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Questions and Answers
What was the concentration of DNA used as input for SNP microarray analysis?
What was the concentration of DNA used as input for SNP microarray analysis?
50 ng/µL
Which platform was used to process the SNP array data?
Which platform was used to process the SNP array data?
Genome Studio 2.0
How many high-quality DNA samples were used to create a pre-existing cluster file?
How many high-quality DNA samples were used to create a pre-existing cluster file?
4405
What was the total number of SNPs left for analysis after removing variants with missing genotypes?
What was the total number of SNPs left for analysis after removing variants with missing genotypes?
What reference genome was used to set the reference alleles in PLINK v2.00?
What reference genome was used to set the reference alleles in PLINK v2.00?
Which tool was used to overlap the identity SNP lists obtained from scATAC-seq data with the WES and GSA reference data?
Which tool was used to overlap the identity SNP lists obtained from scATAC-seq data with the WES and GSA reference data?
Why was individual genetic identification not possible from in-silico mixture?
Why was individual genetic identification not possible from in-silico mixture?
How were the correct individual-specific mixture deconvolutions assessed?
How were the correct individual-specific mixture deconvolutions assessed?
What specific technique was used in this study to perform non-targeted single-cell DNA sequencing (scDNA-seq)?
What specific technique was used in this study to perform non-targeted single-cell DNA sequencing (scDNA-seq)?
What is the significance of separating cells from biological mixtures in forensic science?
What is the significance of separating cells from biological mixtures in forensic science?
What was the complexity of the blood mixtures tested in this study?
What was the complexity of the blood mixtures tested in this study?
What are the two main methods of single-cell DNA analysis mentioned in the text?
What are the two main methods of single-cell DNA analysis mentioned in the text?
What key information was successfully extracted from the deconvoluted mixture samples?
What key information was successfully extracted from the deconvoluted mixture samples?
Explain the advantage of scDNA-seq over scRNA-seq in terms of SNP detection.
Explain the advantage of scDNA-seq over scRNA-seq in terms of SNP detection.
Describe the in-silico experiments conducted to further test the efficacy of the approach.
Describe the in-silico experiments conducted to further test the efficacy of the approach.
What is the potential application of compound markers (two or more autosomal SNPs) in forensic genetics?
What is the potential application of compound markers (two or more autosomal SNPs) in forensic genetics?
What is the significance of the in-silico results regarding mixture complexity?
What is the significance of the in-silico results regarding mixture complexity?
What is a major limitation of using compound markers for forensic purposes?
What is a major limitation of using compound markers for forensic purposes?
What data analysis pipeline was used in this study to deconvolute the single-cell DNA sequencing data?
What data analysis pipeline was used in this study to deconvolute the single-cell DNA sequencing data?
What is the overall conclusion of this study regarding the use of scDNA-seq, specifically scATAC-seq, in forensic applications?
What is the overall conclusion of this study regarding the use of scDNA-seq, specifically scATAC-seq, in forensic applications?
What is the significance of the date "Received 22 August 2023" in the context of the research article?
What is the significance of the date "Received 22 August 2023" in the context of the research article?
Explain the potential impact of this study on forensic science.
Explain the potential impact of this study on forensic science.
What is the meaning of the CC BY license mentioned in the article?
What is the meaning of the CC BY license mentioned in the article?
Identify the two departments at Erasmus MC University Medical Center Rotterdam that are associated with the authors of the research article.
Identify the two departments at Erasmus MC University Medical Center Rotterdam that are associated with the authors of the research article.
How many single-individual scATAC-seq datasets were used to create a highly complex mixture?
How many single-individual scATAC-seq datasets were used to create a highly complex mixture?
What was the purpose of filtering SNPs using bcftools filter?
What was the purpose of filtering SNPs using bcftools filter?
How many barcodes were randomly selected from each of the 11 datasets?
How many barcodes were randomly selected from each of the 11 datasets?
