AUTOMATED SAMPLE TO NGS LIBRARY PREPARATION

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.

Claims

1. A cartridge for automated processing a biological sample, the cartridge comprising: a) a sample compartment for receiving a biological sample; b) means for liberating or purifying nucleic acid from the biological sample received in the sample compartment, said means capable of entering in fluid communication with said sample compartment; and c) a library compartment for preparing a nucleic acid library positioned downstream of the sample compartment and of the means for liberating or purifying nucleic acid, the library compartment configured to receive at least a portion of the liberated or purified nucleic acid and comprising reagents for preparing a nucleic acid library.

2. A cartridge according to claim 1, said cartridge further comprising at least one thermocycling qPCR compartment positioned downstream of the sample compartment and of the means for liberating or purifying nucleic acid, and configured to receive at least a portion of the liberated or purified nucleic acid or at least a portion of the nucleic acid library prepared in the library compartment, wherein said thermocycling qPCR compartment is suitable for amplifying nucleic acids and for allowing detection of signals generated during such amplification and comprises reagents for performing qPCR.

3. A cartridge according to claim 2, wherein the reagents for performing qPCR comprise at least one set of primers, preferably a plurality of sets of primers for amplifying at least one disease-associated target nucleic acid sequence.

4. A cartridge according to claim 1, said cartridge further comprising at least a second one thermocycling qPCR compartment positioned downstream of the sample compartment and of the means for liberating or purifying nucleic acid, the at least second one thermocycling qPCR compartment configured to receive at least a portion of the liberated or purified nucleic acid or a portion of the nucleic acid library prepared in the library compartment, and comprising a at least one set of primers for performing a nucleic acid quality control (QC) qPCR.

5. A cartridge according to claim 4, comprising a plurality of sets of primers for generating amplicons of different sizes.

6. A cartridge according to claim 1, wherein the reagents for preparing a nucleic acid library allow: i) generation of nucleic acid fragments from the portion of the liberated or purified nucleic acid received into the library compartment, and ii) attaching oligonucleotide adapters to at least one, preferably both ends of said generated nucleic acid fragments.

7. A cartridge according to claim 6, wherein the generation of nucleic acid fragments is performed by a PCR, further referred to as library PCR, and wherein the attaching oligonucleotide adapters to the library-PCR-generated nucleic acid fragments is performed by including an adapter sequence in a sequence of at least one primer used in said library PCR.

8. A cartridge according to claim 1, further comprising a cartridge-specific identifier for storing cartridge-specific information.

9. A cartridge according to claim 1, further comprising a recovery compartment positioned downstream of the sample compartment, said recovery compartment providing for recovering any of the following: i) a portion of the biological sample received into the sample compartment; ii) a portion of the nucleic acid liberated or purified from the biological sample received into the sample compartment; iii) at least a portion of the nucleic acid library prepared in the library compartment.

10. An automated method for preparing a next-generation sequencing (NGS) nucleic acid library from a biological sample, said method comprising the steps of: a) receiving a biological sample; b) liberating or purifying at least a part of nucleic acids from the received biological sample; c) providing at least a portion of the liberated or purified nucleic acid into a library compartment for preparing an NGS nucleic acid library and comprising reagents for preparing a nucleic acid library; and d) preparing an NGS nucleic acid library; wherein at least the steps b) to d) are performed on an automated system.

11. An automated method according to claim 10, the method further comprising the step of performing qPCR on said automated system either sequentially or simultaneously with respect to the step of preparing the NGS nucleic acid library, wherein said qPCR is performed on a second portion of the liberated or purified nucleic in a thermocycling qPCR compartment suitable for amplifying nucleic acids and allowing detection of signals generated during such amplification.

12. An automated method according to claim 11, wherein said at least one qPCR amplifies at least one disease-associated target nucleic acid sequence, or is a quality control (QC) qPCR.

13. An automated method according to claim 10, the method performed on a cartridge engageable with the automated system.

14. An automated method according to claim 13, wherein the cartridge comprises a cartridge-specific identifier for storing cartridge-specific information and wherein the method further comprises the step of introducing to the automated system the information stored in the cartridge-specific identifier.

15. Use of a cartridge according to claim 1 for automated preparation of a next-generation sequencing (NGS) library from a biological sample.

Description

BRIEF DESCRIPTION OF FIGURES

[0038] For a fuller understanding of the nature of the present invention, reference is made to the following detailed description taken in conjunction with the accompanying drawings in which:

[0039] FIG. 1: shows 5 DNA bands on an electrophoretic gel, corresponding to 5 products of a 5plex qPCR performed on a liquefied FFPE sample.

[0040] FIG. 2: shows qPCR amplification curves for the 5 products of the 5plex qPCR shown in FIG. 1.

[0041] FIG. 3: shows a Cq to copy number histogram for at least 4 replicates of each of the 5plex qPCR products.

[0042] FIG. 4: shows R squared value determination for each of the 5plex qPCR products.

