Haplotype map of chromosome span, and construction method thereof

A construction method and chromosome technology, applied in the field of haplotype map 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, comprehensive sequencing data, and accuracy. high resolution effect

Active Publication Date: 2015-11-11
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 an

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  • Haplotype map of chromosome span, and construction method thereof
  • Haplotype map of chromosome span, and construction method thereof
  • Haplotype map of chromosome span, and construction method thereof

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

[0029] Name explanation:

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

[0031] Read: In high-throughput sequencing, the length of the sequence to be tested can be read every time the sequencing instrument reads, and the sequence of a short fragment obtained each time is called a read.

[0032] Paired-end reads (PEreads): Paired-end sequencing sequences refer to sequencing inserts in a constructed sequencing library from both ends to obtain sequencing sequences that include sequence information on both ends of the inserts.

[0033] Single-end reads: refers to the sequencing sequence at one end of the paired-end sequencing sequence.

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Abstract

The invention provides a haplotype map of a chromosome span, and a construction method thereof. The construction method comprises the following steps: sequencing a sequencing library which contains the genome crosslinking locus of a sample to be tested to obtain PE (Paired-End) reads; carrying out first-time comparison on the PE reads and a sequence on a reference genome to obtain a first comparison result; according to the first comparison result, constructing a consensus sequence of the PE reads, and obtaining a high-quality SNP (Single Nucleotide Polymorphisms) locus; according to the obtained high-quality SNP locus, screening each reads, and extracting the reads which at least contains two heterozygous SNP loca; and utilizing the heterozygous SNP loca to construct the haplotype map of the chromosome span. The sequencing data of the crosslinking locus based on a whole genome is more comprehensive, and therefore, the obtained haplotype map of the chromosome span is high in accuracy and resolution and has the advantage of being wide in species adaptation range.

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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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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