1

IN THE UNITED STATES DISTRICT COURT

FOR THE WESTERN DISTRICT OF TEXAS

WACO DIVISION

 Natera, Inc.,

Plaintiff,

v.

 Progenity, Inc.,

Defendant.

Civil Action No. 6:20-cv-532

JURY TRIAL DEMANDED

COMPLAINT FOR PATENT INFRINGEMENT

Plaintiff Natera, Inc. (“Natera”), for its Complaint against Defendant Progenity, Inc. 

(“Progenity” or “Defendant”), alleges as follows:

NATURE OF THE ACTION

1. This is a civil action for infringement of United States Patent Nos. 9,228,234 (the 

“’234 Patent”); 9,424,392 (the “’392 Patent”); 10,227,652 (the “’652 Patent”); 10,240,202 (the 

“’202 Patent”); 10,266,893 (the “’893 Patent”); and 10,522,242 (the “’242 Patent”) (collectively 

the “Patents-in-Suit”), arising under the Patent Laws of the United States, 35 U.S.C. §§ 271, et 

seq.

THE PARTIES

2. Natera is a company organized and existing under the laws of Delaware, with its 

principle place of business at 201 Industrial Rd, San Carlos, California 94070.

3. Founded in 2004, Natera (formerly Gene Security Network) is a pioneering 

molecular technology company dedicated to improving disease management for reproductive 

health, oncology, and organ transplantation. For over fifteen years, Natera has been researching 

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and developing non-invasive methods for analyzing DNA to help patients and doctors manage 

diseases. 

4. Natera is a leading developer of highly accurate solutions for non-invasive prenatal 

testing (“NIPT”), genetic-carrier screening, and miscarriage testing. Natera’s PanoramaTM 

Prenatal Screen test is a market-leading NIPT test that analyzes a fetus’s risk for genetic disorders 

as early as nine weeks through a simple blood draw from the mother’s arm. Panorama is a cellfree DNA (“cfDNA”)-based test. Natera is considered the industry leading test in this space, with

over two million tests performed commercially, and with more than twenty-six peer-reviewed 

publications.

5. On information and belief, Progenity is a company organized and existing under 

the laws of Delaware, with its principle place of business located at 4330 La Jolla Village Drive, 

Suite 200, San Diego, California, 92122. Progenity is registered to do business in the state of 

Texas. Progenity has appointed Cogency Global Inc., 1601 Elm St., Suite 4360, Dallas, Texas, 

75201 as its agent for service of process. 

JURISDICTION AND VENUE

6. This action arises under the patent laws of the United States, including 35 U.S.C. 

§§ 271, et. seq. This Court has subject matter jurisdiction over Plaintiff’s claims under 28 U.S.C. 

§§ 1331 and 1338(a).

7. Venue is proper in this District pursuant to 28 U.S.C. §§ 1391(b), (c), (d) and/or 28 

U.S.C. § 1400(b) because Defendant has a permanent and continuous presence in, have committed 

acts of infringement in, and maintain regular and established places of business in this District. 

8. By registering to conduct business in Texas, by having facilities where they 

regularly conduct business in this judicial District, and by having a registered agent in this judicial 

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District, Defendant has a permanent and continuous presence and regular and established places 

of business in the Western District of Texas.

9. Defendant is registered to do business in Texas. (Ex. 1 (registered in TX as 

“Ascendant MDx, Inc.”); Ex. 2 (registration amendment in TX changing the legal name from 

“Ascendant MDx, Inc.” to “Progenity, Inc.”)). The purpose of the registration in Texas was so 

that Defendant could pursue an “Independent clinical laboratory” in Texas. (Ex. 1). 

10. Defendant enlisted “National Corporation Research, Ltd.” to act as its registered 

agent in this judicial District. From 2013-2019, Defendant’s Texas Franchise Tax Reports identify 

800 Brazos, Suite 400, Austin, TX, 78701 as Defendant’s registered agent’s address. (Exs. 3-9). 

11. Defendant is affiliated with Patient Service Centers in this judicial District, 

including at least 15 affiliated centers in Austin, TX; at least 6 affiliated centers in San Antonio, 

TX; at least 10 affiliated centers in El Paso, TX; and at least 2 affiliated centers in Midland and 

Odessa, TX. (Exs. 10-13). For example, Defendant is affiliated with at least the following centers 

in Austin, TX: Clinical Pathology Laboratories – Bailey Square; Clinical Pathology Laboratories 

– Medical Arts Square; Open Draw; Clinical Pathology Laboratories – Medical Park Tower; 

ExamOne Austin; Clinical Pathology Laboratories – Wells Branch; Any Lab Test Now – Austin 

(two locations); Clinical Pathology Laboratories – Southwest Medical Village; Clinical Pathology 

Laboratories – James Casey; Clinical Pathology Laboratories – Four Points PSC; Clinical 

Pathology Laboratories – Medical Oaks Pavilion; Clinical Pathology Laboratories – Renfer Way 

PSC; Clinical Pathology Laboratories – Ladera Park; and Clinical Pathology Laboratories – Brodie 

Lane. (Ex. 10). Defendant also is affiliated with at least the following centers in San Antonio, 

TX: CPL – San Antonio – Somerset; Any Lab Test Now (three locations); CPL – San Antonio –

Pecan Plaza; and Stat-X Medical Services, Inc. (Ex. 11). Defendant is affiliated with at least the 

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following centers in El Paso, TX: CPL – El Paso-Mesa; University Medical Center (UMC) – El 

Paso; University Medical Center (UMC) – Ysleta; University Medical Center (UMC) – West; CPL 

– El Paso-Remcon; University Medical Center (UMC) – Northeast; Insurance Medicals of El Paso; 

CPL – El Paso-Vista Del Sol; University Medical Center (UMC) – Dieter; and University Medical 

Center (UMC) – East. Defendant is affiliated with at least the two following centers in Odessa 

and Midland, TX, respectively: CPL – Odessa and CPL – Midland. (Ex. 12). Defendant’s 

affiliated centers collect specimens from patients for testing. (Ex. 13). Upon information and 

belief, the collected specimens are tested by using the infringing products and/or services.

12. Defendant also has at least 10 employees in this judicial District. For example, 

Defendant’s Chief Operating Officer, Damon Silvestry, represents that he resides and works in 

Austin, TX. (Ex. 14). Additionally, Defendant’s Vice President of Sales and Marketing, Doug 

Sites; Vice President of Medical Affairs, Christina Settler; Vice President of Sales – Specialty 

Division, George Gianakopoulos; Business Development Manager, Liz Opalka; Medical Science 

Liason, Mia Salimbene; and Medical Sales Representative, Matt Cline, represent that they reside 

and work in Austin, TX. (Exs. 15-20). Defendant has additional employees who represent that 

they reside and work in Waco, El Paso, and San Antonio, TX. For example, Defendant’s Medical 

Science Liaison, Victoria H.; Business Development Manager, Raul Tolentino; and Business 

Development Manager, Bethany Moore, represent that they reside and work in Waco, El Paso, and 

San Antonio, TX, respectively. (Exs. 21-23). On information and belief, these employees of the 

Defendant operate from one or more established places of business operated by the Defendant. 

