Torfinn Nome

• Sinani, Valentina Krivenjeva; Wilson, Robert Charles; Nome, Torfinn; Acharya, Ujjwal; Kommisrud, Elisabeth & Wetten, Marte [Show all 7 contributors for this article] (2025). Development and validation of a 70K SNP genotyping array for Atlantic halibut (Hippoglossus hippoglossus). BMC Genomics. 26(1). doi: 10.1186/s12864-025-12128-1. Full text in Research Archive Show summary

  Background The analysis of single nucleotide polymorphism (SNP) genotypes which capture genome-wide polymorphic variation can be used to improve the accuracy of selection in breeding programs and reveal the genetic architecture of quantitative traits. Mid-density SNP genotyping arrays containing > 60 K SNP markers have been developed for numerous production species and have been used to enable enhanced breeding progress. Despite recent genomic advances, Atlantic halibut lacks mid-density genotyping tools, limiting the application of genomic selection and high-resolution association studies in this species. The evolving Atlantic halibut (Hippoglossus hippoglossus) industry is also interested in genetically informed selection of breeding candidates to facilitate genetic improvement. The present study reports the development of the first mid-density SNP-array for use in Atlantic halibut and describes its performance in samples from different breeding populations. Results Variant discovery was performed using whole genome sequencing (WGS) data from 40 individuals and resulted in the detection of more than 8 million small genetic variants including 6,224,375 SNPs and 2,131,436 insertion-deletion variants (INDELS). An Affymetrix Axiom custom array containing 70,824 assays (including 697 for determining genetic gender) was created and used to genotype 1152 Atlantic halibut samples. Assays for 59,491 SNP loci (84% of the array total) performed well and generated reliable genotypes, with an average SNP call rate of 99.64% and genotype concordance of 99.0% with whole-genome sequencing data. Of the gender-specific loci, 133 SNP assays could be used to assign genetic gender. Conclusions This article describes the first mid-density SNP genotyping array for Atlantic halibut. It contains nearly 60 K robust assays for genome-wide dispersed SNP loci, along with those suitable for determining genetic gender. The array is amenable for use as a platform for high-resolution genetics research into traits of evolutionary and economic importance and the results have practical relevance for genomic selection in Atlantic halibut.

• Stenløkk, Kristina S R; Saitou, Marie; Rud-Johansen, Live; Nome, Torfinn; Moser, Michel & Arnyasi, Mariann [Show all 9 contributors for this article] (2022). The emergence of supergenes from inversions in Atlantic salmon. Philosophical Transactions of the Royal Society of London. Biological Sciences. ISSN 0962-8436. 377(1856). doi: 10.1098/rstb.2021.0195. Full text in Research Archive
• Sinclair-Waters, Marion; Nome, Torfinn; Wang, Jing; Lien, Sigbjørn; Kent, Matthew Peter & Sægrov, Harald [Show all 10 contributors for this article] (2022). Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods. Heredity. ISSN 0018-067X. 129(6), p. 356–365. doi: 10.1038/s41437-022-00570-w. Full text in Research Archive Show summary

  Characterizing the role of different mutational effect sizes in the evolution of fitness-related traits has been a major goal in evolutionary biology for a century. Such characterization in a diversity of systems, both model and non-model, will help to understand the genetic processes underlying fitness variation. However, well-characterized genetic architectures of such traits in wild populations remain uncommon. In this study, we used haplotype-based and multi-SNP Bayesian association methods with sequencing data for 313 individuals from wild populations to test the mutational composition of known candidate regions for sea age at maturation in Atlantic salmon (Salmo salar). We detected an association at five loci out of 116 candidates previously identified in an aquaculture strain with maturation timing in wild Atlantic salmon. We found that at four of these five loci, variation explained by the locus was predominantly driven by a single SNP suggesting the genetic architecture of this trait includes multiple loci with simple, non-clustered alleles and a locus with potentially more complex alleles. This highlights the diversity of genetic architectures that can exist for fitness-related traits. Furthermore, this study provides a useful multi-SNP framework for future work using sequencing data to characterize genetic variation underlying phenotypes in wild populations.

