Paternal leakage of plastids rescues inter-lineage hybrids in Silene nutans.

BACKGROUND AND AIMS: Organelle genomes are usually maternally inherited in angiosperms. However, biparental inheritance has been observed, especially in hybrids resulting from crosses between divergent genetic lineages. When it concerns the plastid genome, this exceptional mode of inheritance might rescue inter-lineage hybrids suffering from plastid-nuclear incompatibilities. Genetically differentiated lineages of Silene nutans exhibit strong postzygotic isolation owing to plastid-nuclear incompatibilities, highlighted by inter-lineage hybrid chlorosis and mortality. Surviving hybrids can exhibit variegated leaves, which might indicate paternal leakage of the plastid genome. We tested whether the surviving hybrids inherited the paternal plastid genome and survived thanks to paternal leakage. METHODS: We characterized the leaf phenotype (fully green, variegated or white) of 504 surviving inter-lineage hybrids obtained from a reciprocal cross experiment among populations of four genetic lineages (W1, W2, W3 and E1) of S. nutans from Western Europe and genotyped 560 leaf samples (both green and white leaves for variegated hybrids) using six lineage-specific plastid single nucleotide polymorphisms. KEY RESULTS: A high proportion of the surviving hybrids (≤98 %) inherited the paternal plastid genome, indicating paternal leakage. The level of paternal leakage depended on cross type and cross direction. The E1 and W2 lineages as maternal lineages led to the highest hybrid mortality and to the highest paternal leakage from W1 and W3 lineages in the few surviving hybrids. This was consistent with E1 and W2 lineages, which contained the most divergent plastid genomes. When W3 was the mother, more hybrids survived, and no paternal leakage was detected. CONCLUSIONS: By providing a plastid genome potentially more compatible with the hybrid nuclear background, paternal leakage has the potential to rescue inter-lineage hybrids from plastid-nuclear incompatibilities. This phenomenon might slow down the speciation process, provided hybrid survival and reproduction can occur in the wild.

Antimicrobial activity of lipids extracted from Hermetia illucens reared on different substrates.

As the problem of antimicrobial resistance is constantly increasing, there is a renewed interest in antimicrobial products derived from natural sources, particularly obtained from innovative and eco-friendly materials. Insect lipids, due to their fatty acid composition, can be classified as natural antimicrobial compounds. In order to assess the antibacterial efficacy of Hermetia illucens lipids, we extracted this component from the larval stage, fed on different substrates and we characterized it. Moreover, we analyzed the fatty acid composition of the feeding substrate, to determine if and how it could affect the antimicrobial activity of the lipid component. The antimicrobial activity was evaluated against Gram-positive Micrococcus flavus and Gram-negative bacteria Escherichia coli. Analyzing the fatty acid profiles of larval lipids that showed activity against the two bacterial strains, we detected significant differences for C4:0, C10:0, C16:1, C18:3 n3 (ALA), and C20:1. The strongest antimicrobial activity was verified against Micrococcus flavus by lipids extracted from larvae reared on strawberry, tangerine, and fresh manure substrates, with growth inhibition zones ranged from 1.38 to 1.51 mm, while only the rearing on manure showed the effect against Escherichia coli. Notably, the fatty acid profile of H. illucens seems to not be really influenced by the substrate fatty acid profile, except for C18:0 and C18:2 CIS n6 (LA). This implies that other factors, such as the rearing conditions, larval development stages, and other nutrients such as carbohydrates, affect the amount of fatty acids in insects. KEY POINTS: • Feeding substrates influence larval lipids and fatty acids (FA) • Generally, there is no direct correlation between substrate FAs and the same larvae FAs • Specific FAs influence more the antimicrobial effect of BSF lipids.

The decoupled evolution of the organellar genomes of Silene nutans leads to distinct roles in the speciation process.

