A method and device for screening the combination of complex genomic mutations

Abstract

The present invention discloses a method for screening the combination of complex genomic mutations. The method comprises the following steps: using the Scylla module in the Pisces software to perform mutation combination on the original VCF input file to obtain a preliminary output result and a running record of the mutation combination process, then reading the running record, screening out the valid combination results and the corresponding combination members, marking the screened combination members in the original VCF input file, and then writing the complete information of the combination results into the original VCF input file to obtain the final output result. The method of the present invention can effectively solve the situation of combining two single nucleotide variants (SNVs) that are far apart, avoid the occurrence of invalid combination, retain the original mutation information to the greatest extent, improve the reliability of mutation detection, and at the same time can retain the complete information of the members participating in the combination, providing an original basis for review and confirmation for subsequent report interpretation and improving the traceability of mutation detection.

Description

Technical Field

[0001] The present invention belongs to the field of bioinformatics, and particularly relates to a method and a device for screening the combination of complex genomic mutations. Background Art

[0002] Mutation refers to the sudden and unpredictable variation of the DNA sequence during gene mutation, which causes abnormalities or complete changes in gene products (such as proteins), resulting in changes in genetic information. Gene mutations can occur at the single nucleotide level (referred to as point mutations), or can involve larger parts, such as gene deletions, duplications or inversions, etc. Gene mutations can occur naturally, or can be caused by environmental factors (such as chemicals, radiation, etc.) or genetic defects, etc. Some gene mutations may affect the normal functions of organisms, such as mutations that cause diseases, while other mutations may have no significant effects or may even have adaptive advantages in some cases. Studying gene mutations is of great significance for our understanding of gene structure and function, the etiology of genetic diseases, and the evolutionary process, etc. Common mutations can be roughly classified into the following types:

[0003] 1) Single-base or multi-base deletion (Deletion), that is, the deletion (removal) of a single or multiple bases occurs at a certain position.

[0004] 2) Single-base or multi-base insertion or duplication (Insertion / Duplication), that is, the insertion or duplication of a single or multiple bases occurs at a certain position.

[0005] 3) Substitution mutation (Substitution), that is, a single base or multiple bases at a certain position are replaced by another single or multiple bases, and the substitution mutation of a single base is usually called a single nucleotide variant (SNV).

[0006] 4) Complex variation (Complex Variation). If the above three types of mutation occur continuously in the same sequence or occur continuously within a certain distance, then these mutations can be integrated or degenerate into a more complex mutation composed of the above mutation types.

[0007] Multiple individual mutations may interact to result in a broader range of biological effects. Combining these multiple individual mutations into a complex mutation can more accurately reflect this additive effect. After combining multiple individual mutations into a complex mutation, we can more conveniently interpret its function. Compared with studying and understanding multiple individual mutations separately, the combined complex mutation can more directly reveal changes in protein structure and function, simplify the research process, and provide a more convenient diagnostic method. Especially in the study of genetic diseases, the detection and interpretation of complex mutations can more accurately identify the disease-causing genes related to the diseases compared to the study of single mutations.

[0008] Currently, there are few types of tool software for combining complex mutations. The Scylla module in the Pisces software (https: / / github.com / tamsen / Pisces) can detect, analyze, and combine potential complex mutations in the results obtained from different upstream mutation detection software.

[0009] In practical applications, Scylla combines two SNVs that are relatively far apart, which is often unnecessary in mutation detection applications. The two SNVs in the combined members can be interpreted separately, and this combination makes the mutation expression very long, causing trouble for subsequent interpretation. Moreover, Scylla performs invalid combinations, that is, the final combined result is one of the multiple mutations participating in the combination. This kind of invalid combination cannot produce useful combined results, but will change the relevant information of the original mutations and affect the reliability of mutation detection. The combined results finally produced by Scylla will overwrite the members participating in the combination, making the source of the complex mutation untraceable in the subsequent interpretation process and potentially causing problems for the final reported results. Summary of the Invention

[0010] The purpose of the present invention is to overcome at least one deficiency of the prior art and provide a method and device for screening the combination of genomic complex mutations.

[0011] The technical solution adopted by the present invention is as follows:

[0012] In the first aspect, the present invention provides a method for screening the combination of genomic complex mutations, including the following steps:

[0013] 1) Use the Scylla module in the Pisces software to perform mutation combination on the original VCF input file to obtain a preliminary output result and the operation record of the mutation combination process;

[0014] 2) Read the operation record obtained in step 1), screen out the valid combined results and the corresponding combined members to obtain the screened combined results and combined members;

[0015] 3) From the preliminary output result obtained in step 1), extract the complete information of the merging result obtained in step 2) for backup;

[0016] 4) Mark the merged members obtained in step 2) in the original VCF input file, and then write the complete information extracted in step 3) into the original VCF input file to obtain the final output result;

[0017] Among them, the screening result of step 2) should satisfy the following two conditions simultaneously:

[0018] 1) The lengths of the wild-type sequence and the mutant sequence in the merging result are not equal;

[0019] 2) The merged members do not contain the merging result.

