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14. A collaborative exercise on DNA methylation-based age prediction and body fluid typing

Author

Lee, Ji Eun, Lee, Jeong Min, Naue, Jana, Fleckhaus, Jan, Freire-Aradas, Ana, Neubauer, Jacqueline, Pośpiech, Ewelina, McCord, Bruce, Kalamara, Vivian, Gauthier, Quentin, Mills, Carly, Cao, Yijian, Wang, Zheng, Oh, Yu Na, Feng, Lei, Schneider, Peter M., Phillips, Christopher, Haas, Cordula, Pisarek, Aleksandra, Branicki, Wojciech, Podini, Daniele, Vidaki, Athina, Tejero, Nicole Fernandez, Ambroa-Conde, Adrián, Mosquera-Miguel, Ana, Lareu, Maria Victoria, Hou, Yiping, Lee, Joo Young, and Lee, Hwan Young

Published
2022
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21. Selecting mRNA markers in blood for age estimation of the donor of a biological stain

Author

Dørum, Guro; https://orcid.org/0000-0002-8566-3131, Hänggi, Nadescha Viviane, Burri, Dario, Marti, Yael, Banemann, Regine, Kulstein, Galina, Courts, Cornelius; https://orcid.org/0000-0002-9811-8482, Gosch, Annica, Hadrys, Thorsten, Haas, Cordula; https://orcid.org/0000-0001-8122-1427, Neubauer, Jacqueline; https://orcid.org/0000-0002-9472-7803, Dørum, Guro; https://orcid.org/0000-0002-8566-3131, Hänggi, Nadescha Viviane, Burri, Dario, Marti, Yael, Banemann, Regine, Kulstein, Galina, Courts, Cornelius; https://orcid.org/0000-0002-9811-8482, Gosch, Annica, Hadrys, Thorsten, Haas, Cordula; https://orcid.org/0000-0001-8122-1427, and Neubauer, Jacqueline; https://orcid.org/0000-0002-9472-7803

Abstract

RNA has gained a substantial amount of attention within the forensic field over the last decade. There is evidence that RNAs are differentially expressed with biological age. Since RNA can be co-extracted with DNA from the same piece of evidence, RNA-based analysis appears as a promising molecular alternative for predicting the biological age and hence inferring the chronological age of a person. Using RNA-Seq data we searched for markers in blood potentially associated with age. We used our own RNA-Seq data from dried blood stains as well as publicly available RNA-Seq data from whole blood, and compared two different approaches to select candidate markers. The first approach focused on individual gene analysis with DESeq2 to select the genes most correlated with age, while the second approach employed lasso regression to select a set of genes for optimal prediction of age. We present two lists with 270 candidate markers, one for each approach.

Published
2024

24. HIrisPlex-S system for eye, hair, and skin color prediction from DNA: Massively parallel sequencing solutions for two common forensically used platforms

Author

Breslin, Krystal, Wills, Bailey, Ralf, Arwin, Ventayol Garcia, Marina, Kukla-Bartoszek, Magdalena, Pospiech, Ewelina, Freire-Aradas, Ana, Xavier, Catarina, Ingold, Sabrina, de La Puente, Maria, van der Gaag, Kristiaan J., Herrick, Noah, Haas, Cordula, Parson, Walther, Phillips, Christopher, Sijen, Titia, Branicki, Wojciech, Walsh, Susan, and Kayser, Manfred

Published
2019
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30. Towards broadening Forensic DNA Phenotyping beyond pigmentation: Improving the prediction of head hair shape from DNA

Author

Pośpiech, Ewelina, Chen, Yan, Kukla-Bartoszek, Magdalena, Breslin, Krystal, Aliferi, Anastasia, Andersen, Jeppe D., Ballard, David, Chaitanya, Lakshmi, Freire-Aradas, Ana, van der Gaag, Kristiaan J., Girón-Santamaría, Lorena, Gross, Theresa E., Gysi, Mario, Huber, Gabriela, Mosquera-Miguel, Ana, Muralidharan, Charanya, Skowron, Małgorzata, Carracedo, Ángel, Haas, Cordula, Morling, Niels, Parson, Walther, Phillips, Christopher, Schneider, Peter M., Sijen, Titia, Syndercombe-Court, Denise, Vennemann, Marielle, Wu, Sijie, Xu, Shuhua, Jin, Li, Wang, Sijia, Zhu, Ghu, Martin, Nick G., Medland, Sarah E., Branicki, Wojciech, Walsh, Susan, Liu, Fan, and Kayser, Manfred

