Snædís Kristmundsdóttir
A5042478494- Genomics and Rare Diseases
- Genomics and Phylogenetic Studies
- Genetic Associations and Epidemiology
- Cancer Genomics and Diagnostics
- Genetic factors in colorectal cancer
- Genomic variations and chromosomal abnormalities
- RNA modifications and cancer
- Chromosomal and Genetic Variations
- Genetic Syndromes and Imprinting
- Protein Tyrosine Phosphatases
- RNA and protein synthesis mechanisms
- Cancer-related Molecular Pathways
- Epigenetics and DNA Methylation
- Digestive system and related health
- Nutrition, Genetics, and Disease
- Genomics and Chromatin Dynamics
- Molecular Biology Techniques and Applications
- Genetics and Neurodevelopmental Disorders
- Lipoproteins and Cardiovascular Health
- Mast cells and histamine
- BRCA gene mutations in cancer
- Prenatal Screening and Diagnostics
- Iron Metabolism and Disorders
- Lung Cancer Treatments and Mutations
- Forensic and Genetic Research
deCODE Genetics (Iceland)
2016-2025
Reykjavík University
2016-2023
Detailed knowledge of how diversity in the sequence human genome affects phenotypic depends on a comprehensive and reliable characterization both sequences variation. Over past decade, insights into this relationship have been obtained from whole-exome sequencing or whole-genome large cohorts with rich data1,2. Here we describe analysis 150,119 individuals UK Biobank3. This constitutes set high-quality variants, including 585,040,410 single-nucleotide polymorphisms, representing 7.0% all...
Lipoprotein(a) [Lp(a)] is a causal risk factor for cardiovascular diseases that has no established therapy. The attribute of Lp(a) affects not established. Low levels have been associated with type 2 diabetes (T2D). This study investigated whether conferred by molar concentration or apolipoprotein(a) [apo(a)] size, and the relationship between T2D causal. was case-control 143,087 Icelanders genetic information, including 17,715 coronary artery disease (CAD) 8,734 T2D. used measured...
Analysis of sequence diversity in the human genome is fundamental for genetic studies. Structural variants (SVs) are frequently omitted analysis studies, although each has a relatively large impact on genome. Here, we present GraphTyper2, which uses pangenome graphs to genotype SVs and small using short-reads. Comparison syndip benchmark dataset shows that our SV genotyping sensitive variant segregation families demonstrates accuracy approach. We demonstrate incorporating public assembly...
Abstract Understanding of sequence diversity is the cornerstone analysis genetic disorders, population genetics, and evolutionary biology. Here, we present an update our sequencing set to 15,220 Icelanders who sequenced average genome-wide coverage 34X. We identified 39,020,168 autosomal variants passing GATK filters: 31,079,378 SNPs 7,940,790 indels. Calling de novo mutations (DNMs) a formidable challenge given high false positive rate in datasets relative mutation rate. Here addressed this...
A major challenge to long read sequencing data is their high error rate of up 15%. We present Ratatosk, a method correct reads with short data. demonstrate on 5 human genome trios that Ratatosk reduces the 6-fold average median as low 0.22 %. SNP calls in corrected are nearly 99 % accurate and indel accuracy increased by 37 An assembly from an Ashkenazi individual yields contig N50 45 Mbp less misassemblies than PacBio HiFi assembly.
Abstract Microsatellites are polymorphic tracts of short tandem repeats with one to six base-pair (bp) motifs and some the most variants in genome. Using 6084 Icelandic parent-offspring trios we estimate 63.7 (95% CI: 61.9–65.4) microsatellite de novo mutations (mDNMs) per offspring generation, excluding bp (homopolymers) is 48.2 mDNMs 46.7–49.6). Paternal occur at longer than maternal ones, which turn larger a mean size 3.4 vs 3.1 for paternal ones. increase by 0.97 0.90–1.04) 0.31...
Long-read sequencing (LRS) promises to improve characterization of structural variants (SVs), a major source genetic diversity. We generated LRS data on 3,622 Icelanders using Oxford Nanopore Technologies, and identified median 22,636 SVs per individual (a 13,353 insertions 9,474 deletions), spanning 10 Mb haploid genome. discovered set 133,886 reliably genotyped SV alleles imputed them into 166,281 individuals explore their effects diseases other traits. an association with rare (AF =...
Abstract Motivation Microsatellites, also known as short tandem repeats (STRs), are tracts of repetitive DNA sequences containing motifs ranging from two to six bases. Microsatellites one the most abundant type variation in human genome, after single nucleotide polymorphisms (SNPs) and Indels. Microsatellite analysis has a wide range applications, including medical genetics, forensics construction genetic genealogy. However, microsatellite variations rarely considered whole-genome sequencing...
Urine dipstick tests are widely used in routine medical care to diagnose kidney and urinary tract metabolic diseases. Several environmental factors known affect the test results, whereas effects of genetic diversity largely unknown. We tested 32.5 million sequence variants for association with biomarkers a set 150 274 Icelanders urine measurements. detected 20 signals, which 14 novel, associating at least one five clinical entities defined by dipstick: glucosuria, ketonuria, proteinuria,...
Abstract The corneal endothelium is vital for transparency and proper hydration of the cornea. Here, we conduct a genome-wide association study endothelial cell density (cells/mm 2 ), coefficient size variation (CV), percentage hexagonal cells (HEX) central thickness (CCT) in 6,125 Icelanders find associations at 10 loci, including 7 novel. We assess effects these variants on various ocular biomechanics such as hysteresis (CH), well eye diseases glaucoma dystrophies. Most notably, an...
Genotypes causing pregnancy loss and perinatal mortality are depleted among living individuals therefore difficult to find. To explore genetic causes of recessive lethality, we searched for sequence variants with deficit homozygosity 1.52 million from six European populations. In this study, identified 25 genes harboring protein-altering a strong (10% or less predicted homozygotes). Sequence in 12 the cause Mendelian disease under mode inheritance, two dominant mode, but remaining 11 have...
Objective: Familial hypercholesterolemia (FH) is traditionally defined as a monogenic disease characterized by severely elevated LDL-C (low-density lipoprotein cholesterol) levels. In practice, FH commonly clinical diagnosis without confirmation of causative mutation. this study, we sought to characterize and compare clinically in large sample Icelanders. Approach Results: We whole-genome sequenced 49 962 Icelanders imputed the identified variants into an overall 166 281 chip-genotyped 20...
Abstract We describe the analysis of whole genome sequences (WGS) 150,119 individuals from UK biobank (UKB). This constitutes a set high quality variants, including 585,040,410 SNPs, representing 7.0% all possible human and 58,707,036 indels. The large variants allows us to characterize selection based on sequence variation within population through Depletion Rank (DR) score for windows along genome. DR shows that coding exons represent small fraction regions in subject strong conservation....
popSTR2 is an update and augmentation of our previous work 'popSTR: a population-based microsatellite genotyper'. To make genotyping sensitive to inter-sample differences, we supply kernel estimate sample-specific slippage rates. For clinical sequencing purposes, panel known pathogenic repeat expansions provided along with script that scans flags for manual inspection markers indicative expansion. Like its predecessor, allows joint samples at population scale. We now provide binning method...