WO2019016401A1 - Improved method and kit for the generation of dna libraries for massively parallel sequencing - Google Patents

Improved method and kit for the generation of dna libraries for massively parallel sequencing Download PDF

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Publication number
WO2019016401A1
WO2019016401A1 PCT/EP2018/069845 EP2018069845W WO2019016401A1 WO 2019016401 A1 WO2019016401 A1 WO 2019016401A1 EP 2018069845 W EP2018069845 W EP 2018069845W WO 2019016401 A1 WO2019016401 A1 WO 2019016401A1
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Prior art keywords
seq
primer
sequencing
section
library
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PCT/EP2018/069845
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French (fr)
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Valentina DEL MONACO
Nicolò Manaresi
Genny BUSON
Paola TONONI
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Menarini Silicon Biosystems S.P.A.
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Priority to SG11202000360YA priority Critical patent/SG11202000360YA/en
Priority to JP2020502308A priority patent/JP2020530767A/en
Priority to US16/632,268 priority patent/US11859249B2/en
Priority to CA3070025A priority patent/CA3070025A1/en
Priority to EP18745566.2A priority patent/EP3655541A1/en
Priority to IL272039A priority patent/IL272039B2/en
Application filed by Menarini Silicon Biosystems S.P.A. filed Critical Menarini Silicon Biosystems S.P.A.
Priority to CN201880049144.2A priority patent/CN110959045B/en
Priority to KR1020207004574A priority patent/KR20200054168A/en
Priority to KR1020247015671A priority patent/KR20240069835A/en
Publication of WO2019016401A1 publication Critical patent/WO2019016401A1/en
Priority to JP2023111550A priority patent/JP2023126945A/en
Priority to US18/506,751 priority patent/US20240158850A1/en

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    • 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
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
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    • 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
    • C12Q1/6869—Methods for sequencing
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1093—General methods of preparing gene libraries, not provided for in other subgroups
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
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    • 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
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C12Q1/6855—Ligating adaptors
    • C—CHEMISTRY; METALLURGY
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    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/122—Massive parallel sequencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

Definitions

  • the present invention relates to a method and a kit to generate a massively parallel sequencing library for Whole Genome Sequencing from Whole Genome Amplification products (WGA) .
  • WGA Whole Genome Amplification products
  • the method can advantageously be applied to Deterministic Restriction-Site, Whole Genome Amplification (DRS-WGA) DNA products.
  • the library can advantageously be used for low-pass whole-genome sequencing and genome-wide copy-number profiling .
  • WGA Whole Genome Amplification
  • DRS-WGA Deterministic Restriction Site
  • a LM-PCR based, DRS-WGA commercial kit ⁇ AmplilTM WGA kit, Menarini Silicon Biosystems has been used in Hodgkinson C.L. et al . , Tumorigenicity and genetic profiling of circulating tumor cells in small-cell lung cancer, Nature Medicine 20, 897-903 (2014) .
  • a Copy-Number Analysis by low-pass whole genome sequencing on single-cell WGA material was performed.
  • Illumina libraries required several steps, which included i) digestion of WGA adapters, ii) DNA fragmentation, and standard Illumina workflow steps such as iii) EndRepair iv) A-Tailing v) barcoded adapter ligation, plus the usual steps of vi) sample pooling of barcoded NGS libraries and vii) sequencing.
  • Fig 5b WBC did present few presumably false- positive copy-number calls, although CTCs in general displayed many more aberrations.
  • AmplilTM WGA is compatible with array Comparative Genomic Hybridization (aCGH) ; indeed several groups (Moehlendick B, et al . (2013) A Robust Method to Analyze Copy Number Alterations of Less than 100 kb in Single Cells Using Oligonucleotide Array CGH. PLoS ONE 8(6): e67031; Czyz ZT, et al (2014) Reliable Single Cell Array CGH for Clinical Samples. PLoS ONE 9(1): e85907) showed that it is suitable for high-resolution copy number analysis. However, aCGH technique is expensive and labor intensive, so that different methods such as low-pass whole-genome sequencing (LPWGS) for detection of somatic Copy-Number Alterations (CNA) may be desirable .
  • LWGS low-pass whole-genome sequencing
  • CNA somatic Copy-Number Alterations
  • PCT/EP2017/059075 in the name of the present applicant discloses a method for generating a massively parallel sequencing library -also referred to as an NGS (next generation sequencing) library- starting from a WGA product in a streamlined way.
  • NGS next generation sequencing
  • the method involves amplifying the primary WGA DNA library with two primers, each of which includes a different sequencing adapter at the 5' end that will allow sequencing on a specific sequencing platform.
  • the sequencing platforms that can be used are e.g. the Ion-Torrent platform or the Illumina platform.
  • homoadapter fragments Fragments harboring the same sequencing adapters on both ends (hereinafter referred to as “homoadapter fragments”) are either eluted (if not biotinylated) or remain bound to the streptavidin beads (if biotinylated on both ends) , whereas ssDNA heteroadapter fragments (harboring different sequencing adapters at the two ends) are denatured and eluted so as to be selected.
  • biotinylated primers has some weaknesses. In particular, it leads to a single strand DNA library which is more difficult to quantify and less preferred for storage.
  • the use of a double strand DNA library is preferable. This issue can be addressed by performing a double strand synthesis or further amplification cycles using P5 and P7 primers, but of course this renders the method somewhat more complicated and does not allow a single- tube reaction.
  • the design of a kit is consequently more complex, as it requires e.g. the use of specific buffers designed for the purpose.
  • Other objects of the present invention are to provide a method for low-pass whole genome sequencing and a method for genome-wide copy-number profiling starting from a WGA product, using the library preparation method according to the invention.
  • Figure 1 shows a picture summarizing the steps of the method disclosed in PCT/EP2017/059075 by the applicant to select heteroadapter fragments.
  • FIG. 2A shows a picture summarizing the steps of the method according to the present invention referring in particular to the situation in which the primary WGA DNA library is obtained by DRS-WGA. This is however not intended to limit the scope of the invention to this particular kind of WGA.
  • Figure 2B shows the structure of the primary WGA DNA library and of the four primers used in the method according to the invention as shown in Figure 2A.
  • the acronyms used in the claims and description for the different segments of the primary WGA DNA library and of the four primers are also shown in parenthesis.
  • Figure 3A shows a picture of dual index sequencing on MiSeq, HiSeq 2000/2500 and 1000/1500 with one custom sequencing primer according to the invention.
  • Figure 3B shows a picture of dual index sequencing on
  • FIGS 4A and 4B show sequencing results of a Low-pass Whole Genome Sequencing performed by the method according to the present invention.
  • the figure shows copy number alterations (CNA) profiles of two single cells belonging to NCI-H441 and SW-480 cell lines, sorted by DEPArrayTM
  • Figure 5 shows sequencing results of a Low-pass Whole Genome Sequencing performed by the method according to the present invention.
  • the figure shows copy number alterations (CNA) profiles of a tumor single cell and a population of 50 stromal cells, belonging to disaggregated FFPE section, digitally sorted by DEPArrayTM (Menarini Silicon Biosystems) and whole-genome amplified using the AmplilTM WGA kit.
  • CNA copy number alterations
  • Figures 6A and 6B show inter-method and inter-platform
  • Figure 6A shows copy number alterations (CNA) profiles of a NCI-H23 single cell, obtained with a Low-pass Whole Genome Sequencing method for IonTorrent (presented in PCT/EP2017/059075) and with the method according to the present invention for Illumina platforms.
  • Figure 6B shows NCI-H441 and WBC single-cells hierarchical clustering, based on CNAs profiles.
  • genomic DNA there is intended the genomic DNA (gDNA) prior to amplification with the DRS-WGA.
  • Adapter or "WGA Adapter” or “WGA PCR Primer” or “WGA library universal sequence adapter” there is intended the additional oligonucleotide ligated to each fragment generated by the action of the restriction enzyme, in case of DRS-WGA, or the known polynucleotide sequence present at 5' section of each molecule of the WGA DNA library as a result of extension and PCR process, in case of MALBAC .
  • CNA Codon Number Alteration
  • CNV Codon Number Variation
  • MPS massive-parallel sequencing
  • NGS next generation sequencing
  • Target sequence there is intended a region of interest on the original DNA.
  • MALBAC Multiple Annealing and Looping Based Amplification Cycles
  • DNA library Purification there is intended a process whereby the DNA library material is separated from unwanted reaction components such as enzymes, dNTPs, salts and/or other molecules which are not part of the desired DNA library.
  • Example of DNA library purification processes are purification with paramagnetic bead-based technology (in the scientific literature and hereinafter for simplicity often referred to as "magnetic beads") such as Agencourt AMPure XP or solid-phase reversible immobilization (SPRI) -beads from Beckman Coulter or with spin column purification such as Amicon spin-columns from Merck Millipore.
  • SPRI solid-phase reversible immobilization
  • Another example of DNA library purification processes are purification with magnetic beads conjugated to oligonucleotide baits either directly or through protein-protein interactions such as streptavidin coated magnetic beads interacting with biotinylated oligonucleotides.
  • DNA library Selection there is intended a process whereby either DNA library Purification or DNA library Size selection or both are carried out.
  • SA sequencing adapter
  • a polynucleotide sequence which is required to be present in a massively parallel sequencing library in order for the sequencer to correctly generate an output sequence, but which does not carry information, (as non-limiting examples: a polynucleotide sequence to hybridize a ssDNA to a flow-cell, in case of Illumina sequencing, or to an ion-sphere, in case of Ion Torrent sequencing, or a polynucleotide sequence required to initiate a sequencing-by-synthesis reaction) .
  • sequencing barcode there is intended a polynucleotide sequence which, when sequenced within one sequencer read, allows that read to be assigned to a specific sample associated with that barcode.
  • low-pass whole genome sequencing there is intended a whole genome sequencing at a mean sequencing depth lower than 1.
  • mean sequencing depth the total of number of bases sequenced, mapped to the reference genome divided by the total reference genome size.
  • the total number of bases sequenced and mapped can be approximated to the number of mapped reads times the average read length.
  • normalizing there is intended the act of adjusting the concentration of one or more samples to make them correspond to a desired proportion between them (equalizing being the special case where the proportion is 1) .