[0043] FIG. 5: shows the ability of the 5plex qPCR to distinguish between different degrees of nucleic acid fragmentation. Panel A shows results obtained from 3 FFPE samples having relatively intact DNA; Panel B shows results from another set of 3 FFPE samples with a higher level of fragmentation; lastly, Panel C shows results from 6 different FFPE samples containing heavily fragmented DNA. FIG. 6: shows results of a BRAF-specific qPCR capable of discerning between wt and V600K/R/M BRAF mutants, performed on three FFPE samples each spiked with a plasmid containing a sequence encoding for either wt BRAF, V600M mutant BRAF, or V600K and T149C double-mutant BRAF.

[0044] FIG. 7: shows principles of a one type of NGS-ready library preparation using library PCR with primers containing NGS-specific adapters. Sequences of wild type (Seq ID NO.: 1), V600M (Seq ID NO.: 2) and V600K+V1794C (Seq ID NO.: 3) are represented.

[0045] FIG. 8: shows results of NGS performed on three FFPE samples each spiked with a plasmid containing a sequence encoding for either wt BRAF, V600M mutant BRAF, or V600K and T149C double-mutant BRAF.

[0046] FIG. 9: shows an example of an optimized sample-to-result workflow according to the present invention.

DETAILED DESCRIPTION OF THE INVENTION

[0047] The present invention generally relates to automatic preparation of next-generation sequencing (NGS) libraries from biological samples. In particular, the invention relates to a generic way to generate an NGS-library from any type of sample (blood, stool, urine, FFPE, swab, . . . ) in an automated manner and with the possibility of automatically verifying quantity and quality of the thus obtained library or the nucleic acid used for its construction using a QC qPCR and of almost instantaneously obtaining clinical information from said nucleic acid using an assay qPCR. In case if the latter, it should be noted that exactly the same and identically-processed nucleic acid pool is used for NGS library preparation and qPCR, which further provides unique means for directly comparing the diagnostic information on key target mutations as screened by assay qPCR with a broader genetic landscape as later obtained from the NGS data.

[0048] In particular, the present invention provides a fluidic cartridge for automated processing a biological sample on an automated system and engageable with said system, the cartridge comprising:

[0049] a sample compartment for receiving a biological sample;

[0050] means for liberating or purifying nucleic acid from the biological sample received in the sample compartment, said means capable of entering in fluid communication with said sample compartment either by being connected by a channel to said sample compartment or by being entirely or partially positioned in the sample compartment;

[0051] a library compartment for preparing a nucleic acid library positioned downstream of the sample compartment and of the means for liberating or purifying nucleic acid, the library compartment configured to receive at least a portion of the liberated or purified nucleic acid (e.g. as a result of a pumping action directing the extracted nucleic acids in a channel to the library compartment) and comprising reagents for preparing a nucleic acid library such as enzymes, NGS-specific adapters, any buffering solutions etc.

[0052] One of the objects of the present invention is to provide means for biological sample-to-NGS library processing that is fast, easy-to-use, and requires minimal or virtually no human handling at least from the moment a sample is inserted into the cartridge of the present invention, the cartridge is engaged with its operating automated system, and the automated system is instructed to run the automated library preparation procedure. Thus, it is also one of the objectives of the present invention to provide a cartridge or a platform wherein the library preparation process does not require any human intervention from the moment a biological sample is provided (e.g. inserted into the cartridge or otherwise introduced into the automated system compatible with the cartridge) and the automated processing is initiated by the user.

[0053] Advantageously, the cartridge of the invention not only automatically prepares an NGS library but also is capable of concomitantly providing quantity and quality information related to said library, and/or also performing some clinical characterization of the sample from which the library is being generated. To achieve this, in the present invention further provides a cartridge where in parallel with the library preparation, a real-time PCR (qPCR) can be thermocycled and monitored e.g. through a transparent wall. Thus, in a preferred embodiment a cartridge is provided that further comprises at least one thermocycling qPCR compartment positioned downstream of the sample compartment and of the means for liberating or purifying nucleic acid, and configured to receive at least a portion of the liberated or purified nucleic acid or at least a portion of the nucleic acid library prepared in the library compartment (e.g. by pumping through channels), wherein said thermocycling qPCR compartment is suitable for amplifying nucleic acids and allowing detection of signals generated during such amplification and comprises reagents for performing qPCR, such as at least one set of primers, a signal-generating dye or probe, a DNA polymerase, dNTPs, buffer, etc.

[0054] Preferably, the qPCR performed in the thermocycling qPCR compartment is a multiplex qPCR, i.e. a qPCR simultaneously amplifying and detecting multiple sequences in a single reaction. A multiplex qPCR uses multiple primer sets in a single qPCR mixture and thus generates multiple products in one tube, chamber, or other type of a qPCR thermocycling compartment. Multiplex qPCR using two primer sets (usually pairs) is called a duplex, often denoted 2plex. Similarly, a multiplex qPCR with three primer sets is a triplex or a 3plex. Preferred in the present invention multiplex qPCR arrangements include a 2plex, a 3plex, a 4plex, a 5plex, a 6plex, a 7plex, or more.

[0055] Therefore, preferably, the reagents for performing PCR comprise a plurality of primer sets, each directed to a different amplicon, wherein said plurality is preferably 2, 3, 4, 5, 6, 7, or more.

