EP4100543A1 - Procédés d'amplification d'adn génomique et préparation de banques de séquençage - Google Patents

Procédés d'amplification d'adn génomique et préparation de banques de séquençage

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Publication number
EP4100543A1
EP4100543A1 EP21703257.2A EP21703257A EP4100543A1 EP 4100543 A1 EP4100543 A1 EP 4100543A1 EP 21703257 A EP21703257 A EP 21703257A EP 4100543 A1 EP4100543 A1 EP 4100543A1
Authority
EP
European Patent Office
Prior art keywords
primers
sequence
nucleotides
amplicons
dna
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
EP21703257.2A
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German (de)
English (en)
Inventor
Jean Christoph NIEMÖLLER
Julian RIBA
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Albert Ludwigs Universitaet Freiburg
Original Assignee
Albert Ludwigs Universitaet Freiburg
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Application filed by Albert Ludwigs Universitaet Freiburg filed Critical Albert Ludwigs Universitaet Freiburg
Publication of EP4100543A1 publication Critical patent/EP4100543A1/fr
Pending legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions

Definitions

  • the invention relates to a method of amplifying DNA of more than one samples for generating a sequencing library, the method comprising a.) providing for each of the more than one samples an individual reaction vessel comprising the DNA in single stranded form, b.) adding first primers to the reaction vessel to produce a reaction mixture, wherein the first primers comprise in a 5’ to 3’ orientation a constant sequence and a variable sequence, wherein the constant sequence comprises in a 5’ to 3’ orientation a first part with a sequence that can be common for the more than one samples and a second part with a sequence that is different for each of the more than one samples, c.) adding a DNA polymerase to the reaction vessel, d.) subjecting the reaction mixture to a temperature at which the first primers anneal to the single stranded DNA via the variable sequence, e.) subjecting the reaction mixture to a temperature at which the DNA polymerase extends the 3’-ends of the annealed first primers to produce first-round amplicons
  • genomic DNA In order to analyze the genome of individual cells or other sample comprising only very little amount of genomic DNA, the genomic DNA must first be amplified (whole-genome-amplification, WGA for short). From the amplified genomic DNA, DNA libraries are then prepared for subsequent DNA sequencing using Next-Generation-Sequencing (NGS sequencing library preparation).
  • WGA whole-genome-amplification
  • NGS sequencing library preparation Next-Generation-Sequencing
  • library preparation refers to a method for providing DNA amplicons or fragments thereof that can be used in a NGS reaction.
  • DNA fragments For the most commonly used lllumina sequencing-by- synthesis technology, such DNA fragments must be between 200 and 1000 bp long and must be flanked by sequencing adapters at both ends. Only fragments/amplicons with a known sequence (adapter A) at one end (5’-end) and another known sequence (adapter B) at the other end (3-end) can be sequenced by this technology. Accordingly, since most known WGA technologies result in DNA amplicons that are much longer than 1000 bp, the process of library preparation mostly requires DNA fragmentation and subsequent ligation of adapter sequences.
  • Both the WGA and the NGS library preparation are complex and cost-intensive procedures (due to the expensive reagents).
  • the cost aspect is also a limiting factor for the broad application of genomic analysis of individual single cells.
  • US6977148B2 describes an amplification method called Multiple Displacement Amplification (MDA) that uses phi29 DNA polymerase for isothermal amplification. Due to the high accuracy of the phi29 polymerase, this method usually has relatively low error rates.
  • MDA Multiple Displacement Amplification
  • nonlinear amplification leads to uneven amplification of individual regions of the genome, which is problematic in two respects: First, the amplified DNA is not suitable for the analysis of copy number variations. Furthermore, the unevenly amplified DNA requires a higher sequencing depth (i.e. additional costs) because otherwise the under-represented sections of the genome are not captured during sequencing. MDA results in DNA fragments with an average length of 10 kb (10,000 base pairs), which have to be fragmented before NGS sequencing library preparation can occur. Also, NGS sequencing library preparation has be performed individually for each cell or sample.
  • MALBAC Multiple Annealing and Looping Based Amplification Cycles
  • US2014/0228255A1 discloses primers with a constant 5’ region and a variable 3’ region, where the constant region comprises a barcoding sequence at its 3’ end for use in a MALBAC amplification.
  • the amplification reaction is a non-modified MALBAC reaction with the limitations described above for the method of Zong, C et al.
  • the amplification products resulting from known WGA methods can be subjected to sonication or enzymatic cleavage. Subsequently, the fragmented amplicons can be ligated to sequencing adapters.
  • the ligated sequencing adapter often comprise an individual barcoding-sequence which enables identification of DNA fragments resulting from an individual cell.
  • barcoding of the fragments only occurs after fragmentation, library preparation has to be performed individually for each sample/each cell to be analyzed.
  • asymmetric sequencing adapter sequences could be introduced by primers (single stranded oligonucleotides) that are used for amplifying the dsDNA molecules of the sequencing library.
  • primers single stranded oligonucleotides
  • alternative or improved methods for asymmetric ligation of sequencing adapters to DNA fragments are provided by primers (single stranded oligonucleotides) that are used for amplifying the dsDNA molecules of the sequencing library.
  • the technical problem underlying the present invention is to provide a method of amplifying genomic DNA of more than one sample resulting in amplified DNA fragments that do not have to be further fragmented for library preparation and that comprise an sequence that identifies them as originating from a specific sample, such as a specific single cell.
  • An additional problem is the provision of an alternative or improved method for asymmetric ligation of sequencing adapters to DNA fragments.
  • the invention therefore relates to a method of amplifying DNA of more than one samples for generating a sequencing library, the method comprising a. providing for each of the more than one samples an individual reaction vessel comprising the DNA in single stranded form, b. adding first primers to the reaction vessel to produce a reaction mixture, wherein the first primers comprise in a 5’ to 3’ orientation a constant sequence and a variable sequence, wherein the constant sequence comprises in a 5’ to 3’ orientation a first part with a sequence that can be common for the more than one samples and a second part with a sequence that is different for each of the more than one samples, c. adding a DNA polymerase to the reaction vessel, d.
  • reaction mixture subjecting the reaction mixture to a temperature at which the first primers anneal (hybridize) to the single stranded DNA via the variable sequence, e. subjecting the reaction mixture to a temperature at which the DNA polymerase extends the 3’-ends of the annealed first primers to produce first-round amplicons, f. subjecting the reaction mixture to a temperature to produce single stranded amplicons, g. subjecting the reaction mixture to a temperature at which free first primers anneal to the single stranded DNA and to the first-round amplicons via the variable sequence, h.
  • reaction mixture subjecting the reaction mixture to a temperature at which the DNA polymerase extends the 3’-ends of the annealed first primers to produce first-round amplicons from first primers annealed to the DNA and second-round amplicons from first primers annealed to first-round amplicons, i. subjecting the reaction mixture to a temperature to produce single stranded amplicons, j. repeating the steps (g)-(i) to produce second-round amplicons of the DNA.
  • the invention preferably relates to the amplification of very small amount of DNA provided in each of the more than one samples.
  • the method relates to the amplification of genomic DNA, such as genomic DNA from more than one single cells. Therefore, in embodiments, the invention relates to a method of amplifying genomic DNA of more than one samples for generating a sequencing library, the method comprising a. providing for each of the more than one samples an individual reaction vessel comprising the genomic DNA in single stranded form, b.
  • first primers to the reaction vessel to produce a reaction mixture
  • the first primers comprise in a 5’ to 3’ orientation a constant sequence and a variable sequence
  • the constant sequence comprises in a 5’ to 3’ orientation a first part with a sequence that can be common for the more than one samples and a second part with a sequence that is different for each of the more than one samples
  • c. adding a DNA polymerase to the reaction vessel d. subjecting the reaction mixture to a temperature at which the first primers anneal (hybridize) via the variable sequence to the single stranded genomic DNA, e.
  • reaction mixture subjecting the reaction mixture to a temperature at which the DNA polymerase extends the 3’-ends of the annealed first primers to produce first-round amplicons, f. subjecting the reaction mixture to a temperature to produce single stranded amplicons, g. subjecting the reaction mixture to a temperature at which free first primers anneal via the variable sequence to the single stranded genomic DNA and to the first-round amplicons, h. subjecting the reaction mixture to a temperature at which the DNA polymerase extends the 3’-ends of the annealed first primers to produce first-round amplicons from first primers annealed to genomic DNA and second-round amplicons from first primers annealed to first-round amplicons, i. subjecting the reaction mixture to a temperature to produce single stranded amplicons, j. repeating the steps (g)-(i) to produce second-round amplicons of the genomic DNA.
  • the invention is directed to a method of amplifying genomic DNA of more than one samples, wherein during the initial amplification step the amplified DNA of each sample is labeled or tagged with an individual sequence-label (or an individual sequence barcode or an individual barcoding- sequence). Provision of a barcoding-sequence to the amplicons during the initial amplification step enables pooling of amplicons generated from the initial amplification before a sequencing library is generated by providing the amplicons with adapter sequences for sequencing. The provision of the sequence-labels is not disclosed for amplification methods and in particular WG A methods of the state of the art.
  • the method of the invention in contrast, surprisingly it is possible by means of the method of the invention to generate amplicons of genomic DNA that are short enough to avoid an additional fragmentation step.
  • the amplification method of the invention generates sufficient number amplicons of genomic DNA that have a maximum length of about 1000 nucleotides in order to cover the whole genome. Accordingly, the amplification method of the invention enables subsequent library preparation without a fragmentation step resulting in a sequencing library that covers the whole genomic DNA provided in each of the samples of the method of the invention. Therefore, it is possible to pool reaction mixtures resulting from the amplification method of the invention or amplicons resulting from the amplification method of the invention already after the initial amplification reaction and before library preparation.
  • the amplification products comprise sufficient amplicons of less than about 1000 bp length that cover the complete sequence of genomic DNA initially provided for each sample.
  • the more than one samples are more than one single cells.
  • Such single cells can be prokaryotic cells (such as bacterial or Archaeal cells) or eukaryotic cells (such as mammalian or human cells).
  • the cells can be first isolated by isolating them into the reaction vessels of a microtiter plate.
  • Several methods can be used for separation, such as sorting with a flow sorter or a FACS device, single-cell dispensing, limiting dilution, or micromanipulation.
  • the cells may then be lysed in a suitable lysis buffer (cell lysis), whereby the cell membrane is broken open so that the DNA molecules can be accessed for subsequent amplification.
  • the genomic DNA is now available as the starting material (DNA template) for the subsequent reaction.
  • the necessary reagents and a primer with a cell/well-specific barcoding-sequence can now be added to each well.
  • pre-amplification which is also referred to as the first amplification reaction of the invention, the liquid from all wells can be pooled into a reaction vessel.
  • the subsequent second amplification reaction and creation of the sequencing library by provision of asymmetric adapter sequences to the amplicons of the amplification method of the invention can now be performed in a single reaction vessel without the need for fragmentation of the amplicons.
  • samples comprise small amounts of genomic DNA that require an amplification step prior to use in a sequencing reaction.
  • Samples comprising a single cell only comprise one set of chromosomes representing genomic DNA. Accordingly, there is only one copy of double stranded genomic DNA present in each sample comprising a single cell.
  • the DNA In order to sequence the genomic DNA present in a single cell, the DNA has to be amplified to provide an amount of DNA that is sufficient for sequencing. Ideally, the amplification reaction does not create a bias towards certain sequences by more efficiently amplifying certain sequences, while less efficiently amplifying other sequences of the provided genomic DNA. Many methods of amplifying genomic DNA create a bias towards certain sequences, which are amplified more efficiently in the beginning. Since these efficiently generated amplicons can in certain amplification methods also serve as templates in the next amplification round, a bias for such sequences is generated.
  • the method of the invention may comprise a sample that represents a negative control that does not comprise any genomic DNA or any DNA at all.
  • a positive control sample may be included, for example a sample that comprises a known, defined amount of DNA, such as a defined amount of genomic DNA.
  • the sample can be subjected to a temperature that leads to melting of the double stranded genomic DNA of the sample.
  • This temperature is usually a temperature above 90 °C, such as for example 91 , 92, 93, 94, 95, 96, 97, 98 or 99 °C. In the context of the invention, it preferably about 92 °C to 98 °C.
  • the step of providing single stranded genomic DNA may comprise cell lysis and/or chromatin digestion.
  • the step of cell lysis can also be regarded as an individual method step that occurs in the beginning of the method.
  • a suitable volume of a lysis buffer may be added to each sample.
  • the samples may be mixed and/or heated to an elevated temperature in the range of 60-100 °C.
  • a suitable protease for digestion of the protein components of chromatin may be added to the sample followed by an incubation at a suitable temperature and for a suitable time in order to remove protein components from the DNA material of the samples.
  • the order of the certain method steps may be modified. Possible modifications of the method step order are obvious to a person skilled in the art.
  • method steps (a)-(c) may have a different order, since it is obviously possible to first assemble a reaction mixture comprising first primers (b) and a polymerase (c) and DNA, such as genomic DNA, and subsequently bring the reaction mixture to a temperature at which the provided DNA, which may be double stranded genomic DNA, is broad into a single stranded state (reaction step a). Accordingly, the addition of first primers and a polymerase can occur before heating the sample so that the comprise dsDNA is provided in a single stranded state.
  • the first primer may be added to the sample prior to subjecting the sample to a temperature leading to the melting of double stranded DNA.
  • the DNA polymerase may have been added to the sample before the melting step, preferably at the same time as the first primer.
  • the DNA polymerase to be used in the context of the method of the invention is preferably stable at temperatures up to 100 °C, such as for example a Taq polymerase or a Deep Vent DNA Polymerase or a Deep Vent (exo-) DNA Polymerase, which is preferably used in the context of the method of the invention.
