Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits

BACKGROUND

In medical genetics, discovery and characterization of disease trait contributory genes and alleles depends on genetic reasoning, study design, and patient ascertainment; we suggest a segmental haploid genetics approach to enhance gene discovery and molecular diagnostics.

METHODS

We constructed a genome-wide map for nonallelic homologous recombination (NAHR)-mediated recurrent genomic deletions and used this map to estimate population frequencies of NAHR deletions based on large-scale population cohorts and region-specific studies. We calculated recessive disease carrier burden using high-quality pathogenic or likely pathogenic variants from ClinVar and gnomAD. We developed a NIRD (NAHR deletion Impact to Recessive Disease) score for recessive disorders by quantifying the contribution of NAHR deletion to the overall allele load that enumerated all pairwise combinations of disease-causing alleles; we used a Punnett square approach based on an assumption of random mating. Literature mining was conducted to identify all reported patients with defects in a gene with a high NIRD score; meta-analysis was performed on these patients to estimate the representation of NAHR deletions in recessive traits from contemporary human genomics studies. Retrospective analyses of extant clinical exome sequencing (cES) were performed for novel rare recessive disease trait gene and allele discovery from individuals with NAHR deletions.

RESULTS

We present novel genomic insights regarding the genome-wide impact of NAHR recurrent segmental variants on recessive disease burden; we demonstrate the utility of NAHR recurrent deletions to enhance discovery in the challenging context of autosomal recessive (AR) traits and biallelic variation. Computational results demonstrate new mutations mediated by NAHR, involving recurrent deletions at 30 genomic regions, likely drive recessive disease burden for over 74% of loci within these segmental deletions or at least 2% of loci genome-wide. Meta-analyses on 170 literature-reported patients implicate that NAHR deletions are depleted from the ascertained pool of AR trait alleles. Exome reanalysis of personal genomes from subjects harboring recurrent deletions uncovered new disease-contributing variants in genes including COX10, ERCC6, PRRT2, and OTUD7A.

CONCLUSIONS

Our results demonstrate that genomic sequencing of personal genomes with NAHR deletions could dramatically improve allele and gene discovery and enhance clinical molecular diagnosis. Moreover, results suggest NAHR events could potentially enable human haploid genetic screens as an approach to experimental inquiry into disease biology.

Genome Sequencing in the Parkinson Disease Clinic

Background and Objectives

Genetic variants affect both Parkinson disease (PD) risk and manifestations. Although genetic information is of potential interest to patients and clinicians, genetic testing is rarely performed during routine PD clinical care. The goal of this study was to examine interest in comprehensive genetic testing among patients with PD and document reactions to possible findings from genome sequencing in 2 academic movement disorder clinics.

Methods

In 203 subjects with PD (age = 63 years, 67% male), genome sequencing was performed and filtered using a custom panel, including 49 genes associated with PD, parkinsonism, or related disorders, as well as a 90-variant PD genetic risk score. Based on the results, 231 patients (age = 67 years, 63% male) were surveyed on interest in genetic testing and responses to vignettes covering (1) familial risk of PD (LRRK2); (2) risk of PD dementia (GBA); (3) PD genetic risk score; and (4) secondary, medically actionable variants (BRCA1).

Results

Genome sequencing revealed a LRRK2 variant in 3% and a GBA risk variant in 10% of our clinical sample. The genetic risk score was normally distributed, identifying 41 subjects with a high risk of PD. Medically actionable findings were discovered in 2 subjects (1%). In our survey, the majority (82%) responded that they would share a LRRK2 variant with relatives. Most registered unchanged or increased interest in testing when confronted with a potential risk for dementia or medically actionable findings, and most (75%) expressed interest in learning their PD genetic risk score.

Discussion

Our results highlight broad interest in comprehensive genetic testing among patients with PD and may facilitate integration of genome sequencing in clinical practice.

Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study

BACKGROUND

Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications.

METHODS

We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC).

FINDINGS

In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683-0·717]).

INTERPRETATION

In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required.

FUNDING

British Journal of Surgery Society.

Peritoneal mesothelioma presenting with 'kissing' liver metastases

A 61-year-old woman was diagnosed with an incidental liver lesion with a satellite lesion that had features of a secondary liver metastasis. Investigations for primary sites did not reveal a primary tumour. The lesion was not amenable to biopsy due to location. Intraoperatively, the two lesions were adjacent, but the first was on the diaphragm and the lesion was in segment 7 of the liver. The liver lesion underwent non-anatomical resection and the diaphragmatic lesion was resected separately. The histopathology diagnosed peritoneal mesothelioma in the lesion removed from diaphragm and the liver lesion to be local metastatic spread to an area of liver that was in close contact (a 'kissing' lesion). This report portrays a rare occurrence of liver metastases from peritoneal mesothelioma and discusses the current evidence for diagnosis and treatment.

