A Low-pass sequencing approach to phylogenetic analysis: reconstructing Sardinian and European demographic history with a panel of 1200 Y-chromosome samples

Aim: The origins of contemporary populations can be clarified by studying the genetic variation within the male-specific portion of the Y chromosome (MSY). The phylogenesis over this region has been subject of several studies in the past years. In the present study we took advantage of the large scale whole genome sequencing studies we have been carrying on to build a phylogenetic map of Y chromosome with an unprecedented resolution, over which we calculated the putative age for coalescence for our samples. Methods: The study involves 1,204 male samples from Sardinia. A complete variant call on the samples is performed and a statistical approach at a first stage and a second stage hierarchical approach are applied to respectively discard / correct errors and select informative variants. A phylogenetic tree is built and TMRCA calculations are performed. Results: The following haplogroups have been unambiguously detected (A, E, F, G, I, J, K, P, R) over the 1,204 samples and 11,763 informative markers have been discovered, among which 6,751 have not previously been observed. We calibrated the tree with archaeological data and used it to calculate a putative age for coalescence of (190±10)·10^3 years ago. Conclusion: This study shows that Sardinian population carries most of European variability, doubles the number of previously known human phylogenetically informative markers for Y chromosome and provides an estimate for coalescence which is closer to previous mitochondrial DNA estimates than in previous studies on the MSY.</br

Otturazione endodontica e restauri adesivi: esiste un legame?

RiassuntoObiettiviL'obiettivo di questa relazione è valutare attraverso studi in vitro condotti presso la Dental School di Torino se l'utilizzo di moderne tecniche adesive possa ridurre gli svantaggi in ambito di adesione portati dalla guttaperca, apportata con condensazione verticale piuttosto che con diversi sistemi con carrier.Materiali e metodiSono stati sviluppati test di push-out per valutare la forza di adesione di perni in fibra cementati in diverse condizioni. 1: efficacia di sistemi cementi self-adhesive. 2: efficacia di sistemi di cementazione duali nella cementazione immediata. 3: Forza di adesione di perni cementati in canali chiusi con 3 diverse tecniche: condensazione verticale, Thermafil, Guttacore.RisultatiI risultati mostrano come la cementazione di perni in fibra sia significativamente influenzata da tecniche di otturazione canalare con carrier, mentre i sistemi adesivi duali consentno di cementare immediatamente il perno in fibra.SummaryObjectiveThe aim of this report is to assess through in vitro studies if the use of modern adhesive techniques can reduce the disadvantages in adhesion brought by gutta-percha, employed both with vertical condensation both with carrier systems.Materials and methodsPush-out test were employed to assess the strength of adhesion of fiber posts cemented in different conditions. 1: Efficacy of self-adhesive cements. 2: Efficacy of dual materials on immediate cementation. 3: Bond strength of post luted in canals obturated with 3 different techniques: vertical condensation, Thermafil, Guttacore.ResultsThe results showed that the cementation of fiber posts is significantly affected by root canal obturation techniques with carrier, while the dual adhesive systems allow to immediately cementing the fiber post

Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample

Background: Next-Generation Sequencing methods have led to a great increase in phylogenetically useful markers within the male specific portion of the Y chromosome, but previous studies have limited themselves to the study of the X-degenerate regions. Methods: DNA was extracted from peripheral blood samples of adult males whose paternal grandfathers were born in Sardinia. The DNA samples were sequenced, genotyped and subsequently analysed for variant calling for approximately 23.1 Mbp of the Y chromosome. A phylogenetic tree was built using Network 4.6 software. Results: From low coverage whole genome sequencing of 1,194 Sardinian males, we extracted 20,155 phylogenetically informative single nucleotide polymorphisms from the whole euchromatic region, including the X-degenerate, X-transposed, and Ampliconic regions, along with variants in other unclassified chromosome intervals and in the readable sequences of the heterochromatic region. Conclusions: The non X-degenerate classes contain a significant portion of the phylogenetic variation of the whole chromosome and their inclusion in the analysis, almost doubling the number of informative polymorphisms, refining the known molecular phylogeny of the human Y chromosome

