Sources of gene expression variation in a globally diverse human cohort.

Genetic variation that influences gene expression and splicing is a key source of phenotypic diversity1-5. Although invaluable, studies investigating these links in humans have been strongly biased towards participants of European ancestries, which constrains generalizability and hinders evolutionary research. Here to address these limitations, we developed MAGE, an open-access RNA sequencing dataset of lymphoblastoid cell lines from 731 individuals from the 1000 Genomes Project6, spread across 5 continental groups and 26 populations. Most variation in gene expression (92%) and splicing (95%) was distributed within versus between populations, which mirrored the variation in DNA sequence. We mapped associations between genetic variants and expression and splicing of nearby genes (cis-expression quantitative trait loci (eQTLs) and cis-splicing QTLs (sQTLs), respectively). We identified more than 15,000 putatively causal eQTLs and more than 16,000 putatively causal sQTLs that are enriched for relevant epigenomic signatures. These include 1,310 eQTLs and 1,657 sQTLs that are largely private to underrepresented populations. Our data further indicate that the magnitude and direction of causal eQTL effects are highly consistent across populations. Moreover, the apparent 'population-specific' effects observed in previous studies were largely driven by low resolution or additional independent eQTLs of the same genes that were not detected. Together, our study expands our understanding of human gene expression diversity and provides an inclusive resource for studying the evolution and function of human genomes.

Transcriptomics and chromatin accessibility in multiple African population samples.

Mapping the functional human genome and impact of genetic variants is often limited to European-descendent population samples. To aid in overcoming this limitation, we measured gene expression using RNA sequencing in lymphoblastoid cell lines (LCLs) from 599 individuals from six African populations to identify novel transcripts including those not represented in the hg38 reference genome. We used whole genomes from the 1000 Genomes Project and 164 Maasai individuals to identify 8,881 expression and 6,949 splicing quantitative trait loci (eQTLs/sQTLs), and 2,611 structural variants associated with gene expression (SV-eQTLs). We further profiled chromatin accessibility using ATAC-Seq in a subset of 100 representative individuals, to identity chromatin accessibility quantitative trait loci (caQTLs) and allele-specific chromatin accessibility, and provide predictions for the functional effect of 78.9 million variants on chromatin accessibility. Using this map of eQTLs and caQTLs we fine-mapped GWAS signals for a range of complex diseases. Combined, this work expands global functional genomic data to identify novel transcripts, functional elements and variants, understand population genetic history of molecular quantitative trait loci, and further resolve the genetic basis of multiple human traits and disease.

"Clinicians Are From Mars and Pathologists Are From Venus" Revisited: Synoptic Reports Improve Clinician Comprehension of Pathology Reports in Inflammatory Bowel Disease.

CONTEXT.­: A prior study in this journal, "Clinicians Are from Mars and Pathologists Are From Venus," demonstrated that clinicians can erroneously interpret pathology reports up to 30% of the time. After noticing reporting heterogeneity in the setting of inflammatory bowel disease (IBD), we speculated that a standardized synoptic report could improve gastroenterologist comprehension. OBJECTIVE.­: To investigate the effect of a synoptic table on gastroenterologist comprehension of IBD pathology reports. DESIGN.­: We recruited gastroenterology fellows and faculty to participate in this study. All participants were given 6 pathology reports and asked if the following were present: active inflammation, chronic inflammation, IBD, and dysplasia. Participants were also asked to rate their confidence. After a 6-week washout period, the same questionnaire was distributed with a synoptic report. We performed paired t-tests to compare the mean accuracy and confidence scores between the preintervention and postintervention responses. RESULTS.­: A total of 39 physicians participated: 9 fellows and 30 faculty. Mean accuracy scores were higher after the intervention (0.81 versus 0.86, P < .001). Mean confidence was also higher after intervention, but this was not statistically significant (3.91 versus 3.98, P = .24). CONCLUSIONS.­: The improvement in accuracy scores after intervention confirms that clinician comprehension improved with the synoptic table. A synoptic report may provide a standardized way of communicating diagnostic information to clinicians in the setting of IBD, and potentially other inflammatory conditions.

Familial Clonal Hematopoiesis in a Long Telomere Syndrome.

