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| Open AccessAI-enhanced integration of genetic and medical imaging data for risk assessment of Type 2 diabetes
Type 2 diabetes is a global health threat demanding precise healthcare methods. Here, the authors show that their AI-driven risk assessment models, integrating genetic, imaging, and demographic data, achieve high accuracy in identifying high-risk groups, promising advancements in prevention strategies.
- Yi-Jia Huang
- , Chun-houh Chen
- & Hsin-Chou Yang
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Article
| Open AccessUtility of polygenic scores across diverse diseases in a hospital cohort for predictive modeling
Here, the authors analyze polygenic scores for 457 phenotypes, finding 49 with robust polygenic score predictive models ( > 0.6 AUC). They find that population diversity and environmental factor integration are key considerations to improving the model’s performance.
- Ting-Hsuan Sun
- , Chia-Chun Wang
- & Kai-Cheng Hsu
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Article
| Open AccessA humanized mouse model for adeno-associated viral gene therapy
All natural AAV serotypes transduce murine hepatocytes more efficiently than their human counterparts in human liver chimeric mouse models. Here the authors developed a novel humanized mouse were human transduction of AAV can be studied.
- Mercedes Barzi
- , Tong Chen
- & Karl-Dimiter Bissig
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Article
| Open AccessPrediction and stratification of longitudinal risk for chronic obstructive pulmonary disease across smoking behaviors
Many people who never smoke develop COPD. Here, the authors derive and validate the Socioeconomic and Environmental Risk Score (SERS) which captures cumulative exposure risks beyond tobacco smoking to predict and stratify risk of COPD.
- Yixuan He
- , David C. Qian
- & Chirag J. Patel
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Article
| Open AccessMutation of key signaling regulators of cerebrovascular development in vein of Galen malformations
Vein of Galen malformations (VOGMs) are severe congenital brain arteriovenous malformations. Here the authors work to elucidate the pathogenesis of VOGMs by performing an integrated analysis of 310 VOGM proband family exomes and 336,326 human cerebrovasculature single-cell transcriptomes to identify mutations of key signaling regulators.
- Shujuan Zhao
- , Kedous Y. Mekbib
- & Kristopher T. Kahle
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| Open AccessA large meta-analysis identifies genes associated with anterior uveitis
Anterior Uveitis is a common inflammatory eye disease that can result in vision loss. Here, the authors perform GWAS and whole-exome analyses of Anterior Uveitis to identify the underlying genetics of HLA-B*27 positive and negative forms of the disease.
- Sahar Gelfman
- , Arden Moscati
- & Giovanni Coppola
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Article
| Open AccessSingle-nucleus DNA sequencing reveals hidden somatic loss-of-heterozygosity in Cerebral Cavernous Malformations
Here the authors establish somatic loss-of-heterozygosity as a genetic underpinning of Cerebral Cavernous Malformations (CCMs): using single-nucleus DNA sequencing, they show homozygosity of chromosomes 7p and/or 7q leads to biallelic inactivation of CCM genes in resected lesions.
- Andrew K. Ressler
- , Daniel A. Snellings
- & Douglas A. Marchuk
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| Open AccessDominance vs epistasis: the biophysical origins and plasticity of genetic interactions within and between alleles
The authors examine how mutations combine to alter phenotypes in biophysical models of proteins and conclude that non-additive interactions (epistasis and dominance) are frequent, context-dependent and so challenging to predict in even the simplest of biological systems.
- Xuan Xie
- , Xia Sun
- & Xianghua Li
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Article
| Open AccessAPOGEE 2: multi-layer machine-learning model for the interpretable prediction of mitochondrial missense variants
APOGEE 2 is a machine-learning tool for assessing the fragility of the mitochondrial genome, evaluating genetic variant pathogenicity and ultimately enhancing our understanding of the clinical heterogeneity of mitochondrial genetic diseases.
- Salvatore Daniele Bianco
- , Luca Parca
- & Tommaso Mazza
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Article
| Open AccessStriated muscle-specific base editing enables correction of mutations causing dilated cardiomyopathy
Dilated cardiomyopathy is the second most common cause for heart failure. Here the authors combine CRISPR base editors with the muscle-targeting viral vector AAVMYO to repair patient mutations in the cardiac splice factor Rbm20 in two mouse models.
