Claims for Patent: 9,165,108

Summary for Patent: 9,165,108

Title:	Probes and methods for determining the presence or absence of genetic segments
Abstract:	A method for determining the presence or absence of a genetic segment of interest, such as an exon, an intron or a promoter, in a DNA-containing sample, and probe sets for use in such methods, including probe sets comprising oligonucleotide probes having nucleotides sequences selected from those of SEQ ID NOS: 1-101.
Inventor(s):	Garcia; David (Derio, ES), Simon; Laureano (Derio, ES), Martinez; Antonio (Derio, ES), Ochoa; Jorge (Derio, ES), Tejedor; Diego (Derio, ES), Lopez; Monica (Derio, ES)
Assignee:	Progenika Biopharma, S.A. (Derio, ES)
Application Number:	13/161,779
Patent Claims:	1. A method for determining the presence or absence of a genetic segment of interest in a DNA-containing sample, the method comprising: (i) bringing at least a first probe set comprising a plurality of replicates of at least one oligonucleotide probe that interrogates a first cognate sequence within said segment of interest into contact with (a) a plurality of reference samples in which the genetic segment of interest is absent, and (b) a plurality of reference samples in which the genetic segment of interest is present, under conditions that allow probe-cognate sequence hybridisation to occur; (ii) measuring the intensity of probe-sample hybridisation of each of the reference samples, thereby obtaining a first cluster of hybridisation intensity values for the reference samples in which the genetic segment of interest is absent and a second cluster of hybridisation intensity values for the reference samples in which the genetic segment of interest is present; and (iii) establishing a "no call" region of hybridisation intensity values that lies in the region between said first and second clusters and which is bounded by a lower no call boundary ("LNC") and an upper no call boundary ("UNC"), wherein the LNC and UNC represent statistical confidence limits for assigning a hybridisation intensity value to said first and said second clusters, respectively; iv) contacting the first probe set with at least one DNA-containing test sample under conditions that allow probe-cognate sequence hybridisation to occur; v) measuring the intensity of probe-sample hybridisation of the at least one test sample; and vi) comparing the measured hybridisation intensity with the LNC and the UNC, wherein a measured hybridisation intensity below the LNC indicates that said genetic segment of interest is absent in the test sample and a measured hybridisation intensity above UNC indicates that said genetic segment of interest is present in the test sample; wherein: the DNA of the reference samples and/or the test sample has been labelled with a fluorescent label and wherein measuring hybridisation intensity comprises measuring the fluorescence signal of the fluorescent label at each oligonucleotide probe location; the hybridisation intensity for each probe set is measured as I/B, where: I is determined as a measure of central tendency of the measured fluorescence signal of the replicates of each oligonucleotide probe; and B is determined as a measure of central tendency of the background fluorescence signal of the replicates of each oligonucleotide probe; and the LNC and UNC values are calculated according to the following formulae: .function..times..times..function..times..times. ##EQU00011## .times..times..function..function..times..times. ##EQU00011.2## .times. ##EQU00011.3## .times..times..function..times..times..function..times..times..function..- times..times..function. ##EQU00011.4## aMedianI/B is a measure of central tendency of the measured I/B values of the reference samples in which the genetic segment of interest is absent; pMedianI/B is a measure of central tendency of the measured I/B values of the reference samples in which the genetic segment of interest is present; a(I/B)n is the greatest measured I/B value of the reference samples in which the genetic segment of interest is absent; and p(I/B)1 is the lowest measured I/B value of the reference samples in which the genetic segment of interest is present. 2. A method according to claim 1, wherein said genetic segment of interest is selected from the group consisting of: an exon, an intron and a promoter. 3. A method according to claim 1, wherein at least a second probe set is employed in addition to said first probe set and wherein the second probe set comprises a plurality of replicates of at least one oligonucleotide probe that interrogates a second cognate sequence within said segment of interest, the method further comprising establishing a second no call region bounded by LNC and UNC boundaries for the second probe set. 4. A method according to claim 3, wherein the test sample is classified as having or not having said segment of interest based on a strict consensus between the determinations of the first and second probe sets. 5. A method according to claim 4, wherein said strict consensus is a strict consensus as set forth in Table 1. 6. A method according to claim 3, wherein the test sample is classified as having or not having said segment of interest based on a majority consensus between the determinations of the first and second probe sets in the absence of contradictory determinations. 