Novel genes and sex differences in COVID-19 severity.

Here, we describe the results of a genome-wide study conducted in 11 939 coronavirus disease 2019 (COVID-19) positive cases with an extensive clinical information that were recruited from 34 hospitals across Spain (SCOURGE consortium). In sex-disaggregated genome-wide association studies for COVID-19 hospitalization, genome-wide significance (P < 5 × 10-8) was crossed for variants in 3p21.31 and 21q22.11 loci only among males (P = 1.3 × 10-22 and P = 8.1 × 10-12, respectively), and for variants in 9q21.32 near TLE1 only among females (P = 4.4 × 10-8). In a second phase, results were combined with an independent Spanish cohort (1598 COVID-19 cases and 1068 population controls), revealing in the overall analysis two novel risk loci in 9p13.3 and 19q13.12, with fine-mapping prioritized variants functionally associated with AQP3 (P = 2.7 × 10-8) and ARHGAP33 (P = 1.3 × 10-8), respectively. The meta-analysis of both phases with four European studies stratified by sex from the Host Genetics Initiative (HGI) confirmed the association of the 3p21.31 and 21q22.11 loci predominantly in males and replicated a recently reported variant in 11p13 (ELF5, P = 4.1 × 10-8). Six of the COVID-19 HGI discovered loci were replicated and an HGI-based genetic risk score predicted the severity strata in SCOURGE. We also found more SNP-heritability and larger heritability differences by age (<60 or ≥60 years) among males than among females. Parallel genome-wide screening of inbreeding depression in SCOURGE also showed an effect of homozygosity in COVID-19 hospitalization and severity and this effect was stronger among older males. In summary, new candidate genes for COVID-19 severity and evidence supporting genetic disparities among sexes are provided.

Germline mutations in WNK2 could be associated with serrated polyposis syndrome.

BACKGROUND: Patients with serrated polyposis syndrome (SPS) have multiple and/or large serrated colonic polyps and higher risk for colorectal cancer. SPS inherited genetic basis is mostly unknown. We aimed to identify new germline predisposition factors for SPS by functionally evaluating a candidate gene and replicating it in additional SPS cohorts. METHODS: After a previous whole-exome sequencing in 39 SPS patients from 16 families (discovery cohort), we sequenced specific genes in an independent validation cohort of 211 unrelated SPS cases. Additional external replication was also available in 297 SPS cases. The WNK2 gene was disrupted in HT-29 cells by gene editing, and WNK2 variants were transfected using a lentiviral delivery system. Cells were analysed by immunoblots, real-time PCR and functional assays monitoring the mitogen-activated protein kinase (MAPK) pathway, cell cycle progression, survival and adhesion. RESULTS: We identified 2 rare germline variants in the WNK2 gene in the discovery cohort, 3 additional variants in the validation cohort and 10 other variants in the external cohorts. Variants c.2105C>T (p.Pro702Leu), c.4820C>T (p.Ala1607Val) and c.6157G>A (p.Val2053Ile) were functionally characterised, displaying higher levels of phospho-PAK1/2, phospho-ERK1/2, CCND1, clonogenic capacity and MMP2. CONCLUSION: After whole-exome sequencing in SPS cases with familial aggregation and replication of results in additional cohorts, we identified rare germline variants in the WNK2 gene. Functional studies suggested germline WNK2 variants affect protein function in the context of the MAPK pathway, a molecular hallmark in this disease.

Tcf20 deficiency is associated with increased liver fibrogenesis and alterations in mitochondrial metabolism in mice and humans.

