A case-note review of continued pregnancies found to be at a high risk of Huntington's disease: considerations for clinical practice

Huntington’s disease (HD) is a severe neurodegenerative condition that impacts the whole family. Prenatal diagnosis by direct or exclusion testing is available for couples at risk of transmitting HD to their children. An ethical problem can arise after prenatal diagnosis for HD if a known ‘high risk’ pregnancy is continued to term: international guidelines emphasise that this situation should be avoided where possible, as it removes the resulting child’s future right to make an informed, autonomous decision about predictive testing. The UK Huntington’s Disease Predictive Testing Consortium recorded 21 pregnancies that were tested, identified as high-risk and then continued. In this qualitative study, health professionals reviewed the case notes of 15 of these pregnancies. This analysis generated guidelines for clinical practice. It is recommended that practitioners: (i) remind couples of the long-term consequences of continuing a high risk pregnancy, (ii) ensure couples understand the information provided, (iii) collaborate closely with other professionals involved in the couple’s prenatal care, (iv) prepare couples for the procedural aspects of prenatal diagnosis and a possible termination of pregnancy, (v) allow time for in-depth pre-test counselling, (vi) explain the rationale for only making prenatal diagnosis available subject to conditions, whilst allowing for human ambivalence and acknowledging that these ‘conditions' cannot be enforced, (vii) monitor the whole clinical process to ensure that it works ‘smoothly', (viii) recommend couples do not disclose the result of the prenatal test to protect the confidentiality and autonomy of the future ‘high-risk' child, and (ix) offer on-going contact and support

The perceived impact of the European registration system for genetic counsellors and nurses

The aim of the European Board of Medical Genetics has been to develop and promote academic and professional standards necessary in order to provide competent genetic counselling services. The aim of this study was to explore the impact of the European registration system for genetic nurses and counsellors from the perspectives of those professionals who have registered. Registration system was launched in 2013. A cross-sectional, online survey was used to explore the motivations and experiences of those applying for, and the effect of registration on their career. Fifty-five Genetic Nurses and Counsellors are registered till now, from them, thirty-three agreed to participate on this study. The main motivations for registering were for recognition of their work value and competence (30.3%); due to the absence of a registration system in their own country (15.2%) and the possibility of obtaining a European/international certification (27.3%), while 27.3% of respondents registered to support recognition of the genetic counselling profession. Some participants valued the registration process as an educational activity in its own right, while the majority indicated the greatest impact of the registration process was on their clinical practice. The results confirm that registrants value the opportunity to both confirm their own competence and advance the genetic counselling profession in Europe.</p

Growth and nutrition in children with Ataxia telangiectasia

Background: Ataxia telangiectasia (A-T) is a rare multisystem disease with high early mortality from lung disease and cancer. Nutritional failure adversely impacts outcomes in many respiratory diseases. Several factors influence nutrition in children with A-T. We hypothesised that children with A-T have progressive growth failure and that early gastrostomy tube feeding (percutaneous endoscopic gastrostomy, or PEG) is a favourable management option with good nutritional outcomes. Methods: Data were collected prospectively on weight, height and body mass index (BMI) at the national paediatric A-T clinic. Adequacy and safety of oral intake was assessed. Nutritional advice was given at each multidisciplinary review. Results: 101 children (51 girls) had 222 measurements (32 once, 32 twice, 24 thrice) between 2009 and 2016. Median (range) age was 9.3 (1.5 to 18.4) years. Mean (sd) weight, height and BMI Z-scores were respectively -1.03(1.57), -1.17 (1.18) and -0.36 (1.43). 35/101 children had weight Z-scores below -2 on at least one occasion. Weight, height and BMI Z-scores declined over time. Decline was most obvious after 8 years of age. 14/101 (13.9%) children had a PEG, with longitudinal data available for 12. In a nested case control study, there was a trend for improvement in weight in those with a PEG (p = 0.06). Conclusions: A-T patients decline in growth over time. There is an urgent need for new strategies, including an understanding of why growth falters. We suggest early proactive consideration of PEG from age 8 years onwards in order to prevent progressive growth failure