  • the DNA polymerase of the initial amplification step of the method of the invention is a Deep Vent (exo-) DNA Polymerase with high stability at 95°C and 100 °C and eliminated 3’ to 5’ proofreading exonuclease activity.
  • Polymerases to be used in the context of the invention comprise strand-displacing polymerases, polymerases that possess a 5'-flap endonuclease and/or polymerases 5'-3' exonuclease activity.
  • Strand-displacing polymerases are polymerases that will dislocate downstream fragments as it extends.
  • Strand displacing polymerases include F29 Polymerase, Bst Polymerase, Pyrophage 3173, Vent Polymerase, Deep Vent polymerase, TOPOTaq DNA polymerase, Vent (exo-) polymerase, Deep Vent (exo-) polymerase, 9°Nm Polymerase, Klenow fragment of DNA Polymerase I, MMLV Reverse Transcriptase, AMV reverse transcriptase, HIV reverse transcriptase, a mutant form of T7 phage DNA polymerase that lacks 3'-5' exonuclease activity, or a mixture thereof.
  • One or more polymerases that possess a 5' flap endonuclease or 5 '-3' exonuclease activity such as Taq polymerase, Bst DNA polymerase (full length), E. coli DNA polymerase, LongAmp Taq polymerase, OneTaq DNA polymerase or a mixture thereof may be used to remove residual bias due to uneven priming.
  • the initial amplification reaction comprises a polymerase with 5’- 3’ exonuclease activity and/or a polymerase with strand displacement activity.
  • the first primers comprise in a 5’ to 3’ orientation a constant sequence and a variable sequence.
  • the constant sequence is located upstream (towards the 5’-end) from variable sequence.
  • the constant sequence is located at the 5’-end of the first primers.
  • the sequence of the first primers consists a variable sequence at the 3’- end and a constant sequence at the 5’-end.
  • variable sequence of the first primers comprises between 3 and 12 nucleotides, which are randomly selected from among G, T, A and C, wherein the variable sequence is configured to enable the first primers to anneal randomly to single-stranded DNA molecules, preferably single-stranded genomic DNA molecules.
  • variable sequence of the first primers consists of between 3 and 12 nucleotides, which are randomly selected from among G, T, A and C, wherein the variable sequence is configured to enable the first primers to anneal randomly to single-stranded DNA molecules, preferably single-stranded genomic DNA molecules.
  • variable sequence consists for 4-11 , 5-10, 6-9, 7-8 nucleotides, wherein the indicated ranges include the noted end-values.
  • variable sequence of the first primers consists of between 3 and 12 nucleotides, whereof 1-6 nucleotides are LNA nucleotides. In embodiments, the variable sequence consists of LNA nucleotides. In embodiments, the LNA percentage in the variable sequence is 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100 %. Such embodiments comprising LNA nucleotides are advantageous since LNA nucleotides have a stabilizing effect.
  • variable sequence of the first primers consists of between 3 and 12 nucleotides, where parts of the variable sequence contain bases randomly selected from among G and C and in other parts of the variable sequence are randomly selected from among G, T, A and C.
  • variable sequence of the first primers are GC-rich, which has a stabilizing effect and/or increases primer affinity.
  • the GC-percentage in the variable sequence is above 60, 65, 70, 75, 80, 85, 90, 95 %.
  • the length of the variable sequence is in the range of 6-18, preferably 7-17, 8- 16, 9-15, 10-14, 11-13 or 12 nucleotides.
  • certain or all nucleotides of the variable sequence may be LNA nucleotides.
  • Such variable sequence may also be GC-rich.
  • variable sequences such as variable sequences of at least 6, 7, 8, 9, 10, 11 .
  • the bases upstream from the variable region of the first primer which can be part of the barcoding-sequence (the second part of the constant region of the first primer) or can be located in between the variable sequence and the barcoding sequence, are G and/or C.
  • the first 1 , 2, 3, 4, 5 or 6 bases upstream from the variable region may be G or C.
  • first primer having two G directly upstream from the variable sequence leads to generation of smaller amplicons, in average.
  • Experimental data indicate that surprisingly stabilization of first primer binding, for example through a comparably long variable sequence that may comprise LNA nucleotides and/or may have a high GC-content leads to amplification of shorter fragments which are mostly or almost all below 1000 nucleotides length.
  • the Mg concentration in the reaction mixture is about 0.5 - 5.0 mM. In a specific embodiment, the Mg concentration in the reaction mixture is about 3.5 mM. In further embodiments, the Mg concentration is above 4 mM, preferably above 4.5 mM.
  • the Mg concentration is about 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1 , 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1 , 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1 , 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1 , 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9, 9.5, 10, 10.5, 11 , 11.5, 12, 12.5, 13, 13.5, 14, 14.5, 15,
  • Mg concentrations of 4 mM of more can lead to an increasing stability of binding of the first primers to the DNA via the variable sequence, which leads to the preferential generation of nucleotides of 1000 nucleotides length or less.
  • the reaction mixture comprises betaine, preferably at a concentration of about 0,5 - 2 M.
  • the betaine concentration in the reaction mixture is about 1 M.
  • the betaine concentration is below 1 M, preferably below 0.9, 0.8, 0.7, 0,6, 0.5, 0.4, 0.3, 0.2, 0.1 , 0.09, 0.08, 0.07, 0.06, 0.05 M.
  • Betaine concentrations of less than 1 M can lead to an increasing stability of binding of the first primers to the DNA via the variable sequence, which leads to the preferential generation of nucleotides of 1000 nucleotides length or less.
  • the first primers can initiate overlapping amplicons throughout the genome.
  • the variable sequence may consist of a first part and a second part, wherein the second part is located at the 3’-end of the first primer.
  • variable sequence may be randomly selected or may be purposefully selected commensurate with the frequency of its representation in a source DNA, such as genomic DNA.
  • nucleotides of the variable sequence will prime at target sites in a source DNA, such as a genomic DNA, containing the corresponding Watson- Crick base partners.
  • the variable region is considered degenerate.
  • the first part of the variable sequence may be randomly selected or may be purposefully selected commensurate with the frequency of its representation in a source DNA, such as genomic DNA.
  • the nucleotides of the first part of the variable sequence will prime at target sites in a source DNA, such as a genomic DNA, containing the corresponding Watson- Crick base partners.
  • a source DNA such as a genomic DNA
  • the first part of the variable region is considered degenerate.
  • the first part of the variable sequence can be characterized by a plurality of nucleotides, such as between 3 and 7 nucleotides which are randomly selected from among G, T, A, and C. For example, if the first part of the variable sequence includes 5 nucleotides, then the number of possible random sequences forming primers is 4 5 .
  • the second part of the variable sequence can include or can be composed of between 2 and 4 nucleotides, wherein the second part of the variable sequence avoids self-complementary sequences.
  • the second part of the variable sequence can include three G (i.e., G- G-G) or three T (i.e., T-T-T) orTTG, GAA or ATG.
  • the constant sequence of the first primers comprises in a 5’ to 3’ orientation a first part with a sequence that can be common for the more than one samples and a second part with a sequence that is different for each of the more than one samples.
  • the constant sequence of the first primers comprises between 10 and 70 nucleotides, preferably about 10-40 nucleotides, wherein the first part of the constant sequence comprises between 5 and 66 nucleotides, preferably 5-36 nucleotides and the second part of the constant sequence comprises between 4 and 10 nucleotides.
  • the constant sequence of the first primer may comprise 10-80, 11-79, 12-78, 13-77, 14-76, 15- 75, 16-74, 17-73, 18-72, 19-71 , 20-70, 21-69, 22-68, 23-67, 24-66, 25-65, 26-64, 27-63, 28-62, 29-61 , 30-60, 59-31 , 58-32, 33-57, 34-56, 35-55, 36-54, 37-53, 38-52, 39-51 , 40-50, 41-49, 42- 48, 43-47, 44-46, 45 nucleotides, wherein the indicated ranges include the noted end-values. This holds true for all end-values disclosed herein in the description of a parameter range.
  • the second part of the constant sequence can be, for example, 4, 5, 6, 7, 8, 9, 10,
  • the second part of the constant sequence of the first primers represents the sequence-label (or barcoding-sequence) that is specific for each sample of the method of the present invention.
  • amplicons can be assigned to individual samples also after pooling of amplicons after the initial round amplification step using the first primers.
  • the sequence of the first part of the constant sequence of the first primers is common for all of the more than one samples.
  • Such embodiments are preferable, since the amplicons resulting from all samples of the method have the same 5’ and 3’ ends, which can be targeted by further primers or oligonucleotides used for amplification reactions or library preparation. This enables pooling of the reaction mixtures of the individual samples as early as after method step .
  • the constant sequence can include a nucleic acid sequence that is substantially non-self- complementary and substantially non-complementary to other primers in the plurality of primers used in the reaction mixture.
  • the constant sequence is preferably known and may be a targeted sequence for a primer in amplification or library preparation methods.
  • the first part of the constant sequence of the first primers is common to all first primers used in the context of the method of the invention.
  • the constant sequence or the first part of the constant sequence and is characterized by a plurality of nucleotides, which include G, T, and A, but excluding C. That is, C is not present in the constant sequence or the first part of the constant sequence. In embodiments, C is not present in the second part of the constant sequence.
  • the first primers have a sequence according to SEQ ID N01 , wherein D can be selected from G, A and T, and N can be selected from G, A, T and C.
  • the first primers are HPLC purified oligonucleotides.
  • the primers are phosphorylated at the 5’-end.
  • the first part of the constant sequence of the first primer consists of 30 nucleotides, which can be selected among A, T, G and C.
  • the second part of the constant sequence consists of 5 nucleotides. These can be selected among A, T, G and C.
  • the nucleotides of the second part of the constant sequence can be G, A or T.
  • the variable sequence at the 3’-end consists of 7 nucleotides which are randomly selected among A, G, T and C.
  • variable sequence of first primers of SEQ ID N01 comprises or consists of LNA nucleotides.
  • the primer according to SEQ ID N01 comprises phosphrothioate modifications (phosphrothioate internucleotide linkages) between all nucleotides of the second part of the constant sequence.
  • the first primers comprise in the constant sequence, preferably at the 3’-end of the first part of the constant sequence and/or in the second part of the constant sequence, preferably at the 5’-end of the second part of the constant sequence modified nucleotides resistant to a 5’ to 3’ exonuclease, such as nucleotides with a phosphorothioate modification or LNA nucleotides.
  • modified nucleotides resistant to a 5’ to 3’ exonuclease such as nucleotides with a phosphorothioate modification or LNA nucleotides.
  • all nucleotides of the second part of the constant sequence of the first primers are modified.
  • Such embodiments are particularly useful in case the amplicons resulting from the method of amplifying genomic DNA of the present invention are used as starting material for the method of generating a sequencing library of the present invention.
  • This method of preparing a sequencing library involves subjecting the DNA amplicons or fragments to be sequenced to a 5’-exonuclease treatment. By using primers comprising the nucleotide modifications described herein, it can be ensured that the exonuclease is not removing the barcoding-sequence incorporated into the amplicons.
  • the second part of the constant sequence of the first primers represent a sequence-label, which may also be called a barcoding-sequence, which is different for each kind of first primers that are used for different sample, such as different cells, in the context of the present invention.
  • the first part of the constant sequence is the same for each kind of first primers, which makes it possible to use the amplicons generated for each sample in the first amplification step of the method of the invention in a pooled fashion for subsequent processing steps that use the first part of the constant sequence.
  • the second part of the constant sequence of multiple kinds of primer A that can be used for different samples in parallel initial amplification reactions of the method of the invention consist or comprise one of the sequences, which comprise nucleotides selected from A, T and G, disclosed in Table 1.
  • the reaction mixture is subjected to a temperature at which the first primers anneal (hybridize) via the variable sequence to the single stranded genomic DNA.
  • the reaction mixture which may have been at a temperature above 90 °C before in order to provide single stranded genomic DNA, is cooled down to a temperature suitable for annealing of the first primers to the single stranded DNA of the samples.
  • the reaction mixture is broad to a temperature at which annealing of the first primers to the single stranded DNA takes place, for example a temperature in the range of 0-30 °C, preferably a temperature in the range on 4-25 °C. In embodiments, the reaction mixture remains at the annealing temperature for about 20-120 seconds, preferably 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90 seconds.
  • the temperature may be elevated to a temperature at which the DNA polymerase extends the 3’-ends of the annealed first primers to produce first-round amplicons.
  • the temperature at which this DNA amplification take place may be in the range of about 30-75 °C.
  • the amplification period may be in the range of about 0.5 - 10 minutes (min), such as for example about 1 , 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 minutes.
  • the temperature at which amplification takes place which is the temperature at which the DNA polymerase extends the 3’-ends of the annealed first primers to produce first-round amplicons, may be subsequently elevated within the suitable temperature range.
  • the sample may initially be broad to 30 °C for 45 seconds, subsequently to 40 °C for 45 seconds, to 50 °C for 45 seconds and finally to 70 °C for 120 seconds.
  • the method steps of (d) and (e) and (g) and (h) may be achieved by subjecting the reaction mixture to a temperature gradient, such as a gradient of 10-70°C.
  • the temperature increasing rate may be 0.1 “C/minute. In further embodiments, the temperature increasing rate may be 0.1 °C/second. Suitable increase rates can be determined by a skilled person for a particular application of the method of the invention.
  • the reaction mixture may be first quickly cooled down, for example to about 0-10°C and subsequently be subjected to a temperature gradient of 10-70°C for primer annealing and amplification. Therein, the reaction mixture may remain at 10°C for about 2 minutes, is subsequently broad to 20°C with an increase rate of about 0.3°C/second, remains at 20°C for about 40-60, preferably 50 seconds, is subsequently broad to 30°C with an increase rate of about 0.3°C/second, remains at 30°C for about 40-60, preferably 45 seconds, is subsequently broad to 40°C with an increase rate of about 0.3°C/second, remains at 40°C for about 40-60, preferably 45 seconds, is subsequently broad to 50°C with an increase rate of about 0.3°C/second, remains at 50°C for about 40-60, preferably 45 seconds, and is subsequently broad to 70°C with an increase rate of about 3°C/second, and remains at 70°C for about 2 minutes.