BACKGROUND & AIMS: Transcription co-activator factor 20 (TCF20) is a regulator of transcription factors involved in extracellular matrix remodelling. In addition, TCF20 genomic variants in humans have been associated with impaired intellectual disability. Therefore, we hypothesized that TCF20 has several functions beyond those described in neurogenesis, including the regulation of fibrogenesis. METHODS: Tcf20 knock-out (Tcf20-/- ) and Tcf20 heterozygous mice were generated by homologous recombination. TCF20 gene genotyping and expression was assessed in patients with pathogenic variants in the TCF20 gene. Neural development was investigated by immufluorescense. Mitochondrial metabolic activity was evaluated with the Seahorse analyser. The proteome analysis was carried out by gas chromatography mass-spectrometry. RESULTS: Characterization of Tcf20-/- newborn mice showed impaired neural development and death after birth. In contrast, heterozygous mice were viable but showed higher CCl4 -induced liver fibrosis and a differential expression of genes involved in extracellular matrix homeostasis compared to wild-type mice, along with abnormal behavioural patterns compatible with autism-like phenotypes. Tcf20-/- embryonic livers and mouse embryonic fibroblast (MEF) cells revealed differential expression of structural proteins involved in the mitochondrial oxidative phosphorylation chain, increased rates of mitochondrial metabolic activity and alterations in metabolites of the citric acid cycle. These results parallel to those found in patients with TCF20 pathogenic variants, including alterations of the fibrosis scores (ELF and APRI) and the elevation of succinate concentration in plasma. CONCLUSIONS: We demonstrated a new role of Tcf20 in fibrogenesis and mitochondria metabolism in mice and showed the association of TCF20 deficiency with fibrosis and metabolic biomarkers in humans.

Consolidation of the clinical and genetic definition of a SOX4-related neurodevelopmental syndrome.

BACKGROUND: A neurodevelopmental syndrome was recently reported in four patients with SOX4 heterozygous missense variants in the high-mobility-group (HMG) DNA-binding domain. The present study aimed to consolidate clinical and genetic knowledge of this syndrome. METHODS: We newly identified 17 patients with SOX4 variants, predicted variant pathogenicity using in silico tests and in vitro functional assays and analysed the patients' phenotypes. RESULTS: All variants were novel, distinct and heterozygous. Seven HMG-domain missense and five stop-gain variants were classified as pathogenic or likely pathogenic variant (L/PV) as they precluded SOX4 transcriptional activity in vitro. Five HMG-domain and non-HMG-domain missense variants were classified as of uncertain significance (VUS) due to negative results from functional tests. When known, inheritance was de novo or from a mosaic unaffected or non-mosaic affected parent for patients with L/PV, and from a non-mosaic asymptomatic or affected parent for patients with VUS. All patients had neurodevelopmental, neurological and dysmorphic features, and at least one cardiovascular, ophthalmological, musculoskeletal or other somatic anomaly. Patients with L/PV were overall more affected than patients with VUS. They resembled patients with other neurodevelopmental diseases, including the SOX11-related and Coffin-Siris (CSS) syndromes, but lacked the most specific features of CSS. CONCLUSION: These findings consolidate evidence of a fairly non-specific neurodevelopmental syndrome due to SOX4 haploinsufficiency in neurogenesis and multiple other developmental processes.

Experimental and Bioinformatic Insights into the Effects of Epileptogenic Variants on the Function and Trafficking of the GABA Transporter GAT-1.

In this article, we identified a novel epileptogenic variant (G307R) of the gene SLC6A1, which encodes the GABA transporter GAT-1. Our main goal was to investigate the pathogenic mechanisms of this variant, located near the neurotransmitter permeation pathway, and compare it with other variants located either in the permeation pathway or close to the lipid bilayer. The mutants G307R and A334P, close to the gates of the transporter, could be glycosylated with variable efficiency and reached the membrane, albeit inactive. Mutants located in the center of the permeation pathway (G297R) or close to the lipid bilayer (A128V, G550R) were retained in the endoplasmic reticulum. Applying an Elastic Network Model, to these and to other previously characterized variants, we found that G307R and A334P significantly perturb the structure and dynamics of the intracellular gate, which can explain their reduced activity, while for A228V and G362R, the reduced translocation to the membrane quantitatively accounts for the reduced activity. The addition of a chemical chaperone (4-phenylbutyric acid, PBA), which improves protein folding, increased the activity of GAT-1WT, as well as most of the assayed variants, including G307R, suggesting that PBA might also assist the conformational changes occurring during the alternative access transport cycle.

