ELIXIR and Toxicology: a community in development

Martens,Marvin; Stierum,Rob; Schymanski,EmmaL.; Evelo,ChrisT.; Aalizadeh,Reza; Aladjov,Hristo; Arturi,Kasia; Audouze,Karine; Babica,Pavel; Berka,Karel; Bessems,Jos; Blaha,Ludek; Bolton,EvanE.; Cases,Montserrat; Damalas,DimitriosΕ; Dave,Kirtan; Dilger,Marco; Exner,Thomas; Geerke,DaanP.; Grafström,Roland; Gray,Alasdair; Hancock,JohnM.; Hollert,Henner; Jeliazkova,Nina; Jennen,Danyel; Jourdan,Fabien; Kahlem,Pascal; Klanova,Jana; Kleinjans,Jos; Kondic,Todor; Kone,Boï; Lynch,Iseult; Maran,Uko; MartinezCuesta,Sergio; Ménager,Hervé; Neumann,Steffen; Nymark,Penny; Oberacher,Herbert; Ramirez,Noelia; Remy,Sylvie; Rocca-Serra,Philippe; Salek,RezaM.; Sallach,Brett; Sansone,Susanna-Assunta; Sanz,Ferran; Sarimveis,Haralambos; Sarntivijai,Sirarat; Schulze,Tobias; Slobodnik,Jaroslav; Spjuth,Ola; Tedds,Jonathan; Thomaidis,Nikolaos; Weber,RalfJ.M.; vanWesten,GerardJ.P.; Wheelock,CraigE.; Williams,AntonyJ.; Witters,Hilda; Zdrazil,Barbara; Županič,Anže; Willighagen,EgonL.; Toxicology has been an active research field for many decades, with academic, industrial and government involvement. [Read More]

Epigenetic age prediction in semen - marker selection and model development

Pisarek,A.; Pospiech,E.; Heidegger,A.; Xavier,C.; Papiez,A.; Piniewska-Rog,D.; Kalamara,V.; Potabattula,R.; Bochenek,M.; Sikora-Polaczek,M.; Macur,A.; Wozniak,A.; Janeczko,J.; Phillips,C.; Haaf,T.; Polanska,J.; Parson,W.; Kayser,M.; Branicki,W.; DNA methylation analysis is becoming increasingly useful in biomedical research and forensic practice. The discovery of differentially methylated sites (DMSs) that continuously change over an individual’s lifetime has led to breakthroughs in molecular age estimation. Although semen samples are often used in forensic DNA analysis, previous epigenetic age prediction studies mainly focused on somatic cell types. [Read More]

Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age

Xavier,C.; Eduardoff,M.; Bertoglio,B.; Amory,C.; Berger,C.; Casas-Vargas,A.; Pallua,J.; Parson,W.; The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. [Read More]

Evidence for multi-copy Mega-NUMTs in the human genome

Lutz-Bonengel,S.; Niederstätter,H.; Naue,J.; Koziel,R.; Yang,F.; Sanger,T.; Huber,G.; Berger,C.; Pflugradt,R.; Strobl,C.; Xavier,C.; Volleth,M.; Weiss,S.C.; Irwin,J.A.; Romsos,E.L.; Vallone,P.M.; Ratzinger,G.; Schmuth,M.; Jansen-Durr,P.; Liehr,T.; Lichter,P.; Parsons,T.J.; Pollak,S.; Parson,W.; The maternal mode of mitochondrial DNA (mtDNA) inheritance is central to human genetics. Recently, evidence for bi-parental inheritance of mtDNA was claimed for individuals of three pedigrees that suffered mitochondrial disorders. We sequenced mtDNA using both direct Sanger and Massively Parallel Sequencing in several tissues of eleven maternally related and other affiliated healthy individuals of a family pedigree and observed mixed mitotypes in eight individuals. [Read More]

Exploring STR sequencing for forensic DNA intelligence databasing using the Austrian National DNA Database as an example

Hölzl-Müller,P.; Bodner,M.; Berger,B.; Parson,W.; Here, we present the results from a population study that evaluated the performance of massively parallel sequencing (MPS) of short tandem repeats (STRs) with a particular focus on DNA intelligence databasing purposes. To meet this objective, 247 randomly selected reference samples, earlier being processed with conventional capillary electrophoretic (CE) STR sizing from the Austrian National DNA Database, were reanalyzed with the PowerSeq 46Y kit (Promega). This sample set provides MPS-based population data valid for the Austrian population to increase the body of sequence-based STR variation. [Read More]