13. Defendant’s employees in this judicial District have responsibilities relating to the 

infringing products and/or services. For example, as Business Development Manager in San 

Antonio, TX, Bethany Moore’s responsibilities and experience include:

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Promote complex, molecular, specialized test. Plan, 

develop, and manage accounts with gynecologist, 

oncologist and clinical laboratories to exceed sales targets. 

Exceeded sales goals by prospecting new accounts and 

increasing volume in current accounts. 

(Ex. 23 at 1) (emphasis added). 

14. As another example, as Vice President of Medical Affairs in Austin, TX, Christina 

Settler’s responsibilities and experience relate to the infringing activities and include, among other 

things:

Extensive clinical and commercial experience shaping 

genetic testing products with the ability to provide clinical 

support to promote market adoption. Strong business 

acumen and expertise in genetic testing, clinical affairs, 

managed care, payer relations, and sales and marketing 

support. 

(Ex. 16 at 1) (emphasis added). 

15. Additionally, as Vice President of Sales and Marketing in Austin, TX, Doug Sites’ 

responsibilities and experience relate to the infringing activities and include, among other things: 

Skilled in all areas of healthcare sales and strategic 

marketing, including selecting, training and motivating 

professionals for complex products, business development, 

reimbursement and new product introductions. Proven 

operational team leader with laboratory, finance, billing, 

client services, R&D, quality assurance and marketing 

automation, all integral in achieving revenue goals and 

driving shareholder value. 

(Ex. 15 at 1) (emphasis added). 

16. Defendant also has at least one job opening listed in this judicial District. Upon 

information and belief, this job opening includes responsibilities relating to the infringing products 

and/or services. For example, Defendant has a job opening for a “Business Development 

Manager” listed for El Paso, TX. The “Business Development Manager’s” responsibilities 

include, among other things:

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The business development manager will help train new 

BMDs, meet the sales budget in the territory, manage 

opportunities and internal resources, and schedule events. 

(Ex. 24 at 3). 

17. Upon information and belief, Defendant also has presented multiple studies relating 

to the infringing products and/or services in this judicial District. For example, Defendant 

presented at least two posters at a scientific meeting in Austin, TX in 2018. (Ex. 25 at 5, 

https://www.progenity.com/clinical-publications/carrier-testing-real-life). Additionally, 

Defendant presented at least four posters at two separate scientific meetings in San Antonio, TX 

in 2019. (See Ex. 26 at 1, https://www.progenity.com/news/progenity-presents-data-acg-2019; 

Ex. 27 at 3, https://www.progenity.com/clinical-publications/hereditary-cancer-risk-morecommon-we-thought). 

18. Defendant transacts business within this District by using, offering for sale, and/or 

selling products and/or services that infringe the Patents-in-Suit, including through their website, 

which is accessible in this District. 

19. Defendant is subject to this Court’s jurisdiction pursuant to due process and/or the 

Texas Long Arm Statute due at least to its substantial business in this State and judicial District, 

including at least regularly doing business through its registered agent in Austin, TX, and engaging 

in persistent conduct and/or deriving substantial revenue from goods and services provided to 

customers in the State of Texas, including the Western District of Texas. For example, Defendant 

conducts business in the District, by at least using, offering for sale, and/or selling products and/or 

services that practice the claimed inventions of the Patents-in-Suit, including through its website, 

which are accessible in this District. 

20. This Court has personal jurisdiction over Defendant due, inter alia, to its 

continuous presence in, and systematic contact with, this District and its registration in Texas. 

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Defendant has established minimum contacts within the forum such that the exercise of jurisdiction 

over Defendant will not offend traditional notions of fair play and substantial justice. 

21. Personal jurisdiction exists over Defendant, because Defendant directly and/or 

through subsidiaries or intermediaries has committed and continues to commit acts of infringement 

in this District, by among other things, using, offering for sale, and/or selling products and/or 

services that infringe the Patents-in-Suit, which led to foreseeable harm and injury to Plaintiff.

22. This Court has personal jurisdiction over Defendant in this action because 

Defendant has committed acts within the Western District of Texas, giving rise to this action and 

has established minimum contacts with this forum such that the exercise of jurisdiction over the 

Defendant would not offend traditional notions of fair play and substantial justice. The Defendant, 

directly and through subsidiaries or intermediaries, has committed and continues to commit acts 

of infringement in this District by, among other things, using, offering for sale, and/or selling 

products and/or services that infringe the Patents-in-Suit, which led to foreseeable harm and injury 

to Plaintiff. 

PATENTS-IN-SUIT

23. The ’234 Patent, entitled “Methods for Non-Invasive Prenatal Ploidy Calling,” was 

duly and legally issued by the United States Patent and Trademark Office on January 5, 2016. The 

inventors of the patent are Matthew Rabinowitz, Allison Ryan, George Gemelos, Milena Banjevic, 

and Zachary Demko, and the patent is assigned to Natera. Natera is the exclusive owner of all 

rights, title, and interest in the ’234 Patent, and has the right to bring this suit to recover damages 

for any current or past infringement. A copy of the ’234 Patent is attached as Exhibit 28.

24. The ’392 Patent, entitled “System and Method for Cleaning Noisy Genetic Data 

from Target Individuals Using Genetic Data from Genetically Related Individuals,” was duly and 

legally issued by the United States Patent and Trademark Office on August 23, 2016. The 

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inventors of the patent are Matthew Rabinowitz, Milena Banjevic, Zachary Demko, and David 

Johnson, and the patent is assigned to Natera. Natera is the exclusive owner of all rights, title, and 

interest in the ’392 Patent, and has the right to bring this suit to recover damages for any current 

or past infringement. A copy of the ’392 Patent is attached as Exhibit 29.

25. The ’652 Patent, entitled “System and Method for Cleaning Noisy Genetic Data 

from Target Individuals Using Genetic Data from Genetically Related Individuals,” was duly and 

legally issued by the United States Patent and Trademark Office on March 12, 2019. The inventors 

of the patent are Matthew Rabinowitz, Milena Banjevic, Zachary Demko, and David Johnson, and 

the patent is assigned to Natera. Natera is the exclusive owner of all rights, title, and interest in 

the ’652 Patent, and has the right to bring this suit to recover damages for any current or past 

infringement. A copy of the ’652 Patent is attached as Exhibit 30.

26. The ’202 Patent, entitled “System and Method for Cleaning Noisy Genetic Data 

from Target Individuals Using Genetic Data from Genetically Related Individuals,” was duly and 

legally issued by the United States Patent and Trademark Office on March 26, 2019. The inventors 

of the patent are Matthew Rabinowitz, Milena Banjevic, Zachary Demko, and David Johnson, and 

the patent is assigned to Natera. Natera is the exclusive owner of all rights, title, and interest in 

the ’202 Patent, and has the right to bring this suit to recover damages for any current or past 

infringement. A copy of the ’202 Patent is attached as Exhibit 31.

