Abstract: In one aspect, the invention features a combination of oligonucleotides comprising a forward primer oligonucleotide and a blocking oligonucleotide. The forward primer oligonucleotide has a 3? end region, where the 3? end region includes a portion complementary to a mutation positioned in a region within a polynucleotide. The blocking oligonucleotide contains a blocking moiety and has a 5? end region, where the 5? end region includes a portion complementary to a wild-type sequence of the region corresponding to the position of the mutation. In other aspects, the invention provides kits including the combination of primer oligonucleotides and methods of using the oligonucleotides to detect a mutation in a polynucleotide.

Abstract: Provided are compositions and methods useful to the determination of whether a microbial contaminant is present in a biological therapeutic production process. Specifically, an artificial positive amplification control plasmid and unique quantitative PCR detection probe are provided, which enables the rapid and real-time detection of a false positive result.

Abstract: Provided herein is a real-time PCR-based method of detecting, in a sample, an agent causing onychodystrophy, wherein the agent causing onychodystrophy belongs to a secondary clade member including one or more primary clade members. Also provided are compositions and kits that finds use in implementing the present method.

Abstract: A method for diagnosing or giving a prognosis for anxious temperament or trait-like anxiety in a human or non-human primate subject comprising the steps of (a) obtaining DNA from a blood or saliva sample from the subject and (b) quantifying methylation in a set of differentially methylated regions (DMRs) selected from SEQ ID NOs:1-75 or DMR-associated genes selected from DIP2C, GRB10, INPP5A, C17ORF97, PDXK, CACNA2D4, TRAPPC9, CRTC1, MEGF6, HIVEP3, OPCML, PITPNM2, ZFPM1, RAP1GAP2, NFATC1, RNF126, FSTL3, GNAS, SH3BP2, NEURL1B, MAD1L1, HSPA12B, IGF2, PEG10, PEG3, SLC16A3, SYTL1, and ZIM2, wherein a significant change methylation indicates the present of anxious temperament or trait-like anxiety, wherein the change is relative to DNA from a second human or non-human primate who does not have anxious temperament or trait-like anxiety. Also disclosed is a biomarker panel of DMR and DMR-associated genes for the diagnosis or prognosis of anxious temperament or trait-like anxiety.

Abstract: The present invention relates to a method for enrichment of target DNA with high GC content based on target sequence capture and multiple displacement amplification, as well as a kit suitable for this method. The present invention also relates to a method for constructing a sequencing library of target DNA with high GC content based on the enrichment method of the present invention.

Abstract: Provided includes methods and systems useful in array-based analysis of mixed nucleic acid populations, including for genotyping and copy number analysis of the various subpopulations of the mixed nucleic acid population. Also provided includes methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken from an organism.

Abstract: The present disclosure provides for a method of determining microbial identities and/or abundances in a biological sample. The method may comprise: (a) immobilizing the biological sample in a matrix; (b) fracturing/breaking the matrix (that comprises the biological sample) into clusters; and (c) determining identities and/or abundances of microbes in the clusters.

Abstract: The present invention relates to methods and kits for identifying microsatellite instability (MSI) in a sample. In particular it relates to identifying microsatellite instability in a tumor sample, which may be from a subject suspected of having colorectal cancer or Lynch syndrome. The methods and kits can be used to identify mismatch repair defects. More particularly the invention relates to a panel of markers for a sequencing based MSI test, that can differentiate between MSI-H and MSS CRCs. The invention also allows for determination of biological significance, differentiating between PCR and sequencing errors and MSI induced indels/mutations.

Abstract: The invention features methods panels, cartridges, and systems for detecting pathogens and for diagnosing and treating diseases, including bacteremia and sepsis.

Abstract: Disclosed are formulations, including both liquid and lyophilized formulations, comprising a far-red dye probe and a non-linear surfactant or foamban. Also disclosed are related methods for preparing a lyophilized far-red dye probe formulation as well as related kits and diagnostic products.

Abstract: A cleavage-based real-time PCR assay method is provided. In general terms, the assay method includes subjecting a reaction mixture comprising a) PCR reagents for amplifying a nucleic acid target, and b) flap cleavage reagents for performing a flap cleavage assay on the amplified nucleic acid target to two sets of thermocycling conditions. No additional reagents are added to the reaction between said first and second sets of cycles and, in each cycle of the second set of cycles, cleavage of a flap probe is measured.

Abstract: Biomarkers and methods for identifying, verifying and confirming circulating serum-based microRNAs. The microRNAs (PARKmiRs) can be used to differentiate patient's suffering from Parkinson's disease (PD) from non-PD patients.

Abstract: The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.

Abstract: The inventors initially participated to the identification of LPIN1 mutations as a cause for massive rhabdomyolysis episodes in children, triggered by febrile illness. The inventors have suggested that TLR9 antagonists would be suitable for the treatment of rhabdomyolysis (WO2017085115). The inventors thus treated 2 patients with lipin-1 disease by a TRL9 antagonist (hydroxychloroquine). They showed that the accumulation of mtDNA in plasma of the two patients before treatment decreases under treatment. When the treatment was stopped, the accumulation of mtDNA reappeared, then normalized when treatment was resumed. Accordingly, the present invention relates to a method for determining whether a patient suffering from rhabdomyolysis achieves a response with a TLR9 antagonist comprising determining the amount of mitochondrial DNA (mtDNA) in a blood sample obtained from the patient (e.g. by PCR).

Abstract: The present invention relates to the use of the value of the expression of at least one gene selected from the group comprising: GBP 1 gene, HLF gene, CXCL13 gene and SULT1E1 gene, for the estimation of prognosis of distant relapse-free survival or overall survival of a patient with triple negative breast cancer (TNBC) having received a neoadjuvant chemotherapy (NACT).

Abstract: The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called “Safe-SeqS” for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant (“super-mutants”) if ?95% of them contain the identical mutation.

Abstract: The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called “Safe-SeqS” for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant (“super-mutants”) if ?95% of them contain the identical mutation.

Abstract: The methods and compositions provided herein relate to the discovery of 13 STR markers, found on the human Y chromosome, having surprisingly high mutation rates when compared with 173 other Y-STR markers known today. The set of RM-Y-STRs may overcome the current dilemma of Y-chromosome analysis in forensic applications due to their extraordinary mutation properties. Embodiments of the invention include methods for allelic determination of rapidly-mutating Y-STR markers, amplification primers for the analysis of rapidly-mutating Y-STR markers, allelic ladders for analysis of rapidly-mutating Y-STR markers, and kits for the analysis of rapidly-mutating Y-STR markers.

Abstract: Methods of repairing a partially double-stranded DNA fragment are provided. In some embodiments, the methods comprise (a) contacting the partially double-stranded DNA fragment with one or more primers of a primer population, wherein the partially double-stranded DNA fragment comprises a 3? overhang and the primer population comprises a random target-hybridizing sequence; (b) extending one or more primers of the primer population along the DNA fragment using a DNA polymerase, thereby producing one or more extended primers annealed to the DNA fragment; and (c) ligating the 3? end of one or more extended primers to the 5? end of an extended primer or a strand of the partially double-stranded DNA fragment, thereby providing a repaired DNA fragment.

Abstract: The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.