IP Library › Granted Patent US 12,209,288
Granted Patent B2
US 12,209,288 · App. 18/356,906 · Granted Jan 28, 2025

Methods for sequencing samples

Inventors: Dietrich Stephan (San Francisco, CA); Vern Norviel (San Francisco, CA); Janet Warrington (Los Altos, CA); Doug Dolginow (Basalt, CO)
Assignee: Aqtual, Inc.
C12Q1/6886G01N33/57484C12Q2600/106C12Q2600/112C12Q2600/136C12Q2600/142C12Q2600/154C12Q2600/156C12Q2600/158C12Q2600/16
View Patent ↗
Loading inventors, assignments & file history…
Monitor This Case
Get email alerts when status or documents change.
Order Certified Copies
Most orders are placed with the USPTO same day — all within 24 business hours.
Order via The Patent Place →
Pre-filled with this patent's details
Quick Facts
Patent No.
US 12,209,288
App. No.
18/356,906
Granted
Jan 28, 2025
Kind
B2
Abstract

Personalized medicine involves the use of a patient's molecular markers to guide treatment regimens for the patient. The scientific literature provides multiple examples of correlations between drug treatment efficacy and the presence or absence of molecular markers in a patient sample. Methods are provided herein that permit efficient dissemination of scientific findings regarding treatment efficacy and molecular markers found in patient tumors to health care providers.

Claims (22)

1. A method comprising:

(a) obtaining a cell-free deoxyribonucleic acid (DNA) sample from a subject wherein said cell-free DNA sample comprises molecular markers;

(b) detecting sequences of a panel of said molecular markers, wherein said molecular markers comprise: (1) Receptor Tyrosine Kinase KIT Proto-Oncogene (KIT); (2) Epidermal Growth Factor Receptor (EGFR) gene; and (3) another molecular marker selected from the group consisting of GTPase KRAS Proto-Oncogene (KRAS), Serine/Threonine Kinase B-Raf Proto-Oncogene (BRAF), a microsatellite sequence, chromosome 18q allelic loss, thymidylate synthase gene, and DNA Topoisomerase I (TOP1) gene; and

(c) providing a cancer treatment option in a report based on said sequences of said panel of said molecular markers.

2. The method of claim 1 , wherein said subject is suspected of having cancer.

3. The method of claim 1 , wherein said subject has a cancer.

4. The method of claim 3 , wherein said subject has a lung cancer, a non-small-cell lung cancer, a breast cancer, a prostate cancer, a gastric cancer, a head and neck cancer, an advanced gastric adenocarcinoma, a squamous cell carcinoma, a pancreatic adenocarcinoma, Hodgkin's Disease, non-Hodgkin's lymphoma; a testicular carcinoma, a colon cancer, a rectal cancer, an esophageal cancer, a hepatocellular carcinoma, a cholangiocarcinoma, a chronic myeloid leukemia, a chronic lymphocytic leukemia, a small lymphocytic lymphoma, or a follicular lymphoma.

5. The method of claim 1 , wherein said cell-free DNA sample comprises blood.

6. The method of claim 1 , wherein said cell-free DNA sample comprises genomic DNA.

7. The method of claim 1 , further comprising detecting a presence or absence of a substitution, an insertion, a deletion, a rearrangement, a de novo mutation, a nonsense mutation, a missense mutation, a silent mutation, a frameshift mutation, a gene amplification, an interstitial deletion, a chromosomal inversion, a loss of heterozygosity, a loss of function mutation, a gain of function mutation, or a dominant negative mutation in said sequences of said panel of said molecular markers.

8. The method of claim 1 , further comprising detecting a presence or absence of a point mutation, a single nucleotide polymorphism, a copy number variation, or a chromosomal translocation in said sequences of said panel of said molecular markers.

9. The method of claim 1 , further comprising, prior to (b), amplifying said panel of said molecular markers from said cell-free DNA sample.

10. The method of claim 1 , wherein said cancer treatment option comprises imatinib, cetuximab, panitumumab, adjuvant therapy, 5-fluorouracil (5-FU), or temzolomide.

