Patent Description:
"Liquid biopsy" is a term coined to describe diagnostic procedures done on nucleic acids in the blood or in other bodily fluids (e.g. urine or cerebrospinal fluid (CSF)) of patients <NUM>, <NUM>, <NUM>. Cells dying by apoptosis or necrosis in a variety of diseases (cancer, myocardial infarction, transplant rejection) release DNA from their fragmented genomes into the bloodstream. Also, DNA from a fetus can be detected in the blood of the mother. A specific case are exosomes, <NUM>-<NUM> microvesicles, that next to DNA or RNA also contain proteins and lipids from the originating cell <NUM>, <NUM>, <NUM>. These nucleic acids in the blood can be detected and analyzed using PCR-based methods, next generation sequencing (NGS), or array technologies. Data that have been generated from analyzing liquid biopsies (e.g., nucleic acids obtained from bodily fluids rather than from tumor masses) have shown the enormous potential in this approach that could have a revolutionary impact on medical diagnosis, maybe similar only to the impact of the introduction of magnetic resonance imaging (MRI). Clinical applications that look particularly promising for the liquid biopsy approach are the diagnosis of chromosomal abnormalities in the fetus (in particular trisomy) by analyzing the blood from the mother (called also non-invasive prenatal screening (NIPT) based on cfDNA) <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, the diagnosis and monitoring of graft rejection in transplantation patients (DNA from donor tissue attacked by immune cells of the host can be detected in the patient's blood) <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, and diagnosis and monitoring of cancer disease <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>. Areas with limited data so far are other diseases with tissue necrosis or apoptosis, such as myocardial infarction <NUM>. The use of "liquid biopsy" is most advanced in the detection of fetal chromosomal abnormalities (in particular trisomies) where genomic diagnosis is challenging the traditional combination of nuchal thickness measurement by ultrasound and the triple test (AFP, hCG, and estriol) <NUM>. However, the field with the promise of highest medical impact is clearly oncology, where data generated during the last few years have shown that key cancer mutations can principally be detected by liquid biopsy that mirror those present in traditional tumor biopsies <NUM>, <NUM>, <NUM>.

Liquid biopsies may be superior to standard biopsies, as all parts of a tumor and all metastases are potentially sampled. Recent data indicate that in most cases analysis of circulating tumor DNA is faithfully reflecting mutations found in all known metastases of a cancer, or is even superior to such an approach (e.g. detecting mutations if standard biopsies fail, or showing more mutations than the standard tissue biopsies)<NUM>, suggesting that sequencing circulating tumor DNA can give a much more complete molecular picture of the systemic cancer disease than standard biopsies. Also, access to a patient's blood is unproblematic. Serial liquid biopsies can be easily taken to monitor cancer therapy effects or to screen for reoccurrence of cancer as long as the volume of blood needed for the respective analysis is small (e.g. a few milliliters). Sensitivity of the method may be superior for detecting cancer at a very early stage, e.g. in cases of reoccurrence of cancer disease after curative surgery, or in a population-based screening program. If liquid biopsy can improve early detection of tumors in preventive screening programs will lead to a higher rate of cured cancer disease, especially for tumor types where means of early detection and preventive screenings are limited or non-existent.

Several studies of liquid biopsy approaches in cancer patients have revealed that the success rate of this approach is related to the tumor mass burden and tumor stage of a patient at the time of liquid biopsy, and the approach is not very successful in instances when tumor mass is low, because there are not so many tumor cells dying and releasing DNA into the blood <NUM>, <NUM>. Moreover, the approach works well in some tumor types (e.g. colon carcinoma), but not in others (e.g. glioblastoma) presumably also due to sensitivity issues <NUM>. Limitations due to very small amounts of cfDNA are likely more relevant in cases where cfDNA is to be analyzed by whole exome or whole genome sequencing as opposed to very sensitive PCR-based approaches such as BEAMing <NUM>. Exome sequencing is advantageous to targeted PCR-based approaches, as practically the whole exome-based single-nucleotide mutation landscape can be analyzed as opposed to only few and pre-known mutations that can be assessed by targeted approaches. Therefore, exome sequencing has far more utility for early detection of cancer with high sensitivity, and of serial analyses of the changing clonal landscape of a tumor following treatment. Often, in research laboratories that have only access to standard library preparation and sequencing infrastructure, cell-free DNA amounts of <NUM> ngs are required for library construction <NUM>. With more specialized approaches, exome sequencing has been done from cfDNA amounts of a minimum of <NUM> ng<NUM>. Newman and colleagues have performed exome sequencing ("CAPP-seq") from down to <NUM> ng cfDNA<NUM>. De Mattos-Arruda used down to <NUM> ng of cfDNA input into library construction <NUM>.

A second problem that can diminish the detection power of liquid biopsy approaches is the "contamination" of cell-free DNA with DNA coming from unrelated processes (e.g. nucleated blood cells lysis during plasma isolation). Cell-free DNA present in the blood plasma or other bodily fluids (CSF, urine, ascites) can be broadly divided into the smaller size fragments (<NUM> - <NUM> and <NUM>-3x multiples of this) that originate from apoptotic breakdown of genomic DNA inside a cell, and larger size fragments that originate mainly from necrotic cell death (necrosis), but also exosome shedding, and other less understood processes. DNA fragments of apoptotic origin can also be detected in healthy people and can increase after sports or a cold for example. Current techniques for cell-free DNA analysis are composed of two principal types of methodologies: A) Next-generation sequencing (NGS): next generation exome sequencing <NUM><NUM>, targeted (TAmseq <NUM>; CAPPseq <NUM>), FastSeqS <NUM>, mFAST-SeqS <NUM>, Safe- SeqS <NUM>), or whole genome sequencing <NUM>. Some commercial kits have also been used in this (e.g. Thermo Fisher Ion AmpliSeq Cancer Hotspot Panel v2). B) Digital PCR (BEAMing: beads, emulsions, amplification and magnetics <NUM>, <NUM>, <NUM>, <NUM>, <NUM>; digital PCR ligation assay <NUM>; emulsion based ddPCR with technology from RainDance or Bio-Rad).

