Source: s3://data.kl3m.ai/documents/govinfo/USCOURTS/USCOURTS-cand-3_18-cv-01662/USCOURTS-cand-3_18-cv-01662-3/pdf.json

Nature of Suit Code: 830
Nature of Suit: Patent
Cause of Action: 35:271 Patent Infringement

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United States District Court

Northern District of California

UNITED STATES DISTRICT COURT

NORTHERN DISTRICT OF CALIFORNIA

ILLUMINA, INC.,

Plaintiff,

v.

NATERA, INC.,

Defendant.

Case No. 18-cv-01662-SI 

ORDER RE: CLAIM CONSTRUCTION

On January 16, 2019, the Court heard argument on the parties’ proposed claim constructions. 

Having considered the arguments of the parties and the papers submitted, the Court construes the 

disputed terms as follows. 

BACKGROUND

Plaintiff Illumina, Inc. filed this patent infringement suit against defendant Natera, Inc. on 

March 16, 2018 alleging infringement of U.S. Patent No. 9,493,831 (“the ’831 patent”) entitled 

“Methods of fetal abnormality detection.” See Dkt. No. 1. On August 16, 2018, Natera responded 

and claimed that it does not infringe the ’831 patent and that the ’831 patent is invalid. Dkt. No. 61 

at 18–20. Natera also counterclaimed against Illumina, alleging infringement of U.S. Patent No. 

8,682,592 (“the ’592 patent”) entitled “System and Method for Cleaning Noisy Genetic Data From 

Target Individuals Using Genetic Data from Genetically Related Individuals.” Id. at 20–24. 

REQUESTED CONSTRUCTIONS

1. ’831 Patent - “selectively enriching a plurality of non-random polynucleotide sequences 

of genomic DNA from said fetal and maternal cell-free DNA”

The term “selectively enriching a plurality of non-random polynucleotide sequences of 

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genomic DNA from said fetal and maternal cell-free DNA” is a part of independent claims 1 and 14

of the ’831 Patent. In this context, genomic DNA refers to DNA that comes from a fetus’ genome. 

Testing this genomic DNA can reveal genetic traits about the fetus, including whether the fetus is 

aneuploid.1 Blood from pregnant females includes both maternal and fetal DNA. Selective 

enrichment of fetal DNA can increase its concentration in a sample relative to the concentration of 

the maternal DNA, which makes it possible to test which traits are present in the fetal DNA. By 

enriching a “non-random polynucleotide sequence,” technicians are able to specifically target fetal 

DNA for enrichment, rather than enriching both the fetal and maternal DNA. Illumina proposes this 

term be construed as “enriching a plurality of non-random nucleic acid sequences of genomic DNA 

from a fetal and maternal cell-free DNA sample that meet sequence and/or location criteria selected 

to facilitate aneuploidy detection.” Dkt. No. 69-1. Natera asks the Court to construe the term as 

“enriching a plurality of selected non-random nucleic acid sequences of genomic DNA from fetal 

and maternal cell-free DNA.” Id. 

Claim 1, which is representative of claim 14, reads: 

1. A method for preparing a sequencing library from a maternal blood 

sample, the method comprising: 

a. obtaining a maternal blood sample comprising fetal and maternal 

cell-free DNA;

b. selectively enriching a plurality of non-random polynucleotide 

sequences of genomic DNA from said fetal and maternal cell-free 

DNA to generate a library of enriched non-random polynucleotide 

sequences, wherein said plurality of non-random polynucleotide 

sequences comprises at least 100 different non-random 

polynucleotide sequences selected from a chromosome tested for 

being aneuploid, said enriching comprising: 

(i) a first amplification step to generate a plurality of first reaction 

products, said amplification comprising at least 100 first primers 

configured to amplify at least 100 different non-random 

polynucleotide sequences;

 

1 Aneuploidy refers to any genetic disorder where there is an abnormal number of 

chromosomes. The most well-known type of aneuploidy is trisomy-21 which causes Down 

Syndrome. ’831 patent at 13:41–52. 