• West, Alexander Christopher; Mizoro, Yasutaka; Wood, Shona; Ince, Louise M.; Iversen, Marianne & Jørgensen, Even Hjalmar [Show all 11 contributors for this article] (2021). Immunologic Profiling of the Atlantic Salmon Gill by Single Nuclei Transcriptomics. Frontiers in Immunology. 12. doi: 10.3389/fimmu.2021.669889. Full text in Research Archive Show summary

  Anadromous salmonids begin life adapted to the freshwater environments of their natal streams before a developmental transition, known as smoltification, transforms them into marine-adapted fish. In the wild, smoltification is a photoperiod-regulated process, involving radical remodeling of gill function to cope with the profound osmotic and immunological challenges of seawater (SW) migration. While prior work has highlighted the role of specialized “mitochondrion-rich” cells (MRCs) and accessory cells (ACs) in delivering this phenotype, recent RNA profiling experiments suggest that remodeling is far more extensive than previously appreciated. Here, we use single-nuclei RNAseq to characterize the extent of cytological changes in the gill of Atlantic salmon during smoltification and SW transfer. We identify 20 distinct cell clusters, including known, but also novel gill cell types. These data allow us to isolate cluster-specific, smoltification-associated changes in gene expression and to describe how the cellular make-up of the gill changes through smoltification. As expected, we noted an increase in the proportion of seawater mitochondrion-rich cells, however, we also identify previously unknown reduction of several immune-related cell types. Overall, our results provide fresh detail of the cellular complexity in the gill and suggest that smoltification triggers unexpected immune reprogramming.

• Bertolotti, Alicia C.; Layer, Ryan M.; Gundappa, Manu Kumar; Gallagher, Michael D.; Pehlivanoglu, Ege & Nome, Torfinn [Show all 23 contributors for this article] (2020). The structural variation landscape in 492 Atlantic salmon genomes. Nature Communications. 11. doi: 10.1038/s41467-020-18972-x. Full text in Research Archive Show summary

  Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species.

• West, Alexander Christopher; Mizoro, Yasutaka; Wood, Shona Hiedi; Iversen, Marianne; Ince, Louise & Jørgensen, Even [Show all 10 contributors for this article] (2020). A single nuclei transcriptomic analysis of the Atlantic salmon gill through smoltification and seawater transfer. BioRxiv. ISSN 0362-4331. doi: 10.1101/2020.09.03.281337. Full text in Research Archive
• Mulugeta, Teshome Dagne; Nome, Torfinn; To, Thu-Hien; Gundappa, Manu Kumar; Macqueen, Daniel J. & Våge, Dag Inge [Show all 8 contributors for this article] (2019). SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes. BMC Genomics. 20(1). doi: 10.1186/s12864-019-6051-0. Full text in Research Archive Show summary

  BACKGROUND: Recently developed genome resources in Salmonid fish provides tools for studying the genomics underlying a wide range of properties including life history trait variation in the wild, economically important traits in aquaculture and the evolutionary consequences of whole genome duplications. Although genome assemblies now exist for a number of salmonid species, the lack of regulatory annotations are holding back our mechanistic understanding of how genetic variation in non-coding regulatory regions affect gene expression and the downstream phenotypic effects. RESULTS: We present SalMotifDB, a database and associated web and R interface for the analysis of transcription factors (TFs) and their cis-regulatory binding sites in five salmonid genomes. SalMotifDB integrates TF-binding site information for 3072 non-redundant DNA patterns (motifs) assembled from a large number of metazoan motif databases. Through motif matching and TF prediction, we have used these multi-species databases to construct putative regulatory networks in salmonid species. The utility of SalMotifDB is demonstrated by showing that key lipid metabolism regulators are predicted to regulate a set of genes affected by different lipid and fatty acid content in the feed, and by showing that our motif database explains a significant proportion of gene expression divergence in gene duplicates originating from the salmonid specific whole genome duplication. CONCLUSIONS: SalMotifDB is an effective tool for analyzing transcription factors, their binding sites and the resulting gene regulatory networks in salmonid species, and will be an important tool for gaining a better mechanistic understanding of gene regulation and the associated phenotypes in salmonids. SalMotifDB is available at https://salmobase.org/apps/SalMotifDB .

