Browsing by Subject "Phenotype"
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Item Open Access A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies.(Nature methods, 2022-12) 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 HH; 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, XihongLarge-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 Open Access A Genocentric Approach to Discovery of Mendelian Disorders.(American journal of human genetics, 2019-11) Hansen, Adam W; Murugan, Mullai; Li, He; Khayat, Michael M; Wang, Liwen; Rosenfeld, Jill; Andrews, B Kim; Jhangiani, Shalini N; Coban Akdemir, Zeynep H; Sedlazeck, Fritz J; Ashley-Koch, Allison E; Liu, Pengfei; Muzny, Donna M; Task Force for Neonatal Genomics; Davis, Erica E; Katsanis, Nicholas; Sabo, Aniko; Posey, Jennifer E; Yang, Yaping; Wangler, Michael F; Eng, Christine M; Sutton, V Reid; Lupski, James R; Boerwinkle, Eric; Gibbs, Richard AThe advent of inexpensive, clinical exome sequencing (ES) has led to the accumulation of genetic data from thousands of samples from individuals affected with a wide range of diseases, but for whom the underlying genetic and molecular etiology of their clinical phenotype remains unknown. In many cases, detailed phenotypes are unavailable or poorly recorded and there is little family history to guide study. To accelerate discovery, we integrated ES data from 18,696 individuals referred for suspected Mendelian disease, together with relatives, in an Apache Hadoop data lake (Hadoop Architecture Lake of Exomes [HARLEE]) and implemented a genocentric analysis that rapidly identified 154 genes harboring variants suspected to cause Mendelian disorders. The approach did not rely on case-specific phenotypic classifications but was driven by optimization of gene- and variant-level filter parameters utilizing historical Mendelian disease-gene association discovery data. Variants in 19 of the 154 candidate genes were subsequently reported as causative of a Mendelian trait and additional data support the association of all other candidate genes with disease endpoints.Item Open Access A genome-wide association study of variants associated with acquisition of Staphylococcus aureus bacteremia in a healthcare setting.(BMC Infect Dis, 2014-02-13) Nelson, Charlotte L; Pelak, Kimberly; Podgoreanu, Mihai V; Ahn, Sun Hee; Scott, William K; Allen, Andrew S; Cowell, Lindsay G; Rude, Thomas H; Zhang, Yurong; Tong, Amy; Ruffin, Felicia; Sharma-Kuinkel, Batu K; Fowler, Vance GBACKGROUND: Humans vary in their susceptibility to acquiring Staphylococcus aureus infection, and research suggests that there is a genetic basis for this variability. Several recent genome-wide association studies (GWAS) have identified variants that may affect susceptibility to infectious diseases, demonstrating the potential value of GWAS in this arena. METHODS: We conducted a GWAS to identify common variants associated with acquisition of S. aureus bacteremia (SAB) resulting from healthcare contact. We performed a logistic regression analysis to compare patients with healthcare contact who developed SAB (361 cases) to patients with healthcare contact in the same hospital who did not develop SAB (699 controls), testing 542,410 SNPs and adjusting for age (by decade), sex, and 6 significant principal components from our EIGENSTRAT analysis. Additionally, we evaluated the joint effect of the host and pathogen genomes in association with severity of SAB infection via logistic regression, including an interaction of host SNP with bacterial genotype, and adjusting for age (by decade), sex, the 6 significant principal components, and dialysis status. Bonferroni corrections were applied in both analyses to control for multiple comparisons. RESULTS: Ours is the first study that has attempted to evaluate the entire human genome for variants potentially involved in the acquisition or severity of SAB. Although this study identified no common variant of large effect size to have genome-wide significance for association with either the risk of acquiring SAB or severity of SAB, the variant (rs2043436) most significantly associated with severity of infection is located in a biologically plausible candidate gene (CDON, a member of the immunoglobulin family) and may warrant further study. CONCLUSIONS: The genetic architecture underlying SAB is likely to be complex. Future investigations using larger samples, narrowed phenotypes, and advances in both genotyping and analytical methodologies will be important tools for identifying causative variants for this common and serious cause of healthcare-associated infection.Item Open Access A new non-enzymatic method for isolating human intervertebral disc cells preserves the phenotype of nucleus pulposus cells.