There is growing evidence that cytonuclear incompatibilities (i.e. disruption of cytonuclear coadaptation) might contribute to the speciation process. In a former study, we described the possible involvement of plastid-nuclear incompatibilities in the reproductive isolation between four lineages of Silene nutans (Caryophyllaceae). Because organellar genomes are usually cotransmitted, we assessed whether the mitochondrial genome could also be involved in the speciation process, knowing that the gynodioecious breeding system of S. nutans is expected to impact the evolutionary dynamics of this genome. Using hybrid capture and high-throughput DNA sequencing, we analyzed diversity patterns in the genic content of the organellar genomes in the four S. nutans lineages. Contrary to the plastid genome, which exhibited a large number of fixed substitutions between lineages, extensive sharing of polymorphisms between lineages was found in the mitochondrial genome. In addition, numerous recombination-like events were detected in the mitochondrial genome, loosening the linkage disequilibrium between the organellar genomes and leading to decoupled evolution. These results suggest that gynodioecy shaped mitochondrial diversity through balancing selection, maintaining ancestral polymorphism and, thus, limiting the involvement of the mitochondrial genome in evolution of hybrid inviability between S. nutans lineages.

Implementation behavior of communities regarding relatives caring for people with dementia : A quantitative study among German communities.

BACKGROUND: Actors from the community (CAs) play a fundamental role in the support of caring relatives (CRs) of people with dementia (PWD). As their support is not sufficient, the implementation of support services needs to be optimized; however, little is known about the factors associated with the implementation behavior of CAs. AIM: This study aimed to investigate the association of person-related factors with the implementation behavior of CAs. METHODS: In a cross-sectional study, 205 CAs from 16 German communities were surveyed with the community implementation behaviour questionnaire (CIBQ), which is based on the theoretical domains framework. Logistic regression analyses were conducted to identify person-related factors associated with the implementation behavior regarding support services for CRs of PWD. RESULTS: Implementing support services for CRs of PWD is positively and significantly (p < 0.001) associated with the agreement of CAs with the CIBQ domains. Higher scores in the CIBQ increase the chance that CAs implemented support services for the target group. CONCLUSION: The CIBQ is a tool to determine the status of implementation behavior of communities. This enables an analysis of the areas CAs need to work on in order to optimize the implementation of support services for CRs of PWD or other health and care-related topics.

Reproductive isolation among lineages of Silene nutans (Caryophyllaceae): A potential involvement of plastid-nuclear incompatibilities.

Early stages of speciation in plants might involve genetic incompatibilities between plastid and nuclear genomes, leading to inter-lineage hybrid breakdown due to the disruption between co-adapted plastid and nuclear genes encoding subunits of the same plastid protein complexes. We tested this hypothesis in Silene nutans, a gynodioecious Caryophyllaceae, where four distinct genetic lineages exhibited strong reproductive isolation among each other, resulting in chlorotic or variegated hybrids. By sequencing the whole gene content of the four plastomes through gene capture, and a large part of the nuclear genes encoding plastid subunits from RNAseq data, we searched for non-synonymous substitutions fixed in each lineage on both genomes. Lineages of S. nutans exhibited a high level of dN/dS ratios for plastid and nuclear genes encoding most plastid complexes, with a strong pattern of coevolution for genes encoding the subunits of ribosome and cytochrome b6/f that could explain the chlorosis of hybrids. Overall, relaxation of selection due to past bottlenecks and positive selection have driven the diversity pattern observed in S. nutans plastid complexes, leading to plastid-nuclear incompatibilities. We discuss the possible role of gynodioecy in the evolutionary dynamics of the plastomes through linked selection.

Impact of Anti-Immigrant Rhetoric on Latinx Families' Perceptions of Child Safety and Health Care Access.

BACKGROUND: Political rhetoric from the former U.S. president influences Latinx adults' feelings of safety and their decisions to seek care in the emergency department (ED). OBJECTIVE: Our aim was to examine the impact of political rhetoric on feelings of safety and health care access in the pediatric population. METHODS: This was a cross-sectional study of undocumented Latinx families (ULF), Latinx U.S. citizen families (LCF), and non-Latinx U.S. citizen families (NLF) conducted from November 2018 through February 2020 by means of interviewing a convenience sample of parents and guardians who brought their child to a pediatric clinic and two EDs in California. RESULTS: Of 705 parents approached, 449 (63.7%) agreed to participate: 138 ULF, 150 LCF, and 158 NLF. Most ULF (95%), LCF (88%), and NLF (78%) parents and guardians had heard anti-immigrant statements from the former U.S. president and most (94% ULF, 90% LCF, 86% NLF) believed these measures against immigrants were being enacted or will be enacted. More ULF (75%, 95% confidence interval [CI] 67-81%) reported that these statements made them concerned about their child's safety in the United States compared with 36% (95% CI 28-45%) and 34% (95% CI 26-43%) of LCF and NLF, respectively. More ULF 17% (95% CI 11-24%) said that these statements made them afraid to bring their child for medical care, compared with 5% (95% CI 2-10%) and 3% (95% CI 1-7%) of LCF and NLF, respectively. CONCLUSIONS: Most parents heard statements against undocumented immigrants by the former U.S. president and most believed measures were being enacted. This rhetoric had a substantial negative impact on ULF parents in terms of safety concerns for their child and fear of accessing health care.