What was the DeGoulash pipeline used for?
What was the DeGoulash pipeline used for?
How many times was each barcode selection repeated?
How many times was each barcode selection repeated?
What tool was used to extract SNPs from the barcode selection?
What tool was used to extract SNPs from the barcode selection?
What was the purpose of using a scRNA-seq dataset with a mixture of four individuals?
What was the purpose of using a scRNA-seq dataset with a mixture of four individuals?
What was done to the selected reads after they were mixed?
What was done to the selected reads after they were mixed?
What software was used to determine bi-parental bio-geographic ancestry using autosomal ancestry-informative SNPs?
What software was used to determine bi-parental bio-geographic ancestry using autosomal ancestry-informative SNPs?
How many major populations were used to determine bi-parental bio-geographic ancestry in the 1000 Genomes database?
How many major populations were used to determine bi-parental bio-geographic ancestry in the 1000 Genomes database?
What tool was used to determine chromosome haplogroups from Y-SNP data?
What tool was used to determine chromosome haplogroups from Y-SNP data?
How was paternal biogeographic ancestry inferred from Y haplogroups?
How was paternal biogeographic ancestry inferred from Y haplogroups?
What database was used to determine MtDNA haplogroups from mtDNA SNP data?
What database was used to determine MtDNA haplogroups from mtDNA SNP data?
How was maternal bio-geographic ancestry inferred from mtDNA haplogroups?
How was maternal bio-geographic ancestry inferred from mtDNA haplogroups?
What tool was used to calculate likelihood ratios (LRs) for individual genetic identification?
What tool was used to calculate likelihood ratios (LRs) for individual genetic identification?
What pipeline was used for mixture deconvolution in the scATAC-seq analysis?
What pipeline was used for mixture deconvolution in the scATAC-seq analysis?
Study Notes
Single-cell DNA Sequencing for Mixture Deconvolution
- Non-targeted single-cell DNA sequencing (scDNA-seq) was applied to address challenges of mixture deconvolution in forensic context.
- scATAC-seq (Assay for Transposase-Accessible Chromatin with sequencing) technique was used to deconvolute complex blood mixtures.
- scATAC-seq, together with De-goulash pipeline, can deconvolute mixtures of five individuals from both sexes with varying biogeographic ancestries.
Mixture Deconvolution and Genetic Characterization
- Correct genetic characterization of biological sex and biogeographic ancestry of each mixture contributor was achieved.
- Individual identity was established by analyzing scATAC-seq data mixtures.
- Successful individual-specific mixture deconvolution was demonstrated for:
- Highly complex mixtures of 11 individuals.
- Balanced mixtures containing as few as 20 cells (10 per each individual).
- Imbalanced mixtures with a ratio as low as 1:80.
Comparison with scRNA-seq
- scDNA-seq detects more SNPs from fewer cells, providing higher sensitivity, which is valuable in forensic genetics.
- scDNA-seq is more suitable for mixture deconvolution and individual identification compared to scRNA-seq.
Methodology
- Autosomal SNPs were used for bi-parental bio-geographic ancestry determination using STRUCTURE and 1000 Genomes database.
- Chromosome haplogroups were determined from Y-SNP data using Y-leaf.
- MtDNA haplogroups were determined from mtDNA SNP data using Haplogrep2.
- Individual genetic identification was calculated using likelihood ratios (LRs) in De-goulash.
In-silico Mixture Preparation and Analysis
- In-silico balanced mixtures were created using publicly available single-individual scATAC-seq datasets.
- Mixture deconvolution was performed using the De-goulash pipeline.
- Individual genetic identification could not be performed from in-silico mixtures due to lack of reference data.
- Correct individual-specific mixture deconvolution was assessed based on barcodes known to belong to one individual or the other.
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Description
Learn about the application of single-cell DNA sequencing in forensic science to deconvolute complex blood mixtures using scATAC-seq technique and De-goulash pipeline.