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(ii) a second amplification step to generate a second reaction product, 

said amplification comprising a second set of primers comprising 

sequences contained in the first reaction products; and

(iii) a third amplification step to generate a third reaction product 

comprising said library of enriched non-random polynucleotide 

sequences, said amplification comprising a third set of primers 

comprising sequences contained in the second reaction products;

wherein at least one primer of at least one of the second and third sets 

of primers includes a sequence configured to be added to the different 

non-random polynucleotide sequences to permit the enriched nonrandom polynucleotide sequences of the library to anneal to a same 

sequencing primer for the enriched non-random polynucleotide 

sequences of the library.

’831 Patent at 63:39–64:42. 

2. The ’592 Patent 

The parties dispute the construction of two terms, both of which are part of claim 1. Claim 

1 of the ’592 patent reads: 

1. An ex vivo method for determining a number of copies of a 

chromosome or chromosome segment of interest in the genome of an 

individual, the method comprising: 

using a single nucleotide polymorphism (SNP) genotyping array or 

high throughput DNA sequencing to measure genetic material and 

produce genetic data for some or all possible alleles at a plurality of 

at least 100 loci on the chromosome or chromosome segment of 

interest in the individual, wherein the genetic data is noisy due to a 

small amount of genetic material from the individual; and wherein the 

small amount of genetic material from the individual is from fifty or 

fewer of the individual's cells, 0.3 ng or less of the individual's DNA, 

extracellular DNA from the individual found in maternal blood, or 

combinations thereof;

creating a set of one or more hypotheses specifying the number of 

copies of the chromosome or chromosome segment of interest in the 

genome of the individual;

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

given the produced genetic data; and

using the probabilities associated with each hypothesis to determine 

the most likely number of copies of the chromosome or chromosome 

segment of interest in the genome of the individual.

’592 Patent at 62:39–62.

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A. “Genetic data for some or all possible alleles”

The parties dispute the construction of the term “genetic data for some or all possible 

alleles.”2 Illumina proposes that the term be construed as “data showing the identities of particular 

bases at specific loci so as to reveal the genotype of the individual for some or all possible alternative 

forms of the loci.” Dkt. No. 70-1 at 3. Natera proposes that the term be construed as “genetic data 

for some or all possible alternative forms of a given locus.” Id.

B. “Loci of interest in the individual”

The parties dispute the construction of the term “at least 100 loci on the chromosome or 

chromosome segment of interest in the individual.”3 Illumina proposes that the Court adopt “as 

least 100 loci on the chromosome or chromosome segment of interest from only the individual” as 

the construction. Dkt. No. 70-1 at 1. Natera asserts that no construction is necessary. Id. 

LEGAL STANDARD

Claim construction is a matter of law. Markman v. Westview Instr., Inc., 517 U.S. 370, 372 

(1996). Terms contained in claims are “generally given their ordinary and customary meaning.” 

Phillips v. AWH Corp., 415 F.3d 1303, 1312 (Fed. Cir. 2005). “[T]he ordinary and customary 

meaning of a claim term is the meaning that the term would have to a person of ordinary skill in the 

art in question at the time of the invention.” Id. at 1312. In determining the proper construction of 

a claim, a court begins with the intrinsic evidence of record, consisting of the claim language, the 

patent specification, and, if in evidence, the prosecution history. Id. at 1313; see also Vitronics 

Corp. v. Conceptronic, Inc., 90 F.3d 1576, 1582 (Fed. Cir. 1996). “The appropriate starting 

 

2 An allele is particular variation of a gene. 

3 Loci refers to fixed positions within a chromosome. A locus is examined to determine the 

specific nucleic acid encoded on that part of the chromosome. Examining a number of loci in 

sequence allows geneticists to determine what variant of a gene, i.e. which allele, an individual has 

in their genome. 

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point...is always with the language of the asserted claim itself.” Comark Communications, Inc. v. 

