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Matched Legal Cases: ['Application No. 2001290868', 'Application No. 2001290868', 'Application No. 2422310', 'Application No. 1970920', 'Application No. 1970920', 'Application No. 1970920', 'Application No. 2731467', 'Application No. 2731467', 'Application No. 2002527319', 'Application No. 2002583932']

Patent US7902343 - Detection of microsatellite instability and its use in diagnosis of tumors - Google PatentsSearch Images Maps Play YouTube News Gmail Drive More »Sign inPatentsMethods and kits are disclosed for use in the analysis of microsatellite instability in genomic DNA. Methods and kits are also disclosed which can be used to detect microsatellite instability DNA present in biological materials, such as tumors. The methods and kits of the present invention can be used...http://www.google.com/patents/US7902343?utm_source=gb-gplus-sharePatent US7902343 - Detection of microsatellite instability and its use in diagnosis of tumorsAdvanced Patent SearchPublication numberUS7902343 B2Publication typeGrantApplication numberUS 12/109,775Publication dateMar 8, 2011Filing dateApr 25, 2008Priority dateSep 15, 2000Fee statusPaidAlso published asCA2422310A1, EP1360322A2, US6844152, US7364853, US20050202473, US20090061438, WO2002022879A2, WO2002022879A3Publication number109775, 12109775, US 7902343 B2, US 7902343B2, US-B2-7902343, US7902343 B2, US7902343B2InventorsJeffery W. Bacher, Laura Flanagan, Nadine NassifOriginal AssigneePromega CorporationExport CitationBiBTeX, EndNote, RefManPatent Citations (40), Non-Patent Citations (150), Referenced by (1), Classifications (12), Legal Events (2) External Links: USPTO, USPTO Assignment, EspacenetDetection of microsatellite instability and its use in diagnosis of tumors
US 7902343 B2Abstract
This application is a divisional of U.S. patent application Ser. No. 11/037,321, filed Jan. 18, 2005, which is a continuation of U.S. patent application Ser. No. 09/663,020, filed Sep. 15, 2000, now U.S. Pat. No. 6,844,152, issued Jan. 18, 2005, which applications are incorporated by reference herein in their entireties.
Each microsatellite locus of normal genomic DNA for most diploid species, such as genomic DNA from mammalian species, consists of two alleles at each locus. The two alleles can be the same or different from one another in length and can vary from one individual to the next. Microsatellite alleles are normally maintained at constant length in a given individual and its descendants; but, instability in the length of microsatellites has been observed in some tumor types (Aaltonen et al., 1993, Science 260:812-815; Thibodeau et al., 1993 Science 260:816-819; Peltomaki et al., 1993 Cancer Research 53:5853-5855; Ionov et al., 1993 Nature 363:558-561). This form of genomic instability in tumors, termed microsatellite instability (hereinafter, “MSI”), is a molecular hallmark of the inherited cancer syndrome Hereditary Nonpolyposis Colorectal Cancer (hereinafter, “HNPCC”). The cause of MSI in HNPCC is thought to be a dysfunctional DNA mismatch repair system that fails to reverse errors that occur during DNA replication (Fishel et al., 1993 Cell 75:1027-38; Leach et al., 1993 Cell 75:215-25; Bronner et al., 1994 Nature 368:258-61; Nicolaides et al., 1994 Nature 371:75-80; Miyaki et al., 1997 Nat Genetics 17:271-2). Insertion or deletion of one or more repetitive units during DNA replication persists without mismatch repair and can be detected as length polymorphisms by comparison of allele sizes found in microsatellite loci amplified from normal and tumor DNA samples (Thibodeau et al, 1993, supra).
The genetic basis of HNPCC is thought to be a germ-line mutation in one of several DNA mismatch repair genes (hereinafter “MMR”) (Leach et al., 1993 Cell 75:1215-1225; Fishel et al., 1993 Cell 75:1027-38; Leach et al., 1993 Cell 75:215-25; Bronner et al., 1994 Nature 368:258-61; Nicolaides et al., 1994 Nature 371:75-80; Miyaki et al., 1997 Nat Genetics 17:271-2; Papadopoulos et al., 1994 Science 263:1625-1629). Among HNPCC patients, 50-60% have been reported to carry inherited mutations in two mismatch repair genes, MSH2 and MLH1 (Kolodner et al., 1999 Cancer Research 59:5068:5074). Moreover, 70-100% of HNPCC cases whose tumors manifest a high frequency MSI (hereinafter “MSI-H”) phenotype reportedly have germ-line mutations in these two genes. Few germ-line mutations in MSH6, MSH3, PMS1 and PMS2 genes have been reported in HNPCC patients, indicating that inherited mutations in these mismatch repair genes play a minor role in HNPCC (Peltomaki et al., 1997 Gastroenterology 113:1146-1158; Liu et al., 1996 Nat Med 2:169-174; Kolodner et al., 1999 Cancer Research 59:5068-5074). Without functional repair proteins, errors that occur during replication are not repaired leading to high mutation rates and increased likelihood of tumor development.