<CIT> refers to methods for replicating, amplifying, and sequencing of nucleic acids using the thermostable, bifunctional replicase "TthPrimPol" from Thermus thermophilus HB27. It has been found that purified TthPrimPol displayed a strong DNA primase activity on a single-stranded oligonucleotide in which a potential primase recognition sequence (GTCC) is flanked by thymine residues. Such a tract of pyrimidines has been shown to be the preferred template context for initiation of the priming reaction by several viral, prokaryotic and eukaryotic RNA primases. It has been found that priming occurred only in front of the "TC" sequence, and that there was no priming opposite the poly dT tracks. Further analysis of template sequence requirements revealed an effect of the nucleotide preceding the template initiation site on TthPrimPol's primase activity-C is preferred over A, G or T. Even if TthPrimPol prefers CTC as template initiation site, it is in general able to act as a primase on any sequence of the generic form XTC, where X stands for either of A, C, G, or T. The modest sequence requirement forms an excellent basis for random priming of nearly all natural templates. <CIT> describes systems and methods for clonal replication and amplification of nucleic acid molecules for genomic and therapeutic applications. <CIT> is concerned with a method of amplifying a target nucleic acid by rolling circle amplification. <CIT> relates to the generation of a single-stranded circular DNA from linear self-annealing segments.

Therefore, sensitivity and specificity limitations of current liquid biopsy approaches are an area in need of technical improvement.

The accompanying drawings, which are incorporated herein and form a part of the specification, illustrate exemplary embodiments and, together with the description, further serve to enable a person skilled in the pertinent art to make and use these embodiments and others that will be apparent to those skilled in the art. The invention will be more particularly described in conjunction with the following drawings wherein:.

Analysis of cell-free DNA in oncology and other fields offers huge opportunities to improve diagnosis and treatment in patients. A key problem is the difficulty to obtain results from biological fluids such as plasma, urine or CSF samples with very low cell-free DNA content. Methods disclosed herein provide a solution for this issue by amplifying short double-stranded polynucleotide fragments, including double-stranded DNA. This includes, without limitation those molecules found in cell-free DNA. Amplification is based on an amplification technology called "primase-initiated multiple displacement amplification" ("PI-MDA", also referred to as "TruePrime") combined with a novel set of sample pretreatments that allows its efficient amplification by subsequent steps such as rolling circle DNA amplification. As used herein, "primase-initiated multiple displacement amplification" or "TruePrime" refers to a form of multiple displacement amplification ("MDA") that uses a primase/polymerase to provide primers for primer extension by a DNA polymerase. Typically, the polymerase has a very strong displacement capacity and good fidelity of synthesis to avoid sequence changes during the process. One such polymerase is Phi29 DNA polymerase. While the current gold standard MDA needs short pieces of DNA ("oligonucleotides") to start off the amplification, primase-initiated multiple displacement amplification does not need any synthetic random primers.

The presently disclosed methods address, among other problems, this liquid biopsy sensitivity and specificity issue by an adapted amplification of apoptotic cell-free DNA based on the PI-MDA technology ("TruePrime"), which is a method of DNA amplification by iterative priming, copying and displacement steps. <NUM> TruePrime kits and protocols are available commercially from Expedeon AG and its affiliates. This disclosure provides a combination of existing TruePrime with the added steps of a sample pretreatment, comprising an end-repair, dA tailing, and the ligation of hairpin adaptors (see <FIG>). Individually, these steps may be carried out by methods known in the art, including by use of the New England Biolabs NEBNext Ultra II DNA Library Prep Kit and similar products and methods, and/or for example: (a) for end repair T4 polynucleotide kinase (PNK) + T4 DNA polymerase Klenow fragment and T4 DNA polymerase large fragment are commonly used (b) for dA tailing Taq polymerase is commonly used. This novel combination of methods provides an efficient process for what would otherwise be unworkable or inefficient: the amplification of small fragments of DNA by traditional TruePrime or other methods. The method steps may optionally be followed by the rolling circle DNA amplification method (see <FIG>). Thus, we provide a novel method to amplify short DNA molecules, e.g. but not limited to, apoptotic cell-free DNA without ligation, allowing an increase in the DNA available for any analytical technology, with superior sensitivity and specificity. While the methods disclosed herein provide particular advantage for short DNA fragments they also work well with DNA samples of any length.

Prim Pol is an enzyme obtained from the thermophilic bacteria Thermus thermophilus. PrimPol combines two distinct and complementary activities in a single thermostable protein: primase and polymerase. Conventional polymerases require small stretches of nucleotides (primers) annealed to a template molecule to synthesize the complementary sequence. PrimPol, on the contrary, creates its own primer sequence, thereby offering fully novel applications.

Moreover, PrimPol is able to copy both DNA and RNA. RNA reflects what genetic information is actually expressed in a cell, whereas DNA refers to the general genetic information present in every cell in the body and often only reflects a predisposition of a person to develop a disease. The development of PrimPol will help to simplify technical aspects of DNA and RNA amplification procedures.