[0056] It is well known in the art that designing a robust multiplex qPCR is not easy as the assay requires that the multiplicity of individual primer sets (usually primer pairs) will specifically target their unique amplicons in one reaction tube and thus under a single set of reaction conditions. Primer design will typically take into account primer purity (17 to 30 bases in length); balance G/C and NT-rich domains (20 to 70% G+C); set melting temperature between 55-80 C.; avoid creating complementary 3end base pairs; avoid primer self-complementary; and avoid 1 or more C's or G's at the 3 end of primers, especially when the multiplex is to be performed on complex samples such as eukaryotic genomic DNA. Several web-based primer design software tools are available that help design PCR primers (e.g. Primer3Plus). Other factors, such as the relative concentration of the primers, the right concentration of the PCR buffer components, balance between the magnesium chloride and deoxynucleotide concentrations, cycling temperatures, and DNA thermocycling polymerase etc. also often have to be fine-tuned for a successful multiplex qPCR. Notably, finding an optimal combination of the annealing temperature and buffer concentration is essential in multiplex PCR to obtain highly specific amplification products. Magnesium chloride concentration needs to be proportional to the amount of dNTP, while primer concentration for each target should be relatively robust. A choice of a proper polymerase can also have impact on the outcome of the reaction. In theory, multiplex PCR can be performed with standard PCR polymerase; however in practice it is preferred that highly processive and sensitive DNA polymerases such as GoTaq or AmpliTaq are used. For particularly sensitive applications, further modifications of multiplex qPCR such as the ones using DNAzymes or MNAzymes may be advantageous for the application in the present invention. The list of the mentioned-herein factors and multiplex optimization strategies is by no means to be interpreted as extensive, which will be immediately appreciated by any person skilled in the art.

[0057] In preferred embodiments of the invention, the quantification of the qPCR in the systems and methods of the invention is based on the standard curve method; however, other quantification strategies can also be used, as will be immediately appreciated by any skilled person.

[0058] Similarly, many different general types of fluorescent dyes or detection probes can be used in the systems and methods of the present invention. In preferred embodiments sequence specific probes will be used, e.g. selected from exonuclease probes, hybridization probes, or molecular beacons. Such probes not only add specificity to the assay, but are also key for enabling multiplex applications. As shown in the examples, the methods of the invention were successfully applied with the use of Taqman probes but other probes would be suitable as well.

[0059] Advantageously, together with the NGS library preparation, the cartridge of the present invention provides for simultaneous qPCR screening of the provided therein clinical sample for the presence of therapy actionable alleles or disease-associated sequences. Some examples of such sequences, among many others, include mutant gene sequences associated with cancer, or exogenous pathogenic sequences indicative of an ongoing infection with a pathogenic organism. In line with this, in a preferred embodiment, a cartridge is provided, wherein the reagents for performing qPCR comprise at least one set of primers, preferably a plurality of sets of primers for amplifying at least one disease-associated target nucleic acid sequence.

[0060] In a further aspect of the present invention, the provided herein cartridge can also advantageously comprise means for assessing the quality of the purified nucleic acids or the already obtained library. Thus, in another preferred embodiment, a cartridge is provided wherein the reagents for performing qPCR comprise at least one set of primers, preferably a plurality of sets of primers for performing a quality control (QC) qPCR. In principle, for performing QC qPCR, targets can be selected from any genes or genomic regions. For diagnosis of genetically unstable conditions like cancer, it is better however, to avoid disease-sensitive regions that are likely to have their sequence mutated or change in copy number. Therefore, in a preferred embodiment, the targets of the quality control multiplex qPCR are selected from intra-exon sequences of single copy genes, such as a housekeeping gene. A further advantage of said solution is that the same target sequences directed to intra-exon regions can be used in assessment of both DNA as well as in RNA quality as a library material. Because of the latter, such design of the quality control multiplex qPCR multiplex of the present invention is particularly useful when it is desired to sequence both the genome and the transcriptome from one sample, which requires construction of and thus also quality verification for both DNA- and RNA-based. Thus, in one preferred embodiment, the quality control multiplex qPCR to be used in systems and method of the invention, targets at least one intra-exon sequence in a single copy gene. Possibly, one, two, three, four, five, six, seven or more intra exon sequence in a one, two, three, four, five, six, seven or more single copy genes are targeted. Alternatively to housekeeping genes, in DNA library construction, repetitive sequences (e.g. LINEs, or SINEs such as Alu elements) may be the targets of interest. As a non-limiting example shown in the example section, the methods of the invention are successfully practiced on intra-exon sequences of the RNaseP, HPRT1, Beta-Actin, TRFC and ABCB1 genes.

[0061] In one preferred embodiment, the cartridge of the invention can perform QC qPCR in addition to an assay qPCR that amplifies target disease-associated nucleic acid sequences. Thus, in an advantageous embodiment, a cartridge is provided further comprising at least a second one thermocycling qPCR compartment positioned downstream of the sample compartment and of the means for liberating or purifying nucleic acid, the at least second one thermocycling qPCR compartment configured to receive at least a portion of the liberated or purified nucleic acid or a portion of the nucleic acid library prepared in the library compartment, and comprising a at least one set of primers for performing a nucleic acid quality control (QC) qPCR.

