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A method for population origin inference based on hair shaft proteome nssnp

A technology of people and matter, applied in the field of biology

Active Publication Date: 2022-06-28
INST OF FORENSIC SCI OF MIN OF PUBLIC SECURITY
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Currently, very few studies have performed population inference using nsSNPs in exomes

Method used

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  • A method for population origin inference based on hair shaft proteome nssnp
  • A method for population origin inference based on hair shaft proteome nssnp
  • A method for population origin inference based on hair shaft proteome nssnp

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0040] Example 1. Acquisition of nsSNPs in the hair shaft proteome

[0041] 1. Extraction of hair shaft proteome and detection of proteome by mass spectrometry

[0042] 1. Collection of samples

[0043] The hair shaft samples of 104 Chinese Han and 105 unrelated Uyghur individuals and 209 corresponding oral swabs were collected. The hair shaft samples were cut from the head and tail of the hair to ensure that there were no hair follicles and hair tails. Each hair shaft The sample is 2cm long (two homologous hair shafts are used when the length of a single hair is less than 2cm).

[0044] 2. Hair shaft proteome extraction

[0045] To extract the hair shaft proteome from the hair shaft sample, the specific steps are as follows: wash the hair shaft twice with 10% (volume fraction) methanol and water for 1-2 hours each time, then take out the washed hair shaft and chop it to about 1 -2mm. 100 μL of protein treatment solution (1M urea, 50mM NH) was added to each part of the min...

Embodiment 2

[0080] Example 2. Application of nsSNP site combination (527) in population inference

[0081] 1. Evaluation of nsSNP loci combinations (527) based on 1000 Genomes data

[0082] 1. Principal Component Analysis (PCA)

[0083] Principal Component Analysis (PCA) was performed using Rv3.2.3 software for 27 populations and 2504 samples in the three regions of Africa, East Asia and Europe in the 1000 Genomes Database in Table 1 using 527 nsSNP site combinations. Principal component analysis is used to reduce the dimension of the data, and multiple measured variables with strong correlation are integrated into a small number of comprehensive variables.

[0084] The result is as Figure 4 shown. As can be seen from the figure: Principal Component 1 (PC1) and Principal Component 2 (PC2) explain the difference of 60.5. The combination of 527 nsSNP loci can effectively distinguish the three populations of Africa, East Asia and Europe.

[0085] 2. Cluster analysis

[0086] A total o...

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Abstract

The invention discloses a method for inferring the origin of a human population based on the hair shaft proteome nsSNP. In the present invention, the hair shaft samples of 104 Chinese Han samples and 105 Chinese Uyghur samples were selected to extract the hair shaft proteome, and the hair shaft proteome was detected by mass spectrometry, and 772 specific polypeptide sequences containing SAP were obtained by screening, corresponding to 703 SAP loci, and associate the SAP loci with the SNP loci in the 1000 Genomes database to obtain 527 nsSNP locus combinations. It is proved by experiments that the combination of nsSNP sites provided by the present invention can be used for inference of the three major populations of Africa, East Asia and Europe.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a method for inferring population origin based on the nsSNP of the hair shaft proteome. Background technique [0002] With the development and progress of forensic DNA testing technology, common blood / spots, saliva / spots, semen / spots, exfoliated cells, hair with follicles, and even bones can obtain STR typing. However, the hair shaft is composed of keratinocytes, and the nuclear DNA content is very low and severely degraded. Although it has also been reported that partial STR typing can be obtained by using a low amplification system, increasing the number of cycles and multiple parallel amplifications, due to its accurate poor performance and stability and were not used in case testing. At present, the inspection method for hair shaft is to detect the base difference in the hypervariable region of mitochondrial DNA by sequencing, which has the disadvantages of low recognition rate ...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6888C12N15/11
CPCC12Q1/6888C12Q2600/156C12Q2600/166
Inventor 李彩霞丰蕾江丽季安全王桂强
Owner INST OF FORENSIC SCI OF MIN OF PUBLIC SECURITY
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