[0020] In some instances, the screened merging result of step 2) does not belong to the mutation type of base deletion.

[0021] In some instances, the screened merging result of step 2) does not belong to the mutation type of base insertion.

[0022] In some instances, the screened merging result of step 2) is a complex mutation composed of a single base deletion and a single base substitution.

[0023] In some instances, the screened merging result of step 2) is a complex mutation composed of a single base insertion and a single base substitution.

[0024] In a second aspect, an apparatus for screening genomic complex mutation merging according to the present invention, the apparatus includes:

[0025] A storage module for storing the preliminary output result of mutation merging and the operation record;

[0026] A judgment module for screening out valid merging results and corresponding merged members;

[0027] An output module for writing the information obtained by the judgment module into the original input file to obtain the final output result.

[0028] In a third aspect, the present invention provides a device, including:

[0029] One or more processors;

[0030] A storage device for storing one or more programs;

[0031] When the one or more programs are executed by the one or more processors, the one or more processors implement the method described in the first aspect.

[0032] Fourthly, the present invention provides a storage medium storing computer instructions for being executed by a computer to implement the method described in the first aspect.

[0033] The beneficial effects of the present invention are as follows:

[0034] 1) The method of the present invention can effectively solve the situation of combining two single nucleotide variants (SNVs) with a relatively large distance, improve the readability of the detection results, make the subsequent report interpretation clearer, and thus provide more efficient medication guidance for patients;

[0035] 2) The method of the present invention can avoid the occurrence of invalid combination, retain the original mutation information to the greatest extent, and improve the reliability of mutation detection;

[0036] 3) The method of the present invention can retain the complete information of the members participating in the combination, provide the original basis for review and confirmation for the subsequent report interpretation, and improve the traceability of mutation detection;

[0037] 4) The method of the present invention reduces the complexity of writing the analysis process and improves the code execution efficiency. Description of the Drawings

[0038] Figure 1 It is a software implementation flowchart. Detailed Embodiments

[0039] The following disclosure provides many different embodiments or examples for implementing different solutions of the present invention.

[0040] The flowchart of the present method is as Figure 1 shown. First, according to the format characteristics of the operation record of mutation combination, it is parsed to clarify the relationship between the members participating in the combination and the combination result. The parsing method is to extract the keyword field "accepted" when generating the combination result, and split it according to the delimiter. At the same time, the first two lines of the result of this line are split in the same way as the members participating in the combination, and then the members and the result are stored according to the corresponding relationship.

[0041] The example is as follows: "chr1:A>B": ["chr1:C>D", "chr1:E>F"], where the combination result "chr1:A>B" is combined by the members "chr1:C>D" and "chr1:E>F". Subsequently, certain screening conditions are set according to the requirements, and only the valid and qualified members and results are retained.

[0042] There are mainly 6 screening conditions, and the entries that meet the conditions must first satisfy (5) and (6): (1) Entries where the merged result is not a simple single-base or multi-base deletion, such as ACG>A, which does not belong to complex mutations; (2) Entries where the merged result is not a simple single-base or multi-base insertion or duplication, such as A>ACG, which does not belong to complex mutations; (3) The merged result is a complex mutation composed of a single-base deletion and a single-base substitution, such as AA>T; (4) The merged result is a mutation composed of a single-base insertion and a single-base substitution, such as T>AA; (5) The length of A is not equal to the length of B (taking "chr1:A>B" above as an example); (6) The members do not contain the result.

[0043] Then, according to the results that meet the conditions, extract their complete information from the preliminary running result VCF for backup. That is, extract the complete information from the VCF according to keyword fields such as "chr1:A>B" for backup.

[0044] Finally, according to the members that meet the conditions, mark the members participating in the merge in the original file (VCF) and add the merge result to the original file to obtain the final output file. That is, find the members "chr1:C>D" and "chr1:E>F" in the original file (VCF) and mark them as "merged members", and then write the complete information of "chr1:A>B" into the original file. Thus, the purpose of improving the traceability of mutation detection is achieved.