  • Alternative suitable temperature gradient programs can be developed
  • the initial amplification/primer-extension step of the method of the invention leads to the production of first-round amplicons.
  • These amplicons of the provided DNA material preferably genomic DNA
  • the reaction mixtures are subjected to a temperature to produce single stranded amplicons.
  • This is a temperature suitable for melting the extended first primers and the provided DNA material to which the primers annealed, and which severed as a template for primer extension/amplification.
  • This temperature may be in the range of 85-100 °C, preferably 88-98, 90-96, 91-95, 92-94 or 93 °C.
  • the reaction remains at this temperature for a period sufficient to produce single stranded DNA material, preferably single stranded genomic DNA. This period is preferably in the range of 20-60, 25-55, 30-50, 35-45 or about 30 seconds.
  • This melting step of the amplification method of the invention is followed by subjecting the reaction mixture to a temperature at which free first primers anneal via the variable sequence to the single stranded (genomic) DNA and to the first-round amplicons, preferably to the 3’-end of the first-round amplicons.
  • the temperature and time of this step correspond to the parameters described above for the annealing of the first primers to the single stranded genomic DNA.
  • first-round amplicons are extended first primers that have randomly annealed to the provided DNA
  • the available free first primers can anneal not only to single stranded (genomic) DNA initially provided in the sample, but also to the single stranded first-round amplicons.
  • first-round amplicons are generated from extension of first primers that have annealed to genomic DNA provided in the initial sample and second-round amplicons are generated from first-primers that have annealed to first-round amplicons.
  • First-round amplicons comprise at their 5’-end the sequence of the first-round primer including the constant sequence of a first primer (including the barcoding-sequence and the first part of the constant sequence).
  • Second-round amplicons are generated from first-round primers that have annealed to a first-round amplicon, for example near their 3’-end or in a central region of the first- round amplicons, by extension of the free 3’-end of the annealed first primer, resulting in a primer extension product that comprises at its 3’-end a sequence that is complementary to the sequence at the 5’-end of a first-round amplicon.
  • a second-round amplicon comprises at its 5’- end a constant region of the first primer of the respective sample and at its 3’-end a sequence complementary to the constant region of the first primer of the respective sample.
  • the steps (g.) subjecting the reaction mixture to a temperature at which free first primers anneal via the variable sequence to the single stranded genomic DNA and to the 3'-end of the first-round amplicons, (h.) subjecting the reaction mixture to a temperature at which the DNA polymerase extends the 3’-ends of the annealed first primers to produce first-round amplicons from first primers annealed to genomic DNA and second-round amplicons from first primers annealed to first-round amplicons, and (i.) subjecting the reaction mixture to a temperature to produce single stranded amplicons, are repeated several times in order to generate amplicons of the (genomic) DNA provided in the sample that can be used for a subsequent sequencing reaction.
  • the number of repetitions of steps g-j is in the range of 3-20, 4-19, 4-18, 5-17, 5-16, 6-15, 7-14, 8- 13, 9-12 or 10-11 cycles.
  • step (i) and (j) the reaction mixture is subjected to a temperature at which second-round amplicons form a hairpin structure through hybridization of the complementary constant sequences at the 5’ and 3’ end of the second-round amplicons.
  • the second-round amplicons comprise at their 5’- and 3’-ends complementary sequences that enable formation of a hairpin or panhandle structure by the second-round amplicons.
  • the 5’-end anneals to or hybridizes to the 3’-end of the same second-round amplicon.
  • the second-round amplicons can be withdrawn from the amplification reaction and do not serve as templates in the next amplification step.
  • a temperature at which second-round amplicons form a hairpin structure can be any temperature in the range of 50-80 °C. However, further suitable temperatures can be identified by a skilled person without undue experimentation. This temperature in particular also depends on the length of the constant region of the first primers forming the complementary sequences. In general, it can be expected that the longer the complementary sequence the higher can be the temperature at which second-round amplicons form a hairpin structure.
  • this additional step of subjecting the reaction mixture to a temperature at which second-round amplicons form such a hairpin structure through hybridization of the complementary constant sequences at the 5’ and 3’ end of the second-round amplicons in the amplification cycle of the amplification method of the invention is particularly advantageous, since amplicons, which represent regions of the provided (genomic) DNA that have already been amplified are withdrawn from the reaction and cannot serve as a template in subsequent amplification cycles. This prevents the creation of a bias towards DNA sequences that are most efficiently amplified and results in a quasi-linear initial amplification of the provided (genomic) DNA.
  • the method of amplifying genomic DNA of more than one samples of the invention comprises additionally k. adding to the reaction mixture of step (j) second primers comprising at their 3’-end a sequence comprised by the first part of the constant sequence of the first primers,
  • the second primers comprise at their 3’-end a sequence that enables hybridization and/or annealing of a second primer to a sequence that is complementary to a sequence comprised by the first part of the constant sequence of the first primers. This may be achieved by using second primers that comprise at their 3’-end a sequence comprised by the first part of the constant sequence of the first primers.
  • the nucleotide sequence of the second primers can consist of a sequence that enables hybridization and/or annealing of a second primer to a sequence that is complementary to a sequence comprised by the first part of the constant sequence of the first primers.
  • the nucleotide sequence of the second primers consists of a sequence comprised by the first part of the constant sequence of the first primers.
  • the sequence of the second primers is identical to the sequence of the first part of the constant sequence of the first primers.
  • the second primers have a sequence according to SEQ ID N02.
  • Such second primers can be used in conjunction with first primers that have a sequence according to SEQ ID N01.
  • the second primers are HPLC purified oligonucleotides.
  • the primers are phosphorylated at the 5’-end.
  • the second primers have a sequence length of about 10-70 nucleotides, such as 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69 or 70 nucleotides. It is preferable that second primers have a sequence length in the range of 20-40, more preferably 25-35 nucleotides.
  • the second primers consist of a sequence comprised by the first part of the constant sequence of the first primers, or that enables hybridization to a sequence that is complementary to a sequence comprised by the first part of the constant sequence of the first primers, wherein the second primers preferably consist of 10-66 nucleotides, more preferably of 20-40 nucleotides, most preferably of about 25-35 nucleotides.
  • the second primers such as a primer having a sequence according to SEQ ID N02, comprise near their 3’-end, preferably within the first 10 nucleotides from their 3’-end, preferably at their 3’-end, at least one nucleotide that is resistant to a 5’- exonuclease, such as one or more a nucleotides with a phosphorothioate internucleotide linkages between.
  • the second primers comprise in the sequence at their 3’-end, preferably at their 3’-end, modified nucleotides resistant to a 5’-exonuclease, such as nucleotides with a phosphorothioate modification or LNA nucleotides, wherein preferably 1 -6, 2-5 or 3-4 nucleotides comprised by the sequence at the 3’- end of the second primers are modified, more preferably the 1-6, 2-5 or 3-4 nucleotides at the 3’- end of the second primers are modified.
  • Such embodiments are particularly useful in case the amplicons resulting from the method of amplifying genomic DNA of the present invention are used as starting material for the method of generating a sequencing library of the present invention.
  • This method of preparing a sequencing library involves subjecting the DNA amplicons or fragments to be sequenced to a 5’-exonuclease treatment. By using primers comprising the nucleotide modifications described herein, it can be ensured that the exonuclease is not removing the barcoding-sequence incorporated into the amplicons.
  • the first and second primers are phosphorylated at their 5’-ends. This ensures that the amplicons of the method of amplifying genomic DNA of the invention are accessible to a 5’-exonuclease, which is required for performing the method of generating a sequencing library of the present invention described below.
  • the reaction mixture of step (j) that underwent multiple cycles of initial (preferably quasi-linear) amplification is subjected to a second amplification reaction.
  • the reaction mixture of step (j) is subjected to a temperature to produce single stranded amplicons.
  • This temperature is to be understood as a temperature at which not only hairpin structures formed by second-round amplicons, but also double stranded amplicons or hybrids of amplicons and genomic DNA are melted into single stranded molecules.
  • the reaction mixture should stay at this melting temperature for a time sufficient to ensure complete melting of all hybridized DNA molecules of the reaction mixture, for example a time in the range of 20-120 seconds, such as 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110 or 115 seconds.
  • second primers are added to the reaction mixture.
  • the initial melting step is followed by subjecting the reaction mixture to a temperature at which the second primers anneal to the first part of the constant sequence of the second-round amplicons. Since the second primers can be understood as representing standard PCR primers that are complementary to the 3’-ends of the second-round amplicons of the reaction mixture, a skilled person is able to identify a suitable annealing temperature.
  • a suitable annealing temperature can be in the range of 50-70 °C, such as 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68 or 69 °C.
  • Suitable times of the annealing step can be defined by a skilled person on the specific conditions, and include, without limitation, times in the range of 10-60 seconds, such as 10, 15, 20, 25, 30, 35, 40, 45, 50, 55 or 60 seconds.
  • the reaction mixture is subjected to a temperature at which the DNA polymerase of the reaction mixture extends the 3’-ends of the annealed second primers to produce double stranded third-round amplicons.
  • the one or more polymerases added before the initial amplification step may be used, or additional polymerase may have been added before the second amplification reaction.
  • the temperature depends on the employed polymerase and its ideal or suitable working temperature. Many suitable polymerases operate fine at 72 °C, which may therefore represent a suitable temperature for extending free 3’-ends of annealed second primers.
  • the time for the primer extension reaction/amplification reaction can be defined by a person skilled in the art and depends on the specific reagents, such as the polymerase used in the reaction. However, suitable times can be in the range of 0.75-10 minutes, 1-9, 1.5-8.5, 2-8,
  • the reaction mixture is subjected to a temperature to produce single stranded amplicons (step (o)).
  • This temperature may correspond to the initial melting temperature of the second amplification reaction leading to melting of all double stranded DNA structures comprised by the reaction mixture.
  • the temperature to produce single stranded amplicons of step (o) is a temperature at which hairpin structures formed by second-round amplicons dehybridize and form single-stranded amplicons, while double stranded third-round amplicons do not dehybridize.
  • the melting temperature of a hairpin structures formed by second-round amplicons is lower than the melting temperature of fully hybridized third-round amplicons and can be determined by a person skilled in the art. This temperature is preferably below 90 °C, such as a temperature in the range of 78-89 °C.
  • a temperature of about 85 °C may be employed, at which fully hybridized double stranded DNA of more than about 200 nucleotides does not dehybridize.
  • the steps (m)-(o) of the second amplification reaction of the amplification method of the invention are repeated several times. This enables conversion of all single-stranded second-round amplicons, which may be present as a hairpin structure, to be converted to double- stranded third-round amplicons, which can be used for library preparation.
  • the steps (m)-(o) can be repeated several times. A skilled person is aware or can determine of a suitable number of cycles. In embodiments, 3-15 cycles are performed, in preferred embodiments 5-8 cycles are performed.
  • the amplicons generated by the method of the invention have an average length off less than 1000 nucleotides.
  • the amplicons generated by the method of the invention have a median length off less than 1000 nucleotides.
  • the method of the invention generates amplicons off less than 1000 nucleotides that cover the whole genomic DNA provided in the reaction vessel. Accordingly, the amplicons of less than 1000 nucleotides length of the method are sufficient for use in a NGS reaction after library preparation.
  • This surprising effect enables the direct use of the generated amplicons for library preparation without having to further fragment the generated amplicons.
  • This enables incorporation of barcoding-sequences into the amplicons already during the first amplification reaction of the method of the invention and therefore earlier than in any known method of amplifying genomic DNA of more than one single cells. Due to this early incorporation of sample/cell identifying barcodes into the generated amplicons, it is possible to pool the amplicons of several initial first amplification reactions at an early process step, such as after step (j) of the initial amplification reaction.
  • step (j) or (p) the reaction mixtures of the more than one samples are pooled in a single reaction vessel.
  • the sequence of the first part of the constant sequence is common for all of the more than one samples.
  • the amplification method of the invention involves an additional step of purifying pooled double-stranded third-round amplicons.
  • a magnetic bead purification method may be used, as described in the examples below.
  • the present invention further relates to a method of generating a sequencing library comprising the steps of a. providing in a reaction vessel double-stranded DNAs, such as dsDNA fragments or dsDNA amplicons, b. generating from said double-stranded DNA double-stranded amplicons with overhanging single-stranded 3’-ends, c.
  • the gap-filling primers comprise o at their 3’-end a sequence that enables hybridization/annealing of the gap filling primers to the overhang-sequences at the 3’-ends of the double stranded DNAs, and o a first adapter sequence for a subsequent sequencing of the double- stranded DNAs, a DNA polymerase, and a ligase, d.
  • the reaction mixture subjecting the reaction mixture to a temperature at which a gap-filling primer hybridizes to the overhanging single-stranded 3’-end of a dsDNA, the 3’-end of the third primer is extended by the DNA polymerase and the extended 3’-end of the gap-filling primer is ligated to a 5’-end of a strand of the dsDNA by the ligase.
  • the present invention further relates to a method of generating a sequencing library comprising the steps of a. providing in a reaction vessel double-stranded DNAs, such as dsDNA fragments or dsDNA amplicons, wherein each strand of the dsDNAs comprises near its 5’-end, preferably within nucleotides 20-100, more preferably within the nucleotides 25-40 counted from the 5’-end, at least one modified nucleotide resistant to a 5’- exonuclease, such as nucleotides with a phosphorothioate modification or LNA nucleotides, b. adding a 5’-exonuclease to the reaction vessel to produce a reaction mixture, c.