PrimPol also shows a great tolerance to damaged DNA. DNA is subject to chemical modifications within the cells. Also during the processes necessary to purify the genetic material, and storage of forensic and clinical samples (e.g. formalin-fixed paraffin-embedded tissues) trigger such modifications. Chemical modifications have been shown to play an increasingly important role in several biological processes, such as aging, neurodegenerative diseases, and cancer. Therefore, there is great interest to develop methods for interrogating damaged DNA in the context of sequencing. Thus, an enzyme able to handle modified templates is of particular interest, since current amplification applications as well as second and third generation sequencing technologies are not optimized to use damaged samples.

PrimPol is also suited to be used in different second and third generation sequencing technologies due to its ability to introduce a variety of substrate nucleotides (e.g. fluorescent nucleotides) into DNA and RNA template molecules.

Finally, PrimPol has a role in multiple displacement amplification (MDA) reactions, generating primers for its subsequent use by Phi29 DNA polymerase, thus making unnecessary the use of random synthetic primers and possibly resulting in a more uniform amplification of DNA.

Provided herein are, among other things, methods of amplifying linear, double stranded polynucleotides (e.g., DNA molecules) and, in particular, apoptotic (mononucleosomal) cell-free DNA. Methods of amplifying linear, double stranded DNA include attaching single-stranded hairpin adaptors comprising an XTC priming sequence, wherein X is adenine (A), cytosine (C), guanine (G) or thymine (T), to both ends of the DNA molecules to produce single stranded, covalently closed DNA molecules comprising complementary internal sequences, and wherein the XTC priming sequence is located in the non-complementary portion of the adaptors; and amplifying the single-stranded covalently closed DNA molecules by rolling circle amplification using a DNA polymerase having strand displacement activity and multiple displacement amplification, e.g., primase-initiated multiple displacement amplification using TthPrimPol.

Linear double stranded DNA for use in the amplification methods described herein can be provided from any source. This includes, for example, DNA from eukaryotes, eubacteria, archaebacteria and viruses. Eukaryotic sources of DNA can include plants, animals, vertebrates, mammals, and humans. Microbial sources of DNA can include microbes sourced from a microbiome of an individual or from the environment.

The linear double stranded DNA used in the amplification methods disclosed herein can be of any length. In certain embodiments, the linear double stranded DNA has a length of no more than <NUM> nucleotides, no more than <NUM> nucleotides, no more than <NUM> nucleotides or no more than <NUM> nucleotides. In other embodiments the population of linear double stranded DNA molecules to be amplified can have an average length of no more than <NUM> nucleotides, no more than <NUM> nucleotides, no more than <NUM> nucleotides, no more than <NUM> nucleotides, no more than <NUM> nucleotides, no more than <NUM> nucleotides, no more than <NUM> nucleotides, e.g., about <NUM> nucleotides. DNA molecules to be amplified can include molecules having a length between about <NUM> and about <NUM> nucleotides. The linear double stranded DNA can comprise fragmented chromosomal DNA. Such DNA fragments may have a length greater than <NUM> nucleotides.

Nucleic acids are typically isolated from other components by isolation methods well known in the art including, without limitation, capture on particles having DNA or RNA binding activity, such as silica particles; polyethylene glycol precipitation and SPRI (Solid Phase Reversible Immobilization) beads.

The linear double stranded DNA used in the methods disclosed herein can comprise cell-free DNA ("cfDNA"). Cell-free DNA refers to DNA that is not encapsulated inside a cell. Cell-free DNA can be apoptotic cell-free DNA. (<FIG>, "Apoptotic cell-free DNA". ) Apoptotic cfDNA refers to DNA released from dead or dying cells, e.g., through the apoptosis cell death mechanism, in which the DNA is cut between nucleosomes, producing DNA fragments of <NUM>-<NUM> bp, or multiples thereof, when the cut in the DNA is not produced between every nucleosome. This includes DNA released from normal cells, e.g. having a germline genome. It also includes DNA released from cancer cells (e.g. malignant cells), also referred to as circulating tumor DNA or "ctDNA". This DNA typically carries somatic mutations associated with cancer e.g., in oncogenes or tumor suppressor genes. Apoptotic cfDNA also includes fetal DNA in the maternal circulation. Cell free DNA can be sourced from any of a number of different bodily fluids including, without limitation, blood, plasma, serum, CSF, urine, saliva, tear drops, milk, semen and synovial fluid. Apoptotic cfDNA typically has a size distribution with two peaks; a first mononucleosomal peak between about <NUM> to about <NUM> nucleotides, with a mode of about <NUM> nucleotides, and a second, minor dinucleosomal peak between about <NUM> to <NUM> nucleotides.

Cell-free DNA molecules can be prepared from bodily fluids, such as blood, by conventional methods. Commercial kits for this purpose are available from, e.g., Thermo Fisher Scientific (Waltham, MA, USA), Active Motif (Carlsbad, CA, USA) and Qiagen (North Rhine-Westphalia, Germany). In general, cells are removed from a sample, for example by centrifugation. Silica particles, e.g. magnetic silica beads, are added to the sample from which cells have been removed. The silica particles bind the DNA. The particles are isolated from the supernatant, for example by centrifugation and/or application of magnetic force. Supernatant is removed and the particles are washed. Cell-free DNA is isolated from the particles by dilution with ethanol.

In other embodiments, the double stranded DNA molecules comprise fragmented genomic DNA, for example, isolated from cells or double stranded cDNA molecules produced from reverse transcription of RNA molecules, such as mRNA, rRNA or tRNA molecules.