27. The ’893 Patent, entitled “System and Method for Cleaning Noisy Genetic Data 

and Determining Chromosome Copy Number,” was duly and legally issued by the United States 

Patent and Trademark Office on April 23, 2019. The inventors of the patent are Matthew 

Rabinowitz, Milena Banjevic, Zachary Demko, David Johnson, Dusan Kijacic, Dimitri Petrov, 

Joshua Sweetkind-Singer, and Jing Xu, and the patent is assigned to Natera. Natera is the exclusive 

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owner of all rights, title, and interest in the ’893 Patent, and has the right to bring this suit to recover 

damages for any current or past infringement. A copy of the ’893 Patent is attached as Exhibit 32.

28. The ’242 Patent, entitled “Methods for Non-Invasive Prenatal Ploidy Calling,” was 

duly and legally issued by the United States Patent and Trademark Office on December 31, 2019. 

The inventors of the patent are Matthew Rabinowitz, Allison Ryan, George Gemelos, Milena 

Banjevic, and Zachary Demko, and the patent is assigned to Natera. Natera is the exclusive owner 

of all rights, title, and interest in the ’242 Patent, and has the right to bring this suit to recover 

damages for any current or past infringement. A copy of the ’242 Patent is attached as Exhibit 33.

29. The ’234 Patent is directed to, among other things, novel methods used in the 

detection of genetic disorders. For example, claim 1 of the ’234 Patent recites:

A method for determining the number of copies of a chromosome or chromosome 

segment of interest in the genome of a gestating fetus, the method comprising:

measuring genetic data at a plurality of loci on at least one chromosome that is 

expected to be disomic in both the mother and the fetus in a mixed sample of DNA 

comprising fetal DNA and maternal DNA;

determining a ratio of fetal to maternal DNA in the mixed sample from the 

measured genetic data at the plurality of loci on the at least one chromosome that 

is expected to be disomic in both the mother and the fetus;

measuring genetic data at a plurality of loci on a chromosome or chromosome 

segment of interest in the mixed sample of DNA;

creating one or more hypotheses specifying the number of copies of the 

chromosome or chromosome segment of interest in the genome of the fetus;

determining, on a computer, the probability of each of the hypotheses using the 

measured genetic data for the chromosome or chromosome segment of interest and 

the ratio of fetal to maternal DNA; and

selecting the hypothesis with the greatest probability, thereby determining the 

number of copies of the chromosome or chromosome segment of interest in the 

genome of the fetus.

30. The ’392 Patent is directed to, among other things, novel methods used in the 

detection of genetic disorders. For example, claim 1 of the ’392 Patent recites:

A method for detecting the presence or absence of a chromosomal abnormality in 

a fetus, the method comprising:

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(a) measuring the amount of genetic material at multiple polymorphic loci on a 

chromosome or chromosome segment of interest in a sample comprising DNA from 

the fetus and DNA from the mother of the fetus; wherein the amount of genetic 

material at a particular polymorphic locus is determined irrespective of the identity 

of the alleles at that polymorphic locus;

(b) determining, on a computer, the probability of the presence and the probability 

of the absence of a chromosomal abnormality in the fetus by comparing the amount 

from step (a) to either (i) a threshold value or (ii) an expected amount for a particular 

copy number hypothesis;

(c) identifying the presence or absence of a chromosomal abnormality in the fetus 

by selecting the probability most likely to be true; and

(d) outputting the selected probability as an indication of whether the fetus has a 

chromosomal abnormality.

31. The ’652 Patent is directed to, among other things, novel methods used in the 

detection of genetic disorders. For example, claim 1 of the ’652 Patent recites:

A method for detecting the presence or absence of a chromosomal abnormality in 

a fetus, the method comprising:

(a) measuring an amount of genetic material at multiple loci on a chromosome or 

chromosome segment of interest in a sample comprising cell-free DNA derived 

from the fetus and from the mother of the fetus, wherein the measuring comprises 

amplifying at least 70 loci in a single reaction and using microarray or sequencing 

to detect amplified reaction products, and wherein the multiple loci are loci having 

alleles with 100% penetrance in the population;

(b) determining, on a computer, a probability of the presence and a probability of 

the absence of a chromosomal abnormality in the fetus by comparing the amounts 

from step (a) to either (i) a threshold value or (ii) an expected amount for a particular 

copy number hypothesis;

(c) identifying the presence or absence of a chromosomal abnormality in the fetus 

by selecting the probability most likely to be true; and

(d) outputting the selected probability as an indication of whether the fetus has a 

chromosomal abnormality, thereby detecting the presence or absence of a 

chromosomal abnormality in a fetus.

32. The ’202 Patent is directed to, among other things, novel methods used in the 

detection of genetic disorders. For example, claim 1 of the ’202 Patent recites:

A method for detecting aneuploidy in a fetus, the method comprising: 

(a) measuring the amounts of genetic material at multiple loci on a chromosome or 

chromosome segment of interest in a sample comprising cell-free DNA derived 

from the fetus and from the mother of the fetus, wherein the measuring comprises 

amplifying at least 70 loci in a single reaction and using microarray or sequencing 

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to detect amplified reaction products, and wherein the amount of genetic material 

at a particular locus is determined irrespective of the identity of the alleles at that 

locus;

(b) determining, on a computer, the probability of aneuploidy in the fetus by 

comparing the measured amounts of genetic material to an expected amount for a 

particular copy number; and

(c) outputting the selected probability as an indication of whether the fetus has 

aneuploidy.

33. The ’893 Patent is directed to, among other things, novel methods used in the 

detection of genetic disorders. For example, claim 1 of the ’893 Patent recites:

A method for measuring the amounts of fetal chromosome segments in a maternal 

blood sample, comprising: 

obtaining cell-free DNA comprising fetal and maternal chromosome segments 

from the maternal blood sample;

performing universal amplification on the chromosome segments to generate 

amplified chromosome segments;

performing clonal amplification on the amplified chromosome segments to 

generate clonally amplified chromosome segments; and

measuring the amounts of clonally amplified fetal chromosome segments by 

performing next-generation sequencing.

34. The ’242 Patent is directed to, among other things, novel methods used in the 

detection of genetic disorders. For example, claim 1 of the ’242 Patent recites:

A method for determining the number of copies of a chromosome or chromosome 

segment of interest in the genome of a gestating fetus, the method comprising: 

measuring genetic data at a plurality of polymorphic loci on at least one 

chromosome that is expected to be disomic in both the mother and the fetus and a 

plurality of polymorphic loci on at least chromosome or chromosome segment of 

interest, which comprises amplifying at least 500 polymorphic loci from a mixed 

sample comprising DNA derived from the fetus and DNA derived from the 

mother, wherein the mixed sample is prepared from a maternal blood or plasma 

sample that comprises free floating fetal and maternal DNA;

determining a ratio of DNA derived from the fetus to DNA derived from the 

mother from the measured genetic data at the plurality of polymorphic loci on the 

at least one chromosome that is expected to be disomic in both the mother and the 

fetus;

creating hypotheses specifying the number of copies of the chromosome or 

chromosome segment of interest in the genome of the fetus;

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determining, on a computer, the probability of each of the hypotheses using the 

measured genetic data for the chromosome or chromosome segment of interest 

and the ratio of DNA derived from the fetus to DNA derived from the mother; and

selecting the hypothesis with the greatest probability, thereby determining the 

number of copies of the chromosome or chromosome segment of interest in the 

genome of the fetus.

