Abstract: The present invention generally concerns an automated system capable of performing quantitative PCR (qPCR) analysis of a nucleic acid present in a biological sample together with preparation of a sequencing-ready nucleic acid library from the sample, either simultaneously or sequentially. In a further aspect, the present invention also provides a method for performing qPCR of a nucleic acid present in a biological sample together with simultaneous of sequential preparation of a sequencing-ready nucleic acid library from the sample. Finally, the present invention also provides removable cartridges for use in the automated systems and methods according to the invention.

Abstract: The present invention generally relates to the field of cancer, in particular to cancers having microsatellite instability (MSI) and/or mismatch repair (MMR-) deficiency. Examples of such cancers include many colorectal, gastric, and endometrial tumors. Accordingly, the present invention provides a novel diagnostic marker panel for analyzing MSI loci, together with methods and kits of using said panel in the detection of cancers having microsatellite instability (MSI) and/or mismatch repair (MMR-) deficiency.

Abstract: The present invention is based on the discovery of sensitive and specific methylation detection by a) controlling excessive DNA degradation prior to conversion by incubating DNA conversion reagent (e.g. bisulfite reagent) directly with a nucleic acid containing sample without requiring prior nucleic acid purification from the sample and without requiring prior nucleic acid denaturation at elevated temperatures of 98° C. and, b) optimizing bisulfite removal by controlling the pumping rate flow of the bisulfite treated sample over an extraction membrane inside an automated system. In some embodiments, a cartridge for the detection of methylated DNA is provided.

Abstract: The present application relates to detection of changes in the number of nucleotides in short homopolymeric nucleic acid repeats, in particular in short homopolymeric microsatellites, for example for the purpose of diagnosing microsatellite instability (MSI) and/or mismatch repair (MMR-) deficiency in tumors. Accordingly, methods are provided for detecting changes in the number of nucleotides present in short homopolymeric nucleotide repeat sequences as well as kits and cartridges for automated detection of said changes.

Abstract: The present application relates to detection of changes in the number of nucleotides in short homopolymeric nucleic acid repeats, in particular in short homopolymeric microsatellites, for example for the purpose of diagnosing microsatellite instability (MSI) and/or mismatch repair (MMR-) deficiency in tumors. Accordingly, methods are provided for detecting changes in the number of nucleotides present in short homopolymeric nucleotide repeat sequences as well as kits and cartridges for automated detection of said changes.

Abstract: The present invention relates to a highly automatable method for isolation and/or purification of nucleic acids from a biological sample, which is particularly suitable for nucleic acids-shorter than 250 bp and can be performed without a proteolytic pre-digestion step in an automated system, preferably a cartridge-based system. In a further aspect, the present invention also provides automated nucleic acid detection methods based on said isolation and/or purification method, as well as buffers and kits to be used in performing said methods.

Abstract: The present invention is based on the discovery of sensitive and specific methylation detection by a) controlling excessive DNA degradation prior to conversion by incubating DNA conversion reagent (e.g. bisulfite reagent) directly with a nucleic acid containing sample without requiring prior nucleic acid purification from the sample and without requiring prior nucleic acid denaturation at elevated temperatures of 98° C. and, b) optimizing bisulfite removal by controlling the pumping rate flow of the bisulfite treated sample over an extraction membrane inside an automated system.

Abstract: The present invention is based on the discovery of sensitive and specific methylation detection by a) controlling excessive DNA degradation prior to conversion by incubating DNA conversion reagent (e.g. bisulfite reagent) directly with a nucleic acid containing sample without requiring prior nucleic acid purification from the sample and without requiring prior nucleic acid denaturation at elevated temperatures of 98° C. and, b) optimizing bisulfite removal by controlling the pumping rate flow of the bisulfite treated sample over an extraction membrane inside an automated system.

Abstract: A transfer device for the contamination free transfer of biological material from a sealed chamber to a recipient. The transfer device includes a support having a first docking area and a second docking area. The first docking area has at least one inlet port, each inlet port creating a fluid connection with one sealed chamber. The second docking area has at least one outlet port, each outlet port creating a fluid connection with a recipient. The first docking area further includes a piercing element designed for piercing a sealing element of a sealed chamber in order to allow, together with at least one inlet port, a fluid connection between a pierced sealed chamber and the inlet port, to allow a contamination free transfer of the biological material from the pierced sealed chamber to at least one recipient.

Abstract: The present application relates to detection of changes in the number of nucleotides in short homopolymeric nucleic acid repeats, in particular in short homopolymeric microsatellites, for example for the purpose of diagnosing microsatellite instability (MSI) and/or mismatch repair (MMR-) deficiency in tumors. Accordingly, methods are provided for detecting changes in the number of nucleotides present in short homopolymeric nucleotide repeat sequences as well as kits and cartridges for automated detection of said changes.

