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| Open AccessIdentification of putative causal loci in whole-genome sequencing data via knockoff statistics
Association analyses that capture rare and noncoding variants in whole genome sequencing data are limited by factors like statistical power. Here, the authors present KnockoffScreen, a statistical method using the knockoff framework to detect, localise and prioritise rare and common risk variants at genome-wide scale.
- Zihuai He
- , Linxi Liu
- & Iuliana Ionita-Laza
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Article
| Open AccessDetecting and phasing minor single-nucleotide variants from long-read sequencing data
Cellular genetic heterogeneity is common across biological conditions, yet application of long-read sequencing to this subject is limited by error rates. Here, the authors present iGDA, a tool for detection and phasing of minor variants from long-read sequencing data, allowing accurate reconstruction of haplotypes.
- Zhixing Feng
- , Jose C. Clemente
- & Eric E. Schadt
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Article
| Open AccessNext generation plasma proteome profiling to monitor health and disease
The proximity extension assay (PEA) is a popular tool to measure plasma protein levels. Here, the authors extend the proteome coverage of PEA by combining it with next-generation sequencing, enabling the analysis of nearly 1500 proteins from minute amounts of plasma.
- Wen Zhong
- , Fredrik Edfors
- & Mathias Uhlén
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Article
| Open AccessArginine is an epigenetic regulator targeting TEAD4 to modulate OXPHOS in prostate cancer cells
Alterations in metabolism and amino acid usage are common in cancer cells. Here, the authors show in prostate cancer cells that arginine globally upregulates nuclear-encoded oxidative phosphorylation genes by altering histone acetylation and retaining TEAD4 in the nucleus to transactivate genes.
- Chia-Lin Chen
- , Sheng-Chieh Hsu
- & Hsing-Jien Kung
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Article
| Open AccessMicrobiota-based markers predictive of development of Clostridioides difficile infection
Clostridioides difficile infection (CDI) is the most common cause of antibiotic-associated diarrhoea (AAD); however, markers predictive of CDI or AAD development are as yet lacking. Here, to identify markers predictive of CDI, the authors profile the intestinal microbiota of 945 hospitalised patients from 34 hospitals in 6 different European countries and show distinct microbiota enriched in Enterococcus and depleted of Ruminococcus, Blautia, Prevotella and Bifidobacterium compared to non-CDI patients.
- Matilda Berkell
- , Mohamed Mysara
- & Odile Launay
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Article
| Open AccessVariable number tandem repeats mediate the expression of proximal genes
Variable number tandem repeats (VNTRs) are implicated in human diseases yet have been difficult to analyse computationally. Here, the authors describe a neural network method, adVNTR-NN, that allows rapid and accurate genotyping of VNTRs from large whole genome sequencing datasets.
- Mehrdad Bakhtiari
- , Jonghun Park
- & Vineet Bafna
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Article
| Open AccessDeficiency of TMEM53 causes a previously unknown sclerosing bone disorder by dysregulation of BMP-SMAD signaling
Sclerosing bone disorder (SBD) includes a broad spectrum of monogenic diseases characterised by increased bone density. Here, the authors describe a previously unknown SBD in four families caused by mutations in TMEM53 and demonstrate the role this protein plays in BMP signalling during bone formation.
- Long Guo
- , Aritoshi Iida
- & Shiro Ikegawa
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Article
| Open AccessSARS-CoV-2 in severe COVID-19 induces a TGF-β-dominated chronic immune response that does not target itself
Our understanding on the humoral immunity induced by SARS-CoV-2 is still lacking. Here the authors analyze B cell responses at the single cell level to find that, in severe COVID-19 patients, plasmablasts shift from IFN to TGFβ instruction to produce IgA antibodies that are not specific to dominant SARS-CoV-2 antigens.
- Marta Ferreira-Gomes
- , Andrey Kruglov
- & Mir-Farzin Mashreghi
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Article
| Open AccessEngineered yeast genomes accurately assembled from pure and mixed samples
The cost and complexity of whole genome sequencing limits its use in identifying and validating sequences used for genetic engineering and synthetic biology. Here the authors present Prymetime, an integrated workflow to sequence engineered strains and identify engineering in metagenomes.
