Genome screening, reporting, and genetic counseling for healthy populations.

Rapid advancements of genome sequencing (GS) technologies have enhanced our understanding of the relationship between genes and human disease. To incorporate genomic information into the practice of medicine, new processes for the analysis, reporting, and communication of GS data are needed. Blood samples were collected from adults with a PCR-confirmed SARS-CoV-2 (COVID-19) diagnosis (target N = 1500). GS was performed. Data were filtered and analyzed using custom pipelines and gene panels. We developed unique patient-facing materials, including an online intake survey, group counseling presentation, and consultation letters in addition to a comprehensive GS report. The final report includes results generated from GS data: (1) monogenic disease risks; (2) carrier status; (3) pharmacogenomic variants; (4) polygenic risk scores for common conditions; (5) HLA genotype; (6) genetic ancestry; (7) blood group; and, (8) COVID-19 viral lineage. Participants complete pre-test genetic counseling and confirm preferences for secondary findings before receiving results. Counseling and referrals are initiated for clinically significant findings. We developed a genetic counseling, reporting, and return of results framework that integrates GS information across multiple areas of human health, presenting possibilities for the clinical application of comprehensive GS data in healthy individuals.

Reliability of preoperative breast biopsies showing ductal carcinoma in situ and implications for non-operative treatment: a cohort study.

PURPOSE: The future of non-operative management of DCIS relies on distinguishing lesions requiring treatment from those needing only active surveillance. More accurate preoperative staging and grading of DCIS would be helpful. We identified determinants of upstaging preoperative breast biopsies showing ductal carcinoma in situ (DCIS) to invasive breast cancer (IBC), or of upgrading them to higher-grade DCIS, following examination of the surgically excised specimen. METHODS: We studied all women with DCIS at preoperative biopsy in a large specialist cancer centre during 2000-2014. Information from clinical records, mammography, and pathology specimens from both preoperative biopsy and excised specimen were abstracted. Women suspected of having IBC during biopsy were excluded. RESULTS: Among 606 preoperative biopsies showing DCIS, 15.0% (95% confidence interval 12.3-18.1) were upstaged to IBC and a further 14.6% (11.3-18.4) upgraded to higher-grade DCIS. The risk of upstaging increased with presence of a palpable lump (21.1% vs 13.0%, pdifference = 0.04), while the risk of upgrading increased with presence of necrosis on biopsy (33.0% vs 9.5%, pdifference < 0.001) and with use of 14G core-needle rather than 9G vacuum-assisted biopsy (22.8% vs 7.0%, pdifference < 0.001). Larger mammographic size increased the risk of both upgrading (pheterogeneity = 0.01) and upstaging (pheterogeneity = 0.004). CONCLUSIONS: The risk of upstaging of DCIS in preoperative biopsies is lower than previously estimated and justifies conducting randomized clinical trials testing the safety of active surveillance for lower grade DCIS. Selection of women with low grade DCIS for such trials, or for active surveillance, may be improved by consideration of the additional factors identified in this study.

Delayed surgery in hip fracture patients. Can we afford it?

The aim is to analyze whether time to surgery (TtoS) in hip fracture patients is associated with longer than expected length of stay (LofS) and whether there is any particular group in which this is especially relevant. We developed an observational study in Madrid, Spain. From 771 patients admitted to the orthopedic ward, we selected 723 with surgical delay ≤7 days. Age was characterized as younger (<81), elderly (81-90), very elderly (>90). Modified Barthel Index was classified as very dependent (<41), moderately dependent (41-80), independent (>80). RESULTS: Median (IQR) TtoS was 3 (1-4) days; LofS 12 (7-15). Mean age was 84.3 years, 78.4% were women. TtoS was associated with LofS, which increased by 1.80 days (95% CI, 1.50-2.10) per delayed day (p<0.001). After adjustment for age, sex, functional status, we found an increase of 1.75 days (1.46-2.04) per day (p<0.001). We did not find effect of age or sex. Functional status had a higher effect in moderately dependent patients 2.25 days (1.78-2.72) than in very dependent or independent patients, 1.33 (0.37-2.30) and 1.50 days (1.09-1.91) respectively (p 0.012). As conclusion we could affirm that increasing TtoS leads to longer than expected LofS in hip fracture patients, particularly moderately dependent patients. Copyright © 2016 John Wiley & Sons, Ltd.

Updates on the web-based VIOLIN vaccine database and analysis system.