  • equalizing being the special case where the proportion is 1 .
  • the method of generating a massively parallel sequencing library comprises the following steps .
  • a primary WGA DNA library (pWGAlib) , which includes fragments comprising a known 5' sequence section (5SS) , a middle sequence section (MSS) , and a known 3' sequence section (3SS) reverse complementary to the known 5' sequence section.
  • the known 5' sequence section (5SS) comprises a WGA library universal sequence adapter.
  • the middle sequence section (MSS) comprises at least an insert section (IS), corresponding to a DNA sequence of the original unamplified DNA prior to WGA.
  • the middle sequence section optionally comprises, in addition to the insert section (IS), a flanking 5' intermediate section (F5) and/or a flanking 3' intermediate section (F3) (for example when the primary WGA DNA library is generated by MALBAC or by DRS-WGA according to the teachings of WO 2015/118077) .
  • the known 5' sequence section (5SS) corresponds to the LIB sequence (SEQ ID NO: 50) specific for the DRS-WGA
  • the known 3' sequence section (3SS) is the reverse complementary of the LIB sequence (LIBrc) .
  • a single PCR cycle is performed on the primary WGA DNA library using at least one first primer (1PR), which comprises at least a first primer 5' section (1PR5S) and a first primer 3' section (1PR3S) .
  • the first primer 5' section (1PR5S) comprises at least one first sequencing adapter (1PR5SA) .
  • the first primer 3' section (1PR3S) hybridizes to the known 3' sequence section (3SS) .
  • the result of the single PCR cycle of step b is a first primer extended WGA DNA library.
  • a single PCR cycle includes a double strand DNA denaturation step, a primer annealing step and an annealed primer extension step.
  • a preferred embodiment includes a denaturation step of 30 seconds at 95°C, an annealing step of 30 seconds at 62°C, and an extension step of 3 minutes at 72°C.
  • the first primer (1PR) preferably further comprises at least one read sequencing primer sequence (1PRSEQ) in 3' position of the first primer 5' section (1PR5S) and in 5' position of the first primer 3' section (1PR3S) .
  • the first primer (1PR) preferably has a sequence selected from the group consisting of SEQ ID NO : 1 to SEQ ID NO: 12.
  • the first primer extended WGA DNA library is purified after step b. This purification is preferably carried out with SPRIselect beads (Beckman Coulter) .
  • step c a single PCR cycle is performed on the first primer extended WGA DNA library, using at least one second primer (2PR) comprising a second primer 5' section (2PR5S) and a second primer 3' section (2PR3S) .
  • the second primer 5' section (2PR5S) comprises at least one second sequencing adapter (2PR5SA) different from the at least one first sequencing adapter (1PR5SA) .
  • the second primer 3' section (2PR3S) hybridizes to the known 3' sequence section (3SS) .
  • the result of the single PCR cycle of step c is a first and second primer extended WGA DNA library.
  • a single PCR cycle includes a double strand DNA denaturation step, a primer annealing step and an annealed primer extension step.
  • a preferred embodiment includes a denaturation step of 30 seconds at 95°C, an annealing step of 30 seconds at 60°C, and an extension step of 3 minutes at 72°C.
  • the second primer (2PR) preferably has a sequence selected from the group consisting of SEQ ID NO: 13 to SEQ ID NO: 20.
  • the first and second primer extended WGA DNA library is purified, preferably with 2.5M NaCl PEG 20% solution .
  • step d the first and second primer extended WGA DNA library is amplified by using at least one third primer (3PR) comprising the first sequencing adapter (1PR5SA) and at least one fourth primer (4PR) comprising the second sequencing adapter (2PR5SA) .
  • the result of the PCR amplification of step d is an amplified first and second primer extended WGA DNA library.
  • the yield of this amplification step in terms of DNA library is sufficient to carry out sequencing thereon.
  • the amplified first and second primer extended WGA DNA library is purified, preferably with 2.5M NaCl PEG 20% solution.
  • the third primer (3PR) preferably has sequence SEQ ID NO: 22 and the fourth primer (4PR) preferably has sequence SEQ ID NO:21.
  • the first primer 5' section (1PR5S) of the first primer (1PR) preferably further comprises at least one first sequencing barcode (1PR5BC) in 3' position of the at least one first sequencing adapter (1PR5SA) and in 5' position of the first primer 3' section (1PR3S) .
  • the second primer 5' section (2PR5S) of the second primer (2PR) preferably further comprises at least one second sequencing barcode (2PR5BC) , in 3' position of the at least one second sequencing adapter (2PR5SA) and in 5' position of the second primer 3' section (2PR3S) . This allows for greater multiplexing.
  • each primer containing a different barcode is used as first primer (1PR)
  • each primer containing a different barcode is used as second primer (2PR)
  • second primer (2PR) each primer containing a different barcode
  • the WGA library universal sequence adapter is preferably a DRS-WGA library universal sequence adapter or a MALBAC library universal sequence adapter, more preferably a DRS-WGA library universal sequence adapter.
  • the DRS-WGA library universal sequence adapter preferably has SEQ ID NO: 50 and the MALBAC library universal sequence adapter preferably has SEQ ID NO: 51.
  • the method for low-pass whole genome sequencing according to the present invention comprises the following steps .
  • the step of pooling samples using different sequencing barcodes further comprises the steps of quantitating the DNA in each of the barcoded, massively-parallel sequencing libraries, and of normalizing the amount of barcoded, massively-parallel sequencing libraries.
  • a massively parallel sequencing library preparation kit comprises at least one first primer (1PR), one second primer (2PR) , one third primer (3PR) and one fourth primer (4PR) .
  • the structure of these primers has already been disclosed above.
  • the massively parallel sequencing library preparation kit comprises one or more primers selected from the group consisting of SEQ ID NO : 1 to SEQ ID NO: 12, one or more primers selected from the group consisting of SEQ ID NO:13 to SEQ ID NO:20, and primers SEQ ID NO:21 and SEQ ID NO: 22.
  • the massively parallel sequencing library preparation kit comprises one or more primers selected from the group consisting of SEQ ID NO: 52 to SEQ ID NO: 63, one or more primers selected from the group consisting of SEQ ID NO: 13 to SEQ ID NO:20, and primers SEQ ID NO:21 and SEQ ID NO:22.
  • the massively parallel sequencing library preparation kit comprises one or more primers selected from the group consisting of SEQ ID NO:27 to SEQ ID NO:38, one or more primers selected from the group consisting of SEQ ID NO: 39 to SEQ ID NO: 46, and primers SEQ ID NO:21 and SEQ ID NO:22.
  • the massively parallel sequencing library preparation kit comprises one or more primers selected from the group consisting of SEQ ID NO: 64 to SEQ ID NO: 75, one or more primers selected from the group consisting of SEQ ID NO: 39 to SEQ ID NO: 46, and primers SEQ ID NO:21 and SEQ ID NO:22.
  • the low-pass whole genome sequencing kit comprises at least one primer selected from the group consisting of SEQ ID NO:l to SEQ ID NO: 12; at least one primer selected from the group consisting of SEQ ID NO:13 to SEQ ID NO:20; primers SEQ ID NO:21 and SEQ ID NO: 22; and a custom sequencing primer of SEQ ID NO: 23.
  • the kit preferably also comprises a primer selected from the group consisting of SEQ ID NO:24, SEQ ID NO:25 and SEQ ID NO:26.
  • SEQ ID NO: 24 is particularly preferred.
  • the low-pass whole genome sequencing kit comprises at least one primer selected from the group consisting of SEQ ID NO: 52 to SEQ ID NO: 63; at least one primer selected from the group consisting of SEQ ID NO: 13 to SEQ ID NO:20; primers SEQ ID NO:21 and SEQ ID NO:22; a custom sequencing primer of SEQ ID NO: 23 and a custom index 2 primer selected from the group consisting of SEQ ID NO: 24, SEQ ID NO: 25 and SEQ ID NO: 26.
  • the low-pass whole genome sequencing kit comprises at least one primer selected from the group consisting of SEQ ID NO: 27 to SEQ ID NO: 38; at least one primer selected from the group consisting of SEQ ID NO: 39 to SEQ ID NO: 46; primers SEQ ID NO: 21 and SEQ ID NO: 22; and primer of SEQ ID NO: 47.
  • the kit preferably also comprises SEQ ID NO: 48. Even more preferably, the kit comprises a primer of SEQ ID NO: 49.
  • the low-pass whole genome sequencing kit comprises at least one primer selected from the group consisting of SEQ ID NO: 64 to SEQ ID NO: 75; at least one primer selected from the group consisting of SEQ ID NO: 39 to SEQ ID NO: 46; primers SEQ ID NO: 21 and SEQ ID NO: 22; and primer of SEQ ID NO: 47.
  • the kit preferably also comprises SEQ ID NO: 48. Even more preferably, the kit comprises a primer of SEQ ID NO: 49.
  • the method for genome-wide copy number profiling according to the present invention comprises the steps of:
  • Single cell DNA was amplified using the AmplilTM WGA Kit (Menarini Silicon Biosystems) according to the manufacturer's instructions. 5 ⁇ L of WGA-amplified DNA were diluted by the addition of 5 ⁇ L of Nuclease-Free Water and purified using SPRIselect beads (Beckman Coulter) system (ratio 1.8x) . The DNA was eluted in 12.5 ⁇ L and quantified by dsDNA HS Assay on the Qubit® 2.0 Fluorometer. •P7 single extension
  • a single step of PCR extension was performed in a volume of 15 ⁇ L using AmplilTM PCR Kit (Menarini Silicon Biosystems) and a LIB_IL_index D7xx (one of primers from SEQ ID NO : 1 to SEQ ID NO:12).
  • Each PCR reaction contained: 1.5 ⁇ L AmplilTM PCR Reaction Buffer (10X), 3 ⁇ L of one primer LIB_IL_index D7xx within the following range: from SEQ ID NO : 1 to SEQ ID NO: 12 [2.5 ⁇ ] , 0.51 ⁇ L AmplilTM PCR dNTPs (10 mM) , 0.37 ⁇ L BSA, 0.12 ⁇ L AmplilTM PCR Taq Polymerase, WGA-purified DNA (from 10 to 75 ng) and AmplilTM water to reach a final volume of 15 ⁇ L .
