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Variant calls for multi-sample variation maps

A mutation, variant technology, applied in the field of processing information related to the human genome, which can solve problems such as insufficient compensation for allelic bias and incompatibility

Pending Publication Date: 2022-05-03
KONINKLJIJKE PHILIPS NV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

Furthermore, graph-based methods do not adequately compensate for allelic bias, which makes them unsuitable for many applications

Method used

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  • Variant calls for multi-sample variation maps
  • Variant calls for multi-sample variation maps
  • Variant calls for multi-sample variation maps

Examples

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[0026] It should be understood that the drawings are only schematic and not drawn to scale. It should also be understood that the same reference numbers are used throughout the drawings to indicate the same or similar parts.

[0027] The description and drawings illustrate the principles of various example embodiments. It will be appreciated that those skilled in the art will be able to devise various arrangements that, although not explicitly described or shown herein, embody the principles of the invention and are included within the scope of the invention. Furthermore, all examples described herein are primarily intended specifically for teaching purposes to aid the reader in understanding the principles of the invention and concepts provided by the inventor(s) to advance the art, and all examples do not should be construed as limited to such specific stated examples and conditions. Furthermore, as used herein, the term "or" refers to a non-exclusive or (ie, and / or), unle...

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Abstract

A method for invoking variants in genetic data includes ranking nodes in a graph-based reference genome, assigning identification information to the ranked nodes, assigning depth values to respective ones of the ranked nodes, determining a reference genome path and one or more variant paths, and determining one or more variants in the graph-based reference genome based on the depth values assigned to nodes on the one or more variation paths.

Description

technical field [0001] The present disclosure relates generally to bioinformatics, and more particularly, but not exclusively, to processing information related to the human genome. Background technique [0002] Various methods have been proposed to transform raw genomic data. One approach relies on mapping reads to a linear reference human genome using a de facto reference genome. However, de facto reference genomes represent only a tiny subset of the human population and thus do not reliably reflect the enormous allelic diversity that exists. This leads to so-called allelic bias, where the normal (eg healthy) deviation from the reference genome is not represented. This results in poor read alignment accuracy for those samples that are not similar. [0003] Another approach proposes transforming raw genomic data by sequencing a sample and then comparing it to a graph-based reference genome. Graph-based reference genomes can incorporate more human genomes into a single s...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/10G16B30/20
CPCG16B30/10G16B30/20G16H50/30G16B20/20
Inventor Z·艾哈迈德A·R·曼科维奇张贻谦
Owner KONINKLJIJKE PHILIPS NV