• Pearse, Devon E.; Barson, Nicola; Nome, Torfinn; Gao, Guangtu; Campbell, Matthew & Abadía-Cardoso, Alicia [Show all 32 contributors for this article] (2019). Sex-dependent dominance maintains migration supergene in rainbow trout. Nature Ecology and Evolution. 3(12), p. 1731–1742. doi: 10.1038/s41559-019-1044-6. Full text in Research Archive
• Celestino, Ricardo; Nome, Torfinn; Pestana, Ana; Hoff, Andreas Midbøe; Gonçalves, A. Pedro & Pereira, Luísa [Show all 12 contributors for this article] (2018). CRABP1, C1QL1 and LCN2 are biomarkers of differentiated thyroid carcinoma, and predict extrathyroidal extension. BMC Cancer. 18:68, p. 1–16. doi: 10.1186/s12885-017-3948-3. Full text in Research Archive Show summary

  Background: The prognostic variability of thyroid carcinomas has led to the search for accurate biomarkers at the molecular level. Follicular thyroid carcinoma (FTC) is a typical example of differentiated thyroid carcinomas (DTC) in which challenges are faced in the differential diagnosis. Methods: We used high-throughput paired-end RNA sequencing technology to study four cases of FTC with different degree of capsular invasion: two minimally invasive (mFTC) and two widely invasive FTC (wFTC). We searched by genes differentially expressed between mFTC and wFTC, in an attempt to find biomarkers of thyroid cancer diagnosis and/or progression. Selected biomarkers were validated by real-time quantitative PCR in 137 frozen thyroid samples and in an independent dataset (TCGA), evaluating the diagnostic and the prognostic performance of the candidate biomarkers. Results: We identified 17 genes significantly differentially expressed between mFTC and wFTC. C1QL1, LCN2, CRABP1 and CILP were differentially expressed in DTC in comparison with normal thyroid tissues. LCN2 and CRABP1 were also differentially expressed in DTC when compared with follicular thyroid adenoma. Additionally, overexpression of LCN2 and C1QL1 were found to be independent predictors of extrathyroidal extension in DTC. Conclusions: We conclude that the underexpression of CRABP1 and the overexpression of LCN2 may be useful diagnostic biomarkers in thyroid tumours with questionable malignity, and the overexpression of LCN2 and C1QL1 may be useful for prognostic purposes.

• Kijas, James W.; McWilliam, Sean; Sanchez, Marina Naval; Kube, Peter; King, Harry & Evans, Bradley [Show all 9 contributors for this article] (2018). Evolution of Sex Determination Loci in Atlantic Salmon. Scientific Reports. 8(1). doi: 10.1038/s41598-018-23984-1. Full text in Research Archive
• Gao, Guangtu; Nome, Torfinn; Pearse, Devon E; Moen, Thomas; Naish, Kerry A & Thorgaard, Gary H [Show all 8 contributors for this article] (2018). A new single nucleotide polymorphism database for rainbow trout generated through whole genome resequencing. Frontiers in Genetics. 9. doi: 10.3389/fgene.2018.00147. Full text in Research Archive
• Samy, Jeevan Karloss Antony; Mulugeta, Teshome Dagne; Nome, Torfinn; Sandve, Simen Rød; Grammes, Fabian & Kent, Matthew Peter [Show all 8 contributors for this article] (2017). SalmoBase: An integrated molecular data resource for Salmonid species. BMC Genomics. 18(1). doi: 10.1186/s12864-017-3877-1. Full text in Research Archive
• Olsen, Hanne Gro; Knutsen, Tim Martin; Kohler, Achim; Svendsen, Morten; Gidskehaug, Lars Halvor & Grove, Harald [Show all 12 contributors for this article] (2017). Genome-wide association mapping for milk fat composition and fine mapping of a QTL for de novo synthesis of milk fatty acids on bovine chromosome 13. Genetics Selection Evolution. ISSN 0999-193X. 49:20, p. 1–13. doi: 10.1186/s12711-017-0294-5. Full text in Research Archive Show summary

