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Contains fulltext : 221455.pdf (publisher's version ) (Open Access)

Background: The VATER/VACTERL association (VACTERL) is defined as the non-random occurrence of the following congenital anomalies: Vertebral, Anal, Cardiac, Tracheal-Esophageal, Renal, and Limb anomalies. As no unequivocal candidate gene has been identified yet, patients are diagnosed phenotypically. The aims of this study were to identify patients with monogenic disorders using a genetics-first approach, and to study whether variants in candidate genes are involved in the etiology of VACTERL or the individual features of VACTERL: Anorectal malformation (ARM) or esophageal atresia with or without trachea-esophageal fistula (EA/TEF). Methods: Using molecular inversion probes, a candidate gene panel of 56 genes was sequenced in three patient groups: VACTERL (n = 211), ARM (n = 204), and EA/TEF (n = 95). Loss-of-function (LoF) and additional likely pathogenic missense variants, were prioritized and validated using Sanger sequencing. Validated variants were tested for segregation and patients were clinically re-evaluated. Results: In 7 out of the 510 patients (1.4%), pathogenic or likely pathogenic variants were identified in SALL1, SALL4, and MID1, genes that are associated with Townes-Brocks, Duane-radial-ray, and Opitz-G/BBB syndrome. These syndromes always include ARM or EA/TEF, in combination with at least two other VACTERL features. We did not identify LoF variants in the remaining candidate genes. Conclusions: None of the other candidate genes were identified as novel unequivocal disease genes for VACTERL. However, a genetics-first approach allowed refinement of the clinical diagnosis in seven patients, in whom an alternative molecular-based diagnosis was found with important implications for the counseling of the families.

Contains fulltext : 221455.pdf (publisher's version ) (Open Access)

Contains fulltext : 205341.pdf (publisher's version ) (Open Access)

Introduction Anorectal malformations (ARM) are rare congenital malformations, resulting from disturbed hindgut development. A genetic etiology has been suggested, but evidence for the involvement of specific genes is scarce. We evaluated the contribution of rare and low-frequency coding variants in ARM etiology, as

Contains fulltext : 205341.pdf (publisher's version ) (Open Access)

Contains fulltext : 205341.pdf (publisher's version ) (Open Access)

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We report numerical results of effective attractive forces on the packing properties of two-dimensional elongated grains. In deposits of non-cohesive rods in 2D, the topology of the packing is mainly dominated by the formation of ordered structures of aligned rods. Elongated particles tend to align horizontally and the stress is mainly transmitted from top to bottom, revealing an asymmetric distribution of local stress. However, for deposits of cohesive particles, the preferred horizontal orientation disappears. Very elongated particles with strong attractive forces form extremely loose structures, characterized by an orientation distribution, which tends to a uniform behavior when increasing the Bond number. As a result of these changes, the pressure distribution in the deposits changes qualitatively. The isotropic part of the local stress is notably enhanced with respect to the deviatoric part, which is related to the gravity direction. Consequently, the lateral stress transmission is dominated by the enhanced disorder and leads to a faster pressure saturation with depth

Contains fulltext : 174787.pdf (publisher's version ) (Open Access), Schinzel-Giedion syndrome (SGS) is a rare developmental disorder characterized by multiple malformations, severe neurological alterations and increased risk of malignancy. SGS is caused by de novo germline mutations clustering to a 12bp hotspot in exon 4 of SETBP1. Mutations in this hotspot disrupt a degron, a signal for the regulation of protein degradation, and lead to the accumulation of SETBP1 protein. Overlapping SETBP1 hotspot mutations have been observed recurrently as somatic events in leukemia. We collected clinical information of 47 SGS patients (including 26 novel cases) with germline SETBP1 mutations and of four individuals with a milder phenotype caused by de novo germline mutations adjacent to the SETBP1 hotspot. Different mutations within and around the SETBP1 hotspot have varying effects on SETBP1 stability and protein levels in vitro and in in silico modeling. Substitutions in SETBP1 residue I871 result in a weak increase in protein levels and mutations affecting this residue are significantly more frequent in SGS than in leukemia. On the other hand, substitutions in residue D868 lead to the largest increase in protein levels. Individuals with germline mutations affecting D868 have enhanced cell proliferation in vitro and higher incidence of cancer compared to patients with other germline SETBP1 mutations. Our findings substantiate that, despite their overlap, somatic SETBP1 mutations driving malignancy are more disruptive to the degron than germline SETBP1 mutations causing SGS. Additionally, this suggests that the functional threshold for the development of cancer driven by the disruption of the SETBP1 degron is higher than for the alteration in prenatal development in SGS. Drawing on previous studies of somatic SETBP1 mutations in leukemia, our results reveal a genotype-phenotype correlation in germline SETBP1 mutations spanning a molecular, cellular and clinical phenotype.

