阅读说明：本技术 基因拷贝数评估方法、装置、系统以及计算机可读介质 (Method, apparatus, system and computer readable medium for evaluating gene copy number ) 是由 张水荣 施巍炜 王凯 柳文进 黄璐嘉 于 2019-11-08 设计创作，主要内容包括：本发明提供了一种能提高对基因拷贝数的评估结果的准确性的基因拷贝数评估方法、装置、系统以及计算机可读介质,其中的基因拷贝数评估方法,根据样本中的肿瘤细胞含量和分别对检测样本和对照样本测序分析后得到的包含检测样本和对照样本各自测序深度矫正后的检测矫正测序深度和对照矫正测序深度的测序分析数据,对检测样本中的基因拷贝数进行评估,其特征在于,包括以下步骤：获取样本矫正测序深度和对照矫正测序深度并采用公式(一)计算得到矫正后测序深度比；根据矫正后测序深度比,采用公式(二)计算得到相应的基因拷贝数。(The invention provides a gene copy number evaluation method, a device, a system and a computer readable medium capable of improving the accuracy of an evaluation result of the gene copy number, wherein the gene copy number evaluation method evaluates the gene copy number in a detection sample according to the content of tumor cells in the sample and sequencing analysis data which are obtained after sequencing analysis of the detection sample and a comparison sample and respectively comprise the detection correction sequencing depth and the comparison correction sequencing depth after respective sequencing depth correction of the detection sample and the comparison sample, and is characterized by comprising the following steps of: acquiring a sample correction sequencing depth and a contrast correction sequencing depth, and calculating by adopting a formula (I) to obtain a corrected sequencing depth ratio; and (4) calculating to obtain the corresponding gene copy number by adopting a formula (II) according to the corrected sequencing depth ratio.)

1. A gene copy number evaluation method is used for evaluating the gene copy number in a detection sample according to the content of tumor cells in the sample and sequencing analysis data which are obtained after sequencing analysis of the detection sample and a control sample and contain the detection correction sequencing depth and the control correction sequencing depth after respective sequencing depth correction of the detection sample and the control sample, and is characterized by comprising the following steps:

obtaining the sample correction sequencing depth and the contrast correction sequencing depth, and calculating by adopting a formula (I) to obtain a corrected sequencing depth ratio;

calculating by adopting a formula (II) according to the corrected sequencing depth ratio to obtain the corresponding gene copy number,

wherein, the formula (one) and the formula (two) are respectively as follows:

in the formula (I), the ratio is the corrected sequencing depth ratio,

TD is the corrected sequencing depth of the sample after the sample correction is detected,

CD is the corrected control sequencing depth of the control sample;

in the formula (II), log₂ ^ratioIs the logarithm of the base 2 ratio,

and purity is the content of the tumor cells in the detection sample.

2. The method for evaluating a gene copy number according to claim 1, further comprising:

the tumor cell content in the sample is the tumor cell content in the evaluated detection sample obtained after evaluation,

wherein the sequencing analysis data further comprises each average sample mutation frequency corresponding to each mutation site and each control mutation frequency corresponding to each mutation site, which are obtained by sequencing analysis of the detection sample and the control sample respectively,

evaluating the tumor cell content in the sample to obtain the tumor cell content in the evaluated test sample, wherein the tumor cell content in the evaluated test sample is used as the tumor cell content in the test sample in formula (two):

acquiring the average sample mutation frequency and the contrast mutation frequency of the mutation sites meeting the preset mutation conditions one by one, and calculating by adopting a formula (1) to obtain the content of single tumor cells corresponding to the mutation sites;

once all the single tumor cell contents corresponding to all the mutation sites meeting the preset mutation conditions are obtained, obtaining all the single tumor cell contents and calculating by adopting a formula (2) to obtain the tumor cell contents in the detection sample;

evaluating the tumor cell content in the detection sample obtained by calculation in the formula (2) according to a preset evaluation rule to obtain the tumor cell content in the detection sample after evaluation,

wherein, the formula (1) and the formula (2) are respectively shown as follows,

in the formula (1), for a mutation site satisfying the predetermined mutation condition,

p is the calculated content of the single tumor cell corresponding to the mutation site,