Palatability Enhancement Potential of Hermetia illucens Larvae Protein Hydrolysate in Litopenaeus vannamei Diets.

Marine feed ingredients derived from cephalopods (e.g., squid) and crustaceans (e.g., krill) are commercially used to improve the palatability of shrimp diets. Increase in global demand for shrimps has resulted in overfishing of these marine organisms and is a matter of concern. Insect protein hydrolysate could be a sustainable alternative for the possible replacement of these marine feed ingredients. During this study, four formulations: diet A (control: not containing any palatability enhancer), diet B (containing squid meal and krill oil), diet C (containing 1% insect protein hydrolysate), and diet D (containing 2% insect protein hydrolysate) were tested for (1) time required by first subject to begin feeding (time to strike) and (2) palatability in Litopenaeus vannamei. Additionally, the chemical composition of all four diet formulations was also analyzed. Results indicate that all diets had similar crude composition. The major essential amino acids in all diets were leucine and lysine, whereas eicosapentaenoic acid was the major omega-3 fatty acid in all diets. There were no significant differences between the mean time to strike for all the tested formulations. Palatability of tested formulations was found in the following order: diet D > diet C > diet B = diet A (p < 0.05), indicating that addition of squid meal and krill oil has no effect on palatability in comparison to control, whereas inclusion of insect protein hydrolysates significantly improves the palatability of formulations. Palatability enhancement potential of insect protein hydrolysate could be attributed to the high free amino acid content and water solubility in comparison to squid meal.

Child Sexual Abuse by Catholic Priests, Deacons, and Male Members of Religious Orders in the Authority of the German Bishops' Conference 1946-2014.

This study explores the extent of sexual abuse of minors by members of the Catholic Church in Germany. It is the first comprehensive study to examine this extent in a European country. The goals of this study are as follows: (a) to analyze whether the extent and characteristics of sexual abuse in a European country are comparable to those in the United States and Australia and (b) how discrepancies can be explained. The personnel files of 38,156 Catholic Priests, deacons, and male members of religious orders in the authority of the German Bishops' Conference were analyzed. The study period lasted from 1946 to 2014. All 27 German dioceses took part in this study. A total of 4.4% of all clerics (N = 1,670) from 1946 to 2014 were alleged to have committed sexual abuse, and 3,677 children or adolescents were identified as victims. These results are similar to those from comparable studies in the United States. Sexual abuse of minors within the authority of the Catholic Church seems to be a worldwide phenomenon.

Clinical and laboratory interpretation of mitochondrial mRNA variants.

Interpretation of mitochondrial protein-encoding (mt-mRNA) variants has been challenging due to mitochondrial characteristics that have not been addressed by American College of Medical Genetics and Genomics guidelines. We developed criteria for the interpretation of mt-mRNA variants via literature review of reported variants, tested and refined these criteria by using our new cases, followed by interpreting 421 novel variants in our clinical database using these verified criteria. A total of 32 of 56 previously reported pathogenic (P) variants had convincing evidence for pathogenicity. These variants are either null variants, well-known disease-causing variants, or have robust functional data or strong phenotypic correlation with heteroplasmy levels. Based on our criteria, 65.7% (730/1,111) of variants of unknown significance (VUS) were reclassified as benign (B) or likely benign (LB), and one variant was scored as likely pathogenic (LP). Furthermore, using our criteria we classified 2, 12, and 23 as P, LP, and LB, respectively, among 421 novel variants. The remaining stayed as VUS (91.2%). Appropriate interpretation of mt-mRNA variants is the basis for clinical diagnosis and genetic counseling. Mutation type, heteroplasmy levels in different tissues of the probands and matrilineal relatives, in silico predictions, population data, as well as functional studies are key points for pathogenicity assessments.

Correction: Interpretation of mitochondrial tRNA variants.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Correction: Interpretation of mitochondrial tRNA variants.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Interpretation of mitochondrial tRNA variants.

