@article {111,
	title = {Evaluation of the VISAGE Basic Tool for Appearance and Ancestry Prediction Using PowerSeq Chemistry on the MiSeq FGx System.},
	journal = {Genes (Basel)},
	volume = {11},
	year = {2020},
	month = {2020 06 26},
	abstract = {<p>The study of DNA to predict externally visible characteristics (EVCs) and the biogeographical ancestry (BGA) from unknown samples is gaining relevance in forensic genetics. Technical developments in Massively Parallel Sequencing (MPS) enable the simultaneous analysis of hundreds of DNA markers, which improves successful Forensic DNA Phenotyping (FDP). The EU-funded VISAGE (VISible Attributes through GEnomics) Consortium has developed various targeted MPS-based lab tools to apply FDP in routine forensic analyses. Here, we present an evaluation of the VISAGE Basic tool for appearance and ancestry prediction based on PowerSeq chemistry (Promega) on a MiSeq FGx System (Illumina). The panel consists of 153 single nucleotide polymorphisms (SNPs) that provide information about EVCs (41 SNPs for eye, hair and skin color from HIrisPlex-S) and continental BGA (115 SNPs; three overlap with the EVCs SNP set). The assay was evaluated for sensitivity, repeatability and genotyping concordance, as well as its performance with casework-type samples. This targeted MPS assay provided complete genotypes at all 153 SNPs down to 125 pg of input DNA and 99.67\% correct genotypes at 50 pg. It was robust in terms of repeatability and concordance and provided useful results with casework-type samples. The results suggest that this MPS assay is a useful tool for basic appearance and ancestry prediction in forensic genetics for users interested in applying PowerSeq chemistry and MiSeq for this purpose.</p>},
	keywords = {DNA Fingerprinting, Eye Color, Forensic Genetics, Genetic Markers, Genotype, Hair Color, High-Throughput Nucleotide Sequencing, Humans, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Skin Pigmentation, Software},
	issn = {2073-4425},
	doi = {10.3390/genes11060708},
	author = {Palencia-Madrid, Leire and Xavier, Catarina and de la Puente, Mar{\'\i}a and Hohoff, Carsten and Phillips, Christopher and Kayser, Manfred and Parson, Walther}
}
@article {19,
	title = {Genome-wide profiling of heritable and de novo STR variations.},
	journal = {Nat Methods},
	volume = {14},
	year = {2017},
	month = {2017 Jun},
	pages = {590-592},
	abstract = {<p>Short tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic casework. However, it has proven problematic to genotype STRs from high-throughput sequencing data. Here, we describe HipSTR, a novel haplotype-based method for robustly genotyping and phasing STRs from Illumina sequencing data, and we report a genome-wide analysis and validation of de novo STR mutations. HipSTR is freely available at https://hipstr-tool.github.io/HipSTR.</p>},
	keywords = {Algorithms, Chromosome Mapping, DNA Fingerprinting, Genetic Predisposition to Disease, Genetic Variation, Genome, Human, High-Throughput Nucleotide Sequencing, Humans, Microsatellite Repeats, Sequence Alignment, Sequence Analysis, DNA, Software},
	issn = {1548-7105},
	doi = {10.1038/nmeth.4267},
	author = {Willems, Thomas and Zielinski, Dina and Yuan, Jie and Gordon, Assaf and Gymrek, Melissa and Erlich, Yaniv}
}