(Cytotechnology, 2014-12) Tang, Xinyan; Richardson, William J; Fitch, Robert D; Brown, Christopher R; Isaacs, Robert E; Chen, JunCells isolated from intervertebral disc (IVD) tissues of human surgical samples are one of potential sources for the IVD cellular therapy. The purpose of this study was to develop a new non-enzymatic method, "tissue incubation", for isolating human IVD cells. The IVD tissues of annulus fibrosus (AF) and nucleus pulposus (NP) were incubated separately in tissue culture flasks with culture medium. After 7-10 days incubation, cells were able to migrate out of IVD tissues and proliferate in vitro. After 3-4 weeks culture, expanded cells were harvested by trypsinization, and the remaining tissues were transferred to a new flask for another round of incubation. The molecular phenotype of IVD cells from juvenile and adult human samples was evaluated by both flow cytometry analysis and immunocytochemical staining for the expression of protein markers of NP cells (CD24, CD54, CD239, integrin α6 and laminin α5). Flow cytometry confirmed that both AF and NP cells of all ages positively expressed CD54 and integrin α6, with higher expression levels in NP cells than in AF cells for the juvenile group sample. However, CD24 expression was only found in juvenile NP cells, and not in AF or older disc cells. Similar expression patterns for NP markers were also confirmed by immunocytochemistry. In summary, this new non-enzymatic tissue incubation method for cell isolation preserves molecular phenotypic markers of NP cells and may provide a valuable cell source for the study of NP regeneration strategies.Item Open Access A plant genetic network for preventing dysbiosis in the phyllosphere.(Nature, 2020-04-08) Chen, Tao; Nomura, Kinya; Wang, Xiaolin; Sohrabi, Reza; Xu, Jin; Yao, Lingya; Paasch, Bradley C; Ma, Li; Kremer, James; Cheng, Yuti; Zhang, Li; Wang, Nian; Wang, Ertao; Xin, Xiu-Fang; He, Sheng YangThe aboveground parts of terrestrial plants, collectively called the phyllosphere, have a key role in the global balance of atmospheric carbon dioxide and oxygen. The phyllosphere represents one of the most abundant habitats for microbiota colonization. Whether and how plants control phyllosphere microbiota to ensure plant health is not well understood. Here we show that the Arabidopsis quadruple mutant (min7 fls2 efr cerk1; hereafter, mfec)1, simultaneously defective in pattern-triggered immunity and the MIN7 vesicle-trafficking pathway, or a constitutively activated cell death1 (cad1) mutant, carrying a S205F mutation in a membrane-attack-complex/perforin (MACPF)-domain protein, harbour altered endophytic phyllosphere microbiota and display leaf-tissue damage associated with dysbiosis. The Shannon diversity index and the relative abundance of Firmicutes were markedly reduced, whereas Proteobacteria were enriched in the mfec and cad1S205F mutants, bearing cross-kingdom resemblance to some aspects of the dysbiosis that occurs in human inflammatory bowel disease. Bacterial community transplantation experiments demonstrated a causal role of a properly assembled leaf bacterial community in phyllosphere health. Pattern-triggered immune signalling, MIN7 and CAD1 are found in major land plant lineages and are probably key components of a genetic network through which terrestrial plants control the level and nurture the diversity of endophytic phyllosphere microbiota for survival and health in a microorganism-rich environment.Item Open Access A strategic research alliance: Turner syndrome and sex differences.(American journal of medical genetics. Part C, Seminars in medical genetics, 2019-03) San Roman, Adrianna K; Page, David C; Page, David CSex chromosome constitution varies in the human population, both between the sexes (46,XX females and 46,XY males), and within the sexes (e.g., 45,X and 46,XX females, and 47,XXY and 46,XY males). Coincident with this genetic variation are numerous phenotypic differences between males and females, and individuals with sex chromosome aneuploidy. However, the molecular mechanisms by which sex chromosome constitution impacts phenotypes at the cellular, tissue, and organismal levels remain largely unexplored. Thus, emerges a fundamental question connecting the study of sex differences and sex chromosome aneuploidy syndromes: How does sex chromosome constitution influence phenotype? Here, we focus on Turner syndrome (TS), associated with the 45,X karyotype, and its synergies with the study of sex differences. We review findings from evolutionary studies of the sex chromosomes, which identified genes that are most likely to contribute to phenotypes as a result of variation in sex chromosome constitution. We then explore strategies for investigating the direct effects of the sex chromosomes, and the evidence for specific sex chromosome genes impacting phenotypes. In sum, we argue that integrating the study of TS with sex differences offers a mutually beneficial alliance to identify contributions of the sex chromosomes to human development, health, and disease.Item Open Access Amino acid-level signal-to-noise analysis of incidentally identified variants in genes associated with long QT syndrome during pediatric whole exome sequencing reflects background genetic noise.