Patents

Patent 1

Title: Multi-loci genomic analysis. US Patent No. 6,197,510. Awarded March 6, 2001.

Inventor: T. Vinayagamoorthy
Assignee: Bio-ID Diagnostic Inc.

Abstract: The invention provides a method of sequencing a nucleic acid in a reaction mixture comprising first and second nucleic acid target sequences. The target sequences may be present on the same or different nucleic acid molecules. First and second labelled sequencing primers are provided that are hybridizable, respectively, to the first and second nucleic acid target sequences. The second sequencing primer being at least as long as the total length of the first sequencing primer plus the length of the first target sequence. Each of the sequencing primer extension products beginning with the second sequencing primer will be longer than the primer extension products in the pool beginning with the first sequencing primer. Once the sequencing reactions have been completed, the lengths of the primer extension products in the pool may be detected by known methods, such as by gel electrophoresis.

Patent 2

Title: Determination of variants produced upon replication or transcription of nucleic acid sequences. US Patent No. 9,150,906. Awarded October 6, 2015.

Inventor: T. Vinayagamoorthy
Assignee: Bio-ID Diagnostic Inc.

Abstract: A method of determining whether or not a nucleic acid having an expected sequence, or one or more variants of the expected sequence are present in a sample containing nucleic acids after replication, transcription or editing (or other transformation) of a substrate nucleic acid. The method involves deciding an expected sequence likely to be formed in the sample upon the replication, transcription or editing of the substrate nucleic acid, and possible variants of the expected sequence, providing primer pairs for a polymerase chain reaction, reverse transcriptase polymerase chain reaction or ligase chain reaction, carrying out the polymerase chain reaction or reverse transcriptase polymerase chain reaction in one or more steps to form amplicons, and analyzing the amplicons to determining whether or not a nucleic acid having the expected sequence and/or variants are present in the sample. The primers of the primer pairs are designed to anneal to regions of the nucleic acid of the expected sequence and the variants, the regions being selected to reveal unambiguously the presence or absence in the sample of the nucleic acid of the expected sequence or the variants thereof according to the presence or absence of specific amplicons amplified by the primers.

Patent 3

Title: Use of markers including nucleotide sequence-based codes to monitor methods of detection and identification of genetic material. US Patent No. 8,785,130. Awarded July 22, 2014.

Inventor: T. Vinayagamoorthy
Assignee: Bio-ID Diagnostic Inc.

Abstract: Disclosed is the use of artificially-generated nucleic acid coded markers to monitor nucleic acid amplification and sequencing reactions designed to detect or analyze biological samples. The markers generally include, along with a unique sequence preferably including coded section designed to represent one or more factors of interest, primer annealing sequences so that the marker may be amplified and sequenced in the same process and using the same amplification and sequencing primers as for the sample target. The invention also relates to the marker itself, and other uses, such as identifying the origin of various materials or products.

Patent 4

Title: Synthesis of single-stranded DNA. US Patent No. 7,727,745. Awarded June 1, 2010.

Inventor: T. Vinayagamoorthy
Assignee: Bio-ID Diagnostic Inc.

Abstract: A method of producing single-stranded DNA. In one form, the method involves providing a uracil-containing oligonucleotide template molecule having a sequence that is complementary to a part of a target single-stranded DNA molecule of length greater than the template molecule; providing one or more parts of the target molecule including a base sequence complementary to a part of the template molecule; annealing the part(s) of the target molecule to the template molecule and forming the complete target molecule by ligating together at least two adjacent parts of the target molecule while annealed to the template molecule, and/or extending at least one part of the target molecule to form a sequence complementary to a remainder of the template molecule by nucleotide polymerization, and then separating the template molecule from the target molecule. In another form, an intermediate molecule is annealed to the template and then enzymatically cut, and one part is then extended by DNA polymerization using monomers of increased molecular weight or ionic charge compared to the monomers used to form the intermediate molecule.

Patent 5

Title: Methods for detecting nucleic acid fragments. European Patent. Patent No. EP 3,049,539. Awarded September 17, 2018.