Abstract PS5-29: Insights into the molecular underpinnings of the mevalonate pathway-YAP/TAZ-driven anti-HER2 therapy resistance in HER2+ breast cancer (BC)

Background. We recently reported that the biosynthetic mevalonate (MVA) pathway that produces cholesterol and isoprenoid intermediates, regulates the YAP/TAZ (Y/T) transcriptional co-activators to promote resistance to treatment regimens that effectively inhibit HER2 signaling in HER2+ BC. We further showed that the mTORC1 complex and survivin protein, which contribute to HER2-elicited oncogenic signaling in HER2-driven BC cells, are alternatively activated by the MVA pathway-Y/T axis in anti-HER2 therapy resistant cell models. Of note, other recent reports also showed that increased Y/T activity enables resistant cells to proliferate when other oncogenic pathways (e.g., RAS, EGFR, and FGFR) were effectively inhibited. Here, we sought to further determine the molecular underpinnings of MVA-Y/T axis-driven anti-HER2 therapy resistance to discover novel therapeutic targets and predictive biomarkers for HER2+ BC.Methods. SKBR3 HER2+ BC parental (P) cells and their lapatinib plus trastuzumab (LT) resistant (LTR) derivatives with sustained HER2 inhibition were treated with the MVA pathway inhibitor simvastatin (Sim), with or without the MVA metabolite to rescue Sim’s inhibitory effects. P and LTR cells were also transfected with control or combined Y/T siRNAs. The transcriptomes of all treatment groups were assessed by RNA-seq. Integrative bioinformatics analyses were used to identify differentially expressed (DE) genes and gene sets with functional annotations in LTR vs. P cells upon different interventions.Results. We found that cell cycle and cell proliferation processes were among the top common DE molecular signatures preferentially downregulated (DN) in LTR vs. P cells by both Sim and Y/T knockdown (KD). The top common genes preferentially DN in LTR vs. P cells include the cell cycle regulatory genes CDCA3 and ERCC6L, and the nucleotide metabolism genes TYMS and RRM2. Interestingly, 20% of the genes preferentially DN in LTR vs. P cells by Sim or Y/T KD were predicted to be direct Y/T transcriptional targets based on previously reported ChIP-seq data (PMID: 26258633). Of the Y/T-dependent genes, a significant enrichment of Sim-repressed genes was observed in both P and LTR cells (P = 1.2e-115 and P = 5.5e-138, respectively). The proportion of these enriched genes was higher in LTR vs. P cells (61% vs. 29%). Of note, we found that the global inhibited genes in LTR cells upon Sim or Y/T KD were significantly enriched for the genes DN by short-term LT treatment in P cells (P < 2.2e-16). Likewise, of the genes nominated as putative molecular players in the MVA pathway-Y/T-mediated resistance, BIRC5 (survivin), CDC6, KIF2C, RRM2, and TYMS were recently also reported to be DN in HER2+ tumors treated with neo-adjuvant LT in the PAMELA trial (NCT01973660), a finding that is in line with what we observed in our P cells treated with short-term LT. Conclusions. Upon acquisition of resistance to sustained HER2 inhibition, the MVA pathway-Y/T axis takes over the regulation of pro-proliferative transcriptional programs that are generally downstream of HER2 signaling in treatment-naïve HER2+ BC. The MVA pathway-Y/T axis leads to Y/T-driven transcriptional reprogramming, an emerging mechanism of therapy resistance to anti-HER2 and other targeted therapies that warrants further investigation. The identification of multiple cell cycle related processes as putative targets of the MVA pathway-Y/T axis presents additional targetable vulnerabilities and implies that inhibitors of Y/T and cell cycle checkpoints may help circumvent anti-HER2 resistance in the clinical setting.

Citation Format: Vidyalakshmi Sethunath, Xiaoyong Fu, Pamela L Luna, Sarmistha Nanda, Martin Shea, Jamunarani Veeraraghavan, Carmine De Angelis, Huizhong Hu, Chad Shaw, Mothaffar Rimawi, C. Kent Osborne, Rachel Schiff. Insights into the molecular underpinnings of the mevalonate pathway-YAP/TAZ-driven anti-HER2 therapy resistance in HER2+ breast cancer (BC) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS5-29.

COVID-19 in Kidney Transplant Patients From a Large UK Transplant Center: Exploring Risk Factors for Disease Severity

Background

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has raised concern for the health of immunocompromised individuals, who are potentially at higher risk of more severe infection and poorer outcomes. As a large London transplant center serving a diverse patient population, we report the outcomes of SARS-CoV-2 infection in our cohort of 2848 kidney and/or pancreas transplant patients.

Methods

Data were obtained retrospectively for all transplant patients who attended hospital during the peak of the pandemic and had a positive nasopharyngeal SARS-CoV-2 test.