Colorectal cancer genetic variants are also associated with serrated polyposis syndrome susceptibility.

BACKGROUND: Serrated polyposis syndrome (SPS) is a clinical entity characterised by large and/ormultiple serrated polyps throughout the colon and increased risk for colorectal cancer (CRC). The basis for SPS genetic predisposition is largely unknown. Common, low-penetrance genetic variants have been consistently associated with CRC susceptibility, however, their role in SPS genetic predisposition has not been yet explored. OBJECTIVE: The aim of this study was to evaluate if common, low-penetrance genetic variants for CRC risk are also implicated in SPS genetic susceptibility. METHODS: A case-control study was performed in 219 SPS patients and 548 asymptomatic controls analysing 65 CRC susceptibility variants. A risk prediction model for SPS predisposition was developed. RESULTS: Statistically significant associations with SPS were found for seven genetic variants (rs4779584-GREM1, rs16892766-EIF3H, rs3217810-CCND2, rs992157-PNKD1/TMBIM1, rs704017-ZMIZ1, rs11196172-TCF7L2, rs6061231-LAMA5). The GREM1 risk allele was remarkably over-represented in SPS cases compared with controls (OR=1.573, 1.21-2.04, p value=0.0006). A fourfold increase in SPS risk was observed when comparing subjects within the highest decile of variants (≥65) with those in the first decile (≤50). CONCLUSIONS: Genetic variants for CRC risk are also involved in SPS susceptibility, being the most relevant ones rs4779584-GREM1, rs16892766-EIF3H and rs3217810-CCND2.

Functional analysis of new variants at the low-density lipoprotein receptor associated with familial hypercholesterolemia.

Familial hypercholesterolemia is an autosomal dominant disease of lipid metabolism caused by defects in the genes LDLR, APOB, and PCSK9. The prevalence of heterozygous familial hypercholesterolemia (HeFH) is estimated between 1/200 and 1/250. Early detection of patients with FH allows initiation of treatment, thus reducing the risk of coronary heart disease. In this study, we performed in vitro characterization of new LDLR variants found in our patients. Genetic analysis was performed by Next Generation Sequencing using a customized panel of 198 genes in DNA samples of 516 subjects with a clinical diagnosis of probable or definitive FH. All new LDLR variants found in our patients were functionally validated in CHO-ldlA7 cells. The LDLR activity was measured by flow cytometry and LDLR expression was detected by immunofluorescence. Seven new variants at LDLR were tested: c.518 G>C;p.(Cys173Ser), c.[684 G>T;694 G>T];p.[Glu228Asp;Ala232Ser], c.926C>A;p.(Pro309His), c.1261A>G;p.(Ser421Gly), c.1594T>A;p.(Tyr532Asn), and c.2138delC;p.(Thr713Lysfs*17). We classified all variants as pathogenic except p.(Ser421Gly) and p.(Ala232Ser). The functional in vitro characterization of rare variants at the LDLR is a useful tool to classify the new variants. This approach allows us to confirm the genetic diagnosis of FH, avoiding the classification as "uncertain significant variants", and therefore, carry out cascade family screening.

[Genomic newborn screening. Perspective from the Ethics commission of the Spanish Society for Human Genetics. Part I. Next generation sequencing technologies applied to newborn screening. Challenges and opportunities.] / Cribado neonatal genómico. Perspectiva de la Comisión de ética de la Asociación Española de Genética Humana. Parte I. Las tecnologías de secuenciación masiva (NGS) y su aplicación al cribado neonatal. Desafíos y oportunidades.

