Eija H Seppälä

Publications of Eija H Seppälä

• Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping.

  Authors: Amaury Vaysse, Abhirami Ratnakumar, Thomas Derrien, Erik Axelsson, Gerli Rosengren Pielberg, Snaevar Sigurdsson, Tove Fall, Eija H Seppälä, Mark S T Hansen, Cindy T Lawley [......] Carles Vilà, Hannes Lohi, Francis Galibert, Merete Fredholm, Jens Häggström, Ake Hedhammar, Catherine André, Kerstin Lindblad-Toh, Christophe Hitte, Matthew T Webster

  PLoS genetics. 10/2011; 7(10):e1002316.

  The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysisThe extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease.

• LGI2 truncation causes a remitting focal epilepsy in dogs.

  Authors: Eija H Seppälä, Tarja S Jokinen, Masaki Fukata, Yuko Fukata, Matthew T Webster, Elinor K Karlsson, Sami K Kilpinen, Frank Steffen, Elisabeth Dietschi, Tosso Leeb, Ranja Eklund, Xiaochu Zhao, Jennifer J Rilstone, Kerstin Lindblad-Toh, Berge A Minassian, Hannes Lohi

  PLoS genetics. 07/2011; 7(7):e1002194.

  One quadrillion synapses are laid in the first two years of postnatal construction of the human brain, which are then pruned until age 10 to 500 trillion synapses composing the final network. GeneticOne quadrillion synapses are laid in the first two years of postnatal construction of the human brain, which are then pruned until age 10 to 500 trillion synapses composing the final network. Genetic epilepsies are the most common neurological diseases with onset during pruning, affecting 0.5% of 2-10-year-old children, and these epilepsies are often characterized by spontaneous remission. We previously described a remitting epilepsy in the Lagotto romagnolo canine breed. Here, we identify the gene defect and affected neurochemical pathway. We reconstructed a large Lagotto pedigree of around 34 affected animals. Using genome-wide association in 11 discordant sib-pairs from this pedigree, we mapped the disease locus to a 1.7 Mb region of homozygosity in chromosome 3 where we identified a protein-truncating mutation in the Lgi2 gene, a homologue of the human epilepsy gene LGI1. We show that LGI2, like LGI1, is neuronally secreted and acts on metalloproteinase-lacking members of the ADAM family of neuronal receptors, which function in synapse remodeling, and that LGI2 truncation, like LGI1 truncations, prevents secretion and ADAM interaction. The resulting epilepsy onsets at around seven weeks (equivalent to human two years), and remits by four months (human eight years), versus onset after age eight in the majority of human patients with LGI1 mutations. Finally, we show that Lgi2 is expressed highly in the immediate post-natal period until halfway through pruning, unlike Lgi1, which is expressed in the latter part of pruning and beyond. LGI2 acts at least in part through the same ADAM receptors as LGI1, but earlier, ensuring electrical stability (absence of epilepsy) during pruning years, preceding this same function performed by LGI1 in later years. LGI2 should be considered a candidate gene for common remitting childhood epilepsies, and LGI2-to-LGI1 transition for mechanisms of childhood epilepsy remission.

• A truncating mutation in ATP13A2 is responsible for adult-onset neuronal ceroid lipofuscinosis in Tibetan terriers.

  Authors: Fabiana H G Farias, Rong Zeng, Gary S Johnson, Fred A Wininger, Jeremy F Taylor, Robert D Schnabel, Stephanie D McKay, Douglas N Sanders, Hannes Lohi, Eija H Seppälä, Claire M Wade, Kerstin Lindblad-Toh, Dennis P O'Brien, Martin L Katz

  Neurobiology of disease. 02/2011; 42(3):468-74.