7. A method according to claim 6, wherein said majority consensus is a majority consensus as set forth in Table 2. 8. A method according to claim 1, wherein the oligonucleotide probes are attached to a solid support. 9. A method according to claim 8, wherein the oligonucleotide probes are attached to a substantially planar solid support in the form of an array. 10. A method according to claim 8, wherein the oligonucleotide probes are attached to one or more particles. 11. A method according to claim 10, wherein said particles are selected from the group consisting of: micrometer-sized beads, nanometer-sized beads and cylinders. 12. A method according to claim 1, wherein said test sample comprises DNA amplified from genomic DNA of a test subject, which DNA has been fragmented and/or labelled with a detectable label. 13. A method according to claim 1, wherein each of the reference samples comprises DNA amplified from genomic DNA of a reference subject, which has been fragmented and/or labelled with a detectable label. 14. A method according to claim 1, wherein the measure of central tendency is selected from the group consisting of: the mean and the median. 15. A method according to claim 1, wherein said measured fluorescence signal is determined after trimming extreme readings. 16. A method according to claim 1, wherein said background fluorescence signal is determined after trimming extreme readings. 17. A method according to claim 1, wherein the genetic segment of interest comprises an exon of the human RHD gene. 18. A method according claim 17, wherein the oligonucleotide probes are selected from the probes shown in Table 4. 19. A method according to claim 18, wherein the method further comprises genotyping the test sample to identify at least one allele at a site of single nucleotide polymorphism ("SNP") in the human RHD gene. 20. A method for selecting at least one optimal probe set, the method comprising: (i) providing a plurality of candidate probe sets, each candidate probe set comprising a plurality of replicates of at least one oligonucleotide probe that interrogates a cognate sequence within a genetic segment of interest; (ii) bringing each of the candidate probe sets into contact with (a) a plurality of reference samples in which the genetic segment of interest is absent, and (b) a plurality of reference samples in which the genetic segment of interest is present, under conditions that allow probe-cognate sequence hybridisation to occur; (iii) measuring the intensity of probe-sample hybridisation of each of the reference samples, thereby obtaining for each candidate probe set a first cluster of hybridisation intensity values for the reference samples in which the genetic segment of interest is absent and a second cluster of hybridisation intensity values for the reference samples in which the genetic segment of interest is present; and (iv) scoring each of the candidate probe sets by dividing a measure of the interval between the first and second clusters by the sum of a measure of central tendency of the first and second clusters, thereby obtaining a probe set score for each of the candidate probe sets, wherein a higher probe set score indicates that the candidate probe set is more likely to be optimal for determining the presence or absence of the genetic segment of interest, wherein the reference samples are labelled with a fluorescent label and wherein the hybridisation intensity is measured as I/B, where: I is determined as a measure of central tendency of the measured fluorescence signal of the replicates of each oligonucleotide probe and B is determined as a measure of central tendency of the background fluorescence signal of the replicates of each oligonucleotide probe and wherein the probe set score (S) for each candidate probe set is calculated according to the following formulae: .function..function..times..times..times..times. ##EQU00012## where: aMedianI/B is a measure of central tendency of the measured I/B values of the reference samples in which the genetic segment of interest is absent; pMedianI/B is a measure of central tendency of the measured I/B values of the reference samples in which the genetic segment of interest is present; a(I/B)n is the greatest measured I/B value of the reference samples in which the genetic segment of interest is absent; and p(I/B)1 is the lowest measured I/B value of the reference samples in which the genetic segment of interest is present. 21. A method according to claim 1, wherein at least said first probe set is a probe set that has been selected using a method which comprises the following steps: (i) providing a plurality of candidate probe sets, each candidate probe set comprising a plurality of replicates of at least one oligonucleotide probe that interrogates a cognate sequence within a genetic segment of interest; (ii) bringing each of the candidate probe sets into contact with (a) a plurality of reference samples in which the genetic segment of interest is absent, and (b) a plurality of reference samples in which the genetic segment of interest is present, under conditions that allow probe-cognate sequence hybridisation to occur; (iii) measuring the intensity of probe-sample hybridisation of each of the reference samples, thereby obtaining for each candidate probe set a first cluster of hybridisation intensity values for the reference samples in which the genetic segment of interest is absent and a second cluster of hybridisation intensity values for the reference samples in which the genetic segment of interest is present; and (iv) scoring each of the candidate probe sets by dividing a measure of the interval between the first and second clusters by the sum of a measure of central tendency of the first and second clusters, thereby obtaining a probe set score for each of the candidate probe sets, wherein a higher probe set score indicates that the candidate probe set is more likely to be optimal for determining the presence or absence of the genetic segment of interest. 