Harris Corp., 156 F.3d 1182, 1186 (Fed. Cir. 1998); see also Abtox, Inc. v. Exitron Corp., 122 F.3d 

1019, 1023 (Fed. Cir. 1997).

Accordingly, although claims speak to those skilled in the art, claim terms are construed in 

light of their ordinary and accustomed meaning, unless examination of the specification, prosecution 

history, and other claims indicates that the inventor intended otherwise. See Electro Medical 

Systems, S.A. v. Cooper Life Sciences, Inc., 34 F.3d 1048, 1053 (Fed. Cir. 1994). The written 

description can provide guidance as to the meaning of the claims, thereby dictating the manner in 

which the claims are to be construed, even if the guidance is not provided in explicit definitional 

format. SciMed Life Systems, Inc. v. Advanced Cardiovascular Systems, Inc., 242 F.3d 1337, 1344 

(Fed. Cir. 2001). In other words, the specification may define claim terms “by implication” such 

that the meaning may be “found in or ascertained by a reading of the patent documents.” Vitronics, 

90 F.3d at 1582, 1584 n.6.

In addition, the claims must be read in view of the specification. Markman v. Westview 

Instruments, Inc., 52 F.3d 967, 978 (Fed. Cir. 1995), aff'd, 517 U.S. 370 (1996). Although claims 

are interpreted in light of the specification, this “does not mean that everything expressed in the 

specification must be read into all the claims.” Raytheon Co. v. Roper Corp., 724 F.2d 951, 957 

(Fed. Cir. 1983). For instance, limitations from a preferred embodiment described in the 

specification generally should not be read into the claim language. See Comark, 156 F.3d at 1187. 

However, it is a fundamental rule that “claims must be construed so as to be consistent with the 

specification.” Phillips, 415 F.3d at 1316. Therefore, if the specification reveals an intentional 

disclaimer or disavowal of claim scope, the claims must be read consistently with that limitation. 

Id.

Finally, the Court may consider the prosecution history of the patent, if in evidence. 

Markman, 52 F.3d at 980. The prosecution history limits the interpretation of claim terms so as to 

exclude any interpretation that was disclaimed during prosecution. See Southwall Technologies, 

Inc. v. Cardinal IG Co., 54 F.3d 1570, 1576 (Fed. Cir. 1995). In most situations, analysis of this 

intrinsic evidence alone will resolve claim construction disputes. See Vitronics, 90 F.3d at 1583. 

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Courts should not rely on extrinsic evidence in claim construction to contradict the meaning 

of claims discernable from examination of the claims, the written description, and the prosecution 

history. See Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1308 (Fed. Cir. 1999) 

(citing Vitronics, 90 F.3d at 1583). However, it is entirely appropriate “for a court to consult 

trustworthy extrinsic evidence to ensure that the claim construction it is tending to from the patent 

file is not inconsistent with clearly expressed, plainly apposite, and widely held understandings in 

the pertinent technical field.” Id. Extrinsic evidence “consists of all evidence external to the patent 

and prosecution history, including expert and inventor testimony, dictionaries, and learned 

treatises.” Phillips, 415 F.3d at 1317. All extrinsic evidence should be evaluated in light of the 

intrinsic evidence. Id. at 1319.

DISCUSSION

Pursuant to Patent Local Rule 4-3(a), parties are required to identify up to ten terms whose 

construction will be most significant to the resolution of the case. Patent L. R. 4-6. The parties 

have identified three terms for construction in their joint claim construction statements. The Court 

addresses each of the disputed constructions in turn.

1. ’831 Patent - “selectively enriching a plurality of non-random polynucleotide sequences

of genomic DNA from said fetal and maternal cell-free DNA[.]” 