(Heart rhythm, 2018-07) Landstrom, Andrew P; Fernandez, Ernesto; Rosenfeld, Jill A; Yang, Yaping; Dailey-Schwartz, Andrew L; Miyake, Christina Y; Allen, Hugh D; Penny, Daniel J; Kim, Jeffrey JBACKGROUND:Due to rapid expansion of clinical genetic testing, an increasing number of genetic variants of undetermined significance and unclear diagnostic value are being identified in children. Variants found in genes associated with heritable channelopathies, such as long QT syndrome (LQTS), are particularly difficult to interpret given the risk of sudden cardiac death associated with pathologic mutations. OBJECTIVE:The purpose of this study was to determine whether variants in LQTS-associated genes from whole exome sequencing (WES) represent disease-associated biomarkers or background genetic "noise." METHODS:WES variants from Baylor Genetics Laboratories were obtained for 17 LQTS-associated genes. Rare variants from healthy controls were obtained from the GnomAD database. LQTS case variants were extracted from the literature. Amino acid-level mapping and signal-to-noise calculations were conducted. Clinical history and diagnostic studies were analyzed for WES subjects evaluated at our institution. RESULTS:Variants in LQTS case-associated genes were present in 38.3% of 7244 WES probands. There was a similar frequency of variants in the WES and healthy cohorts for LQTS1-3 (11.2% and 12.9%, respectively) and LQTS4-17 (27.1% and 38.4%, respectively). WES variants preferentially localized to amino acids altered in control individuals compared to cases. Based on amino acid-level analysis, WES-identified variants are indistinguishable from healthy background variation, whereas LQTS1 and 2 case-identified variants localized to clear pathologic "hotspots." No individuals who underwent clinical evaluation had clinical suspicion for LQTS. CONCLUSION:The prevalence of incidentally identified LQTS-associated variants is ∼38% among WES tests. These variants most likely represent benign healthy background genetic variation rather than disease-associated mutations.Item Open Access An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease.(Cell host & microbe, 2018-08) Wang, Liuyang; Pittman, Kelly J; Barker, Jeffrey R; Salinas, Raul E; Stanaway, Ian B; Williams, Graham D; Carroll, Robert J; Balmat, Tom; Ingham, Andy; Gopalakrishnan, Anusha M; Gibbs, Kyle D; Antonia, Alejandro L; eMERGE Network; Heitman, Joseph; Lee, Soo Chan; Jarvik, Gail P; Denny, Joshua C; Horner, Stacy M; DeLong, Mark R; Valdivia, Raphael H; Crosslin, David R; Ko, Dennis CPathogens have been a strong driving force for natural selection. Therefore, understanding how human genetic differences impact infection-related cellular traits can mechanistically link genetic variation to disease susceptibility. Here we report the Hi-HOST Phenome Project (H2P2): a catalog of cellular genome-wide association studies (GWAS) comprising 79 infection-related phenotypes in response to 8 pathogens in 528 lymphoblastoid cell lines. Seventeen loci surpass genome-wide significance for infection-associated phenotypes ranging from pathogen replication to cytokine production. We combined H2P2 with clinical association data from patients to identify a SNP near CXCL10 as a risk factor for inflammatory bowel disease. A SNP in the transcriptional repressor ZBTB20 demonstrated pleiotropy, likely through suppression of multiple target genes, and was associated with viral hepatitis. These data are available on a web portal to facilitate interpreting human genome variation through the lens of cell biology and should serve as a rich resource for the research community.Item Open Access Angiopoietin receptor TEK mutations underlie primary congenital glaucoma with variable expressivity.