Shoa L. Clarke, MD, PhD

All Publications

• The need for polygenic score reporting standards in evidence-based practice: lipid genetics use case. Current opinion in lipidology Wand, H., Knowles, J. W., Clarke, S. L. 2021

  Abstract

  Polygenic scores (PGS) are used to quantify the genetic predisposition for heritable traits, with hypothesized utility for personalized risk assessments. Lipid PGS are primed for clinical translation, but evidence-based practice changes will require rigorous PGS standards to ensure reproducibility and generalizability. Here we review applicable reporting and technical standards for dyslipidemia PGS translation along phases of the ACCE (Analytical validity, Clinical validity, Clinical utility, Ethical considerations) framework for evaluating genetic tests.New guidance suggests existing standards for study designs incorporating the ACCE framework are applicable to PGS and should be adopted. One recent example is the Clinical Genomics Resource (ClinGen) and Polygenic Score Catalog's PRS reporting standards, which define minimal requirements for describing rationale for score development, study population definitions and data parameters, risk model development and application, risk model evaluation, and translational considerations, such as generalizability beyond the target population studied.Lipid PGS are likely to be integrated into clinical practice in the future. Clinicians will need to be prepared to determine if and when lipid PGS is useful and valid. This decision-making will depend on the quality of evidence for the clinical use of PGS. Establishing reporting standards for PGS will help facilitate data sharing and transparency for critical evaluation, ultimately benefiting the efficiency of evidence-based practice.

  View details for DOI 10.1097/MOL.0000000000000733

  View details for PubMedID 33538426

• Cardiorespiratory Fitness, Body-Mass Index, and Markers of Insulin Resistance in Apparently Healthy Women and Men. The American journal of medicine Clarke, S. L., Reaven, G. M., Leonard, D., Barlow, C. E., Haskell, W. L., Willis, B. L., DeFina, L., Knowles, J. W., Maron, D. J. 2020

  Abstract

  BACKGROUND: Insulin resistance may be present in healthy adults and is associated poor health outcomes. Obesity is a risk factor for insulin resistance, but most obese adults do not have insulin resistance. Fitness may be protective, but the association between fitness, weight, and insulin resistance has not been studied in a large population of healthy adults.METHODS: A cross-sectional analysis of cardiorespiratory fitness, body-mass index, and markers of insulin resistance was performed. Study participants were enrolled at the Cooper Clinic (Dallas, Texas). The analysis included 19,263 women and 48,433 men with no history of diabetes or cardiovascular disease. Cardiorespiratory fitness was measured using exercise treadmill testing. Impaired fasting glucose (100-125 mg/dL) and elevated fasting triglycerides (≥150 mg/dL) were used as a markers of insulin resistance.RESULTS: Among normal weight individuals, poor fitness was associated with a 2.2 (1.4-3.6; p=0.001) fold higher odds of insulin resistance in women and a 2.8 (2.1-3.6; p<0.001) fold higher odds in men. The impact of fitness remained significant for overweight and obese individuals, with the highest risk group being the unfit obese. Among obese women, the odds ratio for insulin resistance was 11.0 (8.7-13.9; p<0.001) for fit and 20.3 (15.5-26.5; p<0.001) for unfit women. Among obese men, the odds ratio for insulin resistance was 7.4 (6.7-8.2; p<0.001) for fit and 12.9 (11.4-14.6; p<0.001) for unfit men.CONCLUSION: Independent of weight, poor fitness is associated with risk of insulin resistance. Obese individuals, particularly women, may benefit from the greatest absolute risk reduction by achieving moderate fitness.