Term to be construed Illumina’s Construction Natera’s Construction

“selectively enriching a 

plurality of non-random 

polynucleotide sequences of 

genomic DNA from said fetal 

and maternal cell-free DNA”

enriching a plurality of nonrandom nucleic acid 

sequences of genomic DNA 

from a fetal and maternal 

cell-free DNA sample that 

meet sequence and/or 

location criteria selected to 

facilitate aneuploidy 

detection

enriching a plurality of 

selected non-random nucleic 

acid sequences of genomic 

DNA from fetal and maternal 

cell-free DNA.

Illumina asks the Court to construe the term as one including an aneuploidy detection 

limitation and asserts the contested term should be construed as “enriching a plurality of non-random 

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nucleic acid sequences of genomic DNA from a fetal and maternal cell-free DNA sample that meet 

sequence and/or location criteria selected to facilitate aneuploidy detection.” Dkt. No. 71 at 5. 

Illumina relies on both this Court’s prior claim construction in Verinata Health, Inc., et al. v. Ariosa 

Diagnostics, Inc., et al., 3:12-cv-05501-SI (N.D. Cal.), Dkt. No. 89 (Oct. 16, 2013) and intrinsic 

evidence within the ’831 patent to demonstrate the claim is directed toward aneuploidy detection. 

Natera counters that the “selected to facilitate aneuploidy detection” limitation should not be in the 

construction and argues that the intrinsic evidence shows the claims are not limited to aneuploidy 

detection.

Both Illumina and Natera cite to this Court’s prior claim construction in Verinata. In that 

order, the Court construed “selectively” as “criteria selected to facilitate aneuploidy detection” 

because this limitation was already incorporated into the claim through the preamble and the 

construction did not limit claim scope. 3:12-cv-05501-SI. (N.D. Cal.), Dkt. No. 89 (Oct. 16, 2013) 

at 39.

Illumina now argues the Court should adopt its construction because it is “nearly identical” 

to a construction the Court adopted for a “nearly identical [term]” in Verinata. Dkt. No. 71 at 1, 5. 

See Claim Construction Order, Verinata at 38–40. Illumina notes that the ’831 patent and the ’430 

patent at issue in Verinata stem from the “same parent applications, share identical specifications, 

and have considerable overlap between their claim language and intrinsic records that justify 

construing the claim term of the ’831 Patent [similarly to the Court’s prior construction] for the ’430 

Patent.” Dkt. No. 71 at 1.

Illumina argues this Court’s prior ’430 patent claim construction demonstrates that the 

method in the ’831 patent contains actual testing for aneuploidy. This Court previously construed 

the term “reference chromosome” to mean “a chromosome different from the particular 

chromosome that is being tested for aneuploidy.” Verinata, Dkt. No. 89 (Oct. 16, 2013) at 43 

(emphasis added). Illumina uses this construction to refute Natera’s argument that “tested for being 

aneuploid” merely specifies where the selected sequences come from and not what they are used 

for. Illumina argues that this Court’s prior interpretation indicated the Court interpreted “tested for 

aneuploid” to mean actual testing for aneuploidy. Accordingly, since both the ’831 patent and the 

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’430 patent contain the identical phrase “chromosome tested for being aneuploid,” Illumina asserts 

that the same reasoning and conclusion should apply—there is actual testing for aneuploidy that 

supports Illumina’s construction. Dkt. No. 76 at 3.

Illumina argues that its proposed construction is supported by the patent’s claim language 

and specification. For example, claim 1 contains the phrase “wherein...at least 100 different nonrandom polynucleotide sequences selected from a chromosome tested for being aneuploid.” ’831 

Patent at 64:48–51; Dkt. No. 71 at 6. Illumina argues this language supports its construction that 

“selective enrichment” of the claims is carried out to facilitate aneuploid detection and is based on 

sequence or location criteria. Illumina also points to dependent claims 6 and 13, noting the 

invention is directed toward a method that involves testing for aneuploidy. Claims 6 and 13 mention 

“the chromosome tested for being aneuploid” and “said chromosome tested,” respectively. ’831 

Patent at 65:8, 27–28. Illumina argues that, “the claims themselves...confirm that selective 

enrichment is directed towards enriching nucleic acid sequences that are selected to facilitate 

aneuploidy detection, as recited in Illumina’s proposed construction.” Dkt. No. 71 at 6.