PROGENITY’S INFRINGING ACTIVITIES

A. The Accused Innatal Prenatal Screen

35. Progenity was founded in 2010 and launched its Innatal Prenatal Screen in 2015. 

The Innatal Prenatal Screen is a noninvasive prenatal test offered to women early in pregnancy to 

screen for risk of fetal chromosomal conditions, such as Down syndrome, trisomy 13, and trisomy 

18, and sex chromosome disorders. On April 29, 2019, Progenity announced changes to the Innatal 

Prenatal Screen with “the latest sequencing technology, improved chemistry, and bioinformatic 

analysis.” (https://www.progenity.com/news/progenity-launches-first-commercially-availablecustom-designed-noninvasive-prenatal-test), but did not release what those changes were. In 

March 2020, Progenity published a paper evaluating the Innatal Prenatal Screen. Ex. 34 (Porreco 

et al.. “Evaluation of a novel screening method for fetal aneuploidy using cell-free DNA in 

maternal plasma.” J. Med.Screen. 2020, Vol. 27(1) 1-8.).

36. According to Progenity’s website:

Cell-free DNA (cfDNA) is analyzed from a maternal blood sample to assess the 

pregnancy for common chromosome aneuploidies, including trisomy 21 (Down 

syndrome), trisomy 18, trisomy 13, and sex chromosome abnormalities. This 

noninvasive screen offers providers and their patients accurate information about 

the risk for these conditions during pregnancy, as early as 10 weeks’ gestation.

The Innatal Prenatal Screen utilizes massively parallel sequencing (MPS) across 

the whole genome. This method sequences short fragments of DNA, creating 

millions of reads that are then mapped to the reference genome. The reads are 

counted to determine whether the sample has extra or missing reads from a 

particular chromosome. Abnormal dosage indicating aneuploidy is presumed to be 

fetal in origin. In rare circumstances, there is an alternative explanation.

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Progenity has upgraded the Innatal Prenatal screen with the latest sequencing 

technology and improved chemistry, demonstrating higher sensitivities than 

previous versions of the test. Fetal fraction is determined for each sample using a 

proprietary algorithm.

(Ex. 35, https://www.progenity.com/products/innatal#practice, accessed June 16, 2020).

37. Progenity is currently developing a 4th Generation Innatal Prenatal Screen and 

anticipates a commercial launch by the end of 2021.

COUNT I

(Infringement of the ’234 Patent)

38. Natera incorporates the foregoing paragraphs of this Complaint by reference.

39. The ’234 Patent is valid and enforceable.

40. Progenity has infringed, and continues to infringe, one or more claims of the ’234 

Patent under 35 U.S.C. § 271, either literally and/or under the doctrine of equivalents, by making, 

using, selling, and/or offering for sale in the United States, and/or importing into the United States, 

products and/or methods encompassed by those claims, including Progenity’s Innatal Prenatal 

Screen.

41. For example, Progenity infringes at least exemplary claim 1 of the ’234 Patent by 

using the Innatal Prenatal Screen. For example, use of the Innatal Prenatal Screen is a method for 

determining the number of copies of a chromosome or chromosome segment of interest in the 

genome of a gestating fetus. Progenity has published a paper on the Innatal product, Porreco et 

al.. “Evaluation of a novel screening method for fetal aneuploidy using cell-free DNA in maternal 

plasma.” J. Med.Screen. 2020, Vol. 27(1) 1-8. The Progenity Innatal Prenatal Screen:

a. measures genetic data at a plurality of loci on at least one chromosome that is 

expected to be disomic in both the mother and the fetus in a mixed sample of DNA 

comprising fetal DNA and maternal DNA (see Ex. 36 (Progenity U.S. Patent 

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Application 2019/0309352) at ¶¶ [0037-0039] (“comparing the test ratio to a 

plurality of reference ratios that are computed based on reference nucleic acid 

samples isolated from reference subjects without a copy number variation at the 

target sequences of interest”)); 

b. determines a ratio of fetal to maternal DNA in the mixed sample from the measured 

genetic data at the plurality of loci on the at least one chromosome that is expected 

to be disomic in both the mother and the fetus (see Ex. 34 (Porreco et al., 

“Evaluation of a novel screening method for fetal aneuploidy using cell-free DNA 

in maternal plasma,” J. Med. Screen, 2020 Vol. 27(1) 1-8) at 6 (“A single nucleotide 

polymorphism-based fetal fraction estimator also was developed.”)); 

c. measures genetic data at a plurality of loci on a chromosome or chromosome 

segment of interest in the mixed sample of DNA (see Ex. 34 (Porreco et al.) at 

Appx. A (“The sequencing data from the Progenity assay also contains information 

from 1-2000 SNPs.”));

d. creates one or more hypotheses specifying the number of copies of the chromosome 

or chromosome segment of interest in the genome of the fetus (see Ex. 34 (Porreco 

et al.) at 6: “A ploidy model and aneuploidy calling algorithm was developed at 

Progenity, Inc. to determine fetal ploidy for the common trisomies and sex 

chromosomes from sequencing data generated by the assay. This algorithm is based 

on a likelihood model that fits the count of unique aligned reads at each MIP site in 

the genome to produce a per-chromosome estimate of ploidy and its standard error. 

A T-score (Supplemental Appendix A) representing the ratio of the difference 

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between the estimated value and the hypothesized value to the standard error is 

generated for each chromosome interrogated within each sample.”);

e. determines, on a computer, the probability of each of the hypotheses using the 

measured genetic data for the chromosome or chromosome segment of interest and 

the ratio of fetal to maternal DNA (see Ex. 34 (Porreco et al.) at Appx. A (“The 

ploidy model regresses the site-specific counts against a design matrix composed 

of covariates obtained from the training data. This model results in estimates of 

ploidy for chromosomes 13, 18, and 21 (Figures S1-S3) and their standard errors.”); 

and

f. selects the hypothesis with the greatest probability, thereby determining the number 

of copies of the chromosome or chromosome segment of interest in the genome of 

the fetus (see Ex. 34 (Porreco et al.) at Appx. A (“A T-value statistic is generated 

for these autosomes within each sample where the null hypothesis for ploidy is 2 

(euploidy) for autosomes. This T-value is a test statistic for deviation from the null 

hypothesis of euploidy as obtained from our proprietary ploidy model. Under the 

alternative hypotheses of maternal of fetal nullisomy, trisomy, etc., the expectation 

of the ploidy is a linear function of the maternal ploidy, fetal ploidy and fetal 

fraction. . . . A T-value between 5 and 4 indicate that fetal ploidy is statistically 

indistinguishable from the euploid distribution. A T-value >4 indicates that fetal 

ploidy is significantly higher than the euploid distribution and is classified as 

trisomy.”). 