11. The method of claim 1 , wherein said subject has had a relapse of a cancer.

12. The method of claim 1 , wherein said KIT has or encodes an activating mutation.

13. The method of claim 1 , wherein said KRAS has a mutation in exon 2.

14. The method of claim 1 , wherein said BRAF encodes a V600E mutation.

15. The method of claim 1 , wherein said microsatellite sequence has low-frequency microsatellite instability.

16. The method of claim 1 , wherein said microsatellite sequence has high-frequency microsatellite instability.

17. The method of claim 1 , wherein a copy number of said EGFR gene is increased relative to normal.

18. The method of claim 1 , wherein said EGFR gene has mutations in exons 18-21.

19. The method of claim 1 , wherein (b) comprises massively parallel DNA sequencing.

Assignments (5)
CHANGE OF NAME Recorded Mar 7, 2024
From: BLOODQ, INC.
To: AQTUAL, INC.
Reel/Frame 066761/0440 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Mar 5, 2024
From: AUEON, INC.
To: BLOODQ, INC.
Reel/Frame 066658/0277 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Mar 1, 2024
From: TOMA BIOSCIENCES, INC.
To: AUEON, INC.
Reel/Frame 066623/0571 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Feb 28, 2024
From: AUEON, INC.
To: TOMA BIOSCIENCES, INC.
Reel/Frame 066595/0365 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Feb 27, 2024
From: STEPHAN, DIETRICH; NORVIEL, VERN; WARRINGTON, JANET; DOLGINOW, DOUG
To: AUEON, INC.
Reel/Frame 066580/0885 →
Continuity (10)
Continuation 16154307 · Oct 8, 2018
Continuation 15183655 · Jun 15, 2016
Division 14927254 · Oct 29, 2015
Continuation 14075996 · Nov 8, 2013
Continuation 13060425
Provisional Application 61231287 · Aug 4, 2009
Provisional Application 61173179 · Apr 27, 2009
Provisional Application 61155477 · Feb 25, 2009
Provisional Application 61094855 · Sep 5, 2008
Related Publication 20230407408A1 · Dec 21, 2023
References Cited (400)
US 3575220A · Davis et al. · 1971 [cited by applicant]
US 3996345A · Ullman et al. · 1976 [cited by applicant]
US 4351760A · Khanna et al. · 1982 [cited by applicant]
US 4458066A · Caruthers et al. · 1984 [cited by applicant]
US 4683202A · Mullis · 1987 [cited by applicant]
US 4739044A · Stabinsky · 1988 [cited by applicant]
US 4757141A · Fung et al. · 1988 [cited by applicant]
US 4889818A · Gelfand et al. · 1989 [cited by applicant]
US 4997928A · Hobbs, Jr. · 1991 [cited by applicant]
US 5231191A · Woo et al. · 1993 [cited by applicant]
US 5487972A · Gelfand et al. · 1996 [cited by applicant]
US 5496699A · Sorenson · 1996 [cited by applicant]
US 5538848A · Livak et al. · 1996 [cited by applicant]
US 5539083A · Cook et al. · 1996 [cited by applicant]
US 5585069A · Zanzucchi et al. · 1996 [cited by applicant]
US 5635400A · Brenner · 1997 [cited by applicant]
US 5677152A · Birch et al. · 1997 [cited by applicant]
US 5723591A · Livak et al. · 1998 [cited by applicant]
US 5750341A · Macevicz · 1998 [cited by applicant]
US 5773258A · Birch et al. · 1998 [cited by applicant]
US 5789206A · Tavtigian et al. · 1998 [cited by applicant]
US 5789224A · Gelfand et al. · 1998 [cited by applicant]
US 5804375A · Gelfand et al. · 1998 [cited by applicant]
US 5827480A · Haff et al. · 1998 [cited by applicant]
US 5925517A · Tyagi et al. · 1999 [cited by applicant]
US 5952170A · Stroun et al. · 1999 [cited by applicant]
US 5981179A · Lorinez et al. · 1999 [cited by applicant]
US 5994056A · Higuchi · 1999 [cited by applicant]
US 6008002A · Bodey · 1999 [cited by applicant]
US 6030787A · Livak et al. · 2000 [cited by applicant]
US 6040138A · Lockhart et al. · 2000 [cited by applicant]
US 6063604A · Wick et al. · 2000 [cited by applicant]
US 6090591A · Burg et al. · 2000 [cited by applicant]
US 6103406A · Kumagai · 2000 [cited by applicant]
US 6127155A · Gelfand et al. · 2000 [cited by applicant]
US 6156504A · Gocke et al. · 2000 [cited by applicant]