BACKGROUND: Telomere shortening is a well-characterized cellular aging mechanism, and short telomere syndromes cause age-related disease. However, whether long telomere length is advantageous is poorly understood. METHODS: We examined the clinical and molecular features of aging and cancer in persons carrying heterozygous loss-of-function mutations in the telomere-related gene POT1 and noncarrier relatives. RESULTS: A total of 17 POT1 mutation carriers and 21 noncarrier relatives were initially included in the study, and a validation cohort of 6 additional mutation carriers was subsequently recruited. A majority of the POT1 mutation carriers with telomere length evaluated (9 of 13) had long telomeres (>99th percentile). POT1 mutation carriers had a range of benign and malignant neoplasms involving epithelial, mesenchymal, and neuronal tissues in addition to B- and T-cell lymphoma and myeloid cancers. Five of 18 POT1 mutation carriers (28%) had T-cell clonality, and 8 of 12 (67%) had clonal hematopoiesis of indeterminate potential. A predisposition to clonal hematopoiesis had an autosomal dominant pattern of inheritance, as well as penetrance that increased with age; somatic DNMT3A and JAK2 hotspot mutations were common. These and other somatic driver mutations probably arose in the first decades of life, and their lineages secondarily accumulated a higher mutation burden characterized by a clocklike signature. Successive generations showed genetic anticipation (i.e., an increasingly early onset of disease). In contrast to noncarrier relatives, who had the typical telomere shortening with age, POT1 mutation carriers maintained telomere length over the course of 2 years. CONCLUSIONS: POT1 mutations associated with long telomere length conferred a predisposition to a familial clonal hematopoiesis syndrome that was associated with a range of benign and malignant solid neoplasms. The risk of these phenotypes was mediated by extended cellular longevity and by the capacity to maintain telomeres over time. (Funded by the National Institutes of Health and others.).

A complete reference genome improves analysis of human genetic variation.

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. We show how this reference universally improves read mapping and variant calling for 3202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of variants per sample in previously unresolved regions, showcasing the promise of the T2T-CHM13 reference for evolutionary and biomedical discovery. Simultaneously, this reference eliminates tens of thousands of spurious variants per sample, including reduction of false positives in 269 medically relevant genes by up to a factor of 12. Because of these improvements in variant discovery coupled with population and functional genomic resources, T2T-CHM13 is positioned to replace GRCh38 as the prevailing reference for human genetics.

Haplotype-aware inference of human chromosome abnormalities.

Extra or missing chromosomes-a phenomenon termed aneuploidy-frequently arise during human meiosis and embryonic mitosis and are the leading cause of pregnancy loss, including in the context of in vitro fertilization (IVF). While meiotic aneuploidies affect all cells and are deleterious, mitotic errors generate mosaicism, which may be compatible with healthy live birth. Large-scale abnormalities such as triploidy and haploidy also contribute to adverse pregnancy outcomes, but remain hidden from standard sequencing-based approaches to preimplantation genetic testing for aneuploidy (PGT-A). The ability to reliably distinguish meiotic and mitotic aneuploidies, as well as abnormalities in genome-wide ploidy, may thus prove valuable for enhancing IVF outcomes. Here, we describe a statistical method for distinguishing these forms of aneuploidy based on analysis of low-coverage whole-genome sequencing data, which is the current standard in the field. Our approach overcomes the sparse nature of the data by leveraging allele frequencies and linkage disequilibrium (LD) measured in a population reference panel. The method, which we term LD-informed PGT-A (LD-PGTA), retains high accuracy down to coverage as low as 0.05 × and at higher coverage can also distinguish between meiosis I and meiosis II errors based on signatures spanning the centromeres. LD-PGTA provides fundamental insight into the origins of human chromosome abnormalities, as well as a practical tool with the potential to improve genetic testing during IVF.

Local adaptation and archaic introgression shape global diversity at human structural variant loci.

Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation - a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.

Archaic hominin genomics provides a window into gene expression evolution.

Differences in gene expression are thought to account for most phenotypic differences within and between species. Consequently, gene expression is a powerful lens through which to study divergence between modern humans and our closest evolutionary relatives, the Neanderthals and Denisovans. Such insights complement biological knowledge gleaned from the fossil record, while also revealing general features of the mode and tempo of regulatory evolution. Because of the degradation of ancient RNA, gene expression profiles of archaic hominins must be studied by indirect means. As such, conclusions drawn from these studies are often laden with assumptions about the genetic architecture of gene expression, the complexity of which is increasingly apparent. Despite these challenges, rapid technical and conceptual advances in the fields of ancient genomics, functional genomics, statistical genomics, and genome engineering are revolutionizing understanding of hominin gene expression evolution.

Impact of EMR Automated Results Routing Tool Implementation on Notification of Inpatient Endoscopy Biopsy Results.