  • the reaction mixture subjecting the reaction mixture to a temperature at which the 5’-exonuclease is active to generate dsDNA with overhanging single-stranded 3’-ends, d. adding to the reaction vessel gap-filling primers, wherein the gap-filling primers comprise o at their 3’-end a sequence that enables hybridization/annealing of the gap filling primers to the overhang-sequences at the 3’-ends of the dsDNA, and o a first adapter sequence for a subsequent sequencing of the dsDNAs, a DNA polymerase, and a ligase, e.
  • the reaction mixture subjecting the reaction mixture to a temperature at which a gap-filling primer hybridizes to the overhanging single-stranded 3’-end of a double-stranded third-round amplicon, the 3’-end of the third primer is extended by the DNA polymerase and the extended 3’-end of the third primer is ligated to a 5’-end of a strand of the dsDNA by the ligase.
  • the method of generating a sequencing library can also be referred to as a method for asymmetric ligation of sequencing adapters to DNA fragments or amplicons.
  • the present method of generating a sequencing library can use as a starting material any kind of double stranded DNA (dsDNA), such as amplicons resulting from a DNA amplification reaction, for example a PCR, which should be analyzed in a subsequent sequencing reaction.
  • dsDNA can be genomic DNA, which has been fragmented.
  • the dsDNA may originate from an amplification reaction employed to increase a small amount of DNA, such as a small amount of genomic DNA, which may have been provided by a single cell.
  • the dsDNA provided for the method of generating a sequencing library may originate from an amplification reaction and may have undergone a fragmentation step before use in the method of the invention.
  • the dsDNA may originate directly from an amplification reaction.
  • the method relates to generating a sequencing a library, comprising providing double-stranded amplicons of genomic DNA as a starting material.
  • the average length of the provided dsDNA is less than 1000 nucleotides. In embodiment, the median length of the provided dsDNA is less than 1000 nucleotides.
  • the provided dsDNA molecules are amplicons generated from an amplification of genomic DNA, wherein the amplicons comprise a number of amplicons of about 1000 nucleotides length or less that cover the whole genomic DNA that was provided as a starting material in the amplification reaction. Accordingly, the amplicons of about 1000 nucleotides length or less than 1000 nucleotides length of the method are sufficient for use in a NGS reaction after library preparation.
  • Each strand of the dsDNAs comprises near its 5’-end, preferably within nucleotides 20-100, more preferably within the nucleotides 25-40 counted from the 5’-end, at least one modified nucleotide resistant to a 5’-exonuclease (resistant nucleotide), such as nucleotides with a phosphorothioate modification or LNA.
  • resistant nucleotide such as nucleotides with a phosphorothioate modification or LNA.
  • 5’-exonucleases are enzymes that work by cleaving nucleotides one at a time from the 5’-end (exo) of a polynucleotide chain by promoting a hydrolyzing reaction that breaks phosphodiester bonds at the 5' end. Addition of such an enzyme to a reaction vessel leads to stepwise removal of nucleotides from the 5’ ends of both strands of a provided dsDNA. For some 5’ to 3’- exonucleases it is required that the 5’-ends of the polynucleotide is phosphorylated. Therefore, it is preferred that the dsDNA provided in the method of generating a sequencing library of the invention is phosphorylated at the 5’-end.
  • the 5’- exonuclease is a lambda exonuclease and the 5’-ends of the provided double-stranded amplicons are phosphorylated at their 5’-ends.
  • each strand of the dsDNAs comprises near its 5’-end at least one nucleotide resistant to a 5’-exonuclease
  • addition of the 5’-exonuclease to the reaction mixture and subjection to a temperature at which the 5’-exonuclease is active leads to the generation of dsDNAs with free, overhanging single-stranded 3’-ends, since the complementary 5’-ends have been remove by the 5’-exonuclease until to the position where the one or more nucleotides resistant to the 5’- exonuclease are located.
  • the term “near the 5’-end” of a strand of dsDNA can relate to a length of about 20% of the total length of the strand, counted from the 5’-end. For example, for a strand of 1000 nucleotides, 20 % would correspond to the first 200 nucleotides counted from the 5’-end.
  • the resistant nucleotide(s) are located within the first 100 nucleotides.
  • the one or more resistant nucleotides are located within about 90, 80, 70, 60, 50, 45, 40, 35, 30, 25, 20, 18, 16, 14, 12, 10, 9, 8, 7, 6, 5, 4, 3, 2 nucleotides from the 5’-end.
  • the resistant nucleotide(s) is not located within the first 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 15, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28 or 30 nucleotides from the 5’-end of the DNA strand.
  • the resistant nucleotide(s) is within or between nucleotides 3- -100, 4-99, 5-98, 6-97, 7-96, 8-95, 9-96, 10-95, 12-92, 14-92, 15-91 , 16-90, 17-80, 18-70, 19-60, 20-50, 21-45, 22-42, 23-40, 24-38, 25-36, 26-35, 27-34, 28-33, 29-32 or 30-31 , counted from the 5’-end.
  • the temperature at which the 5’-exonuclease is active depends on the specific exonuclease and can be determined by a person skilled in the art. For example, a lambda exonuclease is active at 37 °C.
  • the time required for the exonuclease to generate the free 3’-ends is dependent on the specific exonuclease, the reaction temperature and the location of the resistant nucleotides. Preferably times are in the range of 1 minute to 8 hours, preferably 2-60 minutes, for example 30 minutes.
  • the 5’-exonuclease is inactivated by heating the reaction mixture to a suitable temperature, for example 75 °C or higher, such as over 90°C, after the free 3’-ends have been generated.
  • gap-filling primers are added to the reaction vessel.
  • Gap-filling primers of the invention are designed to hybridize/anneal to the overhanging single- stranded 3’-ends of the provided dsDNAs.
  • the sequences at the ends of the provided dsDNAs are known and it is therefore possible to provide gap-filling primers that comprise at their 3’-end a sequence that enables annealing to the overhanging 3’-ends of the dsDNA, for example a sequence that is at least partially, preferably completely complementary to a sequence comprised by the overhanging 3’-end of the dsDNA.
  • the 3’-ends of the gap-filling primers hybridize to a sequence comprised by the overhanging single-stranded 3’-ends of the provided dsDNAs, wherein the hybridizing sequence of the overhanging single-stranded 3’-ends of the provided dsDNAs does not comprise the 3’-end (meaning the last base at the 3’-end) of the respective strand of the provided dsDNA.
  • the dsDNA molecule comprises at its end a Y-structure, which is due to the non-complementarity of the adapter sequence of the gap-filling primer that is upstream from the hybridizing sequence at its 3’-end, and the sequence at the very 3-ends of the strands of the provided dsDNAs, which are not hybridizing with the sequences at the 3’-ends of the gap-filling primers.
  • a Y-structure which is due to the non-complementarity of the adapter sequence of the gap-filling primer that is upstream from the hybridizing sequence at its 3’-end, and the sequence at the very 3-ends of the strands of the provided dsDNAs, which are not hybridizing with the sequences at the 3’-ends of the gap-filling primers.
  • Such embodiments leading to Y-structures at the end of the dsDNA molecules are advantageous since extension of the 3’-ends of dsDNAs by the DNA polymerase using the adapter sequence of the gap-filling primer as a template cannot occur. Furthermore, embodiments leading to the formation of such Y-structures are also advantageous, because Y- shaped structures facilitate the generation of asymmetric amplicons, which are needed for next generation sequencing of the amplicons.
  • the gap-filling primers comprise a first adapter sequence for subsequent sequencing of the dsDNAs of the sequencing library.
  • the adapter sequence is preferably located at the 5’-end of the primer.
  • the sequence 3’-end a sequence that enables hybridization/annealing of the gap-filling primers to the overhang-sequences at the 3’-ends of the dsDNAs consists of 2-36 nucleotides, such as 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18 ,19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34 or 35 nucleotides.
  • the adapter sequence which is preferably located at the 5’-end of the gap-filling primers, can consist of 8-36, such as 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18 ,19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34 or 35 nucleotides.
  • the sequence of the gap-filling primers consists of 20-100 nucleotides, such as
  • the gap-filling primers have a sequence according to SEQ ID N03 or SEQ ID N06.
  • gap-filling primers are HPLC or PAGE purified oligonucleotides.
  • a DNA polymerase and a ligase are added to the reaction vessel comprising the reaction mixture.
  • the DNA polymerase and the ligase can be added at the same time as the gap-filling primer after the exonuclease treatment.
  • the DNA polymerase preferably does not have strand-displacement activity.
  • the gap-filling primers Upon subjecting the reaction mixture comprising dsDNAs with overhanging 3’-ends, the gap-filling primers, the DNA polymerase and the ligase to a suitable temperature or to a suitable temperature program (meaning a sequence of different temperatures), the gap-filling primers anneals to the overhang-sequences at the 3’-end of the dsDNAs, the DNA polymerase extends the 3’-ends of the gap-filling primers, and the ligase ligates the extended 3’-ends of the gap-filling primers to the 5’-ends of the dsDNAs. This process occurs at both ends of the dsDNAs on the opposing strands, so that the extended gap-filling primers are ligated to the 5’-end of each strand of the provided dsDNAs.
  • a temperature at which a gap-filling primer hybridizes to the overhanging single-stranded 3’-end of a double-stranded third-round amplicon, the 3’-end of the third primer is extended by the DNA polymerase without SD activity and the extended 3’-end of the third primer is ligated to the 5’-end of the double-stranded third-round amplicon by the ligase may relate to a suitable sequence of temperatures.
  • the reaction mixture may be subjected to a temperature at which the gap-filling primer does not anneal to the free 3’-end, such as a temperature of about 70 °C or higher.
  • a temperature at which the gap-filling primer does not anneal to the free 3’-end such as a temperature of about 70 °C or higher.
  • This temperature depends on the length of the sequence at the 3’-end of the gap-filling primer and other parameters known to a skilled person and can therefore be adjusted as required.
  • this relatively high temperature can be decreased continuously, for example at a rate of 0.1 °C/sec, until a temperature that ensures good activity of the DNA polymerase and the ligase.
  • the gap-filling primers can anneal to the free 3’-ends of the dsDNA.
  • DNA polymerases and ligases are highly active at 37 °C. so the Temperature may be decreased to 37 °C. Subsequently, the reaction mixture can remain at this temperature suited for DNA polymerase and ligase activity to ensure extension annealed gap-filling primers and subsequent ligation to the 5’-ends.
  • the method of the present invention for generating a sequencing library has many advantages in comparison to known methods of the state of the art.
  • the method of the invention does not require dsDNA adapters (ds- adapters), but only ssDNA adaptors (oligonucleotides), i.e. the gap-filling primer and subsequently the adapter primer.
  • ds- adapters dsDNA adapters
  • ssDNA adaptors oligonucleotides
  • the sequence of the 3' overhang generated by the 5’-exonuclease should be known for designing these primers.
  • the method of generating a sequencing library of the invention is preferably performed subsequently to the method of amplifying DNA of more than one samples of the invention, knowledge of the sequence of the 3' overhang can be assured due to the known sequences of the first and second primers used therein. This is in principle true for all primer based gDNA amplification methods using a primer with a constant region (for example DOP PCR) since knowledge of the sequence of this constant region is a prerequisite for the amplification process.
  • the sequence of the 3' overhang is introduced into the DNA via the first primer in the first amplification step and the length of this primer as well as the position of the exonuclease- resistant nucleotide(s) defines the length of the 3' overhang.
  • the provided dsDNAs are amplicons of genomic DNA.
  • these amplicons have been generated from more than one samples, such as more than one single cells.
  • the amplicons of each sample or cell comprise an individual sequence-label (barcoding-sequence), preferably of a length of 4-10 nucleotides. In that case, it is not required that barcoding- sequences are introduced to the amplicons during the present method of generating a sequencing library.
  • the sequence-label of the provided amplicons may be located near the 3’- and 5’-ends of the amplicons, preferably within nucleotides 20-110, more preferably within the nucleotides 25-50 counted from the 3’- and 5’-end.
  • the sequence-label is located within the first 110 nucleotides.
  • the sequence-label is located within about 90, 80, 70, 60, 50, 45, 40, 35, 30, 25 or 20 nucleotides from the end.
  • the sequence-label is not located within the first 8, 9, 10, 11 , 12, 13, 14, 15, 15, 17, 18, 19, 20, 21 ,
  • sequence-label is within or between nucleotides 15-100, 16-90, 17-80, 18-70, 19-60, 20-50, 21-45, 22-42, 23-40, 24-38, 25- 36, 26-35, 27-34 or 28-33.
  • a sequence label comprised by an amplicons of the method of generating a sequencing library is defined as the second part of a first primer, which is a barcoding-sequence, as disclosed herein.
  • the method of generating a sequencing library of the invention comprises after step (e) f. adding adapter primers to the reaction vessel, wherein the adapter primers comprise at their 3’-end a sequence that enables hybridization/annealing of the adapter primers to the 3’-ends of the strands of the provided dsDNAs, preferably with a higher affinity than the sequence at the 3’-end of the gap-filling primers, and a second adapter sequence for a subsequent sequencing of the provided dsDNA, g. subjecting the reaction mixture to a temperature to produce single stranded DNA (ssDNA), h.
  • ssDNA single stranded DNA
  • reaction mixture subjecting the reaction mixture to a temperature at which the adapter primers anneal to the 3’-ends of the single-stranded provided DNA comprising ligated gap-filling primers at their 5’-end, i. subjecting the reaction mixture to a temperature at which the DNA polymerase extends the 3’-ends of the annealed adapter primers and of the single-stranded DNA comprising ligated gap-filling primers to produce double-stranded adapter amplicons.
  • adapter primers are added to the reaction mixture of step (e) of the method of generating a sequencing library.
