Variant in the synaptonemal complex protein SYCE2 associates with pregnancy loss through effect on recombination

Two-thirds of all human conceptions are lost, in most cases before clinical detection. The lack of detailed understanding of the causes of pregnancy losses constrains focused counseling for future pregnancies. We have previously shown that a missense variant in synaptonemal complex central element protein 2 (SYCE2), in a key residue for the assembly of the synaptonemal complex backbone, associates with recombination traits. Here we show that it also increases risk of pregnancy loss in a genome-wide association analysis on 114,761 women with reported pregnancy loss. We further show that the variant associates with more random placement of crossovers and lower recombination rate in longer chromosomes but higher in the shorter ones. These results support the hypothesis that some pregnancy losses are due to failures in recombination. They further demonstrate that variants with a substantial effect on the quality of recombination can be maintained in the population.

A population-based survey of FBN1 variants in Iceland reveals underdiagnosis of Marfan syndrome

Marfan syndrome (MFS) is an autosomal dominant condition characterized by aortic aneurysm, skeletal abnormalities, and lens dislocation, and is caused by variants in the FBN1 gene. To explore causes of MFS and the prevalence of the disease in Iceland we collected information from all living individuals with a clinical diagnosis of MFS in Iceland (n = 32) and performed whole-genome sequencing of those who did not have a confirmed genetic diagnosis (27/32). Moreover, to assess a potential underdiagnosis of MFS in Iceland we attempted a genotype-based approach to identify individuals with MFS. We interrogated deCODE genetics' database of 35,712 whole-genome sequenced individuals to search for rare sequence variants in FBN1. Overall, we identified 15 pathogenic or likely pathogenic variants in FBN1 in 44 individuals, only 22 of whom were previously diagnosed with MFS. The most common of these variants, NM_000138.4:c.8038 C > T p.(Arg2680Cys), is present in a multi-generational pedigree, and was found to stem from a single forefather born around 1840. The p.(Arg2680Cys) variant associates with a form of MFS that seems to have an enrichment of abdominal aortic aneurysm, suggesting that this may be a particularly common feature of p.(Arg2680Cys)-associated MFS. Based on these combined genetic and clinical data, we show that MFS prevalence in Iceland could be as high as 1/6,600 in Iceland, compared to 1/10,000 based on clinical diagnosis alone, which indicates underdiagnosis of this actionable genetic disorder.

Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis

Clonal hematopoiesis (CH) arises when a substantial proportion of mature blood cells is derived from a single hematopoietic stem cell lineage. Using whole-genome sequencing of 45,510 Icelandic and 130,709 UK Biobank participants combined with a mutational barcode method, we identified 16,306 people with CH. Prevalence approaches 50% in elderly participants. Smoking demonstrates a dosage-dependent impact on risk of CH. CH associates with several smoking-related diseases. Contrary to published claims, we find no evidence that CH is associated with cardiovascular disease. We provide evidence that CH is driven by genes that are commonly mutated in myeloid neoplasia and implicate several new driver genes. The presence and nature of a driver mutation alters the risk profile for hematological disorders. Nevertheless, most CH cases have no known driver mutations. A CH genome-wide association study identified 25 loci, including 19 not implicated previously in CH. Splicing, protein and expression quantitative trait loci were identified for CD164 and TCL1A.

Actionable Genotypes and Their Association with Life Span in Iceland

BACKGROUND

In 2021, the American College of Medical Genetics and Genomics (ACMG) recommended reporting actionable genotypes in 73 genes associated with diseases for which preventive or therapeutic measures are available. Evaluations of the association of actionable genotypes in these genes with life span are currently lacking.

METHODS

We assessed the prevalence of coding and splice variants in genes on the ACMG Secondary Findings, version 3.0 (ACMG SF v3.0), list in the genomes of 57,933 Icelanders. We assigned pathogenicity to all reviewed variants using reported evidence in the ClinVar database, the frequency of variants, and their associations with disease to create a manually curated set of actionable genotypes (variants). We assessed the relationship between these genotypes and life span and further examined the specific causes of death among carriers.

RESULTS

Through manual curation of 4405 sequence variants in the ACMG SF v3.0 genes, we identified 235 actionable genotypes in 53 genes. Of the 57,933 participants, 2306 (4.0%) carried at least one actionable genotype. We found shorter median survival among persons carrying actionable genotypes than among noncarriers. Specifically, we found that carrying an actionable genotype in a cancer gene was associated with survival that was 3 years shorter than that among noncarriers, with causes of death among carriers attributed primarily to cancer-related conditions. Furthermore, we found evidence of association between carrying an actionable genotype in certain genes in the cardiovascular disease group and a reduced life span.

CONCLUSIONS

On the basis of the ACMG SF v3.0 guidelines, we found that approximately 1 in 25 Icelanders carried an actionable genotype and that carrying such a genotype was associated with a reduced life span. (Funded by deCODE Genetics-Amgen.).

Sequence variants affecting the genome-wide rate of germline microsatellite mutations

Microsatellites are polymorphic tracts of short tandem repeats with one to six base-pair (bp) motifs and are some of the most polymorphic variants in the genome. Using 6084 Icelandic parent-offspring trios we estimate 63.7 (95% CI: 61.9-65.4) microsatellite de novo mutations (mDNMs) per offspring per generation, excluding one bp repeats motifs (homopolymers) the estimate is 48.2 mDNMs (95% CI: 46.7-49.6). Paternal mDNMs occur at longer repeats than maternal ones, which are in turn larger with a mean size of 3.4 bp vs 3.1 bp for paternal ones. mDNMs increase by 0.97 (95% CI: 0.90-1.04) and 0.31 (95% CI: 0.25-0.37) per year of father's and mother's age at conception, respectively. Here, we find two independent coding variants that associate with the number of mDNMs transmitted to offspring; The minor allele of a missense variant (allele frequency (AF) = 1.9%) in MSH2, a mismatch repair gene, increases transmitted mDNMs from both parents (effect: 13.1 paternal and 7.8 maternal mDNMs). A synonymous variant (AF = 20.3%) in NEIL2, a DNA damage repair gene, increases paternally transmitted mDNMs (effect: 4.4 mDNMs). Thus, the microsatellite mutation rate in humans is in part under genetic control.

Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality

Genotypes causing pregnancy loss and perinatal mortality are depleted among living individuals and are therefore difficult to find. To explore genetic causes of recessive lethality, we searched for sequence variants with deficit of homozygosity among 1.52 million individuals from six European populations. In this study, we identified 25 genes harboring protein-altering sequence variants with a strong deficit of homozygosity (10% or less of predicted homozygotes). Sequence variants in 12 of the genes cause Mendelian disease under a recessive mode of inheritance, two under a dominant mode, but variants in the remaining 11 have not been reported to cause disease. Sequence variants with a strong deficit of homozygosity are over-represented among genes essential for growth of human cell lines and genes orthologous to mouse genes known to affect viability. The function of these genes gives insight into the genetics of intrauterine lethality. We also identified 1077 genes with homozygous predicted loss-of-function genotypes not previously described, bringing the total set of genes completely knocked out in humans to 4785.

Holes in the tundra: Invasive earthworms alter soil structure and moisture in tundra soils

Human introductions have resulted in earthworms establishing in the Arctic, species known to cause cascading ecosystem change. However, few quantitative outdoor experiments have been performed that describe how these soil modifying earthworms are reshaping structures in tundra soils. In this study, we used three-dimensional (3-D) X-ray images of soil cores (approximately 10 cm diameter, 20 cm height, N = 48) to assess how earthworms (Aporrectodea sp. and Lumbricus sp.) affect soil structure and macropore networks in an outdoor mesocosm experiment that lasted four summers. Effects were assessed in both shrub-dominated (heath) and herb-dominated (meadow) tundra. Earthworms almost doubled the macroporosity in meadow soils and tripled macroporosity in heath. Interestingly, the fractal dimension of macropores decreased in response to earthworm burrowing in both systems, indicating that the presence of earthworms reduced the geometric complexity in comparison to other pore-generating processes active in the tundra. Observed effects on soil structure occurred along with a dramatically reduced soil moisture content, which was observed the first winter after earthworm introduction in the meadow. Our findings suggest that predictions of future changes in vegetation and soil carbon pools in the Arctic should include major impacts on soil properties that earthworms induce.

The sequences of 150,119 genomes in the UK Biobank

Detailed knowledge of how diversity in the sequence of the human genome affects phenotypic diversity depends on a comprehensive and reliable characterization of both sequences and phenotypic variation. Over the past decade, insights into this relationship have been obtained from whole-exome sequencing or whole-genome sequencing of large cohorts with rich phenotypic data^1,2. Here we describe the analysis of whole-genome sequencing of 150,119 individuals from the UK Biobank³. This constitutes a set of high-quality variants, including 585,040,410 single-nucleotide polymorphisms, representing 7.0% of all possible human single-nucleotide polymorphisms, and 58,707,036 indels. This large set of variants allows us to characterize selection based on sequence variation within a population through a depletion rank score of windows along the genome. Depletion rank analysis shows that coding exons represent a small fraction of regions in the genome subject to strong sequence conservation. We define three cohorts within the UK Biobank: a large British Irish cohort, a smaller African cohort and a South Asian cohort. A haplotype reference panel is provided that allows reliable imputation of most variants carried by three or more sequenced individuals. We identified 895,055 structural variants and 2,536,688 microsatellites, groups of variants typically excluded from large-scale whole-genome sequencing studies. Using this formidable new resource, we provide several examples of trait associations for rare variants with large effects not found previously through studies based on whole-exome sequencing and/or imputation.

Reconstruction of a large-scale outbreak of SARS-CoV-2 infection in Iceland informs vaccination strategies

OBJECTIVES

The spread of SARS-CoV-2 is dependent on several factors, both biological and behavioural. The effectiveness of nonpharmaceutical interventions can be attributed largely to changes in human behaviour, but quantifying this effect remains challenging. Reconstructing the transmission tree of the third wave of SARS-CoV-2 infections in Iceland using contact tracing and viral sequence data from 2522 cases enables us to directly compare the infectiousness of distinct groups of persons.

METHODS

The transmission tree enables us to model the effect that a given population prevalence of vaccination would have had on the third wave had one of three different vaccination strategies been implemented before that time. This allows us to compare the effectiveness of the strategies in terms of minimizing the number of cases, deaths, critical cases, and severe cases.

RESULTS

We found that people diagnosed outside of quarantine (Rˆ=1.31) were 89% more infectious than those diagnosed while in quarantine (Rˆ=0.70) and that infectiousness decreased as a function of time spent in quarantine before diagnosis, with people diagnosed outside of quarantine being 144% more infectious than those diagnosed after ≥3 days in quarantine (Rˆ=0.54). People of working age, 16 to 66 years (Rˆ=1.08), were 46% more infectious than those outside of that age range (Rˆ=0.74).

DISCUSSION

We found that vaccinating the population in order of ascending age or uniformly at random would have prevented more infections per vaccination than vaccinating in order of descending age, without significantly affecting the expected number of deaths, critical cases, or severe cases.

Diffuse idiopathic skeletal hyperostosis in elderly Icelanders and its association with the metabolic syndrome: the AGES-Reykjavik Study

Objective: To describe the prevalence of diffuse idiopathic skeletal hyperostosis (DISH) in a large population-based study of elderly Icelanders, with particular reference to weight-related factors and the metabolic syndrome.Method: The study population comprised 5321 participants aged 68-96 years (2276 males, mean ± sd age 76 ± 5 , and 3045 females, age 77 ± 6) from the AGES-Reykjavik Study. DISH diagnosis was based on computed tomography (CT) scans, and interpreted strictly by the Resnick criteria and additional suggestions for CT interpretation by Oudkerk et al. Radiology readings were taken by a radiology resident and sample readings by two experienced radiologists.Results: A diagnosis of DISH was made in 13.7% of males and 2.8% of females. There was no association with age, but a strong association was seen with the metabolic syndrome [odds ratio (OR) 2.12, 95% confidence interval (CI) 1.69-2.64, p = 3.9 × 10^-11]. Among the components of the metabolic syndrome, the association with DISH was significant for the insulin resistance criterion (OR 1.66, 95% CI 1.32-2.01, p < 0.001) and the body mass index (BMI) criterion (OR 2.16, 95% CI 1.70-2.74, p < 0.001). Other weight-related variables (midlife BMI, weight, and abdominal circumference) showed similar associations.Conclusions: This study, which to our knowledge is the largest published study on the prevalence of DISH, shows an association with the metabolic syndrome, particularly with the insulin resistance and BMI criteria. This is analogous with previous reports linking DISH with metabolic causes. In this age category, we did not observe any increase in prevalence with age.