US 6171785B1 · Higuchi · 2001 [cited by applicant]
US 6184934B1 · Nishiki · 2001 [cited by applicant]
US 6204375B1 · Lader · 2001 [cited by applicant]
US 6214979B1 · Gelfand et al. · 2001 [cited by applicant]
US 6217866B1 · Schlessinger et al. · 2001 [cited by applicant]
US 6221589B1 · Lane et al. · 2001 [cited by applicant]
US 6262242B1 · Steck et al. · 2001 [cited by applicant]
US 6303312B1 · Dervan et al. · 2001 [cited by applicant]
US 6306597B1 · Macevicz · 2001 [cited by applicant]
US 6321894B1 · Johnsson · 2001 [cited by applicant]
US 6410231B1 · Arnold et al. · 2002 [cited by applicant]
US 6410243B1 · Wyrick et al. · 2002 [cited by applicant]
US 6482795B1 · Steck et al. · 2002 [cited by applicant]
US 6488895B1 · Kennedy · 2002 [cited by applicant]
US 6492161B1 · Hjoerleifsdottir et al. · 2002 [cited by applicant]
US 6492346B1 · Hedgpeth et al. · 2002 [cited by applicant]
US 6521409B1 · Gocke et al. · 2003 [cited by applicant]
US 6524456B1 · Ramsey et al. · 2003 [cited by applicant]
US 6565727B1 · Shenderov · 2003 [cited by applicant]
US 6582919B2 · Danenberg · 2003 [cited by applicant]
US 6586177B1 · Shuber · 2003 [cited by applicant]
US 6759217B2 · Kopreski et al. · 2004 [cited by applicant]
US 6773566B2 · Shenderov · 2004 [cited by applicant]
US 6812018B2 · Wicher et al. · 2004 [cited by applicant]
US 6818425B2 · Hjorleifsdottir et al. · 2004 [cited by applicant]
US 6849403B1 · Shuber · 2005 [cited by applicant]
US 6858394B1 · Chee et al. · 2005 [cited by applicant]
US 6911132B2 · Pamula et al. · 2005 [cited by applicant]
US 6949342B2 · Golub et al. · 2005 [cited by applicant]
US 7041481B2 · Anderson et al. · 2006 [cited by applicant]
US 7056673B2 · Kamme et al. · 2006 [cited by applicant]
US 7105293B2 · Ramaswamy et al. · 2006 [cited by applicant]
US 7115400B1 · Adessi et al. · 2006 [cited by applicant]
US 7129040B2 · Steck et al. · 2006 [cited by applicant]
US 7138226B2 · Vincek et al. · 2006 [cited by applicant]
US 7141377B2 · Gelfand et al. · 2006 [cited by applicant]
US 7153658B2 · Andersen et al. · 2006 [cited by applicant]
US 7208275B2 · Gocke et al. · 2007 [cited by applicant]
US 7211390B2 · Rothberg et al. · 2007 [cited by applicant]
US 7217795B2 · Steck et al. · 2007 [cited by applicant]
US 7223833B1 · Nielsen et al. · 2007 [cited by applicant]
US 7232653B1 · Austrup et al. · 2007 [cited by applicant]
US 7232656B2 · Balasubramanian et al. · 2007 [cited by applicant]
US 7244559B2 · Rothberg et al. · 2007 [cited by applicant]
US 7264929B2 · Rothberg et al. · 2007 [cited by applicant]
US 7268167B2 · Higuchi et al. · 2007 [cited by applicant]
US 7294468B2 · Bell et al. · 2007 [cited by applicant]
US 7303901B2 · Hjorleifsdottir et al. · 2007 [cited by applicant]
US 7323305B2 · Leamon et al. · 2008 [cited by applicant]
US 7324926B2 · Tamayo et al. · 2008 [cited by applicant]
US 7329495B2 · Chen et al. · 2008 [cited by applicant]
US 7332288B2 · Terstappen et al. · 2008 [cited by applicant]
US 7375140B2 · Higuchi et al. · 2008 [cited by applicant]
US 7381818B2 · Lokhov et al. · 2008 [cited by applicant]
US 7410764B2 · Gocke et al. · 2008 [cited by applicant]
US 7442507B2 · Polsky et al. · 2008 [cited by applicant]
US 7445900B2 · Gelfand et al. · 2008 [cited by applicant]
US 7485442B2 · Afonina et al. · 2009 [cited by applicant]
US 7582739B2 · Lukhtanov et al. · 2009 [cited by applicant]
US 7601821B2 · Andersen et al. · 2009 [cited by applicant]
US 7622281B2 · Ronaghi et al. · 2009 [cited by applicant]
US 7638276B2 · Griffiths et al. · 2009 [cited by applicant]
US 7662553B2 · Lenz · 2010 [cited by applicant]
US 7666593B2 · Lapidus · 2010 [cited by applicant]
US 7700283B2 · Evans et al. · 2010 [cited by applicant]
US 7700286B2 · Stroun et al. · 2010 [cited by applicant]
US 7700323B2 · Willis et al. · 2010 [cited by applicant]
US 7717615B2 · Higuchi et al. · 2010 [cited by applicant]
US 7732576B2 · Steck et al. · 2010 [cited by applicant]
US 7745128B2 · Guo et al. · 2010 [cited by applicant]
US 7772287B2 · Higuchi et al. · 2010 [cited by applicant]
US RE41780E · Anderson et al. · 2010 [cited by applicant]
US 7842248B2 · McAvoy et al. · 2010 [cited by applicant]
US 7908091B2 · Harvey et al. · 2011 [cited by applicant]
US 7932026B2 · Seshagiri · 2011 [cited by applicant]
US 7935487B2 · Gocke et al. · 2011 [cited by applicant]
US 7947819B2 · Stratton et al. · 2011 [cited by applicant]
US 7948015B2 · Rothberg et al. · 2011 [cited by applicant]
US 7981618B2 · Yu et al. · 2011 [cited by applicant]
US 7993842B2 · Mckernan et al. · 2011 [cited by applicant]
US 8067159B2 · Brown et al. · 2011 [cited by applicant]
US 8198028B2 · Rigatti et al. · 2012 [cited by applicant]
US 8252539B2 · Quake et al. · 2012 [cited by applicant]
US 8278071B2 · Brown et al. · 2012 [cited by applicant]
US 8349276B2 · Pamula et al. · 2013 [cited by applicant]
US 8349563B2 · Lao et al. · 2013 [cited by applicant]
US 8399192B2 · Rigatti et al. · 2013 [cited by applicant]
US 8583380B2 · Stephan et al. · 2013 [cited by applicant]
US 8834873B2 · Petricoin, III et al. · 2014 [cited by applicant]
US 9090648B2 · Behr et al. · 2015 [cited by applicant]
US 9217167B2 · Heller et al. · 2015 [cited by applicant]
US 9255291B2 · Toloue et al. · 2016 [cited by applicant]
US 9309556B2 · Myllykangas et al. · 2016 [cited by applicant]
US 9340830B2 · Lipson et al. · 2016 [cited by applicant]
US 9650628B2 · Amorese et al. · 2017 [cited by applicant]
US 10072287B2 · Zhou et al. · 2018 [cited by applicant]
US 11965211B2 · Stephan · 2024 [cited by examiner]
US 20010034023A1 · Stanton et al. · 2001 [cited by applicant]
US 20020012921A1 · Stanton · 2002 [cited by applicant]
US 20020048755A1 · Cohen · 2002 [cited by applicant]
US 20020115073A1 · Papadopoulos et al. · 2002 [cited by applicant]
US 20020120409A1 · Cao et al. · 2002 [cited by applicant]
US 20030082543A1 · Su et al. · 2003 [cited by applicant]
US 20030093819A1 · D'Andrea et al. · 2003 [cited by applicant]
US 20030143600A1 · Gocke et al. · 2003 [cited by applicant]
US 20030165940A1 · Traverso et al. · 2003 [cited by applicant]
US 20030211530A1 · Danenberg · 2003 [cited by applicant]
US 20030224385A1 · Pihan · 2003 [cited by applicant]
US 20030224439A1 · Lafferty et al. · 2003 [cited by applicant]
US 20040110193A1 · Castle et al. · 2004 [cited by applicant]
US 20040137539A1 · Bradford · 2004 [cited by applicant]
US 20050019785A1 · Baker et al. · 2005 [cited by applicant]
US 20050021240A1 · Berlin et al. · 2005 [cited by applicant]
US 20050153317A1 · Denise et al. · 2005 [cited by applicant]
US 20050181377A1 · Markovic · 2005 [cited by applicant]
US 20050186584A1 · Stratton et al. · 2005 [cited by applicant]
US 20050191656A1 · Drmanac et al. · 2005 [cited by applicant]
US 20050246314A1 · Eder et al. · 2005 [cited by applicant]
US 20050260646A1 · Baker et al. · 2005 [cited by applicant]
US 20050272083A1 · Seshagiri · 2005 [cited by applicant]
US 20050287543A1 · Yu et al. · 2005 [cited by applicant]
US 20060008824A1 · Ronaghi et al. · 2006 [cited by applicant]
US 20060008834A1 · Margus et al. · 2006 [cited by applicant]
US 20060024721A1 · Pedersen · 2006 [cited by applicant]
US 20060046258A1 · Lapidus et al. · 2006 [cited by applicant]
US 20060068406A1 · Affholter et al. · 2006 [cited by applicant]
US 20060134674A1 · Huang et al. · 2006 [cited by applicant]
US 20060184489A1 · Weiner et al. · 2006 [cited by applicant]
US 20060188909A1 · Willey et al. · 2006 [cited by applicant]
US 20060195269A1 · Yeatman et al. · 2006 [cited by applicant]
US 20060254933A1 · Adachi et al. · 2006 [cited by applicant]
US 20060278241A1 · Ruano · 2006 [cited by applicant]
US 20070042369A1 · Reese et al. · 2007 [cited by applicant]
US 20070054333A1 · Steck et al. · 2007 [cited by applicant]
US 20070065846A1 · Baker et al. · 2007 [cited by applicant]
US 20070071762A1 · Ts'O et al. · 2007 [cited by applicant]
US 20070087394A1 · Siena et al. · 2007 [cited by applicant]
US 20070092902A1 · Di et al. · 2007 [cited by applicant]
US 20070117121A1 · Hutchison et al. · 2007 [cited by applicant]
US 20070141067A1 · Markovic · 2007 [cited by applicant]
US 20070253951A1 · Ng et al. · 2007 [cited by applicant]
US 20070254295A1 · Harvey et al. · 2007 [cited by applicant]
US 20070269817A1 · Shapero · 2007 [cited by applicant]
US 20080014146A1 · Von Hoff et al. · 2008 [cited by applicant]
US 20080044813A1 · Jansson et al. · 2008 [cited by applicant]
US 20080065411A1 · Keeling et al. · 2008 [cited by applicant]
US 20080090239A1 · Shoemaker et al. · 2008 [cited by applicant]
US 20080090244A1 · Knapp et al. · 2008 [cited by applicant]
US 20080124721A1 · Fuchs et al. · 2008 [cited by applicant]
US 20080131887A1 · Stephan et al. · 2008 [cited by applicant]
US 20080138805A1 · Condeelis · 2008 [cited by applicant]
US 20080160580A1 · Adessi et al. · 2008 [cited by applicant]
US 20080161420A1 · Shuber · 2008 [cited by applicant]
US 20080176209A1 · Muller et al. · 2008 [cited by applicant]
US 20080177608A1 · Keeling · 2008 [cited by applicant]
US 20080207615A1 · Bell et al. · 2008 [cited by applicant]
US 20080213774A1 · Chen et al. · 2008 [cited by applicant]
US 20080242622A1 · Lowe et al. · 2008 [cited by applicant]
US 20080255243A1 · Petricoin et al. · 2008 [cited by applicant]
US 20080262062A1 · Ossovskaya et al. · 2008 [cited by applicant]
US 20080268449A1 · Hoon · 2008 [cited by applicant]
US 20080286795A1 · Kawashima et al. · 2008 [cited by applicant]
US 20080293055A1 · Freeman et al. · 2008 [cited by applicant]
US 20090002608A1 · Kameyama et al. · 2009 [cited by applicant]
US 20090010508A1 · Inoue et al. · 2009 [cited by applicant]
US 20090026082A1 · Rothberg et al. · 2009 [cited by applicant]
US 20090029377A1 · Lo et al. · 2009 [cited by applicant]
US 20090035777A1 · Kokoris et al. · 2009 [cited by applicant]
US 20090035792A1 · Singh et al. · 2009 [cited by applicant]
US 20090062138A1 · Curry et al. · 2009 [cited by applicant]
US 20090075267A1 · Siena et al. · 2009 [cited by applicant]
US 20090081674A1 · Li et al. · 2009 [cited by applicant]
US 20090105081A1 · Rodesch et al. · 2009 [cited by applicant]
US 20090117573A1 · Fu et al. · 2009 [cited by applicant]
US 20090117621A1 · Boutell et al. · 2009 [cited by applicant]
US 20090124514A1 · Fu et al. · 2009 [cited by applicant]
US 20090138286A1 · Linder et al. · 2009 [cited by applicant]
US 20090181861A1 · Li et al. · 2009 [cited by applicant]
US 20090186065A1 · Tillman et al. · 2009 [cited by applicant]
US 20090202984A1 · Cantor · 2009 [cited by applicant]
US 20090202989A1 · Hillan · 2009 [cited by applicant]
US 20090226925A1 · Grebe et al. · 2009 [cited by applicant]
US 20090226975A1 · Sabot et al. · 2009 [cited by applicant]
US 20090247415A1 · Van · 2009 [cited by applicant]
US 20090258795A1 · Cowens et al. · 2009 [cited by applicant]
US 20090264298A1 · Lim et al. · 2009 [cited by applicant]
US 20090269344A1 · Siena et al. · 2009 [cited by applicant]
US 20090299645A1 · Colby et al. · 2009 [cited by applicant]
US 20100004253A1 · Aziz et al. · 2010 [cited by applicant]
US 20100029498A1 · Gnirke et al. · 2010 [cited by applicant]
US 20100041048A1 · Diehl et al. · 2010 [cited by applicant]
US 20100069250A1 · White, III et al. · 2010 [cited by applicant]
US 20100074895A1 · Petricoin, III et al. · 2010 [cited by applicant]
US 20100093550A1 · Stuelpnagel et al. · 2010 [cited by applicant]
US 20100129799A1 · Guomundsson et al. · 2010 [cited by applicant]
US 20100129896A1 · Knapp et al. · 2010 [cited by applicant]
US 20100130527A1 · Lehrer et al. · 2010 [cited by applicant]
US 20100137143A1 · Rothberg et al. · 2010 [cited by applicant]
US 20100143932A1 · Lapidus · 2010 [cited by applicant]
US 20100143935A1 · Davis · 2010 [cited by applicant]
US 20100166747A1 · Beltran et al. · 2010 [cited by applicant]
US 20100167954A1 · Earnshaw et al. · 2010 [cited by applicant]
US 20100173294A1 · Langland et al. · 2010 [cited by applicant]
US 20100184099A1 · Pestano et al. · 2010 [cited by applicant]
US 20100184618A1 · Namsaraev et al. · 2010 [cited by applicant]
US 20100196889A1 · Bankaitis-Davis et al. · 2010 [cited by applicant]
US 20100196898A1 · Sugarbaker et al. · 2010 [cited by applicant]
US 20100216153A1 · Lapidus et al. · 2010 [cited by applicant]
US 20100255004A1 · Depinho et al. · 2010 [cited by applicant]
US 20100286143A1 · Dias-Santagata et al. · 2010 [cited by applicant]
US 20100297615A1 · Seshagiri · 2010 [cited by applicant]
US 20100304446A1 · Davies et al. · 2010 [cited by applicant]
US 20100304989A1 · Von Hoff et al. · 2010 [cited by applicant]
US 20110004413A1 · Carnevali et al. · 2011 [cited by applicant]
US 20110053157A1 · Skog et al. · 2011 [cited by applicant]
US 20110091880A1 · Rafnar et al. · 2011 [cited by applicant]
US 20110157322A1 · Bennett et al. · 2011 [cited by applicant]
US 20110159499A1 · Hindson et al. · 2011 [cited by applicant]
US 20110212456A1 · Siena et al. · 2011 [cited by applicant]
US 20110212991A1 · Langland et al. · 2011 [cited by applicant]
US 20110217710A9 · Shapero · 2011 [cited by applicant]
US 20110230360A1 · Stephan et al. · 2011 [cited by applicant]
US 20110244455A1 · Larson et al. · 2011 [cited by applicant]
US 20110275097A9 · Singh et al. · 2011 [cited by applicant]
US 20110299645A1 · Kim et al. · 2011 [cited by applicant]
US 20120003657A1 · Myllykangas et al. · 2012 [cited by applicant]
US 20120028814A1 · Toloue et al. · 2012 [cited by applicant]
US 20120115143A1 · Livak et al. · 2012 [cited by applicant]
US 20120156728A1 · Li et al. · 2012 [cited by applicant]
US 20120157322A1 · Myllykangas et al. · 2012 [cited by applicant]
US 20120208706A1 · Downing et al. · 2012 [cited by applicant]
US 20120264129A1 · Freeman et al. · 2012 [cited by applicant]
US 20130045872A1 · Zhou et al. · 2013 [cited by applicant]
US 20130143276A1 · Zhelkovsky et al. · 2013 [cited by applicant]
US 20130231253A1 · Amorese et al. · 2013 [cited by applicant]
US 20140080733A1 · Stephan et al. · 2014 [cited by applicant]
US 20140141426A1 · Stephan et al. · 2014 [cited by applicant]
US 20140141980A1 · Stephan et al. · 2014 [cited by applicant]
US 20140172319A1 · Von Hoff et al. · 2014 [cited by applicant]
US 20140193860A1 · Bevilacqua et al. · 2014 [cited by applicant]
US 20140287937A1 · So et al. · 2014 [cited by applicant]
US 20140303008A1 · Schutz et al. · 2014 [cited by applicant]
US 20150017635A1 · Myllykangas et al. · 2015 [cited by applicant]
US 20150031086A1 · Heller et al. · 2015 [cited by applicant]
US 20150126377A1 · Gnirke et al. · 2015 [cited by applicant]
US 20150284714A1 · Gormley et al. · 2015 [cited by applicant]
US 20160115553A1 · Stephan et al. · 2016 [cited by applicant]
US 20160115554A1 · Stephan et al. · 2016 [cited by applicant]
US 20160122830A1 · Stephan et al. · 2016 [cited by applicant]
US 20160186267A1 · So et al. · 2016 [cited by applicant]
US 20160222427A1 · So et al. · 2016 [cited by applicant]
US 20160281154A1 · So et al. · 2016 [cited by applicant]
US 20160362749A1 · Stephan et al. · 2016 [cited by applicant]
US 20170101674A1 · So et al. · 2017 [cited by applicant]
US 20180148756A1 · So et al. · 2018 [cited by applicant]
US 20190271044A1 · Stephan et al. · 2019 [cited by applicant]
US 20230357864A1 · Stephan et al. · 2023 [cited by applicant]
EP 0799897A1 · 1997 [cited by applicant]
EP 1207209A2 · 2002 [cited by applicant]
EP 1394272B1 · 2006 [cited by applicant]
EP 1546313B1 · 2008 [cited by applicant]
EP 1995330A1 · 2008 [cited by applicant]
EP 1573316B1 · 2009 [cited by applicant]
EP 0972024B1 · 2011 [cited by applicant]
EP 2318552A2 · 2011 [cited by applicant]
EP 1591541B1 · 2012 [cited by applicant]
EP 2481815A1 · 2012 [cited by applicant]
EP 2396430B1 · 2013 [cited by applicant]
EP 2610352B1 · 2014 [cited by applicant]
EP 2376659B1 · 2015 [cited by applicant]
JP 2002503954A · 2002 [cited by applicant]
JP 2003501071A · 2003 [cited by applicant]
JP 2010041985A · 2010 [cited by applicant]
WO WO9015065A1 · 1990 [cited by applicant]
WO WO9322456A1 · 1993 [cited by applicant]
WO WO9914226A2 · 1999 [cited by applicant]
WO WO0175160A1 · 2001 [cited by applicant]
WO WO2004062483A2 · 2004 [cited by applicant]
WO WO2004111603A2 · 2004 [cited by applicant]
WO WO2005049849A2 · 2005 [cited by applicant]
WO WO2004111603A3 · 2005 [cited by applicant]
WO WO2005085473A2 · 2005 [cited by applicant]
WO WO2005094357A2 · 2005 [cited by applicant]
WO WO2005108583A1 · 2005 [cited by applicant]
WO WO2006012361A2 · 2006 [cited by applicant]
WO WO2005085473A3 · 2006 [cited by applicant]
WO WO2006047787A2 · 2006 [cited by applicant]
WO WO2004062483A3 · 2006 [cited by applicant]
WO WO2006108627A1 · 2006 [cited by applicant]
WO WO2006128463A2 · 2006 [cited by applicant]
WO WO2006128463A3 · 2007 [cited by applicant]
WO WO2007038792A2 · 2007 [cited by applicant]
WO WO2007050465A2 · 2007 [cited by applicant]
WO WO2007091228A1 · 2007 [cited by applicant]
WO WO2007091230A1 · 2007 [cited by applicant]
WO WO2007100243A1 · 2007 [cited by applicant]
WO WO2007106432A2 · 2007 [cited by applicant]
WO WO2007050465A3 · 2007 [cited by applicant]
WO WO2007038792A3 · 2007 [cited by applicant]
WO WO2008038259A1 · 2008 [cited by applicant]
WO WO2008076406A2 · 2008 [cited by applicant]
WO WO2005094357A3 · 2008 [cited by applicant]
WO WO2008147879A1 · 2008 [cited by applicant]
WO WO2008157220A1 · 2008 [cited by applicant]
WO WO2009004335A1 · 2009 [cited by applicant]
WO WO2009038853A2 · 2009 [cited by applicant]
WO WO2009046445A1 · 2009 [cited by applicant]
WO WO2009102957A2 · 2009 [cited by applicant]
WO WO2009108637A1 · 2009 [cited by applicant]
WO WO2009114836A1 · 2009 [cited by applicant]
WO WO2010028288A2 · 2010 [cited by applicant]
WO WO2010036352A1 · 2010 [cited by applicant]
WO WO2010045318A2 · 2010 [cited by applicant]
WO WO2010045318A3 · 2010 [cited by applicant]
WO WO2010094040A1 · 2010 [cited by applicant]
WO WO2011025477A1 · 2011 [cited by applicant]
WO WO2011106314A2 · 2011 [cited by applicant]
WO WO2011140510A2 · 2011 [cited by applicant]
WO WO2012018638A2 · 2012 [cited by applicant]
WO WO2012103154A1 · 2012 [cited by applicant]
WO WO2012142213A2 · 2012 [cited by applicant]
WO WO2013036810A1 · 2013 [cited by applicant]
WO WO2013066641A1 · 2013 [cited by applicant]
WO WO2013112923A1 · 2013 [cited by applicant]
WO WO2013113012A2 · 2013 [cited by applicant]
WO WO2013119690A1 · 2013 [cited by applicant]
WO WO2013173472A1 · 2013 [cited by applicant]
WO WO2013190441A2 · 2013 [cited by applicant]
WO WO2014130890A1 · 2014 [cited by applicant]
WO WO2015089333A1 · 2015 [cited by applicant]
WO WO2017139492A1 · 2017 [cited by applicant]
Longley et al., “Classes of c-KIT activating mutations: proposed mechanisms of action and implications for disease classification and therapy” 25 Leukemia Research 571-576 (Year: 2001). [cited by examiner]
Krypuy et al., “High resolution melting analysis for the rapid and sensitive detection of mutations in clinical samples: KRAS codon 12 and 13 mutations in non-small cell lung cancer” 6 BMC Cancer 295 1-12 (Year: 2006). [cited by examiner]
Samowitz et al. “Poor Survival Associated with the BRAF V600E Mutation in Microsatellite-Stable Colon Cancers” 65(14) Cancer Research 6063-6070 (Year: 2006). [cited by examiner]
Gryfe et al., “Tumor Microsatellite Instability and Clinical Outcome In Young Patients With Colorectal Cancer” 342(2) The New England Journal of Medicine 69-77 (Year: 2000). [cited by examiner]
Hirsch et al., “Combination of EGFR gene copy number and protein expression predicts outcome for advanced non-small-cell lung cancer patients treated with gefitinib” 18 Annals of Oncology 752-760 (Year: 2007). [cited by examiner]