  • the adapter primers of the invention are designed to hybridize/anneal to the 3’-ends of the strands of the provided dsDNAs.
  • the sequences at the ends of the provided dsDNAs are known and it is therefore possible to provide adapter primers that comprise at their 3’-end a sequence that enables annealing to a 3’- ends of the provided dsDNAs, for example a sequence that is at least partially, preferably completely complementary to a sequence comprised by a 3’-end of the strands of the provided dsDNA.
  • the affinity of the adapter primers to a 3’-end of a strand of the provided dsDNA is higher than the affinity of the gap-filling primers to the 3’-end.
  • the sequence at the 3’-end of the adapter primers that is at least partially, preferably completely complementary to a sequence comprised by a 3’-end of the strands of the provided dsDNA comprises and is longer than the sequence at the 3’-end of the gap-filling primer.
  • the sequence at the 3’-end of the adapter primers hybridizes to a sequence at the 3’- end of the provided dsDNAs.
  • This sequence comprises the 3’-end, meaning the last base at the 3’-end of the dsDNAs.
  • the adapter primers comprise a second adapter sequence for subsequent sequencing of the dsDNAs of the sequencing library.
  • the adapter sequence is preferably located at the 5’-end of the primer.
  • the method of generating a sequencing library of the invention is preferably for generating sequencing library to be used in a lllumina sequencing-by-synthesis sequencing method. Therefore, in embodiments, the first and second adapter sequences comprised by the gap-filling and adapter-primers of the method of the invention can be any adapter sequence known in the art and suitable for employing the dsDNA molecules resulting from the present method in such a reaction.
  • the first and second adapter sequences can be the P5 and P7 lllumina adapter sequence.
  • the adapter primers have a sequence according to SEQ ID N07 or SEQ ID NO10, wherein N can be selected from G, A, T and C.
  • adapter primers are HPLC or PAGE purified oligonucleotides.
  • the gap-filling primers and/or the adapter primers do not contain a barcoding-sequence.
  • the gap-filling primers and/or the adapter primers do contain a barcoding- sequence. Inclusion of multiple barcoding sequences via one or more primers of the present invention can be advantageous for sequencing an even higher number of samples, such as single cells, in a single sequencing run. Multiple barcodes would enable unique dual indexing.
  • the reaction mixture is subjected to a temperature to produce ssDNA, preferably single-stranded amplicons.
  • a temperature In order to ensure complete melting of the provided dsDNA, it is preferred to subject the reaction mixture to a temperature of more than 90 °C, preferably 91 , 92, 93, 94, 95, 96, 97 or 98 °C.
  • the initial incubation time at the melting temperature can be determined by a skilled person, for example at least 5 seconds, preferably at least 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55 or 60 seconds.
  • the reaction mixture After melting of the dsDNA, the reaction mixture is subjected to a temperature at which the adapter primers anneal to the 3’-ends of the provide single stranded DNA comprising ligated gap filling primers at their 5’-ends.
  • the adapter primers Preferably, the adapter primers have a higher affinity to the 3’-ends of the provided single stranded DNA and therefore bind/anneal preferentially in comparison to access gap-filling primers that can still be present in the reaction mixture.
  • the reaction mixture is subjected to a temperature at which a polymerase comprised by the reaction mixture extends the free 3’-ends of the annealed adapter primers as well as the free 3’-ends of the single- stranded provided DNA, for example a temperature of about 72 °C.
  • the polymerase may be already comprised in the reaction mixture or may be added at the same time as or after adding the adapter primers.
  • a dsDNA is generated wherein one strand comprises at its 5’-end the sequence of the adapter primer and at its 3’-end a sequence complementary to the gap-filling primer and the other strand comprises at its 5’-end the sequence of the gap-filling primers and at its 3’-end a sequence complementary to the adapter primer.
  • dsDNAs are referred to as double-stranded adapter amplicons.
  • the method of generating a sequencing library of the invention comprises after step (i) j. subjecting the reaction mixture to a temperature to produce single stranded adapter amplicons, k. subjecting the reaction mixture to a temperature at which the adapter primers and gap-filling primers anneal to the 3’-ends of the corresponding single-stranded adapter amplicons,
  • the reaction mixture of step (i) is subjected to a PCR protocol as known to a person skilled in the art, wherein the adapter primers and the gap-filling primers are serving as amplification primers.
  • the reaction mixture comprising double-stranded adapter amplicons is subjected to a melting temperature for generating single-stranded adapter amplicons.
  • this temperature to produce single stranded adapter amplicons is a temperature of more than 90 °C, preferably 91 , 92, 93, 94, 95, 96, 97 or 98 °C.
  • the incubation time at the melting temperature can be determined by a skilled person, for example at least 5 seconds, preferably at least 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55 or60 seconds.
  • the reaction mixture is subjected to a temperature at which adapter primers and gap-filling primers anneal to the 3’-ends of the corresponding single-stranded adapter amplicons.
  • a temperature at which adapter primers and gap-filling primers anneal to the 3’-ends of the corresponding single-stranded adapter amplicons which can be for example at a temperature in the range of about 60-70 °C and which lasts for example for 15-120 seconds, preferably about 40-80 seconds
  • the reaction mixture is subjected to a temperature at which a polymerase comprised by the reaction mixture extends the free 3’-ends of the annealed adapter primers as well as the free 3’- ends of the single-stranded provided DNA, for example a temperature of about 72 °C.
  • the polymerase may be already comprised in the reaction mixture or may be added at the same time as or after adding the adapter primers. Extension of the annealed adapter and gap-filling primers leads to production of double-stranded adapter amplicons.
  • This amplification cycle is repeated several time, such as 5-30 times, preferably about 15-20 times, to produce a amplify double- stranded adapter amplicons comprising the P5 and the P7 adapter at their respective ends, representing a sequencing library for use in an lllumina sequencing reaction.
  • step (m) or steps (j) to (m), which can be a regular PCR additional reagents may be added to the reaction mixture, such as additional DNA polymerase.
  • the method of generating a sequencing library comprises the provision of amplicons of genomic DNA of more than one samples, such as more than one single cells, wherein the amplicons of each single cell comprise an individual sequence-label, the method comprising a. providing in a reaction vessel pooled third-round amplicons generated by the method of amplifying DNA of more than one samples of the present invention, b. adding a 5’-exonuclease to the reaction vessel to produce a reaction mixture, c. subjecting the reaction mixture to a temperature at which the 5’-exonuclease is active to generate double-stranded third-round amplicons with overhanging single-stranded 3’-ends, d.
  • gap-filling primers comprise o at their 3’-end a sequence comprised by the sequence at the 3’-end of the second primers and o a first adapter sequence for a subsequent sequencing of the amplicons, a DNA polymerase, preferably without strand-displacement (SD) activity, and a ligase, e.
  • SD strand-displacement
  • the reaction mixture subjecting the reaction mixture to a temperature at which a gap-filling primer hybridizes to the overhanging single-stranded 3’-end of a double-stranded third-round amplicon, the 3’-end of the third primer is extended by the DNA polymerase without SD activity and the extended 3’-end of the gap-filling primer is ligated to the 5’-end of the double- stranded third-round amplicon by the ligase.
  • the provided third-round amplicons comprise near their 5’-ends one or more modified nucleotides resistant to a 5’-exonuclease, such as nucleotides with a phosphorothioate modification or LNA nucleotides.
  • the method of generating a sequencing library comprising the provision of third- round amplicons generated by the method of amplifying genomic DNA comprised in more than one samples of the present invention disclosed herein also comprises f. adding adapter primers to the reaction vessel, wherein the adapter primers comprise
  • sequence at the 3’-end of the adapter primers comprises or consists of the sequence at the 3’-end of the second primers, wherein more preferably the sequence at the 3’-end of the adapter primers comprises or consists of the sequence of the second primers, and
  • a second adapter sequence for a subsequent sequencing of the amplicons g. subjecting the reaction mixture to a temperature to produce single stranded amplicons, h. subjecting the reaction mixture to a temperature at which the adapter primers anneal to the 3’-ends of the single-stranded third-round amplicons comprising ligated gap filling primers at their 5’-end, i. subjecting the reaction mixture to a temperature at which the DNA polymerase extends the 3’-ends of the annealed adapter primers and of the single-stranded amplicons comprising ligated gap-filling primers to produce double-stranded adapter amplicons.
  • the method of generating a sequencing library comprising amplicons of genomic DNA of more than one samples comprising the provision of third-round amplicons disclosed herein also comprises j. subjecting the reaction mixture to a temperature to produce single stranded adapter amplicons, k. subjecting the reaction mixture to a temperature at which the adapter primers and gap-filling primers anneal to the 3’-ends of the corresponding single-stranded adapter amplicons,
  • the present invention also relates to a kit for amplifying dsDNA of more than one samples, such as more than one single cells, for generating a sequencing library.
  • the invention relates to a kit for amplifying the whole genome of more than one samples, such as more than one single cells, for generating a sequencing library.
  • the kit of the invention comprises at least two kinds of first primers, wherein each kind of first primers is provided in an individual container, wherein each kind of first primer comprises in a 5’ to 3’ orientation a constant sequence and a variable sequence, wherein the constant sequence comprises in a 5’ to 3’ orientation a first part with a sequence that is common for each of the at least two kinds of first primers, and a second part with a sequence that is different for each of the at least two kinds of first primers.
  • the kit for generating a sequencing library of the invention comprises at least 12, preferably at least 96, more preferably at least 384 kinds of first primers, wherein the primers are preferably provided in sealed individual wells or a multiwell plate.
  • each kind of first primers comprises in the constant sequence modified nucleotides resistant to a 5’-exonuclease, such as nucleotides with a phosphorothioate modification or LNA nucleotides.
  • at least 1 , 2, 3, 4, 5, or 6 nucleotides of the second part of the constant region are modified. It is preferable that the modified nucleotides are located at the 5’-end of the second part of the constant region.
  • the first primers can be phosphorylated at their 5’-ends.
  • each kind of first primers comprises between 10 and 70 nucleotides, preferably about 10-40 nucleotides, wherein the first part of the constant sequence comprises between 5 and 66 nucleotides, preferably 5-36 nucleotides and the second part of the constant sequence comprises between 4 and 10 nucleotides.
  • the kit of the invention comprises additionally in an individual container second primers comprising at their 3’-end a sequence comprised by the first part of the constant sequence of the first primers.
  • the second primers comprise at their 3’- end at least one modified nucleotide, preferably at least 3 to 6 modified nucleotides, resistant to a 5’-exonuclease, such as nucleotides with a phosphorothioate modification or LNA nucleotides.
  • such modified nucleotides are not located at the 3’-end of the second primers but near the 3’-end of the second primers, such as within the first 10, 9, 8, 7, 6, 5, 4, 3 or 2 nucleotides from the 3’-end.
  • the second primers are phosphorylated at their 5’-ends.
  • the kit of the invention comprises additionally gap-filling primers comprising at their 3’-end a sequence comprised by the sequence at the 3’-end of the second primers, wherein the sequence at the 3’-end of the gap-filling primers enables hybridization/annealing of the gap filling primers to the sequence at the 3’-end of the second primers, and a first adapter sequence for a subsequent sequencing of the amplicons.
  • the kit for generating a sequencing library of the invention comprises adapter primers comprising at their 3’-end a sequence comprised by the sequence at the 3’-end of the second primers, wherein the sequence at the 3’-end of the adapter primers enables hybridization/annealing of the adapter primers to the sequence at the 3’-end of the second primers with a higher affinity than the sequence at the 3’-end of the gap-filling primers, and a second adapter sequence for a subsequent sequencing of the amplicons.
  • the sequence at the 3’-end of the adapter primers comprises or consists of the sequence of the second primer.
  • the kit for generating a sequencing library of the invention comprises one or more enzymes for performing any of the methods of the present invention, such as a polymerase, a polymerase with strand displacement activity, a polymerase without strand displacement activity, a polymerase with 5’-3’ exonuclease activity, a polymerase without 5’-3’ exonuclease activity, a 5’-exonuclease, such as a lambda exonuclease, and/or a ligase.
  • enzymes for performing any of the methods of the present invention such as a polymerase, a polymerase with strand displacement activity, a polymerase without strand displacement activity, a polymerase with 5’-3’ exonuclease activity, a polymerase without 5’-3’ exonuclease activity, a 5’-exonuclease, such as a lambda exonuclease, and/or a ligase
  • the invention further relates to a kit for generating a sequencing library from provided dsDNA, the kit comprising gap-filling primers comprising o at their 3’-end a sequence that enables hybridization/annealing of the gap filling primers to a sequence at a 3’-end of the strands of the provided dsDNA, and o a first adapter sequence for a subsequent sequencing of the provided dsDNAs, preferably at their 5’-end, and adapter primers comprising o at their 3’-end a sequence that enables hybridization/annealing of the adapter primers to a sequence at a 3’-end of the strands of the provided dsDNAs, preferably with a higher affinity than the sequence at the 3’-end of the gap-filling primers, and o a second adapter sequence for a subsequent sequencing of the provided dsDNA, preferably at their 5’-end, and optionally one or more enzymes for performing the method of generating a sequencing library of the invention
  • the methods and kits of the present invention are in the field of DNA amplification, in particular whole genome amplification, in particular whole genome amplification of single cells.
  • amplifying DNA comprises amplifying genomic DNA and in particular WGA.
  • DNA amplification and WGA in particular are mostly performed on DNA material of samples comprising very little amounts of DNA, such as samples comprising genomic material of one single cell, such as a prokaryotic or eukaryotic cell.
  • DNA amplification can also be performed using DNA of samples that comprise very little amounts of DNA of unknown origin, which are not derived from a single cell.
  • the provided DNA has to be first amplified before it can be subjected to a sequence analysis reaction, such as a NGS, preferably a sequencing reaction using the predominant lllumina technology.