Abstract: A device for sealing liquids inside a selected zone of a fluidic path that runs in a fluidic assembly and then for cutting or removing the thus sealed zone in a spillage- and contamination-free manner from said fluidic assembly. Methods of performing such contamination- and leakage-free sealing and cutting of selected fluidic path zones comprising a liquid of interest from the remaining parts of fluidic assemblies, preferably in a fully automated manner.

Abstract: The present invention relates to a highly automatable method for isolation and/or purification of nucleic acids from a biological sample, which is particularly suitable for nucleic acids-shorter than 250 bp and can be performed without a proteolytic pre-digestion step in an automated system, preferably a cartridge-based system. In a further aspect, the present invention also provides automated nucleic acid detection methods based on said isolation and/or purification method, as well as buffers and kits to be used in performing said methods.

Abstract: The present invention generally concerns an automated system capable of performing quantitative PCR (qPCR) analysis of a nucleic acid present in a biological sample together with preparation of a sequencing-ready nucleic acid library from said sample, either simultaneously or sequentially. In a further aspect, the present invention also provides a method for performing qPCR of a nucleic acid present in a biological sample together with simultaneous of sequential preparation of a sequencing-ready nucleic acid library from said sample. Finally, the present invention also provides removable cartridges for use in the automated systems and methods according to the invention.

Abstract: The present invention generally-relates to cartridges for automated systems and automated methods for fully automated processing of biological samples to next-generation sequencing-ready nucleic acid libraries. In particular, the present invention concerns a fluidic cartridge comprising a compartment for receiving a biological sample, means for liberating and/or purifying nucleic acids from the received sample and for transporting said nucleic acids to a compartment wherein NGS library can be prepared from said nucleic acids using provided therein reagents. In a particular aspect, the present invention also concerns cartridges for automated systems and automated methods for preparing an NGS nucleic acid library from a biological sample simultaneously or sequentially with a qPCR assay performed on the same biological sample.

Abstract: The present invention is based on the discovery of sensitive and specific methylation detection by a) controlling excessive DNA degradation prior to conversion by incubating DNA conversion reagent (e.g. bisulfite reagent) directly with a nucleic acid containing sample without requiring prior nucleic acid purification from the sample and without requiring prior nucleic acid denaturation at elevated temperatures of 98° C. and, b) optimizing bisulfite removal by controlling the pumping rate flow of the bisulfite treated sample over an extraction membrane inside an automated system.

Abstract: A fluid control and processing system comprising a cartridge and an instrument for operating the cartridge. The cartridge comprises a cylinder body comprising a cylinder and a fluid port. It further comprises dispensing ports to drive a fluid flow, each dispensing port being positioned to be connectable, when the instrument is operating the cartridge, with at least a fluid port by rotation of the cylinder body. The instrument comprises a piston driver for driving the piston. The system further comprises: reversible fastening means for fastening the piston when the piston driver is rotated with respect to the piston, so that the movement of the piston is controlled by the piston driver; and rotating means comprising a cylinder driver constitutive of the instrument for rotating the cylinder body around the axis A.

Abstract: The present invention discloses methods, kits-of-parts, and devices for the selective lysis of eukaryotic cells in a sample comprising micro-organisms such as bacteria unicellular fungi. The selective lysis is obtained by incubating the sample in an ionic surfactant under alkaline conditions.

Abstract: The present invention relates to a method for producing a storable dry composition of biomolecule. First a composition is dispensed on a surface. The composition comprises at least a biomolecule, at least a liquid volatile component, at least a polysaccharide being designed for forming together with the at least a biomolecule and a part of the at least a liquid volatile component a matrix displaying a glass transition temperature Tg. Secondly, at least a part of the liquid volatile component is evaporated by adjusting the temperature of said composition to allow the formation of the matrix. Said evaporation step is initiated at an initial temperature T1, and finished up at a final temperature T2, said final temperature T2 being above said initial temperature T1.

Abstract: A method for filtering a sample comprising the steps of: (a) providing a sample with eukaryotic cells and containing or suspected to contain a micro-organism; (b) performing a selective lysis of the eukaryotic cells to obtain a lysed sample; (c) filtering the lysed sample obtained in step (b) through a filter arranged to retain the micro-organism; and (d) washing the filter with a detergent based wash buffer to selectively solubilize proteins originating from the eukaryotic cells retained by the filter, by passing the detergent based wash buffer through the filter, to remove protein clogs from the filter in order to allow an additional step (c) of filtering said lysed sample.