In 2003 at the ending of the Human Genome Project, it aroused the idea that all newborns could be sequenced and its genome archived in the clinical record, in order to manage risks of diseases and response to medicaments along his whole life. Eighteen years later, promises of genomic medicine and tremendous decrease of costs of next generation sequencing technologies, continues feeding this dream that shows important practical, ethical and social challenges and genomic sequencing is presented as the next historical change in newborn screening programs. In this paper we analyze challenges and opportunities of next generation sequencing technologies, their real costs, problems associated to management, storage and protection of the enormous amount of genomic data produced and finally, according to conclusions of recent researches, there are considered the conclusions in two contexts, sick newborn with diagnostic purposes and healthy asymptomatic newborns with public health purposes (newborn screening programs). In a second part of this article it will be considered ethical, legal and social issues (ELSI). Final objective is to contribute to scientific, professional, ethics and social debate in order to promote that genome sequencing in newborn don't be used indiscriminately constituting a risk, but properly done, as a partner in the promotion of health and prevention of consequences of genetic diseases.

En 2003, cuando finalizó el Proyecto Genoma Humano, surgió la idea de secuenciar el genoma a todos los recién nacidos, archivarlo en la historia clínica y usarlo a lo largo de toda la vida para manejar riesgos de enfermedades y respuesta a medicamentos. Dieciocho años más tarde, las promesas de la medicina genómica y el extraordinario abaratamiento de las tecnologías secuenciadoras, siguen alimentando este sueño que todavía plantea grandes desafíos prácticos, éticos y sociales y la secuenciación genómica se presenta como el próximo gran cambio histórico en los programas de cribado neonatal. En el presente artículo, se analizan los retos y oportunidades de las tecnologías secuenciadoras de nueva generación, sus costos reales, la problemática inherente a la gestión, almacenamiento y protección de la enorme cantidad de datos genómicos que generan y finalmente, en base a las conclusiones de investigaciones recientes, se considera el potencial y limitaciones de su aplicación en dos escenarios, el recién nacido enfermo con finalidades diagnósticas y el recién nacido sano, asintomático, con finalidades de salud pública(programas de cribado neonatal). En una segunda parte de este artículo se tendrán en cuenta los aspectos éticos, legales y sociales (AELS). El objetivo final es contribuir al debate científico, profesional, ético y social, promoviendo que la secuenciación genómica en el recién nacido no sea usada indiscriminadamente constituyendo un riesgo, sino que bien empleada sea una aliada en la promoción de la salud y prevención de las consecuencias de las enfermedades genéticas.

[Genomic newborn screening. Perspective from the Ethics Commission of the Spanish Society for Human Genetics. Part II: Ethical, legal and social issues (ELSIs) of the introduction of next generation sequencing technologies in a public health newborn screening program.] / Cribado neonatal genómico. Perspectiva de la Comisión de ética de la Asociación Española de Genética Humana. Parte II: Aspectos Éticos, Legales y Sociales (AELS) de la Introducción de las Tecnologías de Secuenciación Masiva (NGS) en un programa de cribado neonatal de Salud Pública.

Genome sequencing is a very attractive technology as it is also the idea of sequencing children at birth, with the aim to establish medical care and preventive actions during their whole life, tailored to the genome of each newborn. Part I of this article analyses limitations and opportunities of next generation sequencing technologies (NGS). Part II relates scientific knowledge with ethical, legal and social issues (ELSIs) concerning its application to a newborn screening program. This program is offered universally to a vulnerable and asymptomatic population and must be guided by principles of "do not harm" and to act in the "best interest of child". With this purpose, this article considers, first of all, ethical principles of bioethics and public health that govern newborn screening. Then it summarizes main issues of our legal framework. And finally, in social context, it analyzes influences of technological imperative, commercial actors and patient´s advocacy groups, as well as parent's perspective and psychosocial aspects. In this context, conclusion is that whole genome sequencing should not be implemented as universal newborn screening. Nevertheless, the use of NGS could be an opportunity to extend these programs, including treatable infantile diseases that cannot be detected with other technologies. That means realizing a directed approach in order to identify well known genomic variants, highly penetrant, that confer a high risk of preventable or treatable diseases for which treatment must begin at the neonatal period. The implementation of such directed genomic screening should follow current evidence based model for newborn screening. This model shows three features: recognition of the importance of the evaluation of empirical, epidemiological and clinical data before taking the decision to include a disease; evaluation of benefits and risks (proportionality) and evaluation of benefits and costs (distributive justice); and finally, consideration of public consensus, because this kind of decisions have a value that concerns society as a whole.