  • a sequence analysis reaction such as a NGS
  • the amplification is not creating a bias towards certain sequences in order to ensure that quantitative results can be generated from the sequencing analysis. It is an important advantage of the DNA amplification method of the invention that is a quasilinear reaction that avoids introduction of an amplification bias.
  • embodiments are directed to methods for the amplification of substantially the entire genome or entire transcriptome without loss of representation of specific sites (herein defined as “whole genome amplification” and “whole transcriptome amplification”, respectively).
  • whole genome amplification comprises simultaneous amplification of substantially all fragments of a genomic library.
  • substantially entire or substantially all refers to about 80%, about 85%, about 90%, about 95%, about 97%, or about 99% of all sequence in a genome.
  • amplification of the whole genome will, in some embodiments, comprise non-equivalent amplification of particular sequences over others.
  • embodiments of the invention relate to methods of amplifying DNA or generating a sequencing library that can be performed in a single tube or in a micro-titer plate, for example, in a high throughput format.
  • Single cell sequencing examines the sequence information from individual cells with optimized next generation sequencing (NGS) technologies, providing a higher resolution of cellular differences and a better understanding of the function of an individual cell in the context of its microenvironment. Sequencing the DNA of individual cells can give information about mutations carried by small populations of cells, for example in cancer, sequencing the RNAs expressed by individual cells can give insight into the existence and behavior of different cell types, for example in development.
  • Single cell DNA genome sequencing involves isolating a single cell, performing whole-genome-amplification (WGA), constructing sequencing libraries and then sequencing the DNA using a next-generation sequencer, for example an lllumina sequencer.
  • WGA whole-genome-amplification
  • the DNA amplified by the method of the invention can be sequenced and analyzed using methods known to those of skill in the art. Determination of the sequence of a nucleic acid sequence of interest can be performed using a variety of sequencing methods known in the art including, but not limited to, sequencing by hybridization (SBH), sequencing by ligation (SBL) (Shendure et al. (2005) Science 309: 1728), quantitative incremental fluorescent nucleotide addition sequencing (QIFNAS), stepwise ligation and cleavage, fluorescence resonance energy transfer (FRET), molecular beacons, TaqMan reporter probe digestion, pyrosequencing, fluorescent in situ sequencing (FISSEQ), FISSEQ beads (U.S. Pat. No.
  • SBH sequencing by hybridization
  • SBL sequencing by ligation
  • QIFNAS quantitative incremental fluorescent nucleotide addition sequencing
  • FRET fluorescence resonance energy transfer
  • molecular beacons TaqMan reporter probe digestion, pyrosequencing, fluorescent in situ sequencing (FISSEQ), FISSEQ
  • allele-specific oligo ligation assays e.g., oligo ligation assay (OLA), single template molecule OLA using a ligated linear probe and a rolling circle amplification (RCA) readout, ligated padlock probes, and/or single template molecule OLA using a ligated circular padlock probe and a rolling circle amplification (RCA) readout
  • OLA oligo ligation assay
  • RCA rolling circle amplification
  • ligated padlock probes ligated padlock probes
  • RCA rolling circle amplification
  • High-throughput sequencing methods e.g., using platforms such as Roche 454, lllumina Solexa, AB-SOLiD, Helicos, Polonator platforms and the like, can also be utilized.
  • a variety of light-based sequencing technologies are known in the art (Landegren et al. (1998) Genome Res. 8:769-76; Kwok (2000) Pharmacogenomics 1 :95-100; and Shi
  • NGS sequencing using the lllumina technology works in three basic steps: amplify, sequence, and analyze.
  • the process begins with provision of DNA, purified DNA or purified DNA fragments.
  • the DNA gets fragmented up into smaller pieces of mostly less than 1000 nucleotides/base pairs and given adapters, potentially barcoding-sequences and other kinds of molecular modifications that act as reference points during amplification, sequencing, and analysis are added.
  • the modified DNA is loaded onto a specialized chip where amplification and sequencing will take place. Along the bottom of the chip are hundreds of thousands of oligonucleotides (short, synthetic pieces of DNA). They are anchored to the chip and able to grab DNA fragments that have complementary adapter sequences. Once the fragments have attached, cluster generation begins.
  • Cluster generation results in about a thousand copies of each fragment of DNA.
  • primers and modified nucleotides enter the chip and these nucleotides have reversible 3' blockers that force the polymerase to add on only one nucleotide at a time as well as fluorescent tags.
  • a camera takes a picture of the chip.
  • a computer determines what base was added by the wavelength of the fluorescent tag and records it for every spot on the chip.
  • non-incorporated molecules are washed away.
  • a chemical deblocking step is then used in the removal of the 3’ terminal blocking group and the dye in a single step.
  • a method that modifies one or dsDNA molecules, preferably multiple dsDNA fragments or amplicons, that are to be subjected to a NGS reaction, preferably using the lllumina technology, in a way that dsDNA molecules of mostly no more than 1000 bp having two different adapter sequences attached to both of their ends is referred to as a “method of generating a sequencing library”.
  • Usual methods of generating a sequencing library from sample comprising very small amounts of DNA involve fragmentation of the amplicons of genomic DNA generated from WGA, since WGA method of the state of the art generate amplicons that are mostly longer than 1000 bp and do not generate a sufficient number of amplicons of not more than 1000 bp in order to cover the whole DNA provided in a sample, such as the whole genome of a mammalian or human cell. Therefore, amplicons of genomic DNA generated by WGA have to be fragmented prior to ligation or introduction of adapter sequences, which may comprise a barcoding-sequence for identifying DNA material originating from a specific sample. Therefore, pooling of DNA material from different samples can only occur after library preparation, when using methods of the state of the art.
  • dsDNA molecule refers to a dsDNA composed of two complementary strands of DNA that are bound to each other via base-pairing. Although a dsDNA molecules is composed of two individual DNA molecules, the term as used herein refers to the hybridized complex of two DNA strands.
  • the method of amplifying DNA further includes genotype analysis of the amplified DNA product.
  • the method of amplifying DNA preferably further includes identifying a polymorphism such as a single nucleotide polymorphism (SNP) in the amplified DNA product.
  • SNP single nucleotide polymorphism
  • a SNP may be identified in the DNA of an organism by a number of methods well known to those of skill in the art, including but not limited to identifying the SNP by DNA sequencing, by amplifying a PCR product and sequencing the PCR product, by Oligonucleotide Ligation Assay (OLA), by Doublecode OLA, by Single Base Extension Assay, by allele specific primer extension, or by mismatch hybridization.
  • OLA Oligonucleotide Ligation Assay
  • the identified SNP is associated with a phenotype, including disease phenotypes and desirable phenotypic traits.
  • the amplified DNA generated by using the disclosed method of DNA amplification may also preferably be used to generate a DNA library, including but not limited to genomic DNA libraries, microdissected chromosome DNA libraries, BAC libraries, YAC libraries, PAC libraries, cDNA libraries, phage libraries, and cosmid libraries.
  • nucleoside refers to a molecule having a purine or pyrimidine base covalently linked to a ribose or deoxyribose sugar. Exemplary nucleosides include adenosine, guanosine, cytidine, uridine and thymidine.
  • nucleosides include inosine, 1 - methyl inosine, pseudouridine, 5,6-dihydrouridine, ribothymidine, 2 N-methylguanosine and 2 ' 2 N,N- dimethylguanosine (also referred to as "rare" nucleosides).
  • nucleotide refers to a nucleoside having one or more phosphate groups joined in ester linkages to the sugar moiety.
  • Exemplary nucleotides include nucleoside monophosphates, diphosphates and triphosphates.
  • polynucleotide refers to a polymer of nucleotides, either deoxyribonucleotides or ribonucleotides, of any length joined together by a phosphodiester linkage between 5' and 3' carbon atoms.
  • Polynucleotides can have any three-dimensional structure and can perform any function, known or unknown.
  • polynucleotides a gene or gene fragment (for example, a probe, primer, EST or SAGE tag), exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes and primers.
  • a polynucleotide can comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. The term also refers to both double- and single-stranded molecules.
  • any embodiment of this invention that comprises a polynucleotide encompasses both the double-stranded form and each of two complementary single-stranded forms known or predicted to make up the double-stranded form.
  • a polynucleotide is composed of a specific sequence of four nucleotide bases: adenine (A); cytosine (C); guanine (G); thymine (T); and uracil (U) for thymine when the polynucleotide is RNA.
  • A adenine
  • C cytosine
  • G guanine
  • T thymine
  • U uracil
  • polynucleotide sequence is the alphabetical representation of a polynucleotide molecule.
  • RNA RNA molecule
  • DNA DNA molecule
  • deoxyribonucleic acid molecule refers to a polymer of deoxyribonucleotides.
  • DNA and RNA can be synthesized naturally (e.g., by DNA replication or transcription of DNA, respectively). RNA can be post-transcriptionally modified. DNA and RNA can also be chemically synthesized. DNA and RNA can be single-stranded (i.e.
  • mRNA or “messenger RNA” is single- stranded RNA that specifies the amino acid sequence of one or more polypeptide chains. This information is translated during protein synthesis when ribosomes bind to the mRNA.
  • nucleotide analog refers to a nonstandard nucleotide, including non-naturally occurring ribonucleotides or deoxyribonucleotides.
  • nucleotide analogs are modified at any position so as to alter certain chemical properties of the nucleotide yet retain the ability of the nucleotide analog to perform its intended function.
  • positions of the nucleotide which may be derivitized include the 5 position, e.g., 5-(2-amino)propyl uridine, 5-bromo uridine, 5-propyne uridine, 5- propenyl uridine, etc.; the 6 position, e.g., 6-(2- amino) propyl uridine; the 8-position for adenosine and/or guanosines, e.g., 8- bromo guanosine, 8-chloro guanosine, 8-fluoroguanosine, etc.
  • 5 position e.g., 5-(2-amino)propyl uridine, 5-bromo uridine, 5-propyne uridine, 5- propenyl uridine, etc.
  • the 6 position e.g., 6-(2- amino) propyl uridine
  • the 8-position for adenosine and/or guanosines e.g., 8-
  • Nucleotide analogs also include deaza nucleotides, e.g., 7-deaza-adenosine; O- and N-modified (e.g., alkylated, e.g., N6-methyl adenosine, or as otherwise known in the art) nucleotides; and other heterocyclically modified nucleotide analogs such as those described in Herdewijn, Antisense Nucleic Acid Drug Dev., 2000 Aug. 10(4):297-310. Nucleotide analogs may also comprise modifications to the sugar portion of the nucleotides.
  • the 2' OH-group may be replaced by a group selected from H, OR, R, F, Cl, Br, I, SH, SR, NH2, NHR, NR2, COOR, or OR, wherein R is substituted or unsubstituted C1 -C6 alkyl, alkenyl, alkynyl, aryl, etc.Other possible modifications include those described in U.S. Pat. Nos. 5,858,988, and 6,291 ,438.
  • a 5’-exonuclease is used in order to generate free 3’-ends of dsDNA molecules.
  • Any 5’-exonuclease known to a skilled person can be used in the context of the invention.
  • one or both strands of the provided dsDNA molecules such as third- round amplicons generated from the method of amplifying DNA of the present invention, comprise modified nucleotides resistant to a 5’-exonuclease near their 5’-end.
  • modified nucleotides resistant to a 5’-exonuclease are understood as nucleotides that have been modified so they cannot be removed by a 5’-exonuclease. Accordingly, incorporation of modified nucleotides resistant to a 5’-exonuclease into a nucleotide sequence leads to a stop of the continuous hydrolysis reaction degrading the nucleotide sequence of the DNA strand from the 5’-end.
  • Modified nucleotides resistant to a 5’-exonuclease include nucleotides with a phosphorothioate modification or LNA nucleotides.
  • PT phosphorothioate
  • This modification renders the internucleotide linkage resistant to nuclease degradation.
  • Phosphorothioate bonds can be introduced between the last 3-10, preferably 3-5 nucleotides at the 5'- or 3'-end of purchasable oligonucleotides to inhibit exonuclease degradation.
  • LNA stands for locked nucleic acid and is often referred to as inaccessible RNA. It is a modified RNA nucleotide in which the ribose moiety is modified with an extra bridge connecting the 2' oxygen and 4' carbon. The bridge "locks" the ribose in the 3'-endo (North) conformation, which is often found in the A-form duplexes.
  • LNA nucleotides can be mixed with DNA or RNA residues in the oligonucleotide whenever desired and hybridize with DNA or RNA according to Watson-Crick base-pairing rules.
  • the terms “complementary” and “complementarity” are used in reference to nucleotide sequences related by the base-pairing rules.
  • sequence 5'-AGT-3' is complementary to the sequence 5'-ACT-3'.
  • Complementarity can be partial or total. Partial complementarity occurs when one or more nucleic acid bases is not matched according to the base pairing rules. Total or complete complementarity between nucleic acids occurs when each and every nucleic acid base is matched with another base under the base pairing rules. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands.
  • a partially complementary sequence is one that at least partially inhibits a completely complementary sequence from hybridizing to a target nucleic acid and is referred to using the functional term "substantially homologous.”
  • the inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or Northern blot, solution hybridization and the like) under conditions of low stringency.
  • a substantially homologous sequence or probe i.e., an oligonucleotide which is capable of hybridizing to another oligonucleotide of interest
  • conditions of low stringency are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (i.e., selective) interaction.
  • the absence of non-specific binding may be tested by the use of a second target which lacks even a partial degree of complementarity (e.g., less than about 30% identity); in the absence of non-specific binding the probe will not hybridize to the second noncomplementary target.
  • a double-stranded nucleic acid sequence such as a cDNA or genomic clone
  • the term “substantially homologous” refers to any probe or primer or oligonucleotide which can hybridize to either or both strands of the double-stranded nucleic acid sequence under conditions of low stringency.