  • Applied Biosystems® 2720 Thermal Cycler was set as follows: 95°C for 4 minutes, 1 cycle of 95°C for 30 seconds, 62°C for 30 seconds, 72°C for 3 minutes.
  • the library amplification PCR reaction was performed in the presence of beads.
  • Applied Biosystems® 2720 Thermal Cycler was set as follows: 95°C for 4 minutes, 1 cycle of 95°C for 30 seconds, 60°C for 30 seconds, 72°C for 2 minutes, 10 cycles of 95°C for 30 seconds, 60°C for 30 seconds, 72°C for 2 minutes (extended by 20 seconds/cycle) and final extension at 72° C for 7 minutes.
  • the cycles of 95°C for 30 seconds, 60°C for 30 seconds, 72°C for 2 minutes can be extended to 12, to increase the library concentration of at least a 2 (-4) factor by introducing 2 extra cycles during library amplification, thus increasing the total number of cycles from 11 to 13.
  • the amplified library (containing Illumina sequencing adapter sequences) was finally purified using 2.5M NaCl PEG 20% solution (ratio 1.5x) and eluted in 15 ⁇ L of AmplilTM water.
  • the purified libraries were qualified by Agilent DNA 7500, DNA 1000 or DNA HS Kits on the 2100 Bioanalyzer® and quantified by dsDNA HS Assay on Qubit® 2.0 Fluorometer, in order to obtain an equimolar pool.
  • the purified libraries were quantified by Quantitative real-time PCR (qPCR) methodology.
  • the qPCR method accurately quantifies the functional libraries, in particular those fragments that have the correct adapter on each end (heteroadapter fragments) , based on a standard curve generated from a control template dilutions . Sequencing on MiSeq sequencing system
  • Custom readl sequencing primer (SEQ ID NO:23) was then diluted with HTl to obtain a final concentration of 0,5 ⁇ . 600 ⁇ L of diluted Custom readl sequencing primer was loaded on MiSeq reagent cartridge (Illumina) .
  • Single end reads of 100 bases or Paired end reads (100 PE) were generated using the v2 chemistry of the Illumina HiSeq, in Rapid run mode, or using the v4 chemistry of the Illumina HiSeq, in High Output run mode.
  • Custom readl sequencing primer (SEQ ID NO:23) was then diluted with HTl to obtain a final concentration of 0.5 ⁇ .
  • Custom readl sequencing primer SEQ ID NO:23
  • Custom primer index 2A i5 [ LNA-5 ' ] (SEQ ID NO:24) were then diluted with HT1 to obtain a final concentration of 0.5 ⁇ .
  • the LIB reverse complementary is the target for the primers listed in TABLE 1, from SEQ ID NO:l to SEQ ID NO:20, as shown in the figures 2A and 2B.
  • a custom readl sequencing primer (SEQ ID NO: 23) has been designed, because the final library lacks the target sequence of Illumina readl sequencing primer.
  • the custom readl sequencing primer (SEQ ID NO:23) contains the LIB sequence and is complementary to the LIB reverse complementary sequence.
  • the sequencing run are preferably performed using the custom readl sequencing primer (SEQ ID NO:23), the PhiX DNA library lacks the target sequence of custom readl sequencing primer and for this reason the PhiX DNA will not be sequenced.
  • the final library obtained by the method of the present invention does not have the canonical Illumina sequence-adapter used by MiniSeq, NextSeq, HiSeq 3000 and 4000 Illumina systems to read the index 2 (i5) .
  • a custom primer index 2 (SEQ ID NO:24 or SEQ ID NO:25 or SEQ ID NO:26) is used to allow the correct reading of index i5.
  • the custom sequencing primer index 2 contains the LIB sequence.
  • the custom primer index 2A (i5) [LNA- 5'] (SEQ ID NO:24) and the custom primer index 2A (i5) [LNA- 3'] (SEQ ID NO:25) have three LNA (Locked Nucleic Acid [ LNATM] - Exiqon) modified nucleotides indicated in Table 1 with the "+" beside (e.g. "+A") .
  • the custom primer index 2(i5) [RNA] (SEQ ID NO:26) is formed by fifteen RNA nucleotides indicated with the "r” beside (e.g. "rA”) .
  • the following combination of primers can be used: - at least one primer selected from the group consisting of SEQ ID NO: 52 to SEQ ID NO: 63;
  • Primers from SEQ ID NO: 52 to SEQ ID NO: 63 include, instead of the RDSP sequence, a sequence of 8 nucleotides, which are needed 5' of the first primer 3' section to increase the annealing temperature of custom sequencing primers .
  • the second primer (SEQ ID NO: 13 to SEQ ID NO:20) includes the same sequence of 8 nucleotides 5' of the second primer 3' section.
  • the custom sequencing primer of SEQ ID NO: 23 is used for Illumina sequencing platforms to read the Read 1 and/or Read 2; the custom sequencing primer of SEQ ID NO: 24 (or SEQ ID NO: 25 or SEQ ID NO:26) is used for Illumina sequencing platforms to read the Index 1 and Index 2.
  • primer of SEQ ID NO: 48 is used. Even more preferably, also primer of SEQ ID NO: 49 is used.
  • Sequenced reads were aligned to the hg19 human reference 5 genome using the BWA MEM algorithm (Li H. and Durbin R., 2010) .
  • Control-FREEC Boeva V. et al . , 2011
  • Main ploidy parameter was set accordingly to ploidy of the genetic material tested and contamination adjustment was not used.
  • the ploidy values are indicated in the y-axis; providing a better fit of profiles with segmented data (black lines) and improving CNA calling. Dots above the main ploidy assessed can be considered gains; dots below the main ploidy assessed can be considered losses.
  • Figure 5 shows Low-pass Whole Genome Sequencing results performed by the method disclosed above.
  • the figure shows copy number alterations (CNA) profiles, with gains and losses only for the tumor single cell.
  • Figures 6A and 6B show inter-method and inter-platform (IonTorrent and Illumina) comparison results.
  • Figure 6A shows copy number alterations (CNA) profiles of a NCI-H23 single cell, obtained with a Low-pass Whole Genome Sequencing method for IonTorrent (presented in PCT/EP2017/059075) and with the method according to the present invention for Illumina platforms. The results obtained with the two platforms are highly consistent with one another.
  • CNA copy number alterations
  • NCI-H441 and WBC single-cells hierarchical clustering shows that samples are clustered by sample-types (tumor and normal) and not by methods or platforms (Figure 6B) .
  • the first or second primer (1PR and/or 2PR) could be modified so that they are bound at their 5' end to a solid support during at least one step of the procedure.
  • the first primer (1PR) may comprise a Biotinylated 5' end.
  • streptavidin coated beads are added to the reaction tube, capturing the first-primer extended DNA library fragments, whereas non- extended fragments which do not comprise the first primer are eluted away, along with primers dNTPs and polymerase.
  • the second primer (2PR) is provided (along with other PCR reagents) and hybridizes to the first-primer extended DNA library fragments and polymerization occurs using the bead-bound DNA library fragments left in the tube as template, producing a heteroadapter DNA fragment.
  • the heteroadapter can be further amplified by PCR (step d) in the same tube using third (3PR) and fourth (4PR) primers (along with other PCR reagents) .
  • the heteroadapter can be denatured and eluted from the tube for further PCR amplification (step d) using third (3PR) and fourth (4PR) primers in a separate tube.
  • the first primer (1PR) may be bound covalently to magnetic beads.
  • the first-primer extended DNA library fragments are bound to the beads and retained, whereas non-extended fragments which comprise the known 3' sequence section (3SS) but do not comprise the first primer are eluted away.
  • the second primer (2PR) hybridizes to the first-primer extended DNA library fragments known 3' sequence section (3SS) and polymerization occurs using the bead- bound DNA library fragments left in the tube as template, producing a heteroadapter DNA fragment.
  • the heteroadapter can be further amplified by PCR (step d) in the same tube using third (3PR) and fourth (4PR) primers.
  • the heteroadapter can be denatured and eluted from the tube for further PCR amplification (step d) using third (3PR) and fourth (4PR) primers in a separate tube.
  • One advantage of these embodiments is that no size-selective effect linked to the use of SPRIbeads is introduced in the process. This will allow fragments of lengths smaller and/or larger than what normally retained by SPRIbeads, to be represented in the final sequenceable library.
  • One disadvantage is the increased complexity of the kit reagents, inherent to conjugation of primers to beads or to Biotin. The presence of a broader range of fragments may be beneficial especially when pursuing whole genome sequencing at higher depth to achieve complete resquencing beyond the genome- wide copy number profiling by low-pass WGS.
  • step b) after the first primer (1PR) is used in the first PCR cycle (step b) , a SPRI purification is carried out to remove residual first primer, then said second primer (2PR) conjugated to magnetic beads (either directly, through covalent bonds, or indirectly, through biotin modification of second primer and biotin-streptavidin interaction with streptavidin coated magnetic beads) is used in said single PCR cycle of step c, then the residual of reaction mix and mono-adapter fragments are eluted, magnetically retaining in the tube exclusively the resulting heteroadapter fragments, before proceeding to -step d- the PCR amplification with said third (3PR) and fourth (4PR) primer.
  • the method of generating a massively parallel sequencing library allows to obtain a library including only heteroadapter fragments for those sequencing platforms which require so, in a rapid, efficient, reliable and cost-effective manner. Not least, it allows to generate double strand DNA and sequencing-ready libraries with a streamlined, single-day and single-tube workflow.
  • Array CGH is based on the use of differentially labeled test and reference genomic DNA samples that are simultaneously hybridized to DNA targets arrayed on a glass slide or other solid platform.
  • limitations remain for certain applications as it has proved difficult to use low quality/quantity of DNA.
  • chromosomal copy number assessment based on a low-pass whole genome sequencing method may offer several advantages compared to aCGH including reduced DNA sequencing cost, enhanced detection of partial or segmental aneuploidies as a result of the potential increase in chromosomal analysis resolution, control-free calling of copy number alterations.
  • the potential automation of the sequencing library preparation allows to minimize human errors, reduce hands-on time, and enable higher throughput and consistency.