Results

Sixty-six patients were found to be positive for SARS-CoV-2. Twenty percent were treated as outpatients, 59% were admitted to the general ward, and 21% required intensive care. Treatment consisted of reduced immunosuppression, antibiotics for pneumonia or sepsis, and other supportive treatments. Within our cohort, 12 patients died (18%), with an overall mortality of 0.4%. Predictive risk factors for COVID-19 severity were explored.

Conclusions

Severe disease was associated with lower hemoglobin prior to COVID-19 diagnosis and lower lymphocyte count at the time of diagnosis but not age, sex, ethnicity, or preexisting comorbidities. Lower glomerular filtration rate and higher C-reactive protein were associated with more severe disease. Despite no use of hydroxychloroquine, azithromycin, antiviral, or immunomodulatory medications, our mortality rate (kidney and pancreas transplant patients) is similar to current international rates.

Integrated sequencing and array comparative genomic hybridization in familial Parkinson disease

Objective

To determine how single nucleotide variants (SNVs) and copy number variants (CNVs) contribute to molecular diagnosis in familial Parkinson disease (PD), we integrated exome sequencing (ES) and genome-wide array-based comparative genomic hybridization (aCGH) and further probed CNV structure to reveal mutational mechanisms.

Methods

We performed ES on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated ES and aCGH data for pathogenic SNVs and CNVs at Mendelian PD gene loci. We confirmed SNVs via Sanger sequencing and further characterized CNVs with custom-designed high-density aCGH, droplet digital PCR, and breakpoint sequencing.

Results

Using ES, we discovered individuals with known pathogenic SNVs in GBA (p.Glu365Lys, p.Thr408Met, p.Asn409Ser, and p.Leu483Pro) and LRRK2 (p.Arg1441Gly and p.Gly2019Ser). Two subjects were each double heterozygotes for variants in GBA and LRRK2. Based on aCGH, we additionally discovered cases with an SNCA duplication and heterozygous intragenic GBA deletion. Five additional subjects harbored both SNVs (p.Asn52Metfs*29, p.Thr240Met, p.Pro437Leu, and p.Trp453*) and likely disrupting CNVs at the PRKN locus, consistent with compound heterozygosity. In nearly all cases, breakpoint sequencing revealed microhomology, a mutational signature consistent with CNV formation due to DNA replication errors.

Conclusions

Integrated ES and aCGH yielded a genetic diagnosis in 19.3% of our familial PD cohort. Our analyses highlight potential mechanisms for SNCA and PRKN CNV formation, uncover multilocus pathogenic variation, and identify novel SNVs and CNVs for further investigation as potential PD risk alleles.

Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions

Purpose:

The goal of this study was to assess the scale of low-level parental mosaicism in exome sequencing (ES) databases.

Methods:

We analyzed approximately 2000 family trio ES datasets from the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) and Baylor Genetics (BG). Among apparent de novo single nucleotide variants (SNVs) identified in the affected probands, we selected rare unique variants with variant allele fraction (VAF) between 30-70% in the probands and lower than 10% in one of the parents.

Results:

Out of 102 candidate mosaic variants validated using amplicon-based NGS, droplet digital PCR, or blocker displacement amplification, 27 (26.4%) were confirmed to be low- (VAF between 1-10%) or very low- (VAF <1%) level mosaic. Detection precision in parental samples with two or more alternate reads was 63.6% (BHCMG) and 43.6% (BG). In nine investigated individuals, we observed variability of mosaic ratios among blood, saliva, fibroblast, buccal, hair, and urine samples.

Conclusion:

Our computational pipeline enables robust discrimination between true and false positive candidate mosaic variants and efficient detection of low-level mosaicism in ES samples. We confirm that the presence of two or more alternate reads in the parental sample is a reliable predictor of low-level parental somatic mosaicism.

Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study

BACKGROUND

This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery.

METHODS

This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery.

RESULTS

A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498).

CONCLUSION

There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.

CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels

PURPOSE

Improved resolution of molecular diagnostic technologies enabled detection of smaller sized exonic level copy-number variants (CNVs). The contribution of CNVs to autosomal recessive (AR) conditions may be better recognized using a large clinical cohort.

METHODS

We retrospectively investigated the CNVs' contribution to AR conditions in cases subjected to chromosomal microarray analysis (CMA, N = ~70,000) and/or clinical exome sequencing (ES, N = ~12,000) at Baylor Genetics; most had pediatric onset neurodevelopmental disorders.

RESULTS

CNVs contributed to biallelic variations in 87 cases, including 81 singletons and three affected sibling pairs. Seventy cases had CNVs affecting both alleles, and 17 had a CNV and a single-nucleotide variant (SNV)/indel in trans. In total, 94.3% of AR-CNVs affected one gene; among these 41.4% were single-exon and 35.0% were multiexon partial-gene events. Sixty-nine percent of homozygous AR-CNVs were embedded in homozygous genomic intervals. Five cases had large deletions unmasking an SNV/indel on the intact allele for a recessive condition, resulting in multiple molecular diagnoses.