Loss-of-Function Variants in the Tumor-Suppressor Gene PTPN14 Confer Increased Cancer Risk

The success of genome-wide association studies (GWAS) in identifying common, low-penetrance variant-cancer associations for the past decade is undisputed. However, discovering additional high-penetrance cancer mutations in unknown cancer predisposing genes requires detection of variant-cancer association of ultra-rare coding variants. Consequently, large-scale next-generation sequence data with associated phenotype information are needed. Here, we used genotype data on 166,281 Icelanders, of which, 49,708 were whole-genome sequenced and 408,595 individuals from the UK Biobank, of which, 41,147 were whole-exome sequenced, to test for association between loss-of-function burden in autosomal genes and basal cell carcinoma (BCC), the most common cancer in Caucasians. A total of 25,205 BCC cases and 683,058 controls were tested. Rare germline loss-of-function variants in PTPN14 conferred substantial risks of BCC (OR, 8.0; P = 1.9 × 10^-12), with a quarter of carriers getting BCC before age 70 and over half in their lifetime. Furthermore, common variants at the PTPN14 locus were associated with BCC, suggesting PTPN14 as a new, high-impact BCC predisposition gene. A follow-up investigation of 24 cancers and three benign tumor types showed that PTPN14 loss-of-function variants are associated with high risk of cervical cancer (OR, 12.7, P = 1.6 × 10^-4) and low age at diagnosis. Our findings, using power-increasing methods with high-quality rare variant genotypes, highlight future prospects for new discoveries on carcinogenesis. SIGNIFICANCE: This study identifies the tumor-suppressor gene PTPN14 as a high-impact BCC predisposition gene and indicates that inactivation of PTPN14 by germline sequence variants may also lead to increased risk of cervical cancer.

Lifelong Reduction in LDL (Low-Density Lipoprotein) Cholesterol due to a Gain-of-Function Mutation in LDLR

BACKGROUND

Loss-of-function mutations in the LDL (low-density lipoprotein) receptor gene (LDLR) cause elevated levels of LDL cholesterol and premature cardiovascular disease. To date, a gain-of-function mutation in LDLR with a large effect on LDL cholesterol levels has not been described. Here, we searched for sequence variants in LDLR that have a large effect on LDL cholesterol levels.

METHODS

We analyzed whole-genome sequencing data from 43 202 Icelanders. Single-nucleotide polymorphisms and structural variants including deletions, insertions, and duplications were genotyped using whole-genome sequencing-based data. LDL cholesterol associations were carried out in a sample of >100 000 Icelanders with genetic information (imputed or whole-genome sequencing). Molecular analyses were performed using RNA sequencing and protein expression assays in Epstein-Barr virus-transformed lymphocytes.

RESULTS

We discovered a 2.5-kb deletion (del2.5) overlapping the 3' untranslated region of LDLR in 7 heterozygous carriers from a single family. Mean level of LDL cholesterol was 74% lower in del2.5 carriers than in 101 851 noncarriers, a difference of 2.48 mmol/L (96 mg/dL; P=8.4×10^-8). Del2.5 results in production of an alternative mRNA isoform with a truncated 3' untranslated region. The truncation leads to a loss of target sites for microRNAs known to repress translation of LDLR. In Epstein-Barr virus-transformed lymphocytes derived from del2.5 carriers, expression of alternative mRNA isoform was 1.84-fold higher than the wild-type isoform (P=0.0013), and there was 1.79-fold higher surface expression of the LDL receptor than in noncarriers (P=0.0086). We did not find a highly penetrant detrimental impact of lifelong very low levels of LDL cholesterol due to del2.5 on health of the carriers.

CONCLUSIONS

Del2.5 is the first reported gain-of-function mutation in LDLR causing a large reduction in LDL cholesterol. These data point to a role for alternative polyadenylation of LDLR mRNA as a potent regulator of LDL receptor expression in humans.

Humoral Immune Response to SARS-CoV-2 in Iceland

BACKGROUND

Little is known about the nature and durability of the humoral immune response to infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

METHODS

We measured antibodies in serum samples from 30,576 persons in Iceland, using six assays (including two pan-immunoglobulin [pan-Ig] assays), and we determined that the appropriate measure of seropositivity was a positive result with both pan-Ig assays. We tested 2102 samples collected from 1237 persons up to 4 months after diagnosis by a quantitative polymerase-chain-reaction (qPCR) assay. We measured antibodies in 4222 quarantined persons who had been exposed to SARS-CoV-2 and in 23,452 persons not known to have been exposed.

RESULTS

Of the 1797 persons who had recovered from SARS-CoV-2 infection, 1107 of the 1215 who were tested (91.1%) were seropositive; antiviral antibody titers assayed by two pan-Ig assays increased during 2 months after diagnosis by qPCR and remained on a plateau for the remainder of the study. Of quarantined persons, 2.3% were seropositive; of those with unknown exposure, 0.3% were positive. We estimate that 0.9% of Icelanders were infected with SARS-CoV-2 and that the infection was fatal in 0.3%. We also estimate that 56% of all SARS-CoV-2 infections in Iceland had been diagnosed with qPCR, 14% had occurred in quarantined persons who had not been tested with qPCR (or who had not received a positive result, if tested), and 30% had occurred in persons outside quarantine and not tested with qPCR.

CONCLUSIONS

Our results indicate that antiviral antibodies against SARS-CoV-2 did not decline within 4 months after diagnosis. We estimate that the risk of death from infection was 0.3% and that 44% of persons infected with SARS-CoV-2 in Iceland were not diagnosed by qPCR.

Humoral Immune Response to SARS-CoV-2 in Iceland

BACKGROUND

Little is known about the nature and durability of the humoral immune response to infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

METHODS

We measured antibodies in serum samples from 30,576 persons in Iceland, using six assays (including two pan-immunoglobulin [pan-Ig] assays), and we determined that the appropriate measure of seropositivity was a positive result with both pan-Ig assays. We tested 2102 samples collected from 1237 persons up to 4 months after diagnosis by a quantitative polymerase-chain-reaction (qPCR) assay. We measured antibodies in 4222 quarantined persons who had been exposed to SARS-CoV-2 and in 23,452 persons not known to have been exposed.

