Analysis of copy number variation in men with non-obstructive azoospermia

BACKGROUND

Recent findings demonstrate that single nucleotide variants can cause non-obstructive azoospermia (NOA). In contrast, copy number variants (CNVs) were only analysed in few studies in infertile men. Some have reported a higher prevalence of CNVs in infertile versus fertile men.

OBJECTIVES

This study aimed to elucidate if CNVs are associated with NOA.

MATERIALS AND METHODS

We performed array-based comparative genomic hybridisation (aCGH) in 37 men with meiotic arrest, 194 men with Sertoli cell-only phenotype, and 21 control men. We filtered our data for deletions affecting genes and prioritised the affected genes according to the literature search. Prevalence of CNVs was compared between all groups. Exome data of 2,030 men were screened to detect further genetic variants in prioritised genes. Modelling was performed for the protein encoded by the novel candidate gene TEKT5 and we stained for TEKT5 in human testicular tissue.

RESULTS

We determined the cause of infertility in two individuals with homozygous deletions of SYCE1 and in one individual with a heterozygous deletion of SYCE1 combined with a likely pathogenic missense variant on the second allele. We detected heterozygous deletions affecting MLH3, EIF2B2, SLX4, CLPP and TEKT5, in one subject each. CNVs were not detected more frequently in infertile men compared with controls.

DISCUSSION

While SYCE1 and MLH3 encode known meiosis-specific proteins, much less is known about the proteins encoded by the other identified candidate genes, warranting further analyses. We were able to identify the cause of infertility in one out of the 231 infertile men by aCGH and in two men by using exome sequencing data.

CONCLUSION

As aCGH and exome sequencing are both expensive methods, combining both in a clinical routine is not an effective strategy. Instead, using CNV calling from exome data has recently become more precise, potentially making aCGH dispensable.

Genomic testing for copy number and single nucleotide variants in spermatogenic failure

PURPOSE

To identify clinically significant genomic copy number (CNV) and single nucleotide variants (SNV) in males with unexplained spermatogenic failure (SPGF).

MATERIALS AND METHODS

Peripheral blood DNA from 97/102 study participants diagnosed with oligozoospermia, severe oligozoospermia, or non-obstructive azoospermia (NOA) was analyzed for CNVs via array comparative genomic hybridization (aCGH) and SNVs using whole-exome sequencing (WES).

RESULTS

Of the 2544 CNVs identified in individuals with SPGF, > 90% were small, ranging from 0.6 to 75 kb. Thirty, clinically relevant genomic aberrations, were detected in 28 patients (~ 29%). These included likely diagnostic CNVs in 3/41 NOA patients (~ 7%): 1 hemizygous, intragenic TEX11 deletion, 1 hemizygous DDX53 full gene deletion, and 1 homozygous, intragenic STK11 deletion. High-level mosaicism for X chromosome disomy (~ 10% 46,XY and ~ 90% 47,XXY) was also identified in 3 of 41 NOA patients who previously tested normal with conventional karyotyping. The remaining 24 CNVs detected were heterozygous, autosomal recessive carrier variants. Follow-up WES analysis confirmed 8 of 27 (30%) CNVs (X chromosome disomy excluded). WES analysis additionally identified 13 significant SNVs and/or indels in 9 patients (~ 9%) including X-linked AR, KAL1, and NR0B1 variants.

CONCLUSION

Using a combined genome-wide aCGH/WES approach, we identified pathogenic and likely pathogenic SNVs and CNVs in 15 patients (15%) with unexplained SPGF. This value equals the detection rate of conventional testing for aneuploidies and is considerably higher than the prevalence of Y chromosome microdeletions. Our results underscore the importance of comprehensive genomic analysis in emerging diagnostic testing of complex conditions like male infertility.

Annular lipoatrophy of the ankle: Four new pediatric cases and a review of the literature

Annular lipoatrophy of the ankle is a rare and unique acquired lipoatrophic panniculitis that mainly affects children. There is no consensus on treatment, and the long-term course is not well known. We present four new pediatric cases that contribute to the understanding of this rare disease.