CONCLUSIONS

AR-CNVs are often smaller in size, transmitted through generations, and underrecognized due to limitations in clinical CNV detection methods. Our findings from a large clinical cohort emphasized integrated CNV and SNV/indel analyses for precise clinical and molecular diagnosis especially in the context of genomic disorders.

The evolving role of surface electromyography in amyotrophic lateral sclerosis: A systematic review

OBJECTIVE

Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease that leads to inexorable motor decline and a median survival of three years from symptom onset. Surface EMG represents a major technological advance that has been harnessed in the development of novel neurophysiological biomarkers. We have systematically reviewed the current application of surface EMG techniques in ALS.

METHODS

We searched PubMed to identify 42 studies focusing on surface EMG and its associated analytical methods in the diagnosis, prognosis and monitoring of ALS patients.

RESULTS

A wide variety of analytical techniques were identified, involving motor unit decomposition from high-density grids, motor unit number estimation and measurements of neuronal hyperexcitability or neuromuscular architecture. Some studies have proposed specific diagnostic and prognostic criteria however clinical calibration in large ALS cohorts is currently lacking. The most validated method to monitor disease is the motor unit number index (MUNIX), which has been implemented as an outcome measure in two ALS clinical trials.

CONCLUSION

Surface EMG offers significant practical and analytical flexibility compared to invasive techniques. To capitalise on this fully, emphasis must be placed upon the multi-disciplinary collaboration of clinicians, bioengineers, mathematicians and biostatisticians.

SIGNIFICANCE

Surface EMG techniques can enrich effective biomarker development in ALS.

Frailty and hospital outcomes within a low socioeconomic population

BACKGROUND

Clinical frailty scales (CFS) predict hospital-related outcomes. Frailty is more common in areas of higher socioeconomic disadvantage, but no studies exclusively report on the impact of CFS on hospital-related outcomes in areas of known socioeconomic disadvantage.

AIMS

To evaluate the association of the CFS with hospital-related outcomes.

DESIGN

Retrospective observational study in a community hospital within a disadvantaged area in Australia (Social Economic Index for Areas = 0.1%).

METHODS

The CFS was used in the emergency department (ED) for people aged ≥ 75 years. Frailty was defined as a score of ≥4. Associations between the CFS and mortality, admission rates, ED presentations and length of stay (LOS) were analysed using regression analyses.

RESULTS

Between 11 July 2017 and 31 March 2018, there were 5151 ED presentations involving 3258 patients aged ≥ 75 years. Frail persons were significantly more likely to be older, represent to the ED and have delirium compared with non-frail persons. CFS was independently associated with 28-day mortality, with odds of mortality increasing by 1.5 times per unit increase in CFS (95% CI: 1.3-1.7). Frail persons with CFS 4-6 were more likely to be admitted (OR: 1.2; 95% CI: 1.0-1.5), have higher geometric mean LOS (1.43; 95% CI 1.15-1.77 days) and higher rates of ED presentations (IRR: 1.12; 95% CI 1.04-1.21) compared with non-frail persons.

CONCLUSIONS

The CFS predicts community hospital-related outcomes in frail persons within a socioeconomic disadvantage area. Future intervention and allocation of resources could consider focusing on CFS 4-6 as a priority for frail persons within a community hospital setting.

Evaluation of the VIDAS Staph Enterotoxin II (SET 2) Immunoassay Method for the Detection of Staphylococcal Enterotoxins in Selected Foods: Collaborative Study

A multilaboratory study was conducted to determine the limit of detection (LOD) of Staphylococcal enterotoxins (SET) in 5 foods. Cooked chicken, ham, potato salad, pasteurized liquid whole milk, and canned mushrooms were each spiked with a different enterotoxin (A, B, C1, D, or E), and tested at 0.25 and 0.5 ng/g SET levels to determine the LOD of the assay for those foods in a collaborative study. Unspiked controls were also included. A total of 19 laboratories representing government and industry participated. In this study, 1674 test portions were analyzed, of which 1638 were used in the statistical analysis. Of the 1638 test portions used in the statistical analysis, 1104 were spiked test portions, of which 1073 were positive by the VIDAS Staph enterotoxin II (SET 2) method. The detection rates at the 0.25 ng/mL level were cooked chicken, 98.2; ham, 99.0; potato salad, 99.1; liquid whole milk, 85.2; and canned mushrooms, 100. The detection rates at the 0.5 ng/mL level were cooked chicken, 97.4; ham, 98.1; potato salad, 100; liquid whole milk, 99.0; and canned mushrooms, 100. The data indicate that the SET 2 method is capable of detecting SET at 0.25 ng/g in cooked chicken, ham, potato salad, and canned mushrooms and at 0.5 ng/g in pasteurized liquid whole milk.