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Abstract

There is disclosed a method of generating a massively parallel sequencing library comprising the steps of :a) providing a primary WGA DNA library (pWGAlib), including fragments comprising a WGA library universal sequence adapter; b) performing a single PCR cycle on the pWGAlib using a first primer (1PR) comprising from 5' to 3' a first sequencing adapter (1PR5SA) and a first primer 3' section (1PR3S) hybridizing to the reverse complementary of the WGA library universal sequence adapter; c) performing a single PCR cycle on the on the product of step b) using a second primer (2PR) comprising from 5' to 3' a second sequencing adapter (2PR5SA) different from the 1PR5SA, and a second primer 3' section (2PR3S) hybridizing to the WGA library universal sequence adapter reverse complementary; d) amplifying by PCR the product of step c) using a third primer comprising the 1PR5SA and a fourth primer comprising 2PR5SA.

Description

IMPROVED METHOD AND KIT FOR THE GENERATION OF DNA LIBRARIES FOR MASSIVELY PARALLEL SEQUENCING
Cross-Reference to related Applications
This application claims priority from European Patent
Application No. 17182693.6 filed on July 21, 2017, the disclosure of which is incorporated by reference.
Technical Field of the Invention
The present invention relates to a method and a kit to generate a massively parallel sequencing library for Whole Genome Sequencing from Whole Genome Amplification products (WGA) . In particular, the method can advantageously be applied to Deterministic Restriction-Site, Whole Genome Amplification (DRS-WGA) DNA products.
The library can advantageously be used for low-pass whole-genome sequencing and genome-wide copy-number profiling .
Prior Art
With single cells it is useful to carry out a Whole Genome Amplification (WGA) for obtaining more DNA in order to simplify and/or make it possible to carry out different types of genetic analyses, including sequencing, SNP detection etc.
WGA with a LM-PCR based on a Deterministic Restriction Site (as described in e.g. WO/2000/017390) is known from the art (herein below referred to simply as DRS-WGA) . A LM-PCR based, DRS-WGA commercial kit {Amplil™ WGA kit, Menarini Silicon Biosystems) has been used in Hodgkinson C.L. et al . , Tumorigenicity and genetic profiling of circulating tumor cells in small-cell lung cancer, Nature Medicine 20, 897-903 (2014) . In this work, a Copy-Number Analysis by low-pass whole genome sequencing on single-cell WGA material was performed. However, for the standard workflow used in this paper, the creation of Illumina libraries required several steps, which included i) digestion of WGA adapters, ii) DNA fragmentation, and standard Illumina workflow steps such as iii) EndRepair iv) A-Tailing v) barcoded adapter ligation, plus the usual steps of vi) sample pooling of barcoded NGS libraries and vii) sequencing. As shown in the aforementioned article (Fig 5b) , WBC did present few presumably false- positive copy-number calls, although CTCs in general displayed many more aberrations.
Amplil™ WGA is compatible with array Comparative Genomic Hybridization (aCGH) ; indeed several groups (Moehlendick B, et al . (2013) A Robust Method to Analyze Copy Number Alterations of Less than 100 kb in Single Cells Using Oligonucleotide Array CGH. PLoS ONE 8(6): e67031; Czyz ZT, et al (2014) Reliable Single Cell Array CGH for Clinical Samples. PLoS ONE 9(1): e85907) showed that it is suitable for high-resolution copy number analysis. However, aCGH technique is expensive and labor intensive, so that different methods such as low-pass whole-genome sequencing (LPWGS) for detection of somatic Copy-Number Alterations (CNA) may be desirable .
Although the DRS-WGA provides best results in terms of uniform and balanced amplification, current protocols based on aCGH or metaphase CGH are laborious and/or expensive. Low-pass whole-genome sequencing has been proposed as a high- throughput method to analyze several samples with higher processivity and lower cost than aCGH. However, known methods for the generation of a massively parallel sequencing library for WGA products (such as DRS-WGA) still require protocols including several enzymatic steps and reactions.
It would be desirable to have a more streamlined method, combining the reproducibility and quality of DRS-WGA with the capability to analyze genome-wide Copy-Number Variants (CNVs) . In addition, determining a whole-genome copy number profile also from minute amount of cells, FFPE or tissue biopsies would be desirable.
PCT/EP2017/059075 in the name of the present applicant discloses a method for generating a massively parallel sequencing library -also referred to as an NGS (next generation sequencing) library- starting from a WGA product in a streamlined way.
The method involves amplifying the primary WGA DNA library with two primers, each of which includes a different sequencing adapter at the 5' end that will allow sequencing on a specific sequencing platform. The sequencing platforms that can be used are e.g. the Ion-Torrent platform or the Illumina platform.
When using certain sequencing platforms, e.g. the Illumina platform, it is particularly advantageous to select library fragments including the two different sequencing adapters (in the case of Illumina: P5 and P7) on the opposite ends of the fragment. These fragments will be referred to as "heteroadapter fragments". In order to do this, one of the embodiments disclosed in the above mentioned application provides that one of the two primers for amplifying the primary WGA DNA library is biotinylated at the 5' end. Figure 1 summarizes this embodiment. Once the primary WGA DNA library has been amplified with the two primers, the fragments are selected by streptavidin beads. Fragments harboring the same sequencing adapters on both ends (hereinafter referred to as "homoadapter fragments") are either eluted (if not biotinylated) or remain bound to the streptavidin beads (if biotinylated on both ends) , whereas ssDNA heteroadapter fragments (harboring different sequencing adapters at the two ends) are denatured and eluted so as to be selected.
The selection by biotinylated primers has some weaknesses. In particular, it leads to a single strand DNA library which is more difficult to quantify and less preferred for storage. In addition, for Illumina sequencing workflows the use of a double strand DNA library is preferable. This issue can be addressed by performing a double strand synthesis or further amplification cycles using P5 and P7 primers, but of course this renders the method somewhat more complicated and does not allow a single- tube reaction. The design of a kit is consequently more complex, as it requires e.g. the use of specific buffers designed for the purpose.
Summary of the Invention
It is therefore an object of the present invention to provide a method for generating a massively parallel sequencing library starting from a WGA product that overcomes the above mentioned issues.
Other objects of the present invention are to provide a method for low-pass whole genome sequencing and a method for genome-wide copy-number profiling starting from a WGA product, using the library preparation method according to the invention.
Further objects of the present invention are to provide a massively parallel sequencing library preparation kit and a low-pass whole genome sequencing kit for implementing the above mentioned methods. Brief Description of the Drawings
Figure 1 shows a picture summarizing the steps of the method disclosed in PCT/EP2017/059075 by the applicant to select heteroadapter fragments.
Figure 2A shows a picture summarizing the steps of the method according to the present invention referring in particular to the situation in which the primary WGA DNA library is obtained by DRS-WGA. This is however not intended to limit the scope of the invention to this particular kind of WGA.
Figure 2B shows the structure of the primary WGA DNA library and of the four primers used in the method according to the invention as shown in Figure 2A. The acronyms used in the claims and description for the different segments of the primary WGA DNA library and of the four primers are also shown in parenthesis.
Figure 3A shows a picture of dual index sequencing on MiSeq, HiSeq 2000/2500 and 1000/1500 with one custom sequencing primer according to the invention.
Figure 3B shows a picture of dual index sequencing on
MiniSeq, NextSeq, HiSeq 3000/4000 Illumina sequencing platforms, with two custom sequencing primers according to the invention.
Figures 4A and 4B show sequencing results of a Low-pass Whole Genome Sequencing performed by the method according to the present invention. The figure shows copy number alterations (CNA) profiles of two single cells belonging to NCI-H441 and SW-480 cell lines, sorted by DEPArray™
(Menarini Silicon Biosystems) (Figure 4A) ; and blood single cells (Circulating Tumor Cell [CTC] and White Blood Cell
[WBC] ) , sorted by DEPArray™ (Menarini Silicon Biosystems)
(Figure 4B) .
Figure 5 shows sequencing results of a Low-pass Whole Genome Sequencing performed by the method according to the present invention. The figure shows copy number alterations (CNA) profiles of a tumor single cell and a population of 50 stromal cells, belonging to disaggregated FFPE section, digitally sorted by DEPArray™ (Menarini Silicon Biosystems) and whole-genome amplified using the Amplil™ WGA kit.
Figures 6A and 6B show inter-method and inter-platform
(IonTorrent and Illumina) comparison results. In particular, Figure 6A shows copy number alterations (CNA) profiles of a NCI-H23 single cell, obtained with a Low-pass Whole Genome Sequencing method for IonTorrent (presented in PCT/EP2017/059075) and with the method according to the present invention for Illumina platforms. Figure 6B shows NCI-H441 and WBC single-cells hierarchical clustering, based on CNAs profiles.
Definitions
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although many methods and materials similar or equivalent to those described herein may be used in the practice or testing of the present invention, preferred methods and materials are described below. Unless mentioned otherwise, the techniques described herein for use with the invention are standard methodologies well known to persons of ordinary skill in the art.
By the term "Original DNA" there is intended the genomic DNA (gDNA) prior to amplification with the DRS-WGA.
By the term "Adapter" or "WGA Adapter" or "WGA PCR Primer" or "WGA library universal sequence adapter" there is intended the additional oligonucleotide ligated to each fragment generated by the action of the restriction enzyme, in case of DRS-WGA, or the known polynucleotide sequence present at 5' section of each molecule of the WGA DNA library as a result of extension and PCR process, in case of MALBAC .
By the term "Copy Number Alteration (CNA) " there is intended a somatic change in copy-numbers of a genomic region, defined in general with respect to the same individual genome.
By the term "Copy Number Variation (CNV) " there is intended a germline variant in copy-numbers of a genomic region, defined in general with respect to a reference genome. Throughout the description CNA and CNV may be used interchangeably, as most of the reasoning can be applied to both situations. It should be intended that each of those terms refers to both situations, unless the contrary is specified.
By the term "massive-parallel sequencing" (MPS) or "next generation sequencing" (NGS) there is intended a method of sequencing DNA comprising the creation of a library of DNA molecules spatially and/or time separated, clonally sequenced (with or without prior clonal amplification) . Examples include Illumina platform (Illumina Inc) , Ion Torrent platform (ThermoFisher Scientific Inc) , Pacific Biosciences platform, MinlON (Oxford Nanopore Technologies Ltd) .
