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Synthetische drugs worden in Nederland op grote schaal illegaal geproduceerd en elk jaar worden tientallen drugslaboratoria ontdekt en ontmanteld. Bij de productie van synthetische drugs komt veel chemische afval vrij dat onder andere door dumping in het milieu in de voedselketen terecht kan komen. De hieruit volgende risico’s zijn nog onvoldoende bekend. Om potentiële risico’s in de voedselketen in kaart te brengen, is het nodig dat chemische analyses op de aanwezigheid van drugs of grondstoffen daarvan uitgevoerd kunnen worden. Dit kleine project is uitgevoerd met als doel om vast te stellen welke stoffen gemeten moeten kunnen worden.Om deze vraag te kunnen beantwoorden is onderzocht welke stoffen aanwezig kunnen zijn in afval afkomstig van de productie van synthetische drugs. Hiervoor is in kaart gebracht welke productieprocessen er momenteel in Nederland toegepast worden voor het produceren van synthetische drugs en wat voor soort afval hierbij verwacht wordt. Daarbij is bekeken in hoeverre de relevante stoffen met de huidige chemische analysemethodes binnen WFSR aangetoond kunnen worden. Daarnaast is onderzocht in welke mate en waar drugsafval gedumpt wordt en is onderzocht wat er bekend is over de toxiciteit van deze stoffen en het risico op ophoping in de voedselketen, om zo te kunnen beoordelen of en welke voedingsgewassen nader onderzoek en analyse vereisen.Dit onderzoek is uitgevoerd door interviews te houden met onderzoekers binnen WFSR die gespecialiseerd zijn in de analyse van drugsgerelateerde stoffen en met experts van Nederlands Forensisch Instituut en de politie, gespecialiseerd op het gebied van drugsdumpingen in Nederland.In 2021 zijn, overeenkomend met voorgaande jaren, 69 locaties in Nederland gevonden waar synthetische drugs geproduceerd werden. In 86% van de gevallen ging het om MDMA, amfetamine of methylamfetamine. Gevonden drugsafval is dan ook vooral hiervan afkomstig. Naast de productie van synthetische drugs zijn er ook gegevens bekend o

De novo mutations arising in the germline add to genetic variation. The number of de novo mutations occurring every generation, especially structural variants, has not been well studied in most species, including livestock. We used whole-genome sequencing from 46 pig trios from two commercial lines to identify de novo structural variants (dnSVs) present in the offspring. We characterised these dnSV by identifying their parent-of-origin, predicting their causal mechanisms, and identifying their functional annotations. We identified four dnSVs, including two clusters of mutations. One of these clusters contained a deletion, and three duplications, one of which was inverted. This cluster was the only dnSV that could be phased and was located in the paternal haplotype of the proband. All four identified dnSVs were located within the introns of genes. Our study is the first of its kind to identify and characterise dnSVs using whole genome shotgun sequence data in pigs.

