11 Million SNP Reference Profiles for Identity Searching Across Ethnicities, Kinship, and Admixture

High Throughput ◽

Family Relationships ◽

In Silico ◽

High Throughput Sequencing ◽

Genetic Data ◽

Mixture Analysis ◽

Single Nucleotide ◽

Public Repositories

AbstractHigh throughput sequencing (HTS) of single nucleotide polymorphisms (SNPs) provides additional applications for DNA forensics including identification, mixture analysis, kinship prediction, and biogeographic ancestry prediction. Public repositories of human genetic data are being rapidly generated and released, but the majorities of these samples are de-identified to protect privacy, and have little or no individual metadata such as appearance (photos), ethnicity, relatives, etc. A reference in silico dataset has been generated to enable development and testing of new DNA forensics algorithms. This dataset provides 11 million SNP profiles for individuals with defined ethnicities and family relationships spanning eight generations with admixture for a panel with 39,108 SNPs.

SNP Identity Searching Across Ethnicities, Kinship, and Admixture

10.1101/574566 ◽

2019 ◽

Author(s):

Brian S. Helfer ◽

Darrell O. Ricke

Keyword(s):

Single Nucleotide Polymorphism ◽

High Throughput ◽

In Silico ◽

High Throughput Sequencing ◽

Mixture Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Search Results ◽

Comparison Results ◽

Snp Panels

ABSTRACTAdvances in high throughput sequencing (HTS) enables application of single nucleotide polymorphism (SNP) panels for identification and mixture analysis. Large reference sets of characterized individuals with documented relationships, ethnicities, and admixture are not yet available for characterizing the impacts of different ethnicities, kinships, and admixture on identification and mixture search results for relatives and unrelated individuals. Models for the expected results are presented with comparison results on two in silico datasets spanning four ethnicities, extended kinship relationships, and also admixture between the four ethnicities.

High-throughput genotyping of single-nucleotide polymorphisms inace-1gene of mosquitoes using MALDI-TOF mass spectrometry

Insect Science ◽

10.1111/j.1744-7917.2012.01520.x ◽

2012 ◽

Vol 20 (2) ◽

pp. 167-174 ◽

Cited By ~ 3

Author(s):

Yun Mao ◽

Feng Tan ◽

Shuai-Guo Yan ◽

Guo-Xing Wu ◽

Chuan-Ling Qiao ◽

...

Keyword(s):

Mass Spectrometry ◽

High Throughput ◽

Single Nucleotide ◽

Maldi Tof Mass Spectrometry ◽

Maldi Tof

Impact of single nucleotide polymorphisms in HBB gene causing haemoglobinopathies: in silico analysis

New Biotechnology ◽

10.1016/j.nbt.2009.01.004 ◽

2009 ◽

Vol 25 (4) ◽

pp. 214-219 ◽

Cited By ~ 10

Author(s):

C. George Priya Doss ◽

Sethumadhavan Rao

Keyword(s):

In Silico ◽

In Silico Analysis ◽

Single Nucleotide ◽

Silico Analysis

Prediction of single nucleotide polymorphisms (SNPs) in apolipoprotein E gene and their possible associations with a deleterious effect on the structure and functional properties: an in silico approach

Network Modeling Analysis in Health Informatics and Bioinformatics ◽

10.1007/s13721-018-0178-9 ◽

2018 ◽

Vol 7 (1) ◽

Author(s):

Noor AlHuda Ali A. H. Saeed ◽

Israa Hussein Hamzah ◽

Alaa Naseer Mohammed Ali ◽

Abdulwahab Ali Abuderman

Keyword(s):

Apolipoprotein E ◽

Functional Properties ◽

In Silico ◽

Deleterious Effect ◽

Single Nucleotide ◽

E Gene ◽

Apolipoprotein E Gene

Investigation of Genetic Relationships within Miscanthus using SNP Markers Identified using SLAF-Seq

10.21203/rs.3.rs-152687/v1 ◽

2021 ◽

Author(s):

ZHIYONG Chen ◽

Yancen He ◽

Yasir Iqbal ◽

Yanlan Shi ◽

Hongmei Huang ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Genetic Relationships ◽

Female Parent ◽

Snp Markers ◽

Single Nucleotide ◽

Breeding Programs ◽

Sequencing Method ◽

Specific Locus

Abstract Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.