Published
2018
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35. Clinical and experimental evidence suggest a link between KIF7 and C5orf42-related ciliopathies through Sonic Hedgehog signaling

Author

Asadollahi, Reza, Strauss, Justin E, Zenker, Martin, Beuing, Oliver, Edvardson, Simon, Elpeleg, Orly, Strom, Tim M, Joset, Pascal, Niedrist, Dunja, Otte, Christine, Oneda, Beatrice, Boonsawat, Paranchai, Azzarello-Burri, Silvia, Bartholdi, Deborah, Papik, Michael, Zweier, Markus, Haas, Cordula, Ekici, Arif B, Baumer, Alessandra, Boltshauser, Eugen, Steindl, Katharina, Nothnagel, Michael, Schinzel, Albert, Stoeckli, Esther T, and Rauch, Anita

Published
2018
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36. Body Fluid Identification by mRNA and MicroRNA

Author

Houck, Max M, Wilson, Lauren, Eldrige, Heidi, Lewis, Simon W, Lothridge, Kevin, Reedy, Paul, Houck, M M ( Max M ), Wilson, L ( Lauren ), Eldrige, H ( Heidi ), Lewis, S W ( Simon W ), Lothridge, K ( Kevin ), Reedy, P ( Paul ), Haas, Cordula; https://orcid.org/0000-0001-8122-1427, Hänggi, Nadescha Viviane, Hanson, Erin, Ballantyne, Jack, Houck, Max M, Wilson, Lauren, Eldrige, Heidi, Lewis, Simon W, Lothridge, Kevin, Reedy, Paul, Houck, M M ( Max M ), Wilson, L ( Lauren ), Eldrige, H ( Heidi ), Lewis, S W ( Simon W ), Lothridge, K ( Kevin ), Reedy, P ( Paul ), Haas, Cordula; https://orcid.org/0000-0001-8122-1427, Hänggi, Nadescha Viviane, Hanson, Erin, and Ballantyne, Jack

Abstract

Analysis of biological evidence typically begins with a preliminary screening for the presence of biological fluids. Conventional enzymatic and immunological assays are of limited specificity and cannot conclusively identify the presence of several common biological fluids. RNA profiling is a new method for the identification of forensically relevant biological fluids, such as blood, saliva, semen, vaginal secretions and menstrual blood. Here, we provide an overview of the two different types of RNA profiling, particularly messenger RNA and micro RNA. The results of these studies are promising and suggest the future role of molecular-based approaches for the routine identification of the tissue source of origin of forensic biological evidence.

Published
2023

37. Exome analysis focusing on epilepsy-related genes in children and adults with sudden unexplained death

Author

Buerki, Sarah E; https://orcid.org/0000-0003-3054-1791, Haas, Cordula; https://orcid.org/0000-0001-8122-1427, Neubauer, Jacqueline; https://orcid.org/0000-0002-9472-7803, Buerki, Sarah E; https://orcid.org/0000-0003-3054-1791, Haas, Cordula; https://orcid.org/0000-0001-8122-1427, and Neubauer, Jacqueline; https://orcid.org/0000-0002-9472-7803

Abstract

Purpose: Genetic studies in sudden infant death syndrome (SIDS) and sudden unexplained death (SUD) cohorts have indicated that cardiovascular diseases might have contributed to sudden unexpected death in 20–35 % of autopsy-negative cases. Sudden unexpected death can also occur in people with epilepsy, termed as sudden unexpected death in epilepsy (SUDEP). The pathophysiological mechanisms of SUDEP are not well understood, but are likely multifactorial, including seizure-induced hypoventilation and arrhythmias as well as genetic risk factors. The sudden death of some of the SIDS/SUD victims might also be explained by genetic epilepsy, therefore this study aimed to expand the post-mortem genetic analysis of SIDS/SUD cases to epilepsy-related genes. Methods: Existing whole-exome sequencing data from our 155 SIDS and 45 SUD cases were analyzed, with a focus on 365 epilepsy-related genes. Nine of the SUD victims had a known medical history of epilepsy, seizures or other underlying neurological conditions and were therefore classified as SUDEP cases. Results: In our SIDS and SUD cohorts, we found epilepsy-related pathogenic/likely pathogenic variants in the genes OPA1, RAI1, SCN3A, SCN5A and TSC2. Conclusion: Post-mortem analysis of epilepsy-related genes identified potentially disease-causing variants that might have contributed to the sudden death events in our SIDS/SUD cases. However, the interpretation of identified variants remains challenging and often changes over time as more data is gathered. Overall, this study contributes insight in potentially pathophysiological epilepsy-related mechanisms in SIDS, SUD and SUDEP victims and underlines the importance of sensible counselling on the risk and preventive measures in genetic epilepsy.