By the term "Target sequence" there is intended a region of interest on the original DNA.
By the term "Primary WGA DNA library (pWGAlib) " there is indented a DNA library obtained from a WGA reaction.
By the term "Multiple Annealing and Looping Based Amplification Cycles (MALBAC) " there is intended a quasilinear whole genome amplification method (Zong et al . , Genome-wide detection of single-nucleotide and copy-number variations of a single human cell, Science. 2012 Dec 21; 338 (6114) : 1622-6. doi: 10.1126/science .1229164.) . MALBAC primers have a 8 nucleotides 3' random sequence, to hybridize to the template, and a 27 nucleotides 5' common sequence (GTG AGT GAT GGT TGA GGT AGT GTG GAG) . After first extension, semiamplicons are used as templates for another extension yielding a full amplicon which has complementary 5' and 3' ends. Following few cycles of quasi-linear amplification, full amplicon can be exponentially amplified with subsequent PCR cycles.
By the term "DNA library Purification" there is intended a process whereby the DNA library material is separated from unwanted reaction components such as enzymes, dNTPs, salts and/or other molecules which are not part of the desired DNA library. Example of DNA library purification processes are purification with paramagnetic bead-based technology (in the scientific literature and hereinafter for simplicity often referred to as "magnetic beads") such as Agencourt AMPure XP or solid-phase reversible immobilization (SPRI) -beads from Beckman Coulter or with spin column purification such as Amicon spin-columns from Merck Millipore. Another example of DNA library purification processes are purification with magnetic beads conjugated to oligonucleotide baits either directly or through protein-protein interactions such as streptavidin coated magnetic beads interacting with biotinylated oligonucleotides.
By the term "DNA library Selection" there is intended a process whereby either DNA library Purification or DNA library Size selection or both are carried out.
By the term "sequencing adapter (SA)" there is intended one or more molecules which are instrumental for sequencing the DNA insert. Each molecule may comprise none, one or more of the following: a polynucleotide sequence, a functional group. In particular, there is intended a polynucleotide sequence which is required to be present in a massively parallel sequencing library in order for the sequencer to correctly generate an output sequence, but which does not carry information, (as non-limiting examples: a polynucleotide sequence to hybridize a ssDNA to a flow-cell, in case of Illumina sequencing, or to an ion-sphere, in case of Ion Torrent sequencing, or a polynucleotide sequence required to initiate a sequencing-by-synthesis reaction) .
By the term "sequencing barcode" there is intended a polynucleotide sequence which, when sequenced within one sequencer read, allows that read to be assigned to a specific sample associated with that barcode.
By the term "low-pass whole genome sequencing" there is intended a whole genome sequencing at a mean sequencing depth lower than 1.
By the term "mean sequencing depth" there is intended here, on a per-sample basis, the total of number of bases sequenced, mapped to the reference genome divided by the total reference genome size. The total number of bases sequenced and mapped can be approximated to the number of mapped reads times the average read length.
By "equalizing" there is intended the act of adjusting the concentration of one or more samples to make them equal.
By "normalizing" there is intended the act of adjusting the concentration of one or more samples to make them correspond to a desired proportion between them (equalizing being the special case where the proportion is 1) . In the description, for the sake of simplicity, the terms normalizing and equalizing will be used indifferently as they are obviously conceptually identical.
Detailed Description of the Invention
With reference to Figure 2A, which exemplifies the case in which the primary WGA DNA library is obtained by DRS-WGA and the sequencing platform is the Illumina platform, the method of generating a massively parallel sequencing library according to the present invention comprises the following steps .
In step a, there is provided a primary WGA DNA library (pWGAlib) , which includes fragments comprising a known 5' sequence section (5SS) , a middle sequence section (MSS) , and a known 3' sequence section (3SS) reverse complementary to the known 5' sequence section. The known 5' sequence section (5SS) comprises a WGA library universal sequence adapter. The middle sequence section (MSS) comprises at least an insert section (IS), corresponding to a DNA sequence of the original unamplified DNA prior to WGA. The middle sequence section (MSS) optionally comprises, in addition to the insert section (IS), a flanking 5' intermediate section (F5) and/or a flanking 3' intermediate section (F3) (for example when the primary WGA DNA library is generated by MALBAC or by DRS-WGA according to the teachings of WO 2015/118077) . In Figures 2A and 2B, the known 5' sequence section (5SS) corresponds to the LIB sequence (SEQ ID NO: 50) specific for the DRS-WGA, and the known 3' sequence section (3SS) is the reverse complementary of the LIB sequence (LIBrc) .
In step b, a single PCR cycle is performed on the primary WGA DNA library using at least one first primer (1PR), which comprises at least a first primer 5' section (1PR5S) and a first primer 3' section (1PR3S) . The first primer 5' section (1PR5S) comprises at least one first sequencing adapter (1PR5SA) . The first primer 3' section (1PR3S) hybridizes to the known 3' sequence section (3SS) . The result of the single PCR cycle of step b is a first primer extended WGA DNA library.
A single PCR cycle includes a double strand DNA denaturation step, a primer annealing step and an annealed primer extension step. A preferred embodiment includes a denaturation step of 30 seconds at 95°C, an annealing step of 30 seconds at 62°C, and an extension step of 3 minutes at 72°C.
The first primer (1PR) preferably further comprises at least one read sequencing primer sequence (1PRSEQ) in 3' position of the first primer 5' section (1PR5S) and in 5' position of the first primer 3' section (1PR3S) .
The first primer (1PR) preferably has a sequence selected from the group consisting of SEQ ID NO : 1 to SEQ ID NO: 12.
After step b, it is necessary to prevent that the first primer (1PR) polymerizes other primary WGA products or first primer extended WGA DNA library fragments. In a preferred embodiment the first primer extended WGA DNA library is purified after step b. This purification is preferably carried out with SPRIselect beads (Beckman Coulter) .
In step c, a single PCR cycle is performed on the first primer extended WGA DNA library, using at least one second primer (2PR) comprising a second primer 5' section (2PR5S) and a second primer 3' section (2PR3S) . The second primer 5' section (2PR5S) comprises at least one second sequencing adapter (2PR5SA) different from the at least one first sequencing adapter (1PR5SA) . The second primer 3' section (2PR3S) hybridizes to the known 3' sequence section (3SS) .
The result of the single PCR cycle of step c is a first and second primer extended WGA DNA library.
A single PCR cycle includes a double strand DNA denaturation step, a primer annealing step and an annealed primer extension step. A preferred embodiment includes a denaturation step of 30 seconds at 95°C, an annealing step of 30 seconds at 60°C, and an extension step of 3 minutes at 72°C.
The second primer (2PR) preferably has a sequence selected from the group consisting of SEQ ID NO: 13 to SEQ ID NO: 20.
After step c, the first and second primer extended WGA DNA library is purified, preferably with 2.5M NaCl PEG 20% solution .
In step d, the first and second primer extended WGA DNA library is amplified by using at least one third primer (3PR) comprising the first sequencing adapter (1PR5SA) and at least one fourth primer (4PR) comprising the second sequencing adapter (2PR5SA) . The result of the PCR amplification of step d is an amplified first and second primer extended WGA DNA library. The yield of this amplification step in terms of DNA library is sufficient to carry out sequencing thereon.
After step d, the amplified first and second primer extended WGA DNA library is purified, preferably with 2.5M NaCl PEG 20% solution.
The third primer (3PR) preferably has sequence SEQ ID NO: 22 and the fourth primer (4PR) preferably has sequence SEQ ID NO:21. The first primer 5' section (1PR5S) of the first primer (1PR) preferably further comprises at least one first sequencing barcode (1PR5BC) in 3' position of the at least one first sequencing adapter (1PR5SA) and in 5' position of the first primer 3' section (1PR3S) . The second primer 5' section (2PR5S) of the second primer (2PR) preferably further comprises at least one second sequencing barcode (2PR5BC) , in 3' position of the at least one second sequencing adapter (2PR5SA) and in 5' position of the second primer 3' section (2PR3S) . This allows for greater multiplexing. In particular, if SEQ ID NO : 1 to SEQ ID NO: 12 are used as first primer (1PR), each primer containing a different barcode, and SEQ ID NO: 13 to SEQ ID NO:20 are used as second primer (2PR) , each primer containing a different barcode, 96 combinations of barcodes can be obtained, leading to the analysis of 96 libraries.
The WGA library universal sequence adapter is preferably a DRS-WGA library universal sequence adapter or a MALBAC library universal sequence adapter, more preferably a DRS-WGA library universal sequence adapter.
The DRS-WGA library universal sequence adapter preferably has SEQ ID NO: 50 and the MALBAC library universal sequence adapter preferably has SEQ ID NO: 51.
The method for low-pass whole genome sequencing according to the present invention comprises the following steps .
First, there is provided a plurality of barcoded, massively-parallel sequencing libraries obtained according to the above disclosed method of generating a massively parallel sequencing library and samples obtained using different sequencing barcodes (BC) are pooled. Then the pooled library is sequenced.
The step of pooling samples using different sequencing barcodes (BC) further comprises the steps of quantitating the DNA in each of the barcoded, massively-parallel sequencing libraries, and of normalizing the amount of barcoded, massively-parallel sequencing libraries.
A massively parallel sequencing library preparation kit according to the present invention comprises at least one first primer (1PR), one second primer (2PR) , one third primer (3PR) and one fourth primer (4PR) . The structure of these primers has already been disclosed above.
In one preferred embodiment, in which the primary WGA DNA library is a DRS-WGA, the massively parallel sequencing library preparation kit comprises one or more primers selected from the group consisting of SEQ ID NO : 1 to SEQ ID NO: 12, one or more primers selected from the group consisting of SEQ ID NO:13 to SEQ ID NO:20, and primers SEQ ID NO:21 and SEQ ID NO: 22.
In an alternative preferred embodiment, in which the primary WGA DNA library is a DRS-WGA, the massively parallel sequencing library preparation kit comprises one or more primers selected from the group consisting of SEQ ID NO: 52 to SEQ ID NO: 63, one or more primers selected from the group consisting of SEQ ID NO: 13 to SEQ ID NO:20, and primers SEQ ID NO:21 and SEQ ID NO:22.