Global longitudinal strain and mechanical dispersion at rest in exercise stress echocardiography for detecting obstructive coronary artery disease: a pilot study

Funding Acknowledgements

Type of funding sources: None.

BACKGROUND

Exercise stress echocardiography (ESE) is a commonly used investigation for risk stratification in coronary artery disease (CAD). The added value of resting indices such as Global Longitudinal Strain (GLS) and Mechanical Dispersion (MD) to detect obstructive CAD is not well established and would be of significant clinical benefit.

PURPOSE

To evaluate the diagnostic value of GLS and MD at rest and post-exercise during ESE to detect obstructive CAD, defined by angiographic stenosis >70% in any major coronary artery.

METHODS

Retrospective cohort study of 80 consecutive patients who underwent ESE and had coronary angiography (invasive or CT) within 6 months. Retrospective speckle tracking strain analysis was performed on digitally archived video-loops, using vendor independent software. Data on demographics, medications, outcomes and ESE characteristics were collected and analysed.

RESULTS

In 49 (61.3%) patients with any CAD >70%, GLS at rest was lower (-13.9% ± 4.2 vs -16.1% ± 5.2, p-value = 0.04), and MD at rest was higher (81ms ± 43 vs 58ms ± 28, p-value = 0.008), when compared to patients without CAD >70%. GLS and MD measured post-exercise were not significantly different between groups. Ejection fraction (EF) and Wall Motion Score Index (WMSI) at rest and post-exercise were not significantly different between groups. A resting GLS cutpoint of -14% had a sensitivity and specificity of 57/68%, comparable to the development of new regional wall motion abnormalities (71/39%) and peak WMSI >1.2 (59/48%). Additionally, in 39 (48.8%) patients who had >70% stenosis in the left anterior descending (LAD) artery, LS in the LAD territory segments was lower (-16.2% ± 4.4 vs -18.3% ± 4.7, p-value = 0.04), when compared to patients without >70% stenosis in the LAD artery.

CONCLUSION

Resting GLS was lower and MD higher in patients undergoing ESE, who have any CAD >70% compared to patients who do not have any CAD >70%. Resting GLS and MD may increase diagnostic accuracy during ESE to predict obstructive CAD. Further prospective studies evaluating the utility of resting indices to predict functionally significant CAD are required.

Polygenic Risk Score Analysis of Alzheimer's Disease in Cases without APOE4 or APOE2 Alleles

The We and others have previously shown that polygenic risk score analysis (PRS) has considerable predictive utility for identifying those at high risk of developing Alzheimer’s disease (AD) with an area under the curve (AUC) of >0.8. However, by far the greatest determinant of this risk is the apolipoprotein E locus with the E4 allele alone giving an AUC of ∼0.68 and the inclusion of the protective E2 allele increasing this to ∼0.69 in a clinical cohort. An important question is to determine how good PRS is at predicting risk in those who do not carry the E4 allele (E3 homozygotes, E3E2 and E2E2) and in those who carry neither the E4 or E2 allele (i.e. E3 homozygotes). Previous studies have shown that PRS remains a significant predictor of AD risk in clinical cohorts after controlling for APOE ε4 carrier status. In this study we assess the accuracy of PRS prediction in a cohort of pathologically confirmed AD cases and controls. The exclusion of APOE4 carriers has surprisingly little effect on the PRS prediction accuracy (AUC ∼0.83 [95% CI: 0.80-0.86]), and the accuracy remained higher than that in clinical cohorts with APOE included as a predictor. From a practical perspective this suggests that PRS analysis will have predictive utility even in E4 negative individuals and may be useful in clinical trial design.

Society of pediatric liver transplantation: Current registry status 2011-2018

BACKGROUND

SPLIT was founded in 1995 in order to collect comprehensive prospective data on pediatric liver transplantation, including waiting list data, transplant, and early and late outcomes. Since 2011, data collection of the current registry has been refined to focus on prospective data and outcomes only after transplant to serve as a foundation for the future development of targeted clinical studies.

OBJECTIVE

To report the outcomes of the SPLIT registry from 2011 to 2018.