RESULTS

Of the 1797 persons who had recovered from SARS-CoV-2 infection, 1107 of the 1215 who were tested (91.1%) were seropositive; antiviral antibody titers assayed by two pan-Ig assays increased during 2 months after diagnosis by qPCR and remained on a plateau for the remainder of the study. Of quarantined persons, 2.3% were seropositive; of those with unknown exposure, 0.3% were positive. We estimate that 0.9% of Icelanders were infected with SARS-CoV-2 and that the infection was fatal in 0.3%. We also estimate that 56% of all SARS-CoV-2 infections in Iceland had been diagnosed with qPCR, 14% had occurred in quarantined persons who had not been tested with qPCR (or who had not received a positive result, if tested), and 30% had occurred in persons outside quarantine and not tested with qPCR.

CONCLUSIONS

Our results indicate that antiviral antibodies against SARS-CoV-2 did not decline within 4 months after diagnosis. We estimate that the risk of death from infection was 0.3% and that 44% of persons infected with SARS-CoV-2 in Iceland were not diagnosed by qPCR.

Spread of SARS-CoV-2 in the Icelandic Population

BACKGROUND

During the current worldwide pandemic, coronavirus disease 2019 (Covid-19) was first diagnosed in Iceland at the end of February. However, data are limited on how SARS-CoV-2, the virus that causes Covid-19, enters and spreads in a population.

METHODS

We targeted testing to persons living in Iceland who were at high risk for infection (mainly those who were symptomatic, had recently traveled to high-risk countries, or had contact with infected persons). We also carried out population screening using two strategies: issuing an open invitation to 10,797 persons and sending random invitations to 2283 persons. We sequenced SARS-CoV-2 from 643 samples.

RESULTS

As of April 4, a total of 1221 of 9199 persons (13.3%) who were recruited for targeted testing had positive results for infection with SARS-CoV-2. Of those tested in the general population, 87 (0.8%) in the open-invitation screening and 13 (0.6%) in the random-population screening tested positive for the virus. In total, 6% of the population was screened. Most persons in the targeted-testing group who received positive tests early in the study had recently traveled internationally, in contrast to those who tested positive later in the study. Children under 10 years of age were less likely to receive a positive result than were persons 10 years of age or older, with percentages of 6.7% and 13.7%, respectively, for targeted testing; in the population screening, no child under 10 years of age had a positive result, as compared with 0.8% of those 10 years of age or older. Fewer females than males received positive results both in targeted testing (11.0% vs. 16.7%) and in population screening (0.6% vs. 0.9%). The haplotypes of the sequenced SARS-CoV-2 viruses were diverse and changed over time. The percentage of infected participants that was determined through population screening remained stable for the 20-day duration of screening.

CONCLUSIONS

In a population-based study in Iceland, children under 10 years of age and females had a lower incidence of SARS-CoV-2 infection than adolescents or adults and males. The proportion of infected persons identified through population screening did not change substantially during the screening period, which was consistent with a beneficial effect of containment efforts. (Funded by deCODE Genetics-Amgen.).

Quantitative 3D imaging parameters improve prediction of hip osteoarthritis outcome

Osteoarthritis is an increasingly important health problem for which the main treatment remains joint replacement. Therapy developments have been hampered by a lack of biomarkers that can reliably predict disease, while 2D radiographs interpreted by human observers are still the gold standard for clinical trial imaging assessment. We propose a 3D approach using computed tomography—a fast, readily available clinical technique—that can be applied in the assessment of osteoarthritis using a new quantitative 3D analysis technique called joint space mapping (JSM). We demonstrate the application of JSM at the hip in 263 healthy older adults from the AGES-Reykjavík cohort, examining relationships between 3D joint space width, 3D joint shape, and future joint replacement. Using JSM, statistical shape modelling, and statistical parametric mapping, we show an 18% improvement in prediction of joint replacement using 3D metrics combined with radiographic Kellgren & Lawrence grade (AUC 0.86) over the existing 2D FDA-approved gold standard of minimum 2D joint space width (AUC 0.73). We also show that assessment of joint asymmetry can reveal significant differences between individuals destined for joint replacement versus controls at regions of the joint that are not captured by radiographs. This technique is immediately implementable with standard imaging technologies.

GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs

Analysis of sequence diversity in the human genome is fundamental for genetic studies. Structural variants (SVs) are frequently omitted in sequence analysis studies, although each has a relatively large impact on the genome. Here, we present GraphTyper2, which uses pangenome graphs to genotype SVs and small variants using short-reads. Comparison to the syndip benchmark dataset shows that our SV genotyping is sensitive and variant segregation in families demonstrates the accuracy of our approach. We demonstrate that incorporating public assembly data into our pipeline greatly improves sensitivity, particularly for large insertions. We validate 6,812 SVs on average per genome using long-read data of 41 Icelanders. We show that GraphTyper2 can simultaneously genotype tens of thousands of whole-genomes by characterizing 60 million small variants and half a million SVs in 49,962 Icelanders, including 80 thousand SVs with high-confidence.

GWAS of bone size yields twelve loci that also affect height, BMD, osteoarthritis or fractures

Bone area is one measure of bone size that is easily derived from dual-energy X-ray absorptiometry (DXA) scans. In a GWA study of DXA bone area of the hip and lumbar spine (N ≥ 28,954), we find thirteen independent association signals at twelve loci that replicate in samples of European and East Asian descent (N = 13,608 - 21,277). Eight DXA area loci associate with osteoarthritis, including rs143384 in GDF5 and a missense variant in COL11A1 (rs3753841). The strongest DXA area association is with rs11614913[T] in the microRNA MIR196A2 gene that associates with lumbar spine area (P = 2.3 × 10-42, β = -0.090) and confers risk of hip fracture (P = 1.0 × 10-8, OR = 1.11). We demonstrate that the risk allele is less efficient in repressing miR-196a-5p target genes. We also show that the DXA area measure contributes to the risk of hip fracture independent of bone density.