Item does not contain fulltext, De novo, germline variants in DNMT3A cause Tatton-Brown-Rahman syndrome (TBRS). This condition is characterized by overgrowth, distinctive facial appearance, and intellectual disability. Somatic DNMT3A variants frequently occur in hematologic malignances, particularly acute myeloid leukemia. The Arg882 residue is the most common site of somatic DNMT3A variants, and has also been altered in patients with TBRS. Here we present three additional patients with this disorder attributed to DNMT3A germline variants that disrupt the Arg882 codon, suggesting that this codon may be a germline mutation hotspot in this disorder. Furthermore, based on the investigation of previously reported variants in patients with TBRS, we found overlap in the spectrum of DNMT3A variants observed in this disorder and somatic variants in hematological malignancies.

Contains fulltext : 177281.pdf (publisher's version ) (Closed access), Clonal hematopoiesis results from somatic mutations in hematopoietic stem cells, which give an advantage to mutant cells, driving their clonal expansion and potentially leading to leukemia. The acquisition of clonal hematopoiesis-driver mutations (CHDMs) occurs with normal aging and these mutations have been detected in more than 10% of individuals >/=65 years. We aimed to examine the prevalence and characteristics of CHDMs throughout adult life. We developed a targeted re-sequencing assay combining high-throughput with ultra-high sensitivity based on single-molecule molecular inversion probes (smMIPs). Using smMIPs, we screened more than 100 loci for CHDMs in more than 2,000 blood DNA samples from population controls between 20 and 69 years of age. Loci screened included 40 regions known to drive clonal hematopoiesis when mutated and 64 novel candidate loci. We identified 224 somatic mutations throughout our cohort, of which 216 were coding mutations in known driver genes (DNMT3A, JAK2, GNAS, TET2, and ASXL1), including 196 point mutations and 20 indels. Our assay's improved sensitivity allowed us to detect mutations with variant allele frequencies as low as 0.001. CHDMs were identified in more than 20% of individuals 60 to 69 years of age and in 3% of individuals 20 to 29 years of age, approximately double the previously reported prevalence despite screening a limited set of loci. Our findings support the occurrence of clonal hematopoiesis-associated mutations as a widespread mechanism linked with aging, suggesting that mosaicism as a result of clonal evolution of cells harboring somatic mutations is a universal mechanism occurring at all ages in healthy humans.

Radboud University, 8 juni 2017, Promotor : Veltman, J.A. Co-promotores : Hoischen, A., Gilissen, C.F.H.A., Contains fulltext : 173265.pdf (publisher's version ) (Open Access), The work presented in this thesis shows that mutations arise constantly, between one generation and the next but also throughout life. This continuous occurrence of mutations leads to extraordinary genetic diversity between individuals but is also at the origin of the existence of genetically different populations of cells within a single human being. While the occurrence of novel mutations represents an important biological phenomenon in humans with a role on prenatal development, physiology and evolution, novel mutations also contribute to different forms of human disease ranging from rare and severe developmental disorders to adult-onset diseases such as cancer. The work in this thesis supports that in addition to the detection of mutations, NGS can be used as a tool to identify the timing of mutations in order to include the dimension of time in the interpretation of mutations and their possible consequences. De novo mutations have different recurrence risks depending on the exact timing at which they occurred, which can be determined by meticulous analysis with NGS methods. Indeed, genetic mosaicism resulting from mutations occurring during embryogenesis is common and, depending on their timing, postzygotic mutations can be transmitted to the next generation. Additionally, somatic mutations arise in stem cells throughout life and can be detected using highly sensitive sequencing methods. Furthermore, the timing of a mutation can also shape the resulting phenotype, as the same mutation can be involved in different disorders depending on its timing. For instance, overlapping germline and somatic mutations in SETBP1, leading to Schinzel-Giedion syndrome and to myeloid leukemia, respectively. Future work focusing on the role of timing of somatic and germline mutations will provide us with a better understanding of the effect of the expression of a mutation in the dynamic context of a cell, a tissue and a whole organism.

Schinzel-Giedion syndrome (SGS) is a rare developmental disorder characterized by multiple malformations, severe neurological alterations and increased risk of malignancy. SGS is caused by de novo germline mutations clustering to a 12bp hotspot in exon 4 of SETBP1. Mutations in this hotspot disrupt a degron, a signal for the regulation of protein degradation, and lead to the accumulation of SETBP1 protein. Overlapping SETBP1 hotspot mutations have been observed recurrently as somatic events in leukemia. We collected clinical information of 47 SGS patients (including 26 novel cases) with germline SETBP1 mutations and of four individuals with a milder phenotype caused by de novo germline mutations adjacent to the SETBP1 hotspot. Different mutations within and around the SETBP1 hotspot have varying effects on SETBP1 stability and protein levels in vitro and in in silico modeling. Substitutions in SETBP1 residue I871 result in a weak increase in protein levels and mutations affecting this residue are significantly more frequent in SGS than in leukemia. On the other hand, substitutions in residue D868 lead to the largest increase in protein levels. Individuals with germline mutations affecting D868 have enhanced cell proliferation in vitro and higher incidence of cancer compared to patients with other germline SETBP1 mutations. Our findings substantiate that, despite their overlap, somatic SETBP1 mutations driving malignancy are more disruptive to the degron than germline SETBP1 mutations causing SGS. Additionally, this suggests that the functional threshold for the development of cancer driven by the disruption of the SETBP1 degron is higher than for the alteration in prenatal development in SGS. Drawing on previous studies of somatic SETBP1 mutations in leukemia, our results reveal a genotype-phenotype correlation in germline SETBP1 mutations spanning a molecular, cellular and clinical phenotype.