[0045] Example 1

[0046] The wild-type sequence input in this example is GAATTAAGAGAAG, and the mutant sequence is CAAC. The partial original VCF file input is shown in Table 1:

[0047] Table 1

[0048]

[0049] Use the Scylla module in the Pisces software to perform mutation merging on this, and the preliminary output results are as follows:

[0050] VariantSites GGAATTAAGA>G, G>C, GAAG>CAAC, G>C; (merged members)

[0051] VariantPositions 55242465, 55242475, 55242475, 55242478; (mutation sites)

[0052] mnv accepted: chr7, 55242466, GAATTAAGAGAAG, CAAC. (Combined result column)

[0053] Then, the preliminary output results are screened and judged to obtain the members and results that pass the filtering conditions as follows:

[0054] {"chr7:55242466:GAATTAAGAGAAG:CAAC": ["chr7:55242465:GGAATTAAGA:G", "chr7:55242475:G:C", "chr7:GAAG:CAAC", "chr7:55242478:G:C"]}

[0055] Based on the above members and results that pass the filtering conditions, mark the members participating in the merge in the original file (VCF) and add the combined result to the original file to obtain the final output file. Part of this output file is shown in Table 2.

[0056] Table 2

[0057]

[0058] Example 2

[0059] The wild-type sequence input in this example is ATGTTTTTG, and the mutant sequence is TTGTTTTTT. Obviously, this mutation is A>T and G>T at relatively far distances. The Scylla module in the Pisces software is used to merge this mutation, and the preliminary output results are as follows:

[0060] Variant Sites A>T, G>T; (Merged members)

[0061] Variant Positions 116381106, 116381114; (Mutation sites)

[0062] mnv accepted: chr7 116381106, ATGTTTTTG, TTGTTTTTT. (Combined result)

[0063] Obviously, Scylla will merge two mutations at relatively far distances, which is often unnecessary in mutation detection applications. This kind of merge makes the mutation expression very long and brings trouble to subsequent interpretation.

[0064] The preliminary output results are screened and judged. Obviously, this output result does not meet the condition that "the lengths of the wild-type sequence and the mutant sequence in the combined result are not equal", so this type of merge is discarded.

[0065] Example 3

[0066] The wild-type sequence input in this example is C, and the mutant sequence is A. The Scylla module in the Pisces software is used to perform mutation merging on this, and the preliminary output results are as follows:

[0067] VariantSites G>G, G>G, C>A, T>T; (merged members)

[0068] VariantPositions 116381153, 116381160, 116381173, 116381183; (mutation sites)

[0069] mnv accepted:chr7, 116381173, C, A. (merged result)

[0070] Obviously, invalid merging occurred during the operation of Scylla, that is, the four groups of G>G, G>G, C>A, and T>T were merged, which will change the relevant information of the original mutation in the mutation detection application and affect the reliability of mutation detection.

[0071] The preliminary output results are screened and judged. Obviously, this output result does not meet the condition that "the merged members do not include the merged result", so this type of merging is filtered.

[0072] The above is a further detailed description of the present invention, and it should not be regarded as a limitation to the specific implementation of the present invention. For those of ordinary skill in the technical field to which the present invention belongs, simple deductions or replacements without departing from the concept of the present invention are within the protection scope of the present invention.

Claims

1. A method for screening the combination of complex genomic mutations, characterized in that, It includes the following steps: 1) Use the Scylla module in the Pisces software to merge mutations in the original VCF input file to obtain a preliminary output result and a running record of the mutation merging process; 2) Read the running record obtained in step 1), filter out the valid merging results and the corresponding merging members to obtain the filtered merging results and merging members; 3) In the preliminary output result obtained in step 1), extract the complete information of the merging result obtained in step 2) for backup; 4) Mark the merging members obtained in step 2) in the original VCF input file, and then write the complete information extracted in step 3) into the original VCF input file to obtain the final output result; Among them, the screening results in step 2) must satisfy the following two conditions simultaneously: 1) The lengths of the wild-type sequence and the mutant sequence in the merging result are not equal; 2) The merging members do not include the merging result.

2. The method according to claim 1, characterized in that, The filtered merging result in step 2) does not belong to the mutation type of base deletion.

3. The method according to claim 1, characterized in that, The filtered merging result in step 2) does not belong to the mutation type of base insertion.

4. The method according to claim 1, characterized in that The filtered merging result in step 2) is a complex mutation composed of a single base deletion and a single base substitution.

5. The method according to claim 1, wherein The filtered merging result in step 2) is a complex mutation composed of a single base insertion and a single base substitution.

6. An apparatus for screening complex genomic mutation combinations, characterized in that, Using the method for screening and merging complex genomic mutations described in claim 1, the device includes: A storage module for storing the preliminary output result and the running record of mutation merging; A judgment module for screening out valid merging results and the corresponding merging members; An output module for writing the information obtained by the judgment module into the original input file to obtain the final output result.

7. An apparatus for screening genomic complex mutation combinations, characterized in that, It includes: One or more processors; A storage device for storing one or more programs; When the one or more programs are executed by the one or more processors, the one or more processors implement the method described in claim 1.

8. A storage medium storing computer instructions for being executed by a computer to implement the method described in claim 1.

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