Characterizing mutagenic effects of recombination through a sequence-level genetic map

Genetic diversity arises from recombination and de novo mutation (DNM). Using a combination of microarray genotype and whole-genome sequence data on parent-child pairs, we identified 4,531,535 crossover recombinations and 200,435 DNMs. The resulting genetic map has a resolution of 682 base pairs. Crossovers exhibit a mutagenic effect, with overrepresentation of DNMs within 1 kilobase of crossovers in males and females. In females, a higher mutation rate is observed up to 40 kilobases from crossovers, particularly for complex crossovers, which increase with maternal age. We identified 35 loci associated with the recombination rate or the location of crossovers, demonstrating extensive genetic control of meiotic recombination, and our results highlight genes linked to the formation of the synaptonemal complex as determinants of crossovers.

COPA syndrome in an Icelandic family caused by a recurrent missense mutation in COPA

Background

Rare missense mutations in the gene encoding coatomer subunit alpha (COPA) have recently been shown to cause autoimmune interstitial lung, joint and kidney disease, also known as COPA syndrome, under a dominant mode of inheritance.

Case presentation

Here we describe an Icelandic family with three affected individuals over two generations with a rare clinical presentation of lung and joint disease and a histological diagnosis of follicular bronchiolitis. We performed whole-genome sequencing (WGS) of the three affected as well as three unaffected members of the family, and searched for rare genotypes associated with disease using 30,067 sequenced Icelanders as a reference population. We assessed all coding and splicing variants, prioritizing variants in genes known to cause interstitial lung disease. We detected a heterozygous missense mutation, p.Glu241Lys, in the COPA gene, private to the affected family members. The mutation occurred de novo in the paternal germline of the index case and was absent from 30,067 Icelandic genomes and 141,353 individuals from the genome Aggregation Database (gnomAD). The mutation occurs within the conserved and functionally important WD40 domain of the COPA protein.

Conclusions

This is the second report of the p.Glu241Lys mutation in COPA, indicating the recurrent nature of the mutation. The mutation was reported to co-segregate with COPA syndrome in a large family from the USA with five affected members, and classified as pathogenic. The two separate occurrences of the p.Glu241Lys mutation in cases and its absence from a large number of sequenced genomes confirms its role in the pathogenesis of the COPA syndrome.

Electronic supplementary material

The online version of this article (10.1186/s12881-017-0490-8) contains supplementary material, which is available to authorized users.

Physiological changes associated with routine nursing procedures in critically ill are common: an observational pilot study

BACKGROUND

Nursing procedures that are routinely performed in the intensive care unit (ICU) are assumed to have minimal side effects. However, these procedures may sometimes cause physiological changes that negatively affect the patient. We hypothesized that physiological changes associated with routine nursing procedures in the ICU are common.

METHODS

A clinical observational study of 16 critically ill patients in a nine-bed mixed university hospital ICU. All nursing procedures were observed, and physiological data were collected and subsequently analyzed. Minor physiological changes were defined as minimal changes in respiratory or circulatory variables, and major physiological changes were marked as hyper/hypotension, bradycardia/tachycardia, bradypnea/tachypnea, ventilatory distress, and peripheral blood oxygen desaturation.

RESULTS

In the 16 patients, 668 procedures generated 158 major and 692 minor physiological changes during 187 observational hours. The most common procedure was patient position change, which also generated the majority of the physiological changes. The most common major physiological changes were blood oxygen desaturation, ventilatory distress, and hypotension, and the most common minor changes were arterial pressure alteration, coughing, and increase in respiratory rate.

CONCLUSION

In this pilot study, we examined physiological changes in connection with all regular routine nursing procedures in the ICU. We found that physiological changes were common and sometimes severe.

Activation of Complement Following Total Hip Replacement

The aim of this study was to investigate whether complement activation, via the classical and alternative pathways, occurs following a cemented total hip replacement (THR) surgery due to osteoarthritis. Blood samples were collected systematically from 12 patients - six male and six women, with a median age of 75 (range: 59-90 years) - preoperatively, 6 h post-operatively and on the first, second and third post-operative day. Total function of classical (CH50) and alternative pathways (AH50) was evaluated, along with the determination of serum concentrations of the complement proteins C3, C4, C3d, the soluble terminal complement complex (sTCC) sC5b-9, as well as C-reactive protein (CRP) and albumin. Measurements of CRP and albumin levels elucidated a marked inflammatory response following the operation. The CH50, AH50 and C3 and C4 levels were significantly lower 6 h after the surgery compared with the preoperative levels, but elevated above the preoperative levels during the following 3 days. The complement activation product C3d levels increased continually during the whole observation period, from 13.5 AU/ml (range: 8-19 AU/ml) preoperative to 20 AU/ml (range: 12-34 AU/ml) on the third post-operative day. Furthermore, we observed an increase in the sC5b-9 levels between the preoperative and the third post-operative day. These results demonstrate a significant activation of the complement system following cemented THR. Further studies are needed to elucidate the time frame and the pathogenic role of this observed complement activation.

Abstract P2-04-02: Overdiagnosis in mammography screening in two randomised trials in Malmö, Sweden – An age specific analysis

OBJECTIVES: The aim of the current study was to estimate age-specific overdiagnosis due to mammography screening in the two randomized trials in Malmö, Sweden: The Malmö Mammographic Screening Trial I and II (MMST I and MMST II).

SETTING: Women living in Malmö were randomized in a 1:1 proportion to a screening group or a control group. The MMST I included 42,283 women born between 1908 and 1932 and the MMST II included 17,793 women born between 1933 and 1945. Women in the study group were invited from 1976 until 1990 when the control group was invited. The age at randomization was 45-70 years in MMST I and 43-48 years in MMST II.

METHODS: Data from the two trials were merged and overdiagnosis was estimated using age specific incidence rates excluding the first years of screening. The age specific relative breast cancer incidence rate for the screening group versus the control group was estimated and adjusted for lead time. Only the first breast cancer diagnosis was considered and results for invasive cancer and carcinoma in situ combined as well as for invasive cancer were calculated.