Inventor: T. Vinayagamoorthy
Assignee: Bio-ID Diagnostic Inc.

Abstract: Provided are methods for detecting and analyzing polynucleotides in a biological sample or sample derived therefrom for example, using a synthetic template polynucleotide. In some aspects, a target polynucleotide in the sample hybridizes to the template polynucleotide and is extended by a polymerase, generating an extended target polynucleotide. In some examples, the extended target polynucleotide is amplified, for example, by polymerase chain reaction, and sequences of the target polynucleotide determined, for example, by priming in the region of the extended target polynucleotide generated by extension and sequencing towards the region having identity to the target polynucleotide. In some aspects, the target polynucleotide is thereby detected in the sample and its sequence identified. In some aspects, the provided methods can be used to capture polynucleotide fragments in a biological sample, for example, plasma, and determine respective biomarkers they carry, for example, for cancer diagnosis and prognosis.

Patent 6

Title: Determination of variants produced upon replication or transcription of nucleic acid sequences. US Patent No. 10036053. Awarded July 31, 2018.

Inventor: T. Vinayagamoorthy
Assignee: Bio-ID Diagnostic Inc.

Abstract: A method of determining whether or not a nucleic acid having an expected sequence, or one or more variants of the expected sequence are present in a sample containing nucleic acids after replication, transcription or editing (or other transformation) of a substrate nucleic acid. The method involves deciding an expected sequence likely to be formed in the sample upon the replication, transcription or editing of the substrate nucleic acid, and possible variants of the expected sequence, providing primer pairs for a polymerase chain reaction, reverse transcriptase polymerase chain reaction or ligase chain reaction, carrying out the polymerase chain reaction or reverse transcriptase polymerase chain reaction in one or more steps to form amplicons, and analyzing the amplicons to determining whether or not a nucleic acid having the expected sequence and/or variants are present in the sample. The primers of the primer pairs are designed to anneal to regions of the nucleic acid of the expected sequence and the variants, the regions being selected to reveal unambiguously the presence or absence in the sample of the nucleic acid of the expected sequence or the variants thereof according to the presence or absence of specific amplicons amplified by the primers.

Patent 7

Title: An algorithm to evaluate efficacy of detecting cellular variants in a heterogeneous cell population. US Filed and Pending.

Inventor: T. Vinayagamoorthy
Assignee: Bio-ID Diagnostic Inc.

Abstract: Multicellular organisms carry heterogenous cell populations, both in normal and disease conditions. Under disease conditions (e.g. cancer), some cells undergo cellular and molecular changes that are associated with the incidence and/or progression of the disease. Identification of such changes helps in the diagnosis and adoption of treatment protocols (e.g. somatic mutations are associated with cancer progression and treatment using targeted therapies). These changes are not inherited and could be present at low concentrations. Hence, there is a need for more sensitive assays to detect these changes in the background of heterogeneous cell populations. This in turn creates a need to evaluate the efficacy of detection of specific changes. A new algorithm, Detection Index (DI), is proposed to evaluate the efficacy of detection. Detection Index is based on the combination of two basic factors, the number of copies of the target, and the ratio of target to that of wild-type in the sample.

Patent 8

Title: Methods for detecting nucleic acid fragments. US Patent No. 10,351,899. Awarded July 16, 2019.

Inventor: T. Vinayagamoorthy
Assignee: Bio-ID Diagnostic Inc.

Abstract: Provided are methods for detecting and analyzing polynucleotides in a biological sample or sample derived therefrom, for example, using a synthetic template polynucleotide. In some aspects, a target polynucleotide in the sample hybridizes to the template polynucleotide and is extended by a polymerase, generating an extended target polynucleotide. In some examples, the extended target polynucleotide is amplified, for example, by polymerase chain reaction, and sequences of the target polynucleotide determined, for example, by priming in the region of the extended target polynucleotide generated by extension and sequencing towards the region having identity to the target polynucleotide. In some aspects, the target polynucleotide is thereby detected in the sample and its sequence identified. In some aspects, the provided methods can be used to capture polynucleotide fragments in a biological sample, for example, plasma, and determine respective biomarkers they carry, for example, for cancer diagnosis and prognosis.

