Claims for Patent: 6,051,379

Summary for Patent: 6,051,379

Title:	Cancer susceptibility mutations of BRCA2
Abstract:	New mutations have been found in the BRCA2 gene. The mutations are located at nucleotide numbers 2192, 3772, 5193, 5374, 6495 or 6909 of the published nucleotide sequence of BRCA2 gene. A process for identifying a sequence variation in a BRCA2 polynucleotide sequence is disclosed. The identification process includes allele specific sequence-based assays of known sequence variations. The methods can be used for efficient, and accurate detection of a mutation in a test BRCA2 gene sample.
Inventor(s):	Lescallett; Jennifer Lee (Great Falls, VA), Lawrence; Tammy (Laurel, MD), Allen; Antonette Preisinger (Severn, MD), Olson; Sheri Jon (Falls Church, VA), Thurber; Denise Bernadette (Silver Spring, MD), White; Marga Belle (Frederick, MD)
Assignee:	Oncormed, Inc. (Gaithersburg, MD)
Application Number:	08/984,034
Patent Litigation and PTAB cases:	See patent lawsuits and PTAB cases for patent 6,051,379
Patent Claims:	1. An isolated oligonucleotide wherein the oligonucleotide is capable of detecting a G at nucleotide number 2192 of a BRCA2 gene by specifically hybridizing to the region containing nucleotide number 2192 of the BRCA2 gene. 2. An isolated oligonucleotide having the sequence 5'TGA AGA ACC AAC TTT GT3', SEQ ID NO:3, or the complementary oligonucleotide thereto. 3. An isolated oligonucleotide according to claim 1 having the sequence 5'TGA AGA ACG AAC TTT GT3', SEQ ID NO:4, or the complementary oligonucleotide thereto. 4. The isolated oligonucleotide wherein the oligonucleotide is capable of detecting a deletion of TT at nucleotide number 3772 of a BRCA2 gene by specifically hybridizing to the region containing nucleotide number 3772 of the BRCA2 gene. 5. An isolated oligonucleotide having the sequence 5'GCA AGC AAT TTG AAG GT3', SEQ ID NO:7, or the complementary oligonucleotide thereto. 6. An isolated oligonucleotide according to claim 4 having the sequence 5'GCA AGC AAT GAA GGT AC3', SEQ ID NO:8, or the complementary oligonucleotide thereto. 7. An isolated oligonucleotide wherein the oligonucleotide is capable of detecting a substitution of G for C at nucleotide number 5193 of a BRCA2 gene by specifically hybridizing to the region containing nucleotide number 5193 of the BRCA2 gene. 8. An isolated oligonucleotide having the sequence 5'ACT TGT TAC ACA AAT CA3', SEQ ID NO:11, or the complementary oligonucleotide thereto. 9. An isolated oligonucleotide according to claim 7 having the sequence 5'ACT TGT TAG ACA AAT CA3', SEQ ID NO:12, or the complementary oligonucleotide thereto. 10. An isolated oligonucleotide according to claim 1 wherein the oligonucleotide is capable of detecting a deletion of TATG at nucleotide number 5374 of a BRCA2 gene by specifically hybridizing to the region containing nucleotide number 5374 of the BRCA2 gene. 11. An isolated oligonucleotide having the sequence 5'ATT ATT TGT ATG AAA AT3', SEQ ID NO:15, or the complementary oligonucleotide thereto. 12. An isolated oligonucleotide according to claim 10 having the sequence 5'ATT ATT TGA AAA TAA TT3', SEQ ID NO:16, or the complementary oligonucleotide thereto. 