Evaluation of the BAX® System for Detection of Listeria monocytogenes in Foods: Collaborative Study

A multilaboratory study was conducted to compare the automated BAX® system and the standard cultural methods for detection of Listeria monocytogenes in foods. Six food types (frankfurters, soft cheese, smoked salmon, raw, ground beef, fresh radishes, and frozen peas) were analyzed by each method. For each food type, 3 inoculation levels were tested: high (average of 2 CFU/g), low (average of 0.2 CFU/g) and uninoculated controls. A total of 25 laboratories representing government and industry participated. Of the 2335 samples analyzed, 1109 were positive by the BAX system and 1115 were positive by the standard method. A Chi square analysis of each of the 6 food types, at the 3 inoculation levels tested, was performed. For all foods, except radishes, the BAX system performed as well as or better than the standard reference methods based on the Chi square results.

Evaluation of the BAX® System for Detection of Salmonella in Selected Foods: Collaborative Study

A multilaboratory study was conducted to compare the automated BAX® System to the standard cultural methods for detection of Salmonella in selected foods. Five food types—frankfurters, raw ground beef, mozzarella cheese, raw frozen tilapia fish, and orange juice—at 3 inoculation levels, were analyzed by each method. A sixth food type, raw ground chicken, was tested using 3 naturally contaminated lots. A total of 16 laboratories representing government and industry participated. In this study, 1386 samples were analyzed, of which 1188 were paired samples and 198 were unpaired samples. Of the 1188 paired samples, 461 were positive by both methods and 404 were negative by both methods. Thirty-seven samples were positive by the BAX System but negative by the standard reference method, and 11 samples were positive by standard cultural method and negative by the BAX System. Of the 198 unpaired samples, 106 were positive by the BAX System and 60 were positive by the standard cultural method. A Chi square analysis of each of the 6 food types, at the 3 inoculation levels tested, was performed. For all foods, the BAX System demonstrated results comparable to those of the standard reference methods based on the Chi square results.

Key components of international and European governance for quality of care

The legal status and binding nature of various international governance and guidance instruments to foster and support quality strategies in European countries differs substantially. This presentation introduces and discusses the four main elements of an integrated international governance framework for quality in health care: i) raising political awareness of the relevance of health care quality and creating a common vision on how to improve it; ii) implementing this vision into actual policy frameworks by sharing experience and practice between countries; iii) developing and providing standards and models (voluntary or mandatory) that can be transposed into national policy; iv) measuring, assessing and comparing quality by developing better information, better indicators and methodologies as well as dissemination strategies.

The presentation will also focus on how quality in health care is addressed through EU policy, first through EU provisions and policies that are meant to ensure free movement of citizens and goods and establish an internal market, and by means of more horizontal and generic EU policies on quality and safety that stem from the mandate to support, coordinate or supplement national policies. It will further highlight how EU integration and policy touch upon quality in health care and how the approach has evolved over time.

External institutional strategies for health care organizations as a quality strategy

Accreditation, certification and supervision are quality strategies that intend to encourage the compliance of health care organizations with published standards through external assessment. The idea is that health care organizations will increase compliance with standards in advance of a planned external inspection. Despite several common characteristics of the three strategies, their origins and initial objectives differ. This presentation aims to disambiguate these concepts, inform on their utilization in European countries and discuss the evidence on their effectiveness, cost-effectiveness and implementation.

External assessment strategies have been widely implemented in Europe. Most countries make use of several strategies, including basic supervision as part of the licensing process for healthcare providers, coupled with certification or accreditation strategies to ensure and improve the quality of care. The scope of these strategies and their regulation differs substantially between countries. Despite this widespread uptake, there is little robust evidence to support their effectiveness and there is a complete absence of evidence on cost-effectiveness. Furthermore, due to the broad purpose range of external assessments and the lack of consensus in the use of terminology, implementation strategies are sparse or missing. However, this presentation highlights several facilitators and barriers that may affect the implementation of external assessment strategies in health care organizations as well as relevant insights for policy-makers.

Targeting the Mevalonate Pathway to Overcome Acquired Anti-HER2 Treatment Resistance in Breast Cancer