- Joseph H. Collins
- , Kevin W. Keating
- & Eric M. Young
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Article
| Open AccessA multiplexed, automated evolution pipeline enables scalable discovery and characterization of biosensors
Biosensors are key to engineered biological systems. Here the authors demonstrate rapid de novo in vitro evolution of RNA biosensors of small molecules in a fully automated system.
- Brent Townshend
- , Joy S. Xiang
- & Christina D. Smolke
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Article
| Open AccessLysates of Methylococcus capsulatus Bath induce a lean-like microbiota, intestinal FoxP3+RORγt+IL-17+ Tregs and improve metabolism
Dietary changes can impact the microbial constitution of the gastrointestinal tract and modulate the local immune response. Here, the authors show supplementation using lysates of Methylococcus capsulatus Bath result in changes to the microbiota, modulate Treg populations and metabolic read outs in a dietary control murine model.
- Benjamin A. H. Jensen
- , Jacob B. Holm
- & Tor E. Lea
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Article
| Open AccessDissection of intercellular communication using the transcriptome-based framework ICELLNET
Bulk and single-cell transcriptomic data can be a source of novel insights into how cells interact with each other. Here the authors develop ICELLNET, a global, biologically validated, and easy-to-use framework to dissect cell communication from individual or multiple cell-based transcriptomic profiles.
- Floriane Noël
- , Lucile Massenet-Regad
- & Vassili Soumelis
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Article
| Open AccessAutoMap is a high performance homozygosity mapping tool using next-generation sequencing data
Homozygosity mapping is a useful tool for identifying candidate mutations in recessive conditions, however application to next generation sequencing data has been sub-optimal. Here, the authors present AutoMap, which efficiently identifies runs of homozygosity in whole exome/genome sequencing data.
- Mathieu Quinodoz
- , Virginie G. Peter
- & Carlo Rivolta
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Article
| Open AccessDistinct mechanisms control genome recognition by p53 at its target genes linked to different cell fates
The tumor suppressor p53 is a master regulator of cellular stress response pathways, including cell cycle arrest and apoptosis. Here, the authors identify molecular mechanisms of p53 binding to high- and low-affinity p53 response elements in the genome, linked to cell cycle arrest and pro-apoptotic genes, respectively.
- Marina Farkas
- , Hideharu Hashimoto
- & Steven B. McMahon
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Article
| Open AccessWhole-genome sequencing analysis of the cardiometabolic proteome
The human proteome represents a crucial link between complex disease and genetic/environmental factors. Here, the authors investigate 257 cardiometabolic-relevant protein biomarkers in whole genome sequencing data from 1328 individuals, revealing the genetic architecture underlying biomarker variation.
- Arthur Gilly
- , Young-Chan Park
- & Eleftheria Zeggini
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Article
| Open AccessAnalytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis
Nanopore sequencing (ONT) has been used in SARS-CoV-2 studies, however adoption of ONT for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. Here, the authors perform a comprehensive evaluation of ONT analytical performance on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls.
- Rowena A. Bull
- , Thiruni N. Adikari
- & Ira W. Deveson
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Article
| Open AccessDonkey genomes provide new insights into domestication and selection for coat color
A new donkey reference genome and comparisons with wild asses yields insights into the evolutionary history of donkey domestication and identifies a genetic variant that results in the non-Dun coat colours of domestic donkeys.
- Changfa Wang
- , Haijing Li
- & Jifeng Zhong
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Article
| Open AccessMuscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology
Chromatin structure and topology play important roles in the regulation of gene expression. Here the authors study the spatio-temporal re-organization of promoter-enhancer interactions in pluripotent ES and skeletal muscle stem cells and the corresponding impact on gene expression as a consequence of myogenic commitment and differentiation.
- Nan Zhang
- , Julen Mendieta-Esteban
- & Brian David Dynlacht
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Article
| Open AccessUMI-linked consensus sequencing enables phylogenetic analysis of directed evolution
The success of protein evolution is dependent on the sequence context mutations are introduced into. Here the authors present UMIC-seq that allows consensus generation for closely related genes by using unique molecular identifiers linked to gene variants.