In an alternative preferred embodiment, in which the primary WGA DNA library is a MALBAC WGA, the massively parallel sequencing library preparation kit comprises one or more primers selected from the group consisting of SEQ ID NO:27 to SEQ ID NO:38, one or more primers selected from the group consisting of SEQ ID NO: 39 to SEQ ID NO: 46, and primers SEQ ID NO:21 and SEQ ID NO:22.
In an alternative preferred embodiment, in which the primary WGA DNA library is a MALBAC WGA, the massively parallel sequencing library preparation kit comprises one or more primers selected from the group consisting of SEQ ID NO: 64 to SEQ ID NO: 75, one or more primers selected from the group consisting of SEQ ID NO: 39 to SEQ ID NO: 46, and primers SEQ ID NO:21 and SEQ ID NO:22.
The low-pass whole genome sequencing kit according to one embodiment of the present invention comprises at least one primer selected from the group consisting of SEQ ID NO:l to SEQ ID NO: 12; at least one primer selected from the group consisting of SEQ ID NO:13 to SEQ ID NO:20; primers SEQ ID NO:21 and SEQ ID NO: 22; and a custom sequencing primer of SEQ ID NO: 23. The kit preferably also comprises a primer selected from the group consisting of SEQ ID NO:24, SEQ ID NO:25 and SEQ ID NO:26. In particular one of the latter primers is used with MiniSeq, NextSeq, HiSeq 3000/4000 Illumina sequencing platforms to read Index2. Additional explanation will be provided in the following. Among the three primers, SEQ ID NO: 24 is particularly preferred.
In an alternative embodiment, the low-pass whole genome sequencing kit comprises at least one primer selected from the group consisting of SEQ ID NO: 52 to SEQ ID NO: 63; at least one primer selected from the group consisting of SEQ ID NO: 13 to SEQ ID NO:20; primers SEQ ID NO:21 and SEQ ID NO:22; a custom sequencing primer of SEQ ID NO: 23 and a custom index 2 primer selected from the group consisting of SEQ ID NO: 24, SEQ ID NO: 25 and SEQ ID NO: 26.
The low-pass whole genome sequencing kit according to another embodiment of the present invention comprises at least one primer selected from the group consisting of SEQ ID NO: 27 to SEQ ID NO: 38; at least one primer selected from the group consisting of SEQ ID NO: 39 to SEQ ID NO: 46; primers SEQ ID NO: 21 and SEQ ID NO: 22; and primer of SEQ ID NO: 47. The kit preferably also comprises SEQ ID NO: 48. Even more preferably, the kit comprises a primer of SEQ ID NO: 49.
In an alternative embodiment, the low-pass whole genome sequencing kit comprises at least one primer selected from the group consisting of SEQ ID NO: 64 to SEQ ID NO: 75; at least one primer selected from the group consisting of SEQ ID NO: 39 to SEQ ID NO: 46; primers SEQ ID NO: 21 and SEQ ID NO: 22; and primer of SEQ ID NO: 47. The kit preferably also comprises SEQ ID NO: 48. Even more preferably, the kit comprises a primer of SEQ ID NO: 49.
The method for genome-wide copy number profiling according to the present invention comprises the steps of:
- sequencing a DNA library developed using one of the above said sequencing library preparation kits;
- analysing the sequencing read depth across different regions of the genome;
- determining a copy-number value for the regions of the genome by comparing the number of reads in that region with respect to the number of reads expected in the same for a reference genome.
Protocol 1 for Low Pass Whole Genome Sequencing on
Illumina platforms
•Deterministic-Restriction Site Whole Genome
Amplification (DRS-WGA)
Single cell DNA was amplified using the Amplil™ WGA Kit (Menarini Silicon Biosystems) according to the manufacturer's instructions. 5 μL of WGA-amplified DNA were diluted by the addition of 5 μL of Nuclease-Free Water and purified using SPRIselect beads (Beckman Coulter) system (ratio 1.8x) . The DNA was eluted in 12.5 μL and quantified by dsDNA HS Assay on the Qubit® 2.0 Fluorometer. •P7 single extension
A single step of PCR extension was performed in a volume of 15 μL using Amplil™ PCR Kit (Menarini Silicon Biosystems) and a LIB_IL_index D7xx (one of primers from SEQ ID NO : 1 to SEQ ID NO:12). Each PCR reaction contained: 1.5 μL Amplil™ PCR Reaction Buffer (10X), 3 μL of one primer LIB_IL_index D7xx within the following range: from SEQ ID NO : 1 to SEQ ID NO: 12 [2.5 μΜ] , 0.51 μL Amplil™ PCR dNTPs (10 mM) , 0.37 μL BSA, 0.12 μL Amplil™ PCR Taq Polymerase, WGA-purified DNA (from 10 to 75 ng) and Amplil™ water to reach a final volume of 15 μL .
Applied Biosystems® 2720 Thermal Cycler was set as follows: 95°C for 4 minutes, 1 cycle of 95°C for 30 seconds, 62°C for 30 seconds, 72°C for 3 minutes.
•SPRIselect beads clean-up and P5 single extension
15 μL of Amplil™ WGA-amplified from the previous step were purified using SPRIselect beads (Beckman Coulter) system (ratio 1.5x) . The DNA was eluted in 15 μL of PCR reaction mix prepared as following: 1.5 μL Amplil™ PCR Reaction Buffer (10X), 3 μL of one primer LIB_IL_index D5xx (one of primers from SEQ ID NO:13 to SEQ ID NO:20) [2.5 μM] , 0.51 μL Amplil™ PCR dNTPs (10 mM) , 0.37 μL BSA, 0.12 μL Amplil™ PCR Taq Polymeras and 9.5 μL Amplil™ water. The P5 single extension PCR reaction was performed in the presence of beads. Applied Biosystems® 2720 Thermal Cycler was set as follows: 95°C for 4 minutes, 1 cycle of 95°C for 30 seconds, 60°C for 30 seconds, 72°C for 3 minutes.
•2.5M NaCl PEG 20% solution clean-up and library amplification
15 μL of Amplil ™ WGA-amplified from the previous step were purified using 2.5M NaCl PEG 20% solution (ratio 1.5x) . The DNA was eluted in 15 μL of PCR reaction mix prepared as following: 1.5 μL Amplil™ PCR Reaction Buffer (10X), 1 μL of one primer adapter P5 (SEQ ID NO:21) and 1 μL of one primer adapter P7 (SEQ ID NO:22) (7,5 μM each), 0.51 μL Amplil™ PCR dNTPs (10 mM) , 0.37 μL BSA, 0.12 μL Amplil™ PCR Taq Polymerase and 10.5 μL Amplil™ water.
The library amplification PCR reaction was performed in the presence of beads.
Applied Biosystems® 2720 Thermal Cycler was set as follows: 95°C for 4 minutes, 1 cycle of 95°C for 30 seconds, 60°C for 30 seconds, 72°C for 2 minutes, 10 cycles of 95°C for 30 seconds, 60°C for 30 seconds, 72°C for 2 minutes (extended by 20 seconds/cycle) and final extension at 72° C for 7 minutes.
In a preferred embodiment, the cycles of 95°C for 30 seconds, 60°C for 30 seconds, 72°C for 2 minutes can be extended to 12, to increase the library concentration of at least a 2 (-4) factor by introducing 2 extra cycles during library amplification, thus increasing the total number of cycles from 11 to 13.
•Final library clean-up
The amplified library (containing Illumina sequencing adapter sequences) was finally purified using 2.5M NaCl PEG 20% solution (ratio 1.5x) and eluted in 15 μL of Amplil™ water. The purified libraries were qualified by Agilent DNA 7500, DNA 1000 or DNA HS Kits on the 2100 Bioanalyzer® and quantified by dsDNA HS Assay on Qubit® 2.0 Fluorometer, in order to obtain an equimolar pool. Based on library average size (usually an average length of 700bp is observed experimentally on DRS-WGA products obtained using Amplil™ WGA kit -Menarini Silicon Biosystems) , the library concentration generated by the quantification step can be converted to nM as known by those with ordinary skill in the art (for example 1 ng/μL=2.5 nM for 600bp library average size, 1 ng/μL=2 nM for 700bp library average size, 1 ng/μL=1.9 nM for 800bp library average size) -see Illumina Technical Note: DNA Sequencing "Nextera® Library Validation and Cluster Density Optimization" Pub No. 770-2013-003.
•As preferred alternative, the purified libraries were quantified by Quantitative real-time PCR (qPCR) methodology. The qPCR method accurately quantifies the functional libraries, in particular those fragments that have the correct adapter on each end (heteroadapter fragments) , based on a standard curve generated from a control template dilutions . Sequencing on MiSeq sequencing system
4 nM of the pool was denatured 5 minutes with 0. IN NaOH . Denatured sample was then diluted with HTl buffer (Illumina) to obtain a 20 pM denatured library. 600 μL, of denatured library was loaded on MiSeq reagent cartridge (Illumina) .
Single end reads of 150 bases or Paired end reads (75 PE) were generated using the v3 chemistry of the Illumina MiSeq.
Custom readl sequencing primer (SEQ ID NO:23) was then diluted with HTl to obtain a final concentration of 0,5 μΜ . 600 μL of diluted Custom readl sequencing primer was loaded on MiSeq reagent cartridge (Illumina) .
•Sequencing on HiSeq 1000/1500 and 2000/2500 systems 4 nM of the pool was denatured 5 minutes with 0. IN NaOH.
Single end reads of 100 bases or Paired end reads (100 PE) were generated using the v2 chemistry of the Illumina HiSeq, in Rapid run mode, or using the v4 chemistry of the Illumina HiSeq, in High Output run mode.
Custom readl sequencing primer (SEQ ID NO:23) was then diluted with HTl to obtain a final concentration of 0.5 μΜ .
•Sequencing on NextSeq, HiSeq 3000 and 4000, NovaSeq Series and HiSeq X Ten systems
4 nM of the pool was denatured 5 minutes with 0. IN NaOH. Single end reads of 150 bases or Paired end reads (100 PE) were generated using specific chemistry for the Illumina platforms .
