Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences

Dür,A.; Huber,N.; Parson,W.; In this paper, we present a new algorithm for alignment and haplogroup estimation of mitochondrial DNA (mtDNA) sequences. Based on 26,011 vetted full mitogenome sequences, we refined the 5435 original haplogroup motifs of Phylotree Build 17 without changing the haplogroup nomenclature. We adapted 430 motifs (about 8%) and added 966 motifs for yet undetermined subclades. In summary, this led to an 18% increase of haplogroup defining motifs for full mitogenomes and a 30% increase for the mtDNA control region that is of interest for a variety of scientific disciplines, such as medical, population and forensic genetics. [Read More]

Genetic and phylogeographic evidence for Jewish Holocaust victims at the Sobibor death camp

Diepenbroek,M.; Amory,C.; Niederstätter,H.; Zimmermann,B.; Szargut,M.; Zielinska,G.; Dür,A.; Teul,I.; Mazurek,W.; Persak,K.; Ossowski,A.; Parson,W.; Six million Jews were killed by Nazi Germany and its collaborators during World War II. Archaeological excavations in the area of the death camp in Sobibor, Poland, revealed ten sets of human skeletal remains presumptively assigned to Polish victims of the totalitarian regimes. However, their genetic analyses indicate that the remains are of Ashkenazi Jews murdered as part of the mass extermination of European Jews by the Nazi regime and not of otherwise hypothesised non-Jewish partisan combatants. [Read More]

Impact of excessive alcohol abuse on age prediction using the VISAGE enhanced tool for epigenetic age estimation in blood

Piniewska-Rog,D.; Heidegger,A.; Pospiech,E.; Xavier,C.; Pisarek,A.; Jarosz,A.; Wozniak,A.; Wojtas,M.; Phillips,C.; Kayser,M.; Parson,W.; Branicki,W.; VISAGEConsortium; DNA methylation-based clocks provide the most accurate age estimates with practical implications for clinical and forensic genetics. However, the effects of external factors that may influence the estimates are poorly studied. Here, we evaluated the effect of alcohol consumption on epigenetic age prediction in a cohort of extreme alcohol abusers. Blood samples from deceased alcohol abusers and age- and sex-matched controls were analyzed using the VISAGE enhanced tool for age prediction from somatic tissues that enables examination of 44 CpGs within eight age markers. [Read More]

Interpreting NUMTs in forensic genetics: Seeing the forest for the trees

Marshall,C.; Parson,W.; Nuclear mitochondrial DNA (mtDNA) segments (NUMTs) were discovered shortly after sequencing the first human mitochondrial genome. They have earlier been considered to represent archaic elements of ancient insertion events, but modern sequencing technologies and growing databases of mtDNA and NUMT sequences confirm that they are abundant and some of them phylogenetically young. Here, we build upon mtDNA/NUMT review articles published in the mid 2010s and focus on the distinction of NUMTs and other artefacts that can be observed in aligned sequence reads, such as mixtures (contamination), point heteroplasmy, sequencing error and cytosine deamination. [Read More]

Kombinierter Suizid: Methode nach Kusch und Kopfschuss – ein Fallbericht

Weber,A.; Rabl,W.; Die gleichzeitige Anwendung mehrerer Methoden beim Suizid wird als „kombinierter Suizid“ bezeichnet. Vorgestellt wird ein Fall, bei dem zunächst alles auf einen Suizid mittels Schusswaffe hindeutet. Die chemisch-toxikologische Analyse ergibt den Nachweis von Benzodiazepinen und einer potenziell letalen Chloroquinkonzentration im Blutserum, was als Methode nach Kusch bezeichnet wird und mit einer Handlungsunfähigkeit einhergehen kann. Die Kombination von Chloroquin mit Diazepam kann aber, in Abhängigkeit von der Dosierung, auch dazu führen, dass die Handlungsfähigkeit erhalten bleibt und auch hohe Chloroquinkonzentrationen überlebt werden. [Read More]