Published
2023

38. Analytical description of adolescent binge drinking patients

Author

Haas, Cordula; https://orcid.org/0000-0001-8122-1427, Salzmann, Andrea Patrizia, Binz, Tina Maria; https://orcid.org/0000-0001-6783-1202, Staubli, Georg; https://orcid.org/0000-0003-2667-1972, Seiler, Michelle; https://orcid.org/0000-0002-1263-5818, Steuer, Andrea Eva; https://orcid.org/0000-0001-8983-2353, Haas, Cordula; https://orcid.org/0000-0001-8122-1427, Salzmann, Andrea Patrizia, Binz, Tina Maria; https://orcid.org/0000-0001-6783-1202, Staubli, Georg; https://orcid.org/0000-0003-2667-1972, Seiler, Michelle; https://orcid.org/0000-0002-1263-5818, and Steuer, Andrea Eva; https://orcid.org/0000-0001-8983-2353

Abstract

Background Binge drinking is a widespread health compromising behavior among adolescents and young adults, leading to significant health problems, injuries and mortality. However, data on alcohol consumption is often unreliable, as it is mainly based on self-reporting surveys. In this five-year study (2014–2019) at the University Children’s Hospital Zurich, we analyzed blood samples from adolescent binge drinking patients to investigate blood alcohol concentrations (BACs), co-ingestion of drugs, assess compliance between self-reported and measured substance use, and test for genetic components of innate alcohol tolerance. Furthermore, hair analysis was performed to retrospectively access drug exposure and to evaluate the potential of hair analysis to assess binge drinking. Methods In a prospective, single-center study, patients with alcohol intoxications aged 16 years and younger were included. Blood and hair samples were analyzed by sensitive liquid chromatography – tandem mass spectrometry drug analysis. HTTLPR genotyping was performed with PCR and fragment analysis. Results Among 72 cases, 72 blood and 13 hair samples were analyzed. BACs ranged from 0.08–3.20‰ (mean 1.63‰, median 1.60‰), while a mean concentration of 3.64 pg/mg hair (median 3.0 pg/mg) of the alcohol marker ethyl glucuronide (EtG) was detected in eleven hair samples, providing no evidence of chronic excessive drinking. In 47% of the cases, co-ingested drugs were qualitatively detected next to ethanol, but only 9% of the detected drugs had blood concentrations classified as pharmacologically active. Cannabis consumption (22%) and stimulant intake (16%) were the most frequently observed drugs. Compliance between patients’ statements and measured substances matched well. Although we investigated the genetic contribution to innate alcohol tolerance via the 5-HTTLPR polymorphism, the diverse genetic background of the cohort and small sample size did not allow any conclusions to be drawn. Conclusion Alm

Published
2023

39. Comparative evaluation of the MAPlex, Precision ID Ancestry Panel, and VISAGE Basic Tool for biogeographical ancestry inference

Author

Resutik, Peter, Aeschbacher, Simon; https://orcid.org/0000-0001-5217-1926, Krützen, Michael, Kratzer, Adelgunde, Haas, Cordula, Phillips, Christopher, Arora, Natasha, Resutik, Peter, Aeschbacher, Simon; https://orcid.org/0000-0001-5217-1926, Krützen, Michael, Kratzer, Adelgunde, Haas, Cordula, Phillips, Christopher, and Arora, Natasha

Abstract

Biogeographical ancestry (BGA) inference from ancestry-informative markers (AIMs) has strong potential to support forensic investigations. Over the past two decades, several forensic panels composed of AIMs have been developed to predict ancestry at a continental scale. These panels typically comprise fewer than 200 AIMs and have been designed and tested with a limited set of populations. How well these panels recover patterns of genetic diversity relative to larger sets of markers, and how accurately they infer ancestry of individuals and populations not included in their design remains poorly understood. The lack of comparative studies addressing these aspects makes the selection of appropriate panels for forensic laboratories difficult. In this study, the model-based genetic clustering tool STRUCTURE was used to compare three popular forensic BGA panels: MAPlex, Precision ID Ancestry Panel (PIDAP), and VISAGE Basic Tool (VISAGE BT) relative to a genome-wide reference set of 10k SNPs. The genotypes for all these markers were obtained for a comprehensive set of 3957 individuals from 228 worldwide human populations. Our results indicate that at the broad continental scale (K = 6) typically examined in forensic studies, all forensic panels produced similar genetic structure patterns compared to the reference set (G′ ≈ 90%) and had high classification performance across all regions (average AUC-PR > 97%). However, at K = 7 and K = 8, the forensic panels displayed some region-specific clustering deviations from the reference set, particularly in Europe and the region of East and South-East Asia, which may be attributed to differences in the design of the respective panels. Overall, the panel with the most consistent performance in all regions was VISAGE BT with an average weighted AUC̅W score of 96.26% across the three scales of geographical resolution investigated.

