Dataset Information

The anatomical distribution of genetic associations.

ABSTRACT: Deeper understanding of the anatomical intermediaries for disease and other complex genetic traits is essential to understanding mechanisms and developing new interventions. Existing ontology tools provide functional, curated annotations for many genes and can be used to develop mechanistic hypotheses; yet information about the spatial expression of genes may be equally useful in interpreting results and forming novel hypotheses for a trait. Therefore, we developed an approach for statistically testing the relationship between gene expression across the body and sets of candidate genes from across the genome. We validated this tool and tested its utility on three applications. First, we show that the expression of genes in associated loci from GWA studies implicates specific tissues for 57 out of 98 traits. Second, we tested the ability of the tool to identify novel relationships between gene expression and phenotypes. Specifically, we experimentally confirmed an underappreciated prediction highlighted by our tool: that white blood cell count--a quantitative trait of the immune system--is genetically modulated by genes expressed in the skin. Finally, using gene lists derived from exome sequencing data, we show that human genes under selective constraint are disproportionately expressed in nervous system tissues.

SUBMITTER: Wells A

PROVIDER: S-EPMC4678833 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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The anatomical distribution of genetic associations.

Wells Alan A Kopp Nathan N Xu Xiaoxiao X O'Brien David R DR Yang Wei W Nehorai Arye A Adair-Kirk Tracy L TL Kopan Raphael R Dougherty J D JD

Nucleic acids research 20151119 22

Deeper understanding of the anatomical intermediaries for disease and other complex genetic traits is essential to understanding mechanisms and developing new interventions. Existing ontology tools provide functional, curated annotations for many genes and can be used to develop mechanistic hypotheses; yet information about the spatial expression of genes may be equally useful in interpreting results and forming novel hypotheses for a trait. Therefore, we developed an approach for statistically ...[more]

PMID: 26586807

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Project description:BackgroundWhy does a tumor start where it does within an organ? Location is traditionally viewed as a random event, yet the statistics of the location of tumors argues against this being a random occurrence. There are numerous examples including that of breast cancer. More than half of invasive breast cancer tumors start in the upper outer quadrant of the breast near the armpit, even though it is estimated that only 35 to 40% of breast tissue is in this quadrant. This suggests that there is an unknown microenvironmental factor that significantly increases the risk of cancer in a spatial manner and that is not solely due to genes or toxins. We hypothesize that tumors are more prone to form in healthy tissue at microvascular 'hot spots' where there is a high local concentration of microvessels providing an increased blood flow that ensures an ample supply of oxygen, nutrients, and receptors for growth factors that promote the generation of new blood vessels.ResultsTo show the plausibility of our hypothesis, we calculated the fractional probability that there is at least one microvascular hot spot in each region of the breast assuming a Poisson distribution of microvessels in two-dimensional cross sections of breast tissue. We modulated the microvessel density in various regions of the breast according to the total hemoglobin concentration measured by near infrared diffuse optical spectroscopy in different regions of the breast. Defining a hot spot to be a circle of radius 200 μm with at least 5 microvessels, and using a previously measured mean microvessel density of 1 microvessel/mm2, we find good agreement of the fractional probability of at least one hot spot in different regions of the breast with the observed invasive tumor occurrence. However, there is no reason to believe that the microvascular distribution obeys a Poisson distribution.ConclusionsThe spatial location of a tumor in an organ is not entirely random, indicating an unknown risk factor. Much work needs to be done to understand why a tumor occurs where it does.