Contains fulltext : 174787.pdf (publisher's version ) (Open Access), Schinzel-Giedion syndrome (SGS) is a rare developmental disorder characterized by multiple malformations, severe neurological alterations and increased risk of malignancy. SGS is caused by de novo germline mutations clustering to a 12bp hotspot in exon 4 of SETBP1. Mutations in this hotspot disrupt a degron, a signal for the regulation of protein degradation, and lead to the accumulation of SETBP1 protein. Overlapping SETBP1 hotspot mutations have been observed recurrently as somatic events in leukemia. We collected clinical information of 47 SGS patients (including 26 novel cases) with germline SETBP1 mutations and of four individuals with a milder phenotype caused by de novo germline mutations adjacent to the SETBP1 hotspot. Different mutations within and around the SETBP1 hotspot have varying effects on SETBP1 stability and protein levels in vitro and in in silico modeling. Substitutions in SETBP1 residue I871 result in a weak increase in protein levels and mutations affecting this residue are significantly more frequent in SGS than in leukemia. On the other hand, substitutions in residue D868 lead to the largest increase in protein levels. Individuals with germline mutations affecting D868 have enhanced cell proliferation in vitro and higher incidence of cancer compared to patients with other germline SETBP1 mutations. Our findings substantiate that, despite their overlap, somatic SETBP1 mutations driving malignancy are more disruptive to the degron than germline SETBP1 mutations causing SGS. Additionally, this suggests that the functional threshold for the development of cancer driven by the disruption of the SETBP1 degron is higher than for the alteration in prenatal development in SGS. Drawing on previous studies of somatic SETBP1 mutations in leukemia, our results reveal a genotype-phenotype correlation in germline SETBP1 mutations spanning a molecular, cellular and clinical phenotype.

Item does not contain fulltext, De novo, germline variants in DNMT3A cause Tatton-Brown-Rahman syndrome (TBRS). This condition is characterized by overgrowth, distinctive facial appearance, and intellectual disability. Somatic DNMT3A variants frequently occur in hematologic malignances, particularly acute myeloid leukemia. The Arg882 residue is the most common site of somatic DNMT3A variants, and has also been altered in patients with TBRS. Here we present three additional patients with this disorder attributed to DNMT3A germline variants that disrupt the Arg882 codon, suggesting that this codon may be a germline mutation hotspot in this disorder. Furthermore, based on the investigation of previously reported variants in patients with TBRS, we found overlap in the spectrum of DNMT3A variants observed in this disorder and somatic variants in hematological malignancies.

Contains fulltext : 177281.pdf (publisher's version ) (Closed access), Clonal hematopoiesis results from somatic mutations in hematopoietic stem cells, which give an advantage to mutant cells, driving their clonal expansion and potentially leading to leukemia. The acquisition of clonal hematopoiesis-driver mutations (CHDMs) occurs with normal aging and these mutations have been detected in more than 10% of individuals >/=65 years. We aimed to examine the prevalence and characteristics of CHDMs throughout adult life. We developed a targeted re-sequencing assay combining high-throughput with ultra-high sensitivity based on single-molecule molecular inversion probes (smMIPs). Using smMIPs, we screened more than 100 loci for CHDMs in more than 2,000 blood DNA samples from population controls between 20 and 69 years of age. Loci screened included 40 regions known to drive clonal hematopoiesis when mutated and 64 novel candidate loci. We identified 224 somatic mutations throughout our cohort, of which 216 were coding mutations in known driver genes (DNMT3A, JAK2, GNAS, TET2, and ASXL1), including 196 point mutations and 20 indels. Our assay's improved sensitivity allowed us to detect mutations with variant allele frequencies as low as 0.001. CHDMs were identified in more than 20% of individuals 60 to 69 years of age and in 3% of individuals 20 to 29 years of age, approximately double the previously reported prevalence despite screening a limited set of loci. Our findings support the occurrence of clonal hematopoiesis-associated mutations as a widespread mechanism linked with aging, suggesting that mosaicism as a result of clonal evolution of cells harboring somatic mutations is a universal mechanism occurring at all ages in healthy humans.