42. Progenity has had knowledge of the ’234 Patent and its infringement since at least 

the date of this Complaint.

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43. Progenity’s infringement of the ’234 Patent was, and continues to be, willful and 

deliberate since at least the date of this Complaint.

44. Natera has been and continues to be damaged by Defendant’s infringement of the 

’234 Patent, and will suffer irreparable injury unless the infringement is enjoined by this Court.

45. Defendant’s conduct in infringing the ’234 Patent renders this case exceptional 

within the meaning of 35 U.S.C. § 285.

COUNT II

(Infringement of the ’392 Patent)

46. Natera incorporates the foregoing paragraphs of this Complaint by reference.

47. The ’392 Patent is valid and enforceable.

48. Progenity has infringed, and continues to infringe, one or more claims of the ’392 

Patent under 35 U.S.C. § 271, either literally and/or under the doctrine of equivalents, by making, 

using, selling, and/or offering for sale in the United States, and/or importing into the United States, 

products and/or methods encompassed by those claims, including Progenity’s Innatal Prenatal 

Screen.

49. For example, Progenity infringes at least exemplary claim 1 of the ’392 Patent by 

using the Innatal Prenatal Screen. For example, use of the Innatal Prenatal Screen is a method for 

detecting the presence or absence of a chromosomal abnormality in a fetus (see Ex. 34 (Porreco et 

al.)) that includes:

a. measuring the amount of genetic material at multiple polymorphic loci on a 

chromosome or chromosome segment of interest in a sample comprising DNA from 

the fetus and DNA from the mother of the fetus; wherein the amount of genetic 

material at a particular polymorphic locus is determined irrespective of the identity 

of the alleles at that polymorphic locus (see Ex. 34 (Porreco et al.) at 3 (“The 

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 16 of 32
17

cfDNA test described here uses a novel MIP strategy developed at Progenity, Inc. 

to enrich and tag specific genomic sequences for next generation sequencing 

without the need for a highly-multiplexed target capture reaction”); at 5 (“In all, the 

probe captured ~200,000 sites across the genome. . . .”); and Appx. A at 2 (“The 

sequencing data from the Progenity assay also contains information from 1‐2,000 

SNPs with minor allele frequency >0.3%.”; “This model results in estimates of 

ploidy for chromosomes 13, 18, and 21....”);

b. determining, on a computer, the probability of the presence and the probability of 

the absence of a chromosomal abnormality in the fetus by comparing the amount 

from step (a) to either (i) a threshold value or (ii) an expected amount for a particular 

copy number hypothesis (see Ex. 34 (Porreco et al.) at 6 (“A ploidy model and 

aneuploidy calling algorithm was developed at Progenity, Inc. to determine fetal 

ploidy for the common trisomies and sex chromosomes from sequencing data 

generated by the assay. This algorithm is based on a likelihood model that fits the 

count of unique aligned reads at each MIP site in the genome to produce a perchromosome estimate of ploidy and its standard error. A T-score (Supplemental 

Appendix A) representing the ratio of the difference between the estimated value 

and the hypothesized value to the standard error is generated for each chromosome 

interrogated within each sample. A single nucleotide polymorphism-based fetal 

fraction estimator also was developed.”); at Appx. A at 1 (“A T‐value statistic is 

generated for these autosomes within each sample where the null hypothesis for 

ploidy is 2 (euploidy) for autosomes. This T-value is a test statistic for deviation 

from the null hypothesis of euploidy as obtained from our proprietary ploidy model. 

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 17 of 32
18

Under the alternative hypotheses of maternal or fetal nullisomy, trisomy, etc., the 

expectation of the ploidy is a linear function of the maternal ploidy, fetal ploidy and 

fetal fraction. The model T‐value represents the deviation of the estimated ploidy 

from the euploid expectation divided by the standard error obtained from fitting a 

generalized linear model.”); and Appx. A at 2 (“A T‐value between 5 and 4 indicate 

that fetal ploidy is statistically indistinguishable from the euploid distribution. A T‐

value > 4 indicates that fetal ploidy is significantly higher than the euploid 

distribution and is classified as trisomy. Similar methods were used to test 

chromosome X and Y ploidy (data not shown).”);

c. identifying the presence or absence of a chromosomal abnormality in the fetus by 

selecting the probability most likely to be true (see Ex. 34 (Porreco et al.) at Appx. 

A (“The ploidy model regresses the site-specific counts against a design matrix 

composed of covariates obtained from the training data. This model results in 

estimates of ploidy for chromosomes 13, 18, and 21 (Figures S1-S3) and their 

standard errors. A T-value statistic is generated for these autosomes within each 

sample where the null hypothesis for ploidy is 2 (euploidy) for autosomes. This Tvalue is a test statistic for deviation from the null hypothesis of euploidy as obtained 

from our proprietary ploidy model. Under the alternative hypotheses of maternal 

of fetal nullisomy, trisomy, etc., the expectation of the ploidy is a linear function of 

the maternal ploidy, fetal ploidy and fetal fraction. . . . A T-value between 5 and 4 

indicate that fetal ploidy is statistically indistinguishable from the euploid 

distribution. A T-value >4 indicates that fetal ploidy is significantly higher than 

the euploid distribution and is classified as trisomy.” ); and

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 18 of 32
19

d. outputting the selected probability as an indication of whether the fetus has a 

chromosomal abnormality, thereby detecting the presence or absence of a 

chromosomal abnormality in a fetus. See Ex. 34 (Porreco et al.) at Abstract (“Using 

the new sequencing technology, 1414 samples were analyzed. The findings showed 

sensitivities and specificities for the common trisomies and the sex chromosome 

aneuploidies at >99% (Trisomy 21 sensitivity 99.2 CI 95.6–99.2; specificity 99.9 

CI 99.6–99.9). Positive predictive values among the trisomies varied from 85.2% 

(Trisomy 18) to 99.0% (Trisomy 21), reflecting their prevalence rates in the 

study.”)

50. Progenity has had knowledge of the ’392 Patent and its infringement since at least 

the date of this Complaint.

51. Progenity’s infringement of the ’392 Patent was, and continues to be, willful and 

deliberate since at least the date of this Complaint.

52. Natera has been and continues to be damaged by Defendant’s infringement of the 

’392 Patent, and will suffer irreparable injury unless the infringement is enjoined by this Court.

53. Defendant’s conduct in infringing the ’392 Patent renders this case exceptional 

within the meaning of 35 U.S.C. § 285.

COUNT III

(Infringement of the ’652 Patent)

54. Natera incorporates the foregoing paragraphs of this Complaint by reference.

55. The ’652 Patent is valid and enforceable.

56. Progenity has infringed, and continues to infringe, one or more claims of the ’652 

Patent under 35 U.S.C. § 271, either literally and/or under the doctrine of equivalents, by making, 

using, selling, and/or offering for sale in the United States, and/or importing into the United States, 

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 19 of 32
20

products and/or methods encompassed by those claims, including Progenity’s Innatal Prenatal 

Screen.