Despite effective strategies, resistance in HER2⁺ breast cancer remains a challenge. While the mevalonate pathway (MVA) is suggested to promote cell growth and survival, including in HER2⁺ models, its potential role in resistance to HER2-targeted therapy is unknown. Parental HER2⁺ breast cancer cells and their lapatinib-resistant and lapatinib + trastuzumab-resistant derivatives were used for this study. MVA activity was found to be increased in lapatinib-resistant and lapatinib + trastuzumab-resistant cells. Specific blockade of this pathway with lipophilic but not hydrophilic statins and with the N-bisphosphonate zoledronic acid led to apoptosis and substantial growth inhibition of R cells. Inhibition was rescued by mevalonate or the intermediate metabolites farnesyl pyrophosphate or geranylgeranyl pyrophosphate, but not cholesterol. Activated Yes-associated protein (YAP)/transcriptional coactivator with PDZ-binding motif (TAZ) and mTORC1 signaling, and their downstream target gene product Survivin, were inhibited by MVA blockade, especially in the lapatinib-resistant/lapatinib + trastuzumab-resistant models. Overexpression of constitutively active YAP rescued Survivin and phosphorylated-S6 levels, despite blockade of the MVA. These results suggest that the MVA provides alternative signaling leading to cell survival and resistance by activating YAP/TAZ-mTORC1-Survivin signaling when HER2 is blocked, suggesting novel therapeutic targets. MVA inhibitors including lipophilic statins and N-bisphosphonates may circumvent resistance to anti-HER2 therapy warranting further clinical investigation. IMPLICATIONS: The MVA was found to constitute an escape mechanism of survival and growth in HER2⁺ breast cancer models resistant to anti-HER2 therapies. MVA inhibitors such as simvastatin and zoledronic acid are potential therapeutic agents to resensitize the tumors that depend on the MVA to progress on anti-HER2 therapies.

A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing

Background

Although mosaic variation has been known to cause disease for decades, high-throughput sequencing technologies with the analytical sensitivity to consistently detect variants at reduced allelic fractions have only recently emerged as routine clinical diagnostic tests. To date, few systematic analyses of mosaic variants detected by diagnostic exome sequencing for diverse clinical indications have been performed.

Methods

To investigate the frequency, type, allelic fraction, and phenotypic consequences of clinically relevant somatic mosaic single nucleotide variants (SNVs) and characteristics of the corresponding genes, we retrospectively queried reported mosaic variants from a cohort of ~ 12,000 samples submitted for clinical exome sequencing (ES) at Baylor Genetics.

Results

We found 120 mosaic variants involving 107 genes, including 80 mosaic SNVs in proband samples and 40 in parental/grandparental samples. Average mosaic alternate allele fraction (AAF) detected in autosomes and in X-linked disease genes in females was 18.2% compared with 34.8% in X-linked disease genes in males. Of these mosaic variants, 74 variants (61.7%) were classified as pathogenic or likely pathogenic and 46 (38.3%) as variants of uncertain significance. Mosaic variants occurred in disease genes associated with autosomal dominant (AD) or AD/autosomal recessive (AR) (67/120, 55.8%), X-linked (33/120, 27.5%), AD/somatic (10/120, 8.3%), and AR (8/120, 6.7%) inheritance. Of note, 1.7% (2/120) of variants were found in genes in which only somatic events have been described. Nine genes had recurrent mosaic events in unrelated individuals which accounted for 18.3% (22/120) of all detected mosaic variants in this study. The proband group was enriched for mosaicism affecting Ras signaling pathway genes.

Conclusions

In sum, an estimated 1.5% of all molecular diagnoses made in this cohort could be attributed to a mosaic variant detected in the proband, while parental mosaicism was identified in 0.3% of families analyzed. As ES design favors breadth over depth of coverage, this estimate of the prevalence of mosaic variants likely represents an underestimate of the total number of clinically relevant mosaic variants in our cohort.

Electronic supplementary material

The online version of this article (10.1186/s13073-019-0658-2) contains supplementary material, which is available to authorized users.

SPiQE: An automated analytical tool for detecting and characterising fasciculations in amyotrophic lateral sclerosis

OBJECTIVES

Fasciculations are a clinical hallmark of amyotrophic lateral sclerosis (ALS). Compared to concentric needle EMG, high-density surface EMG (HDSEMG) is non-invasive and records fasciculation potentials (FPs) from greater muscle volumes over longer durations. To detect and characterise FPs from vast data sets generated by serial HDSEMG, we developed an automated analytical tool.

METHODS

Six ALS patients and two control patients (one with benign fasciculation syndrome and one with multifocal motor neuropathy) underwent 30-minute HDSEMG from biceps and gastrocnemius monthly. In MATLAB we developed a novel, innovative method to identify FPs amidst fluctuating noise levels. One hundred repeats of 5-fold cross validation estimated the model's predictive ability.

RESULTS

By applying this method, we identified 5,318 FPs from 80 minutes of recordings with a sensitivity of 83.6% (+/- 0.2 SEM), specificity of 91.6% (+/- 0.1 SEM) and classification accuracy of 87.9% (+/- 0.1 SEM). An amplitude exclusion threshold (100 μV) removed excessively noisy data without compromising sensitivity. The resulting automated FP counts were not significantly different to the manual counts (p = 0.394).

CONCLUSION

We have devised and internally validated an automated method to accurately identify FPs from HDSEMG, a technique we have named Surface Potential Quantification Engine (SPiQE).

SIGNIFICANCE

Longitudinal quantification of fasciculations in ALS could provide unique insight into motor neuron health.