- Paul Jannis Zurek
- , Philipp Knyphausen
- & Florian Hollfelder
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Article
| Open AccessQuantitative and multiplexed chemical-genetic phenotyping in mammalian cells with QMAP-Seq
Identifying chemical-genetic interactions in mammalian cells is limited to low-throughput or computational methods. Here, the authors present QMAP-Seq, a broadly accessible and scalable approach that uses NGS for pooled high-throughput chemical-genetic profiling in mammalian cells.
- Sonia Brockway
- , Geng Wang
- & Marc L. Mendillo
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Article
| Open AccessLarge-scale targeted sequencing identifies risk genes for neurodevelopmental disorders
For many neurodevelopmental disorder (NDD) risk genes, the significance for mutational burden is unestablished. Here, the authors sequence 125 candidate NDD genes in over 16,000 NDD cases; case-control mutational burden analysis identifies 48 genes with a significant burden of severe ultra-rare mutations.
- Tianyun Wang
- , Kendra Hoekzema
- & Evan E. Eichler
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Article
| Open AccessA diploid assembly-based benchmark for variants in the major histocompatibility complex
Accurate, phased assemblies are a key tool in understanding the human genome, particularly in highly polymorphic regions like the medically important MHC. Here the authors provide an assembly-based benchmark for this difficult-to-characterize region.
- Chen-Shan Chin
- , Justin Wagner
- & Justin M. Zook
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Article
| Open AccessLoss of MTX2 causes mandibuloacral dysplasia and links mitochondrial dysfunction to altered nuclear morphology
Mandibuloacral dysplasias (MADs) are rare progeroid syndromes characterized by nuclear morphological and functional abnormalities. Here the authors report that loss of mitochondrial membrane protein MTX2 causes a progeroid MAD sharing clinical features with lamin-associated progeroid syndromes.
- Sahar Elouej
- , Karim Harhouri
- & Annachiara De Sandre-Giovannoli
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Article
| Open AccessQuantitative tRNA-sequencing uncovers metazoan tissue-specific tRNA regulation
The relative abundance of specific tRNA can impact protein production rate, folding, and messenger RNA stability. Here the authors describe QuantM-tRNA seq — a method to monitor tRNA abundance and sequence variants — and uncover distinctions in isodecoder expression between tissues that are independent of the anticodon pool of each tRNA family.
- Otis Pinkard
- , Sean McFarland
- & Jeff Coller
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Article
| Open AccessNon-invasive early detection of cancer four years before conventional diagnosis using a blood test
Patients whose disease is diagnosed in its early stages have better outcomes. In this study, the authors develop a non invasive blood test based on circulating tumor DNA methylation that can potentially detect cancer occurrence even in asymptomatic patients.
- Xingdong Chen
- , Jeffrey Gole
- & Li Jin
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Article
| Open AccessPrediction-based highly sensitive CRISPR off-target validation using target-specific DNA enrichment
Off-target mutations that occur at a frequency below 0.5% can be difficult to detect. Here the authors use predicted off-target amplification to increase detection sensitivity.
- Seung-Hun Kang
- , Wi-jae Lee
- & Seung Hwan Lee
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Article
| Open AccessA universal and independent synthetic DNA ladder for the quantitative measurement of genomic features
Standard units of measurement are required for a quantitative description of the genome. Here, the authors present a universal synthetic DNA ladder that can measure genetic abundance in next-generation sequencing libraries.
- Andre L. M. Reis
- , Ira W. Deveson
- & Tim R. Mercer
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Article
| Open AccessDiscovery and quality analysis of a comprehensive set of structural variants and short tandem repeats
The complexity of structural variation (SV) and short tandem repeats (STRs) makes it necessary to apply different calling and filtering strategies to sequencing datasets. Here, Jakubosky et al. report a comprehensive SV and STR callset from whole-genome sequencing of 477 individuals from iPSCORE and HipSci using five algorithms.
- David Jakubosky
- , Erin N. Smith
- & Kelly A. Frazer
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Article
| Open AccessRapid range shifts and megafaunal extinctions associated with late Pleistocene climate change
The impact of late Pleistocene climate change on ecosystems has been hard to assess. Here, the authors sequence ancient DNA from Hall’s Cave, Texas and find that both plant and vertebrate diversity decreased with cooling, and though plant diversity recovered with rewarming, megafauna went extinct.