End-repair refers to a process of providing double stranded DNA molecules having <NUM>' and/or <NUM>' single strand overhangs with either sticky ends or blunt ends. End repair renders double stranded DNA molecules more suitable for attachment to polynucleotide adaptors. Attachment can be by either sticky-end ligation or blunt-end ligation. "Sticky-end ligation" refers to the ligation of two double-stranded polynucleotides, each of which has a <NUM>' overhang complementary to the other <NUM>' overhang. A sticky end can be, for example, a single nucleotide overhang, such as <NUM>' dA and <NUM>' dT, or a longer sticky-end, such as an overhang produced by restriction enzyme digestion. "Blunt-end ligation" refers to the ligation of a double stranded polynucleotide to the blunt-end of another, double stranded polynucleotide.

In either case, modification of the polynucleotide typically initially involves blunt ending the molecules. Typically, this involves using a polymerase to fill in a <NUM>' overhang and a molecule having exonuclease activity to chew back a <NUM>' overhang. Blunt-ending can be performed using a mixture of T4 polymerase and the DNA polymerase I klenow fragment. The klenow fragment possesses <NUM>' - <NUM>' polymerase activity to fill in <NUM>' overhangs and <NUM>' - <NUM>' exonuclease activity to remove <NUM>' overhangs. T4 DNA polymerase possesses a less efficient <NUM>'→ <NUM>' polymerase activity and a more efficient <NUM>' - <NUM>' exonuclease activity. Mung bean nuclease also can be used to eliminate <NUM>' and <NUM>' overhangs. T4 polynucleotide kinase ("T4 PNK") is used to phosphorylate the <NUM>' strand of a molecule and dephosphorylate the <NUM>' strand. Kits for performing blunt-ending of DNA molecules are available from a variety of commercial sources including Thermo Fisher Scientific (Waltham, MA, USA) and New England Biolabs (Ipswich, MA, USA).

In certain embodiments, a blunt-ended polynucleotide can be dA-tailed by a process of adding a terminal <NUM>' deoxy adenosine nucleotide to a DNA molecule. This action can be performed using Taq polymerase. (<FIG>, "End-repaired cfDNA (<NUM>'-dA overhangs)".

Blunt-ended molecules or dA-tailed molecules can be used in the methods described herein by the attachment of single-stranded adaptors.

Polynucleotides that have been end-repaired and, optionally, dA-tailed, can be ligated to adaptors. Adaptors are polynucleotide molecules adapted for attachment to target molecules. Typically, adaptors include nucleotide sequences for priming DNA strand extension. In certain methods of this disclosure the adaptor is a hairpin adaptor. As used herein, the term "hairpin adaptor" refers to a single stranded nucleic acid molecule (e.g., DNA) that includes a second region flanked by a first and third region. The first and third regions have sufficient complementarity to hybridize with each other (e.g., <NUM>%, <NUM>%, or <NUM>% complementary). The second region is not complementary to either the first or the third region. The adaptor can have a length of between <NUM> and <NUM> nucleotides long. The second region can be, for example, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, or fewer than <NUM> nucleotides long. As a consequence, a hairpin adaptor molecule can fold back on itself forming a stem-and-loop structure comprising a double stranded end and a single-stranded, internal segment that is not hybridized. Hairpin adaptors can include a <NUM>' dA overhang, or be blunt-ended, depending on the application. See, e.g., <FIG> and <FIG>.

Adaptors also include internal nucleotide sequences compatible with a DNA primase and/or primer extension. The hairpin adaptor includes a primase/polymerase recognition sequence, e.g., XTC, where X represents nucleotides adenine (A), cytosine (C), guanine (G) or thymine (T) for example, CTC, GTC or GTCC. The primase/polymerase recognition sequence is located in the loop (non-complementary) portion of the adapter, which is recognized by TthPrimPol. In other embodiments the hairpin adaptor comprises an amplification primer binding site.

End repaired, dA-tailed double-stranded polynucleotides can be attached on one or both ends to hairpin adaptors. The end of the adaptor is preferably compatible with the end of the double stranded polynucleotide. So, for example, a dA-tailed double-strand polynucleotide is attached to a dT tailed hairpin adaptor, or a blunt-ended double-stranded polynucleotide is attached to a blunt-ended hairpin adaptor. Attachment is typically performed with a DNA ligase, such as T4 DNA ligase. In certain embodiments hairpin adaptors have a sequence as depicted in <FIG>, i.e., [SEQ ID NO:<NUM>], [SEQ ID NO:<NUM>], [SEQ ID NO:<NUM>], or [SEQ ID NO:<NUM>].

The product of ligation between hairpin adaptors and double-stranded polynucleotides is a single-stranded, covalently closed polynucleotide. See, e.g., <FIG> ("Adaptor ligation"). Such a polynucleotide can also be described as a single stranded, circular polynucleotide. As used herein, the term "covalently closed DNA molecule" refers to a DNA molecule having no free <NUM>' or <NUM>' end. Such molecules are also referred to as "circular DNA". Because they have complementary internal sequences, such molecules can assume a "dumbbell" shape. A polynucleotide insert flanked on one or both ends by hairpin adaptors is referred to as a "adaptor-tagged polynucleotide".

A collection of adaptor-tagged polynucleotides is referred to as a "nucleic acid library". Typically, in the case of cfDNA, a nucleic acid library comprising a population of end-repaired DNA molecules include polynucleotide inserts having different nucleotide sequences.

Single-stranded, covalently closed polynucleotides can be amplified by methods disclosed herein.

In certain embodiments, amplification of single-stranded, covalently closed polynucleotides involves using a DNA-directed primase/polymerase, such as TthPrimPol; a DNA polymerase having strand displacement activity, such as Phi29; and modified or unmodified deoxyribonucleotides. In combination, these reagents effect rolling circle amplification primed by the primase/polymerase and extended by the DNA polymerase. Furthermore, the combination of primase/polymerase and DNA polymerase can effect multiple strand displacement amplification through priming of amplified molecules with the primase/polymerase and/or random oligonucleotide primers and primer extension by the DNA polymerase. Multiple strand displacement amplification produces a branched structure as DNA synthesis is primed and extended from many positions in the amplified molecules.