Radboud University, 08 juni 2017, Promotor : Veltman, J.A. Co-promotores : Hoischen, A., Gilissen, C.F.H.A., Contains fulltext : 173265.pdf (publisher's version ) (Open Access), The work presented in this thesis shows that mutations arise constantly, between one generation and the next but also throughout life. This continuous occurrence of mutations leads to extraordinary genetic diversity between individuals but is also at the origin of the existence of genetically different populations of cells within a single human being. While the occurrence of novel mutations represents an important biological phenomenon in humans with a role on prenatal development, physiology and evolution, novel mutations also contribute to different forms of human disease ranging from rare and severe developmental disorders to adult-onset diseases such as cancer. The work in this thesis supports that in addition to the detection of mutations, NGS can be used as a tool to identify the timing of mutations in order to include the dimension of time in the interpretation of mutations and their possible consequences. De novo mutations have different recurrence risks depending on the exact timing at which they occurred, which can be determined by meticulous analysis with NGS methods. Indeed, genetic mosaicism resulting from mutations occurring during embryogenesis is common and, depending on their timing, postzygotic mutations can be transmitted to the next generation. Additionally, somatic mutations arise in stem cells throughout life and can be detected using highly sensitive sequencing methods. Furthermore, the timing of a mutation can also shape the resulting phenotype, as the same mutation can be involved in different disorders depending on its timing. For instance, overlapping germline and somatic mutations in SETBP1, leading to Schinzel-Giedion syndrome and to myeloid leukemia, respectively. Future work focusing on the role of timing of somatic and germline mutations will provide us with a better understanding of the effect of the expression of a mutation in the dynamic context of a cell, a tissue and a whole organism.

Radboud University, 08 juni 2017, Promotor : Veltman, J.A. Co-promotores : Hoischen, A., Gilissen, C.F.H.A., Contains fulltext : 173265.pdf (publisher's version ) (Open Access), The work presented in this thesis shows that mutations arise constantly, between one generation and the next but also throughout life. This continuous occurrence of mutations leads to extraordinary genetic diversity between individuals but is also at the origin of the existence of genetically different populations of cells within a single human being. While the occurrence of novel mutations represents an important biological phenomenon in humans with a role on prenatal development, physiology and evolution, novel mutations also contribute to different forms of human disease ranging from rare and severe developmental disorders to adult-onset diseases such as cancer. The work in this thesis supports that in addition to the detection of mutations, NGS can be used as a tool to identify the timing of mutations in order to include the dimension of time in the interpretation of mutations and their possible consequences. De novo mutations have different recurrence risks depending on the exact timing at which they occurred, which can be determined by meticulous analysis with NGS methods. Indeed, genetic mosaicism resulting from mutations occurring during embryogenesis is common and, depending on their timing, postzygotic mutations can be transmitted to the next generation. Additionally, somatic mutations arise in stem cells throughout life and can be detected using highly sensitive sequencing methods. Furthermore, the timing of a mutation can also shape the resulting phenotype, as the same mutation can be involved in different disorders depending on its timing. For instance, overlapping germline and somatic mutations in SETBP1, leading to Schinzel-Giedion syndrome and to myeloid leukemia, respectively. Future work focusing on the role of timing of somatic and germline mutations will provide us with a better understanding of the effect of the expression of a mutation in the dynamic context of a cell, a tissue and a whole organism.

Item does not contain fulltext, De novo, germline variants in DNMT3A cause Tatton-Brown-Rahman syndrome (TBRS). This condition is characterized by overgrowth, distinctive facial appearance, and intellectual disability. Somatic DNMT3A variants frequently occur in hematologic malignances, particularly acute myeloid leukemia. The Arg882 residue is the most common site of somatic DNMT3A variants, and has also been altered in patients with TBRS. Here we present three additional patients with this disorder attributed to DNMT3A germline variants that disrupt the Arg882 codon, suggesting that this codon may be a germline mutation hotspot in this disorder. Furthermore, based on the investigation of previously reported variants in patients with TBRS, we found overlap in the spectrum of DNMT3A variants observed in this disorder and somatic variants in hematological malignancies.

Contains fulltext : 177281.pdf (publisher's version ) (Closed access), Clonal hematopoiesis results from somatic mutations in hematopoietic stem cells, which give an advantage to mutant cells, driving their clonal expansion and potentially leading to leukemia. The acquisition of clonal hematopoiesis-driver mutations (CHDMs) occurs with normal aging and these mutations have been detected in more than 10% of individuals >/=65 years. We aimed to examine the prevalence and characteristics of CHDMs throughout adult life. We developed a targeted re-sequencing assay combining high-throughput with ultra-high sensitivity based on single-molecule molecular inversion probes (smMIPs). Using smMIPs, we screened more than 100 loci for CHDMs in more than 2,000 blood DNA samples from population controls between 20 and 69 years of age. Loci screened included 40 regions known to drive clonal hematopoiesis when mutated and 64 novel candidate loci. We identified 224 somatic mutations throughout our cohort, of which 216 were coding mutations in known driver genes (DNMT3A, JAK2, GNAS, TET2, and ASXL1), including 196 point mutations and 20 indels. Our assay's improved sensitivity allowed us to detect mutations with variant allele frequencies as low as 0.001. CHDMs were identified in more than 20% of individuals 60 to 69 years of age and in 3% of individuals 20 to 29 years of age, approximately double the previously reported prevalence despite screening a limited set of loci. Our findings support the occurrence of clonal hematopoiesis-associated mutations as a widespread mechanism linked with aging, suggesting that mosaicism as a result of clonal evolution of cells harboring somatic mutations is a universal mechanism occurring at all ages in healthy humans.