La secuenciación genómica es una tecnología extraordinariamente atractiva, tanto como lo es la idea de poder aplicarla a todos los recién nacidos, estableciendo con ello una etapa de cuidados médicos para toda la vida y acciones preventivas a medida del genoma de cada niño. En la parte I de este artículo se analizaron las limitaciones y oportunidades que presentan las tecnologías de secuenciación de nueva generación (NGS). La parte II relaciona el conocimiento científico con los aspectos éticos, legales y sociales (AELS) de su introducción en un programa de cribado neonatal de salud pública de aplicación universal a población vulnerable y asintomática, que debe ser guiada por los principios fundamentales de "no hacer daño" y de actuar "en el mejor interés del niño". Para ello se contemplan en primer lugar los principios éticos de la medicina y de la salud pública que rigen el cribado neonatal, a continuación se resumen los principales aspectos de nuestro marco legal al respecto y finalmente en el ámbito social se analizan la influencia del imperativo tecnológico, la de los actores comerciales, los grupos de apoyo de pacientes y por último la perspectiva de los padres y aspectos psicosociales. Las conclusiones son que en este contexto la secuenciación genómica completa no debe ser implementada como cribado neonatal universal, sin embargo el uso de las NGS podría ser una oportunidad para ampliar los programas incluyendo enfermedades infantiles tratables que no pudiesen ser detectadas con otros métodos. Realizando para ello una aproximación dirigida a enfermedades/genes concretos, a fin de identificar variantes genómicas bien conocidas, altamente penetrantes confiriendo riesgo elevado de enfermedad prevenible o tratable, para la cual el tratamiento deba iniciarse en el periodo neonatal. Su incorporación al cribado neonatal debería seguir el modelo actual basado en la evidencia, evaluando los datos empíricos, epidemiológicos y clínicos antes de tomar una decisión sobre la inclusión de una enfermedad, así como los beneficios y riesgos (proporcionalidad) y si los beneficios justifican los costes (justicia distributiva), tomando en consideración el consenso público en tanto que las decisiones tienen una carga de valores que conciernen a la sociedad en su conjunto.

Case report: A novel case of parental mosaicism in SMC1A gene causes inherited Cornelia de Lange syndrome.

Ultimate advances in genetic technologies have permitted the detection of transmitted cases of congenital diseases due to parental gonadosomatic mosaicism. Regarding Cornelia de Lange syndrome (CdLS), up to date, only a few cases are known to follow this inheritance pattern. However, the high prevalence of somatic mosaicism recently reported in this syndrome (∼13%), together with the disparity observed in tissue distribution of the causal variant, suggests that its prevalence in this disorder could be underestimated. Here, we report a new case of parental gonadosomatic mosaicism in SMC1A gene that causes inherited CdLS, in which the mother of the patient carries the causative variant in very low allele frequencies in buccal swab and blood. While the affected child presents with typical CdLS phenotype, his mother does not show any clinical manifestations. As regards SMC1A, the difficulty of clinical identification of carrier females has been already recognized, as well as the gender differences observed in CdLS expressivity when the causal variant is found in this gene. Currently, the use of DNA deep-sequencing techniques is highly recommended when it comes to molecular diagnosis of patients, as well as in co-segregation studies. These enable us to uncover gonadosomatic mosaic events in asymptomatic or oligosymptomatic parents that had been overlooked so far, which might have great implications regarding genetic counseling for recurrence risk.

[Half a century of newborn screening in Spain: Evolution of ethical, legal and social issues (ELSIs). Part III, social issues.] / Medio siglo de cribado neonatal en España: evolución de los aspectos éticos, legales y sociales (AELS). Parte III, aspectos sociales.

