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Evidence from literature, including the BRIDGES study, indicates that germline protein truncating variants (PTVs) in FANCM confer moderately increased risk of ER-negative and triple-negative breast cancer (TNBC), especially for women with a family history of the disease. Association between FANCM missense variants (MVs) and breast cancer risk has been postulated. In this study, we further used the BRIDGES study to test 689 FANCM MVs for association with breast cancer risk, overall and in ER-negative and TNBC subtypes, in 39,885 cases (7566 selected for family history) and 35,271 controls of European ancestry. Sixteen common MVs were tested individually; the remaining rare 673 MVs were tested by burden analyses considering their position and pathogenicity score. We also conducted a meta-analysis of our results and those from published studies. We did not find evidence for association for any of the 16 variants individually tested. The rare MVs were significantly associated with increased risk of ER-negative breast cancer by burden analysis comparing familial cases to controls (OR = 1.48; 95% CI 1.07-2.04; P = 0.017). Higher ORs were found for the subgroup of MVs located in functional domains or predicted to be pathogenic. The meta-analysis indicated that FANCM MVs overall are associated with breast cancer risk (OR = 1.22; 95% CI 1.08-1.38; P = 0.002). Our results support the definition from previous analyses of FANCM as a moderate-risk breast cancer gene and provide evidence that FANCM MVs could be low/moderate risk factors for ER-negative and TNBC subtypes. Further genetic and functional analyses are necessary to clarify better the increased risks due to FANCM MVs.

Additional file 1.

Pogosta disease is a mosquito-borne infection, caused by Sindbis virus (SINV), which causes epidemics of febrile rash and arthritis in Northern Europe and South Africa. Resident grouse and migratory birds play a significant role as amplifying hosts and various mosquito species, including Aedes cinereus, Culex pipiens, Cx. torrentium and Culiseta morsitans are documented vectors. As specific treatments are not available for SINV infections, and joint symptoms may persist, the public health burden is considerable in endemic areas. To predict the environmental suitability for SINV infections in Finland, we applied a suite of geospatial and statistical modeling techniques to disease occurrence data. Using an ensemble approach, we first produced environmental suitability maps for potential SINV vectors in Finland. These suitability maps were then combined with grouse densities and environmental data to identify the influential determinants for SINV infections and to predict the risk of Pogosta disease in Finnish municipalities. Our predictions suggest that both the environmental suitability for vectors and the high risk of Pogosta disease are focused in geographically restricted areas. This provides evidence that the presence of both SINV vector species and grouse densities can predict the occurrence of the disease. The results support material for public-health officials when determining area-specific recommendations and deliver information to health care personnel to raise awareness of the disease among physicians.

Sindbis virus (SINV) is a mosquito-borne avian hosted virus that is widely distributed in Europe, Africa, Asia, and Oceania. Disease in humans is documented mainly from Northern Europe and South Africa and associated with genotype I. In 2018 under extremely warm climatic conditions, a small outbreak of 71 diagnosed SINV infections was recorded in Finland. We screened 52 mosquito pools (570 mosquitoes) and 223 human sera for SINV with real-time RT-PCR and the positive samples with virus isolation. One SINV strain was isolated from a pool (n = 13) of genusOchlerotatusmosquitoes and three strains from patient serum samples. Complete genome analysis suggested all the isolates to be divergent from one another and related to previous Finnish, Swedish, and German strains. The study provides evidence of SINV strain transfer within Europe across regions with different epidemiological characteristics. Whether these are influenced by different mosquito genera involved in the transmission remains to be studied.

