Browsing by Subject "Phenotype"
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Item 3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies(Public Library of Science, 2021-05-13) Hoskens, Hanne; Liu, Dongjing; Naqvi, Sahin; Lee, Myoung Keun; Eller, Ryan J.; Indencleef, Karlijne; White, Julie D.; Li, Jiarui; Larmuseau, Maarten H. D.; Hens, Greet; Wysocka, Joanna; Walsh, Susan; Richmond, Stephen; Shriver, Mark D.; Shaffer, John R.; Peeters, Hilde; Weinberg, Seth M.; Claes, Peter; Biology, School of ScienceThe analysis of contemporary genomic data typically operates on one-dimensional phenotypic measurements (e.g. standing height). Here we report on a data-driven, family-informed strategy to facial phenotyping that searches for biologically relevant traits and reduces multivariate 3D facial shape variability into amendable univariate measurements, while preserving its structurally complex nature. We performed a biometric identification of siblings in a sample of 424 children, defining 1,048 sib-shared facial traits. Subsequent quantification and analyses in an independent European cohort (n = 8,246) demonstrated significant heritability for a subset of traits (0.17-0.53) and highlighted 218 genome-wide significant loci (38 also study-wide) associated with facial variation shared by siblings. These loci showed preferential enrichment for active chromatin marks in cranial neural crest cells and embryonic craniofacial tissues and several regions harbor putative craniofacial genes, thereby enhancing our knowledge on the genetic architecture of normal-range facial variation.Item A Cephalometric Study of Non-Cleft Parents of Children with Cleft Lip, Cleft Lip and Palate, and Cleft Palate : Evidence to Support a Different Etiology for Isolated Cleft Palate Versus Cleft Lip?(1993) Sadler, Charles A., Jr.; Ward, Richard E.; Bixler, David; Hathaway, Ronald R.; Shanks, James C.; Roberts, W. EugeneCleft lip with or without cleft palate (CLI P) and isolated cleft palate (CP) have been shown to be separate epidemiologic and embryologic entities. Furthermore, it has been proposed that noncleft biologic parents of children with facial clefts may demonstrate craniofacial differences genetically predisposing them to pass on the cleft phenotype to their offspring. With these two hypotheses in mind, the objective of the present study was to determine if differences exist in the craniofacial morphology between parents of CL/P children and parents of CP children. Twenty-seven measurements were obtained from anterior-posterior (AP) cephalograms on 127 biologic parents of sporadic CL/P and CP children. Each measurement was compared with sex and age-matched normals, and Z-scores were determined. The mean Z-scores for each group were tested for significant differences from normal and from each other. In agreement with past literature, the craniofacial morphology of parents of cleft children was generally found to have greater facial widths and shorter facial heights. Differences between the findings of the present study and the past literature are discussed. Although CL/P and CP are thought to be separate entities, differences between the parents of CL/P and CP children were not statistically evident.Item A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies(Springer Nature, 2022) Li, Zilin; Li, Xihao; Zhou, Hufeng; Gaynor, Sheila M.; Selvaraj, Margaret Sunitha; Arapoglou, Theodore; Quick, Corbin; Liu, Yaowu; Chen, Han; Sun, Ryan; Dey, Rounak; Arnett, Donna K.; Auer, Paul L.; Bielak, Lawrence F.; Bis, Joshua C.; Blackwell, Thomas W.; Blangero, John; Boerwinkle, Eric; Bowden, Donald W.; Brody, Jennifer A.; Cade, Brian E.; Conomos, Matthew P.; Correa, Adolfo; Cupples, L. Adrienne; Curran, Joanne E.; de Vries, Paul S.; Duggirala, Ravindranath; Franceschini, Nora; Freedman, Barry I.; Göring, Harald H. H.; Guo, Xiuqing; Kalyani, Rita R.; Kooperberg, Charles; Kral, Brian G.; Lange, Leslie A.; Lin, Bridget M.; Manichaikul, Ani; Manning, Alisa K.; Martin, Lisa W.; Mathias, Rasika A.; Meigs, James B.; Mitchell, Braxton D.; Montasser, May E.; Morrison, Alanna C.; Naseri, Take; O'Connell, Jeffrey R.; Palmer, Nicholette D.; Peyser, Patricia A.; Psaty, Bruce M.; Raffield, Laura M.; Redline, Susan; Reiner, Alexander P.; Reupena, Muagututi'a Sefuiva; Rice, Kenneth M.; Rich, Stephen S.; Smith, Jennifer A.; Taylor, Kent D.; Taub, Margaret A.; Vasan, Ramachandran S.; Weeks, Daniel E.; Wilson, James G.; Yanek, Lisa R.; Zhao, Wei; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lipids Working Group; Rotter, Jerome I.; Willer, Cristen J.; Natarajan, Pradeep; Peloso, Gina M.; Lin, Xihong; Biostatistics and Health Data Science, School of MedicineLarge-scale whole-genome sequencing studies have enabled analysis of noncoding rare-variant (RV) associations with complex human diseases and traits. Variant-set analysis is a powerful approach to study RV association. However, existing methods have limited ability in analyzing the noncoding genome. We propose a computationally efficient and robust noncoding RV