Correction:Comprehensive genetic screening of early-onset dementia patients in an Austrian cohort-suggesting new disease-contributing genes (Human Genomics, (2023), 17, 1, (55), 10.1186/s40246-023-00499-z)

Following publication of the original article [1], the authors reported an error in Table 1. The correct Table 1 has been provided in this Correction. (Table presented.) Basic clinical and genetic characteristics of all 60 EOD patients ID Diagnosis AAO (years) Sex FH APOE Gene Variant Position Transcript CADD ClinVar Significance for disease EOD-1 EOD-2 c.184G &gt; A; p.R62C chr6:41129208-41129208 NM_001271821.1 25.5 n.r Risk modifier Risk modifier EOD-3 AD 45 f 2 E3/E3 EOD-4 AD 51 f 4 E4/E3 Risk modifier EOD-5 nfPPA 58 f 2 E3/E2 EOD-6 AD 56 f 3 E3/E3 EOD-7 AD/PCA 56 f 4 E3/E3 EOD-8 bvFTD 56 m 4 E3/E3 c.1427T &gt; C; p.M476T chr11:117160361-117160361 NM_012104.3 26.4 n.r Unknown c.9757A &gt; G; p.S3253G chr15:62173781-62173781 NM_020821.2 29.5 n.r Unknown EOD-9 AD 55 f 3,5 E4/E3 Risk modifier EOD-10 AD 58 f 3,5 E3/E3 EOD-11 AD 63 m 4 E3/E3 EOD-12 mixed dementia (AD + VD) 55 m 3,5 E4/E3 Risk modifier EOD-13 AD 61 m 4,5 E3/E3 EOD-14 AD/lpPPA 61 m 4 E4/E3 Risk modifier c.4300C &gt; T; p.V1434I chr15:62244179-62244179 NM_020821.2 24.8 n.r Unknown EOD-15 nfPPA 64 m 2 E3/E3 c.2218C &gt; T; p.E740K chr2:74594514-74594514 NM_004082.4 24.0 n.r Unknown EOD-16 AD 56 f 4 E3/E3 EOD-17 AD (PD) 60 m 1 E4/E3 Risk modifier g.chr16:1816528 A &gt; G; c.2817-2A &gt; G chr16:1816528-1816528 NM_015133.3 22.3 n.r Unknown EOD-18a c.2914C &gt; T; p.P972S chr19:1051537-1051537 NM_019112.3 25.3 n.r Potential risk modifier EOD-19 EOD-19 (2)b EOD-20 AD 57 m 4,5 E3/E3 c.7397T &gt; A; p.L2466H chr12:40760814-40760814 NM_198578.3 25.7 VUS Unknown EOD-21 EOD-22 EOD-23 EOD-24 EOD-25 EOD-26 AD 56 f 4 E3/E3 c.2980G &gt; C; p.P994A chr2:74590268-74590268 NM_023019.3 17.3 VUS Unknown c.2087G &gt; A; p.R696H chr16:1814180-1814180 NM_015133.3 31.0 n.r Unknown EOD-27 AD 57 f 4 E4/E3 Risk modifier EOD-28 AD 54 m 4 E3/E3 EOD-29 AD 54 m 4 E3/E3 EOD-30 AD 64 m 4 E3/E3 EOD-31 mixed dementia (AD + VD) 58 m 3,5 E3/E3 EOD-32 FTD/svPPA 