PURPOSE: To develop criteria to interpret mitochondrial transfer RNA (mt-tRNA) variants based on unique characteristics of mitochondrial genetics and conserved structural/functional properties of tRNA. METHODS: We developed rules on a set of established pathogenic/benign variants by examining heteroplasmy correlations with phenotype, tissue distribution, family members, and among unrelated families from published literature. We validated these deduced rules using our new cases and applied them to classify novel variants. RESULTS: Evaluation of previously reported pathogenic variants found that 80.6% had sufficient evidence to support phenotypic correlation with heteroplasmy levels among and within families. The remaining variants were downgraded due to the lack of similar evidence. Application of the verified criteria resulted in rescoring 80.8% of reported variants of uncertain significance (VUS) to benign and likely benign. Among 97 novel variants, none met pathogenic criteria. A large proportion of novel variants (84.5%) remained as VUS, while only 10.3% were likely pathogenic. Detection of these novel variants in additional individuals would facilitate their classification. CONCLUSION: Proper interpretation of mt-tRNA variants is crucial for accurate clinical diagnosis and genetic counseling. Correlations with tissue distribution, heteroplasmy levels, predicted perturbations to tRNA structure, and phenotypes provide important evidence for determining the clinical significance of mt-tRNA variants.

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.

Assessing Physical Stability Risk Using the Amorphous Classification System (ACS) Based on Simple Thermal Analysis.

The purpose of this study is to develop a classification system utilizing milligram amounts of the compound for physical stability ranking of amorphous pharmaceuticals, which can be used as an early risk assessment tool for amorphous solid dispersion formulations. Simple thermal analysis utilizing a differential scanning calorimeter is used to characterize amorphous pharmaceuticals with respect to their molecular mobility and configurational entropy. Molecular mobility and configurational entropy are considered as two critical factors in determining the physical stability of amorphous phases. Theoretical arguments and numerical simulations suggest that the fragility strength parameter is a good indicator of the molecular mobility below Tg, and the heat capacity change at Tg is a good indicator of the configurational entropy. Using these two indicators, 40 structurally diverse pharmaceuticals with known physical stability were analyzed. Four classes of compounds are defined with class I being the most stable and class IV the least stable. The proposed amorphous classification system and methodology for estimating molecular mobility and configurational entropy provides an easily accessible framework to conduct early risk assessments related to physical stability challenges in developing amorphous formulations.

[Self-design and prevention potential for older people in institutional long-term care]. / Selbstgestaltungs- und Präventionspotenziale hochaltriger Menschen in der stationären Langzeitversorgung.

Healthcare in inpatient long-term care facilities (nursing homes) should not be limited to medical curative measures, but should also include strengthening social participation, autonomy, self-responsibility and joint responsibility of the residents. Prevention and rehabilitation should therefore be even more integrated into care concepts.This article first introduces various areas of prevention physical activity, nutrition, cognitive competence, psychosocial health, abuse, and freedom-removing measures and then discusses their evidence. Essential for the implementation and the success of such measures is the ability and willingness of people in need of care to engage actively in these therapies; here, appropriate and motivating information plays an important role.Subsequently, geriatric rehabilitation is referred to. In the 2013-2017 empirical study Organization and Rehabilitation for Residents in the Nursing Home to Improve Independence and Participation (ORBIT), 215 people in need of care participated in three-month therapeutic interventions, which were followed by three-months of rehabilitative care. Improvements in mobility and quality of life (Barthel index, QOL-AD) could be demonstrated compared to a control group (n = 28). The results have to be considered against the background of a worsening health and reduced functional capacities in old age. A stronger integration of prevention and rehabilitation services into long-term institutional care is functional for strengthening participation and independence - an important condition for the residents' certainty that their dignity will be respected, competence and strive for self-responsibility and self-determination.

Slo3 K+ channel blocker clofilium extends bull and mouse sperm-fertilizing competence.