Custom readl sequencing primer (SEQ ID NO:23) and Custom primer index 2A (i5) [ LNA-5 ' ] (SEQ ID NO:24) were then diluted with HT1 to obtain a final concentration of 0.5 μΜ.
The following table summarizes the sequences of the DRS-WGA compatible primers for all Illumina platforms (sequences in 5' 3' direction, 5' and 3' omitted) :
TABLE 1
Figure imgf000027_0001
The following table summarizes the sequences of the
MALBAC-WGA primers compatible for all Illumina platforms
(sequences in 5' 3' direction, 5' and 3' omitted) :
TABLE 2
Figure imgf000028_0001
When DRS-WGA is used, the LIB reverse complementary is the target for the primers listed in TABLE 1, from SEQ ID NO:l to SEQ ID NO:20, as shown in the figures 2A and 2B. Furthermore, a custom readl sequencing primer (SEQ ID NO: 23) has been designed, because the final library lacks the target sequence of Illumina readl sequencing primer. The custom readl sequencing primer (SEQ ID NO:23) contains the LIB sequence and is complementary to the LIB reverse complementary sequence.
Noteworthy, in the sequencing setup it is possible to avoid to use a PhiX spike-in control (Illumina), because this method enables the construction of high-complexity libraries from our Amplil™ WGA product input.
Furthermore, the sequencing run are preferably performed using the custom readl sequencing primer (SEQ ID NO:23), the PhiX DNA library lacks the target sequence of custom readl sequencing primer and for this reason the PhiX DNA will not be sequenced.
Moreover, the final library obtained by the method of the present invention does not have the canonical Illumina sequence-adapter used by MiniSeq, NextSeq, HiSeq 3000 and 4000 Illumina systems to read the index 2 (i5) .
For this reason, with these platforms, a custom primer index 2 (SEQ ID NO:24 or SEQ ID NO:25 or SEQ ID NO:26) is used to allow the correct reading of index i5. Noteworthy is that the custom sequencing primer index 2 contains the LIB sequence. In detail, the custom primer index 2A (i5) [LNA- 5'] (SEQ ID NO:24) and the custom primer index 2A (i5) [LNA- 3'] (SEQ ID NO:25) have three LNA (Locked Nucleic Acid [ LNA™] - Exiqon) modified nucleotides indicated in Table 1 with the "+" beside (e.g. "+A") . Furthermore, the custom primer index 2(i5) [RNA] (SEQ ID NO:26) is formed by fifteen RNA nucleotides indicated with the "r" beside (e.g. "rA") .
The same considerations above apply mutatis mutandis when using the MALBAC compatible primers listed in Table 2 (SEQ ID NO:27 to SEQ ID NO:49).
As a further alternative embodiment, which allows the production of libraries suitable for all Illumina platforms (and in which the primary WGA library is a DRS-WGA library) , the following combination of primers can be used: - at least one primer selected from the group consisting of SEQ ID NO: 52 to SEQ ID NO: 63;
- at least one primer selected from the group consisting of SEQ ID NO: 13 to SEQ ID NO: 20;
- primers SEQ ID NO:21 and SEQ ID NO:22;
- a custom sequencing primer of SEQ ID NO: 23 and a custom index 2 primer selected from the group consisting of SEQ ID NO: 24, SEQ ID NO: 25 and SEQ ID NO: 26.
Primers from SEQ ID NO: 52 to SEQ ID NO: 63 include, instead of the RDSP sequence, a sequence of 8 nucleotides, which are needed 5' of the first primer 3' section to increase the annealing temperature of custom sequencing primers . It should be noted that the second primer (SEQ ID NO: 13 to SEQ ID NO:20) includes the same sequence of 8 nucleotides 5' of the second primer 3' section. The custom sequencing primer of SEQ ID NO: 23 is used for Illumina sequencing platforms to read the Read 1 and/or Read 2; the custom sequencing primer of SEQ ID NO: 24 (or SEQ ID NO: 25 or SEQ ID NO:26) is used for Illumina sequencing platforms to read the Index 1 and Index 2.
The following table summarizes the sequences of the
DRS-WGA compatible primers for Illumina platforms according to this embodiment (sequences in 5' 3' direction, 5' and 3' omitted)
TABLE 3
Figure imgf000031_0001
As a further alternative embodiment, which allows the production of libraries suitable for all Illumina platforms (and in which the primary WGA library is a MALBAC library) , the following combination of primers can be used:
- at least one primer selected from the group consisting of SEQ ID NO: 64 to SEQ ID NO: 75;
- at least one primer selected from the group consisting of SEQ ID NO: 39 to SEQ ID NO: 46;
- primers SEQ ID NO:21 and SEQ ID NO:22;
- a custom read primer of SEQ ID NO: 47.
Preferably, also primer of SEQ ID NO: 48 is used. Even more preferably, also primer of SEQ ID NO: 49 is used.
The following table summarizes the sequences of the DRS-WGA compatible primers for Illumina platforms according to this embodiment (sequences in 5' 3' direction, 5' and 3' omitted)
TABLE 4
Figure imgf000032_0001
Examples
Example 1
Sequenced reads were aligned to the hg19 human reference 5 genome using the BWA MEM algorithm (Li H. and Durbin R., 2010) .
Control-FREEC (Boeva V. et al . , 2011) algorithm was used to obtain copy-number calls without a control sample. Read counts were corrected by GC content and mappability (uniqMatch option) and window size were determined by software using 10 coefficientOfVariation = 0.06. Main ploidy parameter was set accordingly to ploidy of the genetic material tested and contamination adjustment was not used.
Plots for CNA profiles of two single cells belonging to NCI-441 and SW-480 cell lines, sorted by DEPArray™ (Menarini 15 Silicon Biosystems) and blood single cells, a circulating tumour cell (CTC) and a white blood cell (WBC) sorted by DEPArray™, were obtained using a custom python script, as shown in Figures 4A and 4B.
From the figures it can be noted that significant gains and losses are depicted, along the 22 autosomes, expressed as absolute copy numbers in sorted tumor single cells.
The ploidy values are indicated in the y-axis; providing a better fit of profiles with segmented data (black lines) and improving CNA calling. Dots above the main ploidy assessed can be considered gains; dots below the main ploidy assessed can be considered losses.
On the other hand, there is the absence of gains and losses in WBC normal cell as expected.
Example 2
A tumor single cell and a population of 50 stromal cells, belonging to a disaggregated FFPE section, were digitally sorted by DEPArray™ (Menarini Silicon Biosystems) and whole-genome amplified using the Amplil™ WGA kit. Figure 5 shows Low-pass Whole Genome Sequencing results performed by the method disclosed above. The figure shows copy number alterations (CNA) profiles, with gains and losses only for the tumor single cell. These high-quality CNA profiles demonstrate that the presented method is highly resilient to DNA degradation and proved to be a reliable and valuable method for the molecular characterization of tumour heterogeneity in FFPE tissues down to single level.
Example 3
Figures 6A and 6B show inter-method and inter-platform (IonTorrent and Illumina) comparison results. In particular, Figure 6A shows copy number alterations (CNA) profiles of a NCI-H23 single cell, obtained with a Low-pass Whole Genome Sequencing method for IonTorrent (presented in PCT/EP2017/059075) and with the method according to the present invention for Illumina platforms. The results obtained with the two platforms are highly consistent with one another.
Furthermore, NCI-H441 and WBC single-cells hierarchical clustering, based on CNAs profiles, shows that samples are clustered by sample-types (tumor and normal) and not by methods or platforms (Figure 6B) .
In conclusion, both Amplil™ LowPass methods for IonTorrent and for Illumina sequencing platforms show high concordance of CNA profiles.
Although the present invention has been described with reference to the method for Amplil™ WGA only, the technique described, as will be apparent for the skilled in the art, clearly applies mutatis mutandis also to any other kind of WGA (e.g. MALBAC) which comprises a library with self-complementary 5' and 3' regions.
In an alternative embodiment of the present invention, the first or second primer (1PR and/or 2PR) could be modified so that they are bound at their 5' end to a solid support during at least one step of the procedure.
As an example the first primer (1PR) may comprise a Biotinylated 5' end. After the first PCR cycle (step b) , streptavidin coated beads are added to the reaction tube, capturing the first-primer extended DNA library fragments, whereas non- extended fragments which do not comprise the first primer are eluted away, along with primers dNTPs and polymerase. In step c, the second primer (2PR) is provided (along with other PCR reagents) and hybridizes to the first-primer extended DNA library fragments and polymerization occurs using the bead-bound DNA library fragments left in the tube as template, producing a heteroadapter DNA fragment. After washing the reaction mix of step c, the heteroadapter can be further amplified by PCR (step d) in the same tube using third (3PR) and fourth (4PR) primers (along with other PCR reagents) . Alternatively the heteroadapter can be denatured and eluted from the tube for further PCR amplification (step d) using third (3PR) and fourth (4PR) primers in a separate tube.
As another example, the first primer (1PR) may be bound covalently to magnetic beads. After the first PCR cycle (step b) , the first-primer extended DNA library fragments are bound to the beads and retained, whereas non-extended fragments which comprise the known 3' sequence section (3SS) but do not comprise the first primer are eluted away. In step c, the second primer (2PR) hybridizes to the first-primer extended DNA library fragments known 3' sequence section (3SS) and polymerization occurs using the bead- bound DNA library fragments left in the tube as template, producing a heteroadapter DNA fragment. After washing the reaction mix of step c, the heteroadapter can be further amplified by PCR (step d) in the same tube using third (3PR) and fourth (4PR) primers. Alternatively the heteroadapter can be denatured and eluted from the tube for further PCR amplification (step d) using third (3PR) and fourth (4PR) primers in a separate tube.
One advantage of these embodiments, is that no size-selective effect linked to the use of SPRIbeads is introduced in the process. This will allow fragments of lengths smaller and/or larger than what normally retained by SPRIbeads, to be represented in the final sequenceable library. One disadvantage is the increased complexity of the kit reagents, inherent to conjugation of primers to beads or to Biotin. The presence of a broader range of fragments may be beneficial especially when pursuing whole genome sequencing at higher depth to achieve complete resquencing beyond the genome- wide copy number profiling by low-pass WGS.