57. For example, Progenity infringes at least exemplary claim 1 of the ’652 Patent by 

using the Innatal Prenatal Screen. For example, use of the Innatal Prenatal Screen is a method for 

detecting the presence or absence of a chromosomal abnormality in a fetus. The Innatal Prenatal 

Screen includes:

a. measuring an amount of genetic material at multiple loci on a chromosome or 

chromosome segment of interest in a sample comprising cell-free DNA derived 

from the fetus and from the mother of the fetus, wherein the measuring comprises 

amplifying at least 70 loci in a single reaction and using microarray or sequencing 

to detect amplified reaction products, and wherein the multiple loci are loci having 

alleles with 100% penetrance in the population (see Ex. 34 (Porreco et al.) at 3 

(“The cfDNA test described here uses a novel MIP strategy developed at Progenity, 

Inc. to enrich and tag specific genomic sequences for next generation sequencing 

without the need for a highly-multiplexed target capture reaction”); at 5 (“In all, the 

probe captured ~200,000 sites across the genome. . . .”); and Appx. A at 2 (“The 

sequencing data from the Progenity assay also contains information from 1‐2,000 

SNPs with minor allele frequency >0.3%.”; “This model results in estimates of 

ploidy for chromosomes 13, 18, and 21....”);

b. determining, on a computer, a probability of the presence and a probability of the 

absence of a chromosomal abnormality in the fetus by comparing the amounts from 

step (a) to either (i) a threshold value or (ii) an expected amount for a particular 

copy number hypothesis(see Ex. 34 (Porreco et al.) at 6 (“A ploidy model and 

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 20 of 32
21

aneuploidy calling algorithm was developed at Progenity, Inc. to determine fetal 

ploidy for the common trisomies and sex chromosomes from sequencing data 

generated by the assay. This algorithm is based on a likelihood model that fits the 

count of unique aligned reads at each MIP site in the genome to produce a perchromosome estimate of ploidy and its standard error. A T-score (Supplemental 

Appendix A) representing the ratio of the difference between the estimated value 

and the hypothesized value to the standard error is generated for each chromosome 

interrogated within each sample. A single nucleotide polymorphism-based fetal 

fraction estimator also was developed.”); at Appx. A at 1 (“A T‐value statistic is 

generated for these autosomes within each sample where the null hypothesis for 

ploidy is 2 (euploidy) for autosomes. This T-value is a test statistic for deviation 

from the null hypothesis of euploidy as obtained from our proprietary ploidy model. 

Under the alternative hypotheses of maternal or fetal nullisomy, trisomy, etc., the 

expectation of the ploidy is a linear function of the maternal ploidy, fetal ploidy and 

fetal fraction. The model T‐value represents the deviation of the estimated ploidy 

from the euploid expectation divided by the standard error obtained from fitting a 

generalized linear model.”); and Appx. A at 2 (“A T‐value between 5 and 4 indicate 

that fetal ploidy is statistically indistinguishable from the euploid distribution. A T‐

value > 4 indicates that fetal ploidy is significantly higher than the euploid 

distribution and is classified as trisomy. Similar methods were used to test 

chromosome X and Y ploidy (data not shown).”);

c. identifying the presence or absence of a chromosomal abnormality in the fetus by 

selecting the probability most likely to be true (see Ex. 34 (Porreco et al.) at Appx. 

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 21 of 32
22

A (“The ploidy model regresses the site-specific counts against a design matrix 

composed of covariates obtained from the training data. This model results in 

estimates of ploidy for chromosomes 13, 18, and 21 (Figures S1-S3) and their 

standard errors. A T-value statistic is generated for these autosomes within each 

sample where the null hypothesis for ploidy is 2 (euploidy) for autosomes. This Tvalue is a test statistic for deviation from the null hypothesis of euploidy as obtained 

from our proprietary ploidy model. Under the alternative hypotheses of maternal 

of fetal nullisomy, trisomy, etc., the expectation of the ploidy is a linear function of 

the maternal ploidy, fetal ploidy and fetal fraction. . . . A T-value between 5 and 4 

indicate that fetal ploidy is statistically indistinguishable from the euploid 

distribution. A T-value >4 indicates that fetal ploidy is significantly higher than 

the euploid distribution and is classified as trisomy.” ); and 

d. outputting the selected probability as an indication of whether the fetus has a 

chromosomal abnormality, thereby detecting the presence or absence of a 

chromosomal abnormality in a fetus. See Ex. 34 (Porreco et al.) at Abstract (“Using 

the new sequencing technology, 1414 samples were analyzed. The findings showed 

sensitivities and specificities for the common trisomies and the sex chromosome 

aneuploidies at >99% (Trisomy 21 sensitivity 99.2 CI 95.6–99.2; specificity 99.9 

CI 99.6–99.9). Positive predictive values among the trisomies varied from 85.2% 

(Trisomy 18) to 99.0% (Trisomy 21), reflecting their prevalence rates in the 

study.”)

58. Progenity has had knowledge of the ’652 Patent and its infringement since at least 

the date of this Complaint.

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 22 of 32
23

59. Progenity’s infringement of the ’652 Patent was, and continues to be, willful and 

deliberate since at least the date of this Complaint.

60. Natera has been and continues to be damaged by Defendant’s infringement of the 

’652 Patent, and will suffer irreparable injury unless the infringement is enjoined by this Court.

61. Defendant’s conduct in infringing the ’652 Patent renders this case exceptional 

within the meaning of 35 U.S.C. § 285.

COUNT IV

(Infringement of the ’202 Patent)

62. Natera incorporates the foregoing paragraphs of this Complaint by reference.

63. The ’202 Patent is valid and enforceable.

64. Progenity has infringed, and continues to infringe, one or more claims of the ’202 

Patent under 35 U.S.C. § 271, either literally and/or under the doctrine of equivalents, by making, 

using, selling, and/or offering for sale in the United States, and/or importing into the United States, 

products and/or methods encompassed by those claims, including Progenity’s Innatal Prenatal 

Screen.