RESULTS: The number of breast cancer cases, including carcinoma in situ, for the period 1976-1989 was 867 and 676 for the study group and the control group, respectively. The rate ratio for overdiagnosis in age 43-78 years adjusted for lead time was 1.04 (95% CI, 0.93-1.16). No overdiagnosis from subsequent screening was found for women below the age of 60. In women aged 60-69 and 70-78 years overdiagnosis was estimated at 1.13 (0.95-1.33) and 1.15 (0.85-1.54), respectively. The corresponding results for invasive cancer only was lower and no overdiagnosis was seen except for the age group 60-69 years where the rate ratio was 1.10 (0.92-1.32). For age 43-78 the result was 0.96 (0.85-1.08).

CONCLUSIONS

For the total material overdiagnosis from subsequent screening, including carcinoma in situ, was 4%. This is somewhat lower than an earlier evaluation of MMST I where age were higher and another method was used. For women below the age of 60 no overdiagnosis was seen and indicated that the possible problem with overdiagnosis concern women 60+. However none of the results were statistically significant at the 5% level.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-04-02.

Clinical examination, spondylolysis and adolescent athletes

Symptomatic spondylolysis is a stress reaction caused by microtrauma during physical exercise, an imaging diagnostic subgroup of Adolescent Low Back Pain (ALBP), found in adolescent athletes. Early diagnosis increases the possibility of healing. Thus, it is important to divide ALBP into subgroups. The aim of this study was to evaluate clinical tests that can distinguish symptomatic spondylolysis from other forms of ALBP in order to facilitate early referral for diagnostic imaging. The investigation subjects were a prospective case series with a control group, 25 subjects with ALBP and 13 subjects that had no history of LBP. The 2 groups were examined using the same clinical protocol. MRI of the whole lumbar spine was performed in both the case and control groups and CT investigations of the L4 and L5 vertebrae were performed in the case group. Significant differences between the 2 groups were found in 8 of our clinical tests. No clinical test, alone or in combination, could distinguish between spondylolysis and other forms of ALBP. As 88% of the subjects in the case group had MRI findings and almost 50% had spondylolysis, MRI should be performed at an early age in young athletes with ALBP.

Metabolic risk factors and skin cancer in the Metabolic Syndrome and Cancer Project (Me-Can)

BACKGROUND

Little is known about the associations of metabolic aberrations with malignant melanoma (MM) and nonmelanoma skin cancer (NMSC).

OBJECTIVES

To assess the associations between metabolic factors (both individually and combined) and the risk of skin cancer in the large prospective Metabolic Syndrome and Cancer Project (Me-Can).

METHODS

During a mean follow-up of 12 years of the Me-Can cohort, 1728 (41% women) incident MM, 230 (23% women) fatal MM and 1145 (33% women) NMSC were identified. Most NMSC cases (76%) were squamous cell carcinoma (SCC) (873, 33% women). Hazard ratios (HRs) were estimated by Cox proportional hazards regression for quintiles and standardized z-scores (with a mean of 0 and SD of 1) of body mass index (BMI), blood pressure, glucose, cholesterol, triglycerides and for a combined metabolic syndrome score. Risk estimates were corrected for random error in the measurements.

RESULTS

Blood pressure per unit increase of z-score was associated with an increased risk of incident MM cases in men and women [HR 1·17, 95% confidence interval (CI) 1·04-1·31 and HR 1·18, 95% CI 1·03-1·36, respectively] and fatal MM cases among women (HR 2·39, 95% CI 1·58-3·64). In men, all quintiles for BMI above the reference were associated with a higher risk of incident MM. In women, SCC NMSC risk increased across quintiles for glucose levels (P-trend 0·02) and there was a trend with triglyceride concentration (P-trend 0·09).

CONCLUSION

These findings suggest that mechanisms linked to blood pressure may be involved in the pathogenesis of MM. SCC NMSC in women could be related to glucose and lipid metabolism.

Altered activity of the serratus anterior during unilateral arm elevation in patients with cervical disorders

Altered activity in the axioscapular muscles is considered to be an important feature in patients with neck pain. The activity of the serratus anterior (SA) and trapezius muscles during arm elevation has not been investigated in these patients. The objectives of this study was to investigate whether there is a pattern of altered activity in the SA and trapezius in patients with insidious onset neck pain (IONP) (n=22) and whiplash associated disorders (WAD) (n=27). An asymptomatic group was selected for baseline measurements (n=23). Surface electromyography was used to measure the onset of muscle activation and duration of muscle activity of the SA as well as the upper, middle, and lower trapezius during unilateral arm elevation in the three subject groups. Both arms were tested. With no interaction, the main effect for the onset of muscle activation and duration of muscle activity for serratus anterior was statistically significant among the groups. Post hoc comparison revealed a significantly delayed onset of muscle activation and less duration of muscle activity in the IONP group, and in the WAD group compared to the asymptomatic group. There were no group main effects or interaction effects for upper, middle and lower trapezius. This finding may have implications for scapular stability in these patients because the altered activity in the SA may reflect inconsistent or poorly coordinated muscle activation that may reduce the quality of neuromuscular performance and induce an increased load on the cervical and the thoracic spine.

Insights into the genetic architecture of osteoarthritis from stage 1 of the arcOGEN study

Objectives

The genetic aetiology of osteoarthritis has not yet been elucidated. To enable a well-powered genome-wide association study (GWAS) for osteoarthritis, the authors have formed the arcOGEN Consortium, a UK-wide collaborative effort aiming to scan genome-wide over 7500 osteoarthritis cases in a two-stage genome-wide association scan. Here the authors report the findings of the stage 1 interim analysis.

Methods

The authors have performed a genome-wide association scan for knee and hip osteoarthritis in 3177 cases and 4894 population-based controls from the UK. Replication of promising signals was carried out in silico in five further scans (44 449 individuals), and de novo in 14 534 independent samples, all of European descent.

Results

None of the association signals the authors identified reach genome-wide levels of statistical significance, therefore stressing the need for corroboration in sample sets of a larger size. Application of analytical approaches to examine the allelic architecture of disease to the stage 1 genome-wide association scan data suggests that osteoarthritis is a highly polygenic disease with multiple risk variants conferring small effects.

Conclusions

Identifying loci conferring susceptibility to osteoarthritis will require large-scale sample sizes and well-defined phenotypes to minimise heterogeneity.