The nephrotic syndrome (NS) is characterized by massive proteinuria, edema and hypertriglyceridemia. It can appear as a primary or a secondary disease, idiopathic or familial, monogenic or complex, responsive to medication or progressing inevitably towards end-stage renal disease. As the manifestations of the disease are varied so is the etiologies behind it and still much remains to be discovered. However, structural compromise can be observed in the glomeruli of the NS patients, especially in podocytes, specialized epithelial cells of the glomerular filtration barrier. When causative genetic variants are found they are predominantly in the genes coding proteins involved in the structure and function of the podocytes. To date, over thirty podocyte protein-coding genes have been implicated. In this study we looked into genetic and cellular mechanisms in the podocyte underlying different forms of NS: congenital nephrotic syndrome of the Finnish type (CNF), steroid sensitive nephrotic syndrome (SSNS) and steroid resistant nephrotic syndrome (SRNS). Specifically, we used CNF kidney samples to study how the different compartments of the podocyte are affected by the lack of nephrin, characteristic structural component of the unique cellular junction of the podocytes (slit diaphragm (SDs)). We also looked into genetic variation in the podocyte protein coding genes in the Finnish SRNS patients to map out the variant spectrum and to see if this population shows difference to other populations. In addition, we aimed to find genetic and clinical markers predicting the course and severity of SSNS, which would have significant clinical value. The analyses were carried out using an array of molecular biological methods. Protein expression was studied using immunohistochemistry and light microscopy, genetic variants with PCR and sequence analysis. In addition, immunoprecipitation and western blot analyses were carried out to study the functionality of a particular variant. Genome wide sequencing analysis was carried out to gain wider perspective on the variant spectrum in NS patients. Our results showed that the lack of nephrin leads to widespread effects in the podocyte on protein level, especially on the expression of other proteins of the SD. In other compartments of the cell (basal membrane, actin cytoskeleton, apical membrane) the effect was clear but considering the profound structural damage seen in CNF the orders of magnitude of the observed changes were modest. We also showed that the analyzed clinical features or variants in these key genes coding podocyte proteins cannot reliably predict severity of SSNS. Children with difficult disease (multiple relapses, dependence on steroids) are more likely to suffer from NS in adulthood but other correlations between early patient features and prognosis could not be made. Single nucleotide polymorphisms (SNP) analysis of children with idiopathic NS revealed that variants in some genes (e.g. MDR1) may be useful in predicting responsiveness to steroids but the correlation is not sufficiently strong to warrant routine clinical testing. We found few causative variants in patients with idiopathic SRNS but did uncover a de novo NPHS2 variant co-segregating with familial dominant SRNS and unusual course of the disease. Healthy function of the podocyte relies on interaction and communication between multitudes of protein components in the different compartments of the cell. If any of these components are faulty it may cascade into widespread podocyte damage and proteinuria. The precise nature of the defect may play a significant role in the disease phenotype and not only the function of the damaged gene but also the nature of the variant ought to be considered when carrying out genetic analysis. Not in all cases causative variants or precise faulty structures can be identified. The genetic factors behind complex traits remain elusive, and even though some pieces of the puzzle have been found, in small part by this study, much is still to be discovered. Nefroottiseen syndroomaan (NS) kuuluu väkevä valkuaisvirtsaisuus, turvotukset ja hypertriglyseridemia. Sen ilmentymät vaihtelevat primaarisairauksista sekundaarisiin, ja idiopaattisesta periytyvään. Osa tautimuodoista on monogeenisiä, toiset luonteeltaan monitekijäisiä. Osaan on löydetty tehokas lääkitys, kun taas osa johtaa vääjäämättä munuaisten vajaatoimintaan. Myös eri NS:n muotojen taustatekijät ovat moninaiset, eikä niitä kaikkia vielä tunneta. Usein kuitenkin NS potilaiden munuaiskerästen ja erityisesti niiden suodatuskerroksen epiteelisolujen, podosyyttien, rakenne on vaurioitunut. Löydetyt NS:n kanssa assosioituvat geneettiset muutokset ovat usein geeneissä, jotka koodaavat podosyyttien rakenteeseen ja toimintaan vaikuttavia proteiineja. Tähän mennessä variantteja on löytynyt yli kolmestakymmenestä podosyyttiproteiinia koodavasta geenistä. Tässä tutkimuksessa selvitimme podosyyttien erilaisia geneettisiä ja solubiologisia mekanismeja NS:n eri muodoissa: suomalaistyypin synnynnäisessä nefroosissa (CNF), steroidiresistentissä NS:ssä (SRNS) ja steroidisensitiivisessä NS:ssä (SSNS). CNF-munuaisnäytteistä tutkimme nefriini-proteiinin puutoksen aiheuttamia rakennemuutoksia podosyytin eri osissa. Etsimme myös variantteja yleisimmistä podosyyttiproteiineja koodaavista geeneistä suomalaisista SRNS potilaista nähdäksemme erottuuko tämä populaatio muista varianttien määrässä tai laadussa. Lisäksi etsimme geneettisiä ja kliinisiä tekijöitä joiden avulla voisi ennustaa SSNS:n taudinkuvaa ja kulkua. Tutkimuksessa käytettiin lukuisia molekyylibiologisia menetelmiä. Immunohistokemiaa ja valomikroskopiaa käytettiin proteiiniekspression tutkimiseen, PCR:ää ja sekvessianalyysiä geneettisten varianttien etsintään. Lisäksi immunopresipitaatiota ja Weatern blot menetelmää käytettiin tiettyjen varianttien toiminnallisten vaikutusten selvittämiseen. Koko genomin sekvensoinnilla haettiin laajempaa perspektiiviä NS-potilaiden geneettisten varianttien kirjoon. Osoitimme että proteiinitasolla nefriinin puutteen vaikutukset ilmenevät kaikissa podosyytin osissa, mutta erityisesti slit diaphragm rakenteen ympärillä. Muissa osissa (basaali- ja apikaalikalvot, aktiiniranka) vaikutus oli selvä, mutta huomioiden CNF:ssä havaitun histologisen vaurion laajuuden, mittaluokaltaan varsin hillitty. Näytimme myös etteivät kliiniset muuttujat tai geneettiset variantit keskeisiä podosyyttiproteiineja koodaavissa geeneissä ennusta taudin vakavuutta. Lapsuusiän vakava sairaus (mm. toistuvat relapsit, jatkuvaa steroidilääkitystä vaativa) korreloi aikuisena jatkuvan NS:n kanssa mutta muita yhteyksiä aikaisten kliinisten piirteiden ja taudin etenemisen kanssa ei voi vetää. Nukleotidimuutokset tietyissä geeneissä, kuten MDR1:ssä, voivat ennustaa sairauden steroidivastetta, mutta yhteys ei ole riittävän voimakas oikeuttaakseen rutiininomaisen kliinisen testauksen. Löysimme harvoja tautia aiheuttavia variantteja suomalaisista idiopaattista NS:ää sairastavista potilaista mutta paikansimme de novo variantin NPHS2 geenissä joka kulkeutuu yhdessä periytyvän, dominantin NS:n kanssa, ja assosioituu epätavallisen hitaasti kehittyvään tautimuotoon. Terveiden podosyyttien toiminta nojaa lukuisien proteiinien väliseen interaktioon ja kommunikaatioon solun eri osissa, ja jos jokin näistä komponenteista on vioittunut, se saattaa johtaa laajamittaiseen podosyyttivaurioon ja valkuiasvirtsaisuuteen. Saman geenin sisällä erilaiset muutokset voivat vaikuttaa kehittyvään taudinkuvaan eri tavoilla, joten geneettisissä analyyseissä tulee huomioida vaurioituneen geenin toiminnan lisäksi myös spesifin variantin laatu.