As yet another example of embodiment, after the first primer (1PR) is used in the first PCR cycle (step b) , a SPRI purification is carried out to remove residual first primer, then said second primer (2PR) conjugated to magnetic beads (either directly, through covalent bonds, or indirectly, through biotin modification of second primer and biotin-streptavidin interaction with streptavidin coated magnetic beads) is used in said single PCR cycle of step c, then the residual of reaction mix and mono-adapter fragments are eluted, magnetically retaining in the tube exclusively the resulting heteroadapter fragments, before proceeding to -step d- the PCR amplification with said third (3PR) and fourth (4PR) primer.
Advantages
The method of generating a massively parallel sequencing library according to the present invention allows to obtain a library including only heteroadapter fragments for those sequencing platforms which require so, in a rapid, efficient, reliable and cost-effective manner. Not least, it allows to generate double strand DNA and sequencing-ready libraries with a streamlined, single-day and single-tube workflow.
Finally, the advantages of low pass whole genome sequencing with respect to array CGH (aCGH) - the current leading technology for investigating CNV - should be highlighted. Array CGH (aCGH) is based on the use of differentially labeled test and reference genomic DNA samples that are simultaneously hybridized to DNA targets arrayed on a glass slide or other solid platform. However, limitations remain for certain applications as it has proved difficult to use low quality/quantity of DNA. Moreover, chromosomal copy number assessment based on a low-pass whole genome sequencing method may offer several advantages compared to aCGH including reduced DNA sequencing cost, enhanced detection of partial or segmental aneuploidies as a result of the potential increase in chromosomal analysis resolution, control-free calling of copy number alterations. In addition, the potential automation of the sequencing library preparation allows to minimize human errors, reduce hands-on time, and enable higher throughput and consistency.

Claims

1. A method of generating a massively parallel sequencing library comprising the steps of:
a. providing a primary WGA DNA library (pWGAlib) including fragments comprising a known 5' sequence section (5SS) , a middle sequence section (MSS) , and a known 3' sequence section (3SS) reverse complementary to the known 5' sequence section, the known 5' sequence section (5SS) comprising a WGA library universal sequence adapter, and the middle sequence section (MSS) comprising at least an insert section (IS) , corresponding to a DNA sequence of the original unamplified DNA prior to WGA, the middle sequence section (MSS) optionally comprising, in addition, a flanking 5' intermediate section (F5) and/or a flanking 3' intermediate section (F3) ;
b. performing a single PCR cycle on the primary WGA DNA library using at least one first primer (1PR) comprising at least a first primer 5' section (1PR5S) and a first primer 3' section (1PR3S), the first primer 5' section (1PR5S) comprising at least one first sequencing adapter (1PR5SA), and the first primer 3' section (1PR3S) hybridizing to the known 3' sequence section (3SS) , so as to obtain a first primer extended WGA DNA library;
c. performing a single PCR cycle on the first primer extended WGA DNA library using at least one second primer (2PR) comprising a second primer 5' section (2PR5S) and a second primer 3' section (2PR3S) , the second primer 5' section (2PR5S) comprising at least one second sequencing adapter (2PR5SA) different from the at least one first sequencing adapter (1PR5SA), and the second primer 3' section (2PR3S) hybridizing to the known 3' sequence section (3SS) , so as to obtain a first and second primer extended WGA DNA library; d. amplifying by PCR the first and second primer extended WGA DNA library using at least one third primer (3PR) comprising the first sequencing adapter (1PR5SA) and at least one fourth primer (4PR) comprising the second sequencing adapter (2PR5SA) , so as to obtain an amplified first and second primer extended WGA DNA library.
2. The method according to claim 1, wherein the at least one first primer (1PR) further comprises at least one read sequencing primer sequence (1PRSEQ) in 3' position of the first primer 5' section (1PR5S) and in 5' position of the first primer 3' section (1PR3S) .
3. The method according to claim 1 or 2, wherein the first primer 5' section (1PR5S) further comprises at least one first sequencing barcode (1PR5BC), in 3' position of the at least one first sequencing adapter (1PR5SA) and in 5' position of the first primer 3' section (1PR3S) and/or the second primer 5' section (2PR5S) further comprises at least one second sequencing barcode (2PR5BC) , in 3' position of the at least one second sequencing adapter (2PR5SA) and in 5' position of the second primer 3' section (2PR3S) .
4. The method according to any of claims 1 to 3, further comprising a step of purifying the first primer extended WGA DNA library after step b and/or further comprising a step of purifying the first and second primer extended WGA DNA library after step c and/or further comprising a step of purifying the amplified first and second primer extended WGA DNA library after step d.
5. The method according to any of claims 1 to 4, wherein the WGA library universal sequence adapter is a DRS-WGA library universal sequence adapter or a MALBAC library universal sequence adapter.
6. The method according to claim 5, wherein the WGA library universal sequence adapter is a DRS-WGA library universal sequence adapter.
7. The method according to claim 5 or 6, wherein the DRS-WGA library universal sequence adapter is SEQ ID NO: 50 and the MALBAC library universal sequence adapter is SEQ ID NO:51.
8. A method for low-pass whole genome sequencing comprising the steps of:
- providing a plurality of barcoded, massively-parallel sequencing libraries obtained according to the method according to any of claims 3 to 7 and pooling samples obtained using different sequencing barcodes (BC) ;
- sequencing the pooled library.
9. The method for low-pass whole genome sequencing according to claim 8, wherein the step of pooling samples using different sequencing barcodes (BC) further comprises the steps of:
- quantitating the DNA in each of the barcoded, massively- parallel sequencing libraries;
- normalizing the amount of barcoded, massively-parallel sequencing libraries.
10. A massively parallel sequencing library preparation kit comprising:
- at least one first primer (1PR) comprising at least a first primer 5' section (1PR5S) and a first primer 3' section (1PR3S) , the first primer 5' section (1PR5S) comprising at least one first sequencing adapter (1PR5SA), and the first primer 3' section (1PR3S) hybridizing to a known 3' sequence section (3SS) reverse complementary to a known 5' sequence section (5SS) comprising a WGA library universal sequence adapter of fragments of a primary WGA DNA library (pWGAlib) , the fragments further comprising a middle sequence section (MSS) 3' of the known 5' sequence section (5SS) and 5' of the known 3' sequence section (3SS) ;
- at least one second primer (2PR) comprising at least a second primer 5' section (2PR5S) and a second 3' section (2PR3S) , the second primer 5' section (2PR5S) comprising at least one second sequencing adapter (2PR5SA) different from the at least one first sequencing adapter (1PR5SA), the second 3' section hybridizing to the known 3' sequence section (3SS) of the fragments;
- at least one third primer (3PR) comprising the first sequencing adapter (1PR5SA); and
- at least one fourth primer (4PR) comprising the second sequencing adapter (2PR5SA) .
11. A massively parallel sequencing library preparation kit comprising:
a) one or more primers selected from the group consisting of SEQ ID NO : 1 to SEQ ID NO: 12, one or more primers selected from the group consisting of SEQ ID NO: 13 to SEQ ID NO:20, and primers SEQ ID NO:21 and SEQ ID NO:22;
or
b) one or more primers selected from the group consisting of SEQ ID NO:27 to SEQ ID NO:38, one or more primers selected from the group consisting of SEQ ID NO: 39 to SEQ ID NO: 46, and primers SEQ ID NO:21 and SEQ ID NO:22;
c) one or more primers selected from the group consisting of SEQ ID NO: 52 to SEQ ID NO: 63, one or more primers selected from the group consisting of SEQ ID NO: 13 to SEQ ID NO:20, and primers SEQ ID NO: 21 and SEQ ID NO: 22;
or d) one or more primers selected from the group consisting of SEQ ID NO: 64 to SEQ ID NO: 75, one or more primers selected from the group consisting of SEQ ID NO: 39 to SEQ ID NO: 46, and primers SEQ ID NO: 21 and SEQ ID NO: 22.
12. A low-pass whole genome sequencing kit comprising: a) at least one primer selected from the group consisting of SEQ ID NO:l to SEQ ID NO: 12; at least one primer selected from the group consisting of SEQ ID NO: 13 to SEQ ID NO: 20; primers SEQ ID NO: 21 and SEQ ID NO: 22; and a custom sequencing primer of SEQ ID NO: 23;
or
b) at least one primer selected from the group consisting of SEQ ID NO: 27 to SEQ ID NO: 38; at least one primer selected from the group consisting of SEQ ID NO: 39 to SEQ ID NO: 46; primers SEQ ID NO: 21 and SEQ ID NO: 22; and primer of SEQ ID NO: 47;
or
c) at least one primer selected from the group consisting of SEQ ID NO: 52 to SEQ ID NO: 63; at least one primer selected from the group consisting of SEQ ID NO: 13 to SEQ ID NO: 20; primers SEQ ID NO: 21 and SEQ ID NO: 22; a custom sequencing primer of SEQ ID NO: 23 and a custom index 2 primer selected from the group consisting of SEQ ID NO: 24, SEQ ID NO: 25 and SEQ ID NO: 26;
or
d) at least one primer selected from the group consisting of SEQ ID NO: 64 to SEQ ID NO: 75; at least one primer selected from the group consisting of SEQ ID NO: 39 to SEQ ID NO: 46; primers SEQ ID NO: 21 and SEQ ID NO: 22; and primer of SEQ ID NO: 47.
13. A low-pass whole genome sequencing kit according to claim 12, wherein alternative a) further comprises a primer selected from the group consisting of SEQ ID NO: 24, SEQ ID NO: 25 and SEQ ID NO: 26 and alternative b) or alternative d) further comprises SEQ ID NO: 48.
14. A low-pass whole genome sequencing kit according to claim 13, wherein alternative b) or alternative d) further comprises a primer of SEQ ID NO: 49.
15. A method for genome-wide copy number profiling, comprising the steps of:
- sequencing a DNA library developed using the sequencing library preparation kit of claim 10 or 11;
- analysing the sequencing read depth across different regions of the genome;
- determining a copy-number value for the regions of the genome by comparing the number of reads in that region with respect to the number of reads expected in the same for a reference genome.
PCT/EP2018/069845 2017-07-21 2018-07-20 Improved method and kit for the generation of dna libraries for massively parallel sequencing WO2019016401A1 (en)

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