BACKGROUND: Mucosal biopsies are often obtained during inpatient endoscopies to aid diagnosis. Up to 75% of patients are reported to have pending test results at discharge. Incomplete result communication to patients can lead to patient anxiety and poor outcomes. This study aimed to evaluate the impact of a systemwide electronic medical record (EMR) update on result communication. METHODS: The researchers retrospectively reviewed 100 inpatient endoscopies pending histopathology results at discharge to see if finalized results were communicated to the patients within 30 days. The same metric was studied after implementation of an EMR update that automatically routed results to the supervising endoscopist, by reviewing another 100 inpatient endoscopies during which biopsies were obtained. Follow-up rate pre- and post-EMR update was compared. RESULTS: Prior to the update, 47/77 (61.0%) histopathology results were communicated to the patients. Of the 30 nonreported cases, 17 showed nonspecific/chronic inflammation, 8 had no abnormal findings, 3 showed hyperplastic colon polyps, and 2 had colonic tubular adenomas. Following the EMR update, 65/71 (91.5%) of pathology results were communicated, demonstrating an increase of 30.5 percentage points in the rate of follow-up (95% confidence interval [CI] = 17.7-43.0, p < 0.0001). CONCLUSION: This study observed that 39.0% of inpatient endoscopic mucosal biopsy results in one health care system were not communicated to the patients. Implementation of a systemwide EMR intervention reduced this to 8.5% by shifting the responsibility of result communication to the endoscopy team. Similar EMR enhancements can be applied to other pending test results in health care systems with similar issues.

Comparison of colon adenoma detection rates using cap-assisted and Endocuff-assisted colonoscopy: a randomized controlled trial.

Objectives and study aim Colonoscopy prevents colorectal cancer by removing adenomatous polyps, but missed adenomas lead to interval cancers. Different devices have been used to increase adenoma detection rates (ADR). Two such devices of interest are the transparent cap (Olympus) and Endocuff (ARC Medical). Our study aimed to compare differences in ADR between Endocuff-assisted colonoscopy (EAC), cap-assisted colonoscopy (CAC) and standard colonoscopy (SC). Patients and methods A sample size of 126 subjects was calculated to determine an effect size of 30 %. Patients undergoing screening or surveillance colonoscopy between March 2016 and January 2017 were randomized to SC, CAC or EAC groups. Three experienced endoscopists performed all colonoscopies. Patient demographics, procedure indication, Boston Bowel Prep Score (BBPS), withdrawal time, polyp size, location, histopathology, were analyzed. Results There was no difference in ADR (52 %, 40 % and 54 %) in the SC, CAC and EAC groups respectively ( P  = 0.4). Similar findings were also observed for proximal ADR (45 %, 35 %, and 50 %, P  = 0.4) and SSA detection rate (16 %, 14 %, and 23 %, P  = 0.5). EAC detected higher mean ADR per colonoscopy compared to CAC (1.70 vs 0.76, P  = 0.01). However, there was no significant difference in mean ADR per positive colonoscopy (2.08, 1.63, and 2.59, P  = 0.21). Conclusion In a randomized controlled trial comparing AC to CAC and SC, neither device conferred additional benefits in ADR among high detectors. When comparing each device, EAC may be better than CAC at detecting more total adenomas.

Clinical impact of digital cholangioscopy in management of indeterminate biliary strictures and complex biliary stones: a single-center study.

AIMS: Endoscopic management of indeterminate strictures and complex stones remains a challenge, for which the latest generation single-operator digital cholangioscope (SpyGlass DS) has shown promising results. We aimed to study the clinical impact of single-operator digital cholangioscope at our tertiary academic center. METHODS: We retrospectively reviewed all digital cholangioscopies performed from June 2015 to May 2018. Patient characteristics, procedure characteristics, and post-procedural patient outcomes were recorded. RESULTS: A total of 50 patients (26 men, average age 61.4 years) underwent 67 procedures. Indications were biliary stones (21/50, 42%), strictures and primary sclerosing cholangitis surveillance (22/50, 46%), and miscellaneous (7/50, 14%). The average procedure time was 82 ± 29 min (99.5 min for stones and 74.2 min for strictures). Stone clearance was achieved in 19/21 (90.47%) cases, with electrohydraulic lithotripsy employed in 16/21 and repeat cholangioscopy necessary in 9/21. Malignant strictures (10) were differentiated from benign (12) in all cases both in patients with primary sclerosing cholangitis (9) and in those without (13), based on visual cholangioscopic features (sensitivity and specificity 100%), single-operator digital cholangioscope-directed biopsies (sensitivity 60% and specificity 100%), and brush cytology (sensitivity 37.5% and specificity 100%). Complications included one post-sphincterotomy bleeding and one post-procedural cholangitis despite antibiotic prophylaxis, but no procedure-related mortality. CONCLUSION: Single-operator digital cholangioscope had a high success rate and a low rate of complications for management of indeterminate strictures and difficult biliary stones. Visual cholangioscopic features of biliary strictures had excellent diagnostic accuracy, and targeted biopsies outperformed brush cytology. Early implementation of cholangioscopy for select indications leads to successful patient outcomes and reduces diagnostic delays, cost, and risks of repeat endoscopic retrograde cholangiopancreatographies.