  View details for DOI 10.1016/j.amjmed.2019.11.031

  View details for PubMedID 31926863

• Genome-Wide Association Studies of Coronary Artery Disease: Recent Progress and Challenges Ahead. Current atherosclerosis reports Clarke, S. L., Assimes, T. L. 2018; 20 (9): 47

  Abstract

  Genome-wide association studies (GWAS) have been the primary tool for unbiased assessment of the genetic basis of coronary artery disease (CAD) for more than a decade. We summarize successes as well as shortcomings of recent studies in this context.The number of CAD-associated loci has more than doubled in the past year to 161. This rapid progress has been in large part due to the release of genome-wide genotyping data for the largely European participants of the UK Biobank study which has been combined with existing GWAS from the CARDIoGRAMplusC4D consortium. Additional discoveries have been achieved through large-scale genotyping of participants using custom high-yield genotyping arrays including the Metabochip and the Exome chip. As a consequence, the ability of genetic risk scores in predicting incident CAD events has improved but that improvement has only been shown in European populations. GWAS have proven to be a fruitful approach for uncovering the genetic drivers of CAD. However, determining the mechanisms of association of GWAS findings remains a challenging endeavor requiring long-term investment. Genetic risk scores offer an opportunity for recent findings to have an immediate clinical impact. Going forward, CAD genetics will benefit greatly from the release of more genetic data produced by mega-biobanks. These new data will allow for the more comprehensive examination of underrepresented populations.

  View details for DOI 10.1007/s11883-018-0748-4

  View details for PubMedID 30022313

• Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories. PLoS computational biology Guturu, H., Chinchali, S., Clarke, S. L., Bejerano, G. 2016; 12 (2)

  Abstract

  Although many human diseases have a genetic component involving many loci, the majority of studies are statistically underpowered to isolate the many contributing variants, raising the question of the existence of alternate processes to identify disease mutations. To address this question, we collect ancestral transcription factor binding sites disrupted by an individual's variants and then look for their most significant congregation next to a group of functionally related genes. Strikingly, when the method is applied to five different full human genomes, the top enriched function for each is invariably reflective of their very different medical histories. For example, our method implicates "abnormal cardiac output" for a patient with a longstanding family history of heart disease, "decreased circulating sodium level" for an individual with hypertension, and other biologically appealing links for medical histories spanning narcolepsy to axonal neuropathy. Our results suggest that erosion of gene regulation by mutation load significantly contributes to observed heritable phenotypes that manifest in the medical history. The test we developed exposes a hitherto hidden layer of personal variants that promise to shed new light on human disease penetrance, expressivity and the sensitivity with which we can detect them.

  View details for DOI 10.1371/journal.pcbi.1004711

  View details for PubMedID 26845687

  View details for PubMedCentralID PMC4742230

• The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option. PLoS genetics Wenger, A. M., Clarke, S. L., Notwell, J. H., Chung, T., Tuteja, G., Guturu, H., Schaar, B. T., Bejerano, G. 2013; 9 (8)

  Abstract

  Genetic studies have identified a core set of transcription factors and target genes that control the development of the neocortex, the region of the human brain responsible for higher cognition. The specific regulatory interactions between these factors, many key upstream and downstream genes, and the enhancers that mediate all these interactions remain mostly uncharacterized. We perform p300 ChIP-seq to identify over 6,600 candidate enhancers active in the dorsal cerebral wall of embryonic day 14.5 (E14.5) mice. Over 95% of the peaks we measure are conserved to human. Eight of ten (80%) candidates tested using mouse transgenesis drive activity in restricted laminar patterns within the neocortex. GREAT based computational analysis reveals highly significant correlation with genes expressed at E14.5 in key areas for neocortex development, and allows the grouping of enhancers by known biological functions and pathways for further studies. We find that multiple genes are flanked by dozens of candidate enhancers each, including well-known key neocortical genes as well as suspected and novel genes. Nearly a quarter of our candidate enhancers are conserved well beyond mammals. Human and zebrafish regions orthologous to our candidate enhancers are shown to most often function in other aspects of central nervous system development. Finally, we find strong evidence that specific interspersed repeat families have contributed potentially key developmental enhancers via co-option. Our analysis expands the methodologies available for extracting the richness of information found in genome-wide functional maps.