Published
2023

40. Body Fluid Identification in Samples Collected after Intimate and Social Contact: A Comparison of Two mRNA Profiling Methods and the Additional Information Gained by cSNP Genotypes

Author

Johannessen, Helen; https://orcid.org/0000-0001-7032-2660, Hanson, Erin, Gill, Peter, Haas, Cordula; https://orcid.org/0000-0001-8122-1427, Bergseth, Erik Francisco, Ballantyne, Jack, Fonneløp, Ane Elida, Johannessen, Helen; https://orcid.org/0000-0001-7032-2660, Hanson, Erin, Gill, Peter, Haas, Cordula; https://orcid.org/0000-0001-8122-1427, Bergseth, Erik Francisco, Ballantyne, Jack, and Fonneløp, Ane Elida

Abstract

The ability to associate a contributor with a specific body fluid in a crime stain can aid casework investigation. The detection of body fluids combined with DNA analyses may supply essential information, but as the two tests are independent, they may not be associated. Recently, the analysis of coding region SNPs (cSNPs) within the RNA transcript has been proven to be a promising method to face this challenge. In this study, we performed targeted RNA sequencing of 158 samples (boxershorts, fingernail swabs and penile swabs) collected from 12 couples at different time points post-intimate contact and after non-intimate contact, using the Ion S5™ System and BFID-cSNP-6F assay. The aim of the study was to compare the performance of the MPS and CE methods in the detection of mRNA markers, and to associate body fluids with contributors by their cSNP genotypes. The results of the study show a lower success rate in the detection of vaginal mucosa by the MPS compared to the CE method. However, the additional information obtained with the cSNP genotypes could successfully associate body fluids with contributors in most cases.

Published
2023

44. Body Fluid Identification by mRNA and MicroRNA

Author

Haas, Cordula, Hänggi, Nadescha Viviane, Hanson, Erin, Ballantyne, Jack, University of Zurich, Houck, Max M, Wilson, Lauren, Eldrige, Heidi, Lewis, Simon W, Lothridge, Kevin, and Reedy, Paul

Subjects
Circular RNAs (circRNA), Coding region single nucleotide polymorphisms (cSNPs), 340 Law, 610 Medicine & health, Body fluid identification, 10218 Institute of Legal Medicine, Vaginal secretion, Presumptive test, Blood, Confirmatory test, Messenger RNA (mRNA), Semen, Massive Parallel Sequencing (MPS), MicroRNA (miRNA), Saliva, Menstrual blood, PiwiRNA (piRNA), Skin
Published
2023
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46. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