65. For example, Progenity infringes at least exemplary claim 1 of the ’202 Patent by 

using the Innatal Prenatal Screen. For example, use of the Innatal Prenatal Screen is a method for 

detecting aneuploidy in a fetus, and includes: 

a. measuring the amounts of genetic material at multiple loci on a chromosome or 

chromosome segment of interest in a sample comprising cell-free DNA derived 

from the fetus and from the mother of the fetus, wherein the measuring comprises 

amplifying at least 70 loci in a single reaction and using microarray or sequencing

to detect amplified reaction products, and wherein the amount of genetic material 

at a particular locus is determined irrespective of the identity of the alleles at that 

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 23 of 32
24

locus (see Ex. 34 (Porreco et al.) at 3 (“The cfDNA test described here uses a novel 

MIP strategy developed at Progenity, Inc. to enrich and tag specific genomic 

sequences for next generation sequencing without the need for a highly-multiplexed 

target capture reaction”); at 5 (“In all, the probe captured ~200,000 sites across the 

genome. . . .”); and Appx. A at 2 (“The sequencing data from the Progenity assay 

also contains information from 1‐2,000 SNPs with minor allele frequency >0.3%.”; 

“This model results in estimates of ploidy for chromosomes 13, 18, and 21....”);

b. determining, on a computer, the probability of aneuploidy in the fetus by comparing 

the measured amounts of genetic material to an expected amount for a particular 

copy number (see Ex. 34 (Porreco et al.) at 6 (“A ploidy model and aneuploidy 

calling algorithm was developed at Progenity, Inc. to determine fetal ploidy for the 

common trisomies and sex chromosomes from sequencing data generated by the 

assay. This algorithm is based on a likelihood model that fits the count of unique 

aligned reads at each MIP site in the genome to produce a per-chromosome estimate 

of ploidy and its standard error. A T-score (Supplemental Appendix A) representing 

the ratio of the difference between the estimated value and the hypothesized value 

to the standard error is generated for each chromosome interrogated within each 

sample. A single nucleotide polymorphism-based fetal fraction estimator also was 

developed.”); at Appx. A at 1 (“A T‐value statistic is generated for these autosomes 

within each sample where the null hypothesis for ploidy is 2 (euploidy) for 

autosomes. This T-value is a test statistic for deviation from the null hypothesis of 

euploidy as obtained from our proprietary ploidy model. Under the alternative 

hypotheses of maternal or fetal nullisomy, trisomy, etc., the expectation of the 

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 24 of 32
25

ploidy is a linear function of the maternal ploidy, fetal ploidy and fetal fraction. The 

model T‐value represents the deviation of the estimated ploidy from the euploid 

expectation divided by the standard error obtained from fitting a generalized linear 

model.”); and Appx. A at 2 (“A T‐value between 5 and 4 indicate that fetal ploidy 

is statistically indistinguishable from the euploid distribution. A T‐value > 4 

indicates that fetal ploidy is significantly higher than the euploid distribution and is 

classified as trisomy. Similar methods were used to test chromosome X and Y 

ploidy (data not shown).”); and

c. outputting the selected probability as an indication of whether the fetus has 

aneuploidy. See Ex. 34 (Porreco et al.) at Abstract (“Using the new sequencing 

technology, 1414 samples were analyzed. The findings showed sensitivities and 

specificities for the common trisomies and the sex chromosome aneuploidies at 

>99% (Trisomy 21 sensitivity 99.2 CI 95.6–99.2; specificity 99.9 CI 99.6–99.9). 

Positive predictive values among the trisomies varied from 85.2% (Trisomy 18) to 

99.0% (Trisomy 21), reflecting their prevalence rates in the study.”)

66. Progenity has had knowledge of the ’202 Patent and its infringement since at least 

the date of this Complaint.

67. Progenity’s infringement of the ’202 Patent was, and continues to be, willful and 

deliberate since at least the date of this Complaint.

68. Natera has been and continues to be damaged by Defendant’s infringement of the 

’202 Patent, and will suffer irreparable injury unless the infringement is enjoined by this Court.

69. Defendant’s conduct in infringing the ’202 Patent renders this case exceptional 

within the meaning of 35 U.S.C. § 285.

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 25 of 32
26

COUNT V

(Infringement of the ’893 Patent)

70. Natera incorporates the foregoing paragraphs of this Complaint by reference.

71. The ’893 Patent is valid and enforceable.

72. Progenity has infringed, and continues to infringe, one or more claims of the ’893 

Patent under 35 U.S.C. § 271, either literally and/or under the doctrine of equivalents, by making, 

using, selling, and/or offering for sale in the United States, and/or importing into the United States, 

products and/or methods encompassed by those claims, including Progenity’s Innatal Prenatal 

Screen.

73. For example, Progenity infringes at least exemplary claim 1 of the ’893 Patent by 

using the Innatal Prenatal Screen. For example, use of the Innatal Prenatal Screen is a method for 

measuring the amounts of fetal chromosome segments in a maternal blood sample, that includes: 

a. obtaining cell-free DNA comprising fetal and maternal chromosome segments 

from the maternal blood sample (see Ex. 34 (Porreco et al.) at Abstract (“Objective: 

To evaluate the test performance of a novel sequencing technology using molecular 

inversion probes applied to cell-free DNA screening for fetal aneuploidy.”); and 3 

(“Venous blood (approximately 20mL) was collected from study participants. . . 

.”);

b. performing universal amplification on the chromosome segments to generate 

amplified chromosome segments (see Ex. 34 (Porreco et al.) at 5 (“The single 

stranded circular DNA generated from the capture protocol (Figure 1) was used as 

template in a universal PCR reaction containing primers that bind to the MIP 

backbone.”);

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 26 of 32
27

c. performing clonal amplification on the amplified chromosome segments to 

generate clonally amplified chromosome segments (see Ex. 34 (Porreco et al.) at 5-

6 (“PCR product libraries were purified . . . and samples were pooled into a 

multiplexed sequencing library (including controls). The library was diluted to an 

appropriate concentration for patterned flow cell clustering on a NovaSeq 6000. . . 

.”); and

d. measuring the amounts of clonally amplified fetal chromosome segments by 

performing next-generation sequencing. See Ex. 34 (Porreco et al.) at 3 (“The 

cfDNA test described here uses a novel MIP strategy developed at Progenity, Inc. 

to enrich and tag specific genomic sequences for next generation sequencing 

without the need for a highly-multiplexed target capture reaction”)

74. Progenity has had knowledge of the ’893 Patent and its infringement since at least 

the date of this Complaint.

75. Progenity’s infringement of the ’893 Patent was, and continues to be, willful and 

deliberate since at least the date of this Complaint.

76. Natera has been and continues to be damaged by Defendant’s infringement of the 

’893 Patent, and will suffer irreparable injury unless the infringement is enjoined by this Court.

77. Defendant’s conduct in infringing the ’893 Patent renders this case exceptional 

within the meaning of 35 U.S.C. § 285.

COUNT VI

(Infringement of the ’242 Patent)

78. Natera incorporates the foregoing paragraphs of this Complaint by reference.

79. The ’242 Patent is valid and enforceable.

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 27 of 32
28

80. Progenity has infringed, and continues to infringe, one or more claims of the ’242 

Patent under 35 U.S.C. § 271, either literally and/or under the doctrine of equivalents, by making, 

using, selling, and/or offering for sale in the United States, and/or importing into the United States, 

products and/or methods encompassed by those claims, including Progenity’s Innatal Prenatal 

Screen.