Microsatellite multiplex systems have been primarily developed for use in genotyping, mapping studies and DNA typing applications. These multiplex systems are designed to allow co-amplification of multiple microsatellite loci in a single reaction, followed by detection of the size of the resulting amplified alleles. For DNA typing analysis, the use of multiple microsatellite loci dramatically increases the matching probability over a single locus. Matching probability is a common statistic used in DNA typing that defines the number of individuals you would have to survey before you would find the same DNA pattern as a randomly selected individual. For example, a four locus multiplex system (GenePrint™ CTTv Multiplex System, Promega) has a matching probability of 1 in 252.4 in African-American populations, compared to an eight locus multiplex system (GenePrint™ PowerPlex™ 1.2 System, Promega) which has a matching probability of 1 in 2.74�108 (Proceedings: American Academy of Forensic Sciences (Feb. 9-14, 1998), Schumm, James W. et al., p. 53, B88; Id. Gibson, Sandra D. et al., p. 53, B89; Id., Lazaruk, Katherine et al., p. 51, B83; Sparkes, R. et al., 1996 Int J Legal Med 109:186-194). Other commercially available multiplex systems for DNA typing include AmpF/STR Profiler™ and AmpF/STR COfiler™(AmpFISTR Profiler™ PCR Amplification Kit User's Manual (1997), i-viii and 1-1 to 1-10; and AmpFISTR COfiler™ PCR Amplification Kit User Bulletin (1998), i-iii and 1-1 to 1-10, both published by Perkin-Elmer Corp). In addition to multiplexes for DNA typing, a few multiplex microsatellite systems have been developed for the detection of diseases, such as cancer. One such system has been developed by Roche Diagnostics, the “HNPCC Microsatellite Instability Test”, in which five MSI loci (BAT25, BAT26, D5S436, D17S250, and D2S123) are co-amplified and analyzed. Additional systems are needed, particularly systems that include additional loci displaying high sensitivity to MSI and low stutter for easy and accuracy of analysis.
Tissues and DNA isolation. Matched normal (blood) and neoplastic tissue samples for 39 patients were obtained from the Cooperative Human Tissue Network (hereinafter, “CHTN”) (Ohio State University, Columbus, Ohio). After surgical resection, tissue samples were frozen in liquid nitrogen and stored at −70� C. Blood samples were collected by venipuncture using vacuum tubes. DNA extraction from blood and solid tissues was performed either by standard Phenol/chloroform method (Sambrook et al., 1989 Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Press, Cold Springs Harbor, N.Y.) or with QIAamp Blood and Tissue Kit (QIAGEN, Santa Clarita, Calif.) following manufactures protocol.
PCR and Microsatellite Analysis. Fluorescently labeled primers from 275 microsatellite loci were used to amplify template DNA from normal/tumor pairs of samples. Two hundred and forty-five tetra-nucleotide repeat markers from the Research Genetics CHLC/Weber Human Screening Set Version 9.0 were evaluated (Research Genetics, Huntsville, Ala.). Additional primer sets for tetra-nucleotide and penta-nucleotide repeat markers were obtained from Promega Corporation (Madison, Wis.) (PowerPlex™ 16 System contains D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX, and FGA loci). Penta-nucleotide repeat markers TP53, Penta A, Penta B, Penta C, Penta D, Penta E, Penta F and Penta G or were custom synthesized (Promega Corporation, Madison, Wis.) using sequence data from public databases Di-nucleotide markers included for comparison purposes (D8S254, NM23, D18S35, D5S346, TP53-di, D2S123, D1S2883, D3S1611, D7S501) were obtained from PE Biosystems (now doing business as Applied Biosystems Group, Foster City, Calif.).
Markers from Research Genetics, Human Screening Set Version 9.0, were multiplexed and screened for MSI using 2.5 ng of DNA in 10 μl PCR reactions described below. Other loci were evaluated as monoplexes using 1 ng DNA in 25 μl PCR reactions as described below. All markers were PCR amplified under the same conditions in using a Perkin-Elmer� GeneAmp PCR System 9600 Thermal Cycler, except as indicated otherwise below. Microsatellite markers from the PowerPlex™ 16 System (Technical Manual #TMD012, Promega Corporation, Madison, Wis.) and dinucleotide repeat markers from the Microsatellite RER Assay system (see product literature from PE Biosystems, non Applied Biosystems, Foster City, Calif.) were analyzed following manufacture's protocol.
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