  • the term “substantially homologous” refers to any probe which can hybridize to the single-stranded nucleic acid sequence under conditions of low stringency.
  • reference sequence is a defined sequence used as a basis for a sequence comparison; a reference sequence may be a subset of a larger sequence, for example, as a segment of a full-length cDNA sequence given in a sequence listing or may comprise a complete gene sequence. Generally, a reference sequence is at least 20 nucleotides in length, frequently at least 25 nucleotides in length, and often at least 50 nucleotides in length.
  • two polynucleotides may each (1) comprise a sequence (i.e., a portion of the complete polynucleotide sequence) that is similar between the two polynucleotides, and (2) may further comprise a sequence that is divergent between the two polynucleotides
  • sequence comparisons between two (or more) polynucleotides are typically performed by comparing sequences of the two polynucleotides over a "comparison window" to identify and compare local regions of sequence similarity.
  • a “comparison window”, as used herein, refers to a conceptual segment of at least 20 contiguous nucleotide positions wherein a polynucleotide sequence may be compared to a reference sequence of at least 20 contiguous nucleotides and wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences.
  • Optimal alignment of sequences for aligning a comparison window may be conducted by the local homology algorithm of Smith and Waterman (Smith and Waterman (1981) Adv. Appl. Math.
  • sequence identity means that two polynucleotide sequences are identical (i.e., on a nucleotide-by-nucleotide basis) over the window of comparison.
  • percentage of sequence identity is calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, U, or I) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity.
  • substantially identical denotes a characteristic of a polynucleotide sequence, wherein the polynucleotide comprises a sequence that has at least 85 percent sequence identity, preferably at least 90 to 95 percent sequence identity, more usually at least 99 percent sequence identity as compared to a reference sequence over a comparison window of at least 20 nucleotide positions, frequently over a window of at least 25-50 nucleotides, wherein the percentage of sequence identity is calculated by comparing the reference sequence to the polynucleotide sequence which may include deletions or additions which total 20 percent or less of the reference sequence over the window of comparison.
  • the reference sequence may be a subset of a larger sequence, for example, as a segment of the full-length sequences of the compositions claimed in the present invention.
  • hybridization refers to the pairing of complementary nucleic acids. Hybridization and the strength of hybridization (i.e., the strength of the association between the nucleic acids) is impacted by such factors as the degree of complementary between the nucleic acids, stringency of the conditions involved, the T m of the formed hybrid, and the G:C ratio within the nucleic acids. A single molecule that contains pairing of complementary nucleic acids within its structure is said to be “self-hybridized.”
  • T m melting temperature
  • the melting temperature is the temperature at which a population of double-stranded nucleic acid molecules becomes half dissociated into single strands.
  • T m melting temperature
  • the present invention relates to the amplification and optionally subsequent analysis of genomic DNA of a single cell.
  • cells are identified and then a single cell or a plurality of cells are isolated.
  • Cells within the scope of the present disclosure include any type of cell where understanding the DNA or RNA content is considered by those of skill in the art to be useful.
  • a cell according to the present disclosure includes a cancer cell of any type, hepatocyte, oocyte, embryo, stem cell, iPS cell, ES cell, neuron, erythrocyte, melanocyte, astrocyte, germ cell, oligodendrocyte, kidney cell and the like.
  • the methods of the present invention are practiced with the cellular RNA or cellular DNA from a single cell.
  • the methods of the invention relate to the analysis of more than one sample, preferably more than one cell.
  • a plurality of cells includes from about 2 to about 1 ,000,000 cells, about 2 to about 10 cells, about 2 to about 100 cells, about 2 to about 1 ,000 cells, about 2 to about 10,000 cells, about 2 to about 100,000 cells, about 2 to about 10 cells or about 2 to about 5 cells.
  • Nucleic acids processed by methods described herein may be DNA, RNA, or DNA-RNA chimeras, and they may be obtained from any useful source, such as, for example, a human sample.
  • a double stranded DNA molecule is further defined as comprising a genome, such as, for example, one obtained from a sample from a human.
  • the sample may be any sample from a human, such as blood, serum, plasma, cerebrospinal fluid, cheek scrapings, nipple aspirate, biopsy, semen (which may be referred to as ejaculate), urine, feces, hair follicle, saliva, sweat, immunoprecipitated or physically isolated chromatin, and so forth.
  • the sample comprises a single cell.
  • the amplified nucleic acid molecule from the sample provides diagnostic or prognostic information.
  • the prepared nucleic acid molecule from the sample may provide genomic copy number and/or sequence information, allelic variation information, cancer diagnosis, prenatal diagnosis, paternity information, disease diagnosis, detection, monitoring, and/or treatment information, sequence information, and so forth.
  • a "single cell” refers to one cell.
  • Single cells useful in the methods described herein can be obtained from a tissue of interest, or from a biopsy, blood sample, or cell culture. Additionally, cells from specific organs, tissues, tumors, neoplasms, or the like can be obtained and used in the methods described herein.
  • cells from any population can be used in the methods, such as a population of prokaryotic or eukaryotic single celled organisms including bacteria or yeast.
  • a single cell suspension can be obtained using standard methods known in the art including, for example, enzymatically using trypsin or papain to digest proteins connecting cells in tissue samples or releasing adherent cells in culture, or mechanically separating cells in a sample.
  • Single cells can be placed in any suitable reaction vessel in which single cells can be treated individually.
  • a 96-well plate such that each single cell is placed in a single well.
  • Methods for manipulating single cells include fluorescence activated cell sorting (FACS), single-cell dispensing (Riba et al., “Molecular Genetic Characterization of Individual Cancer Cells Isolated via Single-Cell Printing,” PLoS One, vol. 11 , no. 9, p.
  • the cell can be lysed to release cellular contents including DNA and RNA, using methods known to those of skill in the art.
  • the cellular contents are contained within a vessel.
  • cellular contents such as genomic DNA and RNA, can be released from the cells by lysing the cells. Lysis can be achieved by, for example, heating the cells, or by the use of detergents or other chemical methods, or by a combination of these.
  • any suitable lysis method known in the art can be used. A mild lysis procedure can advantageously be used to prevent the release of nuclear chromatin.
  • cells can be heated to 65°C for 10 minutes in water (Esumi et al., Neurosci Res 60(4):439-51 (2008)); or 70°C for 90 seconds in PCR buffer II (Applied Biosystems) supplemented with 0.5% NP-40 (Kurimoto et al., Nucleic Acids Res 34(5):e42 (2006)); or lysis can be achieved with a protease such as Proteinase K or by the use of chaotropic salts such as guanidine isothiocyanate (U.S. Publication No.
  • Amplification of genomic DNA according to methods described herein can be performed directly on cell lysates, such that a reaction mix can be added to the cell lysates.
  • the cell lysate can be separated into two or more volumes such as into two or more containers, tubes or regions using methods described herein or methods known to those of skill in the art with a portion of the cell lysate contained in each volume container, tube or region.
  • Genomic DNA contained in each container, tube or region may then be amplified by methods described herein or methods known to those of skill in the art.
  • a nucleic acid used in the invention can also include native or non-native bases.
  • a native deoxyribonucleic acid can have one or more bases selected from the group consisting of adenine, thymine, eytosine or guanine and a ribonucleic acid can have one or more bases selected from the group consisting of uracil, adenine, cytosine or guanine.
  • Exemplary nonnative bases that can be included in a nucleic acid, whether having a native backbone or analog structure include, without limitation, inosine, xathanine, hypoxathanine, isocytosine, isoguanine,
  • 6-azo thymine 5-uracil, 4-thiouracil, 8-halo adenine or guanine, 8- amino adenine or guanine, 8- thiol adenine or guanine, 8-thioalkyl adenine or guanine, 8- hydroxyl adenine or guanine, 5-halo substituted uracil or cytosine, 7-methylguanine, 7- methyladenine, 8-azaguanine, 8-azaadenine,
  • a particular embodiment can utilize isocytosine and isoguanine in a nucleic acid in order to reduce nonspecific hybridization, as generally described in U.S. Pat. No.5, 681 ,702.
  • primer generally includes an oligonucleotide, either natural or synthetic, that is capable, upon forming a duplex with a polynucleotide template, of acting as a point of initiation of nucleic acid synthesis and being extended from its 3' end along the template so that an extended duplex is formed.
  • the sequence of nucleotides added during the extension process are determined by the sequence of the template polynucleotide.
  • primers are extended by a DNA polymerase. Primers usually have a length in the range of between 3 to 36 nucleotides, also 5 to 24 nucleotides, also from 14 to 36 nucleotides.
  • Primers within the scope of the invention include orthogonal primers, amplification primers, constructions primers and the like Pairs of primers can flank a sequence of interest or a set of sequences of interest. Primers and probes can be degenerate or quasi-degenerate in sequence. Primers within the scope of the present invention bind adjacent to a target sequence.
  • a "primer” may be considered a short polynucleotide, generally with a free 3' -OH group that binds to a target or template potentially present in a sample of interest by hybridizing with the target, and thereafter promoting polymerization of a polynucleotide complementary to the target.
  • Primers of the instant invention are comprised of nucleotides ranging from 17 to 30 nucleotides.
  • the primer is at least 17 nucleotides, or alternatively, at least 18 nucleotides, or alternatively, at least 19 nucleotides, or alternatively, at least 20 nucleotides, or alternatively, at least 21 nucleotides, or alternatively, at least 22 nucleotides, or alternatively, at least 23 nucleotides, or alternatively, at least 24 nucleotides, or alternatively, at least 25 nucleotides, or alternatively, at least 26 nucleotides, or alternatively, at least 27 nucleotides, or alternatively, at least 28 nucleotides, or alternatively, at least 29 nucleotides, or alternatively, at least 30 nucleotides, or alternatively at least 50 nucleotides, or alternatively at least 75 nucleotides or alternatively at least 100 nucleotides.
  • DNA amplified in a first step using the methods describe herein can be further amplified using methods known to those of skill in the art.
  • amplification is achieved using PCR.
  • the term "polymerase chain reaction" (“PCR") of Mullis (U.S. Pat. Nos. 4,683, 195, 4,683,202, and 4,965, 188) refers to a method for increasing the concentration of a segment of a target sequence in a mixture of nucleic acid sequences without cloning or purification.
  • This process for amplifying the target sequence consists of introducing a large excess of two oligonucleotide primers to the nucleic acid sequence mixture containing the desired target sequence, followed by a precise sequence of thermal cycling in the presence of a polymerase (e.g., DNA polymerase).
  • the two primers are complementary to their respective strands of the double stranded target sequence.
  • the mixture is denatured and the primers then annealed to their complementary sequences within the target molecule.
  • the primers are extended with a polymerase so as to form a new pair of complementary strands.
  • the steps of denaturation, primer annealing, and polymerase extension can be repeated many times (i.e., denaturation, annealing and extension constitute one "cycle;” there can be numerous “cycles”) to obtain a high concentration of an amplified segment of the desired target sequence.
  • the length of the amplified segment of the desired target sequence is determined by the relative positions of the primers with respect to each other, and therefore, this length is a controllable parameter.
  • the method is referred to as the “polymerase chain reaction” (hereinafter "PCR”).
  • the desired amplified segments of the target sequence become the predominant sequences (in terms of concentration) in the mixture, they are said to be "PCR amplified.”
  • PCR it is possible to amplify a single copy of a specific target sequence in genomic DNA to a level detectable by several different methodologies (e.g., hybridization with a labeled probe; incorporation of biotinylated primers followed by avidin-enzyme conjugate detection; incorporation of 32 P-labeled deoxynucleotide triphosphates, such as dCTP or dATP, into the amplified segment).
  • any oligonucleotide or polynucleotide sequence can be amplified with the appropriate set of primer molecules.
  • PCR is a reaction in which replicate copies are made of a target polynucleotide using a pair of primers or a set of primers consisting of an upstream and a downstream primer, and a catalyst of polymerization, such as a DNA polymerase, and typically a thermally-stable polymerase enzyme.
  • a catalyst of polymerization such as a DNA polymerase, and typically a thermally-stable polymerase enzyme.
  • a primer can also be used as a probe in hybridization reactions, such as Southern or Northern blot analyses.
  • the expression "amplification” or “amplifying” refers to a process by which extra or multiple copies of a particular polynucleotide are formed. Amplification includes methods such as PCR, ligation amplification (or ligase chain reaction, LCR) and amplification methods. These methods are known and widely practiced in the art. See, e.g., U.S. Patent Nos.
  • the PCR procedure describes a method of gene amplification which is comprised of (i) sequence-specific hybridization of primers to specific genes within a DNA sample (or library), (ii) subsequent amplification involving multiple rounds of annealing, elongation, and denaturation using a DNA polymerase, and (iii) screening the PCR products for a band of the correct size.
  • the primers used are oligonucleotides of sufficient length and appropriate sequence to provide initiation of polymerization, i.e. each primer is specifically designed to be complementary to each strand of the genomic locus to be amplified.
  • Reagents and hardware for conducting amplification reaction are commercially available.
  • Primers useful to amplify sequences from a particular gene region are preferably complementary to, and hybridize specifically to sequences in the target region or in its flanking regions and can he prepared using the polynucleotide sequences provided herein. Nucleic acid sequences generated by amplification can be sequenced directly.
  • a double-stranded polynucleotide can be complementary or homologous to another polynucleotide, if hybridization can occur between one of the strands of the first polynucleotide and the second.
  • Complementarity or homology is quantifiable in terms of the proportion of bases in opposing strands that are expected to form hydrogen bonding with each other, according to generally accepted base-pairing rules.
  • PCR product refers to the resultant mixture of compounds after two or more cycles of the PCR steps of denaturation, annealing and extension are complete. These terms encompass the case where there has been amplification of one or more segments of one or more target sequences.
