Method for conducting SNP-haplotype analysis by means of multiplex PCR technology
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A haplotype analysis and haplotype technology, applied in the field of molecular biology and bioinformatics, can solve the problems of long distance, easy recombination, high detection cost and long cycle.
Pending Publication Date: 2016-03-09
YIKON GENOMICS SHANGHAI CO LTD +1
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However, each of the above-mentioned technologies has certain defects. For example, the multiplex fluorescent PCR technology uses multiplex PCR combined with fluorescent probes to detect STR typing. Due to fewer STR markers and longer distances and easy recombination, there are fewer available STR sites in practice. The cost is high, so this technology cannot be used for batch detection; compared with the method of capturing SNPs by chips and probes, the cost is relatively high and the cycle is relatively long
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Embodiment 1
[0050] The SNP-haplotype analysis was carried out according to the above steps, and the specific results are shown in Table 1. An autosomal recessive genetic disease model, the causative gene is A. In this family, both father and mother are carriers, carrying Mutation1 and Mutation2 mutation sites respectively.
[0051] After analysis, for A-SNP1, the paternal allelic type is G / G, the maternal allelic type is G / A, and the affected individual's allelic type is G / A, indicating that the base of this site in the maternal A is linked with the pathogenic site in the same haplotype and is inherited to the affected individual. This SNP site is a distinguishing SNP; the alleles of embryos 2, 4 and 6 all have base A, indicating that this All three embryos carried maternal pathogenic loci. According to the principle of Mendelian inheritance, determine whether the embryo carries the disease-causing gene locus: Embryos 1, 3, and 5 are carriers of the paternal mutation, embryos 2 and 6 ar...
Embodiment 2
[0053] The SNP-haplotype analysis was carried out according to the above steps, and the specific results are shown in Table 2. An X-linked recessive genetic disease model, the causative gene is B. In this family, the female parent is a carrier of the B gene Mutation3 mutation site. According to the above analysis, it can be seen that embryo 2 does not carry the pathogenic mutation, and embryos 1 and 3 are carriers of the pathogenic mutation.
[0054] Table 1A Partial SNP genotypes in the gene region
[0055]
[0056]
[0057] Table 2B Partial SNP genotypes in the gene region
[0058]
[0059]
[0060] Notes:
[0061] 1. "_" in the table indicates that the corresponding SNP data cannot be obtained (no data coverage or low depth);
[0063] 3. The haplotype 1 of the father and mother in Table 1 indicates the haplotype of the pathogenic mutation, and the maternal haplotype 1 in Table 2 indicates the haplotype...
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Abstract
The invention discloses a method for conducting SNP-haplotype analysis by means of a multiplex PCR technology. Designed primers are combined into one tube for single primer amplification when synthesis is conducted, and meanwhile whole genome amplification is completed through an MALBAC technology; when multiplex PCR amplification is conducted, a touch down PCR amplification program is adopted, high-throughput sequencing and reasonable data analysis are combined, only one set of SNP detection is needed, different schemes do not need to be designed according to different objects, the working cycle is shortened, and the cost is reduced. In addition, according to the method for conducting the SNP-haplotype analysis by means of the multiplex PCR technology, family and embryonic genome SNP information is captured, embryo SNP information can be effectively and accurately determined, SNP-haplotype analysis is conducted to determine whether an embryo carries mutation sites of a genetic gene or not, and the defects that in the prior art, the technological cost is high, the cycle is long, and the application range is small are effectively overcome.
Description
technical field [0001] The invention relates to the fields of molecular biology and bioinformatics, in particular to a method for SNP-haplotype analysis using multiplex PCR technology. Background technique [0002] According to statistics from the World Health Organization in 2014, birth defects affect about 1 in 33 babies, causing about 3.2 million cases of birth defect-related disabilities each year, and an estimated 270,000 newborns die of birth defects each year. Birth defects can be caused by genetic, infectious or environmental factors. Many birth defects are preventable, such as single-gene genetic diseases. Adequate pre-pregnancy and pre-natal screening is the key. [0003] Preimplantation diagnosis (PGD) technology refers to the preimplantation biopsy and genetic analysis of embryos from patients with genetic risks in the process of in vitro fertilization, so as to select embryos without genetic diseases for implantation into the uterine cavity, so as to obtain norm...
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