Furthermore, amplification can be accomplished without the use of oligonucleotide primer molecules by using hairpin adaptors comprising one or more primase recognition sites together with a primase having DNA priming activity on single stranded DNA, such as TthPrimPol, and a DNA polymerase having strand displacement activity, such as Phi29 and deoxyribonucleotide triphosphates. Using these reagents, a highly branched structure is produced during multiple strand displacement amplification.

As used herein, the term "priming" refers to the generation of an oligonucleotide primer on a polynucleotide template.

For amplification of DNA, the primase/polymerase is a DNA-directed primase/polymerase, and is a PrimPol enzyme. TthPrimPol. Unlike most primases, PrimPol is uniquely capable of starting DNA chains with dNTPs. The TthPrimPol enzymeis a Thermus thermophilus primase/polymerase ("TthPrimPol").

Thermus thermophilus HB27 primase/polymerase is described, for example, in <CIT> ("Methods for amplification and sequencing using thermostable TthPrimPol"). It has an amino acid sequence shown in <FIG> [SEQ ID NO: <NUM>]. It bears Gene ID: NC_005835 in the NCBI Entrez database, protein WP_011173100. <NUM> TthPrimPol can be obtained commercially in kits from Expedeon (Cambridge, UK).

Human PrimPol is also known as MYP22; CCDC111 and Primpol1, and is described herein but is not part of the invention. It bears Gene ID: <NUM> in the NCBI Entrez database.

PrimPols described herein can be a relative of any PrimPol described herein including the following: An allelic variant (a naturally occurring variation of a gene), an artificial variant (a gene or protein comprising one or more genetic modifications to a naturally occurring gene or protein while retaining natural function), a homolog (a naturally occurring gene from another genus or species than the one defined, or a distinct gene in the same strain or species that encodes for a protein having nearly identical folding and function); an ortholog (a homolog that occurs in another genus or species from the one discussed) or a paralog (a homolog that occurs in the same strain or species as the one discussed, e.g., as a result of gene duplication). A PrimPol enzyme described herein can have at least <NUM>%, <NUM>%, <NUM>%, <NUM>%, <NUM>% or <NUM>% amino acid sequence homology with the protein of SEQ ID NO: <NUM>.

Amplification methods can employ a DNA polymerase with strand displacement activity, e.g., a polymerase with strong binding to single-stranded DNA e.g., in preference to double-stranded DNA. Strand displacement activity can be useful in displacing hybridized strands of a DNA molecule while extending a primer position, for example, in the loop area of a hairpin structure.

DNA polymerases with strand displacement activity useful in methods disclosed herein include, for example, Phi29. Phi29 DNA polymerase can be obtained commercially from, for example, New England Biolabs (Ipswich, MA, USA), ThermoFisher Scientific (Waltham, MA, USA and Expedeon (Cambridge, UK). Phi29 polymerase can generate DNA fragments up to <NUM> kb. The enzyme has a <NUM>'→<NUM>' exonuclease proofreading activity and provides up to <NUM>-fold higher fidelity compared to Taq DNA polymerase-based methods. Phi29 polymerase can function on DNA comprising secondary structures such as hairpin loops.

In another embodiment the DNA polymerase can be Bacillus steatothermophilus (Bst) polymerase.

Primer creation and primer extension can be accomplished by providing primase/polymerase enzymes and DNA polymerases with deoxyribonucleotide substrates e.g., deoxyribonucleotide triphosphates. Typically, these include the four standard bases, A, T, G and C. However, in certain embodiments non-natural nucleotides, such as inosine can be included. In certain embodiments nucleotides may bear a label for detection or capture of polynucleotides into which they are incorporated.

Rolling circle amplification is a method of amplifying a covalently closed DNA molecule such as a single stranded, covalently closed DNA molecule. The template DNA molecule is primed with a primer, for example a primer provided by a primase/polymerase. A DNA polymerase performs primer extension on the primer around the closed DNA molecule. The polymerase displaces the hybridized copy and continues polynucleotide extension around the template to produce a concatenated amplification product.

Multiple displacement amplification is an isothermal, non-PCR-based DNA amplification method in which primer extension from a template molecule produces molecules which themselves are primed and copied by primer extension to produce a branch-like structure. Branches are displaced from each other as primers are extended from one DNA molecule template into the branch area. In certain embodiments MDA employs random hexamers as primers to prime amplification at multiple sites on an original template and amplified copies thereof. Multiple strand amplification is further described in, for example, <CIT> ("Multiple Displacement Amplification"). Polymerization that extends primers at multiple priming sites.

In the disclosed methods, priming is accomplished with TthPrimPol. In this case priming includes the provision of deoxyribonucleotide triphosphates as a reagent. In certain embodiments, the deoxyribonucleotides are unmodified. In other embodiments, deoxyribonucleotides can be modified by attachments to a label, for example, a fluorescent molecule. As used herein, the term "label" refers to a chemical moiety attached to a molecule, such as a nucleic acid molecule. Detectable labels include, for example, fluorescent labels, luminescent labels, enzymatic labels, colorimetric labels such as colloidal gold or colored glass or plastic beads and radioactive labels.