The integrative Vaccine Investigation and Online Information Network (VIOLIN) vaccine research database and analysis system (http://www.violinet.org) curates, stores, analyses and integrates various vaccine-associated research data. Since its first publication in NAR in 2008, significant updates have been made. Starting from 211 vaccines annotated at the end of 2007, VIOLIN now includes over 3240 vaccines for 192 infectious diseases and eight noninfectious diseases (e.g. cancers and allergies). Under the umbrella of VIOLIN, >10 relatively independent programs are developed. For example, Protegen stores over 800 protective antigens experimentally proven valid for vaccine development. VirmugenDB annotated over 200 'virmugens', a term coined by us to represent those virulence factor genes that can be mutated to generate successful live attenuated vaccines. Specific patterns were identified from the genes collected in Protegen and VirmugenDB. VIOLIN also includes Vaxign, the first web-based vaccine candidate prediction program based on reverse vaccinology. VIOLIN collects and analyzes different vaccine components including vaccine adjuvants (Vaxjo) and DNA vaccine plasmids (DNAVaxDB). VIOLIN includes licensed human vaccines (Huvax) and veterinary vaccines (Vevax). The Vaccine Ontology is applied to standardize and integrate various data in VIOLIN. VIOLIN also hosts the Ontology of Vaccine Adverse Events (OVAE) that logically represents adverse events associated with licensed human vaccines.

Endometriosis-Associated Angiogenesis and Anti-angiogenic Therapy for Endometriosis.

Endometriosis is a known estrogen-dependent inflammatory disease affecting reproductive-aged women. Common symptoms include pelvic pain, dysmenorrhea, dyspareunia, heavy menstrual bleeding, and infertility. The exact etiology of endometriosis is largely unknown, and, thus, the diagnosis and treatment of endometriosis are challenging. A complex interplay of many molecular mechanisms is thought to aid in the progression of endometriosis, most notably angiogenesis. This mini-review examines our current knowledge of the molecular etiology of endometriosis-associated angiogenesis and discusses anti-angiogenic therapy, in the blockade of endometriosis-associated angiogenesis, as potential non-hormonal therapy for the treatment of endometriosis.

Genome Reporting for Healthy Populations-Pipeline for Genomic Screening from the GENCOV COVID-19 Study.

Genome sequencing holds the promise for great public health benefits. It is currently being used in the context of rare disease diagnosis and novel gene identification, but also has the potential to identify genetic disease risk factors in healthy individuals. Genome sequencing technologies are currently being used to identify genetic factors that may influence variability in symptom severity and immune response among patients infected by SARS-CoV-2. The GENCOV study aims to look at the relationship between genetic, serological, and biochemical factors and variability of SARS-CoV-2 symptom severity, and to evaluate the utility of returning genome screening results to study participants. Study participants select which results they wish to receive with a decision aid. Medically actionable information for diagnosis, disease risk estimation, disease prevention, and patient management are provided in a comprehensive genome report. Using a combination of bioinformatics software and custom tools, this article describes a pipeline for the analysis and reporting of genetic results to individuals with COVID-19, including HLA genotyping, large-scale continental ancestry estimation, and pharmacogenomic analysis to determine metabolizer status and drug response. In addition, this pipeline includes reporting of medically actionable conditions from comprehensive gene panels for Cardiology, Neurology, Metabolism, Hereditary Cancer, and Hereditary Kidney, and carrier screening for reproductive planning. Incorporated into the genome report are polygenic risk scores for six diseases-coronary artery disease; atrial fibrillation; type-2 diabetes; and breast, prostate, and colon cancer-as well as blood group genotyping analysis for ABO and Rh blood types and genotyping for other antigens of clinical relevance. The genome report summarizes the findings of these analyses in a way that extensively communicates clinically relevant results to patients and their physicians. © 2022 Wiley Periodicals LLC. Basic Protocol 1: HLA genotyping and disease association Basic Protocol 2: Large-scale continental ancestry estimation Basic Protocol 3: Dosage recommendations for pharmacogenomic gene variants associated with drug response Support Protocol: System setup.

Obstetric outcomes in pregnancies resulting from in vitro fertilization are not different in fertile, sterilized women compared to infertile women: A Society for Assisted Reproductive Technology database analysis.

OBJECTIVE: To compare obstetric and neonatal outcomes resulting from assisted reproductive technology in couples with a history of female sterilization to couples with other infertility diagnoses. DESIGN: Retrospective cohort study. SETTING: Not applicable. PATIENT(S): Fresh, nondonor cycles excluding gestational surrogacy from 2004 to 2013 in the United States. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Preterm birth rates and low birth weight rates from in vitro fertilization (IVF) pregnancies in couples with infertility and in couples with prior tubal ligation as their sole indication for IVF. RESULT(S): The mean ages of fertile women (N = 8,478) and infertile women (N = 371,488) were 35.3 and 34.6 years, respectively. Of the singletons born to parous women (N = 26,463), the incidence of preterm birth was not significantly different in fertile, sterilized couples compared to infertile couples (13.7% vs. 12.0%). The incidence of low birth weight among term singletons was also not significantly different between fertile couples compared to infertile couples (3.5% vs. 3.2%). CONCLUSION(S): Fertile couples have similar preterm birth and low birth weight rates after IVF compared to infertile couples. This suggests that differences in perinatal outcomes may be due to assisted reproductive technology procedures rather than infertility itself.

