IP Library › Patent Application 17080201

Patent Application

App. No. 17/080,201

GENOMIC ALTERATIONS IN THE TUMOR AND CIRCULATION OF PANCREATIC CANCER PATIENTS

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Quick Facts

Patent No.: US None
App. No.: 17/080,201

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Abstract

Pancreatic adenocarcinoma has the worst overall mortality of any solid tumor, with only 7% of patients surviving after 5 years. To evaluate the clinical implications of genomic alterations in this low cellularity tumor type, we deeply sequenced the genomes of 101 enriched pancreatic adenocarcinomas from patients who underwent potentially curative resections and used non-invasive approaches to examine tumor specific mutations in the circulation of these patients. These analyses revealed somatic mutations in chromatin regulating genes including MLL and ARID1A in 20% of patients that were associated with improved survival. Liquid biopsy analyses of cell free plasma DNA revealed that 43% of patients with localized disease had detectable circulating tumor DNA (ctDNA) in their blood at the time of diagnosis. Detection of ctDNA after resection predicted clinical relapse and poor outcome, and disease recurrence by ctDNA was detected 6.5 months earlier than with standard CT imaging.

Claims (143)

1 - 11 . (canceled)

12 . A probe or primer specific for a mutant chromatin regulating MLL (chromosome 11), MLL2 (chromosome 12), MLL 3 (chromosome 7) or ARID1A gene, said probe or primer comprising a mutation selected from the group consisting of:

ARID1A mutations:

chr1_26928798-

403Q > X

Substitution

Nonsense;

26928798_C_T

chr1_26979465-

Insertion

Frameshift;

26979465_C

chr1_26978312-

1779E > G

Substitution

Nonsynonymous

26978312_A_G

coding;

chr1_26978589-

1871H > Q

Substitution

Nonsynonymous

26978589_C_G

coding;

chr1_26895595-

38E > EA

Insertion

In-frame

26895595_GGC

insertion;

chr1_26960135-

708Q > X

Substitution

Nonsense;

26960135_C_T

chr1_26973560-

1419A > T

Substitution

Nonsynonymous

26973560_G_A

coding;

chr1_26974706-

1682A > E

Substitution

Nonsynonymous

26974706_C_A

coding;

chr1_26972534-

1276R > X

Substitution

Nonsense;

26972534_C_T

chr1_26978518-

Deletion

Frameshift;

26978518_G —

chr1_26979254-

Insertion

Frameshift;

26979254_TT

and MLL (chromosome 11), MLL2 (chromosome 12), or MLL 3 (chromosome 7) mutations:

chr7_151490485-

3704V > L

Substitution

Nonsynonymous

151490485_C_G

coding;

chr11_117854039-

1161C > S

Substitution

Nonsynonymous

117854039_G_C

coding;

chr11_117847769-

229P > T

Substitution

Nonsynonymous

117847769_C_A

coding;

chr12_47718147-

3087R > W

Substitution

Nonsynonymous

47718147_G_A

coding;

chr7_151515732-

Substitution

Splice site donor;

151515732_C_T

chr12_47729834-

Insertion

Frameshift;

47729834_A

chr7_151576224-

743P > L

Substitution

Nonsynonymous

151576224_G_A

coding;

chr7_151476195-

4584R > W

Substitution

Nonsynonymous

151476195_G_A

coding;

chr7_151686622-

Insertion

Frameshift;

151686622_TC

chr12_47711653-

Insertion

Frameshift;

47711653_T

chr12_47731362-

Deletion

Frameshift;

47731362_G —

chr7_151601824-

Insertion

Frameshift;

151601824_T

chr12_47722327-

1974T > M

Substitution

Nonsynonymous

47722327_G_A

coding; and

chr7_151510210-

1890R > X

Substitution

Nonsense.

151510210_G_A

13 . The probe or primer of claim 12 which is labeled with a radionuclide, a fluorescent label, or a chromophore.

14 - 34 . (canceled)

Assignments (1)

ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Oct 26, 2020

From: VELCULESCU, VICTOR; SAUSEN, MARK; ADLEFF, VILMOS; PHALLEN, JILLIAN

To: THE JOHNS HOPKINS UNIVERSITY

Reel/Frame 054167/0351 →