Referring to <FIG>, in methods disclosed herein, a single stranded, covalently closed nucleic acid molecule template ("cfDNA pretreated to add hairpin adaptors at both ends") is provided. TthPrimPol is provided and recognizes recognition sites in the hairpin adapter and primes polymerization by the synthesis of primers. ("TthPrimPol hairpin recognition and primer synthesis". ) A DNA polymerase with preference for binding single-stranded nucleic acid molecules and strand displacement activity amplifies the template through a combination of rolling circle amplification and multiple displacement amplification. Rolling circle amplification provides a concatenated molecule that folds back on itself forming double-stranded segments based on the complementary sequences. These folds also include the adapter sequences comprising primase/polymerase recognition sites. The primase/polymerase synthesizes primers on the concatenated molecule which are, in turn, extended by the DNA polymerase. The result is exponential amplification of the original template molecule, typically in branched fashion. ("Stranded displacement and exponential rolling circle amplification by new priming events".

Described herein are other methods of amplifying single-stranded, covalently closed DNA molecules.

In one method herein described, rather than priming polymerization with a primase/polymerase, amplification is primed with random sequence primers. For example, random sequence primers can be hexamers comprising a degenerate set of sequences. Amplification can continue by multiple displacement amplification.

In another method herein described, amplification of single-stranded, covalently closed DNA molecules is performed by Degenerate Oligonucleotide Primed (DOP)-PCR. (DOP)-PCR uses a single primer for PCR (instead of a forward and reverse primer). This primer is usually an oligomer having about <NUM> bases with a six nucleotide degenerate region in the center, e.g. CGACTCGAGNNNNNNATGTGG [SEQ ID NO: <NUM>]. This degenerate region is a random sequence composed of any of the four DNA nucleotides. The first five steps of the DOP-PCR procedure are a non-specific amplification step. The degenerate primer along with low annealing temperatures will cause random annealing at locations across the entire genome. During PCR, extension will occur from these primers and create long fragments.

In another method described herein, amplification of single-stranded, covalently closed DNA molecules is performed by Primer Extension Preamplification (PEP). Primer Extension Preamplification (PEP) uses random/degenerate primers and a low PCR annealing temperature. The primers can be, for example, about <NUM> nucleotides long.

In another method described herein, amplification of single-stranded, covalently closed DNA molecules is performed by linker-adaptor PCR (LA-PCR). In LA-PCR, double-stranded DNA is digested with Msel, leaving a TA overhang for adapter annealing and subsequent ligation. A single primer, complementary to the adapter, is used to amplify the whole sample by PCR.

In another method described herein, amplification of single-stranded, covalently closed DNA molecules is performed by using any combination of a thermostable DNA polymerase (e.g., Taq polymerase) and a highly processive strand-displacement DNA polymerase (e.g., Phi29 polymerase or Bacillus stearothermophilus (Bst) polymerase). One such method is Multiple Annealing and Looping Based Amplification Cycles (MALBAC). MALBAC is a non-exponential whole genome amplification method. Primers used in MALBAC allow amplicons to have complementary ends which form loops, inhibiting exponential copying.

As used herein, the term "high throughput sequencing" refers to the simultaneous or near simultaneous sequencing of thousands of nucleic acid molecules. High throughput sequencing is sometimes referred to as "next generation sequencing" or "massively parallel sequencing". Platforms for high throughput sequencing include, without limitation, massively parallel signature sequencing (MPSS), Polony sequencing, <NUM> pyrosequencing, Illumina (Solexa) sequencing, SOLiD sequencing, Ion Torrent semiconductor sequencing, DNA nanoball sequencing, Heliscope single molecule sequencing, single molecule real time (SMRT) sequencing (PacBio), and nanopore DNA sequencing (e.g., Oxford Nanopore).

Methods described herein can be used for, without limitation, whole genome sequencing, exome sequencing and amplicon sequencing. To the extent apoptotic cfDNA comprises sequences from the entire genome, the amplification product of methods described herein represent whole genome amplification. However, amplified molecules themselves, can be subject to amplification of specific amplicons. Sequence capture using baits directed to gene sequences in the genome can be used to isolate amplified molecules representing the exome. By reverse transcribing mRNA into double stranded cDNA an amplified transcriptome can be produced for sequencing.

DNA amplified by the methods disclosed herein has properties of double-stranded DNA. This is due, at least in part, to the complementarity within strands which fold back on themselves. Accordingly, amplified DNA can be prepared for sequencing as one might native double-stranded DNA. Library preparation methods depend on both the sequencing platform and the sequencing approach. For example, the sequencing platform may be adapted for short reads, such as Illumina or Ion Torrent, or for long reads, such as PacBio or Oxford Nanopore. Sequencing approaches include targeted, whole exome or whole genome sequencing. For example, to perform whole genome sequencing using Illumina, one can shear the DNA (enzymatically or mechanically) to a length appropriate to the sequencing specifications (e.g., single-end or paired-end reads and chosen lengths (<NUM> nucleotides, <NUM> nucleotides, etc.). After shearing, the libraries are prepared using kits that include the adaptors suitable for the sequencing to occur. In contrast, when using long-read whole genome sequencing, e.g., PacBio and Oxford Nanopore, a first step with T7 endonuclease is recommended to eliminate the multi-branched DNA structure derived from the multiple displacement amplification mechanism produced by all MDA methods. Otherwise, different library prep methods are followed depending on the sequencing platform. In targeted approaches, PCR is used to amplify certain regions of interest, that will be the only ones sequenced afterwards.

Also provided herein are kits for use in performing the methods disclosed herein. As used herein, the term "kit" refers to a collection of items intended for use together.