Project description:Vertebrobasilar dolichoectasia (VBD) is a dilatative arteriopathy associated with intracerebral hemorrhage. In the present study, we sought to evaluate the frequency and anatomical distribution of cerebral microbleeds (cMBs) and intracerebral hemorrhage (ICH) in VBD.From a MRI database 94 VBD patients were identified and analyzed with special emphasis on cMBs and ICH on T2*-weighted gradient echo images (GRE) in relation to the established diagnostic MRI criteria of VBD (diameter, height, and lateral position). cMBs/ICH location was categorized into anterior/posterior circulation. Clinical information like demographic details, clinical symptoms, and comorbidities were abstracted from the case records. An extensive modelling approach using generalized linear mixed-effects models was used.Overall, 79 (84.0%) patients (mean age 72.1±10.0 years, 74.7% male) with a standard stroke MRI protocol including T2*-weighted images were included in the analysis. cMBs were observed in 38/79 (48.1%) patients, ranging from 1 to 84 cMBs per patient. In the posterior circulation cMBs were observed more frequently (34/38 (89.5%)) in comparison to the anterior circulation (24/38 (63.2%)). cMBs were observed in the thalamus in 20/38 (52.6%), hippocampus in 1/38 (2.6%), occipital lobe in 18/38 (47.4%), pons in 6/38 (15.8%), medulla oblongata in 2/38 (5.2%), and cerebellum in 14/38 (36.8%) patients. ICH was observed in only 6/79 (7.6%) patients. There were significantly more cMBs in the posterior- (NCMBs-PC = 1.717, 95%CI: 1.336-2.208, p = 0.0315) than in the anterior circulation. Logistic regression model showed a significant positive effect of clinical symptoms such as ischemic, TIA and hemorrhagic stroke on the presence of cMBs (OR = 3.34, 95%CI [2.0-5.57], p = 0.0184; ndf = 78, AIC = 107.51). General linear model showed that clinical symptoms have a highly significant effect on the number of cMBs (N = 2.78, 95%CI [2.51-3.07], p<2*10-16; ndf = 78, AIC = 1218).cMBs and ICH may be observed in the anterior and posterior circulation in VBD but they occur more frequently in the posterior circulation. Most common anatomical locations of cMBs in VBD were the thalamus, occipital lobe and cerebellum. This posterior dominance of cMBs and ICH in VBD might reflect a specific underlying vascular pathology.

Project description:Graphical abstract Highlights • LCH in bone marrow and lymph node are more likely to have multi-system involvement compared to LHC in other sites.• Craniofacial osseous LCH is more likely to be treated with surgery, vertebral LCH is less likely to be treated with surgery.• A racial disparity in surgery utilization is identified in pediatric patients with bone LCH. Background Langerhans cell histiocytosis (LCH) is a rare monoclonal histiocytic neoplasm. Little is known about clinical factors associated with LCH single- vs multi-system involvement at the time of diagnosis. Methods Data on 1549 LCH patients diagnosed between years 2010 and 2018 were extracted from the Surveillance, Epidemiology and End Results Program. Patterns of single- vs multisystem involvement were examined using multivariable logistic regression analysis. Odd ratio (OR) and 95% confidence interval (CI) were reported. Results 968 children and adolescents (0–19 years; median: 4 years) and 581 adults (≥20 years; median: 49 years) were included in the analysis. Multi-system LCH was reported for 30.9 % patients. Bone marrow (BM) (OR = 3.776; 95 %CI = 1.939–7.351; P < 0.001) and lymph node (LN) (OR = 3.274; 95 %CI = 1.443–7.427; P = 0.005) involvement were most commonly associated with multi-system LCH at the time of diagnosis; similar pattern was also observed in adult patients (OR = 17.780; 95 %CI = 6.469–48.867; P < 0.001 for BM LCH; and OR = 5.156; 95 %CI = 2.131–12.471; P < 0.001 for LN LCH). Among pediatric patients, craniofacial osseous LCH was more likely to be treated with surgery (OR = 2.822; 95 %CI = 1.199–6.639; P = 0.018) compared to skeletal lesions in other sites, whereas vertebral body LCH was less likely to be treated with surgery (OR = 0.175; 95 %CI = 0.058–0.527; P = 0.002). In pediatric patients with bone LCH, the non-white patients were less likely to be treated surgically compared to the white patients (OR = 0.470; 95 %CI = 0.272–0.812; P = 0.007). Conclusions BM and LN LCH are associated with the highest risks of multi-system disease, which may require active surveillance. Furthermore, active attempts are needed to mitigate the racial disparity in surgery utilization in pediatric patients with skeletal LCH.

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The anatomical distribution of genetic associations.

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The anatomical distribution of genetic associations.

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