Morphologic features of cardiac sarcoidosis in native hearts of patients having cardiac transplantation.

Described herein are 10 patients who underwent cardiac transplantation (CT) for severe chronic systolic heart failure resulting from cardiac sarcoidosis. None had the diagnosis of sarcoidosis established before CT except for the 3 patients who earlier had had a portion of left ventricular wall excised for insertion of a left ventricular assist device and non-caseating granulomas were present in the removed myocardium. Although none of the 10 patients had significant narrowing of any of the epicardial coronary arteries, all had focal scarring of the walls of the left and right ventricles and ventricular septum and all had dilated ventricular cavities. The patients with the most ventricular wall scarring tended to have the fewest sarcoid granulomas in the ventricular walls. Two patients had no sarcoid granulomas in the excised heart although one did have typical sarcoid granulomas in the portion of left ventricular wall excised to insert a left ventricular assist device. Patients with cardiac sarcoidosis severe enough to warrant CT had characteristic cardiac ventricular morphologic findings, and no dysfunction of other non-cardiac organs, making clinical diagnosis of cardiac sarcoidosis rather difficult.

Systematic annotation and analysis of "virmugens"-virulence factors whose mutants can be used as live attenuated vaccines.

Live attenuated vaccines are usually generated by mutation of genes encoding virulence factors. "Virmugen" is coined here to represent a gene that encodes for a virulent factor of a pathogen and has been proven feasible in animal models to make a live attenuated vaccine by knocking out this gene. Not all virulence factors are virmugens. VirmugenDB is a web-based virmugen database (http://www.violinet.org/virmugendb). Currently, VirmugenDB includes 225 virmugens that have been verified to be valuable for vaccine development against 57 bacterial, viral, and protozoan pathogens. Bioinformatics analysis has revealed significant patterns in virmugens. For example, 10 Gram-negative and 1 Gram-positive bacterial aroA genes are virmugens. A sequence analysis has revealed at least 50% of identities in the protein sequences of the 10 Gram-negative bacterial aroA virmugens. As a pathogen case study, Brucella virmugens were analyzed. Out of 15 verified Brucella virmugens, 6 are related to carbohydrate or nucleotide transport and metabolism, and 2 involving cell membrane biogenesis. In addition, 54 virmugens from 24 viruses and 12 virmugens from 4 parasites are also stored in VirmugenDB. Virmugens tend to involve metabolism of nutrients (e.g., amino acids, carbohydrates, and nucleotides) and cell membrane formation. Host genes whose expressions were regulated by virmugen mutation vaccines or wild type virulent pathogens have also been annotated and systematically compared. The bioinformatics annotation and analysis of virmugens helps to elucidate enriched virmugen profiles and the mechanisms of protective immunity, and further supports rational vaccine design.

The myth of the Bernheim syndrome.

The Bernheim syndrome has been a topic of discussion for over a century. It has been reported to be caused by severe rightward movement of the ventricular septum resulting in compression of the right ventricular cavity leading to right-sided heart failure without pulmonary congestion. Hemodynamic findings have been described in a few patients with the so-called Bernheim syndrome. We describe a patient in whom the ventricular septum dramatically decreased the size of the right ventricular cavity and yet peak systolic pressures in both the right ventricle and pulmonary trunk were identical. Thus, it is difficult to view the Bernheim syndrome as a real entity.

The clinical and genomic significance of donor-specific antibody-positive/C4d-negative and donor-specific antibody-negative/C4d-negative transplant glomerulopathy.