[0062] It has been observed that a multiplex qPCR generating amplicons of different sizes is particularly suitable for assessing nucleic acid quality. Consequently, in another preferred embodiment, a cartridge is provided comprising a plurality of sets of primers for generating amplicons of different sizes. The size range of the amplicons varies from a smaller size Ax to a higher size Ay (with x<y), typically in the size range of 50-600 bp. Preferably the smaller Ax size ranges from 50 to 110 bp and can be of any length in between that range. Preferably Ax is between 60 bp+/10 bp. As shown further herein in Examples, Ax is 63 bp or 105 bp. Preferably the larger Ay size ranges from 300 to 550 bp and can be any length in between that range. As shown in further in the Examples, Ay is 504 bp (e.g. for the TRFC gene) or alternatively 318 bp (e.g. for the beta-actin gene). In case of RNA sequencing, particularly in applications focusing on microRNA (e.g. 15-35 bp size range), the smaller Ax size range may need to be lowered accordingly. As will be appreciated by any skilled artisan, during the multiplex qPCR design for the purposes of the present invention, the preferred amplicon sizes may advantageously be selected in accordance with the NGS application of choice in order to provide the most adequate estimation about the NGS coverage according to amplicon length.

[0063] In preferred embodiments, the biological sample is a human clinical sample. The clinical sample can be a fresh sample, a fresh frozen sample, a fine needle aspirate, a sample that has been treated for preservation and may contain cross-linking of reactive sites due to fixation treatment, a wax-contacted or wax-embedded sample, an FFPE sample in the form of an FFPE slice, a liquid sample such as a urine sample, a blood sample, a serum sample, or any other clinical sample.

[0064] Once introduced to the cartridge of the invention, a biological sample will usually be processed by contacting it with a composition that provides for releasing of nucleic acids. In preferred embodiments, the composition is optimized for use in microfluidic analyzers and preferably contains surfactants rather than organic solvents. Mixing with said composition usually also facilitates transporting of such processed sample through a microfluidic system. In embodiments wherein the sample is an FFPE sample, the surfactant comprised in said composition will preferably be non-ionic. Nucleic acids obtained from FFPE samples typically contain nucleotide-to-nucleotide and nucleotide-to-protein cross-links, base modifications and other chemical modifications that affect the integrity of the nucleic acid. Preferred methods of the present invention incorporate a non-ionic surfactant and permit automated removal of embedded wax and liberation of the components without use of organic solvents. This is particularly beneficial because it puts the liberated nucleic acids in a condition and environment that interfaces with downscale applications requiring enzymatic activity such as nucleic acid amplification via PCR. In one embodiment, the lysate and/or components released from the sample will be further processed in diagnostic analyzers using microfluidic systems.

[0065] Optionally, the liberated nucleic acid is provided in a form sufficiently pure for being directly used as a template for a qPCR and a nucleic acid library construction according to the invention. In a preferred embodiment, the nucleic acid-liberating means performs its function in a fluidic or microfluidic arrangement. In such instance, the elements forming such nucleic acid-liberating means may comprise a series of consecutive or otherwise fluidly interconnected compartments, like chambers or channels, at least some of which being supplied with reagents like lysis buffers, enzyme solutions, extraction buffers, binding buffers and/or wash buffers; or optionally comprising any of the known in the art physical barriers, such as filters or high-affinity resins, that facilitate processes like mechanical sample clearing or nucleic acid binding, washing, and releasing. Such and alternative means for liberating nucleic acids are well known in the art and therefore will not be discussed herein in greater detail.

[0066] Usually, the fluidic cartridge of the invention will comprise means for dividing nucleic acids liberated and/or purified from a received therein sample between at least the library compartment and the thermocycling qPCR compartment. Such means could e.g. comprise two separate channels extending from the nucleic acid source-receiving compartment or the compartment whereto the liberated from said source nucleic acid is deposited in the last step of the nucleic acid liberation process, into the thermocycling qPCR compartment and into the library compartment, respectively. In order to actively transport the nucleic acid between the compartments of choice, the automated system of the invention could provide a pressure gradient capable of pushing or pulling a desired amount of fluid into prescribed direction. Generation of such pressure gradients by means of pumps, suction devices, manifolds etc. is widely employed in contemporary microfluidic systems and thus well known in the art.

[0067] As will be understood by any skilled person, fluidic or microfluidic cartridges suitable for the present invention may contain at least two reaction chambers comprising the thermocycling qPCR compartment and the library compartment, and one or more fluid chambers. Some of the fluid chambers may hold fluid which is used for producing lysate from the sample. Other chambers may hold fluids such as washing fluids and amplification solution. Separate reaction chambers are used as the thermocycling qPCR compartment and the library compartment. The chamber configured to serve as the thermocycling qPCR compartment comprises a number of primer sets, along with other amplification reagents and enzymes required for performing a qPCR. The other chamber configured to serve as the library compartment is adapted to performing the steps of constructing a nucleic acid library for an NGS application of choice. Parts of the sample will be transferred to the reaction chambers and to make such transfer possible, chambers are connected to one or more fluid channel. In at least one, but preferably each of these fluid channels a valve means may be provided, which valve means preferably normally closes the fluid channel, but opens the fluid channel upon actuation of the valve means therewith placing the respective two chambers in fluid communication. The valve means may be designed as a one-way valve.