(The Journal of clinical investigation, 2016-07) Souma, Tomokazu; Tompson, Stuart W; Thomson, Benjamin R; Siggs, Owen M; Kizhatil, Krishnakumar; Yamaguchi, Shinji; Feng, Liang; Limviphuvadh, Vachiranee; Whisenhunt, Kristina N; Maurer-Stroh, Sebastian; Yanovitch, Tammy L; Kalaydjieva, Luba; Azmanov, Dimitar N; Finzi, Simone; Mauri, Lucia; Javadiyan, Shahrbanou; Souzeau, Emmanuelle; Zhou, Tiger; Hewitt, Alex W; Kloss, Bethany; Burdon, Kathryn P; Mackey, David A; Allen, Keri F; Ruddle, Jonathan B; Lim, Sing-Hui; Rozen, Steve; Tran-Viet, Khanh-Nhat; Liu, Xiaorong; John, Simon; Wiggs, Janey L; Pasutto, Francesca; Craig, Jamie E; Jin, Jing; Quaggin, Susan E; Young, Terri LPrimary congenital glaucoma (PCG) is a devastating eye disease and an important cause of childhood blindness worldwide. In PCG, defects in the anterior chamber aqueous humor outflow structures of the eye result in elevated intraocular pressure (IOP); however, the genes and molecular mechanisms involved in the etiology of these defects have not been fully characterized. Previously, we observed PCG-like phenotypes in transgenic mice that lack functional angiopoietin-TEK signaling. Herein, we identified rare TEK variants in 10 of 189 unrelated PCG families and demonstrated that each mutation results in haploinsufficiency due to protein loss of function. Multiple cellular mechanisms were responsible for the loss of protein function resulting from individual TEK variants, including an absence of normal protein production, protein aggregate formation, enhanced proteasomal degradation, altered subcellular localization, and reduced responsiveness to ligand stimulation. Further, in mice, hemizygosity for Tek led to the formation of severely hypomorphic Schlemm's canal and trabecular meshwork, as well as elevated IOP, demonstrating that anterior chamber vascular development is sensitive to Tek gene dosage and the resulting decrease in angiopoietin-TEK signaling. Collectively, these results identify TEK mutations in patients with PCG that likely underlie disease and are transmitted in an autosomal dominant pattern with variable expressivity.Item Open Access Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.(Database : the journal of biological databases and curation, 2018-01) Dahdul, Wasila; Manda, Prashanti; Cui, Hong; Balhoff, James P; Dececchi, T Alexander; Ibrahim, Nizar; Lapp, Hilmar; Vision, Todd; Mabee, Paula MNatural language descriptions of organismal phenotypes, a principal object of study in biology, are abundant in the biological literature. Expressing these phenotypes as logical statements using ontologies would enable large-scale analysis on phenotypic information from diverse systems. However, considerable human effort is required to make these phenotype descriptions amenable to machine reasoning. Natural language processing tools have been developed to facilitate this task, and the training and evaluation of these tools depend on the availability of high quality, manually annotated gold standard data sets. We describe the development of an expert-curated gold standard data set of annotated phenotypes for evolutionary biology. The gold standard was developed for the curation of complex comparative phenotypes for the Phenoscape project. It was created by consensus among three curators and consists of entity-quality expressions of varying complexity. We use the gold standard to evaluate annotations created by human curators and those generated by the Semantic CharaParser tool. Using four annotation accuracy metrics that can account for any level of relationship between terms from two phenotype annotations, we found that machine-human consistency, or similarity, was significantly lower than inter-curator (human-human) consistency. Surprisingly, allowing curatorsaccess to external information did not significantly increase the similarity of their annotations to the gold standard or have a significant effect on inter-curator consistency. We found that the similarity of machine annotations to the gold standard increased after new relevant ontology terms had been added. Evaluation by the original authors of the character descriptions indicated that the gold standard annotations came closer to representing their intended meaning than did either the curator or machine annotations. These findings point toward ways to better design software to augment human curators and the use of the gold standard corpus will allow training and assessment of new tools to improve phenotype annotation accuracy at scale.Item Open Access Applying active learning to high-throughput phenotyping algorithms for electronic health records data.(Journal of the American Medical Informatics Association : JAMIA, 2013-12) Chen, Yukun; Carroll, Robert J; Hinz, Eugenia R McPeek; Shah, Anushi; Eyler, Anne E; Denny, Joshua C; Xu, HuaObjectives