CSVS, a crowdsourcing database of the Spanish population genetic variability

The knowledge of the genetic variability of the local population is of utmost importance in personalized medicine and has been revealed as a critical factor for the discovery of new disease variants. Here, we present the Collaborative Spanish Variability Server (CSVS), which currently contains more than 2000 genomes and exomes of unrelated Spanish individuals. This database has been generated in a collaborative crowdsourcing effort collecting sequencing data produced by local genomic projects and for other purposes. Sequences have been grouped by ICD10 upper categories. A web interface allows querying the database removing one or more ICD10 categories. In this way, aggregated counts of allele frequencies of the pseudo-control Spanish population can be obtained for diseases belonging to the category removed. Interestingly, in addition to pseudo-control studies, some population studies can be made, as, for example, prevalence of pharmacogenomic variants, etc. In addition, this genomic data has been used to define the first Spanish Genome Reference Panel (SGRP1.0) for imputation. This is the first local repository of variability entirely produced by a crowdsourcing effort and constitutes an example for future initiatives to characterize local variabilityworldwide. CSVS is also part of the GA4GH Beacon network.Spanish Ministry of Economy and Competitiveness SAF2017-88908-R PT17/0009/0006 PI19/00321 CIBERER ACCI-06/07/0036 PI14-948 PI171659Regional Government of Madrid, RAREGenomicsCM B2017/BMD3721 B2017/BMD-3721European Union (EU)European Union (EU) 676559University Chair UAM-IIS-FJD of Genomic MedicineRamon Areces Foundatio

A crowdsourcing database for the copy-number variation of the Spanish population

Background: Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants. Results: Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/. Conclusion: SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database

An European overview of genetic counselling supervision provision

Genetic testing is becoming more commonplace in general and specialist health care, and should always be accompanied by genetic counselling, according to legislation in many European countries and recommendations by professional bodies. Personal and professional competence is necessary to provide safe and effective genetic counselling. Clinical and counselling supervision of genetics healthcare practitioners plays a key role in quality assurance, providing a safe environment not only for patients but for professionals too. However, in many European countries, genetic counsellors are still an emerging professional group and counselling supervision is not routinely offered and there are no enough evidences on the impact of these insufficiencies. This study aimed to explore the current status of genetic counselling supervision provision across Europe and to ascertain factors that might be relevant for the successful implementation of counselling supervision. A total of 100 practitioners responded to an online survey; respondents were from 18 countries, with the majority working in France (27%) and Spain (17%). Only 34 participants reported having access to genetic counselling supervision. Country of origin, the existence of a regulation system and years of experience were factors identified as relevant, influencing access and characteristics of counselling supervision. Although there is a growing number of genetic counsellors trained at European level, just a few countries have implemented and required as mandatory the access to genetic counselling supervision. Nevertheless, this is essential to ensure a safe and effective genetic counselling and should be regulated at the European genetic healthcare services.</p

SMN1 copy-number and sequence variant analysis from next-generation sequencing data

© 2020 The Authors.Spinal muscular atrophy (SMA) is a severe neuromuscular autosomal recessive disorder affecting 1/10,000 live births. Most SMA patients present homozygous deletion of SMN1, while the vast majority of SMA carriers present only a single SMN1 copy. The sequence similarity between SMN1 and SMN2, and the complexity of the SMN locus makes the estimation of the SMN1 copy-number by next-generation sequencing (NGS) very difficult. Here, we present SMAca, the first python tool to detect SMA carriers and estimate the absolute SMN1 copy-number using NGS data. Moreover, SMAca takes advantage of the knowledge of certain variants specific to SMN1 duplication to also identify silent carriers. This tool has been validated with a cohort of 326 samples from the Navarra 1000 Genomes Project (NAGEN1000). SMAca was developed with a focus on execution speed and easy installation. This combination makes it especially suitable to be integrated into production NGS pipelines. Source code and documentation are available at https://www.github.com/babelomics/SMAca.This study is supported by grants SAF2017‐88908‐R from the Spanish Ministry of Economy and Competitiveness and “Plataforma de RecursosBiomoleculares y Bioinformáticos” PT17/0009/0006 from the ISCIII, both cofunded with European Regional Development Funds as well as H2020 Programme of the European Union grants Marie Curie Innovative Training Network “Machine Learning Frontiers in Precision Medicine” (GA 813533) and “ELIXIR‐EXCELERATE fast‐track ELIXIR implementation and drive early user exploitation across the life sciences” (GA 676559)

Characterization of the Common Genetic Variation in the Spanish Population of Navarre

Large-scale genomic studies have significantly increased our knowledge of genetic variability across populations. Regional genetic profiling is essential for distinguishing common benign variants from disease-causing ones. To this end, we conducted a comprehensive characterization of exonic variants in the population of Navarre (Spain), utilizing whole genome sequencing data from 358 unrelated individuals of Spanish origin. Our analysis revealed 61,410 biallelic single nucleotide variants (SNV) within the Navarrese cohort, with 35% classified as common (MAF > 1%). By comparing allele frequency data from 1000 Genome Project (excluding the Iberian cohort of Spain, IBS), Genome Aggregation Database, and a Spanish cohort (including IBS individuals and data from Medical Genome Project), we identified 1069 SNVs common in Navarre but rare (MAF ≤ 1%) in all other populations. We further corroborated this observation with a second regional cohort of 239 unrelated exomes, which confirmed 676 of the 1069 SNVs as common in Navarre. In conclusion, this study highlights the importance of population-specific characterization of genetic variation to improve allele frequency filtering in sequencing data analysis to identify disease-causing variants