METHODS

This is a multicenter, cross-sectional analysis characterizing patients transplanted and enrolled in the SPLIT registry between 2011 and 2018. All patients, <18 years of age, received a first liver-only, a combined liver-kidney, or a combined liver-pancreas transplant during this study period.

RESULTS

A total of 1911 recipients from 39 participating centers in North America were registered. Indications included biliary atresia (38.5%), metabolic disease (19.1%), tumors (11.7%), and fulminant liver failure (11.5%). Greater than 50% of recipients were transplanted as either Status 1A/1B or with a MELD/PELD exception score. Incompatible transplants were performed in 4.1%. Kaplan-Meier estimates of 1-year patient and graft survival were 97.3% and 96.6%. First 30 days of surgical complications included reoperation (31.7%), hepatic artery thrombosis (6.3%), and portal vein thrombosis (3.2%). In the first 90 days, biliary tract complications were reported in 13.6%. Acute cellular rejection during first year was 34.7%. At 1 and 2 years of follow-up, 39.2% and 50.6% had normal liver tests on monotherapy (tacrolimus or sirolimus). Further surgical, survival, allograft function, and complications are detailed.

Polygenic Risk Scoring is an Effective Approach to Predict Those Individuals Most Likely to Decline Cognitively Due to Alzheimer's Disease

BACKGROUND

There is a clear need for simple and effective tests to identify individuals who are most likely to develop Alzheimer's Disease (AD) both for the purposes of clinical trial recruitment but also for improved management of patients who may be experiencing early pre-clinical symptoms or who have clinical concerns.

OBJECTIVES

To predict individuals at greatest risk of progression of cognitive impairment due to Alzheimer's Disease in individuals from the Alzheimer's Disease Neuroimaging Initiative (ADNI) using a polygenic risk scoring algorithm. To compare the performance of a PRS algorithm in predicting cognitive decline against that of using the pTau/Aß1-42 ratio CSF biomarker profile.

DESIGN

A longitudinal analysis of data from the Alzheimer's Disease Neuroimaging Initiative study conducted across over 50 sites in the US and Canada.

SETTING

Multi-center genetics study.

PARTICPANTS

515 subjects who upon entry to the study were diagnosed as cognitively normal or with mild cognitive impairment.

MEASUREMENTS

Use of genotyping and/or whole genome sequencing data to calculate polygenic risk scores and assess ability to predict subsequent cognitive decline as measured by CDR-SB and ADAS-Cog13 over 4 years.

RESULTS

The overall performance for predicting those individuals who would decline by at least 15 ADAS-Cog13 points from a baseline mild cognitive impairment in 4 years was 72.8% (CI:67.9-77.7) AUC increasing to 79.1% (CI: 75.6-82.6) when also including cognitively normal participants. Assessing mild cognitive impaired subjects only and using a threshold of greater than 0.6, the high genetic risk participant group declined, on average, by 1.4 points (CDR-SB) more than the low risk group over 4 years. The performance of the PRS algorithm tested was similar to that of the pTau/Aß1-42 ratio CSF biomarker profile in predicting cognitive decline.

CONCLUSION

Calculating polygenic risk scores offers a simple and effective way, using DNA extracted from a simple mouth swab, to select mild cognitively impaired patients who are most likely to decline cognitively over the next four years.

Culture-independent and dependent evaluation of the equine paranasal sinus microbiota in health and disease

BACKGROUND

Horses with bacterial sinusitis frequently undergo empirical treatment with antimicrobials, however, in some cases bacterial culture of the affected sinus is used to direct therapy. Data regarding which organisms are part of the commensal microbiota of the equine sinus are lacking making it difficult to interpret culture results and guide empiric antimicrobial selection.

OBJECTIVES

Our objectives were to describe the bacterial and fungal microbiota of the paranasal sinuses in clinically normal horses using culture-dependent and independent approaches and to compare the bacterial culture and susceptibility patterns of normal horses with those from horses affected with primary and secondary sinusitis.

STUDY DESIGN

Experimental study and descriptive retrospective review of case records.

