrant.

To the knowledge of the Reporting Persons, none of the Covered Persons directly owns any shares of Common Stock; provided, however, that because of each Covered Persons’ status as a director, executive officer, manager, member or partner of a Reporting Person, a Covered Person may be deemed to be the beneficial owner of the shares of Common Stock beneficially owned by such Reporting Person. Except to the extent of their pecuniary interest, each of the Covered Persons disclaims beneficial ownership of the shares of the Common Stock reported herein and the filing of this Schedule 13D shall not be construed as an admission that any such Covered Person is the beneficial owner of any securities covered by this statement.

In accordance with the SEC Release No. 34-39538 (January 12, 1998) (the “Release”), this Schedule 13D reflects the securities beneficially owned by certain operating units (collectively, the “NB Alts Reporting Units”) of Neuberger Berman Group LLC and its subsidiaries and affiliates (collectively, “NBG”). This Schedule 13D does not reflect securities, if any, beneficially owned by any operating units of NBG whose ownership of securities is disaggregated from that of the NB Alts Reporting Units in accordance with the Release.

(c) Except as described in Item 3 of this Schedule 13D, none of the Reporting Persons or, to their knowledge, none of the Covered Persons, has had any transactions in the Common Stock during the past 60 days.

(d) Except as set forth herein, to the knowledge of the Reporting Persons, no other person has the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, any shares of Common Stock.

(e) Not applicable.

Fourth Amended and Restated Investors’ Rights Agreement

On August 27, 2019, the Joint Funds, Co-Invest LP and Acquisition LP (the “Athyrium Parties”) entered into a fourth amended and restated investors’ rights agreement (the “Investors’ Rights Agreement”) with the Company and the other stockholders of the Company. The Investors’ Rights Agreement provides that the stockholders of the Company have certain registration rights described below. On November 12 2019, in connection with its acquisition of the securities of the Company previously held by Acquisition LP, Acquisition 2 LP signed a joinder agreement to the Investors’ Rights Agreement and became one of the Athyrium Parties discussed below.

The registration rights described below will expire (i) five years after the completion of the Company’s initial public offering, (ii) with respect to any Athyrium Party, at the time such Athyrium Party can sell all of its registrable securities under Rule 144 or another similar exemption under the Securities Act without limitation during a three-month period without registration or (iii) upon termination of the Investors’ Rights Agreement.

The key registration rights under the Investors’ Rights Agreement are as follows:

Lock-Up Agreement

On June 19, 2020, Jeffrey A. Ferrell and each of the Funds entered into a lock-up agreement (“Lock-Up Agreement”) with Piper Sandler & Co. and Wells Fargo Securities, LLC, as representatives of the underwriters of the Company’s initial public offering, whereby Mr. Ferrell and each of the Funds agreed with the underwriters that, for a period of 180 days following the date of the final prospectus used for the Company’s initial public offering, subject to certain exceptions, each of them will not, directly or indirectly, offer, pledge, announce the intention to sell, contract to sell, sell any option or contract to purchase, sell any option or contract to purchase, grant any option, right or warrant to purchase, make any short sale or otherwise transfer or dispose of any of shares of Common Stock, or any options or warrants to purchase any shares of Common Stock, or any securities convertible into, or exchangeable for or that represent the right to receive shares of Common Stock. Piper Sandler & Co. and Wells Fargo Securities, LLC may, in their sole discretion, release all or any portion of the shares from these restrictions.

Series B Preferred Stock Purchase Warrant

On October 27, 2017, the Company issued a Series B Preferred Stock Purchase Warrant (as amended, modified, restated, refinanced, replaced or supplemented from time to time, the “Warrant”) to Co-Invest LP as registered holder. Following the initial public offering of the Company, the Warrant is exercisable into 400,160 shares of Common Stock at an exercise price of $13.90 per share, at any time on or prior to its expiration on October 27, 2022.

The foregoing summary of the Investors’ Rights Agreement, Lock-Up Agreement and Warrant is qualified in its entirety by reference to the complete text of such agreements, copies of which are filed as exhibits hereto and are incorporated herein by reference.

Pursuant to Rule 13d-1(k) promulgated under the Securities Exchange Act of 1934, as amended, the Reporting Persons have entered into an agreement with respect to the joint filing of this Schedule 13D, which agreement is set forth on the signature page to this Schedule 13D.

Except as described above and herein in this Schedule 13D, there are no other contracts, understandings or relationships (legal or otherwise) among the parties named in Item 2 hereto and between such persons and any person with respect to any of the common stock of the Company owned by the Funds.

SIGNATURES

After reasonable inquiry and to the best of his or its knowledge and belief, each of the undersigned certifies that the information set forth in this statement is true, complete and correct.

In accordance with Rule 13d-1(k)(1)(iii) under the Securities Exchange Act of 1934, as amended, the persons named below agree to the joint filing on behalf of each of them of this Schedule 13D with respect to the common stock of the Company.

Dated as of July 6, 2020.

ANNEX A

Other than as set forth below, and in the Schedule 13D to which this Annex A is attached, none of the Reporting Persons have appointed any executive officers or directors.

Athyrium Opportunities Associates GP LLC

The name and principal occupation of each of the members and executive officers of Athyrium Opportunities Associates GP LLC are listed below:

Athyrium Capital Management, LP

The name and principal occupation of each of the members and executive officers of Athyrium Capital Management, LP are listed below:

Athyrium Capital Holdings, LLC

The name and principal occupation of each of the members of Athyrium Capital Holdings, LLC is listed below:

Athyrium Opportunities Advisers LLC

The name and principal occupation of each of the members and executive officers of Athyrium Opportunities Advisers LLC are listed below:

NB Alternatives Advisers LLC

The name and principal occupation of each of the members and executive officers of NB Alternatives Advisers LLC are listed below:

NB Alternatives GP Holdings LLC

The name and principal occupation of each of the members and executive officers of NB Alternatives GP Holdings LLC are listed below:

NB Alternatives Holdings LLC

The name and principal occupation of each of the members and executive officers of NB Alternatives Holdings LLC are listed below:

Athyrium Opportunities Co-Invest LLC

The name and principal occupation of each of the members and executive officers of Athyrium Opportunities Co-Invest LLC are listed below:

Athyrium Opportunities Associates III GP LLC

The name and principal occupation of each of the members and executive officers of Athyrium Opportunities Associates III GP LLC are listed below: