CN114717314A

CN114717314A - Reference substance for detecting tumor-related mutant genes in circulating free DNA

Info

Publication number: CN114717314A
Application number: CN202210293003.3A
Authority: CN
Inventors: 王涛; 司慧娟; 闫慧慧; 马亚茹
Original assignee: Hangzhou Repugene Technology Co ltd
Current assignee: Hangzhou Repugene Technology Co ltd
Priority date: 2022-03-23
Filing date: 2022-03-23
Publication date: 2022-07-08

Abstract

The invention provides a reference substance for a tumor-related mutant gene detection technology, in particular to a reference substance for detecting free DNA mutation of blood plasma. The invention also provides a reference plate containing the reference, a kit containing the reference or the reference plate, and applications of the reference plate and the kit.

Description

Reference substance for detecting tumor-related mutant genes in circulating free DNA

Technical Field

The invention relates to the field of gene detection, in particular to a reference substance used in detection. The invention provides a reference substance for detecting tumor-associated mutant genes in plasma free DNA, in particular to a positive mutant reference substance of circulating free DNA (cfDNA). Reference plates comprising the reference, kits and methods of making the reference are also provided.

Background

Currently, the main source for obtaining information about tumor genes is still the tumor tissue sample of a subject. However, tumor tissue samples are not available for some patients with advanced cancer, and dynamic monitoring is not suitable.

A number of clinical studies have demonstrated that circulating free DNA (or cfDNA) is present in peripheral blood, whereas circulating tumor DNA (ctDNA) is contained in cfDNA in peripheral blood of tumor patients. The detection of free DNA such as cfDNA or ctDNA in plasma (or serum) can avoid invasive tissue biopsy and facilitate repeated sample collection.

Using cfDNA or ctDNA in a plasma sample, mutation information on tumor-associated genes can be obtained. This information helps predict disease progression in tumor patients, helps select targeted drugs, and helps predict treatment prognosis. Therefore, ctDNA gene detection of plasma samples of partial cancers has been recommended by clinical consensus.

The detection of tumor ctDNA in vitro requires high detection techniques due to the low content of tumor ctDNA in the sample. In recent years, only methods such as digital pcr (ddpcr) and high-throughput sequencing (NGS) have been widely used to detect ctDNA mutations.

Reference products are important components in vitro diagnostic procedures based on gene detection. The reference substance plays an important role in the whole process of research and development of therapeutic drugs and diagnostic reagents. In the development process of medicines and reagents, proper reference substances are needed in quality inspection of raw materials, semi-finished products, finished products and the like, confirmation of reagent performance and the like.

In the detection of ctDNA mutation, the requirements on parameters such as the type, stability and detection lower limit of a reference substance are more strict. The reasonability of the setting of the reference product and the performance of the reference product play a key role in controlling the quality of the reagent.

In addition, the links of using reference substances in the whole process of developing the kit products are numerous, so that the reference substances also closely influence the development cost.

Meanwhile, the number of detected reactions is reduced by designing the configuration of the reference substance, so that the cost of clinical detection can be greatly reduced, and the medical burden of patients and society is reduced.

Currently, many companies have introduced tumor mutation cfDNA detection kits. In these kits, most of the DNA constituting the reference is obtained by mechanical disruption or enzymatic cleavage. By combining these DNAs according to the distribution of the target mutation and mixing them with the wild-type DNA, a reference is finally formed. In such a reference, the target mutation is included at a certain mutation frequency. For example, CN110578002A (guangzhou fire stone medical laboratory ltd) discloses various quality controls for detecting mutations in circulating tumor DNA.

However, the reference materials used in the kits of companies on the market at present cannot satisfy the above requirements at the same time. These references are used in larger numbers, covering fewer gene types and mutation sites.

Thus, it is desirable to achieve simultaneous coverage of a greater variety of genes and/or multiple mutation sites with a smaller number of references.

Disclosure of Invention

The inventor innovatively develops an optimized human tumor mutation detection reference disc. By optimizing the combination mode and the preparation process of the reference substance, the performance is improved, and the cost is obviously reduced.

The reference plate of the present invention is suitable for samples of free DNA (including cfDNA and ctDNA) in plasma. The reference plate of the present invention comprises positive references, in particular 9 independently usable positive references, each of which comprises a set of mutations. The 9 positive reference products cover 33 hot spot tumor related gene mutation sites, can meet the detection requirements of multiple genes and multiple mutations in the market, and have excellent quality control performance.

In a first aspect, the present invention provides a reference for the detection of plasma free DNA mutations, wherein the reference comprises wild type DNA fragments and one or more mutant DNA fragments, each of the mutant DNA fragments has one or more base mutations and encodes an amino acid sequence having the amino acid mutations listed in table 1.

Preferably, the amino acid sequence encoded by the mutant DNA fragment in the reference comprises a combination of a plurality of amino acid mutations selected from any one of (a) to (i) and does not comprise any amino acid mutation of the other group,

(a) the amino acid mutation of EGFR, p.E746_ A750del,

amino acid mutation of EGFR p.T790M,

the amino acid mutation p.L858R of EGFR,

amino acid mutation p.g12c of KRAS;

(b) the amino acid mutation of EGFR, p.G719A,

the amino acid mutation of EGFR, p.E746_ A750del,

amino acid mutation of NRAS p.Q61K,

amino acid mutation p.g12v of KRAS;

(c) an amino acid mutation of EGFR, p.G719S,

amino acid mutation of ALK EML4-ALK,

the amino acid mutation of BRAF is p.V600E,

amino acid mutation of KRAS p.G12D,

amino acid mutation of PIK3CA p.h 1047r;

(d) the amino acid mutation p.L747_ P753 indel S of EGFR,

the amino acid mutation p.S768I of EGFR,

amino acid mutation of KRAS p.G13C,

amino acid mutation p.a775_ G776insYVMA of ERBB 2;

(e) amino acid mutation of EGFR p.c797s,

KRAS amino acid mutation p.G13D,

the amino acid mutation of PIK3CA p.ej5k;

(f) KRAS amino acid mutation p.G12S,

amino acid mutation of EGFR p.L747_ A750delinsP,

amino acid mutation p.ej542k of PIK3 CA;

(g) amino acid mutation of ALK EML4-ALK,

amino acid mutation p.g12a of KRAS;

(h) amino acid mutation of KRAS p.Q61H,

an amino acid mutation of EGFR p.L861Q,

amino acid mutation of MET 14exon skiping;

(i) the amino acid mutation p.E746_ S752delinsV of EGFR,

the amino acid mutation D770_ N771insG of EGFR,

amino acid mutation of RET KIF5B-RET,

amino acid mutation of ROS1 CD74-ROS1,

amino acid mutation of EGFR p.g719c.

In one embodiment, the mutant DNA fragment and the wild-type DNA fragment have a similar molecular weight distribution as native cfDNA. In another embodiment, the mutant DNA fragment and the wild-type DNA fragment have an average length of 130-170bp fragments.

In one embodiment, the ratio of the mutant DNA fragments to the wild-type DNA fragments in the reference is such that the frequency of each base mutation in the reference is from 0.1 to 10%, preferably from 1 to 5%, more preferably about 3%.

In a preferred embodiment, the reference comprises base mutations corresponding to the amino acid mutations listed in table 1.

In a specific embodiment, the reference comprises a base mutation selected from any one of the following groups (a) - (i),

in the (a), the base mutation of p.E746_ A750del is c.2235_2249del15,

the base mutation of p.T790M is c.2369C > T,

the base mutation of the p.L858R is c.2573T > G,

the base mutation of the p.G12C is c.34G > T;

in the (b), the base mutation of p.G719A is c.2156G > C,

the base mutation of p.E746_ A750del is c.2236_2250del15,

the base mutation of the p.Q61K is c.181C > A,

the base mutation of the p.G12V is c.35G > T;

in the I, the base mutation of the p.G719S is c.2155G > A,

the subtype of the EML4-ALK is E6; a, 20, and the method is that,

the base mutation of the p.V600E is c.1799T > A,

the base mutation of the p.G12D is c.35G > A,

the base mutation of the p.H1047R is c.3140A > G;

in the step (d), the base mutation of the p.L747_ P753 indel S is c.2240_2257del18,

the base mutation of the p.S768I is c.2303G > T,

the base mutation of the p.G13C is c.37G > T,

the base mutation of the p.A775_ G776insYVMA is c.2324_2325ins 12;

wherein the p.C797S base mutation is c.2389T > A,

the base mutation of the p.G13D is c.38G > A,

the base mutation of the p.E545K is c.1633G > A;

in the step (f), the base mutation of p.G12S is c.34G > A,

the base mutation of the p.L747_ A750delinsP is c.2239_2248delinsC,

the base mutation of the p.E542K is c.1624G > A;

in the step (g), the subtype of the EML4-ALK is E13; a, 20, and the method is that,

the base mutation of the p.G12A is c.35G > C;

in the step (h), the base mutation of p.Q61H is c.183A > T,

the base mutation of the p.L861Q is c.2582T > A,

the base mutation of the 14exon skiping is c.3082+1G > T;

in the step (i), the base mutation of p.E746_ S752delinsV is c.2237_2255delinsT,

the base mutation of D770_ N771insG is c.2310_2311insGGT,

the KIF5B-RET is K15; the content of R12 is shown in the specification,

the subtype of the CD74-ROS1 is C6; the content of R34 is shown in the specification,

the base mutation of p.G719C is c.2155G > T.

In a specific embodiment, the wild-type DNA fragment and the mutant DNA fragment are obtained by fragmenting a nucleotide molecule known to contain the base mutation, for example genomic DNA of a cell line known to contain the base mutation, into fragments of suitable length. Preferably, the fragmentation is performed by enzymatic digestion or sonication.

In a specific embodiment, the DNA fragment is obtained by digesting genomic DNA of a cell line known to contain the base mutation, with respect to a reference substance containing the mutation of any one of groups (a) to (h). In a preferred embodiment, the enzymatic digestion is performed using the Atlantis enzyme to obtain DNA fragments similar to cfDNA in native plasma.

In a specific embodiment, for a reference comprising a mutation of group (i), the DNA fragment is obtained by ultrasonication of DNA from a sample derived from a clinical specimen or the like.

In a specific embodiment, the mixing of the wild-type DNA fragment and the mutant DNA fragment may be performed in a human plasma matrix.

A second aspect is a reference pan comprising a reference as described in the first aspect as a positive reference. In a preferred embodiment the reference plate comprises or only 9 positive references, said 9 positive references comprising one set of mutations in said (a) to (i) respectively and not any mutations in the other sets.

A third aspect is a kit comprising the reference plate of the second aspect described above. The kit preferably further comprises one or more, preferably all, of a negative reference, a detection limit reference and a reproducibility reference.

In particular embodiments, the detection limit reference has the same combination of mutations and a different mutation frequency as a positive reference, preferably a combination of mutations from group (c). In a specific embodiment, the frequency of mutations in the detection-limited reference other than the fusion mutation is 0.3%, and the mutation frequency of the fusion mutation is 0.4%. In a preferred embodiment, the kit comprises a plurality, preferably 9, of detection limit references. The 9 detection limit reference products respectively correspond to the 9 positive reference products.

In a specific embodiment, the kit contains 9 positive references, 9 detection limit references, 2 negative references, and 2 replicate references prepared in the examples of the invention.

In a specific embodiment, the 2 duplicate references are a positive duplicate reference R1 with the same combination of mutations as one of the positive references, and a negative duplicate reference R2 without mutations. In a specific embodiment, the frequency of mutations in the repetitive reference is 1%.

In particular embodiments, the kit has a composition as shown in table 7.

A fourth aspect is the use of the reference of the first aspect, the reference plate of the second aspect, or the kit of the third aspect, for detecting ctDNA mutations. Preferably, the detection is performed by a method selected from the group consisting of: micro-droplet digital pcr (ddpcr), amplification-blocking mutation system pcr (arms), and high-throughput sequencing (NGS).

The fifth aspect is a DNA library prepared by the above reference. The DNA library is prepared by procedures commonly used in the art. In particular embodiments, the library is used for sequencing and the like.

A sixth aspect is a method of making a reference plate of the second aspect comprising 9 positive references, comprising:

(1) for each mutation, providing genomic DNA comprising a wild-type gene and genomic DNA comprising a mutant gene;

(2) fragmenting the genomic DNA of step (1) into fragments similar in size to the naturally occurring cfDNA to obtain wild type DNA fragments (mock WT-cfDNA) and mutant DNA fragments (mock cfDNA) corresponding to each mutation;

(3) the mutant DNA fragments (mock cfDNA) obtained in step (2) were mixed with the wild type DNA fragments (mock WT-cfDNA) according to the frequency of the base mutation according to the grouping shown in table 1 to obtain reference plates containing 9 positive references.

Preferably, the fragmentation is performed by enzymatic digestion or sonication.

In a specific embodiment, the reference substance comprising a mutation of any one of groups (a) to (h) is obtained by digesting genomic DNA of a cell line known to contain the base mutation. In a preferred embodiment, the enzymatic digestion is performed using the Atlantis enzyme to obtain DNA fragments similar to cfDNA in native plasma.

In a particular embodiment, for a reference comprising a mutation of group (i), said DNA fragment is obtained by ultrasonication of DNA from a sample derived from a clinical specimen or the like.

TABLE 1 reference contains the mutation types (HGVS format)

Preferably, the predetermined base mutation frequency is 0.1% to 10%, preferably 0.3% to 3%.

Preferably, the genomic DNA in step (1) is derived from a cell line.

For example, the genomic DNA is nucleosome DNA.

Preferably, the step (2) fragments the genomic DNA into a 130-and 170-bp fragment.

In a seventh aspect, the present invention provides a reference disc prepared by the method of the sixth aspect.

In an eighth aspect, the invention relates to a kit comprising the reference plate of the seventh aspect.

In a ninth aspect, the invention relates to a method of detecting gene mutations in circulating tumour dna (ctdna) or circulating episomal dna (cfdna), comprising the use of a reference according to the first aspect, a reference disc according to the second or seventh aspect, or a kit according to the third or eighth aspect.

In specific embodiments, the detecting of the ninth aspect may be performed by a method selected from the group consisting of: micro-droplet digital pcr (ddpcr), amplification-blocking mutation system pcr (arms), and high-throughput sequencing (NGS).

The advantages of the present invention are at least shown in the following aspects.

1. Compared with the existing reference product, the reference product disc and the kit can greatly reduce the number of required reactions and reduce the cost for using the reference product through proper mutation combination on the premise of monitoring the gene type to be equivalent to the mutation type. Particularly, when the reference product is used as an internal reference product of an enterprise, the development and quality control cost of products (medicines and reagents) can be greatly reduced;

2. detection using cfDNA or ctDNA as a sample has a strict requirement on the lower limit of detection. The reference plate and the kit have good efficiency and low detection limit, and are suitable for detection with strict detection lower limit requirements.

3. The positive reference substance, the reference substance tray and the kit cover four concentration gradients of high, medium, low and negative, and can meet the requirements of various detection methods. The sample source of the positive reference substance does not comprise plasmid source, accords with the regulation of the national food and drug administration, and has guarantee on safety.

Detailed Description

The terms of the present application are defined below. Terms not defined are to be construed as commonly understood by one of ordinary skill in the relevant art.

Definition of

"cfDNA" is an acronym for circulating free DNA (circulating free DNA), and refers to a DNA fragment released into the blood, typically 50-200bp in length.

By "mock cfDNA" or "mock … … cfDNA" is meant that the artificially prepared DNA fragment is comparable in molecular weight size and/or length to cfDNA. Specifically, it refers to a DNA fragment having a molecular weight distribution and/or length distribution similar to that of natural cfDNA. The molecular weight distribution means that the percentage of DNA fragments of various molecular weights in a certain collection of DNA fragments in the collection is approximately the same. Similarly, a distribution of lengths means that the percentage of DNA fragments of each nucleotide length in a collection of DNA fragments in said collection is approximately the same

"ctDNA" is an acronym for circulating tumor DNA (circulating tumor DNA), and refers to a DNA fragment derived from a tumor and released into the blood (in an assay, e.g., in a plasma sample).

"genomic DNA" herein refers to chromosomal DNA, which is distinguished from extrachromosomal DNA such as episomal DNA. This term emphasizes the presence and origin of DNA, without limiting that the referred DNA must include the complete genome. For example, the genomic DNA may be a portion of a complete genome.

"microdroplet digital PCR" or "ddPCR" is digital PCR performed using water-in-oil emulsion droplets. Unlike conventional PCR, the amplification reaction of ddPCR does not occur in Eppendorf tubes or microplate wells, but rather occurs within a droplet. In ddPCR, the sample is divided into nanoliter-scale droplets, and the reactions in each droplet occur independently, or can be measured independently.

"reference" specifically refers to a reference sample used in the detection of a reagent associated with human gene testing, which has one or more properties that have been determined and can be used for quality control, e.g., to control the positive-fit rate of the reagent.

"reference plate" refers to the combination of all references used in an assay.

"Positive reference" refers to a reference known to contain a certain target mutation to be detected (sometimes also referred to as a mutation-positive reference).

"negative" refers to a reference known to be free of some mutation of interest to be detected, e.g., a reference free of disease-related genetic mutations. Examples of negative references are references derived from Wild Type (WT) or healthy samples.

"negative reference" refers to a reference that does not contain the mutation to be detected, and is also referred to as a test gene locus negative reference, and is sometimes referred to as a wild-type and other homologous gene locus positive reference.

The 'repeatability reference substance' can also be called as precision reference substance and is used for reflecting the repeatability of product detection and the stability of repeated detection. Repetitive references of the invention may comprise one or more common types of mutations.

The "detection limit reference substance" is used as distinguished from the "detection limit reference substance" and the "lowest detection limit reference substance".

"mutation frequency" refers to the proportion of mutated DNA in a population of DNA fragments. In a specific embodiment, a sample having a predetermined mutation frequency is obtained by mixing wild-type DNA with mutant-type DNA, wherein the mutation frequency is the weight percentage of mutant-type DNA to the total DNA in the sample.

In preferred embodiments, the present reference disc encompasses multiple mutation frequencies. Since the mutation frequency is the weight percentage of mutant DNA to total DNA, different mutation frequencies can be considered as concentration gradients of mutations. For point mutation and insertion deletion, the reference plate covers gradients of 3% (high concentration), 1% (medium concentration) and 0.3% (low concentration), and is consistent with the setting requirements of national detection reference. For the fusion gene, 3% (high concentration), 1% (medium concentration), 0.4% (low concentration) were used. 0% is negative concentration.

"tumor" refers to an abnormal tissue with independent and unrestricted growth propensity arising from existing body cells. Herein, "tumor" is used indiscriminately with "cancer" and "cancerous" tumors.

"wild-type" (WT) refers to a gene, line, or characteristic that is ubiquitous in individuals of the natural population. In this context, wild type can also be interpreted as the absence of a (to be tested) mutation which is the object of detection.

"mutant" means that a mutation has occurred as compared with the wild type. Mutant is also understood to have a disease-related mutation to be tested.

"wild-type DNA fragment" means a DNA fragment having a base sequence identical to that of the wild type, and is understood not to be an intact DNA strand. Commercially available BEAS-2B, GM12878 and GM24385 cell lines can be used as wild type cell lines of origin.

"mutant DNA fragment" means a DNA in the form of a fragment having a base sequence containing a mutation as compared with the wild type, and is understood not to be an intact DNA strand, and herein, particularly means a DNA fragment having a mutation to be detected.

"tumor-associated mutant gene" means that the mutation of the gene is associated with the generation, progression, and prognosis of a tumor.

"High Throughput Sequencing" (High-Throughput Sequencing) is also known as Next Generation Sequencing (NGS).

"mutation exclusion" refers to the assignment of mutation sites from the same exon to different references, or to the assignment of different base mutations occurring in the same mutation site from different cell lines to different references.

Substrate

In the reference, the nucleic acid molecule needs to be dissolved in a matrix for use. As the substrate, a negative (WT) substrate having the same or similar properties as those of the clinical specimen, for example, a healthy human plasma substrate, or the like may be used. In the subsequent examples of the present invention, when the mutant DNA fragment is mixed with the wild-type DNA fragment, the substrate may not be used.

Type of mutation

The types of mutations described in the present invention are all described using the Human Genome Variation Society (HGVS: Human Genome Variation Society) rule nomenclature.

For example, the prefix "p." denotes a human protein reference sequence; the prefix "c." denotes a human cDNA reference sequence.

Substitution (>): one nucleotide is replaced by another, using ">".

Deletion (del): one or more nucleotides are removed and described using "del".

Inversion (inv): a new nucleotide sequence (greater than 1 nucleotide) reverse complementary to the original sequence replaces the original sequence.

Repeat (dup): one or more nucleotide copies are inserted directly downstream of the original sequence, denoted by "dup".

Insertion (ins): one or more nucleotides are inserted into the sequence, and the inserted sequence is not a copy of the upstream sequence.

Deletion-insertion (delins/indel): one or more nucleotides are replaced by other nucleotides, but substitution, inversion and transposition do not occur.

Conversion (con): one particular type of deletion-insertion, in which the nucleotide sequence that replaces the original sequence is a copy of the sequence from another site in the genome.

For example, herein, p.e746_ a750del indicates that E at position 746 to a at position 750 are deleted compared to the human protein reference sequence; T790M indicates that T at position 790 has become M compared with the human protein reference sequence, i.e., T represents (Threonine) Threonine, M represents (Methionine) Methionine, and T790M indicates that the C-to-T conversion occurs at code 790 of the EGFR gene, resulting in the conversion of the amino acid at the position from Threonine to Methionine; p.775 _ G776insYVMA shows that the amino acid sequence YVMA is inserted between a at position 775 and G at position 776 compared with the human protein reference sequence; l747_ a750delinsP indicates that the sequence between L at position 747 and a at position 750 is substituted (replaced) by amino acid P compared to the human protein reference sequence and not by substitution (substistition), inversion (inversion) and conversion (conversion). "c." indicates the comparison with the reference sequence of human cDNA, for example, the + 1in c.3082+1G > T represents the first base of the next following intron of this exon. For example, EML4-ALK refers to the fusion gene of EML4 and ALK, and 14exon skiping refers to the skipping deletion of exon 14 at the mRNA level. The meaning of these codes can be determined without error by those skilled in the art.

With regard to the expression of mutations in fusion genes, such as the EML4-ALK fusion gene, it is known that the general classification divides patients into E13; a20, E20; a20, E6; a20 and other subtype 4 groups, as determined by one skilled in the art as E13; mutation information represented by subtype A20 and the like.

"reaction number" the reaction number corresponding to the reference plate of the present invention can be calculated by the following formula:

reaction number positive reference product, negative reference product, repeatability reference product 10+ detection limit reference product

Reference plate

One embodiment of the invention is a reference plate for detecting mutations in tumor-associated genes. The reference plate comprises positive references which are at least 1, 2, 3, 4, 5, 6, 7, 8 or 9, preferably 9, of the positive references 1-9 shown in table 1.

The reference plate may further comprise at least 1, 2, 3, 4, 5, 6, 7, 8 or 9, preferably 9, of the 9 detection limit references S1-S9 shown in table 1.

The reference plate may further comprise a repeatability reference and a negative reference.

The reproducibility references may include at least one positive reproducibility reference and at least one negative reproducibility reference.

The positive repeatability reference substance is preferably obtained by diluting the positive reference substance in the table 1, more preferably by diluting the positive reference substance p3, and the dilution factor is preferably 3 times. After dilution, the frequency of mutations in the repetitive reference was 1%. The negative repetitive reference substance is prepared by the same preparation method of the positive reference substance, and is prepared by a normal wild cell line WT.

Each reference in the reference tray can be used independently or in any combination according to actual requirements.

For example, at least 1, 2, 3, 4, 5, 6, 7, 8 or 9 selected from the positive reference substances 1 to 9 can be used as the positive reference substance. At least 1, 2, 3, 4, 5, 6, 7, 8 or 9 selected from the detection limit references S1-S9 may be used. At least 1 or 2 of the repetitive references may be used. At least 1 or 2 of the negative references may be used.

In one embodiment, the reference plate comprises 22 references, wherein the references comprise 1-9 positive references, 2 negative references and 2 repetitive references, and the detection limit references are from S1 to S9.

Reagent kit

One embodiment is a kit comprising 1, 2, 3, 4, 5, 6, 7, 8, or 9 of the positive references P1-9 shown in table 1.

Preferably, the kit further comprises a negative reference, a detection limit reference and a repeatability reference.

The kit may further comprise other commonly used sequencing reagents such as sequencing reaction solution, sequencing primers and the like.

Preparation method

One embodiment of the present invention is a method for preparing a reference for detecting a tumor mutation, the reference comprising:

(1) enzyme cutting is carried out on genomic DNA by using an enzyme cutting method, and wild cfDNA1 and mutant cfDNA1 are obtained from a normal cell line and a tumor cell line;

(2) disrupting genomic dna (gdna) of the cell line using sonication to obtain wild-type cfDNA2 and mutant cfDNA 2;

(3) mixing the mutant cfDNA1 with wild cfDNA1 according to a certain combination and proportion to obtain a corresponding reference substance;

(4) and (3) mixing the mutant cfDNA in the step (2) with wild cfDNA according to a certain proportion to obtain a corresponding reference substance.

In a specific embodiment, the enzyme is a nickelis double-stranded dnase, which cleaves genomic DNA. The inventors demonstrated in previous experiments that the nucleic acid distribution of the mock cfDNA obtained using the enzyme was very similar to that of the native cfDNA.

The source of the mutant DNA fragment containing a mutation, for example, a specific cell line, is not limited as long as such a DNA fragment can be obtained.

For example, a mutant DNA fragment containing a mutation can be obtained from a cell known to contain such a mutation by the above-mentioned enzymatic cleavage method or the like. In addition, the mutant DNA fragment may be derived from clinical specimens, immortalized cell lines, gene-editing cell lines, genetically engineered products, recombinant plasmids, and the like. In other words, the mutant DNA fragment can be obtained from commercially available plasmids, or can be obtained from cell lines known to contain these mutations by means of PCR techniques, genetic engineering, or the like, or artificially synthesized from sequence information, or the like.

When the reference of the present invention is used as part of a test kit in which the subject is a human, preferably, the plasmid is not included in the source of the mutant DNA fragment.

Among them, the cell line from which the mutant DNA fragment of the present invention is derived is preferably a tumor cell line. Specifically, the cell lines from which the mutant DNA fragments of the present invention are derived include those shown in Table 2.

Use of

One embodiment of the present invention is the use of the above reference in methods for detecting ctDNA mutations, such as in digital micro-pcr (ddpcr), amplification-retarded mutation system pcr (arms), and high-throughput sequencing (NGS) methods.

The reference plate or kit of the invention can be used to detect cfDNA forms of tumor-associated mutant genes. The disease/tumor type corresponding to the gene mutation detectable in the present invention is, for example, non-small cell lung cancer, colorectal cancer, melanoma, breast cancer, endometrial cancer, ovarian cancer, lung cancer, etc.

The reference plate or kit of the invention may be used for clinical use. Specifically, the use of the ctDNA can be used for predicting the drug administration (e.g., gefitinib, erlotinib hydrochloride, oxitinib mesylate, crizotinib) and the curative effect of the drug to a cancer patient based on the ctDNA mutation frequency, and can also be used for early screening of cancer, detecting the sensitivity of an immune checkpoint inhibitor therapy, predicting the recurrence risk and/or survival of the patient, and the like.

The reference plate or kit of the invention can also be used in reagent development or performance verification, quality control, comparison of platform result consistency under different methods, and the like. Specific examples thereof include:

1) as an enterprise reference product, raw materials, semi-finished products and finished products of products (a kit for detecting the plasma DNA, including but not limited to an NGS method, a PCR method and the like) can be detected;

2) when the staff gauge is used for clinical detection, the staff gauge can be used for training and checking internal staff; can be used as a negative and positive reference substance to monitor the experimental process and prove whether the experimental process is effective or not.

Examples

The scheme of the invention will be explained with reference to the examples. It will be appreciated by those skilled in the art that the following examples are illustrative of the invention only and should not be taken as limiting the scope of the invention.

The examples, where specific techniques or conditions are not indicated, are to be construed according to the techniques or conditions described in the literature in the art or according to the product specifications. The reagents or instruments used are not indicated by the manufacturer, and are all conventional products commercially available.

Example 1 preparation and detection of reference

In this example, a positive reference and a negative reference, a repetitive reference and a detection limit reference containing a tumor-associated mutation according to the present invention were prepared.

In order to achieve the object of the present invention, the detection kit can simultaneously cover multiple genes and multiple mutation sites by using a small number of reference substances, and the inventors have optimized the design of the reference substances to obtain the groups in table 1.

In the grouping, different mutations of the same gene are tried to be located in different reference samples. However, if the same gene contains more than 9 mutations, different mutations from the same exon of the gene are not placed in the same reference. Efforts were made to make a particular mutation in one reference originate from only one cell line, and to make mutations in different cell lines mutually exclusive (the same cell line does not contain different base mutations occurring in the same mutation site at the same time).

For example, 8 KRAS mutations, 3 RIK3CA mutations and 2 ALK mutations were placed in different references, respectively; for 14 EGFR mutations, involving exons 18(3 mutations), 19(5 mutations), 20(3 mutations) and 21(2 mutations) of the EGFR gene, respectively, mutation sites from the same exon (e.g., the sites of KRAS are all in exon 2, and the same base would be of 3 types) were assigned to different references, which advantageously reduced the probability of PCR false positives or false negatives.

For the cell line to be used as a source, a commercially available cell line can be used, and generally one cell line contains 1 mutation, and each cell contains two mutations. The cell lines are not limited to those exemplified in Table 2, as long as they have corresponding mutations.

Finally, the inventors obtained 9 positive references shown in table 1, which contain 33 mutation sites in total, and could be used as 9 enterprise disks. The specific preparation method and effect test process are as follows.

1.1 selection of raw materials

1.1.1 cells and culture Medium

The sources of the samples in the preparation of the reference plates are shown in table 2 below.

TABLE 2 correspondence of mutations to source cell lines

Among them, there are 5 mutation sites, which have no corresponding cell line, and thus clinical samples or standards were used, as shown in table 3 below:

TABLE 3 additional mutation sites

Note: the standard substance is a standard substance and a reference substance approved by China food and drug testing institute (middle school).

1.1.2 enzymes

Attributes double stranded DNase, Atlantis dsDNase (available, for example, from ZOMO research, 2030,12.5u, or sold as part of the EZ nucleic DNA Prep Kit (D5220)).

1.2 preparation Process

1.2.1 preparation and detection of Positive reference P1-P8

Mock cfDNA was prepared using a ditlanius double-stranded dnase digestion. Specifically, mutant DNA fragments (mock tumor cfDNA) were prepared using the cell lines shown in table 2, and wild-type DNA fragments (mock WT-cfDNA) were prepared using human healthy negative cell lines.

The preparation method comprises the following specific steps:

(1) the cells were cultured using the corresponding medium as described in 1.1.1, taking about 1X 10 cells per experiment⁶(ii) individual cells;

(2) washing the cells with phosphate buffer, centrifuging at 200 Xg, and collecting the cells; cleaning is repeated for one time;

(3) discarding the supernatant, resuspending the cells with 1 ml of phosphate buffer, and transferring to a 1.5 ml centrifuge tube;

(4) the supernatant was discarded by centrifugation, and 100. mu.l of a nucleic acid preparation (containing 0.25% trypsin as a main component and NaHCO as a main component) was added thereto₃Adjusting the pH to 8.0), blowing or reversing the test tube by using a pipette gun to resuspend the cell sediment, and incubating for 5 minutes on ice;

(5) centrifuging to collect cell nucleic acid, and discarding supernatant;

(6) washing cells with 100 μ l of Asia-Telius digest (mainly containing 20mg/mL proteinase K and 50mM Tris-HCl1, pH 8.0), mixing by up-and-down reversal for 2-3 times, centrifuging, and discarding the supernatant;

(7) repeating the step (6) once;

(8) gently resuspending the cellular nucleic acids with 100 μ l of methylene blue digest;

(9) adding 10 microliters of methylene blue double-stranded DNA enzyme, and flicking the test tube wall to mix uniformly;

(10) digesting and incubating for 40 minutes at 42 ℃;

(11) adding 20 μ l of reaction termination solution (containing 0.5M EDTANA2 as main ingredient, and adjusting pH to 8.0 with NaOH), vortex, mixing, and terminating reaction;

(12) adding 600 microliters of DNA binding solution (the main components are 5M hydrochloride, 20% propylene glycol and 0.12M acetate), and uniformly mixing by vortex;

(13) transferring to a centrifugal column (installed in a collecting tube), centrifuging for 30 seconds at 10000- & 13000 multiplied by g, and discarding the filtrate;

(14) adding 300 microliter DNA cleaning solution (the main component is 80% ethanol, 10000-;

(15) repeating step (14) once;

(16) centrifuging the empty tube for 1 minute, removing residual cleaning solution, and transferring the centrifugal column to a new 1.5 ml centrifuge tube;

(17) adding 30 μ l DNA eluate (main ingredient is 0.01M Tris-HC1, 0.01MEDTA) into centrifugal column, standing at room temperature for 3 min;

(18) and centrifuging for 30 seconds, and collecting the purified DNA, namely the enzyme-cut cfDNA.

Wild type DNA fragment WT-cfDNA was used as a negative sample, and mutant DNA fragments were used as positive samples, and mixed in the combinations shown in Table 1 based on the amount of DNA so that the expected mutation frequency of each mutation in the respective reference was 3%. No reagents other than the sample were added during the mixing.

Mutations covered by the positive references P1-P8 are shown in table 4, respectively.

1.2.2 preparation and detection of Positive reference P9

For reference P9, simulated cfDNA was prepared using ultrasound disruption. Specifically, mutant DNA fragments were prepared using the sample sources shown in Table 3, and wild-type DNA fragment WT-cfDNA was prepared using human negative clinical samples.

The procedure for treating cells with ultrasound is specifically as follows.

1. Turning on a Covaris M220 instrument switch and a computer desktop 'SonoLab' software, adding ultrapure water into a water tank, wherein the water level needs to be flush with or slightly higher than the required position of the sample tube bracket, and the interruption can be carried out when the 'Run' is green;

2. prepare a PCR tube and a DNA break tube for each FFPE sample, and mark the tubes separately.

Taking 55ng of FFPE sample DNA in a PCR tube, and complementing the DNA to 55 mu L by using nucleic-free water;

note: if the total DNA of the FFPE sample is less than 55ng, the maximum volume of the sample DNA is used for establishing a library.

4. And (3) oscillating and uniformly mixing the DNA diluent, centrifuging for a short time, transferring all the liquid into corresponding DNA breaking tubes, centrifuging for a short time, and putting the breaking tubes into a breaking instrument.

5. Interrupting the parameters: duty Factor 25%; average incorporated Power 18.8; peak Incident Power (PIP) 75; cycleper Burst 1000; water Temperature 9 ℃ (max), 5 ℃ (min); treatment Time 300 s;

6. after the disruption was completed, the DNA disruption tube was removed, after brief centrifugation all the liquid was transferred to a new labeled PCR tube, another 30. mu.L of disrupted DNA was used for library construction, and the remaining DNA was stored at-20 ℃.

Wild type DNA (WT-DNA) was used as a negative sample without mutation, and other DNAs after ultrasonic disruption were used as positive samples with mutation, and mixed and prepared so that the expected mutation frequency of each mutation in the respective reference was 3% (by mass fraction, the same applies hereinafter), and mixed in accordance with the composition of P9 in Table 1 to obtain a positive reference P9.

TABLE 4 mutation information of Positive reference

1.2.3 preparation of negative reference

Negative reference N1 was prepared using the NCI-H1395 cell line and negative reference N2 was prepared using the healthy human cell line GM24631 using the same method as in 1.2.1. Negative reference N1 did not contain the mutations described in table 1, and negative reference N2 did not contain any known disease-causing positive mutations.

1.2.4 preparation of detection Limit reference

Detection limit references S1-S8 were prepared using the same methods and sources as in 1.2.1.

S1 to S8 were identical in composition to the mutations of P1 to P8, respectively, but were different from P1 to P8 in the mixing ratio of the wild type DNA fragment and the mutant type DNA fragment.

Specifically, the detection limit reference product S1-S8 was obtained by mixing a wild-type DNA fragment and a mutant DNA fragment at an expected mutation frequency of 0.3% for each mutation (wherein the mutation frequency of the fusion mutation is 0.4%).

The detection limit reference S9 was prepared using the same method and source as in 1.2.2. S9 has the same mutation composition as that of P9, but differs in the mixing ratio of the wild-type DNA fragment and the mutant-type DNA fragment.

The wild type DNA fragment and the mutant type DNA fragment were mixed at 0.3% of the expected mutation frequency corresponding to each mutation (wherein, the mutation frequency of the fusion mutation was 0.4%), to obtain a detection limit reference S9.

1.2.5 preparation of repetitive reference

A duplicate positive reference R1 and a duplicate negative reference R2 were prepared using the same method as in 1.2.1.

R1 has the same mutation composition as that of the positive reference P3, but is different from P3 in the mixing ratio of the wild-type DNA fragment and the mutant-type DNA fragment. The wild-type DNA fragment and the mutant-type DNA fragment were mixed at an expected mutation frequency of 1% for each mutation to obtain a detection limit reference R1.

R2 was obtained by dilution with mock WT-cfDNA.

1.3 quality control

1.3.1 Positive reference quality test

The detection values of the mutation frequencies of the positive reference products P1-P9 were detected by the internal quality inspection and the third-party quality inspection by the microdroplet digital PCR method, and are shown in Table 5 below.

Table 5 ddPCR quality test results for the reference products

As a result, the internal detection results of the 33 mutation sites contained in the positive reference products P1-P9 were all consistent with the detection results of ddPCR. The positive reference substance of the invention is proved to have better consistency with the gold standard accepted in the industry and meet the requirements.

1.3.2 quality control of detection Limit reference

The prepared detection limit reference products S1-S9 are sent to a third party detection company for ddPCR detection. After the comparison, the detection results of NGS at 33 mutation sites contained in the reference sample are all consistent with the detection result of ddPCR, and the results are shown in table 6. This result demonstrates that the detection limit reference can be detected and function properly.

TABLE 6 internal detection and ddPCR detection of detection Limit references

1.3.3 NGS detection

Considering that the application scenario of the reference substance is a plasma sample, the matrix of the plasma sample is studied. Wherein, the DNA of the negative cell WT is replaced by the DNA of the negative plasma of the normal person, the positive DNA sample is added into the negative plasma matrix of the normal person according to a certain proportion, and the DNA extraction is carried out by utilizing a nucleic acid extraction or purification reagent. The extracted DNA was pooled and sequenced on the machine, and the final NGS detection results were in agreement with expectations, as shown in table 8.

1.4 reference plate combinations

The positive reference substance of the present invention is preferably used in combination with the negative reference substance, the detection limit reference substance, and the repetitive reference substance described above as a reference substance tray.

Example 2 comparison with other reference disks

In this example, the compositions of the reference products of the present invention and a part of commercially available reference products/kits were counted and compared, and the results are shown in table 7. The reaction numbers in Table 7 were calculated as follows.

In table 7, a ═ guangzhou stone burning medical examination limited, "egfr akbrafkras gene mutation joint detection kit (reversible end termination sequencing)"; b ═ south beijing and genebiotech gmbh, "egfr akros 1BRAFKRASHER2 gene mutation detection kit (reversible end termination sequencing method)"; "human EGFR-KRAS-BRAF-PIK3CA-ALK-ROS1 gene mutation detection kit (semiconductor sequencing method)", tianjinnuo grassy bioinformatics science and technology ltd; "human 10 gene mutation joint detection kit (reversible end-termination sequencing method)", xiamen edd biomedical science and technology ltd.

TABLE 7 comparison with other commercial kits

From the results, compared with the reference A, the number of the mutant gene types and the mutant site types of the reference plate is the same, but the total number of the reference is reduced by 56.86%, and the reaction number of the reference is reduced by 78.49%; compared with a reference product B, the types of the mutant genes and the types of the mutant sites of the reference product disk are respectively increased by about 1.5 times and 1.54 times, the total quantity of the reference products is reduced by 47.62 percent, and the reaction number of the reference products is reduced by 54.02 percent; compared with a reference product C, the reference product disk mutant gene types and the mutant site types are respectively increased by about 0.67 time and 0.65 time, the total number of the reference products is reduced by 4.35%, and the reaction number of the reference products is reduced by 32.2%; compared with the reference D, although the types of the mutant sites of the reference disc are reduced by about 0.15 times, the types of the mutant genes are increased by 0.67 times, the total number of the references is reduced by 77.32%, and the reaction number of the references is reduced by 75%.

In conclusion, compared with the reference products of other companies in the market, the reference product disc provided by the invention has more mutant gene types and mutation types, and can meet the detection requirements of multiple mutations of multiple genes in the market. Meanwhile, the total number of the reference substances contained in the reference substance tray is only 22, and the total number of the reference substance reactions is only 40, so that the development cost and the detection cost of a related detection kit containing the reference substances are remarkably reduced.

Example 3 operational repeatability verification

In this example, operation repeatability verification was performed in order to explore the effect of different batches of cell sources used to prepare the reference and different experimenters on the detection of reference mutations.

First, 9 samples of the reference disks P1-9 having a mutation frequency of 3% were prepared by the operator 1 according to the same formulation procedure as in example 1. NGS detection is carried out on the samples, the mutation frequency in a reference substance is determined, and meanwhile, the result is verified by a ddPCR method, and the NGS result is in accordance with expectation.

Thereafter, nucleosome DNAs of different batches of cells were extracted by operator 2, and the preparations of reference products P1 to P9 were repeated using the extracted DNAs in the same preparation method as described above, and the same verification was carried out.

The NGS measurements obtained from the standards prepared by operators 1, 2 were compared and the results are shown in table 8.

TABLE 8.3 results of second generation sequencing (NGS) assay of the reference plate

The results show that, as can be seen from table 5, the reference plate prepared using the preparation method of the present invention can obtain similar results even though different batches of cells are used and operated by different persons, and the difference from the expected mutation frequency is within an acceptable range.

Industrial applicability

The reference plate of the present invention can be used in detection applications for detecting tumor-associated gene mutations in cfDNA. The reference plate of the invention can be used not only in clinical detection, but also in reagent development, for example, to verify reagent performance, perform quality control, compare the consistency of results of different methods and platforms, and the like.

Claims

1. A reference for the detection of mutations in circulating free DNA, wherein said reference comprises:

a wild-type DNA fragment, and

one or more mutant DNA fragments, each of said mutant DNA fragments having one or more base mutations and encoding an amino acid sequence having one or more amino acid mutations listed in table 1.

2. The reference product according to claim 1, wherein the amino acid sequence encoded by the mutant DNA fragment in the reference product comprises a combination of amino acid mutations selected from any one of the following groups (a) to (i), and does not comprise any amino acid mutation from the other group:

(a) the amino acid mutation of EGFR, p.E746_ A750del,

the amino acid mutation p.T790M of EGFR,

the amino acid mutation p.L858R of EGFR,

amino acid mutation p.g12c of KRAS;

(b) the amino acid mutation of EGFR, p.G719A,

the amino acid mutation of EGFR, p.E746_ A750del,

amino acid mutation of NRAS p.Q61K,

amino acid mutation of KRAS p.g12v;

(c) the amino acid mutation p.G719S of EGFR,

amino acid mutation of ALK EML4-ALK,

the amino acid mutation of BRAF is p.V600E,

amino acid mutation of KRAS p.G12D,

amino acid mutation of PIK3CA p.h 1047r;

(d) the amino acid mutation p.L747_ P753 indel S of EGFR,

the amino acid mutation p.S768I of EGFR,

amino acid mutation of KRAS p.G13C,

amino acid mutation p.a775_ G776insYVMA of ERBB 2;

(e) amino acid mutation of EGFR p.c797s,

amino acid mutation of KRAS p.G13D,

an amino acid mutation of PIK3CA p.ej5k;

(f) amino acid mutation of KRAS p.G12S,

amino acid mutation of EGFR p.L747_ A750delinsP,

amino acid mutation p.ej542k of PIK3 CA;

(g) amino acid mutation of ALK EML4-ALK,

amino acid mutation of KRAS p.g12a;

(h) amino acid mutation of KRAS p.Q61H,

an amino acid mutation of EGFR p.L861Q,

amino acid mutation of MET 14exon skiping;

(i) the amino acid mutation p.E746_ S752delinsV of EGFR,

the amino acid mutation D770_ N771insG of EGFR,

amino acid mutation of RET, KIF5B-RET,

amino acid mutation of ROS1 CD74-ROS1,

amino acid mutation of EGFR p.g719c.

3. The reference according to claim 1 or 2, wherein the mutant and wild type DNA fragments have similar lengths as cfDNA, e.g. an average length of 130-170 bp.

4. The reference according to any one of claims 1 to 3, wherein the ratio of the mutant DNA fragments to the wild type DNA fragments in the reference is such that the frequency of the base mutations is 0.1 to 10%, preferably 1 to 5%, more preferably about 3%.

5. A reference according to any one of claims 2 to 4, which comprises a combination of base mutations selected from any one of the following groups (a) to (i), and which is free of any base mutation from the other group:

(a) a base mutation c.2235-2249 del15 corresponding to p.E746-A750 del,

a base mutation c.2369C > T corresponding to said p.T790M,

a base mutation c.2573T > G corresponding to the p.L858R,

a base mutation c.34g > T corresponding to said p.g12c;

(b) a base mutation c.2156G > C corresponding to said p.G719A,

a base mutation c.2236_2250del15 corresponding to p.E746_ A750del,

the base mutation c.181C > A corresponding to the p.Q61K,

a base mutation c.35G > T corresponding to the p.G12V;

(c) a base mutation c.2155G > A corresponding to said p.G719S,

subtype E6 corresponding to the EML 4-ALK; at the time of the A20, the number of the main chain is,

a base mutation c.1799T > A corresponding to the p.V600E,

a base mutation c.35G > A corresponding to the p.G12D,

a base mutation c.3140A > G corresponding to said p.H1047R;

(d) a base mutation c.2240_2257del18 corresponding to the p.L747_ P753 indel S,

a base mutation c.2303G > T corresponding to the p.S768I,

a base mutation c.37G > T corresponding to the p.G13C,

a base mutation c.2324_2325ins12 corresponding to the p.775 _ G776 insYVMA;

(e) a base mutation c.2389T > A corresponding to said p.C797S,

a base mutation c.38G > A corresponding to the p.G13D,

a base mutation c.1633G > A corresponding to the p.E545K;

(f) a base mutation c.34G > A corresponding to the p.G12S,

a base mutation c.2239-2248 delinsC corresponding to p.L747_ A750delinsP,

the base mutation c.1624G > A corresponding to the p.E542K;

(g) subtype E13 corresponding to the EML 4-ALK; a, 20, and the method is that,

a base mutation c.35g > C corresponding to the p.g12a;

(h) a base mutation c.183A > T corresponding to the p.Q61H,

a base mutation c.2582T > A corresponding to the p.L861Q,

the base mutation c.3082+1G > T corresponding to the 14exon skiping;

(i) a base mutation c.2237_2255delinsT corresponding to p.E746_ S752delinsV,

a base mutation c.2310-2311 insGGT corresponding to the D770-N771 insG,

subtype K15 corresponding to said KIF 5B-RET; the content of R12 is shown in the specification,

subtype C6 corresponding to said CD74-ROS 1; the content of R34 is shown in the specification,

the base mutation c.2155G > T corresponding to said p.G719C.

6. Reference according to claims 1 to 5, wherein said wild-type and mutant DNA fragments are obtained by enzymatic digestion or sonication of nucleotide molecules known to contain said base mutations, such as genomic DNA of a cell line, preferably said enzymatic digestion is carried out using the enzyme Atlantis.

7. A reference pan comprising as a positive reference the reference of any one of claims 1 to 6; preferably, the reference plate comprises 9 positive references, and the 9 positive references comprise the sets of mutations in (a) - (i), respectively.

8. A kit comprising the reference pan of claim 7; preferably further comprising one or more of a negative reference, a detection limit reference and a repetitive reference,

wherein the detection limit reference has the same combination of mutations and a different mutation frequency from a positive reference, preferably the combination of mutations of group (c).

9. Use of the reference of any one of claims 1-6, the reference plate of claim 8, or the kit of claim 9 in a method of detecting a circulating tumor DNA (ctDNA) mutation,

the methods are preferably digital PCR in microdroplet (ddPCR), PCR in the amplification-blocking mutation system (ARMS) and high-throughput sequencing (NGS).

10. A DNA library prepared from the reference of any one of claims 1 to 6.