A type method and application of abo blood group system based on sequencing data
A technology of ABO blood type and sequencing data, which is applied in the field of blood type analysis, can solve the problems of missed detection of SNP sites, time-consuming and laborious, and inability to distinguish haplotypes, and achieve the effects of improving accuracy, improving efficiency, and saving manpower and material resources
Active Publication Date: 2022-03-25
SHENZHEN HUADA GENE INST
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Problems solved by technology
The current PCR-SBT typing method is mainly aimed at determining the genotype of exons 6 and 7 of the ABO gene with relatively concentrated polymorphic sites. Exons 1-5 are not sequenced, and each Differences between ABO blood types may be caused by only a single or a few nucleotide variations, therefore, the PCR-SBT method is likely to cause missed detection of SNP sites
Moreover, the PCR-SBT method is time-consuming and laborious, and is not suitable for ABO blood group identification of large-scale samples
In addition, due to the presence of heterozygotes, in the case of diploid sequencing, the PCR-SBT method cannot distinguish haplotypes, resulting in ambiguous results
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[0088] In this example, the ABO blood grouping system is based on the whole genome sequencing data of 1 autism family with ~30×. The ABO blood grouping system based on the sequencing data is as follows:
[0089] (1) Download the ABO genotype and sequence data from the dbRBC database of NCBI, that is, the public BGMUT database, wherein the sequence data includes the gene coding sequence and the full-length gene sequence. Given that among the sequences downloaded from the database, only a few sequences contain all exons and introns, and most of the other sequences have more or less deletions of certain exons or introns; therefore, this For example, according to sequence similarity, exons 2 to 7 of the sequence are completed.
[0090] (2) Cut the downloaded ABO gene coding sequence according to the exons, take out the sequences of exons 2-7, and extend 100 bp on both sides, as the reference sequence of the sample to be typed. If its own exon sequence is long enough, the extended...
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The present application discloses an ABO blood group system typing method based on sequencing data and its application. The method of this application includes using the reference sequence and the Bayesian classification training data set to analyze the sequencing data of the sample to be tested, specifically, comparing the sequencing data of the sample to be tested to obtain the position and variation information relative to the reference sequence; the reads on the comparison For each exon, assemble overlapping reads with consistent overlapping sequences as a haplotype; according to the number of supported reads and coverage score, take out the haplotype according to the score from high to low, and construct a candidate haplotype ;Permutate and combine the variations of all candidate haplotypes, and score based on the distance between the haplotype obtained by the permutation and combination and the haplotype in the database, the P value of Bayesian classification, the number of supported reads, and the non-contradictory type , select the two with the highest scores as the final ABO blood type of the sample to be tested. The method of the present application improves the accuracy of blood typing, can also analyze potential new blood types, and can perform mass analysis.
Description
technical field [0001] The present application relates to the field of blood group analysis methods, in particular to an ABO blood group system typing method based on sequencing data and its application. Background technique [0002] The ABO blood group system is the most common blood group system. The H antigen is encoded by the gene encoding the H antigen, and then the H antigen is modified by the transferase encoded by the ABO gene to make it an A antigen or a B antigen. When the nonsense mutation of the ABO gene leads to the loss of transferase activity, the H antigen has not undergone any modification, which is the antigen of type O blood. A blood group system, such as the ABO blood group system, is a purely genetic characterization that enables accurate red blood cell surface antigen prediction, known as blood group prediction, for individuals of unknown blood type using a known variant-phenotype database. This is extremely important for patients with multiple blood ...
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IPC IPC(8): G16B20/20G16B30/00G16B50/00G16B5/00
Inventor 杨焕杰马玉婷张智霖仝欣张涛
Owner SHENZHEN HUADA GENE INST