© 2017 Elsevier Inc. Wastewater is increasingly being recognized as a key water resource, and reclaimed water (or treated wastewater) is used for irrigating vegetables destined for human consumption. The aim of the present study was to determine the diversity and prevalence of Aeromonas spp. both in reclaimed water used for irrigation and in the three types of vegetables irrigated with that water. Seven of the 11 (63.6%) samples of reclaimed water and all samples of vegetables were positive for the presence of Aeromonas. A total of 216 Aeromonas isolates were genotyped and corresponded to 132 different strains that after identification by sequencing the rpoD gene belonged to 10 different species. The prevalence of the species varied depending on the type of sample. In the secondary treated reclaimed water A. caviae and A. media dominated (91.4%) while A. salmonicida, A. media, A. allosaccharophila and A. popoffii represented 74.0% of the strains in the irrigation water. In vegetables, A. caviae (75.0%) was the most common species, among which a strain isolated from lettuce had the same genotype (ERIC pattern) as a strain recovered from the irrigation water. Furthermore, the same genotype of the species A. sanarellii was recovered from parsley and tomatoes demonstrating that irrigation water was the source of contamination and confirming the risk for public health.

Four Aeromonas strains from clinical and environmental samples differed from known species on the basis of rpoD gene sequence. Multilocus Phylogenetic Analysis and in silico DNA-DNA Hybridization confirmed them as four new species, despite their 16S rRNA gene sequence similarity with their closest relative was >98.7%, as occurred for other Aeromonas spp.

Contains fulltext : 165722.pdf (publisher's version ) (Open Access), Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing studies of parent-offspring trios have provided the first insights into the number and distribution of these de novo mutations in health and disease, pointing to risk factors that increase their number in the offspring. De novo mutations have been shown to be a major cause of severe early-onset genetic disorders such as intellectual disability, autism spectrum disorder, and other developmental diseases. In fact, the occurrence of novel mutations in each generation explains why these reproductively lethal disorders continue to occur in our population. Recent studies have also shown that de novo mutations are predominantly of paternal origin and that their number increases with advanced paternal age. Here, we review the recent literature on de novo mutations, covering their detection, biological characterization, and medical impact.

Contains fulltext : 165722.pdf (publisher's version ) (Open Access), Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing studies of parent-offspring trios have provided the first insights into the number and distribution of these de novo mutations in health and disease, pointing to risk factors that increase their number in the offspring. De novo mutations have been shown to be a major cause of severe early-onset genetic disorders such as intellectual disability, autism spectrum disorder, and other developmental diseases. In fact, the occurrence of novel mutations in each generation explains why these reproductively lethal disorders continue to occur in our population. Recent studies have also shown that de novo mutations are predominantly of paternal origin and that their number increases with advanced paternal age. Here, we review the recent literature on de novo mutations, covering their detection, biological characterization, and medical impact.

Contains fulltext : 165722.pdf (publisher's version ) (Open Access), Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing studies of parent-offspring trios have provided the first insights into the number and distribution of these de novo mutations in health and disease, pointing to risk factors that increase their number in the offspring. De novo mutations have been shown to be a major cause of severe early-onset genetic disorders such as intellectual disability, autism spectrum disorder, and other developmental diseases. In fact, the occurrence of novel mutations in each generation explains why these reproductively lethal disorders continue to occur in our population. Recent studies have also shown that de novo mutations are predominantly of paternal origin and that their number increases with advanced paternal age. Here, we review the recent literature on de novo mutations, covering their detection, biological characterization, and medical impact.

© 2016 The Society for Applied Microbiology Aims: To perform a comparative study for determining the optimum culture method (direct plating or enrichment) and medium (ampicillin dextrin agar (ADA), starch ampicillin agar (SAA), bile salts irgasan brilliant green modified (BIBG-m)) for recovering Aeromonas species from water and shellfish samples. Methods and Results: By direct culture, Aeromonas was detected in 65% (13/20) of the water samples and in 54·5% (6/11) of the shellfish samples. However, when a pre-enrichment step was included, the number of positive water samples increased to 75% (15/20) and the ones of shellfish to 90·1% (10/11). The enriched culture significantly favoured (P < 0·05) the isolation of Aeromonas allosaccharophila from water, Aeromonas salmonicida from shellfish and Aeromonas caviae from both types of samples. The most specific (P < 0·05) culture medium for detecting Aeromonas from water was ADA. However, no differences were observed in the case of shellfish samples (P > 0·05). Isolation of Aeromonas media from water was favoured (P < 0·05) in the ADA medium, while SAA enhanced (P < 0·05) the isolation of Aer. salmonicida from shellfish. Conclusions: The culture method and medium used influenced the recovery of some Aeromonas species from water and shellfish samples. Significance and Impact of the Study: This fact should be considered in future prevalence studies to avoid overestimating the above mentioned Aeromonas species.