VAFa is the average mutation frequency of the sample corresponding to the mutation site in the detection sample,

VAFt is the mutation frequency of the tumor cells corresponding to the mutation site in the sample,

VAFn is the corresponding control mutation frequency of the mutation site in the control sample,

in the formula (2), P is the content of tumor cells in the test sample, n is the total number of mutation sites satisfying the predetermined mutation condition, and the individual tumor cell contents P corresponding to each of the n mutation sites are represented by P1, P2, P3 and P4 … Pn, respectively.

3. The method for evaluating a gene copy number according to claim 2, wherein:

wherein the predetermined mutation condition is that the control mutation frequency corresponding to one of the mutation sites is 0.4 or more and 0.6 or less.

4. The method for evaluating a gene copy number according to claim 2 or 3, wherein:

the predetermined evaluation rule is: directly evaluating the tumor cell content in the detection sample obtained by calculation in the formula (2) as the tumor cell content in the detection sample after evaluation.

5. The method for evaluating a gene copy number according to claim 2 or 3, wherein:

wherein the predetermined evaluation rule is: correcting the content of the tumor cells in the detection sample obtained by calculation by adopting the following tumor cell content correction model, and evaluating the content of the tumor cells obtained after correction as the content of the tumor cells in the detection sample after evaluation,

y＝ax-b (3)

in the formula (3), y is the content of tumor cells in the detection sample obtained after the rectification;

x is the tumor cell content p in the detection sample obtained by calculation,

a and b are model parameters, the value of a is 1.4, and the value range of b is 0.23-0.26.

6. A gene copy number evaluation device, comprising:

the corrected sequencing depth calculating unit is used for obtaining the sample corrected sequencing depth and the contrast corrected sequencing depth and calculating by adopting a formula (I) to obtain a corrected sequencing depth ratio;

a gene copy number calculation unit, which calculates the corresponding gene copy number by adopting a formula (II) according to the corrected sequencing depth ratio,

wherein, the formula (one) and the formula (two) are respectively as follows:

in the formula (I), the ratio is the corrected sequencing depth ratio,

TD is the corrected sequencing depth of the sample after the sample correction is detected,

CD is the corrected control sequencing depth of the control sample;

in the formula (II), log₂ ^ratioIs the logarithm of the base 2 ratio;

and purity is the content of the tumor cells in the detection sample.

7. The apparatus for evaluating a gene copy number according to claim 6, further comprising:

a tumor cell content evaluation unit for evaluating the tumor cell content in the sample to obtain the tumor cell content in the sample after evaluation, which is used as the tumor cell content in the detection sample in formula (two), and which has:

a single tumor cell content calculation part, which acquires the average sample mutation frequency and the contrast mutation frequency of the mutation sites meeting the preset mutation conditions one by one and calculates the single tumor cell content corresponding to the mutation sites by adopting a formula (1);

a tumor cell content calculation unit for obtaining the contents of all the single tumor cells corresponding to all the mutation sites satisfying the predetermined mutation conditions and calculating the contents of the tumor cells in the test sample by using the formula (2),

a content evaluation section for evaluating the tumor cell content in the test sample calculated by the formula (2) according to a predetermined evaluation rule to obtain the tumor cell content in the evaluated test sample,

wherein, the formula (1) and the formula (2) are respectively shown as follows,

in the formula (1), for a mutation site satisfying the predetermined mutation condition,

p is the calculated content of the single tumor cell corresponding to the mutation site,

VAFa is the average mutation frequency of the sample corresponding to the mutation site in the detection sample,

VAFt is the mutation frequency of the tumor cells corresponding to the mutation site in the sample,

VAFn is the corresponding control mutation frequency of the mutation site in the control sample,

in the formula (2), P is the calculated tumor cell content in the test sample, n is the total number of mutation sites satisfying the predetermined mutation condition, and the individual tumor cell contents P corresponding to each of the n mutation sites are respectively represented by P1, P2, P3 and P4 … Pn.