- Markus Grosch
- , Laura Schraft
- & Lars M. Steinmetz
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Article
| Open AccessGenetics implicates overactive osteogenesis in the development of diffuse idiopathic skeletal hyperostosis
The genetic contribution to risk of Diffuse Idiopathic Skeletal Hyperostosis has been unclear. Here, the authors find genetic variation associated with Diffuse Idiopathic Skeletal Hyperostosis, finding phenotypic and genetic association with increased bone mass throughout the skeletal system.
- Anurag Sethi
- , J. Graham Ruby
- & Eugene Melamud
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Article
| Open AccessThe SOD1-mediated ALS phenotype shows a decoupling between age of symptom onset and disease duration
Analysis of age of onset and disease duration in a large, international cohort of people with SOD1-ALS shows that there is a distinct phenotype and that onset and progression are decoupled.
- Sarah Opie-Martin
- , Alfredo Iacoangeli
- & Christopher E. Shaw
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Article
| Open AccessThe inner junction protein CFAP20 functions in motile and non-motile cilia and is critical for vision
Motile and non-motile cilia have distinct functions and protein complexes associated with them. Here, the authors show the conserved protein CFAP20 is important for both motile and non-motile cilia and is distinct from other ciliopathy-associated domains or macromolecular complexes.
- Paul W. Chrystal
- , Nils J. Lambacher
- & Michel R. Leroux
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Article
| Open AccessGenome-wide rare variant score associates with morphological subtypes of autism spectrum disorder
Morphological subtypes of autism spectrum disorder (ASD) may differ in their genetic bases. Chan et al. develop a method for calculating a patient-level, genome-wide rare variant score and find significant differences in rare and common variant associations between dysmorphic and nondysmorphic ASD groups.
- Ada J. S. Chan
- , Worrawat Engchuan
- & Stephen W. Scherer
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Article
| Open AccessTransferability of genetic loci and polygenic scores for cardiometabolic traits in British Pakistani and Bangladeshi individuals
Most genetic studies of disease have been done in European ancestry cohorts, and the relevance to other populations is not guaranteed. Here, the authors use data from 22,000 British South Asian individuals and find that the transferability of polygenic scores was high for lipids and blood pressure, and lower for BMI and coronary artery disease.
- Qin Qin Huang
- , Neneh Sallah
- & Karoline Kuchenbaecker
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Article
| Open AccessAn automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases
Rapid diagnosis and implementation of treatments is crucial in many genetic conditions. Here the authors describe Genome-to-Treatment, a virtual disease management system that can achieve a rapid diagnosis by expedited whole genome sequencing in 13.5 hours and provide guidance to clinicians for possible therapies.
- Mallory J. Owen
- , Sebastien Lefebvre
- & Stephen F. Kingsmore
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Article
| Open AccessThe contribution of common regulatory and protein-coding TYR variants to the genetic architecture of albinism
Albinism is a rare disorder often caused by high-effect rare variants in the TYR gene. Here, the authors study a large albinism cohort and find that a common variant in the TYR promoter contributes to albinism by modifying the penetrance of other common variants, demonstrating a complex genetic architecture.
- Vincent Michaud
- , Eulalie Lasseaux
- & Panagiotis I. Sergouniotis
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Article
| Open AccessInherited basis of visceral, abdominal subcutaneous and gluteofemoral fat depots
The inherited basis of body fat distribution is not fully understood. Here, the authors use genetic data and MRI-derived measures of local adiposity to highlight fat depot-specific genetic architecture with implications for cardiometabolic health.
- Saaket Agrawal
- , Minxian Wang
- & Amit V. Khera
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| Open AccessCommon genetic variation associated with Mendelian disease severity revealed through cryptic phenotype analysis
The severity of rare genetic diseases often varies between individuals, but small sample sizes make it difficult to identify contributing factors. Here, the authors use biobank-scale clinical and genetic data to investigate a role for common genetic variation.
- David R. Blair
- , Thomas J. Hoffmann
- & Joseph T. Shieh
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Article
| Open AccessDesmoplakin and periplakin genetically and functionally contribute to eosinophilic esophagitis
Eosinophilic esophagitis (EoE) is a chronic allergic inflammatory disease with a complex underlying genetic etiology. Here, the authors identify a series of rare variants in DSP and PPL in multiplex families with EoE and uncover a pathogenic role for desmosomal dysfunction in EoE.
- Tetsuo Shoda
- , Kenneth M. Kaufman
- & Marc E. Rothenberg
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| Open AccessHuman MLH1/3 variants causing aneuploidy, pregnancy loss, and premature reproductive aging
Proper meiotic chromosome segregation requires mismatch repair genes MLH1 and MLH3, of which variants occur in the human population. Here, the authors use computational predictions and yeast assays to select human MLH1/3 variants for modelling in mice, observing reproductive defects from abnormal levels of crossing over.