Metabolic syndrome and rare gynecological cancers in the metabolic syndrome and cancer project (Me-Can)

BACKGROUND

Risk factors for rare gynecological cancers are largely unknown. Initial research has indicated that the metabolic syndrome (MetS) or individual components could play a role.

MATERIALS AND METHODS

The Metabolic syndrome and Cancer project cohort includes 288,834 women. During an average follow-up of 11 years, 82 vulvar, 26 vaginal and 43 other rare gynecological cancers were identified. Hazard ratios (HRs) were estimated fitting Cox proportional hazards regression models for tertiles and standardized z-scores [with a mean of 0 and a standard deviation (SD) of 1] of body mass index (BMI), blood pressure, glucose, cholesterol, triglycerides and MetS. Risk estimates were corrected for random error in the measurement of metabolic factors.

RESULTS

The MetS was associated with increased risk of vulvar [HR 1.78, 95% confidence interval (CI) 1.30-2.41) and vaginal cancer (HR 1.87, 95% CI 1.07-3.25). Among separate MetS components, 1 SD increase in BMI was associated with overall risk (HR 1.43, 95% CI 1.23-1.66), vulvar (HR 1.36, 95% CI 1.11-1.69) and vaginal cancer (HR 1.79, 95% CI 1.30-2.46). Blood glucose and triglyceride concentrations were associated with increased risk of vulvar cancer (HR 1.98, 95% CI 1.10-3.58 and HR 2.09, 95% CI 1.39-3.15, respectively).

CONCLUSION

The results from this first prospective study on rare gynecological cancers suggest that the MetS and its individual components may play a role in the development of these tumors.

A Method of Correcting for Tilt from Horizontal in Downwelling Shortwave Irradiance Measurements on Moving Platforms

The downwelling shortwave irradiance typically consists of both a direct component of radiation from the sun, and a diffuse component of scattered sunlight from the sky. Significant offsets can occur in downwelling shortwave irradiance measurements made from moving platforms due to the tilt of the instruments from horizontal which changes the angular orientation of the direct component of sunlight to the instrument and causes an artificial variation in the measured signal. To properly correct for this tilt, a-priori knowledge of the partitioning between the direct and diffuse components of the total shortwave irradiance is needed to properly apply a correction for tilt. This partitioning information can be adequately provided using a newly available commercial radiometer named the SPN1 that produces reasonable measurements of the total and diffuse shortwave irradiance (and by subtraction the direct shortwave irradiance) with no moving parts and regardless of azimuthal orientation. We have developed methodologies for determining the constant pitch and roll offsets of the radiometers for aircraft applications, and for applying a tilt correction to the total shortwave irradiance data. Results suggest that the methodology is accurate for tilt up to +/-10°, with 90% of the data corrected to within 10 Wm-2 at least for clear-sky data. Without a proper tilt correction, even data limited to 5° of tilt can still exhibit large errors, greater than 100 Wm-2 in some cases. Given the low cost, low weight, and low power consumption of the SPN1 total and diffuse radiometer, opportunities previously excluded for moving platform measurements such as small Unmanned Aerial Vehicles and solar powered buoys now become feasible using our methodology. The increase in measurement accuracy is important, given current concerns over long-term climate variability and change especially over the 70% of the Earth's surface covered by ocean where long-term records of these measurements are sorely needed and must be made on ships and buoys.

Prevalence of gastric ulceration in Swedish Standardbreds in race training

REASONS FOR PERFORMING STUDY

There is little information about the prevalence of gastric ulcers in Standardbred trotters and potential correlations between ulcers and various traits, e.g. age, sex, performance, temperament and feeding regimens, need further elucidation.

OBJECTIVES

The prevalence of ulcers in the gastric squamous mucosa of Swedish Standardbreds was estimated and the associations between ulcer score and age, sex, performance, temperament and feeding regimens were determined.

METHODS

Eighty Swedish Standardbreds in active race training, trained by 9 different trainers, underwent gastroscopy. Information on age, gender, status of training, performance over the last 4 months compared with the trainer's expectations before that period, behaviour, eating habits, feed type, bedding type, time spent outdoors per day and medical treatment during the last month was collected. Gastroscopy was performed and lesions in the squamous gastric mucosa were scored from 0 to 4 (0 = no lesions; 4 = > 5 lesions with haemorrhage, > 10 lesions with no haemorrhage, or a large area of diffuse loss of surface epithelium).

RESULTS

Twenty-four (30%) of the horses had no lesions in the squamous mucosa, 22 (27.5%) had a score of 1; 21 (26.2%) score 2; 9 (11.2%) score 3; and 4 (5%) score 4. Horses that were in preparatory training and those that had raced during the last month were significantly more affected than horses that were fit for racing but had not raced during the last month, using a logistic regression model with trainer incorporated as a random effect.

CONCLUSIONS

The study confirmed a high prevalence of ulcers in the gastric squamous mucosa of Standardbreds in race training. Of the studied parameters only status of training showed a significant association with gastric ulcers of the squamous mucosa.

POTENTIAL RELEVANCE

Gastric ulceration is a common disease and diagnosis should be made by endoscopic examination of the gastric mucosa, since parameters such as age, gender, performance, behaviour, eating habits provide only weak clues as to which horses might be affected. Further studies are needed to determine the aetiology of the syndrome and to find ways to reduce, if possible, the frequency of gastric ulcers.

Hand radiology characteristics of patients carrying the T303M mutation in the gene for matrilin‐3

OBJECTIVE

To determine whether the recently described hand osteoarthritis (HOA)-associated T(303)M mutation in the gene for matrilin-3 (MATN3) is associated with specific radiological changes on hand radiographs.

METHOD

Standard hand radiographs from 26 HOA patients carrying the T(303)M missense mutation in the MATN3 gene (T(303)M patients) were compared with those from 52 HOA controls matched for sex, age, and clinical disease severity. Two blinded readers scored the radiographs, using the Verbruggen-Veys anatomical scoring system for the interphalangeal and metacarpophalangeal joints and the OARSI atlas scoring system for the first carpometacarpal (CMC1) joints. A scoring system based on the latter was used for the scaphoid-trapezoid-trapezoideum (STT) joints.