  View details for DOI 10.1371/journal.pgen.1003728

  View details for PubMedID 24009522

  View details for PubMedCentralID PMC3757057

• PRISM offers a comprehensive genomic approach to transcription factor function prediction. Genome research Wenger, A. M., Clarke, S. L., Guturu, H., Chen, J., Schaar, B. T., McLean, C. Y., Bejerano, G. 2013; 23 (5): 889-904

  Abstract

  The human genome encodes 1500-2000 different transcription factors (TFs). ChIP-seq is revealing the global binding profiles of a fraction of TFs in a fraction of their biological contexts. These data show that the majority of TFs bind directly next to a large number of context-relevant target genes, that most binding is distal, and that binding is context specific. Because of the effort and cost involved, ChIP-seq is seldom used in search of novel TF function. Such exploration is instead done using expression perturbation and genetic screens. Here we propose a comprehensive computational framework for transcription factor function prediction. We curate 332 high-quality nonredundant TF binding motifs that represent all major DNA binding domains, and improve cross-species conserved binding site prediction to obtain 3.3 million conserved, mostly distal, binding site predictions. We combine these with 2.4 million facts about all human and mouse gene functions, in a novel statistical framework, in search of enrichments of particular motifs next to groups of target genes of particular functions. Rigorous parameter tuning and a harsh null are used to minimize false positives. Our novel PRISM (predicting regulatory information from single motifs) approach obtains 2543 TF function predictions in a large variety of contexts, at a false discovery rate of 16%. The predictions are highly enriched for validated TF roles, and 45 of 67 (67%) tested binding site regions in five different contexts act as enhancers in functionally matched cells.

  View details for DOI 10.1101/gr.139071.112

  View details for PubMedID 23382538

  View details for PubMedCentralID PMC3638144

• Human Developmental Enhancers Conserved between Deuterostomes and Protostomes PLOS GENETICS Clarke, S. L., VanderMeer, J. E., Wenger, A. M., Schaar, B. T., Ahituv, N., Bejerano, G. 2012; 8 (8)

  Abstract

  The identification of homologies, whether morphological, molecular, or genetic, is fundamental to our understanding of common biological principles. Homologies bridging the great divide between deuterostomes and protostomes have served as the basis for current models of animal evolution and development. It is now appreciated that these two clades share a common developmental toolkit consisting of conserved transcription factors and signaling pathways. These patterning genes sometimes show common expression patterns and genetic interactions, suggesting the existence of similar or even conserved regulatory apparatus. However, previous studies have found no regulatory sequence conserved between deuterostomes and protostomes. Here we describe the first such enhancers, which we call bilaterian conserved regulatory elements (Bicores). Bicores show conservation of sequence and gene synteny. Sequence conservation of Bicores reflects conserved patterns of transcription factor binding sites. We predict that Bicores act as response elements to signaling pathways, and we show that Bicores are developmental enhancers that drive expression of transcriptional repressors in the vertebrate central nervous system. Although the small number of identified Bicores suggests extensive rewiring of cis-regulation between the protostome and deuterostome clades, additional Bicores may be revealed as our understanding of cis-regulatory logic and sample of bilaterian genomes continue to grow.

  View details for DOI 10.1371/journal.pgen.1002852

  View details for Web of Science ID 000308529300014

  View details for PubMedID 22876195

  View details for PubMedCentralID PMC3410860

• Coding exons function as tissue-specific enhancers of nearby genes GENOME RESEARCH Birnbaum, R. Y., Clowney, E. J., Agamy, O., Kim, M. J., Zhao, J., Yamanaka, T., Pappalardo, Z., Clarke, S. L., Wenger, A. M., Loan Nguyen, L., Gurrieri, F., Everman, D. B., Schwartz, C. E., Birk, O. S., Bejerano, G., Lomvardas, S., Ahituv, N. 2012; 22 (6): 1059-1068