Illumina also points to the specification to support its proposed construction. Specifically, 

Illumina highlights language in the “Abstract” and “Background of the Invention.” The Abstract 

states “[m]ethods of using selectively enriched non-random polynucleotide sequences for detection 

of fetal aneuploidy are provided.” The Background states “[t]here is a need for a means of 

selectively enriching non-random fetal and maternal polynucleotide sequences in a way that 

facilitates aneuploidy detection by massively parallel sequencing techniques and increases the 

sensitivity of aneuploidy detection. . .” ’831 Patent at 1:34–39. 

Natera argues that Illumina misapplies the ’430 patent’s claim construction. Dkt. No. 73 at 

10–12. Natera points out that there is one important difference between the ’430 patent and ’831 

patent at issue: the preamble of the ’430 patent states “determining a presence or absence of a fetal 

aneuploidy,” while the preamble of the ’831 patent does not mention aneuploidy. Natera argues the 

’430 patent claims show Verinata knew how to specify that facilitating aneuploidy detection was 

the purpose of the claimed invention, and because Verinata failed to include similar limiting 

language in ’831’s preamble, the claim here should not be limited to aneuploidy detection. 

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Natera argues that the patent’s claim language and specification support its construction. 

Natera argues that the phrase in claim 1, “tested for being aneuploid...merely specifies where the 

selected sequences come from—not what they must be used for.” Dkt. No. 73 at 9. In addition, 

Natera argues that the specification does not support Illumina’s contention that the invention is 

directed only toward aneuploidy detection. Natera points out that throughout the specification, 

aneuploidy analysis is discussed as an exemplary embodiment and not the entire invention, e.g.,

“[i]n another embodiment, said sequenced enriched sequences are used to determine the presence 

or absence of fetal aneuploidy.” ’831 Patent at 3:29–41. 

The Court finds that the patent’s claim language supports a finding that the ’831 is directed 

to aneuploidy detection. The claim imposes limitations on how non-random sequences are to be 

selected—that is, they are selected from a chromosome “tested for being aneuploid.” This Court’s 

interpretation of that same phrase in the ’430 patent demonstrates the claim methods include 

chromosomes that are actually tested for aneuploidy. Although the preamble of the ’831 patent 

lacks the phrase “determining a presence or absence of fetal aneuploidy,” which is present in the 

’430 patent, the Court finds that the ’831 patent is directed to aneuploidy detection. Ultimately, the 

’831 claims language “tested for being aneuploid” is persuasive in showing the method is directed 

to aneuploidy detection.

The Court also finds that the specification supports a finding that the ’831 patent is directed 

toward aneuploidy detection. The Abstract and Background state that the invention contains 

methods for detecting aneuploidy and that there is a need for such detection methods. The fact that 

the specification frames aneuploidy detection as examples or embodiments is not dispositive and 

does not overcome the plain language from the Abstract and Background, which inform the bounds 

of the invention. 

For the reasons stated above, the Court to construes “selectively enriching a plurality of nonrandom polynucleotide sequences of genomic DNA from said fetal and maternal cell-free DNA” to 

mean: “enriching a plurality of non-random nucleic acid sequences of genomic DNA from a fetal 

and maternal cell-free DNA sample that meet sequence and/or location criteria selected to facilitate 

aneuploidy detection.”

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2. ’592 Patent

A. “genetic data for some or all possible alleles” 

Term to be construed Illumina’s Construction Natera’s Construction

“genetic data for some or all 

possible alleles”

data showing the identities of 

particular bases at specific 

loci so as to reveal genotype 

of the individual for some or 

all possible alternative forms 

of the loci

genetic data for some or all 

possible alternative forms of 

a given locus 

The parties dispute whether “genetic data” should be construed broadly as the plain and 

ordinary meaning of “genetic data” or more narrowly as “data showing the identities of particular 

bases at specific loci so as to reveal genotype of the individual.” Dkt. No. 70-1. 

