Dana-farber-cancer Institute Inc.

The Brigham and Women's Hospital, Inc.

Northeastern University

The Broad Institute, Inc.

Gerassimos M Makrigiorgos

Srinivas Sridhar

Wilfred F Ngwa

Rajiv Kumar

Viktor A Adalsteinsson

Stephanie Dougan

Robert Cormack

Chen Song

The present disclosure provides methods for preparing a target mutant nucleic acid for subsequent enrichment relative to a wild type nucleic acid using nucleases that have a substantially higher activity on double stranded DNA versus single stranded DNA or RNA. The present disclosure also includes methods for enriching a target mutant nucleic acid and for preparing unmethylated/methylated nucleic acids of interest for subsequent enrichment.

Selective degradation of wild-type DNA and enrichment of mutant alleles using nuclease

Provided herein are methods to determine the original abundance of mutant alleles of one or more barcoded target sequences following mutation enrichment and sequencing.

Compositions and methods for molecular barcoding of DNA molecules prior to mutation enrichment and/or mutation detection

The present invention is directed to methods, compositions and software for enriching low abundance alleles in a sample. It is directed in particular to the use of an excess amount of reference blocking sequence in an amplification reaction mixture in order to improve the enrichment efficiency, and reduce cycle time, of full COLD-PCR.

Full COLD-PCR enrichment with reference blocking sequence

This disclosure relates to compositions and methods for single-step, multi-stage amplification reactions that combine many stages of sample preparation process in a single tube reaction. The disclosed technology provides a mean of performing multiplexed nested PCR in a single vessel, without any need of purification steps, and is based on the use of three sets of primers: a pair of outer primers, a pair of inner primers that are nested within the pair of outer primers, and tail primers that are complementary to tails on the inner primers. By adjusting the temperature conditions, annealing temperatures of the primers, number of amplification cycles, and the concentrations of the outer, inner, and tail primers, it is possible to carry out multiplexed nested PCR in a single vessel.

Methods and compositions for selecting and amplifying DNA targets in a single reaction mixture

The present invention is directed to methods, compositions and reaction mixtures for multiplexing COLD-PCR/ice-COLD-PCR to enrich simultaneously several low abundance alleles (mutant target sequences) from a sample. The invention also involves COLD-PCR/ice-COLD-PCR amplification performed on DNA fragments that have different melting temperatures, and therefore different critical denaturation temperatures, in a graded temperature approach such that mutation enrichment is achieved on all diverse DNA fragments simultaneously (temperature-independent COLD-PCR or TI-COLD-PCR). The invention also involves methods for enabling identification of variant-sequence alleles in the presence of a large excess of non-variant alleles in nucleic acids without the complication of polymerase-introduced errors or other primer-introduced artifacts.

Methods and compositions to enable multiplex COLD-PCR

The present invention is directed to methods, compositions and reaction mixtures for conducting COLD-PCR, by controlling and varying a preferential denaturation time.

Methods and compositions to enable enrichment of minor DNA alleles by limiting denaturation time in PCR or simply enable enrichment of minor DNA alleles by limiting the denaturation time in PCR

Compositions and methods for the radiological and immunotherapeutic treatment of cancer are provided. Metallic nanoparticles conjugated with an immunoadjuvant are dispersed within a biodegradable polymer matrix that can be implanted in a patient and released gradually. The implant may be configured as, or be a component of, brachytherapy spacers and applicators, or radiotherapy fiducial markers. The composition may be combined with marginless radiotherapy, allowing for lower doses of radiation and enhancing the immune response against cancer, including at non-irradiated sites.

Biomaterials for combined radiotherapy and immunotherapy of cancer

A method of detecting migration of tumor cells is provided by implanting in a region of tumor cells one or more implants having a matrix material of a biocompatible and biodegradable polymer, and a plurality of nanoparticles dispersed within the matrix material and functionalized to bind tumor cells. Nanoparticles bound to the tumor cells that have migrated out of the region can be detected by various imaging modalities. The implant can be in the shape of a brachytherapy spacer or radiotherapy fiducial maker or can be a coating on a brachytherapy spacer or fiducial marker. A method of treating cancer is provided by implanting one or more brachytherapy spacers or fiducial markers including the matrix material and an anti-cancer therapeutic agent dispersed within the matrix material.

Biopolymer-nanoparticle composite implant for tumor cell tracking

Full cold-PCR enrichment with reference blocking sequence

The present invention is directed to methods, compositions, software and devices for enriching low abundance alleles from a sample. The method is based in part on a modified nucleic acid amplification protocol that includes incubating the reaction mixture at a critical denaturing temperature or 'Tc'. By employing the present invention the current detection limits of all PCR-based technologies are greatly improved.

Enrichment of a target sequence

The present method is directed to using a mutation scanning array to identify mismatches or polymorphisms in multiple genes or the same gene in multiple individuals. The array can be a chip or a microsphere. Preferably, the array has elements containing immobilized oligonucleotides that collectively span at least 10 different whole genes.

Growing community of inventors

Brookline, MA, United States of America

Gerassimos M Makrigiorgos