  Background Bovine milk is widely regarded as a nutritious food source for humans, although the effects of individual fatty acids on human health is a subject of debate. Based on the assumption that genomic selection offers potential to improve milk fat composition, there is strong interest to understand more about the genetic factors that influence the biosynthesis of bovine milk and the molecular mechanisms that regulate milk fat synthesis and secretion. For this reason, the work reported here aimed at identifying genetic variants that affect milk fatty acid composition in Norwegian Red cattle. Milk fatty acid composition was predicted from the nation-wide recording scheme using Fourier transform infrared spectroscopy data and applied to estimate heritabilities for 36 individual and combined fatty acid traits. The recordings were used to generate daughter yield deviations that were first applied in a genome-wide association (GWAS) study with 17,343 markers to identify quantitative trait loci (QTL) affecting fatty acid composition, and next on high-density and sequence-level datasets to fine-map the most significant QTL on BTA13 (BTA for Bos taurus chromosome). Results The initial GWAS revealed 200 significant associations, with the strongest signals on BTA1, 13 and 15. The BTA13 QTL highlighted a strong functional candidate gene for de novo synthesis of short- and medium-chained saturated fatty acids; acyl-CoA synthetase short-chain family member 2. However, subsequent fine-mapping using single nucleotide polymorphisms (SNPs) from a high-density chip and variants detected by resequencing showed that the effect was more likely caused by a second nearby gene; nuclear receptor coactivator 6 (NCOA6). These findings were confirmed with results from haplotype studies. NCOA6 is a nuclear receptor that interacts with transcription factors such as PPARγ, which is a major regulator of bovine milk fat synthesis. Conclusions An initial GWAS revealed a highly significant QTL for de novo-synthesized fatty acids on BTA13 and was followed by fine-mapping of the QTL within NCOA6. The most significant SNPs were either synonymous or situated in introns; more research is needed to uncover the underlying causal DNA variation(s).

• Kirubakaran, Tina Graceline; Grove, Harald; Kent, Matthew Peter; Sandve, Simen Rød; Baranski, Matthew & Nome, Torfinn [Show all 13 contributors for this article] (2016). Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod. Molecular Ecology. ISSN 0962-1083. 25(10), p. 2130–2143. doi: 10.1111/mec.13592. Full text in Research Archive
• Lien, Sigbjørn; Koop, Ben F; Sandve, Simen Rød; Miller, Jason R.; Kent, Matthew Peter & Nome, Torfinn [Show all 45 contributors for this article] (2016). The Atlantic salmon genome provides insights into rediploidization. Nature. ISSN 0028-0836. 533(7602), p. 200–205. doi: 10.1038/nature17164. Full text in Research Archive Show summary

  The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.