Decision making for the development of newborn screening programs is based on not only medical but also social concerns and involves different stakeholders. Part III of the article focuses on their role in the governance of the programs. First of all, we consider the proactive role that health authorities has played in the evolution to an evidentiary model of policy development currently based on evidence, just as in the preparation of an expert, impartial and transparent opinion on health policy and its coordination with the national health system. And, in accordance with this evidence and with the consensus, health autorities following quality criteria have made an attempt to achieve a more homogeneous approach of the neonatal screening program throughout the territory. Secondly, we address the role of several scientific and professional societies in newborn screening. Among them, it deserves to be mentioned the Spanish Society for Clinical Chemistry, currently Spanish Society of Laboratory Medicine (SEQCML), and its Commission of inborn errors of metabolism and the Spanish Society for Newborn Screening (AECNE), which since 1985 and for thirty three years collected the activity of newborn screening centers and established a forum for debate, sharing of knowledge and cooperation among screening centers and with health authorities. Since 1999, the Spanish Society for Inborn Errors of Metabolism (AECOM) exercises an important activity in the field of diagnosis treatment and follow up of patients. Finally, we consider the role of families and the psychosocial aspects of the programme, and the associative activity of patient organizations. In 1990 the Spanish federation of PKU and other disorders (FAEPKU) was found, renamed currently as The Spanish Federation of Inherited Metabolic Diseases; together with the Spanish Federation for Rare Diseases (FEDER), found in 1999, they both have clearly contributed to the patient's empowerment, supporting research and education and establishing a network of cooperation and support for patients and their families. Patient organizations collaborate with health authorities but they have not participated in policy decision making yet. During this half century, the evolution of newborn screening programs have been characterized for a spirit of improvement, by including the development of ethical, legal and social issues. Important technological challenges lie ahead and it will be necessary to know how to use them efficiently, proportionally and fairly in the best interest of newborns and by extension of their family and society.

Las bases para la toma de decisiones acerca del desarrollo de los programas de cribado de Salud Pública no son exclusivamente médicas, sino también sociales. En esta parte III del artículo se contemplan los actores que intervienen en la gobernanza de los programas, cómo son las autoridades sanitarias, las sociedades científicas y profesionales, así como las familias y su movimiento asociativo. En primer lugar, se analiza el papel de las instituciones/autoridades sanitarias en el desarrollo de los programas y en la evolución del modelo para la toma de decisiones, hasta el actual basado en la evidencia, así como en la elaboración de una opinión experta, imparcial y transparente en política sanitaria y su coordinación en el marco del Sistema Nacional de Salud (SNS). Y, de acuerdo con dicha evidencia y con el consenso, las instituciones/autoridades sanitarias han tratado de conseguir un abordaje más homogéneo y conforme a criterios de calidad del programa de cribado neonatal en todo el territorio. A continuación, se aborda el papel de las sociedades científicas y profesionales, especialmente de la Sociedad Española de Química Clínica (actualmente Sociedad Española de Medicina de Laboratorio (SEQCML), a través de la Comisión de Errores Congénitos del Metabolismo, y de la Asociación Española de Cribado Neonatal (AECNE), que desde 1985 y durante 33 años recogieron los datos de actividad de los centros de cribado y establecieron un foro de debate, intercambio de conocimientos y colaboración entre ellos y con las autoridades sanitarias. De ellas, destaca el importante papel de la Asociación Española de Errores Congénitos del Metabolismo (AECOM) desde 1999 en el diagnóstico, seguimiento y tratamiento de los pacientes. Finalmente, se contempla el papel de las familias y los aspectos psicosociales del programa, así como la evolución del movimiento asociativo, con especial mención a la fundación en 1990 de la Federación Española de PKU y otros trastornos (FAEPKU) (que pasó después a llamarse la Federación Española de Enfermedades Metabólicas Hereditarias) y en 1999 de la Federación Española de Enfermedades Raras (FEDER). Estas asociaciones han contribuido notablemente al empoderamiento de los pacientes, a apoyar la investigación y la formación y a establecer una red de colaboración y soporte para los pacientes y sus familias. Y aunque están en contacto y colaboran con las autoridades sanitarias, hasta el momento no han participado en la elaboración de decisiones y en la gobernanza de los programas. El espíritu de superación y mejora ha marcado la evolución de los programas durante este medio siglo al incluir el desarrollo de sus aspectos éticos, legales y sociales. Se avecinan desafíos tecnológicos importantes y habrá que saber utilizarlos con eficiencia, proporcionalidad y justicia en el mejor interés del niño y, por extensión, de la familia y de la sociedad.