[0068] In another embodiment, the library compartment and the one or more of the thermocycling qPCR compartments of the present cartridge can be operated in the automated system engaging the cartridge simultaneously or sequentially. This means that three modes of operation can be envisaged: (i) both compartments operate once nucleic acid is fed into them, thus library preparation is independent of and proceeds in parallel with qPCR; and (ii) first, qPCR is made, then library is made; like this the decision to prepare a library for sequencing is made once the results of the qPCR are known and may depend on these results; (iii) first, the library is made, then qPCR is performed on the library for the verification of the library quality.

[0069] The option (i) above describes the simultaneous operation in which the preparation of a library for NGS from a part of a nucleic acid sample is run simultaneously with a qPCR assay on another part of the same nucleic acid sample, and both are preferably performed in parallel in a cartridge-based microfluidic system. As used herein the term simultaneously or in parallel refers to happening or being done at the same time. In such arrangement, the qPCR is being performed on a part from a nucleic acid sample at the same time as the nucleic acid library for NGS application is being constructed from another part from the same nucleic acid sample. In other words, during the simultaneous operation, both the sample analysis via qPCR and library construction are executed by the automated system of the invention at the same time.

[0070] Conversely, the options (ii) and (iii) above can both be described as operating sequentially. In one possible embodiment of the sequential operation at least two thermocycling qPCR compartments operate on the automated system of the invention. For example, first qPCR can be done to read the expression of interesting markers and verify the quality of nucleic acid source fed into the system. Following this first qPCR (sequentially), or to save time in parallel with said first qPCR (simultaneously), a library is constructed. Then, a second or control qPCR can be performed on the thus constructed library to verify whether its quality is sufficient for subjecting it to further applications, such as sequencing.

[0071] With regard to the NG sequencing library preparation or construction, currently there exist many different ways of generating a sequencing-ready library, and their choice naturally depends on which NGS strategy is intended to be performed. In general, NGS library generation involves generation of nucleic acid fragments, which are compatible with given NGS. Therefore, in a preferred embodiment, a cartridge is provided wherein the reagents for preparing a nucleic acid library in the library allow: [0072] generation of nucleic acid fragments from the portion of the liberated or purified nucleic acid received into the library compartment, and [0073] attaching oligonucleotide adapters to at least one, preferably both ends of said generated nucleic acid fragments.

[0074] For most of the commercially available NGS platforms, amplification of nucleic acid fragments is necessary to generate sufficient copies of sequencing templates. Thus, preferably, a cartridge is provided wherein the generation of nucleic acid fragments is performed by a PCR, further referred to as library PCR, and wherein the attaching oligonucleotide adapters to the library-PCR-generated nucleic acid fragments is performed by including an adapter sequence in a sequence of at least one primer used in said library PCR. Suitable library PCRs are known in the art and include methods such as bridge amplification or emulsion PCR.

[0075] As already state above, nucleic acid library construction is needed for DNA sequencing, RNA sequencing, and other applications such as sequencing-based methylation analysis. RNA sequencing (RNA-seq) is a method of investigating the transcriptome of an organism using deep-sequencing techniques. Total RNA generally contains only a very small percentage of coding or functional RNA; ribosomal RNA (rRNA: up to 80-90% of the total RNA), and to a lesser degree transfer RNA (tRNA), make up the majority of the RNA in a sample. Often, In order not to use 80-90% of one's sequencing capacity on repetitive rRNA sequences, rRNA can be removed from the sample prior to sequencing. The RNA after removal of rRNA is made into a library. This involves creating double-stranded cDNA through reverse transcription from the RNA (or fragmented RNA). This double-stranded cDNA may then be handled as normal genomic DNA throughout the remaining library construction process, including linking it with appropriate NGS-strategy specific adapters.

[0076] As the cartridges of present invention provide a convenient way for generating parallel datasets from several assays including NGS, sample quality assessment by QC qPCR, and possibly several target specific qPCR assays, in a particularly practical embodiment, cartridges of the present invention may advantageously be equipped with an element, i.e. an identifier, capable of storing cartridge- or patient-specific information, which would allow to easily keep track of all the assays performed on one cartridge or on samples from one patients. Such identifier could for example be a cartridge-unique code or a barcode containing data like a cartridge number, its batch or series number, production and expiry dates, types of target specific assays that the cartridge carries etc. Alternatively, the identifier could be not only readable but also writable storage medium like a disc or a microchip, where a patient-specific data (like name, age, date of the assay etc.) could be introduced, stored, and then retrieved at will in order to facilitate automated patient identification and minimize mixing of samples. The identifier could be conveniently scanned or otherwise introduced into the automated system engaging with and processing such cartridge, which would save the time of the operator performing the run on typing the required data and also eliminate a stage in the workflow where a human error can be introduced. Furthermore, thanks to the association of runs with one specific cartridge-identifier or patient-identifier, different tests performed on samples from the same patient could become easily traceable, retrievable, and associated with one another also in an automated way. Thus in an advantageous embodiment, the present invention provides a cartridge in accordance with the previous embodiments, further comprising a cartridge-specific identifier like a unique code, barcode, or a microchip etc., for storing cartridge-specific information.