Generalizable, high-throughput phenotyping methods based on supervised machine learning (ML) algorithms could significantly accelerate the use of electronic health records data for clinical and translational research. However, they often require large numbers of annotated samples, which are costly and time-consuming to review. We investigated the use of active learning (AL) in ML-based phenotyping algorithms.Methods
We integrated an uncertainty sampling AL approach with support vector machines-based phenotyping algorithms and evaluated its performance using three annotated disease cohorts including rheumatoid arthritis (RA), colorectal cancer (CRC), and venous thromboembolism (VTE). We investigated performance using two types of feature sets: unrefined features, which contained at least all clinical concepts extracted from notes and billing codes; and a smaller set of refined features selected by domain experts. The performance of the AL was compared with a passive learning (PL) approach based on random sampling.Results
Our evaluation showed that AL outperformed PL on three phenotyping tasks. When unrefined features were used in the RA and CRC tasks, AL reduced the number of annotated samples required to achieve an area under the curve (AUC) score of 0.95 by 68% and 23%, respectively. AL also achieved a reduction of 68% for VTE with an optimal AUC of 0.70 using refined features. As expected, refined features improved the performance of phenotyping classifiers and required fewer annotated samples.Conclusions
This study demonstrated that AL can be useful in ML-based phenotyping methods. Moreover, AL and feature engineering based on domain knowledge could be combined to develop efficient and generalizable phenotyping methods.Item Open Access Associations of genotypes and haplotypes of IL-17 with risk of gastric cancer in an eastern Chinese population.(Oncotarget, 2016-12) Zhou, Fei; Qiu, Li-Xin; Cheng, Lei; Wang, Meng-Yun; Li, Jin; Sun, Meng-Hong; Yang, Ya-Jun; Wang, Jiu-Cun; Jin, Li; Wang, Ya-Nong; Wei, Qing-YiInterleukin-17 plays a crucial role in inflammation-related carcinogenesis. We hypothesize that genetic variants in IL-17 are associated with gastric cancer (GCa) risk, and we genotyped five potentially functional single nucleotide polymorphisms (SNPs) (rs1974226 G > A, rs2275913 A > G, rs3819024 A > G, rs4711998 A > G, and rs8193036 C > T) of IL-17 in 1121 GCa patients and 1216 cancer-free controls in an eastern Chinese population. Logistic regression analysis was used to calculate odds ratios (OR) and 95% confidence intervals (CI). Meta-analysis and genotype-mRNA expression correlation were performed to further validate positive associations. We found that an increased GCa risk was independently associated with rs1974226 (adjusted OR = 2.60, 95% CI = 1.27-5.32 for AA vs. GG + GA) and rs2275913 (adjusted OR = 1.33, 95% CI = 1.03-1.72 for GA + AA vs. GG), while a decreased GCa risk was independently associated with rs3819024 (adjusted OR = 0.72, 95% CI = 0.54-0.96 for GG vs. AA + AG). Additional meta-analyses confirmed the observed risk association with rs2275913. We also found that two IL-17 haplotypes (G-G-G-A-C) and (A-G-G-A-C) (in the order of rs1974226, rs2275913, rs3819024, rs4711998 and rs8193036) were associated with a reduced GCa risk (adjusted OR = 0.64, 95% CI = 0.46-0.89 and adjusted OR = 0.38, 95% CI = 0.17-0.81, respectively). However, the expression Quantitative Trait Locus (eQTL) analysis for the genotype-phenotype correlation did not find mRNA expression changes associated with either the genotypes. In conclusions, genetic variants of IL-17 are likely to be associated with risk of GCa, and additional larger studies with functional validation are needed to explore the molecular mechanisms underlying the observed associations.Item Open Access Behavior genetics and postgenomics.(Behav Brain Sci, 2012-10) Charney, EvanThe science of genetics is undergoing a paradigm shift. Recent discoveries, including the activity of retrotransposons, the extent of copy number variations, somatic and chromosomal mosaicism, and the nature of the epigenome as a regulator of DNA expressivity, are challenging a series of dogmas concerning the nature of the genome and the relationship between genotype and phenotype. According to three widely held dogmas, DNA is the unchanging template of heredity, is identical in all the cells and tissues of the body, and is the sole agent of inheritance. Rather than being an unchanging template, DNA appears subject to a good deal of environmentally induced change. Instead of identical DNA in all the cells of the body, somatic mosaicism appears to be the normal human condition. And DNA can no longer be considered the sole agent of inheritance. We now know that the epigenome, which regulates gene expressivity, can be inherited via the germline. These developments