81. For example, Progenity infringemes at least exemplary claim 1 of the ’242 Patent 

by using the Innatal Prenatal Screen. For example, use of the Innatal Prenatal Screen is a method

for determining the number of copies of a chromosome or chromosome segment of interest in the 

genome of a gestating fetus. The test includes: 

a. measuring genetic data at a plurality of polymorphic loci on at least one 

chromosome that is expected to be disomic in both the mother and the fetus and a 

plurality of polymorphic loci on at least chromosome or chromosome segment of 

interest, which comprises amplifying at least 500 polymorphic loci from a mixed 

sample comprising DNA derived from the fetus and DNA derived from the mother, 

wherein the mixed sample is prepared from a maternal blood or plasma sample that 

comprises free floating fetal and maternal DNA (see Ex. 34 (Porreco et al.) at 5 

(“In all, the probe captured ~200,000 sites across the genome. . . .”); and Appx. A 

at 2 (“The sequencing data from the Progenity assay also contains information from 

1‐2,000 SNPs with minor allele frequency >0.3%.”; “This model results in 

estimates of ploidy for chromosomes 13, 18, and 21....”);

b. determining a ratio of DNA derived from the fetus to DNA derived from the mother 

from the measured genetic data at the plurality of polymorphic loci on the at least 

one chromosome that is expected to be disomic in both the mother and the fetus

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 28 of 32
29

(see Ex. 34 (Porreco et al.) at 6 (“A single nucleotide polymorphism-based fetal 

fraction estimator also was developed.”));

c. creating hypotheses specifying the number of copies of the chromosome or 

chromosome segment of interest in the genome of the fetus (see Ex. 34 (Porreco et 

al.) at 6: “A ploidy model and aneuploidy calling algorithm was developed at 

Progenity, Inc. to determine fetal ploidy for the common trisomies and sex 

chromosomes from sequencing data generated by the assay. This algorithm is based 

on a likelihood model that fits the count of unique aligned reads at each MIP site in 

the genome to produce a per-chromosome estimate of ploidy and its standard error. 

A T-score (Supplemental Appendix A) representing the ratio of the difference 

between the estimated value and the hypothesized value to the standard error is 

generated for each chromosome interrogated within each sample.”);

d. determining, on a computer, the probability of each of the hypotheses using the 

measured genetic data for the chromosome or chromosome segment of interest and 

the ratio of DNA derived from the fetus to DNA derived from the mother (see Ex. 

34 (Porreco et al.) at 6 (“A ploidy model and aneuploidy calling algorithm was 

developed at Progenity, Inc. to determine fetal ploidy for the common trisomies 

and sex chromosomes from sequencing data generated by the assay. This algorithm 

is based on a likelihood model that fits the count of unique aligned reads at each 

MIP site in the genome to produce a per-chromosome estimate of ploidy and its 

standard error. A T-score (Supplemental Appendix A) representing the ratio of the 

difference between the estimated value and the hypothesized value to the standard 

error is generated for each chromosome interrogated within each sample. A single 

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 29 of 32
30

nucleotide polymorphism-based fetal fraction estimator also was developed.”); at 

Appx. A at 1 (“A T‐value statistic is generated for these autosomes within each 

sample where the null hypothesis for ploidy is 2 (euploidy) for autosomes. This Tvalue is a test statistic for deviation from the null hypothesis of euploidy as obtained 

from our proprietary ploidy model. Under the alternative hypotheses of maternal or 

fetal nullisomy, trisomy, etc., the expectation of the ploidy is a linear function of 

the maternal ploidy, fetal ploidy and fetal fraction. The model T‐value represents 

the deviation of the estimated ploidy from the euploid expectation divided by the 

standard error obtained from fitting a generalized linear model.”); and Appx. A at 

2 (“A T‐value between 5 and 4 indicate that fetal ploidy is statistically 

indistinguishable from the euploid distribution. A T‐value > 4 indicates that fetal 

ploidy is significantly higher than the euploid distribution and is classified as 

trisomy. Similar methods were used to test chromosome X and Y ploidy (data not 

shown).”); and

e. selecting the hypothesis with the greatest probability, thereby determining the 

number of copies of the chromosome or chromosome segment of interest in the 

genome of the fetus. See Ex. 34 (Porreco et al.) at Appx. A (“The ploidy model 

regresses the site-specific counts against a design matrix composed of covariates 

obtained from the training data. This model results in estimates of ploidy for 

chromosomes 13, 18, and 21 (Figures S1-S3) and their standard errors. A T-value 

statistic is generated for these autosomes within each sample where the null 

hypothesis for ploidy is 2 (euploidy) for autosomes. This T-value is a test statistic 

for deviation from the null hypothesis of euploidy as obtained from our proprietary 

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 30 of 32
31

ploidy model. Under the alternative hypotheses of maternal of fetal nullisomy, 

trisomy, etc., the expectation of the ploidy is a linear function of the maternal 

ploidy, fetal ploidy and fetal fraction. . . . A T-value between 5 and 4 indicate that 

fetal ploidy is statistically indistinguishable from the euploid distribution. A Tvalue >4 indicates that fetal ploidy is significantly higher than the euploid 

distribution and is classified as trisomy.” )

82. Progenity has had knowledge of the ’242 Patent and its infringement since at least 

the date of this Complaint.

83. Progenity’s infringement of the ’242 Patent was, and continues to be, willful and 

deliberate since at least the date of this Complaint.

84. Natera has been and continues to be damaged by Defendant’s infringement of the 

’242 Patent, and will suffer irreparable injury unless the infringement is enjoined by this Court.

85. Defendant’s conduct in infringing the ’242 Patent renders this case exceptional 

within the meaning of 35 U.S.C. § 285.

PRAYER FOR RELIEF

WHEREFORE, Natera prays for judgment as follows:

A. That Progenity has infringed each of the Patents-in-Suit;

B. That Progenity’s infringement of each of the Patents-in-Suit has been willful;

C. That Natera be awarded an order enjoining Progenity and its officers, directors, 

agents, servants, affiliates, employees, divisions, subsidiaries, parents, and all other acting in active 

concert therewith from further infringement of the Patents-in-Suit;

D. That Natera be awarded all damages adequate to compensate it for Defendant’s past 

infringement and any continuing or future infringement of the Patents-in-Suit up until the date 

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 31 of 32
32

such judgment is entered, including pre- and post-judgment interest, costs, and disbursements as 

justified under 35 U.S.C. § 284;

E. That any award of damages be enhanced under 35 U.S.C. § 284 as result of 

Progenity’s willful infringement;

F. That this case by declared an exceptional case within the meaning of 35 U.S.C. 

§285 and that Natera be awarded the attorney fees, costs, and expenses incurred in connection with 

this action;

G. That Natera be awarded costs and expenses in this action; and

H. That Natera be awarded such other and further relief at law or equity as this Court 

deems just and proper.

DEMAND FOR JURY TRIAL

Pursuant to Rule 38(b) of the Federal Rules of Civil Procedure, Plaintiff Natera demands a 

trial by jury on all issues so triable.

Dated: June 17, 2020

Respectfully submitted,

/s/Stephen M. Hash

Stephen M. Hash 

Texas Bar No. 24012800

BAKER BOTTS L.L.P.

98 San Jacinto Blvd, Suite 1500

Austin, TX 78701

Telephone: (512) 322-2587

Facsimile: (512) 322-3687

stephen.hash@bakerbotts.com

Attorneys for Plaintiff Natera, Inc.

Case 6:20-cv-00532-ADA Document 1 Filed 06/17/20 Page 32 of 32