Patent 9

Title: Method of detecting gene expression and/or of preventing such expression in cells. US Patent No. 5,994528. Awarded November 30, 1999.

Inventor: T. Vinayagamoorthy
Assignee: Bio-ID Diagnostic Inc.

Abstract: A method of amplifying a nucleotide sequence complementary to an mRNA template derived from genomic DNA. The method involves the following steps. A sample mixture containing an mRNA template and corresponding genomic DNA is provided, the genomic DNA including at least two exons separated by at least one intron. A pair of intron-blockers are introduced into the mixture, the intron-blockers comprising a sequence of intron-specific oligonucleotides modified to prevent nucleotide extension in conditions promoting polymerase chain reaction. A primer pair promoting amplification of cDNA derived from the mRNA template is introduced into the mixture and then reverse transcription polymerase chain reaction is carried out to amplify cDNA. Detection of the cDNA is proof of the existence of mRNA in the sample, and thus proof of expression of the corresponding gene. The method avoids false positives caused by amplification of genomic DNA as well as cDNA based on an mRNA template. The invention includes a method of suppressing gene expression in vivo, which comprises exposing cells containing a gene to be suppressed, made up of exons and at least one intron, to intron-blockers having nucleotide sequences that bind to the intron to prevent gene expression.

Patent 10

Title: Method of detecting gene expression and/or of preventing such expression in cells. US Patent No. 5,989,873. Awarded November 23, 1999.

Method of detecting gene expression and/or of preventing such expression in cells.

Inventor: T. Vinayagamoorthy
Assignee: Bio-ID Diagnostic Inc.

Abstract: A method of amplifying a nucleotide sequence complementary to an mRNA template derived from genomic DNA. The method involves the following steps. A sample mixture containing an mRNA template and corresponding genomic DNA is provided, the genomic DNA including at least two exons separated by at least one intron. A pair of intron-blockers are introduced into the mixture, the intron-blockers comprising a sequence of intron-specific oligonucleotides modified to prevent nucleotide extension in conditions promoting polymerase chain reaction. A primer pair promoting amplification of cDNA derived from the mRNA template is introduced into the mixture and then reverse transcription polymerase chain reaction is carried out to amplify cDNA. Detection of the cDNA is proof of the existence of mRNA in the sample, and thus proof of expression of the corresponding gene. The method avoids false positives caused by amplification of genomic DNA as well as cDNA based on an mRNA template. The invention includes a method of suppressing gene expression in vivo, which comprises exposing cells containing a gene to be suppressed, made up of exons and at least one intron, to intron-blockers having nucleotide sequences that bind to the intron to prevent gene expression.

Patent 11

Title: Simultaneous detection of multiple nucleic acid templates using modified primers. European Patent Filed 2018, Pending.

Inventor: T. Vinayagamoorthy
Assignee: Bio-ID Diagnostic Inc.

Abstract: The invention refers to a method of detecting one or more deoxyribose nucleotide (DNA) template(s) by amplifying segments of the DNA template by polymerase 5 chain reaction using upper and lower primers, generating a nucleotide sequence and aligning the generated nucleotide sequence with a reference nucleotide sequence to determine the location of an indicator nucleotide in the reference nucleotide sequence and the DNA template, and to identify the DNA template. In addition, the invention is directed to a kit for detecting one or more DNA templates.

Patent 12

Title: Simultaneous detection of multiple nucleic acid templates using modified primers. US Patent No. 11,028,442. Awarded June 8, 2021.

Inventor: T. Vinayagamoorthy
Assignee: Bio-ID Diagnostic Inc.

Abstract: The invention refers to a method of detecting one or more deoxyribose nucleotide (e.g. DNA) template(s) in a heterogenous sample by generation of template specific surrogate nucleotide sequences. This invention is applied to but not restricted in detecting genetic variations including cancer markers and pathogens.