Illumina advocates for a narrow construction, arguing that claim 1 should be limited to 

genotyping, i.e., “allele-specific” genetic data.

4 Natera argues that claim 1 has a broader scope and 

should encompass both “allele-specific” and “allele-agnostic” genetic data.5 Dkt. No. 75 at 4. 

Natera supports its broader construction with three main arguments. First, Natera argues that 

there is a heavy presumption for its construction because it reflects the ordinary and customary 

meaning. Second, Natera presents examples from the claims and specification of allele-agnostic, 

i.e., non-genotyping, techniques for measuring genetic data. Third, Natera supports its construction 

based on a theory of claim differentiation between independent claim 1 and dependent claim 10.

Natera asserts that its broader construction should receive a heavy presumption because it 

reflects the term’s ordinary and customary meaning. Dkt. No. 75 at 6–7. Natera argues that Illumina 

has not shown “alternative lexicography” or a “clear disavowal” of non-genotyping methods to 

 

4 An “allele specific” interpretation correlates with “genotyping,” “making an allele call,” 

and determining the identification of a base pair at a specific location, or locus, on a chromosome. 

Dkt. No. 72 at 17. An “allele agnostic” interpretation is not synonymous with any of the terms 

described above. 

5 Allele-agnostic techniques are techniques that do not require genotyping, i.e., “nongenotyping.” In other words, allele-agnostic techniques “ignore the identities of any particular 

nucleotides at a locus.” Dkt. No. 75 at 3.

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overcome the presumption. Id. at 3, 6. 

Natera presents multiple examples of non-genotyping methods from the claim language and 

specification. In one example, Natera cites to the language of claim 1, “using a [SNP] genotyping 

array or high throughput DNA sequencing to measure genetic material.” ’592 patent 62:42–44.

Natera argues that this claim language explicitly contemplates both a genotyping technique, “[SNP] 

genotyping array” and a non-genotyping technique, “high throughput DNA sequencing.” Dkt. No. 

72 at 13. 

Natera also asserts that one “aspect of the invention” is “the direct measurements of the 

amount of genetic material,” which is a non-genotyping technique. Dkt. No. 72 at 14; Dkt. No. 75 

at 7–8. Specifically, Natera points to “Sanger DNA sequencing” and “pyrosequencing” from claim 

19 and “mini-sequencing..., pyrosequencing..., and genomic sequencing...” from the specification

to demonstrate examples of non-genotyping techniques. ’592 Patent at 64:5, 3:63, 5:13–14, 8:12; 

Dkt. No. 72 at 13, 16; Dkt. No. 75 at 8.

Natera finally supports its claim construction under a theory of claim differentiation. Natera 

argues that dependent claim 10 narrows claim 1, and therefore claim 1 cannot be limited in the way 

Illumina’s construction requires. Dkt. No. 72 at 15. Specifically, Natera asserts that because claim 

10 narrows the method to genotyping, claim 1 cannot also have such a narrow interpretation. Id.

Illumina supports its narrower construction with three main arguments. First, Illumina 

argues that “sequencing,” in light of the specification, refers only to genotyping and not nongenotyping methods. Second, Illumina asserts that the patentee acted as a lexicographer and limited 

the claim term “alleles” to genotyping. Third, Illumina asserts that the prosecution history, which 

only mentions genotyping techniques, should limit the claim scope.

Illumina asserts that the claim language “high throughput DNA sequencing” and 

“pyrosequencing” must be limited to genotyping. Illumina rejects Natera’s assertion that such types 

of sequencing are examples of non-genotyping techniques. To support this argument, Illumina 

states that the specification never suggests that “sequencing” is used for anything else but 

genotyping and SNP determination. Dkt. No. 74 at 20.

