Haplotype map of chromosome span and its construction method

A construction method and haplotype technology, applied in the field of chromosome-span haplotype map and its construction, can solve the problems affecting the accuracy and comprehensiveness of SNP detection, error amplification, long time, etc., and achieve a wide range of species adaptation, The effects of comprehensive sequencing data, high accuracy and high resolution

Active Publication Date: 2018-02-02
天津诺禾医学检验所有限公司
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Problems solved by technology

Some errors will be introduced during the amplification process, and the errors will be further amplified with the continuous amplification
Moreover, the base preference in the amplification process will affect the accuracy and comprehensiveness of SNP detection, thus causing certain errors in the results of the final haplotype construction.
In addition, the whole experimental process of the above method takes a long time, usually more than 3 months

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  • Haplotype map of chromosome span and its construction method
  • Haplotype map of chromosome span and its construction method
  • Haplotype map of chromosome span and its construction method

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Embodiment Construction

[0028] It should be noted that, in the case of no conflict, the embodiments in the present application and the features in the embodiments can be combined with each other. The present invention will be described in detail below in conjunction with examples.

[0029] Name explanation:

[0030]Haplotype diagram: A haplotype diagram refers to a linear arrangement of genotypes at multiple loci that are co-inherited on the same chromosome.

[0031] Read: refers to the length of the sequence to be tested that can be read by the sequencing instrument each time during high-throughput sequencing, and then a short fragment sequence obtained by each read is called a read.

[0032] Paired-end reads (PE reads): Paired-end sequencing sequences refer to sequencing the insert fragments in the constructed sequencing library from both ends to obtain sequence information including sequence information at both ends of the insert fragments.

[0033] Single-end reads: Refers to the sequencing seq...

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Abstract

The invention provides a haplotype map of chromosome span and a construction method thereof. The construction method includes sequencing the sequencing library containing the cross-linking sites of the genome of the sample to be tested to obtain PE reads; comparing the PE reads with the sequence on the reference genome for the first time to obtain the first comparison result; according to the first Construct the consensus sequence of PE reads by comparing the results to obtain high-quality SNP sites; screen each read according to the obtained high-quality SNP sites, and extract reads containing at least 2 heterozygous SNP sites ; and use heterozygous SNP loci to construct a haplotype map of chromosome span. The sequencing data of cross-linking sites based on the whole genome is more comprehensive, so the accuracy and resolution of the obtained haplotype map of the chromosome span are very high, and it has the advantage of a wide range of species adaptation.

Description

technical field [0001] The invention relates to the field of haplotype map construction, in particular to a chromosome-span haplotype map and a construction method thereof. Background technique [0002] SNP refers to a DNA sequence polymorphism caused by a single nucleotide variation at the chromosomal genome level. A group of SNP alleles located on a chromosome or in a certain region is called a haplotype. Haplotype is the abbreviation of haploid type, which refers to the combination of alleles at multiple loci that are co-inherited on the same chromosome. A haplotype can even refer to at least two loci or an entire chromosome, according to the amount of genetic recombination that occurs at a given locus. High-quality haplotypes are of great value in the evolutionary history of species and association analysis of phenotypic traits. [0003] At present, the methods used in the construction of haplotypes in China are mainly based on long fragment sequences (long fragment s...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/18C12N15/11
Inventor 赵洪卫
Owner 天津诺禾医学检验所有限公司
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