# US 12,205,676 B2 · Methods for treating Barrett's metaplasia and esophageal adenocarcinoma

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- Number: US 12,205,676 B2
- Document ID: US12205676B2
- Status: Granted
- Kind: B2
- Application number: 16/285,604
- Filed: 2019-02-26
- Published: 2020-01-30
- Granted: 2025-01-21
- Earliest claimed: 2011-12-01
- Assignees: Interpace Diagnostics Corporation
- Applicants: Interpace Diagnostics Corporation
- Inventors: Eric Matthew Gayle Ellsworth; Sydney David Finkelstein; Sara Ann Jackson; Brendan Corcoran; Dennis Morgan Smith
- Web page: https://patentgrep.com/patent/US12205676B2

## CPC

- G16B 40/00: ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
- A61B 17/3205: Excision instruments
- A61B 17/3209: Incision instruments
- A61B 18/18: by applying electromagnetic radiation, e.g. microwaves
- A61N 5/0613: {Apparatus adapted for a specific treatment}
- A61N 5/062: {Photodynamic therapy, i.e. excitation of an agent}
- G16B 30/00: ICT specially adapted for sequence analysis involving nucleotides or amino acids
- A61B 18/02: by cooling, e.g. cryogenic techniques
- A61B 18/12: by passing a current through the tissue to be heated, e.g. high-frequency current
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- A61B: DIAGNOSIS; SURGERY; IDENTIFICATION (usefulness limited to only animals A61D)
- A61N: ELECTROTHERAPY; MAGNETOTHERAPY; RADIATION THERAPY; ULTRASOUND THERAPY (measurement of bioelectric currents A61B; surgical instruments, devices or methods for transferring non-mechanical forms of energy to or from the body A61B18/00; anaesthetic apparatus in general A61M; incandescent lamps H01K; infrared radiators for heating H05B)

## Abstract

Disclosed herein are methods for treating Barrett's metaplasia and esophageal adenocarcinoma and methods for determining mutational load as a predictor of the risk of disease progression from Barrett's metaplasia to esophageal adenocarcinoma.

## Claims

### Claim 1

A method of treating Barrett's metaplasia, the method comprising:
amplifying DNA complementary to the microsatellite regions of 1q22, 1p34.2, 1p22.3, 1p36.21, 1p36.21, B Catenin E3, 3p25, 3p12.3, 3p22.3, 3p24.3, 3p26.3, 3p11.2, 3p24.2, C-KIT Ell, C-KIT E17, 5q23.1, 5q23.2, BRAF E15, EGFR E 19, EGFR E 21, 7p12.3, 7p12.1, 9p21.1, 9p23, 10q23.32, 10q23.33, HRAS1 E1, Kras2.E1, Kras2.E2, 17q22, 17q21.2, 17q11.2, 17p13.1 17p13, 17p13.1, 18q21.33, 19q13.2, 19q13.32, 21q21.2, 22q13.2, and Xp22.2 from a subject;
detecting the presence or absence of a mutation in the microsatellite regions;
categorizing clonality of each mutation;
calculating a mutational load based on the sum of low and high clonality mutations;
comparing the mutational load with a series of pre-determined mutational load cut-offs defining risk categories;
assigning the subject to a risk category corresponding to the subject's mutational load, wherein each risk category is indicative of the risk of disease progression;
determining if the subject is in a high risk category for disease progression from Barrett's metaplasia to esophageal adenocarcinoma; and
administering to the subject identified in the high risk category at least one treatment modality selected from endoscopic mucosal resection, endoscopic submucosal dissection, a therapeutically effective amount of radiofrequency ablation, a therapeutically effective amount of cryoablation, a therapeutically effective amount of photodynamic therapy and combinations thereof.

### Claim 2 (depends on 1)

The method of claim 1, wherein the pre-determined mutational load cut-offs defining risk categories are derived from a pre-determined patient population distribution with known mutational loads corresponding to a known disease state diagnosis.

### Claim 3 (depends on 2)

The method of claim 2, wherein the known disease state diagnosis is selected from normal squamous, columnar epithelium without Barrett's metaplasia, Barrett's metaplasia, Barrett's metaplasia intermediate for dysplasia, low grade dysplasia and high grade dysplasia.