Illumina also argues that the patentee acted as its own lexicographer and limited the 

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definition of “alleles” to genotyping. Dkt. No. 74 at 20–21. Illumina cites the definition section of 

the specification where “to call an allele” is defined as “to call a SNP.” ’592 Patent at 62:13.

Accordingly, because calling an SNP equates to genotyping, Illumina argues that the term “alleles” 

must correspond to genotyping. Thus, the claim should be construed as containing a genotyping 

limitation. Dkt. No. 74 at 20.

Illumina argues that the prosecution history also limits the claim term to genotyping. Dkt. 

No. 74 at 22–23. Illumina asserts that the only type of techniques disclosed in the 2005 provisional 

application are based on genotyping. Id. at 22. Thus, Illumina argues, the patent should also be 

limited to only genotyping techniques. Id. at 23. 

The Court finds that both the claims and specification demonstrate that the claimed method 

includes both genotyping and non-genotyping techniques. For example, claim 1 states “[SNP] 

genotyping array or high throughput DNA sequencing.” ’592 Patent at 62:42–43. This language 

supports the argument that one disclosed technique is genotyping and the other is non-genotyping. 

The claims and specification also clearly state that one aspect of the invention is measuring the 

amount of genetic material, which supports a claim interpretation that includes non-genotyping 

techniques. 

Accordingly, the Court construes the term as it proposed during oral argument, which is with 

the slight modification construing “genetic data for some or all possible alleles” to mean: “genetic 

data for some or all possible base pairs at a given locus.” 

B. “at least 100 loci on the chromosome or chromosome segment of interest in the

individual”

Term to be construed Illumina’s Construction Natera’s Construction

“at least 100 loci on the 

chromosome or chromosome 

segment of interest in the 

individual”

at least 100 loci on the 

chromosome or chromosome 

segment of interest from only 

the individual

No construction necessary 

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The parties dispute the phrase immediately preceding “the individual.” Illumina seeks a 

construction specifying “from only the individual”; Natera seeks to leave the term in its original 

form, “in the individual.” The parties dispute whether, according to the patent claims, an 

individual’s genetic data must be measured separately from the genetic material of another 

individual, i.e., whether fetal and maternal DNA must be measured separately. Dkt. No. 74 at 10; 

Dkt. No. 75 at 12. 

Natera supports its position with two main arguments. First, Natera points to the technical 

definition of the claim term “an” to mean more than one. Second, Natera points to “mixed samples” 

and “foreign DNA” in the specification to argue that the patent is not limited to analyzing an 

individual’s DNA separate from another individual’s DNA.

Although the precise claim term being construed is “the individual,” Natera argues that the 

language in the claim’s preamble referring to “an individual” supports its construction, since “an”

should carry the meaning of “one or more” in open-ended claims that use the transitional phrase, 

“comprising.” Dkt. No. 72 at 18–19, 23. While there is an exception to this rule when “the patentee 

evinces a clear intent to so limit the article,” Natera argues that the exception does not apply here. 

Dkt. No. 75 at 13; KCJ Corp. v. Kinetic Concepts, Inc., 223 F.3d 1351, 1356 (Fed. Cir. 2000) (the 

Federal Circuit “has repeatedly emphasized that an indefinite article ‘a’ or ‘an’ in patent parlance carries 

the meaning of ‘one or more’ in open-ended claims containing the transitional phrase ‘comprising,’”); 

Baldwin Graphic Systems, Inc. v. Siebert, 512 F.3d 1338, 1342 (Fed. Cir. 2008) (The fact that “‘a’ or 

‘an’ can mean ‘one or more’ is best described as a rule, rather than merely as a presumption or even a 

convention.”). 

Natera also argues that two examples in the specification support its construction. The 

specification discusses “mixed samples” that contain DNA from multiple individuals and “foreign 

DNA,” which may contaminate the genetic material of an individual being analyzed. See, e.g., ’592 

Patent at 29:53–57, 40:5–58:54; Dkt. No. 72 at 22– 23. Natera argues that “mixed samples” and 

“foreign DNA” show that the patent claims are not limited to measuring genetic data for only one

individual separately from another individual. 

