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Method for assessing genome alignment basis

A genome and reference genome technology, applied in genomics, proteomics, instruments, etc., can solve problems such as slow calculation, not using known mutations, and expensive

Pending Publication Date: 2021-05-07
KONINKLJIJKE PHILIPS NV
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Problems solved by technology

However, not only is this method slow and computationally expensive, but it cannot account for all variation among the many polymorphic positions within a population, and does not take advantage of the known variation of the sequenced genome

Method used

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  • Method for assessing genome alignment basis
  • Method for assessing genome alignment basis
  • Method for assessing genome alignment basis

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Embodiment Construction

[0024] The present disclosure describes various embodiments of systems and methods for analyzing genome sequencing using an alternative reference genome generated from heterozygous alleles identified in the analyzed genome. More generally, Applicants have recognized and appreciated that it would be beneficial to provide methods for reducing alignment bias during alignment of sequencing reads. The system, which may optionally include a sequencing platform, generates or receives sequencing data, including sequencing reads from a genome of interest. The reads are aligned to the reference genome to identify the heterozygous positions, the variant alleles at each heterozygous position, and the ratio of the variant alleles at each heterozygous position. An alternate reference genome is generated using the identified non-reference allelic variants for each of the identified heterozygous positions. The system then aligns the same set of reads to the generated alternative reference ge...

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Abstract

A method (100) for analyzing a target genome, comprising: (i) aligning (120) sequencing data from the target genome to a reference genome; (ii) identifying (130) heterozygous locations, comprising an identification of allele variants and a frequency of each allele, the allele variants comprising both a reference allele variant and a non-reference allele variant; (iii) generating (140) an alternate reference genome, wherein the identified non-reference allele variant for the identified heterozygous locations replaces the reference allele variant in the reference genome; (iv) aligning (150) sequencing data to the alternate reference genome; (v) identifying (160) a frequency of the allele variants at each of the heterozygous locations; (vi) assessing (170) alignment bias at the identified heterozygous locations, comprising comparing the frequency of allele variants from the reference genome alignment to the frequency of allele variants from the alternate genome alignment; and (vii) generating (190) a report comprising the assessment of alignment bias.

Description

technical field [0001] The present disclosure generally relates to methods and systems for assessing alignment bias in next-generation sequencing analyses. Background technique [0002] Many next-generation sequencing methods fragment DNA and generate sequencing reads that are then aligned to a reference genome. This identifies sites of change in the analyzed genome relative to the reference genome. The human genome, for example, includes approximately one million polymorphic positions where there is evidence of two or more alleles across different populations. [0003] All downstream analyzes of the alignment are contingent on the accuracy of the alignment and correct identification of changes within the sequenced genome. However, since a reference genome is that of an individual or a consensus sequence from multiple individuals, it cannot include all variation within a population. Thus, when sequence reads are aligned to the reference genome, reads that match the refere...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/10
CPCG16B30/10G16B20/20G16B45/00
Inventor V·阿格拉瓦尔
Owner KONINKLJIJKE PHILIPS NV
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