Certain kits disclosed herein include <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, elements selected from: (<NUM>) a PrimPol enzyme (e.g., TthPrimPol); (<NUM>) a DNA polymerase (e.g., Phi29); (<NUM>) a single strand hairpin adaptor; (<NUM>) one or more enzymes for dsDNA end repair (e.g., T4 DNA polymerase, klenow fragment and/or Taq polymerase); (<NUM>) one or more enzymes for DNA ligation; (<NUM>) dNTPs; (<NUM>) an enhancer, e.g. to increase DNA ligation efficiency, e.g., polyethylene glycol; (<NUM>) reaction buffer and (<NUM>) a buffer for use with any of the aforementioned elements. In particular, the invention provides a kit wherein the kit can perform RCA and MDA in a single operation, comprising: (a) TthPrimPol; (b) a polymerase having strand displacement activity suitable for rolling circle amplification (RCA) of circular DNA; (c) deoxyribonucleotide triphosphates; and (d) a single stranded hairpin adaptor suitable for attachment to linear double stranded DNA molecules, wherein the adaptor comprises an XTC priming sequence, wherein X is adenine (A), cytosine (C), guanine (G) or thymine (T). The polymerase may be Phi29 polymerase. The kit may further comprise one or more enzymes for dsDNA end repair, such as T4 DNA polymerase, klenow fragment and/or Taq polymerase. The kits can comprise containers to hold these reagents for. Kits can include containers to hold reagents. Containers, themselves, can be placed into a shipping container. The container can be transmitted by hand delivery or by a common carrier, such as a national postal system or a delivery service such as FedEx. Kits also can contain a container for shipping collected blood to a central facility, such as a box or a bag. Kits can also typically include instructions for use as well as and software for data analysis and interpretation.

Shown in <FIG> is the amplification of short DNA molecules (<NUM> bp) obtained by PCR amplification. The end-repair and dA-tailing reaction, and the addition of the hairpin adaptors enables the efficient amplification of the short DNA input by TruePrime.

The presence in DNA <NUM> of a single restriction recognition site for EcoRI enzyme allowed us to obtain single units of the amplified material (see <FIG>), demonstrating the amplification mechanism illustrated in <FIG>.

Shown in <FIG> is the amplification of short DNA molecules (<NUM> bp) obtained by PCR amplification and subjected to the procedure of the disclosure: end-repair, dA-tailing, hairpin-adaptor ligation and rolling circle amplification. The rolling circle amplification can be carried out either with TthPrimPol (TruePrime) or random synthetic primers (RPs) to trigger the amplification, using two independently- prepared DNA samples as substrate (Prep <NUM> and Prep <NUM>). The amplification yield is much higher when using random primers (see <FIG> upper part). However, the analysis of the same amount of amplified DNA (<NUM> ng) by restriction enzyme digestion reveals that TruePrime (based on TthPrimPol) produces more target molecules (<NUM> bp) than random primers, probably due to the amplification of primer dimers, which is a well-known drawback of MDA methods based on random synthetic primers.

Shown in <FIG> is the amplification of DNA molecules ranging from <NUM> bp up to <NUM> bp (<NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM> and <NUM> bp) obtained by PCR amplification. The end-repair and dA-tailing reaction, and the addition of the hairpin adaptors enables the efficient amplification of the different DNA molecules by TruePrime.

Shown in <FIG> are the different hairpin adaptors tested. All the adaptors have self-complementary sequences that allow auto-hybridization of the molecules forming a hairpin. The hairpin sequence and length differ in each case.

Shown in <FIG> is the DNA primase activity of TthPrimPol, the enzyme in charge of synthesizing the DNA primers for Phi29 DNA pol in TruePrime, using adaptors with different hairpin sizes and sequences. Adaptor <NUM> shows the highest activity, as can be deduced from the amount of DNA primers generated, as well as the almost complete absence of the unincorporated labelled nucleotide (G*), which highlights the efficiency of the DNA primase activity using this molecule. Surprisingly, the other three adaptors that contain a more accessible TthPrimPol recognition sequence (<NUM>' CTCC <NUM>') <NUM>show less activity, especially in the case of adaptor <NUM>. Adaptor <NUM> shows the highest activity and the shortest sequence, so it becomes the best candidate to be used in the cfDNA amplification workflow.

<NUM> cancer patients were recruited for this study under informed consent. <NUM> mls of blood were extracted using Streck Cell-free DNA BCT® tubes. <NUM> mls pf plasma were immediately isolated through a double-spin centrifugation protocol to avoid genomic DNA contamination from nucleated blood cells. Cell-free DNA was purified from <NUM> of plasma samples using the gold-standard cfDNA purification kit (Qiagen QIAamp Circulating Nucleic Acid Kit). Different yields were obtained in each case quantified by Qubit (ranging from <NUM> up to <NUM> ng/µl). Cell-free DNA size profile was analyzed using the Bioanalyzer HS kit to confirm the presence of the apoptotic cell-free DNA molecules of interest (size ∼<NUM>-<NUM> bp) and the absence of other longer DNA molecules.

<NUM> ng of cfDNA in each case followed the disclosure workflow for cfDNA amplification (steps shown in <FIG>, left part); i.e. beginning with the steps of end-repair, dA-tailing and adaptor <NUM> ligation. After that, resulting samples (<NUM>µl) were amplified using the TruePrime technology. Shown in <FIG> (right part) are the amplification yields obtained. All cell-free DNA samples were efficiently amplified.

Shown in <FIG> are the excellent sensitivity and efficiency of the disclosure workflow, which achieves DNA amplification yields in the range of micrograms starting from picograms of cell-free DNA. It is remarkable the proportionality between the input amount and the amplification yield observed.

<NUM> ng of cell-free DNA from a colon cancer patient (T3N1aM0) were subjected to the disclosure workflow for cfDNA amplification in duplicate.

Long-read (Oxford Nanopore MinION) whole genome sequencing: <NUM> ng of each amplified cell-free DNA were pre-treated with T7 endonuclease I before preparing the library to eliminate the multi-branched DNA structure. Ligation ID sequencing kit SQK-LSK108 was used and protocol ID genomic DNA sequencing for the MinION device using SQK-LSK <NUM> was followed. The flow cell was run for <NUM> hours.