Item does not contain fulltext, BACKGROUND: Resistance to thyroid hormone is characterised by a lack of response of peripheral tissues to the active form of thyroid hormone (triiodothyronine, T3). In about 85% of cases, a mutation in THRB, the gene coding for thyroid receptor beta (TRbeta), is the cause of this disorder. Recently, individual reports described the first patients with thyroid hormone receptor alpha gene (THRA) defects. METHODS: We used longitudinal clinical assessments over a period of 18 years at one hospital setting combined with biochemical and molecular studies to characterise a novel thyroid hormone resistance syndrome in a cohort of six patients from five families. FINDINGS: Using whole exome sequencing and subsequent Sanger sequencing, we identified truncating and missense mutations in the THRA gene in five of six individuals and describe a distinct and consistent phenotype of mild hypothyroidism (growth retardation, relatively high birth length and weight, mild-to-moderate mental retardation, mild skeletal dysplasia and constipation), specific facial features (round, somewhat coarse and flat face) and macrocephaly. Laboratory investigations revealed anaemia and slightly elevated cholesterol, while the thyroid profile showed low free thyroxine (fT4) levels coupled with high free T3 (fT3), leading to an altered T4 : T3 ratio, along with normal thyroid-stimulating hormone levels. We observed a genotype-phenotype correlation, with milder outcomes for missense mutations and more severe phenotypical effects for truncating mutations. INTERPRETATION: THRA mutations may be more common than expected. In patients with clinical symptoms of mild hypothyreosis without confirmation in endocrine studies, a molecular study of THRA defects is strongly recommended.

Item does not contain fulltext, De novo mutations are recognized both as an important source of genetic variation and as a prominent cause of sporadic disease in humans. Mutations identified as de novo are generally assumed to have occurred during gametogenesis and, consequently, to be present as germline events in an individual. Because Sanger sequencing does not provide the sensitivity to reliably distinguish somatic from germline mutations, the proportion of de novo mutations that occur somatically rather than in the germline remains largely unknown. To determine the contribution of post-zygotic events to de novo mutations, we analyzed a set of 107 de novo mutations in 50 parent-offspring trios. Using four different sequencing techniques, we found that 7 (6.5%) of these presumed germline de novo mutations were in fact present as mosaic mutations in the blood of the offspring and were therefore likely to have occurred post-zygotically. Furthermore, genome-wide analysis of "de novo" variants in the proband led to the identification of 4/4,081 variants that were also detectable in the blood of one of the parents, implying parental mosaicism as the origin of these variants. Thus, our results show that an important fraction of de novo mutations presumed to be germline in fact occurred either post-zygotically in the offspring or were inherited as a consequence of low-level mosaicism in one of the parents.

Item does not contain fulltext, BACKGROUND: Resistance to thyroid hormone is characterised by a lack of response of peripheral tissues to the active form of thyroid hormone (triiodothyronine, T3). In about 85% of cases, a mutation in THRB, the gene coding for thyroid receptor beta (TRbeta), is the cause of this disorder. Recently, individual reports described the first patients with thyroid hormone receptor alpha gene (THRA) defects. METHODS: We used longitudinal clinical assessments over a period of 18 years at one hospital setting combined with biochemical and molecular studies to characterise a novel thyroid hormone resistance syndrome in a cohort of six patients from five families. FINDINGS: Using whole exome sequencing and subsequent Sanger sequencing, we identified truncating and missense mutations in the THRA gene in five of six individuals and describe a distinct and consistent phenotype of mild hypothyroidism (growth retardation, relatively high birth length and weight, mild-to-moderate mental retardation, mild skeletal dysplasia and constipation), specific facial features (round, somewhat coarse and flat face) and macrocephaly. Laboratory investigations revealed anaemia and slightly elevated cholesterol, while the thyroid profile showed low free thyroxine (fT4) levels coupled with high free T3 (fT3), leading to an altered T4 : T3 ratio, along with normal thyroid-stimulating hormone levels. We observed a genotype-phenotype correlation, with milder outcomes for missense mutations and more severe phenotypical effects for truncating mutations. INTERPRETATION: THRA mutations may be more common than expected. In patients with clinical symptoms of mild hypothyreosis without confirmation in endocrine studies, a molecular study of THRA defects is strongly recommended.