Nutritional Ketosis for Weight Management and Reversal of Metabolic Syndrome.

PURPOSE OF REVIEW: The goal of this paper is to review current literature on nutritional ketosis within the context of weight management and metabolic syndrome, namely, insulin resistance, lipid profile, cardiovascular disease risk, and development of non-alcoholic fatty liver disease. We provide background on the mechanism of ketogenesis and describe nutritional ketosis. RECENT FINDINGS: Nutritional ketosis has been found to improve metabolic and inflammatory markers, including lipids, HbA1c, high-sensitivity CRP, fasting insulin and glucose levels, and aid in weight management. We discuss these findings and elaborate on potential mechanisms of ketones for promoting weight loss, decreasing hunger, and increasing satiety. Humans have evolved with the capacity for metabolic flexibility and the ability to use ketones for fuel. During states of low dietary carbohydrate intake, insulin levels remain low and ketogenesis takes place. These conditions promote breakdown of excess fat stores, sparing of lean muscle, and improvement in insulin sensitivity.

Destabilizing mutations encode nongenetic variation that drives evolutionary innovation.

Evolutionary innovations are often achieved by repurposing existing genes to perform new functions; however, the mechanisms enabling the transition from old to new remain controversial. We identified mutations in bacteriophage λ's host-recognition gene J that confer enhanced adsorption to λ's native receptor, LamB, and the ability to access a new receptor, OmpF. The mutations destabilize λ particles and cause conformational bistability of J, which yields progeny of multiple phenotypic forms, each proficient at different receptors. This work provides an example of how nongenetic protein variation can catalyze an evolutionary innovation. We propose that cases where a single genotype can manifest as multiple phenotypes may be more common than previously expected and offer a general mechanism for evolutionary innovation.

Ectopic splenic tissues mimicking gastro-intestinal stromal tumour in a patient after splenectomy for a giant epithelial cyst of spleen: A case report.

INTRODUCTION: Ectopic splenic tissues left after a previous splenectomy can masquerade as a gastro-intestinal stromal tumour (GIST). PRESENTATION OF CASE: Splenectomy was carried out for a 17-year-old girl with a giant epithelial cyst of spleen. Four years later, an upper endoscopy carried out for dyspepsia revealed two sub-mucosal lesions at the posterior wall of the gastric fundus. Computed tomography diagnosed a GIST. At operation, a dump-bell shaped extragastric mass was excised. Histology showed normal splenic tissues. DISCUSSION: Giant epithelial cyst of spleen is rare. It is even rarer for ectopic splenic tissues left after splenectomy to masquerade as a GIST. CONCLUSION: Ectopic splenic tissues should be included as a differential diagnosis in a patient who has a history of splenectomy presenting with a sub-mucosal gastric tumour.

Repression of glucocorticoid-stimulated angiopoietin-like 4 gene transcription by insulin.

Angiopoietin-like 4 (Angptl4) is a glucocorticoid receptor (GR) primary target gene in hepatocytes and adipocytes. It encodes a secreted protein that inhibits extracellular LPL and promotes adipocyte lipolysis. In Angptl4 null mice, glucocorticoid-induced adipocyte lipolysis and hepatic steatosis are compromised. Markedly, insulin suppressed glucocorticoid-induced Angptl4 transcription. To unravel the mechanism, we utilized small molecules to inhibit insulin signaling components and found that phosphatidylinositol 3-kinase and Akt were vital for the suppression in H4IIE cells. A forkhead box transcription factor response element (FRE) was found near the 15 bp Angptl4 glucocorticoid response element (GRE). Mutating the Angptl4 FRE significantly reduced glucocorticoid-induced reporter gene expression in cells. Moreover, chromatin immunoprecipitation revealed that GR and FoxO1 were recruited to Angptl4 GRE and FRE in a glucocorticoid-dependent manner, and cotreatment with insulin abolished both recruitments. Furthermore, in 24 h fasted mice, significant occupancy of GR and FoxO1 at the Angptl4 GRE and FRE was found in the liver. In contrast, both occupancies were diminished after 24 h refeeding. Finally, overexpression of dominant negative FoxO1 mutant abolished glucocorticoid-induced Angptl4 expression, mimicking the insulin suppression. Overall, we demonstrate that both GR and FoxO1 are required for Angptl4 transcription activation, and that FoxO1 negatively mediates the suppressive effect of insulin.