For artificial insemination (AI) to be successful, it is essential that sperm delivery be perfectly timed relative to ovulation, as sperm lifespan is limited due to oxidative metabolism induced by capacitation. Extending the window of sperm capacitation could therefore increase sperm lifespan, prolong sperm-fertilizing competence and increase AI efficiency. Hyperpolarization of sperm is a crucial step in capacitation and is induced by activation of the potassium calcium-activated channel subfamily U member 1 (KCNU1, also named Slo3 or KSper). Given the essential role played by KCNU1 in capacitation, this study assessed the impact of its pharmacological inhibition on sperm lifespan. We showed that treatment of murine sperm with sub-micromolar concentrations of clofilium, a specific inhibitor of KCNU1, slowed down capacitation, decreased the rate of acrosome reaction and extended the fertilizing competence of capacitated sperm for 12 h. Clofilium also extended fertilizing competence and motility of bovine-capacitated sperm, and increased the rate of fertilization with sperm capacitated for 24 h by 100%, and the rate of blastocyst formation by 150%. Finally, toxicity experiments showed clofilium to have no impact on sperm DNA and no embryotoxicity at the concentration used to extend sperm lifespan. Our results demonstrate that clofilium prolongs fertilizing competence of aging capacitated sperm in vitro in both rodent and bovine species. To our knowledge, this is the first time the duration of sperm-fertilizing competence is shown to be extended by potassium channels blockers.

[Sexual Abuse of Minors: Development in Light Field Statistics and Dark Field Research Since 1953 and Implications For The Health Care System]. / Sexueller Missbrauch an Kindern ­ Entwicklungen im Hell- und Dunkelfeld seit 1953 und Implikationen für das Gesundheitswesen.

Data on sexual abuse of minors can be obtained from official Police Crime Statistics and from dark field surveys. This article deals with the longitudinal development of the offense in the last 63 years in Germany. The criminal offenses of sexual abuse of children according to § 176 StGB (German Criminal Code) in the Police Crime Statistics show a decrease of frequency in the reporting period (1953-2016). The empirical results of the dark field research are inconsistent, but partially show a decline in frequency. In this study, the importance of these findings for prevention and health policy is discussed.

New methods for high-accuracy insect chitin measurement.

BACKGROUND: There is a growing interest in the use of insects in poultry, swine and aquaculture feed, as well as pet food applications. All insects produce chitin-based exoskeletons. With regard to chitin content, a precise determination in agricultural applications is crucial because it has favorable functional properties, although it is also difficult to digest for some species of livestock. Three measurement methods were compared to determine the most reliable method of chitin content determination in different insects and selected Hermetia illucens products: acid detergent fiber (ADF) provides the fiber content and the acid detergent lignin (ADL) additionally considers the catecholic compounds. Acetyl group measurement relates the acetate content to the chitin content. RESULTS: Comparing different insect species, the highest chitin value via ADF measurement was determined for the Tenebrio molitor larvae (155 g kg-1 ). Chitin values higher than 200 g kg-1 revealed that H. illucens residues are a much better valuable source of chitin. For the larval exoskeletons, a chitin content for all measurement methods of more than 350 g kg-1 was determined. In general, the ADF measurement is approximately 5% higher than the ADF-ADL and acetyl measurements. ADF-ADL and acetyl group determinations are approximately equivalent measurement methods. CONCLUSION: According to statistical analysis, ADF-ADL represents a compromise between accuracy and equipment demand and is a suitable method for determining the chitin content of both insects and their residues. © 2018 Society of Chemical Industry.

Spermaurin, an La1-like peptide from the venom of the scorpion Scorpio maurus palmatus, improves sperm motility and fertilization in different mammalian species.