Item does not contain fulltext, De novo mutations are recognized both as an important source of genetic variation and as a prominent cause of sporadic disease in humans. Mutations identified as de novo are generally assumed to have occurred during gametogenesis and, consequently, to be present as germline events in an individual. Because Sanger sequencing does not provide the sensitivity to reliably distinguish somatic from germline mutations, the proportion of de novo mutations that occur somatically rather than in the germline remains largely unknown. To determine the contribution of post-zygotic events to de novo mutations, we analyzed a set of 107 de novo mutations in 50 parent-offspring trios. Using four different sequencing techniques, we found that 7 (6.5%) of these presumed germline de novo mutations were in fact present as mosaic mutations in the blood of the offspring and were therefore likely to have occurred post-zygotically. Furthermore, genome-wide analysis of "de novo" variants in the proband led to the identification of 4/4,081 variants that were also detectable in the blood of one of the parents, implying parental mosaicism as the origin of these variants. Thus, our results show that an important fraction of de novo mutations presumed to be germline in fact occurred either post-zygotically in the offspring or were inherited as a consequence of low-level mosaicism in one of the parents.

Item does not contain fulltext, De novo mutations are recognized both as an important source of genetic variation and as a prominent cause of sporadic disease in humans. Mutations identified as de novo are generally assumed to have occurred during gametogenesis and, consequently, to be present as germline events in an individual. Because Sanger sequencing does not provide the sensitivity to reliably distinguish somatic from germline mutations, the proportion of de novo mutations that occur somatically rather than in the germline remains largely unknown. To determine the contribution of post-zygotic events to de novo mutations, we analyzed a set of 107 de novo mutations in 50 parent-offspring trios. Using four different sequencing techniques, we found that 7 (6.5%) of these presumed germline de novo mutations were in fact present as mosaic mutations in the blood of the offspring and were therefore likely to have occurred post-zygotically. Furthermore, genome-wide analysis of "de novo" variants in the proband led to the identification of 4/4,081 variants that were also detectable in the blood of one of the parents, implying parental mosaicism as the origin of these variants. Thus, our results show that an important fraction of de novo mutations presumed to be germline in fact occurred either post-zygotically in the offspring or were inherited as a consequence of low-level mosaicism in one of the parents.

Contains fulltext : 154293.pdf (Publisher’s version ) (Open Access), BACKGROUND: Resistance to thyroid hormone is characterised by a lack of response of peripheral tissues to the active form of thyroid hormone (triiodothyronine, T3). In about 85% of cases, a mutation in THRB, the gene coding for thyroid receptor beta (TRbeta), is the cause of this disorder. Recently, individual reports described the first patients with thyroid hormone receptor alpha gene (THRA) defects. METHODS: We used longitudinal clinical assessments over a period of 18 years at one hospital setting combined with biochemical and molecular studies to characterise a novel thyroid hormone resistance syndrome in a cohort of six patients from five families. FINDINGS: Using whole exome sequencing and subsequent Sanger sequencing, we identified truncating and missense mutations in the THRA gene in five of six individuals and describe a distinct and consistent phenotype of mild hypothyroidism (growth retardation, relatively high birth length and weight, mild-to-moderate mental retardation, mild skeletal dysplasia and constipation), specific facial features (round, somewhat coarse and flat face) and macrocephaly. Laboratory investigations revealed anaemia and slightly elevated cholesterol, while the thyroid profile showed low free thyroxine (fT4) levels coupled with high free T3 (fT3), leading to an altered T4 : T3 ratio, along with normal thyroid-stimulating hormone levels. We observed a genotype-phenotype correlation, with milder outcomes for missense mutations and more severe phenotypical effects for truncating mutations. INTERPRETATION: THRA mutations may be more common than expected. In patients with clinical symptoms of mild hypothyreosis without confirmation in endocrine studies, a molecular study of THRA defects is strongly recommended.

© 2015 Beaz-Hidalgo et al. January Around 27,000 prokaryote genomes are presently deposited in the Genome database of GenBank at the National Center for Biotechnology Information (NCBI) and this number is exponentially growing. However, it is not known how many of these genomes correspond correctly to their designated taxon. The taxonomic affiliation of 44 Aeromonas genomes (only five of these are type strains) deposited at the NCBI was determined by a multilocus phylogenetic analysis (MLPA) and by pairwise average nucleotide identity (ANI). Discordant results in relation to taxa assignation were found for 14 (35.9%) of the 39 non-type strain genomes on the basis of both the MLPA and ANI results. Data presented in this study also demonstrated that if the genome of the type strain is not available, a genome of the same species correctly identified can be used as a reference for ANI calculations. Of the three ANI calculating tools compared (ANI calculator, EzGenome and JSpecies), EzGenome and JSpecies provided very similar results. However, the ANI calculator provided higher intraand inter-species values than the other two tools (differences within the ranges 0.06 -0.82% and 0.92-3.38%, respectively). Nevertheless each of these tools produced the same species classification for the studied Aeromonas genomes. To avoid possible misinterpretations with the ANI calculator, particularly when values are at the borderline of the 95% cutoff, one of the other calculation tools (EzGenome or JSpecies) should be used in combination. It is recommended that once a genome sequence is obtained the correct taxonomic affiliation is verified using ANI or a MLPA before it is submitted to the NCBI and that researchers should amend the existing taxonomic errors present in databases.