  A recessive, adult-onset neuronal ceroid-lipofuscinosis (NCL) occurs in Tibetan terriers. A genome-wide association study restricted this NCL locus to a 1.3Mb region of canine chromosome 2 whichA recessive, adult-onset neuronal ceroid-lipofuscinosis (NCL) occurs in Tibetan terriers. A genome-wide association study restricted this NCL locus to a 1.3Mb region of canine chromosome 2 which contains canine ATP13A2. NCL-affected dogs were homozygous for a single-base deletion in ATP13A2, predicted to produce a frameshift and premature termination codon. Homozygous truncating mutations in human ATP13A2 have been shown by others to cause Kufor-Rakeb syndrome (KRS), a rare neurodegenerative disease. These findings suggest that KRS is also an NCL, although analysis of KRS brain tissue will be needed to confirm this prediction. Generalized brain atrophy, behavioral changes, and cognitive decline occur in both people and dogs with ATP13A2 mutations; however, other clinical features differ between the species. For example, Tibetan terriers with NCL develop cerebellar ataxia not reported in KRS patients and KRS patients exhibit parkinsonism and pyramidal dysfunction not observed in affected Tibetan terriers. To see if ATP13A2 mutations could be responsible for some cases of human adult-onset NCL (Kufs disease), we resequenced ATP13A2 from 28 Kufs disease patients. None of these patients had ATP13A2 sequence variants likely to be causal for their disease, suggesting that mutations in this gene are not common causes of Kufs disease.

• Segregation of point mutation heteroplasmy in the control region of dog mtDNA studied systematically in deep generation pedigrees.

  Authors: Cornelya F C Klütsch, Eija H Seppälä, Mathias Uhlén, Hannes Lohi, Peter Savolainen

  International journal of legal medicine. 11/2010; 125(4):527-35.

  Heteroplasmy, the presence of two or more variants in an organism, may render mitochondrial DNA (mtDNA)-based individual identification challenging in forensic analysis. However, the variation ofHeteroplasmy, the presence of two or more variants in an organism, may render mitochondrial DNA (mtDNA)-based individual identification challenging in forensic analysis. However, the variation of heteroplasmic proportions and the segregation of heteroplasmic variants through generations and within families have not been systematically described at a large scale in animals such as the domestic dog. Therefore, we performed the largest study to date in domestic dogs and screened a 582-bp-long fragment of the mtDNA control region in 180 individuals in 58 pedigrees for signs of heteroplasmy. We identified three pedigrees (5.17%) with heteroplasmic point mutations. To follow the segregation of the point mutations, we then analyzed 131 samples from these three independent pedigrees and found significant differences in heteroplasmy between generations and among siblings. Frequently (10% of cases), the proportion of one base changed from 0-10% to 80-90% (as judged from Sanger electropherograms) between generations and varied to a similar extent among siblings. We included also a literature review of heteroplasmic and potential mutational hot spot positions in the studied region which showed that all heteroplasmic positions appear to be mutational hot spots. Thus, although heteroplasmy may be used to increase the significance of a match in forensic case work, it may also cause erroneous exclusion of related individuals because of sharp switches from one state to the other within a single generation or among siblings especially in the presented mutational hot spots.

• KLF6 IVS1 -27G>A variant and the risk of prostate cancer in Finland.

  Authors: Eija H Seppälä, Ville Autio, Priya Duggal, Tarja Ikonen, Ulf-Håkan Stenman, Anssi Auvinen, Joan E Bailey-Wilson, Teuvo L J Tammela, Johanna Schleutker

  European urology. 11/2007; 52(4):1076-81.