BACKGROUND: This study investigated the mechanisms involved in development of donor-specific antibody (DSA) and/or C4d-negative transplant glomerulopathy (TGP) by allograft gene expression profiles using microarrays. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: This cohort study was conducted in kidney transplant recipients. Patients were eligible for inclusion if they required a clinically indicated biopsy at any time point after their transplant. They were then classified according to their histopathology findings and DSA and C4d results. Eighteen chronic antibody-mediated rejection (CAMR), 14 DSA+/C4d- TGP, 25 DSA-/C4d- TGP, and 47 nonspecific interstitial fibrosis/tubular atrophy (IFTA) biopsy specimens were identified. In a subset of patients from the study population, biopsy specimens in each group and normal transplant kidney specimens were analyzed with Affymetrix Human Gene 1.0 ST Arrays. RESULTS: The mean sum score of glomerulitis and peritubular capillaritis increased from 0.28±0.78 in IFTA specimens to 0.75±0.85 in DSA-/C4d- TGP specimens, 1.71±1.49 in DSA+/C4d-/TGP specimens, and 2.11±1.74 in CAMR specimens (P<0.001). During a median follow-up time of 2 (interquartile range, 1.4-2.8) years after biopsy, graft loss was highest in CAMR specimens (27.8%) compared to IFTA specimens (8.5%), DSA+/C4d- TGP specimens (14.3%), and DSA-/C4d- TGP specimens (16%) (P=0.01). With use of microarrays, comparison of the gene expression profiles of DSA-/C4d- TGP specimens with glomerulitis + peritubular capillaritis scores > 0 to normal and IFTA biopsy specimens revealed higher expression of quantitative cytotoxic T cell-associated transcripts (QCAT). However, both CAMR and DSA+/C4d- TGP specimens had higher expression of not only QCAT but also IFN-γ and rejection-induced, constitutive macrophage-associated, natural killer cell-associated, and DSA-selective transcripts. Endothelial cell-associated transcript expression was upregulated only in CAMR biopsy specimens. CONCLUSIONS: These results suggested that DSA+/C4d- TGP biopsy specimens may be classified as CAMR. In contrast, DSA-/C4d- TGP specimens showed increased cytotoxic T cell-associated transcripts, suggesting T cell activation as a mechanism of injury.

The clinical and molecular significance of C4d staining patterns in renal allografts.

BACKGROUND: We investigated the clinical and molecular significance of minimal peritubular capillary (PTC) and isolated glomerular C4d+ staining using microarrays. METHODS: Two hundred fifty-five clinically indicated transplant biopsies were included in the analyses. C4d staining was performed on paraffin sections using a polyclonal rabbit anti-C4d antibody. Gene expression profiles in a subset of patients were studied using Affymetrix HuGene 1.0ST arrays. RESULTS: Immunohistochemistry for C4d of 255 biopsies showed 51% C4d negative, 4% minimal PTC C4d+, 15% focal or diffuse PTC C4d+, and 31% isolated glomerular C4d+ biopsies. Patients with minimal and focal/diffuse PTC C4d+ staining had higher frequency of donor-specific anti-HLA antibodies (DSA) (67% and 82%) and antibody mediated rejection (AMR) (66% and 89%) when compared with C4d-negative biopsies (25% and 19%, respectively) (P<0.001). The glomerulitis, interstitial inflammation, and peritubular capillaritis scores were also significantly higher in minimal (0.88, 1.25, and 1.5) and focal/diffuse PTC C4d+ biopsies (0.65, 1.41, and 1.5), compared with C4d-negative biopsies (0.25, 079, and 0.34), respectively. There were no differences in the DSA frequency, AMR rate, or Banff scores between isolated glomerular C4d+ and C4d-negative patients. Although both minimal and focal/diffuse C4d+ biopsies showed increased expression of genes related to the immune response, interferon-gamma and rejection-induced, cytotoxic T cell and constitutive macrophage-associated pathogenesis-based transcripts, there was no activation of immune-response-related genes in isolated glomerular C4d+ biopsies. CONCLUSION: Minimal PTC C4d+ staining but not isolated glomerular C4d+ staining is associated with AMR, circulating DSAs and immune-response-related gene activation.

Prognosis of different types of atrial fibrillation in the primary angioplasty era.

BACKGROUND: Atrial fibrillation (AF) has been associated with a poor prognosis in patients with ST-segment elevation myocardial infarction. There is considerable controversy regarding the prognostic implications of different types of AF. METHODS AND RESULTS: We analyzed 913 patients consecutively admitted to our center with ST-segment elevation myocardial infarction undergoing a primary percutaneous coronary intervention. Clinical, ECG, and angiographic data were collected. We carried out univariate and multivariate analysis, using a combined endpoint of death, reinfarction, stroke, and clinically relevant bleeding. AF was documented in 117 patients. Among them, 25 presented AF at admission (previous AF) and 92 developed new-onset AF (66% transient, 13% persistent). Patients with AF were older, more frequently men, and had a worse Killip class, and a poorer left-ventricular ejection fraction. When analyzing the different types of AF, patients with new-onset AF (persistent and transient) had a higher Killip class and a worse left-ventricular ejection fraction. AF was associated with significantly higher in-hospital mortality and with a greater incidence of in-hospital adverse events. An increase in in-hospital mortality was recorded both for previous and for new-persistent AF, but after adjusting for confounding factors, only persistent AF was found to carry a worse short-term prognosis. CONCLUSION: In patients undergoing primary angioplasty in the stent era, AF is associated with a poor prognosis. This risk appears to be particularly high among patients with persistent AF.