• Lorenz, Susanne; Barøy, Tale; Sun, Jinchang; Nome, Torfinn; Vodak, Daniel & Bryne, Jan Christian [Show all 21 contributors for this article] (2016). Unscrambling the genomic chaos of osteosarcoma reveals extensive transcript fusion, recurrent rearrangements and frequent novel TP53 aberrations. OncoTarget. 7(5), p. 5273–5288. doi: 10.18632/oncotarget.6567. Full text in Research Archive Show summary

  In contrast to many other sarcoma subtypes, the chaotic karyotypes of osteosarcoma have precluded the identification of pathognomonic translocations. We here report hundreds of genomic rearrangements in osteosarcoma cell lines, showing clear characteristics of microhomology-mediated break-induced replication (MMBIR) and end-joining repair (MMEJ) mechanisms. However, at RNA level, the majority of the fused transcripts did not correspond to genomic rearrangements, suggesting the involvement of trans-splicing, which was further supported by typical trans-splicing characteristics. By combining genomic and transcriptomic analysis, certain recurrent rearrangements were identified and further validated in patient biopsies, including a PMP22-ELOVL5 gene fusion, genomic structural variations affecting RB1, MTAP/CDKN2A and MDM2, and, most frequently, rearrangements involving TP53. Most cell lines (7/11) and a large fraction of tumor samples (10/25) showed TP53 rearrangements, in addition to somatic point mutations (6 patient samples, 1 cell line) and MDM2 amplifications (2 patient samples, 2 cell lines). The resulting inactivation of p53 was demonstrated by a deficiency of the radiation-induced DNA damage response. Thus, TP53 rearrangements are the major mechanism of p53 inactivation in osteosarcoma. Together with active MMBIR and MMEJ, this inactivation probably contributes to the exceptional chromosomal instability in these tumors. Although rampant rearrangements appear to be a phenotype of osteosarcomas, we demonstrate that among the huge number of probable passenger rearrangements, specific recurrent, possibly oncogenic, events are present. For the first time the genomic chaos of osteosarcoma is characterized so thoroughly and delivered new insights in mechanisms involved in osteosarcoma development and may contribute to new diagnostic and therapeutic strategies.

• Olsen, Hanne Gro; Knutsen, Tim; Lewandowska-Sabat, Anna; Grove, Harald; Nome, Torfinn & Svendsen, Morten [Show all 15 contributors for this article] (2016). Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production. Genetics Selection Evolution. ISSN 0999-193X. 48(1). doi: 10.1186/s12711-016-0257-2. Full text in Research Archive
• Bruun, Jarle; Kolberg, Matthias; Ahlquist, Terje Cruickshank; Røyrvik, Ellen Christine; Nome, Torfinn & Leithe, Edward [Show all 18 contributors for this article] (2015). Regulator of chromosome condensation 2 identifies high-risk patients within both major phenotypes of colorectal cancer. Clinical Cancer Research. ISSN 1078-0432. 21(16), p. 3759–3770. doi: 10.1158/1078-0432.CCR-14-3294. Full text in Research Archive
• Barson, Nicola; Aykanat, Tutku; Hindar, Kjetil; Baranski, Matthew; Bolstad, Geir Hysing & Fiske, Peder [Show all 22 contributors for this article] (2015). Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon. Nature. ISSN 0028-0836. 528(7582), p. 405–408. doi: 10.1038/nature16062. Full text in Research Archive
• Hoff, Andreas Midbøe; Johannessen, Bjarne; Alagaratnam, Sharmini; Zhao, Sen; Nome, Torfinn & Løvf, Marthe [Show all 11 contributors for this article] (2015). Novel RNA variants in colorectal cancers. OncoTarget. 6(34), p. 36587–36602. doi: 10.18632/oncotarget.5500. Full text in Research Archive
• Løvf, Marthe; Nome, Torfinn; Bruun, Jarle; Eknæs, Mette; Bakken, Anne Cathrine & Mpindi, John-Patrick [Show all 12 contributors for this article] (2014). A novel transcript, VNN1-AB, as a biomarker for colorectal cancer. International Journal of Cancer. ISSN 0020-7136. 135(9), p. 2077–2084. doi: 10.1002/ijc.28855. Full text in Research Archive
• Nome, Torfinn; Hoff, Andreas Midbøe; Bakken, Anne Cathrine; Rognum, Torleiv Ole; Nesbakken, Arild & Skotheim, Rolf Inge (2014). High frequency of fusion transcripts involving TCF7L2 in colorectal cancer: Novel fusion partner and splice variants. PLOS ONE. 9(3). doi: 10.1371/journal.pone.0091264. Full text in Research Archive Show summary