### Claim 4 (depends on 2)

The method of claim 2, wherein the risk categories are selected from no mutational load, low mutational load, and high mutational load.

### Claim 5 (depends on 4)

The method of claim 4, wherein the subject is assigned to the no mutational load risk category when the subject has mutational load of 0.0.

### Claim 6 (depends on 4)

The method of claim 4, wherein the wherein no mutational load is indicative of no risk of disease progression from Barrett's metaplasia to esophageal adenocarcinoma.

### Claim 7 (depends on 4)

The method of claim 4, wherein the subject is assigned to the low mutational load risk category when the subject has a mutational load greater than 0.0 but less than or equal to 2.0.

### Claim 8 (depends on 4)

The method of claim 4, wherein the subject is assigned to the high mutational load risk category when the subject has a mutational load greater than 2.0.

### Claim 9 (depends on 1)

The method of claim 1, wherein the subject is a human diagnosed with Barrett's esophagus.

### Claim 10 (depends on 1)

The method of claim 1, wherein the biological specimen is a mucosal lining of the esophagus.

### Claim 11 (depends on 1)

The method of claim 1, wherein amplifying DNA sequences comprises:
selecting a primer pair corresponding to the micro satellite regions;
adding the primer pair to the DNA sequences; and
performing quantitative polymerase chain reaction on the DNA sequences with the primer.

### Claim 12 (depends on 1)

The method of claim 1, wherein detecting mutations comprises determining the sequence of the amplified DNA and comparing the amplified DNA to a known wild type control sequence for the microsatellite regions and identifying differences between the sequence of the amplified DNA and the known wild type control sequence.

### Claim 13 (depends on 1)

The method of claim 1, wherein categorizing clonality of each mutation comprises assigning one of three categories selected from the group consisting of no clonality, low clonality and high clonality.

### Claim 14 (depends on 13)

The method of claim 13, wherein high clonality is assigned where loss of heterozygosity is present in greater than about 75% of DNA analyzed.

### Claim 15 (depends on 13)

The method of claim 13, wherein low clonality is assigned where loss of heterozygosity is present in about 50% to about 75% of DNA analyzed.

### Claim 16 (depends on 13)

The method of claim 13, wherein no clonality is assigned where loss of heterozygosity is present in less than about 50% of DNA analyzed.

### Claim 17 (depends on 1)

The method of claim 1, wherein calculating the mutational load comprises assigning a score to each mutation based on a categorization of low or high clonality of each mutation, wherein the score for low clonality is 0.5x, wherein x is the number of low clonality mutations and the score for high clonality is y, wherein y is the number of high clonality mutations; and wherein the overall mutational load is y+0.5x.

### Claim 18 (depends on 1)

The method of claim 1, wherein calculating the mutational load further comprises assigning a score to each mutation based on detection of DNA microsatellite instability at a particular locus, wherein DNA microsatellite instability at a single locus is defined as 0.75z, wherein z is the number of loci displaying DNA microsatellite instability; wherein the score for low clonality is 0.5x, wherein x is the number of low clonality mutations and the score for high clonality is y, wherein y is the number of high clonality mutations; and wherein the overall mutational load is y+0.5x+0.75z.

### Claim 19 (depends on 1)

The method of claim 1, wherein calculating the mutational load further comprises assigning a score to each mutation based on detection of DNA microsatellite instability at multiple loci, wherein DNA microsatellite instability at multiple loci is defined as 2z, wherein z is the number of loci displaying DNA microsatellite instability; wherein the score for low clonality is 0.5x, wherein x is the number of low clonality mutations and the score for high clonality is y, wherein y is the number of high clonality mutations; and wherein the overall mutational load is y+0.5x+2z.

### Claim 20 (depends on 1)

The method of claim 1, wherein calculating a mutational load further comprises summing the clonality weighting for each specific microsatellite region showing a mutation or DNA microsatellite instability.

### Claim 21 (depends on 1)

The method of claim 1, wherein the method does not comprises performing a histological analysis.