  OBJECTIVES: A recent report demonstrated that KLF6 IVS1 -27G>A substitution increases the transcription of alternatively spliced isoforms; this action was suggested to be associated with prostateOBJECTIVES: A recent report demonstrated that KLF6 IVS1 -27G>A substitution increases the transcription of alternatively spliced isoforms; this action was suggested to be associated with prostate cancer (pCA). To evaluate these findings among the Finnish population, a total of 3348 samples were analysed. METHODS: The variant was genotyped in 164 patients with familial pCA, 852 patients with unselected pCA, 459 patients with benign prostate hyperplasia (BPH), 923 male population controls, and 950 men from a Finnish prostate-specific antigen (PSA) screening trial with PSA levels less than 1.0ng/ml. Odds ratios (ORs) and corresponding 95% confidence intervals (95%CIs) were calculated by using logistic regression to estimate pCA risk. RESULTS: Association testing revealed no significant differences between familial prostate cancer patients and population controls (OR: 0.84; 95%CI, 0.56-1.28; p=0.42), unselected cases and controls (OR: 0.95; 95%CI, 0.76-1.19; p=0.63), or BPH cases and controls (OR: 1.12; 95%CI, 0.86-1.46; p=0.39). pCA and BPH cases were also compared with PSA-screened controls. None of these analyses revealed any significant associations. CONCLUSIONS: Our results do not support the suggested association of KLF6 IVS1 -27G>A germline polymorphism with pCA risk and also suggest that the variant is not a risk allele for BPH in the Finnish population.

• Profiling genetic variation along the androgen biosynthesis and metabolism pathways implicates several single nucleotide polymorphisms and their combinations as prostate cancer risk factors.

  Authors: Nina Mononen, Eija H Seppälä, Priya Duggal, Ville Autio, Tarja Ikonen, Pekka Ellonen, Juha Saharinen, Janna Saarela, Mauno Vihinen, Teuvo L J Tammela, Olli Kallioniemi, Joan E Bailey-Wilson, Johanna Schleutker

  Cancer research. 02/2006; 66(2):743-7.

  Several candidate genes along androgen pathway have been suggested to affect prostate cancer risk but no single gene seems to be overwhelmingly important for a large fraction of the patients. In thisSeveral candidate genes along androgen pathway have been suggested to affect prostate cancer risk but no single gene seems to be overwhelmingly important for a large fraction of the patients. In this study, we first screened for variants in candidate genes and then chose to explore the association between 18 variants and prostate cancer risk by genotyping DNA samples from unselected (n = 847) and familial (n = 121) prostate cancer patients and population controls (n = 923). We identified a novel single nucleotide polymorphism (SNP) in the CYP19A1 gene, T201M, with a mild significant association with prostate cancer [odds ratio (OR), 2.04; 95% confidence interval (95% CI), 1.03-4.03; P = 0.04]. Stratified analysis revealed that this risk was most apparent in patients with organ-confined (T(1)-T(2)) and low-grade (WHO grade 1) tumors (OR, 5.42; 95% CI, 2.33-12.6; P < 0.0001). In contrast, CYP17A1 -34T>C alteration was associated with moderate to poorly differentiated (WHO grade 2-3) organ-confined disease (OR, 1.42; 95% CI, 1.09-1.83; P = 0.007). We also tested a multigenic model of prostate cancer risk by calculating the joint effect of CYP19A1 T201M with five other common SNPs. Individuals carrying both the CYP19A1 and KLK3 -252A>G variant alleles had a significantly increased risk for prostate cancer (OR, 2.87; 95% CI, 1.10-7.49; P = 0.03). In conclusion, our results suggest that several SNPs along the androgen pathway, especially in CYP19A1 and CYP17A1, may influence prostate cancer development and progression. These genes may have different contributions to distinct clinical subsets as well as combinatorial effects in others illustrating that profiling and joint analysis of several genes along each pathway may be needed to understand genetic contributions to prostate cancer etiology.

• Germ-line alterations in MSR1 gene and prostate cancer risk.

  Authors: Eija H Seppälä, Tarja Ikonen, Ville Autio, Annika Rökman, Nina Mononen, Mika P Matikainen, Teuvo L J Tammela, Johanna Schleutker

  Clinical cancer research : an official journal of the American Association for Cancer Research. 11/2003; 9(14):5252-6.