  • amplification reagents refers to those reagents (deoxyribonucleotide triphosphates, buffer, etc.), needed for amplification except for primers, nucleic acid template, and the amplification enzyme. Typically, amplification reagents along with other reaction components are placed and contained in a reaction vessel (test tube, microwell, etc.).
  • Amplification methods include PCR methods known to those of skill in the art and also include rolling circle amplification (Blanco et al., J. Biol. Chem., 264, 8935-8940, 1989), hyperbranched rolling circle amplification (Lizard et al., Nat. Genetics, 19, 225-232, 1998), and loop- mediated isothermal amplification (Notomi et al., Nuc. Acids Res., 28, e63, 2000) each of which are hereby incorporated by reference in their entireties. "Identity,” “homology” or “similarity” are used interchangeably and refer to the sequence similarity between two nucleic acid molecules.
  • Identity can be determined by comparing a position in each sequence which can be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are homologous at that position.
  • a degree of identity between sequences is a function of the number of matching or identical positions shared by the sequences.
  • An unrelated or nonhomologous sequence shares less than 40% identity, or alternatively less than 25% identity, with one of the sequences of the present invention.
  • a polynucleotide has a certain percentage (for example, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or 99%) of "sequence identity" to another sequence means that, when aligned, that percentage of bases are the same in comparing the two sequences.
  • This alignment and the percent sequence identity or homology can be determined using software programs known in the art, for example those described in Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, New York, N.Y., (1993).
  • default parameters are used for alignment.
  • One alignment program is BLAST, using default parameters.
  • Figure 1 Overview of the workflow implementing the method of the present invention.
  • Figure 2 Overview of the first amplification reaction of the method of amplifying genomic DNA of the invention.
  • Figure 3 Overview of the second amplification reaction of the method of amplifying genomic DNA of the invention.
  • Figure 4 Overview of the method of preparing a sequencing library of the invention using third- round amplicons from the method of amplifying DNA of the invention.
  • FIG. 5 Single-cell barcoding WGA; pooling of 3 cells.
  • Figure 6 Single-cell barcoding WGA; PTC; 30 pg gDNA.
  • FIG. 7 Single-cell barcoding WGA; NTC.
  • Figure 8 Single-cell barcoding WGA; regular MALBAC PCR after quasilinear Amplification
  • FIG. 9 Example B; Single-cell barcoding WGA; pooling of 3 cells.
  • FIG. 10 Example B; Single-cell barcoding WGA; pooling of 3 cells; after size selection.
  • Figure 11 Example B; per base sequence quality, per sequence quality scores and per sequence GO content for single cell 1.
  • Figure 12 Example B; per base sequence quality, per sequence quality scores and per sequence GO content for single cell 2.
  • Figure 13 Example B; per base sequence quality, per sequence quality scores and per sequence GC content for single cell 3.
  • Figure 1 shows an overview of the efficient workflow for highly parallel genome analysis of individual cells, which is made possible by the invention.
  • the workflow outlined here allows for the first time to apply DNA barcodes to the single cell DNA directly during whole genome amplification. This enables pooling of the single cell amplification reaction before ligation of adapter sequences in a single reaction for all cells for library preparation. This enables the cost-intensive library preparation for a large number of cells to be carried out in a single adapter ligation reaction.
  • Figure 2 After the lysis of a single cell, specially developed first primers and other components necessary for the amplification reaction (dNTPs, salt ions, polymerase, water) are added to the reaction mixture.
  • the first primers depicted here consist of a variable sequence at the 3’-end of the primers, a reaction-specific barcoding-sequence, and a constant sequence at the 5’-end of the primers.
  • the constant sequence and the barcoding-sequence consists exclusively of G, A and T nucleotides.
  • the primer hybridizes at a random location to the genomic DNA.
  • the cell-specific barcoding-sequence is used to clearly mark the amplicons generated from a sample.
  • self-complementary sequences are formed at the ends of the second-round amplicons, which enable the formation of hairpin structures, which protects already copied sequences from further amplification (quasi-linear amplification).
  • nucleotides of the barcoding-sequence can comprise several phosphorothioate modifications (alternatively LNA bases) to protect the amplicons against degradation by an exonuclease used during the subsequent library preparation method of the invention.
  • LNA bases alternatively LNA bases
  • This first amplification reaction enables a quasilinear pre-amplification and can be performed with an strand displacement polymerase.
  • the generated second-round amplicons are protected from further amplification due to hairpin structure formation preventing the molecules from serving as template molecules during the amplification reaction.
  • Figure 3 Before the second amplification reaction of the amplification method of the invention is started, second primers are added to the reaction.
  • the second primers contain the distal end of the first primers used in the first amplification reaction of the method of the invention.
  • the second primers also contain several phosphorothioate modifications at the 3'- end.
  • the second primers do not contain the cell-specific barcoding-sequence. This makes it possible to use a universal primer for all reactions in this step. Accordingly, it is possible to pool all reaction mixtures of the first amplification reaction corresponding to individual samples, such as individual cells, as a variant of the method of the invention.
  • double- stranded DNA is necessary.
  • the primary amplification products (second-round amplicons), which are present in form of hairpins, into double stranded products, these are first denatured at 95°C. Then the annealing of the second primers takes place as in a normal PCR. The added primers compete with the self-complementary ends of the primary hairpin products for binding to the 3' end of the denatured DNA (a balance is formed between the renewed formation of hairpin structures and the binding of the primer).
  • the denaturing temperature is chosen so high that already formed double stranded DNA molecules do not denature anymore (in the current protocol 85° C) and thus the hairpin DNA is completely converted into double stranded DNA.
  • the individual reactions for the individual samples or cells are brought together/pooled after the second amplification reaction of the method of the invention.
  • the amplicons of 10-10000, preferably 48, 96, or 384, such reactions can be combined.
  • the pooling can be followed by a purification step, wherein the combined amplicons are purified, e.g. using functionalized magnetic beads, from the other reagents contained in the reaction mixtures.
  • Figure 4 By adding a 5’-exonuclease (e.g. lambda exonuklease) and a suitable reaction buffer, the nucleotides at the 5' ends of the double-stranded DNA are selectively degraded. If lambda exonuclease is used, the used primers have phosphate groups at their 5' ends, which allow a selective and efficient degradation of the 5' ends. Since the barcoding-sequence is protected by phosphorothioate bonds, degradation is stopped at this point (see Figure 3). In the next step, another primer (gap-filling primer) is added which contains the 5'-sided sequencing adapter.
  • a 5’-exonuclease e.g. lambda exonuklease
  • This primer is designed to hybridize to the single-stranded part (3' ends) of the amplicons.
  • a polymerase without strand-displacement activity e.g. Taq polymerase
  • a ligase e.g. ampligase
  • the hybridized primer can be fully incorporated into the amplicons. This results in the desired asymmetric Y-structure.
  • a so-called adapter primer containing the 3'-sided sequencing adapter is added.
  • the amplicons equipped with the adapters are then amplified by PCR.
  • the fragments are now available as double-stranded DNA with P5 and P7 adapters at each end. After further purification, the sequencing can be started directly.
  • Figure 5 Chromatogram showing the size distribution of a final sequencing library derived from 3 pooled single cell reactions (Step 6).
  • the Library exhibits a main peak at around 400 bp.
  • the majority of library amplicons is smaller than 1000 bp.
  • Figure 6 Chromatogram showing the size distribution of a final sequencing library derived from a single reaction (positive control) with 30 pg gDNA (Step 6).
  • the Library exhibits a main peak at around 350 bp.
  • the majority of library amplicons is smaller than 1000 bp.
  • Figure 7 Chromatogram showing the size distribution of adapter dimers and template independent products from a single reaction without template (negative control).
  • Figure 8 Chromatogram showing the size distribution of amplicons derived from a single reaction (1 single cell) with regular MALBAC PCR performed after quasilinear amplification (Step 4).
  • the Library exhibits a main peak at around 880 bp. A large portion of library amplicons are larger than 1000 bp.
  • Figure 9 Example B; Chromatogram showing the size distribution of a final sequencing library derived from 3 pooled single cell reactions. The Library exhibits a broad size distribution of approximately 300 - 1200 nucleotides in length.
  • FIG. 10 Example B; Chromatogram showing the size distribution of a final sequencing library derived from 3 pooled single cell reactions after double size selection in order to further increase sequencing efficiency.
  • the Library exhibits a broad size distribution of approximately 300 - 1000 nucleotides in length.
  • Figure 11 Example B; Single cell 1 ; Sequencing quality assessment using FasQC.
  • A) shows the phred quality score across all bases over the position of the reads.
  • B) shows the quality score distribution over all sequences and
  • C) displays the GC content distribution of the data in comparison to the theoretical modeled distribution.
  • Figure 12 Example B; Single cell 2; Sequencing quality assessment using FasQC. A)shows the phred quality score across all bases over the position of the reads. B) shows the quality score distribution over all sequences and C) displays the GC content distribution of the data in comparison to the theoretical modeled distribution.
  • Figure 13 Example B; Single cell 3; Sequencing quality assessment using FasQC. A)shows the phred quality score across all bases over the position of the reads. B) shows the quality score distribution over all sequences and C) displays the GC content distribution of the data in comparison to the theoretical modeled distribution.
  • Figure 14 Example B; Copy number estimation from sequence read coverage using the online tool Ginkgo and a variable bin size of 5Mb and standard settings. CNVs of single cells 1-3 largely resemble those of the Kasumi-1 cell bulk.
  • NAD+ b-Nicotinamide adenine dinucleotide
  • Step 4 regular MALBAC PCR after Quasilinear Amplification
  • Step 5 Conversion to double stranded DNA
  • the dsDNA amplicons can be stored at -20 °C over night.
  • T ransfer and pool all single cell reactions (each 15pl) in a 1 .5 ml DNA low binding tube using the same pipette tip. Up to 24 single-cell reactions can be pooled in one 1.5 ml DNA low binding tube.
  • pooling beads in a 1 :1.1 ratio to the pooled single cell reactions (e.g. per reaction 15mI single cell reaction + 15mI 0.5x TE + 33 mI pooling beads). Mix carefully but thoroughly by Pipetting.
  • Step 8 Gap-filling / Ligation
  • Step 9 Sequencing Library PCR
  • Primer A was used with the following barcode sequences to individually barcode each single cell:
  • the fragment size distribution of the primary single cell library was analyzed using the High Sensitivity D1000 ScreenTape with High Sensitivity D1000 Reagents (Agilent) according to the manufacturer's recommendations. This revealed a size distribution of approximately 300 - 1200 nucleotides in length which is appropriate for next generation sequencing with lllumina systems ( Figure 9).
  • adapter dimers i.e. 255 bp peak
  • fragments larger than 1000 bp were removed using a double size selection protocol with two consecutive AMPure XP purification steps with 25pl of library DNA input.
  • the generated NGS single cell library was sequenced on an lllumina MiSeq system using the 250 bp paired-end mode with 10 % PhiX spike in.
  • the library was additional multiplexed with 20% lllumina TruSeq library containing 13 individually barcoded (lllumina 6bp Index) bulk gDNA samples to further increase nucleotide diversity in the first five sequencing cycles of the run (i.e. which correspond to the single cell barcodes) and in the index read.
  • primers used in Step 8 and 9 contain custom 3’ sequences which differ from the commonly used lllumina adapter sequences, custom READ 1 , INDEX READ and READ 2 primers were added to the MiSeq cartridge wells in position 12, 13 and 14 to a final concentration of 0.5 mM, respectively. All primers contain LNA nucleotides which increase the melting temperature of each primer to a temperature greater than 65 °C to ensure stable annealing to the template during cycling.
  • CNVs copy number variations
  • SNVs single-nucleotide variants
  • duplications additional copies of sequence
  • CNVs are highly important for cancer research because they are, besides of SNVs, a major factor contributing to intra-tumor heterogeneity (ITH) which describes the phenomenon when one tumor is composed of multiple subclones, each characterized by a distinct set of mutations.
  • ITH intra-tumor heterogeneity

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Abstract

L'invention concerne un procédé d'amplification d'ADN de plus d'un échantillon pour générer une banque de séquençage, le procédé comprenant les étapes suivantes : a) fourniture, pour chacun des plus d'un échantillon, d'un récipient de réaction individuel comprenant l'ADN sous forme monocaténaire ; b) ajout des premières amorces au récipient de réaction pour produire un mélange réactionnel, les premières amorces comprenant dans une orientation 5' à 3' une séquence constante et une séquence variable, la séquence constante comprenant dans une orientation de 5' à 3' une première partie ayant une séquence qui peut être commune pour les plus d'un échantillon et une seconde partie ayant une séquence qui est différente pour chacun des plus d'un échantillon ; c) ajout d'une ADN polymérase au récipient de réaction ; d) soumission du mélange réactionnel à une température à laquelle les premières amorces s'hybrident à l'ADN monocaténaire par l'intermédiaire de la séquence variable ; e) soumission du mélange réactionnel à une température à laquelle l'ADN polymérase étend les extrémités 3' des premières amorces recuites pour produire des amplicons de premier cycle ; f) soumission du mélange réactionnel à une température pour produire des amplicons simple brin ; g) soumission du mélange réactionnel à une température à laquelle des premières amorces libres s'hybrident à l'ADN monocaténaire et aux amplicons de premier cycle par l'intermédiaire de la séquence variable ; h) soumission du mélange réactionnel à une température à laquelle l'ADN polymérase étend les extrémités 3' des premières amorces recuites pour produire des amplicons de premier cycle à partir de premières amorces recuites aux ADN fournis et des amplicons de second cycle à partir de premières amorces recuites en amplicons de premier cycle ; i) soumission du mélange réactionnel à une température pour produire des amplicons monocaténaires, répétition des étapes g) à i) pour produire des amplicons de second cycle de l'ADN fourni.
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