8. The gene copy number evaluation device according to claim 7, wherein:

wherein the predetermined evaluation rule is: directly evaluating the tumor cell content in the detection sample obtained by calculation in the formula (2) as the tumor cell content in the detection sample after evaluation.

9. The gene copy number evaluation device according to claim 7, wherein:

wherein the predetermined evaluation rule is: correcting the content of the tumor cells in the detection sample obtained by calculation by adopting the following tumor cell content correction model, and evaluating the content of the tumor cells obtained after correction as the content of the tumor cells in the detection sample after evaluation,

y＝ax-b (3)

in the formula (3), y is the content p' of the tumor cells in the corrected detection sample;

x is the tumor cell content p in the detection sample obtained by calculation,

a and b are the parameters of the model,

the value of a is 1.4, and the value of b ranges from 0.23 to 0.26.

10. A gene copy number evaluation system, comprising:

the sequencing analysis device is used for respectively carrying out sequencing analysis on the detection sample and the control sample to obtain sequencing analysis data for gene copy number evaluation;

a gene copy number evaluating device for evaluating the gene copy number in the test sample based on the sequencing analysis data,

wherein the gene copy number evaluation device is the gene copy number evaluation device according to any one of claims 6 to 8.

11. A gene copy number evaluation apparatus, comprising:

a memory for storing computer program instructions; and

a processor for executing the instructions of the computer program,

wherein the computer program instructions, when executed by the processor, cause the apparatus to perform the steps of the gene copy number evaluation method of any one of claims 1 to 5.

12. A computer-readable medium, characterized in that:

the computer-readable medium stores a computer program,

wherein the computer program is executable by a processor to implement the steps of the gene copy number evaluation method according to any one of claims 1 to 5.

Technical Field

The invention belongs to the field of biology, and particularly relates to a method, a device and a system for evaluating gene copy number and a computer readable medium.

Background

The gene copy number is often needed to be analyzed when the genetic variation detection analysis is performed on the tumor tissue, however, the genetic tumor cells in the tumor tissue also have normal cells, and due to the existence of the normal cells, if the actual content of the tumor cells is not considered, the content of the normal cells is included, so that the analysis result of the gene copy number is greatly influenced.

Disclosure of Invention

The invention provides a method, a device and a system for evaluating gene copy number and a computer readable medium, aiming at improving the accuracy of evaluating the gene copy number.

In order to achieve the purpose, the invention adopts the following technical scheme:

the invention provides a gene copy number evaluation method, which evaluates the gene copy number in a detection sample according to the content of tumor cells in the sample and sequencing analysis data which are obtained after sequencing analysis of the detection sample and a comparison sample and contain detection correction sequencing depth and comparison correction sequencing depth after respective sequencing depth correction of the detection sample and the comparison sample, and is characterized by comprising the following steps: acquiring a sample correction sequencing depth and a contrast correction sequencing depth, and calculating by adopting a formula (I) to obtain a corrected sequencing depth ratio; and (3) calculating to obtain the corresponding gene copy number by adopting a formula (II) according to the corrected sequencing depth ratio, wherein the formula (I) and the formula (II) are respectively as follows:

in the formula (I), the ratio is the corrected sequencing depth ratio,

TD is the corrected sequencing depth of the sample after the sample correction is detected,

CD is the corrected control sequencing depth of the control sample;

in the formula (II), log₂ ^ratioIs the logarithm of the base 2 ratio,

and purity is the content of tumor cells in a detected sample.

