A5086044464- Genetic diversity and population structure
- Forest ecology and management
- Plant and animal studies
- Ecology and Vegetation Dynamics Studies
- Genetic Mapping and Diversity in Plants and Animals
- Cancer Genomics and Diagnostics
- DNA Repair Mechanisms
- Genomic variations and chromosomal abnormalities
- Genetic and phenotypic traits in livestock
- BRCA gene mutations in cancer
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- Forest Insect Ecology and Management
- Species Distribution and Climate Change
- Plant Water Relations and Carbon Dynamics
- Chromosomal and Genetic Variations
- Genomics and Rare Diseases
- Tree-ring climate responses
- Genomics and Chromatin Dynamics
- Telomeres, Telomerase, and Senescence
- Genetic factors in colorectal cancer
- Botany and Plant Ecology Studies
- Molecular Biology Techniques and Applications
- Chronic Lymphocytic Leukemia Research
- Immunodeficiency and Autoimmune Disorders
University of Oulu
2020-2025
NordLab
2020-2023
The fluorescence in situ hybridization (FISH) technique plays an important role the risk stratification and clinical management of patients with chronic lymphocytic leukemia (CLL). For genome-wide analysis, FISH needs to be complemented other cytogenetic methods, including karyotyping and/or chromosomal microarrays. However, this is often not feasible a diagnostic setup. Optical genome mapping (OGM) novel for high-resolution detection structural variants (SVs), previous studies have...
Abstract Purpose Several variants in DNA damage response (DDR) genes increase the probability to develop breast cancer and show enrichment Northern Finland. Here, population prevalence risk estimations were refined for sixteen recurrent pathogenic/likely pathogenic DDR gene variants. Methods Variant genotyping was performed 2343 unselected Finnish cases 4607 cancer-free controls, tumor features family history of carriers examined. Results Based on their carrier history, studied BRCA1 BRCA2...
Pinus sylvestris (Scots pine) is the most widespread coniferous tree in boreal forests of Eurasia, with major economic and ecological importance. However, its large repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping genomic selection. We present new 50K single-nucleotide polymorphism (SNP) genotyping array Scots pine research, breeding other applications. To select SNP set, we first genotyped 480 samples on 407 540...
Abstract Motivation Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide in leaf traits from seven the most ecologically economically important tree Europe. Sample collection trait assessment are embedded GenTree project (EU‐Horizon 2020), which aims at characterizing phenotypic variability forest optimize management sustainable use resources. Our...
Summary Understanding the dynamics of selection is key to predicting response tree species new environmental conditions in current context climate change. However, patterns acting on early recruitment stages and their climatic drivers remain largely unknown most species, despite being a critical period life cycle. We measured phenotypic Pinus sylvestris seed mass, emergence time growth rate over 2 yr four common garden experiments established along latitudinal gradient Europe. Significant...
New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes spectrum new that can occur along a genome, is, therefore, vital interest in evolutionary biology. Recent work has uncovered striking similarities DFE between closely related species, prompting us to ask whether there is variation among populations same or species with different degrees divergence, at levels evolution. Using exome capture data from six tree sampled across...
Progress in the field of evolutionary forest ecology has been hampered by huge challenge phenotyping trees across their ranges natural environments, and limitation high-resolution environmental information. The GenTree Platform contains phenotypic data from 4,959 12 ecologically economically important European tree species: Abies alba Mill. (silver fir), Betula pendula Roth. birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra (Swiss stone...
Breast cancer is strongly influenced by hereditary risk factors. Yet, the known susceptibility genes and genomic loci explain only about half of familial component disease. To identify novel breast predisposing gene defects, here we have performed massive parallel sequencing for Northern Finnish cases.Ninety-eight cases with indication disease were exome sequenced. Data filtering strategy focused on predictably deleterious rare variants that still enriched in sequenced cohort. Findings...
The masking theory states that genes expressed in a haploid stage will be under more efficient selection. In contrast, selection less diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can hidden from heterozygous form. This difference influence several evolutionary processes such as maintenance genetic variation, adaptation rate, and load. Masking expectations have been confirmed single-cell organisms. However, multicellular organisms, plants, are not...
Abstract CHEK2 is a well-established breast cancer susceptibility gene. The most frequent pathogenic variant 1100delC, loss-of-function mutation conferring 2-fold risk for cancer. This gene also harbors other rare variants encountered in the clinical panels hereditary One of these c.1312 G > T, p.(Asp438Tyr) kinase domain protein, but due to its rarity significance predisposition has remained unclear. Here, we tested prevalence allele showing enrichment Northern Finnish population, total...
Abstract Parallel clines in traits related to adaptation a species can be due independent selection on pair of traits, or one trait resulting parallel cline correlated trait. To distinguish between the mechanisms giving rise adaptive population divergence multiple along an environmental gradient we need study variation, correlations, and selective forces within individual populations gradient. In many tree species, budset timing (BST) forms latitudinal cline, clinal variation is also found...
ABSTRACT Background Rare protein truncating variants of NTHL1 gene are causative for the recently described, recessively inherited tumor syndrome that is characterized by an increased lifetime risk colorectal cancer, polyposis, and breast cancer. Although there strong evidence cancer being a part spectrum in these families, role pathogenic susceptibility general population remains unclear. Methods We tested prevalence nonsense variant c.268C>T, p.Q90*, which major allele families also...
Abstract Large and highly repetitive genomes are common. However, research interests usually lie within the non-repetitive parts of genome, as they more likely functional, can be used to answer questions related adaptation, selection, evolutionary history. Exome capture is a cost-effective method for providing sequencing data from protein-coding genes. C0t-1 DNA blockers consist in exome captures prevent hybridization sequences baits or bait-bound genomic DNA. Universal target regions shared...
Large and highly repetitive genomes are common. However, research interests usually lie within the non-repetitive parts of genome, as they more likely functional, can be used to answer questions related adaptation, selection evolutionary history. Exome capture is a cost-effective method for providing sequencing data from protein-coding genes. C0t-1 DNA blockers consist in exome captures prevent hybridisation sequences baits or bait-bound genomic DNA. Universal target regions shared by many...
Abstract TINF2 is a critical subunit of the shelterin complex, which protects and maintains length telomeres. Pathogenic missense truncating mutations are causative for dyskeratosis congenita (DC), rare, dominantly inherited bone marrow failure syndrome characterized by mucocutaneous abnormalities cancer predisposition. Recent reports indicate that specific act as high penetrance predisposition alleles outside DC context, including breast in their tumor spectrum. Here, we have evaluated role...
Abstract The masking theory states that genes expressed in haploid stage will be under more efficient selection. In contrast, selection less diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can hidden from heterozygous form. This difference influence several evolutionary processes such as maintenance genetic variation, adaptation rate, and load. Masking expectations have been confirmed single-cell organisms. However, multicellular organisms, plants,...
Copy number variants (CNVs) are a major source of genetic variation and can disrupt genes or affect gene dosage. They known to be causal underlie predisposition various diseases. However, the role CNVs in inherited breast cancer susceptibility has not been thoroughly investigated. To address this, we performed whole-exome sequencing based analysis rare 98 high-risk Northern Finnish cases. After filtering, selected candidate alleles were validated characterized with combination orthogonal...
Summary Scots pine ( Pinus sylvestris ) is the most widespread coniferous tree in boreal forests of Eurasia and has major economic ecological importance. However, its large repetitive genome presents a challenge for conducting genome-wide analyses such as association studies genomic selection. We present new 50K SNP genotyping array research, breeding programs, other applications. To select set, we first genotyped 480 samples on 407 540 screening array, identified 47 712 high-quality SNPs...