Germline and Somatic Whole-Exome Sequencing Identifies New Candidate Genes Involved in Familial Predisposition to Serrated Polyposis Syndrome.

The serrated polyposis syndrome (SPS) is the most common and yet underdiagnosed colorectal polyposis syndrome. It is characterized by multiple and/or large colonic serrated polyps and a higher associated risk for colorectal cancer (CRC). The main objective of this study was to identify new candidate genes involved in the germline predisposition to SPS/CRC. Thirty-nine SPS patients from 16 families (≥2 patients per family) were recruited without alterations in well-known hereditary CRC genes, and germline and somatic whole-exome sequencing were performed. Germline rare variants with plausible pathogenicity, located in genes involved in cancer development, senescence and epigenetic regulation were selected. Somatic mutational profiling and signature analysis was pursued in one sample per family, when possible. After data filtering, ANXA10, ASXL1, CFTR, DOT1L, HIC1, INO80, KLF3, MCM3AP, MCM8, PDLIM2, POLD1, TP53BP1, WNK2 and WRN were highlighted as the more promising candidate genes for SPS germline predisposition with potentially pathogenic variants shared within families. Somatic analysis characterized mutational profiles in advanced serrated polyps/tumors, revealing a high proportion of hypermutated samples, with a prevalence of clock-like mutational signatures in most samples and the presence of DNA mismatch repair-defective signatures in some cases. In conclusion, we identified new candidate genes to be involved in familial SPS. Further functional studies and replication in additional cohorts are required to confirm the selected candidates.

Identification of a Novel Candidate Gene for Serrated Polyposis Syndrome Germline Predisposition by Performing Linkage Analysis Combined With Whole-Exome Sequencing.

OBJECTIVES: Serrated polyposis syndrome (SPS) is a complex disorder with a high risk of colorectal cancer for which the germline factors remain largely unknown. Here, we combined whole-exome sequencing (WES) and linkage studies in families with multiple members affected by SPS to identify candidate genes harboring rare variants with higher penetrance effects. METHODS: Thirty-nine affected subjects from 16 extended SPS families underwent WES. Genome-wide linkage analysis was performed under linear and exponential models. The contribution of rare coding variants selected to be highly pathogenic was assessed using the gene-based segregation test. RESULTS: A significant linkage peak was identified on chromosome 3p25.2-p22.3 (maxSNP = rs2293787; LODlinear = 2.311, LODexp = 2.11), which logarithm of the odds (LOD) score increased after fine mapping for the same marker (maxSNP = rs2293787; LODlinear = 2.4, LODexp = 2.25). This linkage signal was replicated in 10 independent sets of random markers from this locus. To assess the contribution of rare variants predicted to be pathogenic, we performed a family-based segregation test with 11 rare variants predicted to be deleterious from 10 genes under the linkage intervals. This analysis showed significant segregation of rare variants with SPS in CAPT7, TMEM43, NGLY1, and FBLN2 genes (weighted P value > 0.007). DISCUSSION: Protein network analysis suggested FBLN2 as the most plausible candidate genes for germline SPS predisposition. Etiologic rare variants implicated in disease predisposition may be identified by combining traditional linkage with WES data. This powerful approach was effective for the identification of a new candidate gene for hereditary SPS.

Role of copy number variants in sudden cardiac death and related diseases: genetic analysis and translation into clinical practice.