61 m 4 E3/E3 EOD-33 AD 62 f 4,5 E4/E3 Risk modifier c.521G &gt; A; p.S174L chr2:74598788-74598788 NM_004082.4 24.4 VUS Unknown EOD-34 AD 59 f 2 E4/E3 Risk modifier EOD-35 AD 55 m 3,5 E4/E3 Risk modifier EOD-36c AD 64 m 2 E4/E3 c.140G &gt; A; p.R47H chr6:41129252-41129252 NM_018965.3 9.7 LB Risk modifier Risk modifier EOD-37 AD 52 f 3,5 E3/E3 c.7397T &gt; A; p.L2466H chr12:40760814-40760814 NM_198578.3 25.7 VUS Unknown EOD-38 AD 52 f 3,5 E4/E3 Risk modifier EOD-39 AD 63 f 3 E4/E3 Risk modifier EOD-40 AD 55 f 4 E4/E3 Risk modifier EOD-41 AD 58 m 3,5 E3/E3 EOD-42 AD 39 m 4 E3/E2 EOD-43 AD 63 m 4 E3/E3 c.3148A &gt; G; p.I1050V chr15:62256964-62256964 NM_020821.2 0.001 VUS Unknown EOD-44 AD/lpPPA 58 f 3,5 E3/E3 c.3014T &gt; G; p.M1005R chr11:121430331-121430331 NM_003105.5 27.9 n.r Potential risk modifier EOD-45 AD 65 m 4 E3/E3 EOD-46 CBS + AD 51 f 3,5 E3/E3 c.4606G &gt; A; p.G1536S chr11:121474988-121474988 NM_003105.5 25.2 B Risk modifier EOD-47 AD 54 f 4 E3/E3 EOD-48 bvFTD 57 m 4 E3/E3 EOD-49 FTD/nfPPA + ALS 58 m 4 E3/E3 c.986T &gt; C; p.L276P chr12:64875636-64875636 NM_013254.3 n.r Potential risk modifier c.7436T &gt; C; p.I2429T chr15:62212307-62212307 NM_020821.2 n.r Unknown EOD-50 Risk modifier EOD-51 FTD/svPPA 62 f 4 E3/E3 EOD-52 AD 57 m 4 E4/E3 Risk modifier EOD-53 c.7377G &gt; A; p.M2459I chr12:40758839-40758839 NM_198578.3 17.7 n.r Unknown EOD-54 AD 59 m 1 E4/E3 Risk modifier EOD-55 AD 49 m 4 E3/E3 EOD-56 AD 61 m 3,5 E3/E3 EOD-57 AD/lpPPA 57 f 4 E3/E3 EOD-58 AD + VD 64 f 3 E3/E3 c.823C &gt; T; p.R141C chr2:74598126-74598126 NM_004082.3 29.3 VUS Unknown EOD-59 bvFTD 52 m 4 E4/E3 Risk modifier EOD-60 a, EOD-18: The APP duplication of was confirmed to be 'de novo'. Both parents did not show this duplication b, EOD-19 (2) is the brother of EOD19. He was also affected by AD and carrier of the same duplication. EOD 19 (2) was not included in the analyses of AAO and FH c, EOD-36: ClinVar assessment of TREM2 p.R47H of LB (likely benign) refers to Nasu-Hakola disease. However, p.R47H is an established risk variant for dementia (Ref. 15) The original article [1] has been corrected.</p

