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A method and primers for detecting index sequence contamination of a sequencing platform

An index sequence and sequencing platform technology, which is applied in biochemical equipment and methods, microbial measurement/inspection, DNA/RNA fragments, etc., can solve the problems of inability to clearly or accurately find index pollution sources, high detection costs, and no record of operational errors and other issues, to achieve the effect of easy promotion and use, simple and convenient operation, and high accuracy

Active Publication Date: 2021-12-21
WUHAN BGI CLINICAL LAB CO LTD
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  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] The first method is easy to find the source of index pollution clearly or accurately due to human memory deviation or unrecorded operation errors
The second method, although it can accurately determine which sub-library has index contamination; however, on the one hand, re-sequencing requires expensive sequencing reagents, and the detection cost is high; on the other hand, re-sequencing takes at least 1-2 days Delay, and the process of re-sequencing is not only easy to cause subsequent further expansion of index pollution

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  • A method and primers for detecting index sequence contamination of a sequencing platform
  • A method and primers for detecting index sequence contamination of a sequencing platform

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Embodiment

[0035]In this example, the sequencing library WHTRDRPEP00000082 is used as an example for testing, and the sequencing platform uses the illuminahiseq platform.

[0036] In the experimental design of WHTRDRPEP00000082, theoretically, only libraries with 5 indexes, 201, 202, 203, 204 and 205 should be included; The five indexes 204 and 205 also contain 2.17% of index 87. The results of data splitting are shown in Table 1, which means that one of the five sub-libraries has index 87 sequence contamination.

[0037] Table 1 Index split results of WHTRDRPEP00000082 library

[0038] sample index sequence 0mismatch 1mismatch total reads bases index87 ATGAGG 2.11% 0.06% 2.17% 4458446 802520280 201 ATCACG 17.04% 0.35% 17.40% 35795615 6443210700 11 202 CGATGT 20.42% 0.62% 21.04% 43293453 7792821540 11 203 TTAGGC 20.99% 0.68% 21.67% 44580695 8024525100 11 204 TGACCA 22.08% 0.60% 22.69% 46678174 8402071320...

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Abstract

The application discloses a method and primers for detecting index sequence contamination of a sequencing platform. The method for detecting contamination of the index sequence of the sequencing platform of the present application includes using specific primers for the contamination index sequence to perform PCR amplification on all sub-libraries of the contaminated sequencing channel, and according to whether there is specific amplification in the PCR amplification result , to judge whether there is index sequence pollution in the corresponding sub-library, so as to detect the pollution source of the index sequence of the sequencing platform. The index sequence contamination detection method of the sequencing platform of the present application provides a brand-new solution and idea for the detection of index sequence contamination on the sequencing platform, which can quickly and specifically detect the source of index sequence contamination, and has low cost, high accuracy, and easy operation. Simple and convenient, easy to promote and use.

Description

technical field [0001] The present application relates to the field of nucleic acid sequencing, in particular to a method and primers for detecting index sequence contamination of a sequencing platform. Background technique [0002] In the process of nucleic acid sequencing, especially for some genomes with relatively large sequencing volumes, it is usually necessary to construct multiple sub-libraries, each sub-library contains one or more index sequences (index in English), and the sequencing results are analyzed according to different index sequences. Split to get the complete genome sequence. [0003] However, when the data is split, index pollution occasionally occurs, that is, additional index sequences that are not designed in each sub-library appear, which means that the sequencing platform has index sequence pollution. The contamination of index sequences directly affects the results of data splitting and the accuracy of sequencing results. Therefore, it is necess...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/686C12N15/11
CPCC12Q1/686C12Q2563/101
Inventor 刘莉玲刘舒田志坚刘娜
Owner WUHAN BGI CLINICAL LAB CO LTD
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