Healthy eating interventions in adults living with and beyond colorectal cancer: a systematic review

BACKGROUND

Rates of cancer survival are increasing, with more people living with and beyond cancer. Lifestyle recommendations for cancer survivors are based largely on extrapolation from cancer prevention recommendations. The present study aimed to systematically review the literature on randomised controlled trials (RCTs) focusing on healthy eating interventions in people with colorectal cancer (CRC).

METHODS

A structured search of electronic databases was conducted in March 2018 using medical subject headings (MeSH) and text words related to CRC and diet. The results of the literature searches were uploaded to online software for data management. Titles and abstracts were screened based on the inclusion and exclusion criteria and data were extracted. Quality of data was assessed using the Cochrane Handbook.

RESULTS

Seven studies were identified, including six RCTs and one RCT protocol, with a total of 2233 participants from six studies, of whom 1010 (45%) had CRC. Three studies assessed anthropometrics demonstrating participants who received dietary intervention had a greater reduction in measurements. Six studies assessed changes in dietary components; however, only one demonstrated an increase in dietary fibre. Two studies reported improvements in quality of life favouring dietary intervention groups.

CONCLUSIONS

The quality of identified studies was variable, with limited evidence to support dietary intervention improving dietary intake in people living with or after CRC. Studies to date have not been based on robust study design that has combined all dietary interventions linked to CRC. As a result of the heterogeneity of the studies identified, it was difficult to draw strong conclusions.

Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies

PURPOSE

Defects in the cohesin pathway are associated with cohesinopathies, notably Cornelia de Lange syndrome (CdLS). We aimed to delineate pathogenic variants in known and candidate cohesinopathy genes from a clinical exome perspective.

METHODS

We retrospectively studied patients referred for clinical exome sequencing (CES, N = 10,698). Patients with causative variants in novel or recently described cohesinopathy genes were enrolled for phenotypic characterization.

RESULTS

Pathogenic or likely pathogenic single-nucleotide and insertion/deletion variants (SNVs/indels) were identified in established disease genes including NIPBL (N = 5), SMC1A (N = 14), SMC3 (N = 4), RAD21 (N = 2), and HDAC8 (N = 8). The phenotypes in this genetically defined cohort skew towards the mild end of CdLS spectrum as compared with phenotype-driven cohorts. Candidate or recently reported cohesinopathy genes were supported by de novo SNVs/indels in STAG1 (N = 3), STAG2 (N = 5), PDS5A (N = 1), and WAPL (N = 1), and one inherited SNV in PDS5A. We also identified copy-number deletions affecting STAG1 (two de novo, one of unknown inheritance) and STAG2 (one of unknown inheritance). Patients with STAG1 and STAG2 variants presented with overlapping features yet without characteristic facial features of CdLS.

CONCLUSION

CES effectively identified disease-causing alleles at the mild end of the cohensinopathy spectrum and enabled characterization of candidate disease genes.

Reliable detection of subchromosomal deletions and duplications using cell-based noninvasive prenatal testing

Objective

To gather additional data on the ability to detect subchromosomal abnormalities of various sizes in single fetal cells isolated from maternal blood, using low‐coverage shotgun next‐generation sequencing for cell‐based noninvasive prenatal testing (NIPT).

Method

Fetal trophoblasts were recovered from approximately 30 mL of maternal blood using maternal white blood cell depletion, density‐based cell separation, immunofluorescence staining, and high‐resolution scanning. These trophoblastic cells were picked as single cells and underwent whole genome amplification for subsequent genome‐wide copy number analysis and genotyping to confirm the fetal origin of the cells.

Results

Applying our fetal cell isolation method to a series of 125 maternal blood samples, we detected on average 4.17 putative fetal cells/sample. The series included 15 cases with clinically diagnosed fetal aneuploidies and five cases with subchromosomal abnormalities. This method was capable of detecting findings that were 1 to 2 Mb in size, and all were concordant with the microarray or karyotype data obtained on a fetal sample. A minority of fetal cells showed evidence of genome degradation likely related to apoptosis.

Conclusion

We demonstrate that this cell‐based NIPT method has the capacity to reliably diagnose fetal chromosomal abnormalities down to 1 to 2 Mb in size.

What is already known about this topic?

Fetal trophoblastic cells can be isolated from maternal blood and be used for the detection of fetal aneuploidies and copy number variants. The data on the detection of subchromosomal deletions and duplications is currently limited.

What does this study add?

Cell‐based NIPT can be used for the detection of copy number abnormalities of greater than or equal to 1 Mb in the fetus by low‐coverage next‐generation sequencing after single cell whole genome amplification. Data are provided here for five cases in which different subchromosomal deletions and duplications ranging from 1.2 to 18.9 Mb were detected in single cells.