RESULTS

No particular distinguishing features were found in the T(303)M patients and the prevalence of erosive and cystic changes was similar to the control group. As a group, however, the T(303)M patients had more severe thumb-base affection, particularly in the STT joint. Thus, definite radiological OA in both CMC1 and STT joints and higher STT scores compared with CMC1 were significantly more common in patients carrying the T(303)M mutation. Radiological scores for joint-space narrowing (CMC1 and STT) and osteophytes (STT) were also significantly higher in the T(303)M patients.

CONCLUSION

Patients carrying the T(303)M mutation in the gene for matrilin-3 express a form of HOA that is radiologically indistinguishable from idiopathic HOA in individual patients but they have more severe thumb-base involvement, particularly in the STT joint. This is the first described genetic mutation that is associated with a common form of osteoarthritis.

Hand osteoarthritis in older women is associated with carotid and coronary atherosclerosis: the AGES Reykjavik study

OBJECTIVE

There is evidence that atherosclerosis may contribute to the initiation or progression of osteoarthritis. To test this hypothesis, the presence and severity of hand osteoarthritis (HOA) was compared with markers of atherosclerotic vascular disease in an elderly population.

PATIENTS AND METHODS

The AGES Reykjavik Study is a population-based multidisciplinary study of ageing in the elderly population of Reykjavik. In a study of 2264 men (mean age 76 years; SD 6) and 3078 women (mean age 76 years; SD 6) the severity of HOA, scored from photographs, was compared with measures of atherosclerosis. These included carotid intimal thickness and plaque severity, coronary calcifications (CAC) and aortic calcifications and reported cardiac and cerebrovascular events.

RESULTS

After adjustment for confounders, both carotid plaque severity and CAC were significantly associated with HOA in women, with an odds ratio of 1.42 (95% CI 1.14 to 1.76, p = 0.002) for having CAC and 1.25 (95% CI 1.04 to 1.49, p = 0.016) for having moderate or severe carotid plaques. Both carotid plaques and CAC also exhibited significant linear trends in relation to HOA severity in women in the whole AGES Reykjavik cohort (p<0.001 and p = 0.027, respectively, for trend). No significant associations were seen in men. Despite this evidence of increased atherosclerosis, women with HOA did not report proportionally more previous cardiovascular or cerebrovascular events.

CONCLUSIONS

The results indicate a linear association between the severity of HOA and atherosclerosis in older women. The pathological process of HOA seems to have some components in common with atherosclerosis. Prospective studies may help elucidate the possible mechanisms of this relationship.

Fifty-year follow-up of mortality among a cohort of iron-ore miners in Sweden, with specific reference to myocardial infarction mortality

OBJECTIVES

This study investigates both general mortality and mortality from myocardial infarction among men employed in iron-ore mines in Sweden.

METHODS

The mortality of employees (surface and underground workers) at the iron-ore mines in Malmberget and Kiruna, Sweden was investigated. The study cohort comprised men who had been employed for at least 1 year between 1923 and 1996. The causes of death were obtained from the national cause of death register from 1952 to 2001. Indirect standardised mortality ratios (SMR) were calculated for four main causes. Mortality specifically from myocardial infarction was also analysed.

RESULTS

4504 deaths in the cohort gave an SMR for total mortality of 1.05 (95% CI 1.02 to 1.09). Mortality was significantly higher for lung cancer (SMR 1.73, 95% CI 1.52 to 1.97). There was an increased risk of injuries and poisonings (SMR 1.34, 95% CI 1.24 to 1.46) and respiratory diseases (SMR 1.14, 95% CI 1.00 to 1.28). There were 1477 cases of myocardial infarction, resulting in an SMR of 1.12 (95% CI 1.07 to 1.18). SMR was higher (1.35, 95% CI 1.22 to 1.50) for men aged <or=60 years than for those >60 years of age (1.06, 95% CI 1.00 to 1.13).

CONCLUSIONS

Mortality from myocardial infarction was higher than expected. There was also an increased risk of death from injuries and poisonings, lung cancer and respiratory diseases, as well as higher general mortality. Our findings support the results of previous studies that there is an association between working in the mining industry and adverse health outcomes.

Complexities in the estimation of overdiagnosis in breast cancer screening

There is interest in estimating and attributing temporal changes in incidence of breast cancer in relation to the initiation of screening programmes, in particular to estimation of overdiagnosis of breast cancer as a result of screening. In this paper, we show how screening introduces complexities of analysis and interpretation of incidence data. For example, lead time brings forward time- and age-related increases in incidence. In addition, risk factors such as hormone replacement therapy use have been changing contemporaneously with the introduction of screening. Although we do not indicate exactly how such complexities should be corrected for, we use some simple informal adjustments to show how they may account for a substantial proportion of increased incidence, which might otherwise erroneously have been attributed to overdiagnosis. We illustrate this using an example of analysis of breast cancer incidence data from Sweden.

Fracture mechanisms and fracture pattern in men and women aged 50 years and older: a study of a 12-year population-based injury register, Umeå, Sweden

In a study of a 12-year population-based injury register, Umeå, Sweden, we analyzed the fracture mechanisms and fracture pattern in men and women 50 years and older. Low-energy trauma was responsible for the major and costliest part of the fracture panorama, but the pattern differs between age groups.

INTRODUCTION

Osteoporosis-related fracture is a major health problem: the number of hip fractures is expected to double to 2030. While osteoporosis is one of many risk factors, trauma is almost always involved. Therefore, we analyzed injury mechanisms in patients aged over 50.

METHODS

We registered injury mechanism, cause, diagnosis in all trauma patients at Umeå University hospital, Sweden. This population-based register (1993-2004) comprises a total of 113,668 injuries (29,189 fractures). Patients >or=50 years contributed to 13,279 fractures.

RESULTS

Low-energy trauma (fall <1 m) caused 53% of all fractures >or=50 years and older. In those over 75 low-energy trauma caused >80%. The seasonal variation of fractures was maximally 25%. With increasing age, proximal fractures became more common, in both upper and lower extremities. Proximal locations predominate in older age groups.

CONCLUSIONS

Low-energy trauma was responsible for the largest and costliest part of the fracture panorama. In fact, almost all fractures in middle-aged and old people were caused by low-energy mechanisms; thus, most fractures in these patients have a fragility component, and the contribution of osteoporosis-related fractures is more important than previously thought. A better understanding of injury mechanisms also in low-energy trauma is a prerequisite for preventive interventions.