13. An isolated oligonucleotide wherein the oligonucleotide is capable of detecting a deletion of GC at nucleotide number 6495 of a BRCA2 gene by specifically hybridizing to the region containing nucleotide number 6495 of the BRCA2 gene. 14. An isolated oligonucleotide having the sequence 5'GAA CTG AGC ATA GTC TT3', SEQ ID NO:19, or the complementary oligonucleotide thereto. 15. An isolated oligonucleotide according to claim 13 having the sequence 5'GAA CTG AAT AGT CTT CA3', SEQ ID NO:20, or the complementary oligonucleotide thereto. 16. An isolated oligonucleotide wherein the oligonucleotide is capable of detecting an insertion of G at nucleotide number 6909 of a BRCA gene by specifically hybridizing to the region containing nucleotide number 6909 of the BRCA2 gene. 17. An isolated oligonucleotide having the sequence 5'CAG AAG CAG TAG AAA TT3', SEQ ID NO:23, or the complementary oligonucleotide thereto. 18. An isolated oligonucleotide according to claim 16 having the sequence 5'CAG AAG CAG GTA GAA AT3', SEQ ID NO:24, or the complementary oligonucleotide thereto. 19. The isolated oligonucleotide according to any one of claims 1, 4, 7, 10, 13 and 16 further comprising a label bound thereto. 20. The isolated oligonucleotide according to claim 19 wherein the label is selected from the group consisting of a radiolabel, a fluorescent label, a bioluminescent label, a chemiluminescent label, an enzyme label and a ligand label. 21. A pair of isolated oligonucleotide primers which specifically hybridize to the BRCA2 gene, said pair of primers selected from the group consisting of: BRCA-2-11F: 5'TGG TAC TTT AAT TTT GTC ACT T3' (SEQ ID NO:1), and BRCA-2-11R: 5'TGC AGG CAT GAC AGA GAA T3' (SEQ ID NO: 2); BRCA-2-11F: 5'CTC AGA TGT TAT TTT CAA AGC3' (SEQ ID NO: 5); and BRCA-2-11R: 5'CTG TTA AAT AAC CAG AAG CAC3' (SEQ ID NO: 6); BRCA-2-11F: 5'GCA AAG ACC CTA AAG TAC AG3' (SEQ ID NO: 9), and BRCA-2-11R: 5'CAT CAA ATA TTC CTT CTC TAA G3' (SEQ ID NO: 10); BRCA-2-11F: 5'GAA AAT TCA GCC TTA GC3' (SEQ ID NO: 13), and BRCA-2-11R: 5'ATC AGA ATG GTA GGA AT3' (SEQ ID NO: 14); BRCA-2-11F: 5'TAC AGC AAG TGG AAA GC3' (SEQ ID NO: 17), and BRCA-2-11R: 5'AAG TTT CAG TTT TAC CAA T3' (SEQ ID NO: 18); and BRCA-2-11F: 5'ACT TTT TCT GAT GTT CCT GTG3' (SEQ ID NO: 21), and BRCA-2-11R: 5'TAA AAA TAG TGA TTG GCA ACA3' (SEQ ID NO: 22). 22. The pair of isolated oligonucleotide primers according to claim 21, wherein each primer is bound to a label. 23. The pair of primers according to claim 22 wherein each of said label is selected from the group consisting of a radiolabel, a fluorescent label, a bioluminescent label, a chemiluminescent label, an enzyme label and a ligand label. 24. A method for determining the presence or absence of a sequence variation in the BRCA2 gene at nucleotide number 2192, 3772, 5193, 5374, 6495 or 6909 comprising: (a) performing an allele specific detection assay for the presence or absence of one or more of said sequence variations; and (b) determining the presence or absence of a sequence variation in the BRCA2 gene in the BRCA2 gene sample at nucleotide number 2192, 3772, 5193, 5374, 6495 or 6909. 25. The method according to claim 24 wherein the said sequence variation is C2192G, 3772delTT, C5193G, 5374del4, 6495delGC or 6909insG. 26. The method of claim 24 wherein the allele specific detection assay is performed as part of a multiplex amplification assay format. 