BACKGROUND: Genetic testing for breast cancer susceptibility is widely used, but for many genes, evidence of an association with breast cancer is weak, underlying risk estimates are imprecise, and reliable subtype-specific risk estimates are lacking. METHODS: We used a panel of 34 putative susceptibility genes to perform sequencing on samples from 60,466 women with breast cancer and 53,461 controls. In separate analyses for protein-truncating variants and rare missense variants in these genes, we estimated odds ratios for breast cancer overall and tumor subtypes. We evaluated missense-variant associations according to domain and classification of pathogenicity. RESULTS: Protein-truncating variants in 5 genes (ATM, BRCA1, BRCA2, CHEK2, and PALB2) were associated with a risk of breast cancer overall with a P value of less than 0.0001. Protein-truncating variants in 4 other genes (BARD1, RAD51C, RAD51D, and TP53) were associated with a risk of breast cancer overall with a P value of less than 0.05 and a Bayesian false-discovery probability of less than 0.05. For protein-truncating variants in 19 of the remaining 25 genes, the upper limit of the 95% confidence interval of the odds ratio for breast cancer overall was less than 2.0. For protein-truncating variants in ATM and CHEK2, odds ratios were higher for estrogen receptor (ER)-positive disease than for ER-negative disease; for protein-truncating variants in BARD1, BRCA1, BRCA2, PALB2, RAD51C, and RAD51D, odds ratios were higher for ER-negative disease than for ER-positive disease. Rare missense variants (in aggregate) in ATM, CHEK2, and TP53 were associated with a risk of breast cancer overall with a P value of less than 0.001. For BRCA1, BRCA2, and TP53, missense variants (in aggregate) that would be classified as pathogenic according to standard criteria were associated with a risk of breast cancer overall, with the risk being similar to that of protein-truncating variants. CONCLUSIONS: The results of this study define the genes that are most clinically useful for inclusion on panels for the prediction of breast cancer risk, as well as provide estimates of the risks associated with protein-truncating variants, to guide genetic counseling. (Funded by European Union Horizon 2020 programs and others.).

2 We assessed the PREDICT v 2.2 for prognosis of breast cancer patients with pathogenic germline BRCA1 3 and BRCA2 variants, using follow-up data from 5453 BRCA1/2 carriers from the Consortium of Investigators 4 of Modifiers of BRCA1/2 (CIMBA) and the Breast Cancer Association Consortium (BCAC). 5 PREDICT for estrogen receptor (ER)-negative breast cancer had modest discrimination for BRCA1 carrier 6 patients overall (Gönen & Heller unbiased concordance 0.65 in CIMBA, 0.64 in BCAC), but it distinguished 7 clearly the high-mortality group from lower risk categories. In an analysis of low to high risk categories by 8 PREDICT score percentiles, the observed mortality was consistently lower than the expected mortality, but 9 the confidence intervals always included the calibration slope. Altogether, our results encourage the use of 10 the PREDICT ER-negative model in management of breast cancer patients with germline BRCA1 variants. 11 For the PREDICT ER-positive model, the discrimination was slightly lower in BRCA2 variant carriers 12 (concordance 0.60 in CIMBA, 0.65 in BCAC). Especially, inclusion of the tumor grade distorted the 13 prognostic estimates. The breast cancer mortality of BRCA2 carriers was under-estimated at the low end of 14 the PREDICT score distribution, whereas at the high end, the mortality was over-estimated. These data 15 suggest that BRCA2 status should also be taken into consideration with tumor characteristics, when 16 estimating the prognosis of ER-positive breast cancer patients. 17 Keywords: PREDICT, breast cancer, prognosis, BRCA1, BRCA2, validation, survival