WO2019017806A1 - Appareil et procédé d'identification d'haplotypes - Google Patents

Appareil et procédé d'identification d'haplotypes Download PDF

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Publication number
WO2019017806A1
WO2019017806A1 PCT/RU2017/000538 RU2017000538W WO2019017806A1 WO 2019017806 A1 WO2019017806 A1 WO 2019017806A1 RU 2017000538 W RU2017000538 W RU 2017000538W WO 2019017806 A1 WO2019017806 A1 WO 2019017806A1
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WO
WIPO (PCT)
Prior art keywords
allele
sequences
allele sequences
sequence
aggregated
Prior art date
Application number
PCT/RU2017/000538
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English (en)
Inventor
Dmitry Yurievich IGNATOV
Alexander Nikolaevich Filippov
Xuecang ZHANG
Original Assignee
Huawei Technologies Co., Ltd
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Huawei Technologies Co., Ltd filed Critical Huawei Technologies Co., Ltd
Priority to CN201780093397.5A priority Critical patent/CN111344794B/zh
Priority to PCT/RU2017/000538 priority patent/WO2019017806A1/fr
Publication of WO2019017806A1 publication Critical patent/WO2019017806A1/fr

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Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search

Definitions

  • the state-of-the-art MixSIH method has several critical problems as follows: the MixSIH method performs merely single individual haplotyping and cannot be applied to the multiple genomes; the MixSIH method specializes in single individual haplotyping and, thus, cannot produce more than two haplotypes; the MixSIH method uses complex formulas in the process of haplotype inferring and thus cannot provide optimal performances; the MixSIH method does not support de-novo assembly of haplotypes and can lose the quality of haplotyping in the regions with a high frequency of repetitions; the MixSIH method does not take into account the Phred quality of nucleotide identification and thus cannot produce results with best precision.
  • the invention relates to an apparatus and method for identifying haplotypes in a plurality of sample nucleotide sequences. More specifically, a novel apparatus and method are provided for overlapping haplotyping in the regions with a low frequency of repetitions of nucleotide subsequences in order to overcome the drawbacks of conventional haplotyping methods.
  • the present invention offers several significant advantages compared to the prior art: firstly, the invention provides a method of identifying haplotypes in a sample of multiple genomes. In contrast to existing solutions, this method can take into account all available alleles and their possible combinations. Secondly, the invention develops a method for selection of an expected number of haplotypes.
  • Fig. 6 shows a schematic diagram illustrating a method for haplotyping implemented in an apparatus according to an embodiment
  • Fig. 7 shows a schematic diagram illustrating different stages of a method for haplotyping implemented in an apparatus according to an embodiment
  • Fig. 10 shows a diagram illustrating the generation of unique hash codes for nucleotide sequences as implemented in an apparatus according to an embodiment
  • the method of adaptive haplotyping can efficiently perform haplotyping on the regions of a genome with different frequencies of repetitions of nucleotide sequences by generating a unique Hash-Code for quick identification of repetitive subsequences of a predefined length, and hence can determine to apply the novel method, i.e., overlapping haplotyping, which is applicable to the regions with a low frequency of repetitions, or to apply the de-novo assembly method, which is applicable to the regions with a high frequency of repetitions.

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  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

L'invention concerne un appareil (400) permettant d'identifier des haplotypes dans une pluralité de séquences nucléotidiques d'échantillons d'après une séquence nucléotidique de référence. L'appareil (400) comprend une unité de traitement (401) configurée pour générer un ensemble initial de séquences d'allèles en extrayant une pluralité de séquences d'allèles de la pluralité de séquences nucléotidiques d'échantillon d'après la séquence nucléotidique de référence, chaque allèle de chaque séquence de la pluralité de séquences d'allèles étant associé à un site nucléotidique dans la séquence nucléotidique de référence ; générer un premier ensemble agrégé de séquences d'allèles d'après l'ensemble initial de séquences d'allèles en combinant les séquences d'allèles de l'ensemble initial de séquences d'allèles, qui possèdent les mêmes allèles dans des parties de séquence en chevauchement et appartiennent au même haplotype, dans une séquence d'allèles agrégée, le premier ensemble agrégé de séquences d'allèles comprenant les séquences d'allèles agrégées et les séquences d'allèles de l'ensemble initial des séquences d'allèles qui ne sont pas combinées dans une séquence d'allèles agrégée ; générer un second ensemble agrégé de séquences d'allèles d'après le premier ensemble agrégé de séquences d'allèles en concaténant des paires de séquences d'allèles voisines du premier ensemble agrégé de séquences d'allèles, les séquences d'allèles voisines comprenant des allèles dans des sites nucléotidiques voisins, mais pas d'allèles en chevauchement ; et identifier des haplotypes dans la pluralité de séquences nucléotidiques d'échantillon d'après le second ensemble agrégé de séquences d'allèles.
PCT/RU2017/000538 2017-07-20 2017-07-20 Appareil et procédé d'identification d'haplotypes WO2019017806A1 (fr)

Priority Applications (2)

Application Number Priority Date Filing Date Title
CN201780093397.5A CN111344794B (zh) 2017-07-20 2017-07-20 用于鉴定单体型的装置和方法
PCT/RU2017/000538 WO2019017806A1 (fr) 2017-07-20 2017-07-20 Appareil et procédé d'identification d'haplotypes

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
PCT/RU2017/000538 WO2019017806A1 (fr) 2017-07-20 2017-07-20 Appareil et procédé d'identification d'haplotypes

Publications (1)

Publication Number Publication Date
WO2019017806A1 true WO2019017806A1 (fr) 2019-01-24

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CN (1) CN111344794B (fr)
WO (1) WO2019017806A1 (fr)

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CN112289376B (zh) * 2020-10-26 2021-07-06 北京吉因加医学检验实验室有限公司 一种检测体细胞突变的方法及装置

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MATSUMOTO H.; KIRYU H.: "MixSIH: a mixture model for single individual haplotyping", BMC GENOMICS, vol. 14, 2013, pages S5, XP021138646, DOI: doi:10.1186/1471-2164-14-S2-S5
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CN111344794B (zh) 2024-04-23
CN111344794A (zh) 2020-06-26

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