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Illumina supports its construction, “...from only the individual,” with two main arguments. 

First, Illumina points to repeated use of “the individual” in the claim language to show that the 

claims require DNA measurement of only one individual. Second, Illumina cites to the specification 

that describe isolating fetal DNA from maternal DNA as part of the invention. 

Specifically, Illumina highlights the repeated use of the phrase “the individual” to support 

its construction that the claimed genetic analysis is applied to only one individual separate from 

another individual. For example, claim 1 states that “the small amount of genetic material from the 

individual is from fifty or fewer of the individual's cells, 0.3 ng or less of the individual’s DNA, 

extracellular DNA from the individual found in the maternal blood...” ’592 Patent 62:49–52; Dkt. 

No. 74 at 11. Illumina argues that such language shows that the genetic material of the “individual”

is analyzed separately from the DNA of other individuals. Dkt. No. 74 at 11.

Illumina also cites multiple examples in the specification where genetic material, such as 

“cell-free fetal DNA” is isolated from maternal blood. Dkt. No. 74 at 12–13. Illumina argues that 

language in the Abstract and Summary of the Invention show that the patent covers reconstructing 

“noisy” data from the “individual” and cleaning incomplete or noisy genetic data. Dkt. No. 74 at 

13. Illumina argues that a prerequisite to these techniques is isolating cells or DNA from a single

individual and not from a mixture of multiple individuals. Id. at 13–14. 

Finally, Illumina rejects Natera’s examples of “mixed samples” and “foreign DNA,”

arguing that the claims “do not cover techniques based on the analysis of truly mixed maternal blood 

samples that have not been subject to ‘isolation’ of fetal cells or fetal cell-free DNA.” Dkt. No. 74 

at 17. Illumina argues that the experiment regarding “mixed samples” is not an embodiment of the 

patent because it is not limited to “an individual.” Id. Illumina dismisses the example of a mixed 

sample as “hypothetical control samples.” Id. Illumina also states that “nowhere did the 

experiments assess the number of X chromosomes in the genomes of individuals from whom the 

mixed samples were prepared.” Id. Illumina contends that the analysis of foreign DNA 

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contaminating the sample, which Natera raises, is consistent with Illumina's construction. Id. 

The Court looks to the language of claims and the specification to determine whether an 

individual’s genetic data must be measured separately from the genetic material of another 

individual, i.e., whether fetal and maternal DNA must be measured separately. Dkt. No. 74 at 10; 

Dkt. No. 75 at 12. The Court finds that both the claims and specification demonstrate that the 

claimed method is directed to the analysis of samples containing the DNA of only one individual. 

The claim language mentions genetic material from “the individual” many times, often referring to 

“DNA from the individual found in maternal blood.” ’592 62:52. The claims repeatedly identify 

the genetic material’s source—“the individual”—as distinct from genetic material from another 

individual, e.g. maternal genetic material. This supports the position that fetal and maternal DNA 

are measured separately. The specification also repeatedly states that fetal genetic material (e.g. 

“cell-free fetal DNA”) is isolated from the maternal blood prior to analysis. The specification makes 

clear that the target of analysis is fetal DNA. Accordingly, fetal and maternal DNA are measured 

separately. Additionally, Illumina stated that the technology for simultaneously analyzing a mixture 

of maternal and fetal DNA is a “modern approach” that had not yet been invented at the priority 

date of the ’592 patent. Dkt. No. 80 at 112–113.

Accordingly, the Court construes “at least 100 loci on the chromosome or chromosome 

segment of interest in the individual” to mean: “at least 100 loci on the chromosome or chromosome 

segment of interest from only the individual.”

///

///

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CONCLUSION

For the foregoing reasons and for good cause shown, the Court adopts the constructions set 

forth in this memorandum. 

IT IS SO ORDERED.

Dated: January 30, 2019

______________________________________

SUSAN ILLSTON

United States District Judge

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