Several studies have identified copy number variants (CNVs) as responsible for cardiac diseases associated with sudden cardiac death (SCD), but very few exhaustive analyses in large cohorts of patients have been performed, and they have been generally focused on a specific SCD-related disease. The aim of the present study was to screen for CNVs the most prevalent genes associated with SCD in a large cohort of patients who suffered sudden unexplained death or had an inherited cardiac disease (cardiomyopathy or channelopathy). A total of 1765 European patients were analyzed with a homemade algorithm for the assessment of CNVs using high-throughput sequencing data. Thirty-six CNVs were identified (2%), and most of them appeared to have a pathogenic role. The frequency of CNVs among cases of sudden unexplained death, patients with a cardiomyopathy or a channelopathy was 1.4% (8/587), 2.3% (20/874), and 2.6% (8/304), respectively. Detection rates were particularly high for arrhythmogenic cardiomyopathy (5.1%), long QT syndrome (4.7%), and dilated cardiomyopathy (4.4%). As such large genomic rearrangements underlie a non-neglectable portion of cases, we consider that their analysis should be performed as part of the routine genetic testing of sudden unexpected death cases and patients with SCD-related diseases.

Tetraploidy acute myeloid leukaemia after chromosome 16 inversion.

Our patient is a 36-year-old man referred by his general physician to the Department of Hematology because of mild neutropenia in a routine analysis at work. There was no history of previous diseases, and examination was normal. Blood investigations confirmed the neutropenia and showed elongation of prothrombin time. A bone marrow examination was performed revealing about 10% of myeloblasts on the aspirate smears. A cytogenetic study showed chromosome 16 inversion in all of these cells and tetraploidy only in some of them, which were extremely large in size. According to the revised WHO classification of tumours (2008), the patient was diagnosed as a case of acute myeloid leukaemia with chromosome 16 inversion.

Additional value of screening for minor genes and copy number variants in hypertrophic cardiomyopathy.

INTRODUCTION: Hypertrophic cardiomyopathy (HCM) is the most prevalent inherited heart disease. Next-generation sequencing (NGS) is the preferred genetic test, but the diagnostic value of screening for minor and candidate genes, and the role of copy number variants (CNVs) deserves further evaluation. METHODS: Three hundred and eighty-seven consecutive unrelated patients with HCM were screened for genetic variants in the 5 most frequent genes (MYBPC3, MYH7, TNNT2, TNNI3 and TPM1) using Sanger sequencing (N = 84) or NGS (N = 303). In the NGS cohort we analyzed 20 additional minor or candidate genes, and applied a proprietary bioinformatics algorithm for detecting CNVs. Additionally, the rate and classification of TTN variants in HCM were compared with 427 patients without structural heart disease. RESULTS: The percentage of patients with pathogenic/likely pathogenic (P/LP) variants in the main genes was 33.3%, without significant differences between the Sanger sequencing and NGS cohorts. The screening for 20 additional genes revealed LP variants in ACTC1, MYL2, MYL3, TNNC1, GLA and PRKAG2 in 12 patients. This approach resulted in more inconclusive tests (36.0% vs. 9.6%, p<0.001), mostly due to variants of unknown significance (VUS) in TTN. The detection rate of rare variants in TTN was not significantly different to that found in the group of patients without structural heart disease. In the NGS cohort, 4 patients (1.3%) had pathogenic CNVs: 2 deletions in MYBPC3 and 2 deletions involving the complete coding region of PLN. CONCLUSIONS: A small percentage of HCM cases without point mutations in the 5 main genes are explained by P/LP variants in minor or candidate genes and CNVs. Screening for variants in TTN in HCM patients drastically increases the number of inconclusive tests, and shows a rate of VUS that is similar to patients without structural heart disease, suggesting that this gene should not be analyzed for clinical purposes in HCM.

Pruebas genéticas de venta directa a los consumidores. Perspectiva de la Comisión de Ética de la Asociación Española de Genética Humana / Directed to consumer genetic testing. Perspective from the Ethics commission of the Spanish Society for Human Genetics

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Variabilidad fenotípica del síndrome de Marfan en una familia con una nueva mutación en el gen FBN1 / Phenotypic variability in Marfan syndrome in a family with a novel nonsense FBN1 gene mutation

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