[0077] In another aspect, a cartridge is provided further comprising a recovery compartment positioned downstream of the sample compartment, said recovery compartment providing for recovering any of the following: [0078] a portion of the biological sample received into the sample compartment; [0079] a portion of the nucleic acid liberated or purified from the biological sample received into the sample compartment; [0080] at least a portion of the nucleic acid library prepared in the library compartment

[0081] Such recovery compartment may comprise or simply be made of another chamber wherein no reaction takes place during the operation of the system of the invention. Such recovery would preferably be easily accessible from outside the present automated system or a cartridge of the automated system. For example, it could comprise a wall made of a pierceable material (e.g. a foil or a film) that can be pierced by a needle of a syringe or a pipette, allowing aspiration of its contents. Alternatively, the recovery compartment could be selectively brought in fluid communication and filled in with any of the above by means on pumping and following instructions given by the user through an interface of the automated system of the invention.

[0082] In a possible embodiment, such recovery compartment could be an external container e.g. plastic tube or a vial, engageable with or connectable to the automated system of the invention. In such instance, any of the compartments as follows: [0083] a compartment housing at least a part of the biological sample introduced into the cartridge or at least a part of the nucleic acid liberated from said sample; [0084] the library compartment; [0085] at least one thermocycling qPCR compartment;
could comprise a structure (e.g. an extension like a channel or an zone engageable with an element forming a channel) capable of brining it in fluid communication with the recovery compartment by any means capable of transporting at least a part of the content comprised in any one of said above-listed compartments into the recovery compartments.

[0086] In an advantageous embodiment, the library compartment can comprise a structure capable of brining it in fluid communication directly with a compartment where NGS is performed, possibly wherein said compartment is comprised in another subsystem comprising an automatic sequencer being part of the automated system processing the cartridge.

[0087] In a further aspect, the present invention also provides an automated method for preparing a next-generation sequencing (NGS) nucleic acid library from a biological sample, said method comprising the steps of: [0088] a) receiving a biological sample; [0089] b) liberating or purifying at least a part of nucleic acids from the received biological sample; [0090] c) providing at least a portion of the liberated or purified nucleic acid into a library compartment for preparing an NGS nucleic acid library and comprising reagents for preparing a nucleic acid library; and [0091] d) preparing an NGS nucleic acid library;
wherein at least the steps b) to d) are performed on an automated system without any human manual intervention, at least after the biological sample has been received in said automated system.

[0092] In a preferred embodiment, the step of preparing an NGS nucleic acid library is performed by PCR.

[0093] In another particularly preferred embodiment in accordance with the above embodiments of the method of the invention, the method further comprises the step of performing qPCR on said automated system either sequentially or simultaneously with respect to the step of preparing the NGS nucleic acid library, wherein said qPCR is performed on a second portion of the liberated or purified nucleic in a thermocycling qPCR compartment suitable for amplifying nucleic acids and allowing detection of signals generated during such amplification.

[0094] As explained above, one of the aspects of the invention involves preparing an NGS library concomitantly with running either an assay qPCR and/or a QC qPCR using nucleic acid obtained from the same sample. Consequently, another embodiment, a method is provided wherein said at least one qPCR amplifies at least one disease-associated target nucleic acid sequence, or is a quality control (QC) qPCR.

[0095] In a particularly preferred embodiment, the method of the invention is performed on a cartridge engageable with the automated system. Thus, most preferably the afore mentioned steps of obtaining nucleic acid from a sample, NGS library preparation, assay qPCR, and QC PCR are performed in one cartridge, preferably being a fluidic or microfluidic cartridge engageable with an analyzer-type apparatus so that the cartridge is a self-contained disposable platform for performing the steps of the method according to the present invention. In such advantageous embodiment, all of the reagents required for performing the method of the invention are pre-positioned within such cartridge, for storage considerations preferably in a dried-down or a lyophilized form.

[0096] In another preferred embodiment, for the advantageous considerations as described above, desirably a method is provided wherein the cartridge comprises a cartridge-specific identifier for storing cartridge-specific information and wherein the method further comprises the step of introducing to the automated system the information stored in the cartridge-specific identifier.

[0097] In summary, the present invention provides an effective automation of workflow with integrated sample-in, quality checked nucleic acid library-out strategy. The presented herein approach has a great potential for providing a minimal turn-around times, lower costs, and improved NGS success rates. Furthermore, the cartridges, automated systems, and methods of the invention not only afford for simplification and acceleration of the library construction workflow, but they are also universally adaptable for the use with different sample types, even the challenging ones like FFPE samples. Thus, in a final aspect of the invention, use is provided of cartridges, automated systems, and methods of the invention for automated preparation of a next-generation sequencing (NGS) library from a biological sample.

[0098] It is to be understood that both the foregoing general description and detailed description are only exemplary and explanatory and are not restrictive for the invention as claimed. In this application, the use of singular includes the plural unless specifically stated otherwise. In this application the use of or means and/or unless stated otherwise. The use of the terms including, includes or included is not limiting.