- Priti Singh
- , Robert Fragoza
- & John C. Schimenti
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| Open AccessSystematic analysis of exonic germline and postzygotic de novo mutations in bipolar disorder
The significance of rare and de novo variants in bipolar disorder is not well understood. Here, the authors have analyzed whole exome/genome data from trios to identify deleterious de novo variants associated with bipolar disorder.
- Masaki Nishioka
- , An-a Kazuno
- & Atsushi Takata
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| Open AccessPopulation-specific causal disease effect sizes in functionally important regions impacted by selection
Trans-ethnic genetic correlation is significantly less than 1 for many diseases. Here, the authors stratify this correlation by genomic annotations, finding that loci whose causal disease effect sizes differ between ethnicities are likely impacted by selection, particularly positive selection.
- Huwenbo Shi
- , Steven Gazal
- & Alkes L. Price
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Article
| Open AccessThe contribution of X-linked coding variation to severe developmental disorders
Developmental disorders (DDs) are more prevalent in males, thought to be due to X-linked genetic variation. Here, the authors investigate the burden of X-linked coding variants in 11,044 DD patients, showing that this contributes to ~6% of both male and female cases and therefore does not solely explain male bias in DDs.
- Hilary C. Martin
- , Eugene J. Gardner
- & Matthew E. Hurles
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Article
| Open AccessSomatic mosaicism and common genetic variation contribute to the risk of very-early-onset inflammatory bowel disease
Adult forms of inflammatory bowel disease (IBD) are of a polygenic nature, but paediatric and very early onset (VEO) IBD also occur as monogenic forms. Here, using whole exome sequencing, the authors explore both the monogenic and polygenic contribution to VEO-IBD and characterize a rare somatic mosaic VEO-IBD patient.
- Eva Gonçalves Serra
- , Tobias Schwerd
- & Carl A. Anderson
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Article
| Open AccessCold-induced urticarial autoinflammatory syndrome related to factor XII activation
Systemic autoinflammatory syndromes such as cryopyrin-associated periodic syndrome (CAPS) are rare and often involve genes related to the inflammasome. Here, the authors report a syndrome characterised by systemic inflammation and cold-induced urticarial rash associated with a Factor XII-activating mutation.
- Jörg Scheffel
- , Niklas A. Mahnke
- & Karoline Krause
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Article
| Open AccessQuantifying the polygenic contribution to variable expressivity in eleven rare genetic disorders
Rare genetic disorders (RGDs) often exhibit significant clinical variability among affected individuals. Here, Oetjens et al. systematically study the contribution of common genetic variation to variable expressivity of RGDs and find it is frequently influenced by polygenic factors identified in genome-wide association studies of relevant traits.
- M. T. Oetjens
- , M. A. Kelly
- & D. H. Ledbetter
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Article
| Open AccessBi-allelic variants in RNF170 are associated with hereditary spastic paraplegia
Disturbances in IP3 receptor-mediated release of Ca2+ from the endoplasmatic reticulum are associated with neurodegenerative disease. Here, the authors identify in four families with hereditary spastic paraplegia biallelic mutations in RNF170 that associate with increased basal levels of IP3 receptors.
- Matias Wagner
- , Daniel P. S. Osborn
- & Rebecca Schüle
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| Open AccessABCC9-related Intellectual disability Myopathy Syndrome is a KATP channelopathy with loss-of-function mutations in ABCC9
ABCC9 encodes the SUR2 subunit of KATP channels and dominant genetic variants in ABCC9 have been associated with cardiac phenotypes. Here, the authors report recessive ABCC9 mutations in individuals with mild intellectual disability, myopathy and cardiac systolic dysfunction which is associated with loss of KATP channel function.
- Marie F. Smeland
- , Conor McClenaghan
- & Gijs van Haaften
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| Open AccessHuman PI3Kγ deficiency and its microbiota-dependent mouse model reveal immunodeficiency and tissue immunopathology
Causally linking a mutation to clinical phenotypes in rare hereditary diseases is both challenging and illuminating. Here the authors identify PI3Kɣ mutations in a patient with immune dysregulation, and recapitulate the phenotypes in PI3Kɣ-deficient mice by exposing them to natural microbiota from pet-shop mice.