  VTI1A-TCF7L2 was reported as a recurrent fusion gene in colorectal cancer (CRC), found to be expressed in three out of 97 primary cancers, and one cell line, NCI-H508, where a genomic deletion joins the two genes [1]. To investigate this fusion further, we analyzed high-throughput DNA and RNA sequencing data from seven CRC cell lines, and identified the gene RP11-57H14.3 (ENSG00000225292) as a novel fusion partner for TCF7L2. The fusion was discovered from both genome and transcriptome data in the HCT116 cell line. By triplicate nested RT-PCR, we tested both the novel fusion transcript and VTI1A-TCF7L2 for expression in a series of 106 CRC tissues, 21 CRC cell lines, 14 normal colonic mucosa, and 20 normal tissues from miscellaneous anatomical sites. Altogether, 42% and 45% of the CRC samples expressed VTI1A-TCF7L2 and TCF7L2-RP11-57H14.3 fusion transcripts, respectively. The fusion transcripts were both seen in 29% of the normal colonic mucosa samples, and in 25% and 75% of the tested normal tissues from other organs, revealing that the TCF7L2 fusion transcripts are neither specific to cancer nor to the colon and rectum. Seven different splice variants were detected for the VTI1A-TCF7L2 fusion, of which three are novel. Four different splice variants were detected for the TCF7L2-RP11-57H14.3 fusion. In conclusion, we have identified novel variants of VTI1A-TCF7L2 fusion transcripts, including a novel fusion partner gene, RP11-57H14.3, and demonstrated detectable levels in a large fraction of CRC samples, as well as in normal colonic mucosa and other tissue types. We suggest that the fusion transcripts observed in a high frequency of samples are transcription induced chimeras that are expressed at low levels in most samples. The similar fusion transcripts induced by genomic rearrangements observed in individual cancer cell lines may yet have oncogenic potential as suggested in the original study by Bass et al.

• Nome, Torfinn; Thomassen, Gard O Sundby; Bruun, Jarle; Ahlquist, Terje Cruickshank; Bakken, Anne Cathrine & Hoff, Andreas Midbøe [Show all 17 contributors for this article] (2013). Common fusion transcripts identified in colorectal cancer cell lines by high throughput RNA sequencing. Translational Oncology. ISSN 1944-7124. 6(5), p. 546–553. doi: 10.1593/tlo.13457. Full text in Research Archive
• Nyquist, Kaja Beate; Panagopoulos, Ioannis; Thorsen, Jim; Haugom, Lisbeth; Gorunova, Ludmila & Bjerkehagen, Bodil [Show all 13 contributors for this article] (2012). Whole-Transcriptome Sequencing Identifies Novel IRF2BP2-CDX1 Fusion Gene Brought about by Translocation t(1;5)(q42;q32) in Mesenchymal Chondrosarcoma. PLOS ONE. 7(11). doi: 10.1371/journal.pone.0049705. Full text in Research Archive
• Olsen, Hanne Gro; Hayes, Ben J.; Kent, Matthew Peter; Nome, Torfinn; Svendsen, Morten & Larsgaard, Anne-Guro [Show all 7 contributors for this article] (2011). Genome-wide association mapping in Norwegian Red cattle identifies quantitative trait loci for fertility and milk production on BTA12. Animal Genetics. ISSN 0268-9146. 42(5), p. 466–474. doi: 10.1111/j.1365-2052.2011.02179.x. Full text in Research Archive
• Grindflek, Eli; Meuwissen, Theodorus; Aasmundstad, T.; Hamland, Hanne; Hansen, Marianne H S & Nome, Torfinn [Show all 9 contributors for this article] (2011). Revealing genetic relationships between compounds affecting boar taint and reproduction in pigs. Journal of Animal Science. ISSN 0021-8812. 89(3), p. 680–692. doi: 10.2527/jas.2010-3290. Full text in Research Archive
• Olsen, Hanne Gro; Hayes, Ben J.; Kent, Matthew Peter; Nome, Torfinn; Svendsen, Morten & Lien, Sigbjørn (2010). A genome wide association study for QTL affecting direct and maternal effects of stillbirth and dystocia in cattle. Animal Genetics. ISSN 0268-9146. 41(3), p. 273–280. doi: 10.1111/j.1365-2052.2009.01998.x. Full text in Research Archive Show summary