22. A method for determining a lower no call boundary ("LNC") and an upper no call boundary ("UNC") for at least a first probe set, the method comprising: (i) bringing at least said first probe set comprising a plurality of replicates of at least one oligonucleotide probe that interrogates a first cognate sequence within a genetic segment of interest into contact with (a) a plurality of reference samples in which the genetic segment of interest is absent, and (b) a plurality of reference samples in which the genetic segment of interest is present; (ii) measuring the intensity of probe-sample hybridisation of each of the reference samples, thereby obtaining a first cluster of hybridisation intensity values for the reference samples in which the genetic segment of interest is absent and a second cluster of hybridisation intensity values for the reference samples in which the genetic segment of interest is present; and (iii) establishing a "no call" region of hybridisation intensity values that lies in the region between said first and second clusters and which is bounded by LNC and UNC, wherein the LNC and UNC represent statistical confidence limits for assigning a hybridisation intensity value to said first and said second clusters, respectively; wherein: the DNA of the reference samples and/or the test sample has been labelled with a fluorescent label and wherein measuring hybridisation intensity comprises measuring the fluorescence signal of the fluorescent label at each oligonucleotide probe location; the hybridisation intensity for each probe set is measured as I/B, where: I is determined as a measure of central tendency of the measured fluorescence signal of the replicates of each oligonucleotide probe; and B is determined as a measure of central tendency of the background fluorescence signal of the replicates of each oligonucleotide probe; and the LNC and UNC values are calculated according to the following formulae: .function..times..times..function..times..times. ##EQU00013## .times..times..function..function..times..times. ##EQU00013.2## .times. ##EQU00013.3## .times..times..function..times..times..function..times..times..function..- times..times..function. ##EQU00013.4## aMedianI/B is a measure of central tendency of the measured I/B values of the reference samples in which the genetic segment of interest is absent; pMedianI/B is a measure of central tendency of the measured I/B values of the reference samples in which the genetic segment of interest is present; a(I/B)n is the greatest measured I/B value of the reference samples in which the genetic segment of interest is absent; and p(I/B)1 is the lowest measured I/B value of the reference samples in which the genetic segment of interest is present. 23. A method for determining the presence or absence of a genetic segment of interest in a DNA-containing sample, the method comprising: (i) bringing at least a first probe set comprising a plurality of replicates of at least one oligonucleotide probe that interrogates a first cognate sequence within said segment of interest into contact with at least one DNA-containing test sample under conditions that allow probe-cognate sequence hybridisation to occur; (ii) measuring the intensity of probe-sample hybridisation of the at least one test sample; and (iii) comparing the measured hybridisation intensity with a pre-determined lower no call boundary ("LNC") and a pre-determined upper no call boundary ("UNC"), and wherein a measured hybridisation intensity below the LNC indicates that said genetic segment of interest is absent in the test sample and a measured hybridisation intensity above UNC indicates that said genetic segment of interest is present in the test sample, wherein said LNC and said UNC are determined by the method of claim 22. 24. A method according to claim 1, wherein said cognate sequence comprises a polymorphic site and wherein said first probe set comprises a plurality of replicates of at least two, at least three or at least four allele-specific oligonucleotide probes that distinguish the alleles of said polymorphic site. 25. A method according to claim 24, wherein said test sample comprises said genetic segment of interest, the method further comprising genotyping said test sample to identify an allele at said polymorphic site.

Details for Patent 9,165,108

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		2030-06-18
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	For Injection	103132			2030-06-18
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	Injection	103132			2030-06-18