EXAMPLES

Example 1: Development of a QC qPCR for an Automated Sample-to-Output Assessment of Nucleic Acids

[0099] First, a quality control (QC) qPCR assay was developed for the purpose of assessing the amount and quality of nucleic acids present in a sample in a fully automated manner. The present QC qPCR tests for the presence of amplicons of various lengths, each derived from a different single copy human gene, and serves to assess nucleic acid suitability for NGS application. The amplicons and their lengths are as follows: (1) 63 bp fragment from human RNaseP gene; (2) 105 bp fragment from HPRT; (3) 149 bp fragment from TFRC; (4) 213 bp fragment from ABCB; and (5) 318 bp fragment from -actin. The amplification of the fragments in one PCR reaction (5plex) was initially verified using a qPCR performed on a liquefied FFPE sample (Horizon FFPE sample) with a GoTaq polymerase and Taqman probes (composition as specified by the supplier). The qPCR programme was 5 hold 95 C., followed by 50 cycles of 5 95 C. 44 64 C. FIG. 1 shows the obtained fragments (left lane) next to a DNA ladder (right lane) on a SYBR green stained 10% polyacrylamide gel following electrophoresis in TBE. The corresponding qPCR profile of the same sample shown in FIG. 2 (sizes of amplicons indicated next to the corresponding curves). The Cq values determined with the regression algorithm contained within the Biorad CFX Manager 3.1 are: (1) 26.1 for the 63 bp fragment (RNaseP); (2) 25.6 for the 105 bp fragment (HPRT); (3) 26.0 for the 149 bp fragment (TFRC); (4) 26.2 for the 213 bp fragment (ABCB); and (5) 27.4 for the 318 bp fragment (-actin).

[0100] Next, the 5plex performance on unfragmented human genomic DNA was assessed to obtain standard curves with R squared values for each of the 5 amplicons. To do so, non-fragmented human genomic DNA at 173 g/ml (Promega) was used as a substrate and the copy number was deduced using 3.3 pg/haploid genome as a premise. 4 replicates at 24000 copies per PCR, 4 replicates at 6000 copies, 8 replicates at 1500 copies, 8 replicates at 375 copies, 12 replicates at 94, 16 replicates at 23 copies, 20 replicates at 5.9 copies and 24 replicates at 1.5 copies per PCR were amplified and the Cqs determined as described above. The median Cq values were determined while omitting non-amplifications (so called flatliners). The histogram representing this experiment is shown in FIG. 3. The standard curves were deduced for each amplicon using logarithmic regression and the R squared value was determined as exemplified in FIG. 4 for the complete dataset and the dataset without the Cq values from both 5.9 and 1.5 copies per PCR, respectively. As expected, the R squared values approach 1 better with only data points in double digits copy number. For Cq values below 34, equations with the highest R squared values were used. Notably, for Cq values above 34, the quantification is known to be less accurate due to stochastic effects. The thus calculated according to said equations copy numbers of each of the 5 amplicons allow for the determination of both the useful DNA content and the degree of nucleic acid fragmentation in a given sample. An analysis of the direction coefficient of the linear regression between the log 2 (copy number input) and the Cq provides further indication of the efficiency of amplification in 5plex qPCR of each of the amplicons. As known in the art, a perfect qPCR would be assumed to double amount of amplicon (and hence also the net Taqman fluorescence) per cycle, leaving an absolute direction coefficient of 1. In line with this, as shown in FIG. 4, the absolute direction coefficients for all amplicons except for the largest amplicon of 318 bp are 0.9 or higher, indicating a robust amplification close to doubling Taqman probe degradation per PCR cycle. The largest amplicons size shows >0.8 absolute direction coefficient indicating that the largest fragment amplifies slower and that there is little point in designing a PCR QC test with longer amplicons for this type of Taqman probe-based assay.

Example 2. Automated FFPE Sample Processing, Nucleic Acid Quality Assessment, Target Actionable Marker Screening, and Library Construction

[0101] For the purpose of demonstrating the feasibility of the present invention, a set of Biocartis Idylla cartridges was prepared, each cartridge comprising in separate PCR chambers: (i) reagents for performing the above-described QC 5plex qPCR, (ii) reagents for performing target qPCR for detecting wt and V600M/R mutant BRAF, and (iii) reagents for constructing a DNA library compatible with Illumina MiSeq sequencer. Next, a set of FFPE samples to be analyzed on said cartridges were spiked with plasmids encoding for human BRAF. To simulate clinical reality, different BRAF sequences were used including a fragment containing a wild type (wt) BRAF sequence, a fragment encoding for a V600M mutation, and a fragment encoding for two mutations V600K and T149C. The two mutated fragments were spiked in different amounts with respect to the amount of the wild type copies present in the FFPE samples to obtain a relative concentration of 10% and 5%, respectively. Each of the different BRAF-spiked FFPE samples was introduced into a separate cartridge and processed in a fully automated manner on the Biocartis Idylla instrument. In brief, the processing involved sample liquefaction (as described in e.g. WO2014128129), followed by nucleic acid purification on a silica membrane provided in the cartridge, and then followed by three independent and individually-controlled PCR reactions performed in parallel, which included: (i) verification of the quality of the purified nucleic acids via quality control 5plex QC q PCR, as described above; (ii) real time detection of selected BRAF targets (qPCR for target actionable mutations); and (iii) construction of a DNA library using BRAF-specific or standard random-priming primers comprising linkers compatible with Illumina MiSeq sequencer. The latter library-construction PCR was performed using a Q5 high fidelity hot start polymerase (New England Biolabs) and cycled according to the following programme: 5 at 95 C. and 50 cycles of 90 at 60 C., 5 at 94 C.