  Dystocia and stillbirth are significant causes of female and neonatal death in many species and there is evidence for a genetic component to both traits. Identifying causal mutations affecting these traits through genome wide association studies could reveal the genetic pathways involved and will be a step towards targeted interventions. Norwegian Red cattle are an ideal model breed for such studies as very large numbers of records are available. We conducted a genome wide association study for direct and maternal effects of dystocia and stillbirth using almost 1 million records of these traits. Genotyping costs were minimized by genotyping the sires of the recorded cows, and using daughter averages as phenotypes. A dense marker map containing 17 343 single nucleotide polymorphisms covering all autosomal chromosomes was utilized. The genotyped sires were assigned to one of two groups in an attempt to ensure independence between the groups. Associations were only considered validated if they occurred in both groups. Strong associations were found and validated on chromosomes 4, 5, 6, 9, 12, 20, 22 and 28. The QTL region on chromosome 6 was refined using LDLA analysis. The results showed that this chromosome most probably contains two QTL for direct effect on dystocia and one for direct effect on stillbirth. Several candidate genes may be identified close to these QTL. Of these, a cluster of genes expected to affect bone and cartilage formation (i.e. SPP1, IBSP and MEPE) are of particular interest and we suggest that these genes are screened in candidate gene studies for dystocia and stillbirth in cattle as well as other species.

• Nilsen, Heidi; Olsen, Hanne Gro; Hayes, Ben J.; Nome, Torfinn; Sehested, Erling & Svendsen, Morten [Show all 8 contributors for this article] (2009). Characterization of a QTL region affecting clinical mastitis and protein yield on BTA6. Animal Genetics. ISSN 0268-9146. 40(5), p. 701–712. doi: 10.1111/j.1365-2052.2009.01908.x. Full text in Research Archive Show summary

  P>Quantitative trait loci affecting clinical mastitis were detected and fine mapped to a narrow region on bovine chromosome 6 in the Norwegian Red cattle population. The region includes the casein gene cluster and several candidate genes thought to influence clinical mastitis. The most significant results were found for SNPs within the Mucin 7 gene. This gene encodes an antimicrobial peptide and constitutes part of the first line of defence for the mucosal immune system. Detection of long haplotypes extending several Mb may indicate that artificial selection has influenced the haplotype structures in the region. A search for selection sweeps supports this observation and coincides with association results found both by single SNP and haplotype analyses. Our analyses identified haplotypes carrying quantitative trait loci alleles associated with high protein yield and simultaneously fewer incidences of clinical mastitis. The fact that such haplotypes are found in relative high frequencies in Norwegian Red may reflect the combined breeding goal that is characterized by selection for both milk production and disease resistance. The identification of these haplotypes raises the possibility of overcoming the unfavourable genetic correlation between these traits through haplotype-assisted selection.