Clonal hematopoiesis as a pitfall in germline variant interpretation in the context of Mendelian disorders

Clonal hematopoiesis because of somatic mutations in hematopoietic stem/progenitor cells is an age-related phenomenon and commonly observed when sequencing blood DNA in elderly individuals. Several genes that are implicated in clonal hematopoiesis are also associated with Mendelian disorders when mutated in the germline, potentially leading to variant misinterpretation. We performed a literature search to identify genes associated with age-related clonal hematopoiesis followed by an OMIM query to identify the subset of genes in which germline variants are associated with Mendelian disorders. We retrospectively screened for diagnostic cases in which the presence of age-related clonal hematopoiesis confounded exome sequencing data interpretation. We found 58 genes in which somatic mutations are implicated in clonal hematopoiesis, while germline variants in the same genes are associated with Mendelian (mostly neurodevelopmental) disorders. Using five selected cases of individuals with suspected monogenic disorders, we illustrate how clonal hematopoiesis in either variant databases or exome sequencing datasets poses a pitfall, potentially leading to variant misclassification and erroneous conclusions regarding gene-disease associations

Episignature analysis of moderate effects and mosaics

DNA methylation classifiers (episignatures) help to determine the pathogenicity of variants of uncertain significance (VUS). However, their sensitivity is limited due to their training on unambiguous cases with strong-effect variants so that the classification of variants with reduced effect size or in mosaic state may fail. Moreover, episignature evaluation of mosaics as a function of their degree of mosaicism has not been developed so far. We improved episignatures with respect to three categories. Applying (i) minimum-redundancy-maximum-relevance feature selection we reduced their length by up to one order of magnitude without loss of accuracy. Performing (ii) repeated re-training of a support vector machine classifier by step-wise inclusion of cases in the training set that reached probability scores larger than 0.5, we increased the sensitivity of the episignature-classifiers by 30%. In the newly diagnosed patients we confirmed the association between DNA methylation aberration and age at onset of KMT2B-deficient dystonia. Moreover, we found evidence for allelic series, including KMT2B-variants with moderate effects and comparatively mild phenotypes such as late-onset focal dystonia. Retrained classifiers also can detect mosaics that previously remained below the 0.5-threshold, as we showed for KMT2D-associated Kabuki syndrome. Conversely, episignature-classifiers are able to revoke erroneous exome calls of mosaicism, as we demonstrated by (iii) comparing presumed mosaic cases with a distribution of artificial in silico-mosaics that represented all the possible variation in degree of mosaicism, variant read sampling and methylation analysis

MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome

The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations inNIPBLaccount for most cases ofthe rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report aMAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus.Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable fornormal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fataloutcome of an out-of-frame single nucleotide duplication inNIPBL, engineered in two different cell lines,alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interactwith MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protectiveagainst out-of-frame mutations that is potentially relevant for other genetic conditions

Dystonia Linked to EIF4A2 Haploinsufficiency: A Disorder of Protein Translation Dysfunction

Background: Protein synthesis is a tightly controlled process, involving a host of translation-initiation factors and microRNA-associated repressors. Variants in the translational regulator EIF2AK2 were first linked to neurodevelopmental-delay phenotypes, followed by their implication in dystonia. Recently, de novo variants in EIF4A2, encoding eukaryotic translation initiation factor 4A isoform 2 (eIF4A2), have been described in pediatric cases with developmental delay and intellectual disability. Objective: We sought to characterize the role of EIF4A2 variants in dystonic conditions. Methods: We undertook an unbiased search for likely deleterious variants in mutation-constrained genes among 1100 families studied with dystonia. Independent cohorts were screened for EIF4A2 variants. Western blotting and immunocytochemical studies were performed in patient-derived fibroblasts. Results: We report the discovery of a novel heterozygous EIF4A2 frameshift deletion (c.896_897del) in seven patients from two unrelated families. The disease was characterized by adolescence- to adulthood-onset dystonia with tremor. In patient-derived fibroblasts, eIF4A2 production amounted to only 50% of the normal quantity. Reduction of eIF4A2 was associated with abnormally increased levels of IMP1, a target of Ccr4-Not, the complex that interacts with eIF4A2 to mediate microRNA-dependent translational repression. By complementing the analyses with fibroblasts bearing EIF4A2 biallelic mutations, we established a correlation between IMP1 expression alterations and eIF4A2 functional dosage. Moreover, eIF4A2 and Ccr4-Not displayed significantly diminished colocalization in dystonia patient cells. Review of international databases identified EIF4A2 deletion variants (c.470_472del, c.1144_1145del) in another two dystonia-affected pedigrees. Conclusions: Our findings demonstrate that EIF4A2 haploinsufficiency underlies a previously unrecognized dominant dystonia-tremor syndrome. The data imply that translational deregulation is more broadly linked to both early neurodevelopmental phenotypes and later-onset dystonic conditions. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society