Method for filtering modern DNA pollution from ancient DNA data and application thereof

A DNA damage and data technology, applied in the fields of instruments, biological systems, genomics, etc., can solve the problem of non-contamination assessment, and achieve the effect of good universal practicability

Pending Publication Date: 2020-04-07
SHENZHEN BGI AGRI & CYCLE ECONOMIC TECH
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Problems solved by technology

However, in many cases, the pollution cannot be evaluated by the later bioinformatics analysis method, or the evaluation result is greater than 1%. In these cases, some methods must be used to remo

Method used

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  • Method for filtering modern DNA pollution from ancient DNA data and application thereof
  • Method for filtering modern DNA pollution from ancient DNA data and application thereof
  • Method for filtering modern DNA pollution from ancient DNA data and application thereof

Examples

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Embodiment

[0114] In this case, based on the Illumina platform's next-generation sequencing data and bioinformatics analysis methods, a method for obtaining endogenous ancient DNA from paleontological genome sequencing data, that is, a method for filtering modern DNA pollution, was developed. The method in this example, such as figure 1 As shown, it mainly includes the following steps: 1) Acquisition of Illumina next-generation sequencing data; 2) Fastq quality control of original off-machine data; 3) Analysis of ancient DNA damage patterns; 4) Analysis of the advantages and disadvantages of comparison algorithms; Explore the best parameter combination under the comparison algorithm; 6) Filter modern DNA pollution based on C->T and G->A mutations caused by deamination; 7) Filter modern DNA pollution based on fragmentation characteristics caused by depurination; 8) Filter modern human DNA contamination based on ancient DNA length analysis; 9) Statistics and comparison of final results and...

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Abstract

The invention discloses a method for filtering modern DNA pollution from ancient DNA data and an application thereof. The method comprises a step: carrying out paleo-DNA feature filtering on Illuminanext-generation sequencing original data of paleo-DNA, and specifically comprises the following steps: performing modern DNA pollution filtration on Illumina next-generation sequencing original data according to paleo-DNA deamination characteristics, namely reserving at least N C->T mutations at the 5' end and/or at least M C->T mutations at the 3' end caused by paleo-DNA deamination after filtration. According to the method provided by the invention, the Illumina platform data which is widely used at present can be processed; the method employs a comparison algorithm and parameters most suitable for ancient DNA, can enable the pollution rate after filtering to reach 0 under the suitable N and M values, is one of methods with the maximum filtering intensity at present, and lays a foundation for subsequent deep research of the ancient DNA.

Description

technical field [0001] This application relates to the field of ancient DNA detection and analysis, in particular to a method for filtering modern DNA contamination from ancient DNA data and its application. Background technique [0002] Ancient DNA refers to the DNA information of ancient organisms obtained from archaeological materials, paleontological fossils, biological remains, remains, or sediments. It mainly comes from museum specimens, paleontological tissues preserved under special conditions such as amber or permafrost, and forensic samples. Modern DNA is the DNA information of modern biological materials relative to ancient DNA. [0003] With the emergence and development of PCR technology and sequencing technology, ancient DNA research has developed rapidly in the past 30 years. In 1984, Higuchi et al. successfully extracted and amplified 228bp DNA from the ancient muscle tissue of the extinct quagga, marking the first time that humans successfully extracted an...

Claims

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Application Information

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IPC IPC(8): G16B5/00G16B20/30G16B30/00
CPCY02A90/10
Inventor 兰天明徐文浩罗忻郭小森
Owner SHENZHEN BGI AGRI & CYCLE ECONOMIC TECH
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