Abstract: The field of the invention generally relates to detection of nucleic acid targets in a multiplex reaction setting. In particular, disclosed herein are methods, kits, kits of parts, systems or components thereof for performing a multiplex PCR detection using custom genetic target panels in a generic detection cartridge. The disclosed methods and kits can typically be utilized for quickly designing automated multiplex PCR-based detection assays for a large number, i.e. tens or multiples of tens, of personalized and/or customized genetic targets, including mutations, SNPs, pathogenic sequences, epigenetic lesions etc.

Abstract: A method of target DNA genome analysis is provided. The method comprises the steps of: —obtaining non-overlapping segments of target DNA stretches with segment boundaries defined by the presence of particular restriction enzyme recognition sites, whereby the assembly of said non-overlapping segments compose a reduced representation library of said target DNA genome; —obtaining for said segments, raw metrics from a sequencing process applied on said reduced representation library; —clustering non-overlapping, nearby segments with similar raw metrics to provide master segments; —providing metrics describing the master segments, —making a final discrete DNA call based on the master segments and its metrics.

Abstract: The present teachings concern a method for determining the presence or absence of a fetal chromosomal aneuploidy and/or loss of heterozygosity (LOH) in a biological sample obtained from a pregnant female, the method comprising: obtaining sequence information indicative of targeted-capture massively parallel sequencing of the biological sample comprising both maternal and fetal nucleic acids; determining the amount of off-target reads obtained from said targeted capture massively parallel sequencing; and deriving from said off-target read counts information for determining the absence or presence of said aneuploidy or LOH.

Abstract: Improved compositions for and methods of processing and analyzing samples are described. In particular, the compositions and methods liberate nucleic acids from a biological sample allowing direct downstream processing of the nucleic acids in microfluidic systems. These compositions, methods and kits are useful in diagnosing, staging or otherwise characterizing various biological conditions.

Abstract: The present teachings describe a method for determining the presence or absence of a fetal chromosomal aneuploidy in a pregnant female, the method comprising the calculation of a parameter p from sequences obtained from a biological sample from said pregnant female. The present teachings equally provide a method for determining the fetal fraction of said sample.

Abstract: A method of target DNA genome analysis is provided. The method comprises the steps of: —obtaining non-overlapping segments of target DNA stretches with segment boundaries defined by the presence of particular restriction enzyme recognition sites, whereby the assembly of said non-overlapping segments compose a reduced representation library of said target DNA genome; —obtaining for said segments, raw metrics from a sequencing process applied on said reduced representation library; —clustering non-overlapping, nearby segments with similar raw metrics to provide master segments; —providing metrics describing the master segments, —making a final discrete DNA call based on the master segments and its metrics.

Abstract: Improved compositions for and methods of processing and analyzing samples are described. In particular, the compositions and methods liberate nucleic acids from a biological sample allowing direct downstream processing of the nucleic acids in microfluidic systems. These compositions, methods and kits are useful in diagnosing, staging or otherwise characterizing various biological conditions.