association detection framework, STAARpipeline, to automatically annotate a whole-genome sequencing study and perform flexible noncoding RV association analysis, including gene-centric analysis and fixed window-based and dynamic window-based non-gene-centric analysis by incorporating variant functional annotations. In gene-centric analysis, STAARpipeline uses STAAR to group noncoding variants based on functional categories of genes and incorporate multiple functional annotations. In non-gene-centric analysis, STAARpipeline uses SCANG-STAAR to incorporate dynamic window sizes and multiple functional annotations. We apply STAARpipeline to identify noncoding RV sets associated with four lipid traits in 21,015 discovery samples from the Trans-Omics for Precision Medicine (TOPMed) program and replicate several of them in an additional 9,123 TOPMed samples. We also analyze five non-lipid TOPMed traits.Item Associations Between Dysmenorrhea Symptom-Based Phenotypes and Vaginal Microbiome: A Pilot Study(Wolters Kluwer, 2021) Chen, Chen X.; Carpenter, Janet S.; Gao, Xiang; Toh, Evelyn; Dong, Qunfeng; Nelson, David E.; Mitchell, Caroline; Fortenberry, J. DennisBACKGROUND: Dysmenorrhea is highly prevalent; it places women at risk for other chronic pain conditions. There is a high degree of individual variability in menstrual pain severity, the number of painful sites, and co-occurring gastrointestinal symptoms. Distinct dysmenorrhea symptom-based phenotypes were previously identified, but the biological underpinnings of these phenotypes are less known. One underexplored contributor is the vaginal microbiome. The vaginal microbiota differs significantly among reproductive-age women and may modulate as well as amplify reproductive tract inflammation, which may contribute to dysmenorrhea symptoms. OBJECTIVES: The objective of this study was to examine associations between dysmenorrhea symptom-based phenotypes and vaginal microbiome compositions on- and off-menses. METHODS: We conducted a prospective, longitudinal, pilot study of 20 women (aged 15-24 years) grouped into three dysmenorrhea symptom-based phenotypes: "mild localized pain," "severe localized pain," and "severe multiple pain and gastrointestinal symptoms." Over one menstrual cycle, participants provided vaginal swabs when they were on- and off-menses. We assayed the vaginal microbiome using 16S rRNA gene sequencing. Permutational multivariate analysis of variance tests were used to compare microbiome compositions across phenotypes, with heat maps generated to visualize the relative abundance of bacterial taxa. RESULTS: The vaginal microbiome compositions (n = 40) were different across the three phenotypes. After separating the on-menses (n = 20) and off-menses (n = 20) specimens, the statistically significant difference was seen on-menses, but not off-menses. Compared to the "mild localized pain" phenotype, participants in the "multiple severe symptoms" phenotype had a lower lactobacilli level and a higher abundance of Prevotella, Atopobium, and Gardnerella when on-menses. We also observed trends of differences across phenotypes in vaginal microbiome change from off- to on-menses. DISCUSSION: The study provides proof-of-concept data to support larger studies on associations between dysmenorrhea symptom-based phenotypes and vaginal microbiome that might lead to new intervention targets and/or biomarkers for dysmenorrhea. This line of research has the potential to inform precision dysmenorrhea treatment that can improve women's quality of life.Item Craniofacial Morphology in familial cases of cleft lip/palate: phenotypic heterogeneity and genetic predisposition in unaffected family members(1993) Litz, Stephanie M.; Bixler, David; Fleener, Donald E.; Hennon, David Kent, 1933-; Sadove, A. Michael; Ward, Richard E.; Avery, David R.This study investigated familial cases of cleft lip with or without cleft palate to determine whether the unaffected members of each family can be identified as gene carriers for the cleft trait. This research presumes that such carriers will have henotypic features identifiable by cephalometric analysis that are associated with an increased risk to cleft offspring. Using population genetics methodology, a pedigree analysis was made for each family member was assigned to one of four groups: (1) obligate normal, (2) affected, (3) carrier, and (4) unknown. LA and PA cephalographs were taken on each subject and a clinical oral-facial examination carried out on participating family members. Various anatomic landmarks located on the LA and PA films were digitized and from them, a total of 28 linear measurements were made. To eliminate the effect of sex and differential age responses, Z scores were calculated. Through univariate analysis, only one variable, NCR-MO, was shown to be significantly different between the two groups. This variable difference by itself is not adequate to differentiate those in the normal group from the carrier group. Even though only one variable was significant, other differences