Co-pending U.S. Appl. No. 18/356,900, inventors Stephan; Dietrich et al., filed on Jul. 21, 2023. [cited by applicant]
Lips et al., “Reliable High-Throughput Genotyping and Loss-of-Heterozygosity Detection inf Formalin-Fixed, Paraffn-Embedded Tumors Using single Nucleotide Polyorphism Arrays” Cancer Research, 65(22): 2005; 10188-10891. [cited by applicant]
U.S. Appl. No. 15/183,655 Office Action dated Apr. 6, 2018. [cited by applicant]
U.S. Appl. No. 16/154,307 Office Action dated Feb. 24, 2023. [cited by applicant]
U.S. Appl. No. 16/154,307 Office Action dated Jul. 20, 2022. [cited by applicant]
Agrawal, et al. Tetrahedron Letters. 1990; vol. 31: 1543-1546. [cited by applicant]
Alazzouzi, et al. SMAD4 as a prognostic marker in colorectal cancer. Clin Cancer Res. Apr. 1, 2005;11(7):2606-11. [cited by applicant]
Albert, et al. Direct selection of human genomic loci by microarray hybridization. Nature Methods (2007), 4 (11):903-5. [cited by applicant]
Alizadeh, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. Feb. 3, 2000;403(6769):503-11. [cited by applicant]
Altschul, et al. Basic local alignment search tool. Journal of molecular biology. 1990; vol. 215. No. 3: 403-410. [cited by applicant]
Anker, et al. K-ras mutations are found in DNA extracted from the plasma of patients with colorectal cancer. Gastroenterology. Apr. 1997;112(4):1114-20. [cited by applicant]
Applied Biosystems: Designing TaqMan® MGB Probe and Primer Sets for Allelic Discrimination Assays Using Primer Express® Software Version 2.0 (2002). [cited by applicant]
Arber, et al. Celecoxib for the prevention of colorectal adenomatous polyps. N Engl J Med. Aug. 31, 2006;355(9):885-95. [cited by applicant]
Aureon Laboratories. Available at http://www.aureon.com. Accessed Feb. 5, 2009. [cited by applicant]
Bashiardes, et al. Direct genomic selection. Nat Methods. Jan. 2005;2(1):63-9. [cited by applicant]
Bazan, et al. Specific codon 13 K-ras mutations are predictive of clinical outcome in colorectal cancer patients, whereas codon 12 K-ras mutations are associated with mucinous histotype. Ann Oncol. Sep. 2002;13(9):1438-… [cited by applicant]
Beaucage, et al. Tetrahedron Lett. 1981; vol. 22: 1859-1862. [cited by applicant]
Beck; et al., Profile of the circulating DNA in apparently healthy individuals. Clin Chem. Apr. 2009;55(4):730-8. doi: 10.1373/clinchem.2008.113597. Epub Jan. 30, 2009. [cited by applicant]
Belloch, et al. Detection of BRAF V600E mutation in colorectal cancer: comparison of automatic sequencing and real-time chemistry methodology. J Mol Diagn. Nov. 2006;8(5):540-3. [cited by applicant]
Bentley, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. Nov. 6, 2008;456(7218):53-9. doi: 10.1038/nature07517. [cited by applicant]
Bertagnolli, et al. Celecoxib for the prevention of sporadic colorectal adenomas. N Engl J Med. Aug. 31, 2006;355(9):873-84. [cited by applicant]
Bishop; E., Indicators, vol. 1. Pergamon Press, Oxford, 1972. [cited by applicant]
Blondal et al. Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties. Nucleic Acid Research 33(1):135-142 (2005). [cited by applicant]
Braun, et al. Predictive biomarkers of chemotherapy efficacy in colorectal cancer: results from the UK MRC FOCUS trial. Journal of clinical oncology. Jun. 1, 2008; 26(16):2690-2698. [cited by applicant]
Brenner, et al. In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc Natl Acad Sci U S A. Feb. 15, 2000;97(4):1665-70. [cited by applicant]
Brown et al. Chemical synthesis and cloning of a tyrosine tRNA gene. Methods Enzymol. 68:109-51 (1979). [cited by applicant]
Bunzli. Luminescent lanthanide probes as diagnostic and therapeutic tools. Metal Ions in Biological Systems. 2004; 42 ch2:39-75. [cited by applicant]
Campbell, et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet. Jun. 2008;40(6):722-9. Epub Apr. 27, 2008. [cited by applicant]
Cited By (1)
US 12,467,099