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Method for detecting genomic variations using circularised mate-pair library and shotgun sequencing

A genome and sequencing technology, applied in biochemical equipment and methods, microbial determination/inspection, etc., can solve problems such as time consumption

Inactive Publication Date: 2018-04-06
JACKSON LAB THE
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, it will involve multiple experimental and analytical pipelines, which will be time and resource consuming

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  • Method for detecting genomic variations using circularised mate-pair library and shotgun sequencing
  • Method for detecting genomic variations using circularised mate-pair library and shotgun sequencing
  • Method for detecting genomic variations using circularised mate-pair library and shotgun sequencing

Examples

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Embodiment 1

[0186] Using the method of the present invention, identified various genomic variations in autistic patient P46107, and listed the characterized genomic variations based on the size in the table below. "DNA-PET" stands for MP sequencing data.

[0187] Specifically, patient samples were obtained from hospitals, and samples were anonymized prior to sequencing and analysis. Genomic DNA was extracted from the samples using the AllPrep DNA / RNA Mini Kit (Qiagen) according to the manufacturer's instructions. DNA sequencing libraries were prepared using the methods of the invention as described above. Briefly, genomic DNA samples were simultaneously fragmented and labeled with paired transposomes configured using Illumina to bind adapters. After tagging, short single-stranded sequence gaps in the tagged DNA are filled by a strand displacement reaction using a polymerase. Genomic DNA fragments of 6-8kb were selected by Sage PippinPrep. The size-selected fragments were then circular...

Embodiment 2

[0192] Using the methods of the present invention, various genomic variants were identified in five autistic patients, and the results were compared to those identified from the same patients using current standard assays based on array CGH and exome sequencing.

[0193] The comparison shows that for each CNV structural variant identified by the traditional aCGH assay, there is a perfect match identified by the method of the present invention. However, the methods of the present invention identified many more genomic variations that were not identified by CGH, thus representing an opportunity to identify many more novel variants using the methods of the present invention.

[0194] For example, for patient DBS0005 (autism spectrum disorder), Postpartum high-density SNP array testing revealed a 383.4 kb deletion in the chromosomal region of 5q23.3, including the LYRM7 and HINT1 genes. A 383.591 bp deletion in the same chromosomal region (Chr5: 130140673-130520365) was identifi...

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Abstract

The invention described herein provides methods and systems for comprehensive genomic analysis that enables the detection of a broad range of genomic variations, INC.luding single nucleotide polymorphisms (SNPs), small insertions or deletions (indels), Tandem Base Mutations (TBM), copy number variations (CNVs), structural variations (SVs), and combination thereof, in a single assay. The method employs circularising genomic DNA fragments with a ligated tag sequence, optionally by tagmentation with a transposase, fragmentation by shotgun fragmentation and sequencing of both mate-pair fragments and shotgun fragments and determining genomic variations based on both shotgun and mate-pair fragments. The invention can be used, for example, to analyze the complicated underlying genomic defects indiseases and conditions such as Autism spectrum disorders (ASD), cancers, Alzheimer's disease, and other neurological disorders.

Description

[0001] References to related applications [0002] This international patent application claims the benefit of the filing date of U.S. Provisional Patent Application No. 62 / 142,088, filed April 2, 2015, the entire contents of which are incorporated herein by reference. Background technique [0003] Genetic variation is known to occur in populations at all levels from single nucleotide substitutions to large scale structural variations. Many genomic variants represent normal phenotypic variation for diverse human traits, while some variants are associated with disease. However, the detection and characterization of disease-associated genetic variants is technically challenging, especially in complex disorders including autism. [0004] Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by difficulties or deficits in communication and social interaction. According to the CDC, ASD diagnosis rates have risen dramatically since 2000, from about 1 in 15...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6869
CPCC12Q1/6869C12Q2523/301C12Q2523/303C12Q2535/122C12Q2521/501C12Q2525/191C12Q1/6806
Inventor 阮一骏
Owner JACKSON LAB THE