- Andrew J. Takeda
- , Timothy J. Maher
- & Carrie L. Lucas
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Article
| Open AccessCiliary exclusion of Polycystin-2 promotes kidney cystogenesis in an autosomal dominant polycystic kidney disease model
The molecular role of ciliary Polycystin-2 (PC2) in cyst formation and polycystic kidney disease (ADKPD) is unclear. Here, the authors identify a PC2 mutant lacking ciliary localisation but with active Ca2+ channel function in mice, that is sufficient to generate an ADPKD phenotype.
- Rebecca V. Walker
- , Jennifer L. Keynton
- & Dominic P. Norris
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Article
| Open AccessDefects in t6A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome
The biosynthesis of N6-threonylcarbamoylated adenosine 37 in tRNA (t6A) involves the YRDC enzyme and the KEOPS complex. Here, the authors report mutations in YRDC and the KEOPS component GON7 in Galloway-Mowat syndrome and determine the crystal structure of a GON7-containg subcomplex that suggests a role in KEOPS complex stability.
- Christelle Arrondel
- , Sophia Missoury
- & Géraldine Mollet
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| Open AccessMutations in topoisomerase IIβ result in a B cell immunodeficiency
Topoisomerases are required to release topological stress on DNA during replication and transcription. Here, Broderick et al. report genetic variants in TOP2B that cause a syndromic B cell immunodeficiency associated with reduced TOP2B function, defects in B cell development and B cell activation.
- Lori Broderick
- , Shawn Yost
- & Hal M. Hoffman
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Article
| Open AccessPaternal-age-related de novo mutations and risk for five disorders
Advanced paternal age associates with increased risk for psychiatric and developmental disorders in offspring. Here, Taylor et al. utilize parent-child trio exome sequencing data sets to estimate the contribution of paternal age-related de novo mutations to multiple disorders, including heart disease and schizophrenia.
- Jacob L. Taylor
- , Jean-Christophe P. G. Debost
- & Elise B. Robinson
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| Open AccessImproving the diagnostic yield of exome- sequencing by predicting gene–phenotype associations using large-scale gene expression analysis
A genetic diagnosis remains unattainable for many individuals with a rare disease because of incomplete knowledge about the genetic basis of many diseases. Here, the authors present the web-based tool GADO (GeneNetwork Assisted Diagnostic Optimization) that uses public RNA-seq data for prioritization of candidate genes.
- Patrick Deelen
- , Sipko van Dam
- & Lude Franke
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Article
| Open AccessGenome-wide analysis of dental caries and periodontitis combining clinical and self-reported data
Dental caries and periodontitis are among the most common medical conditions. Here, the authors report a GWAS for measures of oral health that reveals 47 risk loci for caries, find genetic correlation with 31 other complex traits and use Mendelian randomization analyses to explore potential causal relationships.
- Dmitry Shungin
- , Simon Haworth
- & Ingegerd Johansson
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Article
| Open AccessMyoglobinopathy is an adult-onset autosomal dominant myopathy with characteristic sarcoplasmic inclusions
Myoglobin is a hemeprotein that reversibly binds oxygen and gives muscle its red color. Here, the authors report a genetic variant in the MB gene that associates with myoglobinopathy, an autosomal dominant progressive myopathy, and altered oxygen binding properties of the mutant protein.
- Montse Olivé
- , Martin Engvall
- & Nigel G. Laing
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Article
| Open AccessHomozygous frameshift mutations in FAT1 cause a syndrome characterized by colobomatous-microphthalmia, ptosis, nephropathy and syndactyly
Loss of the cadherin FAT1 has been associated with nephropathy and epithelial cell adhesion defects. Here, the authors report five families with a syndromic form of coloboma associated with homozygous frameshift variants in FAT1 and recapitulate the phenotype in mutant mice and zebrafish.
- Najim Lahrouchi
- , Aman George
- & Abdelaziz Sefiani
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Article
| Open AccessCombined loss of LAP1B and LAP1C results in an early onset multisystemic nuclear envelopathy
Nuclear envelopathies are a group of diseases caused by genetic mutations in essential nuclear envelope genes. Here, the authors report a nuclear envelopathy with a homozygous nonsense variant in TOR1AIP1 which leads to changes in the nuclear morphology including large nuclear-spanning channels in patients’ fibroblasts.