  Abstract

  Enhancers are essential gene regulatory elements whose alteration can lead to morphological differences between species, developmental abnormalities, and human disease. Current strategies to identify enhancers focus primarily on noncoding sequences and tend to exclude protein coding sequences. Here, we analyzed 25 available ChIP-seq data sets that identify enhancers in an unbiased manner (H3K4me1, H3K27ac, and EP300) for peaks that overlap exons. We find that, on average, 7% of all ChIP-seq peaks overlap coding exons (after excluding for peaks that overlap with first exons). By using mouse and zebrafish enhancer assays, we demonstrate that several of these exonic enhancer (eExons) candidates can function as enhancers of their neighboring genes and that the exonic sequence is necessary for enhancer activity. Using ChIP, 3C, and DNA FISH, we further show that one of these exonic limb enhancers, Dync1i1 exon 15, has active enhancer marks and physically interacts with Dlx5/6 promoter regions 900 kb away. In addition, its removal by chromosomal abnormalities in humans could cause split hand and foot malformation 1 (SHFM1), a disorder associated with DLX5/6. These results demonstrate that DNA sequences can have a dual function, operating as coding exons in one tissue and enhancers of nearby gene(s) in another tissue, suggesting that phenotypes resulting from coding mutations could be caused not only by protein alteration but also by disrupting the regulation of another gene.

  View details for DOI 10.1101/gr.133546.111

  View details for Web of Science ID 000304728100007

  View details for PubMedID 22442009

  View details for PubMedCentralID PMC3371700

• Control of Pelvic Girdle Development by Genes of the Pbx Family and Emx2 DEVELOPMENTAL DYNAMICS Capellini, T. D., Handschuh, K., Quintana, L., Ferretti, E., Di Giacomo, G., Fantini, S., Vaccari, G., Clarke, S. L., Wenger, A. M., Bejerano, G., Sharpe, J., Zappavigna, V., Selleri, L. 2011; 240 (5): 1173-1189

  Abstract

  Genes expressed in the somatopleuric mesoderm, the embryonic domain giving rise to the vertebrate pelvis, appear important for pelvic girdle formation. Among such genes, Pbx family members and Emx2 were found to genetically interact in hindlimb and pectoral girdle formation. Here, we generated compound mutant embryos carrying combinations of mutated alleles for Pbx1, Pbx2, and Pbx3, as well as Pbx1 and Emx2, to examine potential genetic interactions during pelvic development. Indeed, Pbx genes share overlapping functions and Pbx1 and Emx2 genetically interact in pelvic formation. We show that, in compound Pbx1;Pbx2 and Pbx1;Emx2 mutants, pelvic mesenchymal condensation is markedly perturbed, indicative of an upstream control by these homeoproteins. We establish that expression of Tbx15, Prrx1, and Pax1, among other genes involved in the specification and development of select pelvic structures, is altered in our compound mutants. Lastly, we identify potential Pbx1-Emx2-regulated enhancers for Tbx15, Prrx1, and Pax1, using bioinformatics analyses.

  View details for DOI 10.1002/dvdy.22617

  View details for Web of Science ID 000289942300023

  View details for PubMedID 21455939

  View details for PubMedCentralID PMC3081414

• GREAT improves functional interpretation of cis-regulatory regions NATURE BIOTECHNOLOGY McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M., Bejerano, G. 2010; 28 (5): 495-U155

  Abstract

  We developed the Genomic Regions Enrichment of Annotations Tool (GREAT) to analyze the functional significance of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. Applying GREAT to data sets from chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) of multiple transcription-associated factors, including SRF, NRSF, GABP, Stat3 and p300 in different developmental contexts, we recover many functions of these factors that are missed by existing gene-based tools, and we generate testable hypotheses. The utility of GREAT is not limited to ChIP-seq, as it could also be applied to open chromatin, localized epigenomic markers and similar functional data sets, as well as comparative genomics sets.

  View details for DOI 10.1038/nbt.1630

  View details for Web of Science ID 000277452700030

  View details for PubMedID 20436461