STUDY QUESTION: Is it possible to identify original compounds that are able to enhance sperm motility from the venom of the scorpion Scorpio maurus palmatus? SUMMARY ANSWER: We identified a potent disulfide-rich peptide (DRP) of 73 amino acids that significantly improved the motility of fresh and frozen-thawed sperm in different mammalian species, including human, and improved fertilization outcome in mouse IVF experiments. WHAT IS KNOWN ALREADY: Any disturbance of sperm motility has a strong impact on fertilization and can lead to subfertility or infertility. Significant efforts have, therefore,  been made to identify pharmacological drugs that might improve sperm motility. Such compounds are particularly useful in azoospermia to improve testicular sperm extraction and in the domain of cryopreservation because the motility of frozen-thawed sperm is reduced. STUDY DESIGN, SIZE, DURATION: This was a basic science/medical research study aimed at identifying original compounds from a library of venoms able to enhance mammalian sperm motility, including human. We first identified in the venom of a scorpion S. m. palmatus a fraction able to potently activate sperm motility. We next purified and characterized the compound by liquid chromatography, mass spectrometry and peptide synthesis. Finally, the potency and toxicity of both purified and synthetic versions of the identified compound on sperm motility were assessed using different in vitro tests in different mammalian species. PARTICIPANTS/MATERIALS, SETTING, METHODS: For human sperm, biological samples were collected from normozoospermic donors and subfertile patients attending a reproduction department for diagnostic semen analysis. Testicular sperm was collected from cynomolgus monkeys (Macaca fascicularis) euthanized for the needs of specific authorized research projects. The peptide was also tested on bovine and mouse epidydimal sperm. We measured different sperm motility parameters with a computer-assisted sperm analysis system in the presence or absence of the peptide. MAIN RESULTS AND THE ROLE OF CHANCE: Size exclusion chromatography enabled us to isolate a fraction of the venom of S. m. palmatus able to increase sperm motility. By liquid chromatography and mass spectrometry, a peptide comprising 73 amino acids with 4 disulfide bridges was identified as responsible for the biological activity and called 'spermaurin'. The identity of spermaurin was confirmed by chemical synthesis. We showed that the peptide increased the motility of fresh and frozen-thawed human sperm. We observed that the potency of the peptide was higher on fresh ejaculated spermatozoa with a low motility, achieving a 100% increase of curvilinear velocity in poorly performing sperm. We also demonstrated that peptide is effective on bovine and mouse fresh epididymal, bovine frozen-thawed ejaculated and fresh non-human primate testicular sperm. Finally, in mouse IVF, the production of 2-cell embryos was increased by 24% when sperm were treated with the peptide. LIMITATIONS, REASONS FOR CAUTION: This work is an in vitro evaluation of the ability of spermaurin to improve sperm motility parameters. Another limitation of this study is the small number of human sperm samples tested with the natural (n = 36) and synthetic (n = 12) peptides. Moreover, the effect of the peptide on IVF outcome was only tested in mouse and further tests with human and bovine gametes are required to confirm and extend this result in other mammalian species. WIDER IMPLICATIONS OF THE FINDINGS: This work confirms our initial study showing that venoms represent an interesting source of molecules that are able to modify sperm physiology. Moreover, this work presents the first demonstrated biological action of a venom peptide from the scorpion S. m. palmatus with sequence similarities to La1 peptide from Liocheles australasiae (Wood scorpion), a widespread family of DRPs. LARGE SCALE DATA: Not applicable. STUDY FUNDING/COMPETING INTEREST(S): This work is part of the project 'LAB COM-14 LAB7 0004 01-LIPAV', funded by the program LabCom 2014 from the French Research Agency (ANR). Dr Arnoult reports grants from IMV Technologies during the conduct of the study. In addition, Drs Arnoult, Martinez, Ray and Schmitt have a patent EP16305642.7 pending containing some of the information presented in this manuscript.

The next generation of population-based spinal muscular atrophy carrier screening: comprehensive pan-ethnic SMN1 copy-number and sequence variant analysis by massively parallel sequencing.

PURPOSE: To investigate pan-ethnic SMN1 copy-number and sequence variation by hybridization-based target enrichment coupled with massively parallel sequencing or next-generation sequencing (NGS). METHODS: NGS reads aligned to SMN1 and SMN2 exon 7 were quantified to determine the total combined copy number of SMN1 and SMN2. The ratio of SMN1 to SMN2 was calculated based on a single-nucleotide difference that distinguishes the two genes. SMN1 copy-number results were compared between the NGS and quantitative polymerase chain reaction and/or multiplex ligation-dependent probe amplification. The NGS data set was also queried for the g.27134T>G single-nucleotide polymorphism (SNP) and other SMN1 sequence pathogenic variants. RESULTS: The sensitivity of the test to detect spinal muscular atrophy (SMA) carriers with one copy of SMN1 was 100% (95% confidence interval (CI): 95.9-100%; n = 90) and specificity was 99.6% (95% CI: 99.4-99.7%; n = 6,648). Detection of the g.27134T>G SNP by NGS was 100% concordant with an restriction fragment-length polymorphism method (n = 493). Ten single-nucleotide variants in SMN1 were detectable by NGS and confirmed by gene-specific amplicon-based sequencing. This comprehensive approach yielded SMA carrier detection rates of 90.3-95.0% in five ethnic groups studied. CONCLUSION: We have developed a novel, comprehensive SMN1 copy-number and sequence variant analysis method by NGS that demonstrated improved SMA carrier detection rates across the entire population examined.Genet Med advance online publication 19 January 2017.