are particularly significant for behavior genetics for at least three reasons: First, epigenetic regulation, DNA variability, and somatic mosaicism appear to be particularly prevalent in the human brain and probably are involved in much of human behavior; second, they have important implications for the validity of heritability and gene association studies, the methodologies that largely define the discipline of behavior genetics; and third, they appear to play a critical role in development during the perinatal period and, in particular, in enabling phenotypic plasticity in offspring. I examine one of the central claims to emerge from the use of heritability studies in the behavioral sciences, the principle of minimal shared maternal effects, in light of the growing awareness that the maternal perinatal environment is a critical venue for the exercise of adaptive phenotypic plasticity. This consideration has important implications for both developmental and evolutionary biology.Item Open Access Biogenetic mechanisms predisposing to complex phenotypes in parents may function differently in their children.(J Gerontol A Biol Sci Med Sci, 2013-07) Kulminski, Alexander M; Arbeev, Konstantin G; Christensen, Kaare; Stallard, Eric; Miljkovic, Iva; Barmada, Michael; Yashin, Anatoliy IThis study focuses on the participants of the Long Life Family Study to elucidate whether biogenetic mechanisms underlying relationships among heritable complex phenotypes in parents function in the same way for the same phenotypes in their children. Our results reveal 3 characteristic groups of relationships among phenotypes in parents and children. One group composed of 3 pairs of phenotypes confirms that associations among some phenotypes can be explained by the same biogenetic mechanisms working in parents and children. Two other groups including 9 phenotype pairs show that this is not a common rule. Our findings suggest that biogenetic mechanisms underlying relationships among different phenotypes, even if they are causally related, can function differently in successive generations or in different age groups of biologically related individuals. The results suggest that the role of aging-related processes in changing environment may be conceptually underestimated in current genetic association studies using genome wide resources.Item Open Access Cancer and longevity--is there a trade-off? A study of cooccurrence in Danish twin pairs born 1900-1918.(J Gerontol A Biol Sci Med Sci, 2012-05) Christensen, Kaare; Pedersen, Jacob K; Hjelmborg, Jacob VB; Vaupel, James W; Stevnsner, Tinna; Holm, Niels V; Skytthe, AxelBACKGROUND: Animal models and a few human studies have suggested a complex interaction between cancer risk and longevity indicating a trade-off where low cancer risk is associated with accelerating aging phenotypes and, vice versa, that longevity potential comes with the cost of increased cancer risk. This hypothesis predicts that longevity in one twin is associated with increased cancer risk in the cotwin. METHODS: A total of 4,354 twin pairs born 1900-1918 in Denmark were followed for mortality in the Danish Civil Registration System through 2008 and for cancer incidence in the period 1943-2008 through the Danish Cancer Registry. RESULTS: The 8,139 twins who provided risk time for cancer occurrence entered the study between ages 24 and 43 (mean 33 years), and each participant was followed up to death, emigration, or at least 90 years of age. The total follow-up time was 353,410 person-years and, 2,524 cancers were diagnosed. A negative association between age at death of a twin and cancer incidence in the cotwin was found in the overall analyses as well as in the subanalysis stratified on sex, zygosity, and random selection of one twin from each twin pair. CONCLUSIONS: This study did not find evidence of a cancer-longevity trade-off in humans. On the contrary, it suggested that longevity in one twin is associated with lower cancer incidence in the cotwin, indicating familial factors associated with both low cancer occurrence and longevity.Item Open Access Cardiac phenotype in ATP1A3-related syndromes: A multicenter cohort study.(Neurology, 2020-11) Balestrini, Simona; Mikati, Mohamad A; Álvarez-García-Rovés, Reyes; Carboni, Michael; Hunanyan, Arsen S; Kherallah, Bassil; McLean, Melissa; Prange, Lyndsey; De Grandis, Elisa; Gagliardi, Alessandra; Pisciotta, Livia; Stagnaro, Michela; Veneselli, Edvige; Campistol, Jaume; Fons, Carmen; Pias-Peleteiro, Leticia; Brashear, Allison; Miller, Charlotte; Samões, Raquel; Brankovic, Vesna; Padiath, Quasar S; Potic, Ana; Pilch, Jacek; Vezyroglou, Aikaterini; Bye, Ann ME; Davis, Andrew M; Ryan, Monique M; Semsarian, Christopher; Hollingsworth, Georgina; Scheffer, Ingrid E; Granata, Tiziana; Nardocci, Nardo; Ragona, Francesca; Arzimanoglou, Alexis; Panagiotakaki, Eleni; Carrilho, Inês; Zucca, Claudio; Novy, Jan; Dzieżyc, Karolina; Parowicz, Marek; Mazurkiewicz-Bełdzińska, Maria; Weckhuysen, Sarah; Pons, Roser; Groppa, Sergiu; Sinden, Daniel S; Pitt, Geoffrey S; Tinker, Andrew; Ashworth, Michael; Michalak, Zuzanna; Thom, Maria; Cross, J Helen; Vavassori, Rosaria; Kaski, Juan P; Sisodiya, Sanjay MObjective