The gene copy number evaluation method provided by the present invention is characterized by further comprising: the method comprises the following steps of (1) evaluating the content of tumor cells in a sample to obtain the content of tumor cells in an evaluated detection sample, wherein sequencing analysis data further comprises average sample mutation frequencies respectively corresponding to mutation sites and control mutation frequencies respectively corresponding to the mutation sites, which are obtained by respectively sequencing and analyzing the detection sample and a control sample, and the content of tumor cells in the evaluated detection sample is used as the content of tumor cells in the detection sample in a formula (II): obtaining the average sample mutation frequency and the contrast mutation frequency of the mutation sites meeting the preset mutation conditions one by one, and calculating by adopting a formula (1) to obtain the content of single tumor cells corresponding to the mutation sites; once all the single tumor cell contents corresponding to all the mutation sites meeting the preset mutation conditions are obtained, obtaining all the single tumor cell contents and calculating by adopting a formula (2) to obtain the tumor cell contents in the detection sample; evaluating the tumor cell content in the test sample calculated by the formula (2) according to a predetermined evaluation rule to obtain the tumor cell content in the evaluated test sample, wherein the formula (1) and the formula (2) are respectively as follows,

in the formula (1), for a mutation site satisfying a predetermined mutation condition, P is the calculated content of a single tumor cell corresponding to the mutation site,

VAFa is the average mutation frequency of a sample corresponding to the mutation site in a detection sample,

VAFt is the mutation frequency of the tumor cells corresponding to the mutation site in the sample, VAFn is the control mutation frequency corresponding to the mutation site in the control sample,

in the formula (2), P is the content of tumor cells in the sample, n is the total number of mutation sites satisfying the predetermined mutation condition, and the individual tumor cell contents P corresponding to each of the n mutation sites are represented by P1, P2, P3 and P4 … Pn, respectively.

The method for evaluating a gene copy number according to the present invention is characterized in that the predetermined mutation condition is such that the control mutation frequency corresponding to one mutation site is 0.4 or more and 0.6 or less.

The gene copy number evaluation method provided by the invention is characterized in that: the predetermined evaluation rule is: directly evaluating the tumor cell content in the detection sample obtained by calculation in the formula (2) as the tumor cell content in the detection sample after evaluation.

The gene copy number evaluation method provided by the invention is characterized in that: wherein, the predetermined evaluation rule is as follows: correcting the content of the tumor cells in the detection sample obtained by calculation by adopting the following tumor cell content correction model, evaluating the content of the tumor cells obtained after correction as the content of the tumor cells in the detection sample after evaluation,

y＝ax-b (3)

in the formula (3), y is the content of tumor cells in the detection sample obtained after correction;

x is the calculated content p of the tumor cells in the detection sample,

a and b are model parameters, the value of a is 1.4, and the value range of b is 0.23-0.26.

The present invention also provides a gene copy number evaluation device, comprising: the corrected sequencing depth calculating unit is used for obtaining the corrected sequencing depth of the sample and the corrected sequencing depth of the contrast and calculating by adopting a formula (I) to obtain a corrected sequencing depth ratio; the gene copy number calculating unit calculates the corresponding gene copy number by adopting a formula (II) according to the corrected sequencing depth ratio,

wherein, the formula (one) and the formula (two) are respectively as follows:

in the formula (I), the ratio is the corrected sequencing depth ratio,

TD is the corrected sequencing depth of the sample after the sample correction is detected,

CD is the corrected control sequencing depth of the control sample;

in the formula (II), log₂ ^ratioIs the logarithm of the base 2 ratio;

and purity is the content of tumor cells in a detected sample.

The gene copy number evaluation device according to the present invention is characterized by further comprising: the tumor cell content evaluation unit is used for evaluating the tumor cell content in the sample to obtain the tumor cell content in the sample after evaluation, and the tumor cell content in the sample is used as the tumor cell content in the detection sample in the formula (II), and the tumor cell content evaluation unit comprises: a single tumor cell content calculation part, which obtains the average sample mutation frequency and the contrast mutation frequency of the mutation sites meeting the preset mutation conditions one by one, and calculates the single tumor cell content corresponding to the mutation sites by adopting a formula (1); a tumor cell content calculation part for obtaining all the single tumor cell contents corresponding to all the mutation sites meeting the predetermined mutation conditions once the single tumor cell contents are obtained, and calculating the tumor cell contents in the detection sample by adopting a formula (2), a content evaluation part for evaluating the tumor cell contents in the detection sample obtained by the calculation of the formula (2) according to a predetermined evaluation rule to obtain the tumor cell contents in the detection sample after evaluation, wherein the formula (1) and the formula (2) are respectively shown as follows,