METHODS

Sinus washes were collected from 23 healthy horses. Washes were submitted for routine culture and susceptibility testing and DNA was isolated for next generation sequencing of bacterial and fungal marker genes. For clinical cases of sinusitis, medical records from 2010 to 2017 were reviewed and horses diagnosed with primary and/or secondary sinusitis were included.

RESULTS

The paranasal sinus cavity hosts multiple bacterial and fungal organisms. The bacterial microbiota of healthy horses consists largely of uncultivable, aerobic bacteria. While few anaerobes were isolated from normal horses, the majority of clinical cases resulted in growth of anaerobic organisms with no difference in the proportion of aerobic and anaerobic bacteria isolated from clinical cases.

MAIN LIMITATIONS

Small sample size in both populations of horses and heterogeneity of the population prevent a more in-depth analysis.

CONCLUSIONS

The microbiota of the paranasal sinuses of horses consists primarily of aerobic bacteria and fungal organisms, the majority of which are uncultivable via common clinical methods. Anaerobic bacteria are found in the majority of horses with clinical sinusitis. These findings suggest anaerobic bacteria are associated with sinusitis and their presence should be considered when treating horses with sinusitis.

Clinical Profile of Methotrexate-resistant Juvenile Localised Scleroderma

Methotrexate has demonstrated its efficiency for the treatment of juvenile localized scleroderma but some patients may be resistant. The aim of our study was to define the profile of such patients. We performed an observational retrospective multicenter study between 2007 and 2016 and included all children seen in the French Paediatric Dermatology and Rheumatology departments with active localized scleroderma treated by methotrexate for a minimum of 4 months. Metho-trexate efficacy was assessed clinically and/or by imaging between the fourth to twelfth months of treatment. A total of 57 patients were included. Metho-trexate dosage ranged from 7 to 15 mg/m2/week. Only 4 patients were resistant. No common features could be identified between these 4 patients. Children with localized scleroderma are rarely resistant to metho-trexate and we did not identify a clinical profile for those resistant patients.

Whole-exome sequencing of the BDR cohort: evidence to support the role of the PILRA gene in Alzheimer's disease

AIM

Late-onset Alzheimer's disease (LOAD) accounts for 95% of all Alzheimer's cases and is genetically complex in nature. Overlapping clinical and neuropathological features between AD, FTD and Parkinson's disease highlight the potential role of genetic pleiotropy across diseases. Recent genome-wide association studies (GWASs) have uncovered 20 new loci for AD risk; however, these exhibit small effect sizes. Using NGS, here we perform association analyses using exome-wide and candidate-gene-driven approaches.

METHODS

Whole-exome sequencing was performed on 132 AD cases and 53 control samples. Exome-wide single-variant association and gene burden tests were performed for 76 640 nonsingleton variants. Samples were also screened for known causative mutations in familial genes in AD and other dementias. Single-variant association and burden analysis was also carried out on variants in known AD and other neurological dementia genes.

RESULTS

Tentative single-variant and burden associations were seen in several genes with kinase and protease activity. Exome-wide burden analysis also revealed significant burden of variants in PILRA (P = 3.4 × 10-5 ), which has previously been linked to AD via GWAS, hit ZCWPW1. Screening for causative mutations in familial AD and other dementia genes revealed no pathogenic variants. Variants identified in ABCA7, SLC24A4, CD33 and LRRK2 were nominally associated with disease (P < 0.05) but did not withstand correction for multiple testing. APOE (P = 0.02) and CLU (P = 0.04) variants showed significant burden on AD.

CONCLUSIONS

In addition, polygenic risk scores (PRS) were able to distinguish between cases and controls with 83.8% accuracy using 3268 variants, sex, age at death and APOE ε4 and ε2 status as predictors.