To define the risks and consequences of cardiac abnormalities in ATP1A3-related syndromes.Methods
Patients meeting clinical diagnostic criteria for rapid-onset dystonia-parkinsonism (RDP), alternating hemiplegia of childhood (AHC), and cerebellar ataxia, areflexia, pes cavus, optic atrophy, and sensorineural hearing loss (CAPOS) with ATP1A3 genetic analysis and at least 1 cardiac assessment were included. We evaluated the cardiac phenotype in an Atp1a3 knock-in mouse (Mashl+/-) to determine the sequence of events in seizure-related cardiac death.Results
Ninety-eight patients with AHC, 9 with RDP, and 3 with CAPOS (63 female, mean age 17 years) were included. Resting ECG abnormalities were found in 52 of 87 (60%) with AHC, 2 of 3 (67%) with CAPOS, and 6 of 9 (67%) with RDP. Serial ECGs showed dynamic changes in 10 of 18 patients with AHC. The first Holter ECG was abnormal in 24 of 65 (37%) cases with AHC and RDP with either repolarization or conduction abnormalities. Echocardiography was normal. Cardiac intervention was required in 3 of 98 (≈3%) patients with AHC. In the mouse model, resting ECGs showed intracardiac conduction delay; during induced seizures, heart block or complete sinus arrest led to death.Conclusions
We found increased prevalence of ECG dynamic abnormalities in all ATP1A3-related syndromes, with a risk of life-threatening cardiac rhythm abnormalities equivalent to that in established cardiac channelopathies (≈3%). Sudden cardiac death due to conduction abnormality emerged as a seizure-related outcome in murine Atp1a3-related disease. ATP1A3-related syndromes are cardiac diseases and neurologic diseases. We provide guidance to identify patients potentially at higher risk of sudden cardiac death who may benefit from insertion of a pacemaker or implantable cardioverter-defibrillator.Item Open Access Characterization of the standard and recommended CODIS markers.(Journal of forensic sciences, 2013-01) Katsanis, Sara H; Wagner, Jennifer KAs U.S. courts grapple with constitutional challenges to DNA identification applications, judges are resting legal decisions on the fingerprint analogy, questioning whether the information from a DNA profile could, in light of scientific advances, reveal biomedically relevant information. While CODIS loci were selected largely because they lack phenotypic associations, how this criterion was assessed is unclear. To clarify their phenotypic relevance, we describe the standard and recommended CODIS markers within the context of what is known currently about the genome. We characterize the genomic regions and phenotypic associations of the 24 standard and suggested CODIS markers. None of the markers are within exons, although 12 are intragenic. No CODIS genotypes are associated with known phenotypes. This study provides clarification of the genomic significance of the key identification markers and supports--independent of the forensic scientific community--that the CODIS profiles provide identification but not sensitive or biomedically relevant information.Item Open Access Classification and genetic characterization of pattern-forming Bacilli.(Mol Microbiol, 1998-02) Rudner, R; Martsinkevich, O; Leung, W; Jarvis, EDOne of the more natural but less commonly studied forms of colonial bacterial growth is pattern formation. This type of growth is characterized by bacterial populations behaving in an organized manner to generate readily identifiable geometric and predictable morphologies on solid and semi-solid surfaces. In our first attempt to study the molecular basis of pattern formation in Bacillus subtilis, we stumbled upon an enigma: some strains used to describe pattern formation in B. subtilis did not have the phenotypic or genotypic characteristics of B. subtilis. In this report, we show that these strains are actually not B. subtilis, but belong to a different class of Bacilli, group I. We show further that commonly used laboratory strains of B. subtilis can co-exist as mixed cultures with group I Bacilli, and that the latter go unnoticed when grown on frequently used laboratory substrates. However, when B. subtilis is grown under more stringent semiarid conditions, members of group I emerge in the form of complex patterns. When B. subtilis is grown under less stringent and more motile conditions, B. subtilis forms its own pattern, and members of group I remain unnoticed. These findings have led us to revise some of the mechanistic and evolutionary hypotheses that have been proposed to explain pattern growth in Bacilli.Item Open Access Classifying Patients Operated for Spondylolisthesis: A K-Means Clustering Analysis of Clinical Presentation Phenotypes.