The sequences from the Oxford Nanopore MinION run were analyzed and tested for the occurrence of the hairpin adaptor sequence [SEQ ID NO:<NUM>]. Although the sequencing quality was not high, the sequence of the hairpin adaptor [SEQ ID NO:<NUM>] could be found in almost every read and separated sequence fragments with a high similarity (proven by BLAST of those fragments, which had identical genetic region as hit).

Shown in <FIG> is the high correlation of fragments separated by the hairpin adaptor sequence [SEQ ID NO:<NUM>] in respect to the length of the MinION read.

Short-read (Illumina) whole genome sequencing: <NUM> ng of each amplified cell-free DNA were sheared with Covaris to obtain <NUM> bp fragments. Sheared DNA was purified using AMPure beads and the library was prepared using the NxSeq AmpFREE Low DNA Library kit (Lucigen). Dual indices were added by PCR and the samples were sequenced in an Illumina HiSeq <NUM> using paired-end reads (<NUM> x <NUM> bp).

Shown in <FIG> are the coverage and copy number variant (CNV) detection results. The coverage of two samples from the same patient looks nearly identical and highly even, as does the CNV plot, in which except for single parts both samples have an identical composition of ploidies. The reads were analyzed by CLC Genomics Workbench, combined into one read and then separated again at the position of the hairpin. The hairpin sequence could be found in almost all combined reads. The again separated and artificially created new paired reads were aligned to the human genome and analyzed for the coverage statistics, reproducibility and CNV content.

Shown in <FIG> is the coverage plot from the two samples from one patient in different resolutions. It is remarkable the almost identical amplification and results from the post-sequencing process.

<NUM>, <NUM> and <NUM> ng of cell-free DNA from three different colon cancer patients (T3/<NUM>) were subjected to disclosure workflow for cfDNA amplification, obtaining <NUM>, <NUM> and <NUM>µgs respectively. <NUM> ng of the non-amplified cfDNA and <NUM> ng of the amplified cfDNA from each patient were sequenced using the Oncomine™ Colon cfDNA Assay with tag molecular barcodes for multiplexing in an Ion Proton™ sequencing system, using an Ion Proton™ Chip. Libraries were prepared using the Ion Chef™ system. Read alignment was carried out using the Torrent Suite Software and the variant calling was performed using the CLC software with the following settings: Ploidy = <NUM>. Ignore positions with coverage above = <NUM>. Restrict calling to target regions = Oncomine_Colon_cfDNA. Designed_BED. Ignore broken pairs = No. Ignore non-specific matches = Reads. Minimum coverage = <NUM>. Minimum count = <NUM>. Minimum frequency (%) = <NUM>-<NUM>. Base quality filter = No. Read direction filter = No. Relative read direction filter = No. Read position filter = No. Remove pyro-error variants = No. Create track = Yes. Create annotated table = No..

Variant calling was carried out for single nucleotide variants, multiple nucleotide variants, insertions and deletions at different frequencies, from <NUM>% to <NUM>%. Shown in <FIG> are the number of annotated and non-annotated variants detected in each patient comparing the amplified and non-amplified cfDNA samples in each case.

In the three cases, more variants were detected in the amplified sample than in the non-amplified one, independently of the mutation allele frequency threshold. Additionally, the number of annotated variants is also higher in the amplified samples than in the non-amplified ones.

Shown in <FIG> are the results obtained for the first patient and the higher number of clinically relevant variants in the amplified sample in comparison to the non-amplified cfDNA sample from the same patient at two different allele frequencies (<NUM>% and <NUM>%). For the <NUM>% frequency, <NUM> clinically relevant (ClinVar) mutations are detected in the amplified sample, while only <NUM> in the non-amplified one. From those <NUM>, <NUM> are also detected in the amplified sample. For the <NUM>% frequency, <NUM> ClinVar mutations are detected in the non-amplified sample. Those <NUM> and <NUM> additional ClinVar mutations are found in the amplified material.

Shown in <FIG> are the results obtained for the second patient and the higher number of clinically relevant variants in the amplified sample in comparison to the non-amplified cfDNA sample from the same patient at two different allele frequencies (<NUM>% and <NUM>%). For the <NUM>% frequency, <NUM> ClinVar mutations are detected in the amplified sample, while only <NUM> in the non-amplified one. From those <NUM>, <NUM> are also covered in the amplified sample.

Shown in <FIG> are the results obtained for the third patient and the higher number of clinically relevant variants in the amplified sample in comparison to the non-amplified cfDNA sample from the same patient at two different allele frequencies (<NUM>% and <NUM>%). For the <NUM>% frequency, <NUM> ClinVar mutations are detected in the amplified sample, while only <NUM> in the non-amplified one. From those <NUM>, <NUM> are also covered in the amplified sample.

Therefore, the use of the procedure of the disclosure before amplicon sequencing increases the sensitivity of the analysis, enabling the detection of more clinically relevant variants.

Claim 1:
A method of amplifying DNA comprising:
a) providing linear double stranded DNA molecules;
b) attaching single-stranded adaptors comprising an XTC priming sequence, wherein X is adenine (A), cytosine (C), guanine (G) or thymine (T), to both ends of the linear double stranded DNA molecules to produce single stranded, covalently closed DNA molecules comprising complementary internal sequences, wherein the XTC priming sequence is located in the non-complementary portion of the adaptors; and
c) amplifying the single-stranded, covalently closed DNA molecules in a single operation by (i) rolling circle amplification using a DNA polymerase having strand displacement activity and (ii) multiple displacement amplification using TthPrimPol.