[0102] FIG. 5 shows the results of the 5plex QC qPCR on the different FFPE samples, which provide information with regard to the integrity of the DNA present in said samples. Panel A shows three examples of FFPE tissue samples that contain relatively intact DNA. Panel B shows three other examples that have a slightly higher degree of DNA fragmentation. Lastly, Panel C shows 6 examples of FFPE tissue samples that contain heavily fragmented DNA, which is a counter-indication for subjecting such samples to further analysis by NGS.

[0103] Based on the results of the 5plex QC qPCR, three samples with relatively intact DNA and containing three different forms of spiked BRAF (wt, V600M mutant, or double mutant V600K+T149C) were selected further investigation. Firstly, the results obtained from the assay qPCR capable of detecting wt BRAF and V600M BRAF mutation were checked to confirm the presence of the correct BRAF form. The results are shown in FIG. 6 They demonstrate that in all of the screened three FFPE samples, wt BRAF signal could be detected (FIG. 6, left column, the term target refers to wt BRAF sequence). This result was expected as all FFPE samples prior to spiking with different BRAF plasmids were known to contain wt genomic BRAF sequence. Concerning the detection of the V600M mutant (FIG. 6, right column, the term target refers to V600M/K BRAF sequence), as expected, in the sample spiked only with the wt BRAF-encoding plasmid, no V600M mutant could be detected (FIG. 6, top right pane; flat signal line for the target). However, in the FFPE samples spiked with either the V600M mutant, or the double mutant V600K+T149C, the mutation V600M was correctly detected at the expected amounts (FIG. 6, right column, bottom and middle pane). Because the used-herein BRAF-specific qPCR did not include a specific probe for the T1794C mutation, said mutation could not be detected in the double mutant BRAF-spiked sample.

Example 3. Sequencing of the Selected NGS Libraries

[0104] To confirm the results of the BRAF-specific qPCR and to also detect the presence of the undetected T1794C mutation, the NGS libraries constructed from the same three selected FFPE samples plasmid (wt, V600M, or V600K and T149C) were then subjected to Illumina MiSeq sequencing. The library PCR used for constructing these libraries is schematically shown in FIG. 7 and, as mentioned above, was performed on the same cartridges as and in parallel with the 5ples QC PCR and the BRAF-specific assay qPCR. The library PCR included 50 cycles and used simplified BRAF-specific fusion primers (also known as tailed primers). The fusion primers (shown in middle pane of FIG. 7) in addition to the target (BRAF)-specific sequence also contained sequencing primer sequence and a tag (P5 and P7) for flow cell attachment. In addition, the reverse primer also contained a barcode (or and index) that during a sequencing run allows to discern between samples obtained from different sources. The reason for introducing such barcode is that typically, libraries constructed from different samples or patients are pooled and sequenced on the same NGS instrument. Thus, in order to differentiate between libraries obtained from the three different FFPE samples, each cartridge contained a slightly different reverse primer having a unique barcode sequence.

[0105] Before sequencing, the three NGS libraries were recovered from respective cartridges using a needled syringe, after which the samples were pooled and purified further on the bench to remove any unreacted primers and primer-dimers. It should be noted that the latter purification step can also be performed automatically. Finally, the purified NGS-libraries were loaded into a flow cell of the MiSeq Illimina instrument and sequenced.

[0106] The results of the sequencing run are shown in FIG. 8. In line with the afore-described results of the BRAF-specific qPCR, in the first sample that contained only wt BRAF no mutations were detected. For the two other samples, all the expected BRAF gene mutations were correctly identified during sequencing, even if they could not be captured in the BRAF-specific qPCR. In particular, NGS not only detected the T1794C BRAF mutation missed on the target-specific qPCR, but also allowed to discriminate between the V600M and V600K mutations in mutant- and double mutant-spiked FFPE samples, respectively, thus providing even more exact identification of the already detected mutations. The present results demonstrate the unprecedented robustness of the present invention, wherein desired results are not only provided in a fast and efficient way, but also can be successfully followed up at will if deeper insight is desired.

[0107] For the fuller appreciation of the present invention, the above-described workflow is schematically illustrated in FIG. 9. It starts from providing an FFPE sample into a cartridge, after which the subsequent steps till obtaining of the final qPCR results (of both QC qPCR and target actionable marker qPCR, here BRAF) and ready-to-use library are performed in a fully automated and rapid manner (real time frames provided). It should be noted that all these results and the library are obtained from the same and identically-processed sample, which ensures high-comparability of the data from different assays. Notably, by concomitant NGS library construction and providing information with regard to said library's quality, the present approach not only allows to quickly subject a given sample to an NGS clinical follow-up, but also allows to decide whether such rather costly follow-up is feasible in view of that sample's quality. In view of the above, the present invention opens new possibilities in the current diagnostic practice.