Contains fulltext : 136372.pdf (Publisher’s version ) (Closed access), Neu-Laxova syndrome (NLS) is a rare autosomal-recessive disorder characterized by a recognizable pattern of severe malformations leading to prenatal or early postnatal lethality. Homozygous mutations in PHGDH, a gene involved in the first and limiting step in L-serine biosynthesis, were recently identified as the cause of the disease in three families. By studying a cohort of 12 unrelated families affected by NLS, we provide evidence that NLS is genetically heterogeneous and can be caused by mutations in all three genes encoding enzymes of the L-serine biosynthesis pathway. Consistent with recently reported findings, we could identify PHGDH missense mutations in three unrelated families of our cohort. Furthermore, we mapped an overlapping homozygous chromosome 9 region containing PSAT1 in four consanguineous families. This gene encodes phosphoserine aminotransferase, the enzyme for the second step in L-serine biosynthesis. We identified six families with three different missense and frameshift PSAT1 mutations fully segregating with the disease. In another family, we discovered a homozygous frameshift mutation in PSPH, the gene encoding phosphoserine phosphatase, which catalyzes the last step of L-serine biosynthesis. Interestingly, all three identified genes have been previously implicated in serine-deficiency disorders, characterized by variable neurological manifestations. Our findings expand our understanding of NLS as a disorder of the L-serine biosynthesis pathway and suggest that NLS represents the severe end of serine-deficiency disorders, demonstrating that certain complex syndromes characterized by early lethality could indeed be the extreme end of the phenotypic spectrum of already known disorders.

We present experimental and numerical results for particle alignment and stress distribution in packings of faceted particles deposited in a small-scale bi-dimensional silo. First, we experimentally characterize the deposits’ morphology in terms of the particles’ aspect ratio and feeding rate. Then we use the experimental results to validate our discrete element method (DEM) based on spheropolygons. After achieving excellent agreement, we use contact forces and fabric provided by the simulations to calculate the coarse-grained stress tensor. For low feeding rates, square particles display a strong tendency to align downwards, i.e., with a diagonal parallel to gravity. This morphology leads to stress transmission towards the walls, implying a quick development of pressure saturation, in agreement with the Janssen effect. When the feed rate is increased, both the disorder and the number of horizontal squares in the silo increase, hindering the Janssen effect. Conversely, for elongated particles the feed rate has a weak effect on the final deposit properties. Indeed, we always observe highly ordered structures of horizontal rods where the stress is transmitted mainly in the vertical direction.

Contains fulltext : 136372.pdf (Publisher’s version ) (Closed access), Neu-Laxova syndrome (NLS) is a rare autosomal-recessive disorder characterized by a recognizable pattern of severe malformations leading to prenatal or early postnatal lethality. Homozygous mutations in PHGDH, a gene involved in the first and limiting step in L-serine biosynthesis, were recently identified as the cause of the disease in three families. By studying a cohort of 12 unrelated families affected by NLS, we provide evidence that NLS is genetically heterogeneous and can be caused by mutations in all three genes encoding enzymes of the L-serine biosynthesis pathway. Consistent with recently reported findings, we could identify PHGDH missense mutations in three unrelated families of our cohort. Furthermore, we mapped an overlapping homozygous chromosome 9 region containing PSAT1 in four consanguineous families. This gene encodes phosphoserine aminotransferase, the enzyme for the second step in L-serine biosynthesis. We identified six families with three different missense and frameshift PSAT1 mutations fully segregating with the disease. In another family, we discovered a homozygous frameshift mutation in PSPH, the gene encoding phosphoserine phosphatase, which catalyzes the last step of L-serine biosynthesis. Interestingly, all three identified genes have been previously implicated in serine-deficiency disorders, characterized by variable neurological manifestations. Our findings expand our understanding of NLS as a disorder of the L-serine biosynthesis pathway and suggest that NLS represents the severe end of serine-deficiency disorders, demonstrating that certain complex syndromes characterized by early lethality could indeed be the extreme end of the phenotypic spectrum of already known disorders.

© 2014 Hossain et al. Aeromonas aquatica and Aeromonas lacus are two new species that have been found in association with cyanobacterial blooms from recreational Finnish lakes where adverse human health effects have been recorded. Here, we present the draft genome sequences of their type strains.

© 2014 Figueras et al. The average nucleotide identity (ANI) determines if two genomes belong to the same species. Using ANI, we detected mislabeled genomes and recommend verifying with ANI and multilocus phylogenetic analysis the species affiliations of the announced genomes. The slightly different results obtained with different ANI calculation software can potentially mislead taxonomic inferences.