in the variables between these groups become obvious when the group variables were plotted as Z scores. Since Z scores are pure values with no limits (2--the number of standard deviations in a given variable differs from normal). Thereby, age-related growth differences were minimized. Further information is gained when these Z scores are plotted as pattern profiles, Figures 5-7. These profiles of mean Z scores for each variable pointed out areas of the face in which the differences were so great that specific anatomic areas appeared to be associated with one of the four groups. For example, gene carriers demonstrated specific alterations in facial height that might conceivably be used to discriminate that group from the other three groups. The family normals and carriers were then analyzed by using a stepwise multivariate analysis. By this approach, a discriminant function was generated consisting of six variables (three each from the lateral and frontal headplates), which proved to be significant in distinguishing an individual's phenotype. These variables define facial height, width and depth. The specific findings included a decrease in mid-facial height and depth along with an increased lower facial height and width in the gene carrier population as compared to the normals. The function then was used to predict group membership of the same two groups. Comparing this analytical prediction to that of the grouping system that resulted from the pedigree analysis, all but one individual was classified correctly in both the normal and carrier population. A discriminant score was also determined for the unknown population of family members which were defined as non-cleft blood relatives of cleft probands. Thus, they were a mixture of two types--those unaffected who carried a genetic liability for producing a cleft child and those unaffected who did not. A prediction of their placement into either the normal or carrier group was made with the discriminate function. One-third were classed in the normal group and two-thirds as gene carriers. The results of this study confirm that the phenotype of these unaffected family members designated as obligate gene carriers differs significantly from that of the family normals. This information is not only quite useful for genetic counselling but gives both a better understanding or the genetic control of clefting and can lead to molecular research to identify the specific gene in question.Item Dendritic Cell Therapy in Transplantation, Phenotype Governs Destination and Function(Lippincott, Williams & Wilkins, 2018-10) Samy, Kannan P.; Brennan, Todd V.; Surgery, School of MedicineItem Derivation, validation, and transcriptomic assessment of pediatric septic shock phenotypes identified through latent profile analyses: Results from a prospective multi-center observational cohort(Research Square, 2023-12-06) Atreya, Mihir R.; Huang, Min; Moore, Andrew R.; Zheng, Hong; Hasin-Brumshtein, Yehudit; Fitzgerald, Julie C.; Weiss, Scott L.; Cvijanovich, Natalie Z.; Bigham, Michael T.; Jain, Parag N.; Schwarz, Adam J.; Lutfi, Riad; Nowak, Jeffrey; Thomas, Neal J.; Quasney, Michael; Dahmer, Mary K.; Baines, Torrey; Haileselassie, Bereketeab; Lautz, Andrew J.; Stanski, Natalja L.; Standage, Stephen W.; Kaplan, Jennifer M.; Zingarelli, Basilia; Sweeney, Timothy E.; Khatri, Purvesh; Sanchez-Pinto, L. Nelson; Kamaleswaran, Rishikesan; Pediatrics, School of MedicineBackground: Sepsis poses a grave threat, especially among children, but treatments are limited due to clinical and biological heterogeneity among patients. Thus, there is an urgent need for precise subclassification of patients to guide therapeutic interventions. Methods: We used clinical, laboratory, and biomarker data from a prospective multi-center pediatric septic shock cohort to derive phenotypes using latent profile analyses. Thereafter, we trained a support vector machine model to assign phenotypes in a hold-out validation set. We tested interactions between phenotypes and common sepsis therapies on clinical outcomes and conducted transcriptomic analyses to better understand the phenotype-specific biology. Finally, we compared whether newly identified phenotypes overlapped with established gene-expression endotypes and tested the utility of an integrated subclassification scheme. Findings: Among 1,071 patients included, we identified two phenotypes which we named 'inflamed' (19.5%) and an 'uninflamed' phenotype (80.5%). The 'inflamed' phenotype had an over 4-fold risk of 28-day mortality relative to those 'uninflamed'. Transcriptomic analysis revealed overexpression of genes implicated in the innate immune response and suggested an overabundance of developing neutrophils, pro-T/NK cells, and NK cells among those 'inflamed'. There was no significant overlap between endotypes and phenotypes. However, an integrated subclassification scheme demonstrated varying survival probabilities when comparing endophenotypes. Interpretation: Our research underscores the reproducibility of latent