Author

Purps, Josephine, Siegert, Sabine, Willuweit, Sascha, Nagy, Marion, Alves, Cíntia, Salazar, Renato, Angustia, Sheila M.T., Santos, Lorna H., Anslinger, Katja, Bayer, Birgit, Ayub, Qasim, Wei, Wei, Xue, Yali, Tyler-Smith, Chris, Bafalluy, Miriam Baeta, Martínez-Jarreta, Begoña, Egyed, Balazs, Balitzki, Beate, Tschumi, Sibylle, Ballard, David, Court, Denise Syndercombe, Barrantes, Xinia, Bäßler, Gerhard, Wiest, Tina, Berger, Burkhard, Niederstätter, Harald, Parson, Walther, Davis, Carey, Budowle, Bruce, Burri, Helen, Borer, Urs, Koller, Christoph, Carvalho, Elizeu F., Domingues, Patricia M., Chamoun, Wafaa Takash, Coble, Michael D., Hill, Carolyn R., Corach, Daniel, Caputo, Mariela, D’Amato, Maria E., Davison, Sean, Decorte, Ronny, Larmuseau, Maarten H.D., Ottoni, Claudio, Rickards, Olga, Lu, Di, Jiang, Chengtao, Dobosz, Tadeusz, Jonkisz, Anna, Frank, William E., Furac, Ivana, Gehrig, Christian, Castella, Vincent, Grskovic, Branka, Haas, Cordula, Wobst, Jana, Hadzic, Gavrilo, Drobnic, Katja, Honda, Katsuya, Hou, Yiping, Zhou, Di, Li, Yan, Hu, Shengping, Chen, Shenglan, Immel, Uta-Dorothee, Lessig, Rüdiger, Jakovski, Zlatko, Ilievska, Tanja, Klann, Anja E., García, Cristina Cano, de Knijff, Peter, Kraaijenbrink, Thirsa, Kondili, Aikaterini, Miniati, Penelope, Vouropoulou, Maria, Kovacevic, Lejla, Marjanovic, Damir, Lindner, Iris, Mansour, Issam, Al-Azem, Mouayyad, Andari, Ansar El, Marino, Miguel, Furfuro, Sandra, Locarno, Laura, Martín, Pablo, Luque, Gracia M., Alonso, Antonio, Miranda, Luís Souto, Moreira, Helena, Mizuno, Natsuko, Iwashima, Yasuki, Neto, Rodrigo S. Moura, Nogueira, Tatiana L.S., Silva, Rosane, Nastainczyk-Wulf, Marina, Edelmann, Jeanett, Kohl, Michael, Nie, Shengjie, Wang, Xianping, Cheng, Baowen, Núñez, Carolina, Pancorbo, Marian Martínez de, Olofsson, Jill K., Morling, Niels, Onofri, Valerio, Tagliabracci, Adriano, Pamjav, Horolma, Volgyi, Antonia, Barany, Gusztav, Pawlowski, Ryszard, Maciejewska, Agnieszka, Pelotti, Susi, Pepinski, Witold, Abreu-Glowacka, Monica, Phillips, Christopher, Cárdenas, Jorge, Rey-Gonzalez, Danel, Salas, Antonio, Brisighelli, Francesca, Capelli, Cristian, Toscanini, Ulises, Piccinini, Andrea, Piglionica, Marilidia, Baldassarra, Stefania L., Ploski, Rafal, Konarzewska, Magdalena, Jastrzebska, Emila, Robino, Carlo, Sajantila, Antti, Palo, Jukka U., Guevara, Evelyn, Salvador, Jazelyn, Ungria, Maria Corazon De, Rodriguez, Jae Joseph Russell, Schmidt, Ulrike, Schlauderer, Nicola, Saukko, Pekka, Schneider, Peter M., Sirker, Miriam, Shin, Kyoung-Jin, Oh, Yu Na, Skitsa, Iulia, Ampati, Alexandra, Smith, Tobi-Gail, Calvit, Lina Solis de, Stenzl, Vlastimil, Capal, Thomas, Tillmar, Andreas, Nilsson, Helena, Turrina, Stefania, De Leo, Domenico, Verzeletti, Andrea, Cortellini, Venusia, Wetton, Jon H., Gwynne, Gareth M., Jobling, Mark A., Whittle, Martin R., Sumita, Denilce R., Wolańska-Nowak, Paulina, Yong, Rita Y.Y., Krawczak, Michael, Nothnagel, Michael, and Roewer, Lutz

Published
2014
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47. Collaborative EDNAP exercise on the IrisPlex system for DNA-based prediction of human eye colour

Author

Chaitanya, Lakshmi, Walsh, Susan, Andersen, Jeppe Dyrberg, Ansell, Ricky, Ballantyne, Kaye, Ballard, David, Banemann, Regine, Bauer, Christiane Maria, Bento, Ana Margarida, Brisighelli, Francesca, Capal, Tomas, Clarisse, Lindy, Gross, Theresa E., Haas, Cordula, Hoff-Olsen, Per, Hollard, Clémence, Keyser, Christine, Kiesler, Kevin M., Kohler, Priscila, Kupiec, Tomasz, Linacre, Adrian, Minawi, Anglika, Morling, Niels, Nilsson, Helena, Norén, Lina, Ottens, Renée, Palo, Jukka U., Parson, Walther, Pascali, Vincenzo L., Phillips, Chris, Porto, Maria João, Sajantila, Antti, Schneider, Peter M., Sijen, Titia, Söchtig, Jens, Syndercombe-Court, Denise, Tillmar, Andreas, Turanska, Martina, Vallone, Peter M., Zatkalíková, Lívia, Zidkova, Anastassiya, Branicki, Wojciech, and Kayser, Manfred

Published
2014
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