- Boris Fichtman
- , Fadia Zagairy
- & Ronen Spiegel
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Article
| Open AccessLoss-of-function mutations in QRICH2 cause male infertility with multiple morphological abnormalities of the sperm flagella
Multiple morphological abnormalities of the sperm flagella (MMAF) is a cause of male infertility. Here the authors identify homozygous nonsense mutations of the glutamine rich 2 (QRICH2) gene in two MMAF patients from 2 consanguineous families and show using QRICH2 knockout mice that the protein is required for sperm flagellar formation and motility.
- Ying Shen
- , Feng Zhang
- & Wenming Xu
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Article
| Open AccessGenome-wide meta-analysis implicates mediators of hair follicle development and morphogenesis in risk for severe acne
Acne vulgaris is a chronic inflammation of the skin, the genetic basis of which is incompletely understood. Here, Petridis et al. perform GWAS and meta-analysis for acne in 26,722 individuals and identify 12 novel risk loci that implicate structure and maintenance of the skin in severe acne risk.
- Christos Petridis
- , Alexander A. Navarini
- & Michael A. Simpson
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Article
| Open AccessGenome-wide association meta-analysis yields 20 loci associated with gallstone disease
Genome-wide association studies have so far identified eight risk loci for gallstone disease. Here, the authors perform meta-analysis in cohorts from Iceland and the UK which reveals further 21 common and low-frequency risk variants that highlight the role of bile acid homeostasis in gallstone disease.
- Egil Ferkingstad
- , Asmundur Oddsson
- & Kari Stefansson
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Article
| Open AccessBAFopathies’ DNA methylation epi-signatures demonstrate diagnostic utility and functional continuum of Coffin–Siris and Nicolaides–Baraitser syndromes
Mutations in genes encoding subunits of the BAF complex can cause Coffin–Siris and Nicolaides–Baraitser syndromes. Here the authors identify overlapping DNA methylation signatures in individuals with subtypes of these two syndromes that suggest a functional link and can be used to diagnose subjects with unclear clinical presentations.
- Erfan Aref-Eshghi
- , Eric G. Bend
- & Bekim Sadikovic
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Article
| Open AccessRare truncating variants in the sarcomeric protein titin associate with familial and early-onset atrial fibrillation
Common genetic variants in structural proteins contribute to risk of atrial fibrillation (AF). Here, using whole-exome sequencing, the authors identify rare truncating variants in TTN that associate with familial and early-onset AF and show defects in cardiac sarcomere assembly in ttn.2-mutant zebrafish.
- Gustav Ahlberg
- , Lena Refsgaard
- & Morten S. Olesen
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Article
| Open AccessPathogenic variants in glutamyl-tRNAGln amidotransferase subunits cause a lethal mitochondrial cardiomyopathy disorder
Mitochondrial protein synthesis requires charging a mitochondrial tRNA with its amino acid. Here, the authors describe pathogenic variants in the GatCAB protein complex genes required for the generation of glutaminyl-mt-tRNAGln, that impairs mitochondrial translation and presents with cardiomyopathy.
- Marisa W. Friederich
- , Sharita Timal
- & Johan L. K. Van Hove
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Article
| Open AccessMAP1B mutations cause intellectual disability and extensive white matter deficit
Intellectual disability (ID) is characterized by an intelligence quotient of below 70 and impaired adaptive skills. Here, analyzing whole genome sequences from 31,463 Icelanders, Walters et al. identify variants in MAP1B associated with ID and extensive brain-wide white matter deficits.
- G. Bragi Walters
- , Omar Gustafsson
- & Kari Stefansson
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Article
| Open AccessSLC10A7 mutations cause a skeletal dysplasia with amelogenesis imperfecta mediated by GAG biosynthesis defects
The majority of skeletal dysplasia are caused by pathogenic variants in genes required for glycosaminoglycan (GAG) metabolism. Here, Dubail et al. identify genetic variants in the solute carrier family protein SLC10A7 in families with skeletal dysplasia and amelogenesis imperfecta that disrupt GAG synthesis.
- Johanne Dubail
- , Céline Huber
- & Valérie Cormier-Daire
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| Open AccessA critical view on transgenerational epigenetic inheritance in humans
- Bernhard Horsthemke
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| Open AccessSystematic discovery of germline cancer predisposition genes through the identification of somatic second hits
Inherited germline variants and somatic mutations contribute to cancer. Here, the authors present the statistical method ALFRED that tests the two-hit hypothesis of tumorigenesis and apply it to ~10,000 tumor exomes to identify rare germline variants that affect putative cancer predisposition genes, contributing substantially to cancer risk.
- Solip Park
- , Fran Supek
- & Ben Lehner