profile analyses to identify clinical and biologically informative pediatric septic shock phenotypes with high prognostic relevance. Pending validation, an integrated subclassification scheme, reflective of the different facets of the host response, holds promise to inform targeted intervention among those critically ill.Item THE DEVELOPMENT AND COMMITMENT OF T HELPER SUBSETS(2011-03-09) Stritesky, Gretta L.; Kaplan, Mark H.; Blum, Janice Sherry, 1957-; Dent, Alexander L.; Harrington, Maureen A.T helper cells play a crucial role in providing protection against a wide variety of pathogens. The differentiation and effector function of T helper cell subsets is dependent on cytokine activation of Signal Transducer and Activator of Transcription (STAT) family members. The development of Th17 cells, which are important for immunity to fungi and extracellular bacteria, relies on STAT3. We show that IL-23 in combination with IL-1β promotes maintenance of the Th17 phenotype following multiple rounds of stimulation. However, IL-23 does not promote commitment of Th17 cells, and when Th17 cells are cultured with IL-12 or IL-4 they switch to a Th1 and Th2 phenotype, respectively. The maintenance of the Th17 phenotype by IL-23 also requires STAT4. STAT4-deficient memory cells cultured with IL-23 have reduced IL-17 production following stimulation with either anti-CD3 or IL-18+IL-23 stimulation compared to wild type memory cells. Furthermore, STAT4-deficient mice have impaired in vivo Th17 development following immunization with ovalbumin. This challenges a one-STAT/one-subset paradigm and suggests that multiple STAT proteins can contribute to a single phenotype. To test this further we examined whether STAT3 is required for the development of Th2 cells, a subset known to depend upon the IL-4-induced activation of STAT6 for immunity to parasites and promoting allergic inflammation. We demonstrate that in the absence of STAT3, the expression of Th2-associated cytokines and transcription factors is dramatically reduced. STAT3 is also required for in vivo development of Th2 cells. Moreover, allergic inflammation is diminished in mice that have T cells lacking expression of STAT3. STAT3 does not affect STAT6 activation, but does impact how STAT6 functions in binding target genes. Thus, multiple STAT proteins can cooperate in promoting the development of specific T helper subsets.Item Effect of Epigallocatechin-3-gallate on Skeletal and Cognitive Phenotypes in a Down Syndrome Mouse Model(2014) Abeysekera, Irushi Shamalka; Roper, Randall J.; Goodlett, Charley; Li, Jiliang; Yost, RobertDown syndrome (DS), a genetic disorder that affects ~1 in 700 live births, is caused by trisomy of human chromosome 21 (Hsa21). Individuals with DS are affected by a wide spectrum of phenotypes which vary in severity and penetrance. However, cognitive and skeletal impairments can be commonly observed in all individuals with DS. To study these phenotypes, we utilized the Ts65Dn mouse model that carries three copies of approximately half the gene orthologs found on Hsa21 and exhibit similar phenotypes as observed in humans with DS. Individuals with DS and Ts65Dn mice have deficits in bone mineral density (BMD), bone architecture, bone strength, learning and memory. Over-expression of DYRK1A, a serine-threonine kinase encoded on Hsa21, has been linked to deficiencies in DS bone homeostasis and cognition. Epigallocatechin-3-gallate (EGCG), an aromatic polyphenol found in high concentrations in green tea, is a selective inhibitor of DYRK1A activity. Normalization of DYRK1A activity by EGCG therefore may have the potential to ameliorate skeletal and cognitive deficits. We hypothesized that supplements containing EGCG obtained from health food stores/ online vendors will not be as effective as EGCG from a chemical company in correcting bone deficits associated with DS. Our results suggest that EGCG improves the bone mineral density of trisomic femurs significantly better than the supplements while the EGCgNOW supplement from NOW FOODS improves trabecular and cortical bone structure. The results from HPLC analysis of supplements showed the presence of other catechins in EGCgNOW and degradation analysis revealed the rapid degradation of supplements. Therefore we hypothesize that the presence of EGCG degradation products and other green tea catechins in supplements may play a role in the differential skeletal effects we observed. We further hypothesized that a three week treatment of adolescent mice with EGCG will lead to an improvement in the learning and memory deficits that are observed in trisomic animals in comparison to control mice. However, our results indicate that three weeks of low-dose EGCG treatment during adolescence is insufficient to improve hippocampal dependent learning and memory deficits of Ts65Dn mice. The possibility remains that a higher dose of EGCG that begins at three weeks but lasts throughout the behavioral test period may result in improvement in learning and memory deficit of Ts65Dn mice.