(Neurosurgery, 2021-11) Chan, Andrew K; Wozny, Thomas A; Bisson, Erica F; Pennicooke, Brenton H; Bydon, Mohamad; Glassman, Steven D; Foley, Kevin T; Shaffrey, Christopher I; Potts, Eric A; Shaffrey, Mark E; Coric, Domagoj; Knightly, John J; Park, Paul; Wang, Michael Y; Fu, Kai-Ming; Slotkin, Jonathan R; Asher, Anthony L; Virk, Michael S; Kerezoudis, Panagiotis; Alvi, Mohammed A; Guan, Jian; Haid, Regis W; Mummaneni, Praveen VBackground
Trials of lumbar spondylolisthesis are difficult to compare because of the heterogeneity in the populations studied.Objective
To define patterns of clinical presentation.Methods
This is a study of the prospective Quality Outcomes Database spondylolisthesis registry, including patients who underwent single-segment surgery for grade 1 degenerative lumbar spondylolisthesis. Twenty-four-month patient-reported outcomes (PROs) were collected. A k-means clustering analysis-an unsupervised machine learning algorithm-was used to identify clinical presentation phenotypes.Results
Overall, 608 patients were identified, of which 507 (83.4%) had 24-mo follow-up. Clustering revealed 2 distinct cohorts. Cluster 1 (high disease burden) was younger, had higher body mass index (BMI) and American Society of Anesthesiologist (ASA) grades, and globally worse baseline PROs. Cluster 2 (intermediate disease burden) was older and had lower BMI and ASA grades, and intermediate baseline PROs. Baseline radiographic parameters were similar (P > .05). Both clusters improved clinically (P < .001 all 24-mo PROs). In multivariable adjusted analyses, mean 24-mo Oswestry Disability Index (ODI), Numeric Rating Scale Back Pain (NRS-BP), Numeric Rating Scale Leg Pain, and EuroQol-5D (EQ-5D) were markedly worse for the high-disease-burden cluster (adjusted-P < .001). However, the high-disease-burden cluster demonstrated greater 24-mo improvements for ODI, NRS-BP, and EQ-5D (adjusted-P < .05) and a higher proportion reaching ODI minimal clinically important difference (MCID) (adjusted-P = .001). High-disease-burden cluster had lower satisfaction (adjusted-P = .02).Conclusion
We define 2 distinct phenotypes-those with high vs intermediate disease burden-operated for lumbar spondylolisthesis. Those with high disease burden were less satisfied, had a lower quality of life, and more disability, more back pain, and more leg pain than those with intermediate disease burden, but had greater magnitudes of improvement in disability, back pain, quality of life, and more often reached ODI MCID.Item Open Access Common genetic variation and the control of HIV-1 in humans.(PLoS Genet, 2009-12) Fellay, Jacques; Ge, Dongliang; Shianna, Kevin V; Colombo, Sara; Ledergerber, Bruno; Cirulli, Elizabeth T; Urban, Thomas J; Zhang, Kunlin; Gumbs, Curtis E; Smith, Jason P; Castagna, Antonella; Cozzi-Lepri, Alessandro; De Luca, Andrea; Easterbrook, Philippa; Günthard, Huldrych F; Mallal, Simon; Mussini, Cristina; Dalmau, Judith; Martinez-Picado, Javier; Miro, José M; Obel, Niels; Wolinsky, Steven M; Martinson, Jeremy J; Detels, Roger; Margolick, Joseph B; Jacobson, Lisa P; Descombes, Patrick; Antonarakis, Stylianos E; Beckmann, Jacques S; O'Brien, Stephen J; Letvin, Norman L; McMichael, Andrew J; Haynes, Barton F; Carrington, Mary; Feng, Sheng; Telenti, Amalio; Goldstein, David B; NIAID Center for HIV/AIDS Vaccine Immunology (CHAVI)To extend the understanding of host genetic determinants of HIV-1 control, we performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects. The study was powered to detect common genetic variants explaining down to 1.3% of the variability in viral load at set point. We provide overwhelming confirmation of three associations previously reported in a genome-wide study and show further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC). We also examined the polymorphisms reported in previous candidate gene studies and fail to support a role for any variant outside of the MHC or the chemokine receptor cluster on chromosome 3. In addition, we evaluated functional variants, copy-number polymorphisms, epistatic interactions, and biological pathways. This study thus represents a comprehensive assessment of common human genetic variation in HIV-1 control in Caucasians.