in the formula (1), for a mutation site satisfying a predetermined mutation condition, P is the calculated content of a single tumor cell corresponding to the mutation site,

VAFa is the average mutation frequency of a sample corresponding to the mutation site in a detection sample,

VAFt is the mutation frequency of the tumor cells corresponding to the mutation site in the sample, VAFn is the control mutation frequency corresponding to the mutation site in the control sample,

in the formula (2), P is the calculated tumor cell content in the test sample, n is the total number of mutation sites satisfying the predetermined mutation condition, and the individual tumor cell contents P corresponding to each of the n mutation sites are represented by P1, P2, P3 and P4 … Pn, respectively.

The gene copy number evaluation apparatus according to the present invention is further characterized in that the predetermined evaluation rule is: directly evaluating the content of the tumor cells in the detection sample obtained by the calculation of the formula (2) as the content of the tumor cells in the detection sample after evaluation.

The gene copy number evaluation apparatus according to the present invention is further characterized in that the predetermined evaluation rule is: correcting the content of the tumor cells in the detection sample obtained by calculation by adopting the following tumor cell content correction model, evaluating the content of the tumor cells obtained by correction as the content of the tumor cells in the detection sample after evaluation,

y＝ax-b (3)

in the formula (3), y is the content p' of the tumor cells in the corrected detection sample;

x is the calculated content p of the tumor cells in the detection sample,

a and b are the parameters of the model,

the value of a is 1.4, and the value of b ranges from 0.23 to 0.26.

The present invention also provides a gene copy number evaluation system, comprising: the sequencing analysis device is used for respectively carrying out sequencing analysis on the detection sample and the control sample to obtain sequencing analysis data for gene copy number evaluation; and a gene copy number evaluation device for evaluating the gene copy number in the detection sample according to the sequencing analysis data, wherein the gene copy number evaluation device is the above-mentioned gene copy number evaluation device.

The present invention also provides a gene copy number evaluation apparatus, characterized by comprising: a memory for storing computer program instructions; and a processor for executing computer program instructions, wherein the computer program instructions, when executed by the processor, cause the apparatus to perform the steps of the gene copy number evaluation method described above.

The present invention is also a computer-readable medium characterized by: the computer readable medium stores a computer program, wherein the computer program is executable by a processor to implement the steps of the gene copy number evaluation method according to claim.

Action and Effect of the invention

The gene copy number evaluation method, the gene copy number evaluation device, the gene copy number evaluation system and the computer readable medium provided by the invention have the advantages that the reliability of the evaluation result of the gene copy number can be improved compared with the evaluation of the copy number without considering the content of the tumor cells due to the fact that the content of the tumor cells is considered.

Drawings

FIG. 1 is a block diagram showing the construction of a gene copy number evaluation system according to example 1 of the present invention;

FIG. 2 is a block diagram showing the structure of a tumor cell content evaluation module according to example 1 of the present invention;

FIG. 3 is a flowchart showing the operation of the gene copy number evaluation system according to example 1 of the present invention;

FIG. 4 is a block diagram showing the construction of a gene copy number evaluation system according to example 2 of the present invention;

fig. 5 is a result of verifying the tumor cell content evaluation unit and method according to example 1 of the present invention.

Detailed Description

The following describes embodiments of the present invention with reference to the drawings. For the specific methods or materials used in the embodiments, those skilled in the art can make routine alternatives based on the existing technologies based on the technical idea of the present invention, and not limited to the specific descriptions of the embodiments of the present invention.