• Nilsen, Heidi; Olsen, Hanne Gro; Hayes, Ben J.; Sehested, Erling; Svendsen, Morten & Nome, Torfinn [Show all 8 contributors for this article] (2009). Casein haplotypes and their association with milk production traits in Norwegian Red cattle. Genetics Selection Evolution. ISSN 0999-193X. 41(art. 24), p. 12–12. doi: 10.1186/1297-9686-41-24. Full text in Research Archive Show summary

  A high resolution SNP map was constructed for the bovine casein region to identify haplotype structures and study associations with milk traits in Norwegian Red cattle. Our analyses suggest separation of the casein cluster into two haplotype blocks, one consisting of the CSN1S1, CSN2 and CSN1S2 genes and another one consisting of the CSN3 gene. Highly significant associations with both protein and milk yield were found for both single SNPs and haplotypes within the CSN1S1-CSN2-CSN1S2 haplotype block. In contrast, no significant association was found for single SNPs or haplotypes within the CSN3 block. Our results point towards CSN2 and CSN1S2 as the most likely loci harbouring the underlying causative DNA variation. In our study, the most significant results were found for the SNP CSN2_67 with the C allele consistently associated with both higher protein and milk yields. CSN2_67 calls a C to an A substitution at codon 67 in beta-casein gene resulting in histidine replacing proline in the amino acid sequence. This polymorphism determines the protein variants A1/B (CSN2_67 A allele) versus A2/A3 (CSN2_67 C allele). Other studies have suggested that a high consumption of A1/B milk may affect human health by increasing the risk of diabetes and heart diseases. Altogether these results argue for an increase in the frequency of the CSN2_67 C allele or haplotypes containing this allele in the Norwegian Red cattle population by selective breeding.

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• Pearse, Devon E.; Barson, Nicola; Nome, Torfinn; Gao, Guangtu; Campbell, Matthew A. & Abadía-Cardoso, Alicia [Show all 32 contributors for this article] (2020). Publisher Correction: Sex-dependent dominance maintains migration supergene in rainbow trout (Nature Ecology & Evolution, (2019), 3, 12, (1731-1742), 10.1038/s41559-019-1044-6). Nature Ecology and Evolution. 4(1), p. 170–170. doi: 10.1038/s41559-019-1076-y. Full text in Research Archive
• Namouchi, Amine; Nome, Torfinn; To, Thu-Hien; Grønvold, Lars; Sandve, Simen Rød & Våge, Dag Inge (2019). SalmoBase2.0: An integrative genomic data resource for salmonids. Full text in Research Archive
• To, Thu-Hien; Grønvold, Lars; Nome, Torfinn; Namouchi, Amine; Våge, Dag Inge & Sandve, Simen Rød (2019). A salmonid ohnology pipeline. Full text in Research Archive
• Sandve, Simen Rød; Hvidsten, Torgeir Rhoden; Lien, Sigbjørn; Rori, Rohlfs; Jakobsen, Kjetill Sigurd & Nome, Torfinn [Show all 9 contributors for this article] (2017). Evolution after whole genome duplication - insights from the salmonids. Full text in Research Archive
• Nome, Torfinn; Sandve, Simen Rød; Lien, Sigbjørn & Kent, Matthew Peter (2017). Development of exome capture sequencing for the Atlantic salmon (Salmo salar). Full text in Research Archive
• Barson, Nicola; Aykanat, Tutku; Hindar, Kjetil; Baranski, Matthew; Bolstad, Geir Hysing & Fiske, Peder [Show all 22 contributors for this article] (2016). Sex-Dependent Dominance At A Single Locus Maintains Variation In Age At Maturity In Salmon. Full text in Research Archive
• Skotheim, Rolf Inge; Nome, Torfinn; Thomassen, Gard O Sundby; Johannessen, Bjarne; Bakken, Anne Cathrine & Bruun, Jarle [Show all 10 contributors for this article] (2012). Identification of Fusion Transcripts in Colorectal Cancer by Combined RNA-seq and Exon Microarray Analyses. European Journal of Cancer. ISSN 0959-8049. 48, p. S121–S121. Full text in Research Archive

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