  PURPOSE: The MSR1 gene maps to 8p22-23, a novel susceptibility locus for hereditary prostate cancer (HPC). Mutations in MSR1 have been reported to associate with prostate cancer (PRCA) risk. Here wePURPOSE: The MSR1 gene maps to 8p22-23, a novel susceptibility locus for hereditary prostate cancer (HPC). Mutations in MSR1 have been reported to associate with prostate cancer (PRCA) risk. Here we report a follow-up study from Finland to evaluate the association between PRCA and MSR1 gene. EXPERIMENTAL DESIGN: The youngest affected patient from each of 120 HPC families was initially used for the screening of MSR1 mutations by single-strand conformational polymorphism analysis. Selected variants of MSR1 gene were then screened in 537 unselected PRCA cases and in 480 controls. RESULTS: Among 120 HPC families, five MSR1 sequence variants were identified. The carrier frequencies of the R293X, P275A, and -14743A>G variants were compared between the probands with HPC, unselected PRCA cases, and healthy male blood donors. No significant differences were observed. The odds ratios for R293X, P275A, and -14743A>G mutations were also calculated to estimate the PRCA risk. No significantly elevated or lowered risks for PRCA among these three variants were detected. However, the mean age at diagnosis of the R293X mutation carriers among HPC probands was significantly lower compared with noncarriers (55.4 versus 65.4 years; t test, P = 0.04). The same trend was observed among unselected PRCA cases (65.7 versus 68.7 years; t test, P = 0.37). CONCLUSIONS: Our results do not support a major role for the MSR1 gene in the causation of hereditary or unselected PRCAs but suggest a possible modifying role in cancer predisposition.

• Germline alterations of the RNASEL gene, a candidate HPC1 gene at 1q25, in patients and families with prostate cancer.

  Authors: Annika Rökman, Tarja Ikonen, Eija H Seppälä, Nina Nupponen, Ville Autio, Nina Mononen, Joan Bailey-Wilson, Jeffrey Trent, John Carpten, Mika P Matikainen, Pasi A Koivisto, Teuvo L J Tammela, Olli-P Kallioniemi, Johanna Schleutker

  American journal of human genetics. 06/2002; 70(5):1299-304.

  The RNASEL gene (2',5'-oligoisoadenylate-synthetase dependent) encodes a ribonuclease that mediates the antiviral and apoptotic activities of interferons. The RNASEL gene maps to theThe RNASEL gene (2',5'-oligoisoadenylate-synthetase dependent) encodes a ribonuclease that mediates the antiviral and apoptotic activities of interferons. The RNASEL gene maps to the hereditary-prostate-cancer (HPC)-predisposition locus at 1q24-q25 (HPC1) and was recently shown to harbor truncating mutations in two families with linkage to HPC1. Here, we screened for RNASEL germline mutations in 66 Finnish patients with HPC, and we determined the frequency of the changes in the index patients from 116 families with HPC, in 492 patients with unselected prostate cancer (PRCA), in 223 patients with benign prostatic hyperplasia (BPH), and in 566 controls. A truncating mutation, E265X, was found in 5 (4.3%) of the 116 patients from families with HPC. This was significantly higher (odds ratio [OR] =4.56; P=.04) than the frequency of E265X in controls (1.8%). The highest mutation frequency (9.5%) was found in patients from families with four or more affected members. Possible segregation was detected only in a single family. However, the median age at disease onset for E265X carriers was 11 years less than that for noncarriers in the same families. In addition, of the four missense variants found, R462Q showed an association with HPC (OR=1.96; P=.07). None of the variants showed any differences between controls and either patients with BPH or patients with PRCA. We conclude that, although RNASEL mutations do not explain disease segregation in Finnish families with HPC, the variants are enriched in families with HPC that include more than two affected members and may also be associated with the age at disease onset. This suggests a possible modifying role in cancer predisposition. The impact that the RNASEL sequence variants have on PRCA burden at the population level seems small but deserves further study.