27. The method of claim 24 wherein the allele specific detection assay is performed using a dot blot format, reverse dot blot format, a MASDA format, or a chip array format. 28. The method according to claim 24 further comprising (a) performing an allele specific detection assay for the presence or absence of one or more reference sequences without said sequence variations. 29. The method according to claim 28 wherein said reference sequence is a BRCA2 coding sequence. 30. The method according to claim 28 wherein said reference sequence is a BRCA2 genomic sequence. 31. The method according to claim 28 wherein said reference sequence is one or more exons of the BRCA2 gene. 32. A method of detecting a predisposition or higher susceptibility to cancer in an individual, comprising: (a) digesting DNA from an individual to obtain DNA fragments; (b) separating said DNA fragments; (c) detecting a DNA fragment containing nucleotide number 2192, 3772, 5193, 5374, 6495 or 6909 of the BRCA2 gene sequence or a sequence variation at nucleotide number 2192, 3772, 5193, 5374, 6495 or 6909 of the BRCA2 gene sequence by sequencing; (d) comparing the sequence of said fragment with the BRCA2 gene sequence to determine the presence or absence of a sequence variation at nucleotide number 2192, 3772, 5193, 5374, 6495 or 6909, wherein the presence of a sequence variation indicates a predisposition or higher susceptibility to cancer. 33. A method according to claim 32 further comprising amplifying said DNA fragments prior to the detecting step (c). 34. A method according to claim 32 wherein the DNA fragment containing the sequence variation is amplified with an oligonucleotide primer having a sequence of: 5'TGG TAC TTT AAT TTT GTC ACT T3' SEQ ID NO:1, 5'TGC AGG CAT GAC AGA GAA T3' SEQ ID NO:2, 5'CTC AGA TGT TAT TTT CCA AGC3' SEQ ID NO:5, 5'CTG TTA AAT AAC CAG AAG CAC3' SEQ ID NO:6, 5'GCA AAG ACC CTA AAG TAC AG3' SEQ ID NO:9, 5'CAT CAA ATA TTC CTT CTC TAA G3' SEQ ID NO:10, 5'GAA AAT TCA GCC TTA GC3' SEQ ID NO:13, 5'ATC AGA ATG GTA GGA AT3' SEQ ID NO:14, 5'TAC AGC AAG TGG AAA GC3' SEQ ID NO:17, 5'AAG TTT CAG TTT TAC CAA T3' SEQ ID NO:18, 5'ACT TTT TCT GAT GTT CCT GTG3' SEQ ID NO:21, 5'TAA AAA TAG TGA TTG GCA ACA3' SEQ ID NO:22 or a sequence capable of specific hybridization to and initiation of DNA synthesis on a complementary oligonucleotide or polynucleotide. 35. A method according to claim 34 wherein said oligonucleotide primer is labeled with a radiolabel, a fluorescent label a bioluminescent label, a chemiluminescent label, an enzyme label, or a ligand label. 36. A method of detecting a predisposition or higher susceptibility to cancer in an individual, comprising: (a) digesting DNA from said individual to obtain DNA fragments, (b) separating said DNA fragments obtained from said digestion, (c) subjecting said DNA fragments to hybridization with an allele specific oligonucleotide having a nucleotide sequence capable of specifically hybridizing to a polynucleotide having a sequence variation at nucleotide number 2192, 3772, 5193, 5374, 6495 or 6909 of the BRCA2 gene sequence, thereby determining the absence or presence of said sequence variation in the BRCA2 gene of said individual, and (d) correlating the presence of said sequence variation with a predisposition or higher susceptibility to cancer. 