Using the Gene Ontology to Annotate Key Players in Parkinson's Disease

The Gene Ontology (GO) is widely recognised as the gold standard bioinformatics resource for summarizing functional knowledge of gene products in a consistent and computable, information-rich language. GO describes cellular and organismal processes across all species, yet until now there has been a considerable gene annotation deficit within the neurological and immunological domains, both of which are relevant to Parkinson’s disease. Here we introduce the Parkinson’s disease GO Annotation Project, funded by Parkinson’s UK and supported by the GO Consortium, which is addressing this deficit by providing GO annotation to Parkinson’s-relevant human gene products, principally through expert literature curation. We discuss the steps taken to prioritise proteins, publications and cellular processes for annotation, examples of how GO annotations capture Parkinson’s-relevant information, and the advantages that a topic-focused annotation approach offers to users. Building on the existing GO resource, this project collates a vast amount of Parkinson’s-relevant literature into a set of high-quality annotations to be utilized by the research community.

Alzheimer's disease

Alzheimer's disease, the commonest cause of dementia, is a growing global health concern with huge implications for individuals and society. In this review, current understanding of the epidemiology, genetics, pathology and pathogenesis of Alzheimer's disease is outlined, before its clinical presentation and current treatment strategies are discussed. Finally, the review discusses how our enhanced understanding of Alzheimer pathogenesis, including the recognition of a protracted preclinical phase, is informing new therapeutic strategies with the aim of moving from treatment to prevention.

Tedera proves its value as a summer and autumn feed for sheep in Mediterranean-like climates

Tedera (Bituminaria bituminosa C.H Stirt. vars. albomarginata and crassiuscula) is a traditional forage species for goats in the Canary Islands, Spain. It has agronomic characteristics ideally suited to Mediterranean-like climates that allows it to provide high quality green forage for grazing animals during summer and autumn. It can be used to extend the growing season into late spring and early summer and/or to reduce or eliminate the need for expensive hand feeding of grain and hay to sheep to fill the ‘feed gap’ during the dry season in southern Australian farming systems. Three sheep grazing experiments were carried out with the objective to evaluate sheep production during summer and autumn with tedera as the sole diet. A 3-ha site at Dandaragan, Western Australia was grazed during the summer and autumn of 2014–2015 and 2016 and a 2.4-ha site was grazed at Kojonup, Western Australia during the same period in 2016. At each site, two grazing treatments were evaluated, continuous grazing and rotational grazing with six plots (14 days of grazing and 70 days of recovery). The first hypothesis tested was that tedera plants would not survive continuous grazing during summer and autumn. The second hypothesis tested was that without hand feeding, 10 dry sheep equivalents/ha would be able to at least maintain weight and condition score during summer and autumn. The third hypothesis tested was that rotational grazing would improve the production of the sheep (liveweight and condition score) compared with continuous grazing. The first hypothesis was rejected, the population of tedera plants did not significantly decline due to being continuously grazed during summer and autumn. The second hypothesis was confirmed, at the three experimental sites, 10 dry sheep equivalents/ha were able to at least maintain weight and condition score without any hand feeding. The third hypothesis was partially rejected; continuous grazing had a better performance of the sheep than rotational grazing. However, the rotational grazing plots had more tedera on offer in the remaining grazing plots in the rotation with the potential for a longer grazing time. These three experiments clearly demonstrate that tedera can be used to reduce or eliminate expensive hand feeding during summer and autumn using the simplest and least expensive grazing management; continuous grazing.

Review: Induced pluripotent stem cell models of frontotemporal dementia

The increasing prevalence of dementia in the ageing population combined with the lack of treatments and the burden on national health care systems globally make dementia a public health priority. Despite the plethora of important research findings published over the past two decades, the mechanisms underlying dementia are still poorly understood and the progress in pharmacological interventions is limited. Recent advances in cellular reprogramming and genome engineering technologies offer an unprecedented new paradigm in disease modeling. Induced pluripotent stem cells (iPSCs) have enabled the study of patient-derived neurons in vitro, a significant progress in the field of dementia research. The first studies using iPSCs to model dementia have recently emerged, holding promise for elucidating disease pathogenic mechanisms and accelerating drug discovery. In this review, we summarize the major findings of iPSC-based studies in frontotemporal dementia (FTD) and FTD overlapping with amyotrophic lateral sclerosis (FTD/ALS). We also discuss some of the main challenges in the use of iPSCs to model complex, late-onset neurodegenerative diseases such as dementias.