Somatic mutation profile of thyroid cancer in dogs has not been investigated. We previously reported a familial thyroid follicular cell carcinoma (FCC) in a large number of Dutch German longhaired pointers and identified two deleterious mutations in the TPO gene associated with the disease predisposition. In this study, we comprehensively investigated the somatic mutations in the tumors that potentially contribute to the inherited tumor formation and development using high depth whole-genome sequencing. A GNAS A204D missense mutation was identified in 4 of 7 tumors by whole-genome sequencing and xx of 36 FCC tumors by PCR-RFLP. In humans, somatic mutations in the GNAS gene were also identified but in low prevalence. Meanwhile, the homologous mutation has not been reported. It suggested the potential interaction between germline risk factor and driver mutation by comparing to prevalence of GNAS mutations in human samples. Moreover, tumors with GNAS A204D mutation had significantly less somatic SNVs and Indels, suggesting that this mutation could be a marker for less malignant form of thyroid tumor in dogs., Background We previously reported a familial thyroid follicular cell carcinoma (FCC) in a large number of Dutch German longhaired pointers and identified two deleterious germline mutations in the TPO gene associated with disease predisposition. However, the somatic mutation profile of the FCC in dogs has not been investigated at a genome-wide scale. Results Herein, we comprehensively investigated the somatic mutations that potentially contribute to the inherited tumor formation and progression using high depth whole-genome sequencing. A GNAS p.A204D missense mutation was identified in 4 out of 7 FCC tumors by whole-genome sequencing and in 20 out of 32 dogs’ tumors by targeted sequencing. In contrast to this, in the human TC, mutations in GNAS gene have lower prevalence. Meanwhile, the homologous somatic mutation in humans has not been reported. These findings suggest a difference in the somatic mutation landscape between TC in these dogs and human TC. Moreover, tumors with the GNAS p.A204D mutation had a significantly lower somatic mutation burden in these dogs. Somatic structural variant and copy number alterations were also investigated, but no potential driver event was identified. Conclusion This study provides novel insight in the molecular mechanism of thyroid carcinoma development in dogs. German longhaired pointers carrying GNAS mutations in the tumor may be used as a disease model for the development and testing of novel therapies to kill the tumor with somatic mutations in the GNAS gene.

The growth of animals is a complex trait, in chicken resulting in a diverse variety of forms, caused by a heterogeneous genetic basis. Bantam chicken, known as an exquisite form of dwarfism, has been used for crossbreeding to create corresponding dwarf counterparts for native fowls in the Dutch populations. Here, we demonstrate the heterogeneity of the bantam trait in Dutch chickens and reveal the underlying genetic causes, using whole‐genome sequence data from matching pairs of bantam and normal‐sized breeds. During the bantam‐oriented crossbreeding, various bantam origins were used to introduce the bantam phenotype, and three major bantam sources were identified and clustered. The genome‐wide association studies revealed multiple genetic variants and genes associated with bantam phenotype, including HMGA2 and PRDM16, genes involved in body growth and stature. The comparison of associated variants among studies illustrated differences related to divergent bantam origins, suggesting a clear heterogeneity among bantam breeds. We show that in neo‐bantam breeds, the bantam‐related regions underwent a strong haplotype introgression from the bantam source, outcompeting haplotypes from the normal‐sized counterpart. The bantam heterogeneity is further confirmed by the presence of multiple haplotypes comprising associated alleles, which suggests the selection of the bantam phenotype is likely subject to a convergent direction across populations. Our study demonstrates that the diverse history of human‐mediated crossbreeding has contributed to the complexity and heterogeneity of the bantam phenotype.

Genetic modification techniques, in particular novel gene editing technologies, hold the yet unfulfilled promise of altering genetic traits in farm animals more efficiently than by crossbreeding, allowing for a more rapid development of new cattle breeds with distinct traits. Gene editing technologies allow for the directed alteration of specific traits and thereby have the potential to enhance, for instance, disease resilience, production yield and the production of desired substances in milk. The potential implications of these technological advancements, which are often combined with animal cloning methods, are discussed both for animal health and for consumer safety, also with consideration of available methods for the detection and identification of the related products in the food supply chain. Finally, an overview is provided of current regulatory approaches in the EU and major countries exporting beef to the EU, for products from animals bred through established practices as well as modern biotechnologies.

Repository for the study: Martijn F.L. Derks, Barbara Harlizius, Marcos S. Lopes, Sylvia W.M. Greijdanus-van der Putten, Bert Dibbits, Kimberley Laport, Hendrik-Jan Megens, Martien A.M. Groenen. Detection of a frameshift deletion in the SPTBN4 gene leads to prevention of severe myopathy and postnatal mortality in pigs. 2019. Published in Frontiers in Genetics, doi: 10.3389/fgene.2019.01226

The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non-European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole-genome sequencing data. Additionally, we also employed unlinked and phased SNP-based approaches on high-density SNP array data to characterize non-European cattle ancestry in several southern European cattle breeds. Using heterozygosity-based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross-bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non-European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might ac