Nutritional status, the development and persistence of malnutrition and dietary intake in oesophago-gastric cancer: a longitudinal cohort study

BACKGROUND

Patients with oesophago-gastric (OG) cancer may be at risk of malnutrition, troublesome gastrointestinal symptoms (GI) and reduced dietary intake in view of the tumour location and multimodality curative treatment approach. Longitudinal research is lacking. The present study aimed to assess (i) nutritional status and how it evolved over the first year; (ii) the association between nutritional status scores and GI symptom scores; and (iii) the nutrient and food group intake pattern.

METHODS

This was a prospective, observational study of patients with an OG lesion planned for radical treatment, with assessment at diagnosis, 3 months and 12 months after the start of treatment. Nutritional assessment was performed using the Patient-Generated Subjective Global Assessment, GI symptoms measured using the modified Gastrointestinal Symptom Rating Scale and dietary intake assessed using a semi-quantitative food frequency approach.

RESULTS

Eighty patients (61 males, 19 females; aged 46-89 years) were recruited. At baseline, 3 (n = 68) and 12 months (n = 57), 61%, 62% and 60%, respectively, were moderately/severely malnourished. Higher symptom burden was associated with poorer nutritional status at baseline (r = 0.55, P < 0.001), 3 months (r = 0.51, P < 0.001) and 12 months (r = 0.42, P = 0.001). At each respective time point, 37%, 38% and 42% were meeting their estimated average requirement for energy. No change in mean (SD) intake of energy, fibre, nutrient and food groups was observed over time.

CONCLUSIONS

Patients with OG cancer have progressive weight loss, with malnutrition present over the majority of the 12-month study period. Optimising nutritional status and symptom management throughout the treatment pathway should be a clinical priority.

Effects of genetic variation in protease activated receptor 4 after an acute coronary syndrome: Analysis from the TRACER trial

Variation in platelet response to thrombin may affect the safety and efficacy of PAR antagonism. The Thr120 variant of the common single nucleotide polymorphism (SNP) rs773902 in the protease-activated receptor (PAR) 4 gene is associated with higher platelet aggregation compared to the Ala120 variant. We investigated the relationship between the rs773902 SNP with major bleeding and ischemic events, safety, and efficacy of PAR1 inhibition in 6177 NSTE ACS patients in the TRACER trial. There was a lower rate of GUSTO moderate/severe bleeding in patients with the Thr120 variant. The difference was driven by a lower rate in the smaller homozygous group (recessive model, HR 0.13 [0.02-0.92] P = 0.042). No significant differences were observed in the ischemic outcomes. The excess in bleeding observed with PAR1 inhibition was attenuated in patients with the Thr120 variant, but the interactions were not statistically significant. In summary, lower major bleeding rates were observed in the overall TRACER cohort with the hyperreactive PAR4 Thr120 variant. The increase in bleeding with vorapaxar was attenuated with the Thr120 variant, but we could not demonstrate an interaction with PAR1 inhibition. These findings warrant further exploration, including those of African ancestry where the A allele (Thr120) frequency is ~65%.

Abstract 015: PAR4 Ala120Thr Variant Alters PAR4 Desensitization, Sensitivity to Platelet Antagonists and Risk of Large Vessel Stroke

F2RL3 encodes protease-activated receptor 4 (PAR4) and harbors a A/G SNP (rs773902) with racially dimorphic allelic frequencies. This SNP mediates an alanine to threonine substitution at residue 120 that alters platelet PAR4 activation by the artificial PAR4-activation peptide (PAR4-AP), AYPGKF, which does not occur in vivo. Platelet function studies from healthy human donors demonstrated that compared to rs773902 GG donors, platelets from rs773902 AA donors had increased aggregation to low concentrations (<1 nM) of thrombin, increased Ca 2+ signaling, increased granule secretion and decreased PAR4 desensitization. The increased thrombin sensitivity of rs773902 AA platelets required both PAR4 and PAR1. Whereas receptor cleavage, dimerization, or lipid raft localization were not different between platelets from the two F2RL3 genotypes, rs773902 AA platelets required more than 3-fold amounts of PAR4-AP for receptor desensitization. PAR4-AP stimulation of PAR4-transfected COS-7 cells increased PAR4 levels on the cell surface. Thrombin-stimulated platelets from rs773902 AA donors displayed reduced inhibition by P2Y12 and PAR1 blockers, but not aspirin. Finally, the association of rs773902 alleles with stroke was assessed using the Stroke Genetics Network (SiGN) study. Patients carrying at least one copy of the rs773902 A allele had an increased risk of both large vessel stroke and diabetes in the SiGN dataset. In summary, both PAR4 and PAR1 are required for platelet activation to sub-nanomolar thrombin concentrations. Compared to rs773902 GG platelets, rs773902 AA platelets have a lower EC50 for thrombin and are relatively resistant to receptor desensitization, perhaps due to anterograde trafficking of internal PAR4 to the plasma membrane post-stimulation. The association of the rs773902 A variant with large vessel stroke, diabetes and partial resistance to PAR1 and P2Y12 inhibition must be considered for development of personalized anti-platelet agents.