37. A method according to claim 36 herein said allele specific oligonucleotide is: 5'TGA AGA ACC AAC TTT GT3' SEQ ID NO:3, 5'TGA AGA ACG AAC TTT GT3' SEQ ID NO:4, 5'GCA AGC AAT TTG AAG GT3' SEQ ID NO:7, 5'GCA AGC AAT GAA GGT AC3' SEQ ID NO:8, 5'ACT TGT TAC ACA AAT CA3' SEQ ID NO:11, ' ACT TGT TAG ACA AAT CA3' SEQ ID NO:12, 5'ATT ATT TGT ATG AAA AT3' SEQ ID NO:15, 5'ATT ATT TGA AAA TAA TT3' SEQ ID NO:16, 5'GAA CTG AGC ATA GTC TT3' SEQ ID NO:19, 5'GAA CTG AAT AGT CTT CA3' SEQ ID NO:20, 5'CAG AAG CAG TAG AAA TT3' SEQ ID NO:23, or 5'CAG AAG CAG GTA GAA AT3' SEQ ID NO:24. 38. A method according to claim 36 further comprising amplifying said DNA fragment prior to sequencing. 39. A method according to claim 36 wherein said oligonucleotide is labeled with a radiolabel, a fluorescent label, a bioluminescent label, a chemiluminescent label, an enzyme label, or a ligand label. 40. A kit comprising a carrier means being compartmentalized to receive in close confinement one or more container means, and at least one container means, wherein said at least one container means contains the oligonucleotide of any one of claims 1, 4, 7, 10, 13, 16. 41. The kit according to claim 40 further comprising at least one container means containing: BRCA-2-11F: 5'TGG TAC TTT AAT TTT GTC ACT T3' (SEQ ID NO:1), BRCA-2 11R: 5'TGC AGG CAT GAC AGA GAA T3' (SEQ ID NO: 2), BRCA-2-11F: 5'CTC AGA TGT TAT TTT CAA AGC3' (SEQ ID NO:5), BRCA-2-11R: 5'CTG TTA AAT AAC CAG AAG CAC3' (SEQ ID NO: 6), BRCA-2-11F: 5'GCA AAG ACC CTA AAG TAC AG3' (SEQ ID NO:9), BRCA-2-11R: 5'CAT CAA ATA TTC CTT CTC TAA G3' (SEQ ID NO: 10), BRCA-2-11F: 5'GAA AAT TCA GCC TTA GC3' (SEQ ID NO: 13), BRCA-2-11R: 5'ATC AGA ATG GTA GGA AT3' (SEQ ID NO:14), BRCA-2-11F: 5'TAC AGC AAG TGG AAA GC3' (SEQ ID NO: 17), BRCA-2-11R: 5'AAG TTT CAG TTT TAC CAA T3' (SEQ ID NO:18), BRCA-2-11F: 5'ACT TTT TCT GAT GTT CCT GTG3' (SEQ ID NO: 21), or BRCA-2-11R: 5'TAA AAA TAG TGA TTG GCA ACA3' (SEQ ID NO: 22). 42. The kit according to claim 40 further comprising at least one container means containing a pair of isolated oligonucleotide primers which specifically hybridize to the BRCA2 gene, one of which can effectively hybridize to exon 11 of the BRCA2 gene, and the other can effectively hybridize to either exon 11 or one of the two intron regions flanking exon 11. 43. A kit comprising a carrier means being compartmentalized to receive in close confinement one or more container means, and at least one container means, wherein at least one container means contains the pair of oligonucleotide primers of claim 21. 44. A method of determining whether a C2192G, 3772delTT, C5193G, 5374del4, 6495delGC, or 6909insG mutation is present in a BRCA2 gene comprising sequencing at least a portion of the BRCA2 gene containing either: a sequence complementary to SEQ ID NO:4, SEQ ID NO:8, SEQ ID NO:12, SEQ ID NO:16:, SEQ ID NO:20 or SEQ ID NO:24, or an isolated DNA sequence while in the complement thereof, or at least one mutation from the list: C2192G, 3772delTT, C5193G, 5374del4, 6495delGC or 6909insG.

Details for Patent 6,051,379

Applicant	Tradename	Biologic Ingredient	Dosage Form	BLA	Approval Date	Patent No.	Expiredate
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	For Injection	103132	06/04/1986		2017-09-23
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	For Injection	103132			2017-09-23
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	Injection	103132			2017-09-23