- Frederik V. Seersholm
- , Daniel J. Werndly
- & Michael Bunce
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Article
| Open AccessHigh-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing
Until now, the transcriptome of preimplantation mouse embryos has only been analysed by short-read sequencing. Here, the authors perform long-read sequencing to provide a more detailed transcriptome of the preimplantation mouse embryo, identifying various novel transcripts, for example Kdm4dl.
- Yunbo Qiao
- , Chao Ren
- & Wenjie Shu
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Article
| Open AccessChromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution
Horseshoe crabs have been morphologically stable across evolutionary time. Here, the authors generate a chromosome-level assembly for the mangrove horseshoe crab, with implications for innate immunity, and challenging assumptions about the role of genome duplication in adaptive radiation.
- Prashant Shingate
- , Vydianathan Ravi
- & Byrappa Venkatesh
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Article
| Open AccessCollagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis
Collagen production by lung cells is critical to maintain organ architecture but can also drive pathological scarring. Here the authors perform single cell RNA sequencing of collagen-producing lung cells identifying a subset of pathologic fibroblasts characterized by Cthrc1 expression which are concentrated within fibroblastic foci in fibrotic lungs and show a pro-fibrotic phenotype.
- Tatsuya Tsukui
- , Kai-Hui Sun
- & Dean Sheppard
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Article
| Open AccessIncreased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia
Common variants identified by large-scale genomewide association studies cannot account fully account for the heritability of schizophrenia (SCZ). Here, the authors report high-coverage whole-genome sequencing of 1162 SCZ cases and 936 controls and explore the contribution of different types of variants to SCZ.
- Matthew Halvorsen
- , Ruth Huh
- & Jin P. Szatkiewicz
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Article
| Open AccessOXPHOS remodeling in high-grade prostate cancer involves mtDNA mutations and increased succinate oxidation
The re-wiring of the metabolic machinery is a common feature in cancer. Here, the authors show, using paired normal and prostate cancer samples that the cancer samples exhibit a shift to succinate respiration, which is associated with elevated levels of mitochondrial DNA mutations.
- Bernd Schöpf
- , Hansi Weissensteiner
- & Helmut Klocker
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Article
| Open AccessDissecting the early steps of MLL induced leukaemogenic transformation using a mouse model of AML
The oncogene MLL is frequently translocated in leukemia, resulting in oncogenic fusion proteins. Here, the authors report a temporally controlled mouse model of MLL-ENL driven leukemia AND identify therapeutic targets associated with early MLL-ENL driven leukaemogenesis.
- Silvia Basilico
- , Xiaonan Wang
- & Berthold Göttgens
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Article
| Open AccessMajor antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape
Antigenic site B in influenza A virus hemagglutinin (HA) is immunodominant in circulating human H3N2 strains. Using deep mutational scanning, Wu et al. here define the local fitness landscapes of HA antigenic site B in six human H3N2 strains, providing insights into evolvability of influenza antigenicity.
- Nicholas C. Wu
- , Jakub Otwinowski
- & Ian A. Wilson
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Article
| Open AccessCharacterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling
Most currently available statistical tools for the analysis of ATAC-seq data were repurposed from tools developed for other functional genomics data (e.g. ChIP-seq). Here, Gabitto et al develop ChromA, a Bayesian statistical approach for the analysis of both bulk and single-cell ATAC-seq data.
- Mariano I. Gabitto
- , Anders Rasmussen
- & Richard Bonneau
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Article
| Open AccessHigh-throughput identification of synthetic riboswitches by barcode-free amplicon-sequencing in human cells
Riboswitches can mediate ligand-dependent RNA cleavage and splicing to control gene expression. Here the authors present a method to functionally screen large libraries and identify functional variants.
- Benjamin Strobel
- , Maike Spöring
- & Sebastian Kreuz
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Article
| Open AccessBridging non-overlapping reads illuminates high-order epistasis between distal protein sites in a GPCR
Epistasis effects among amino acids at distal sites within binding pockets can have important impacts on protein fitness landscapes. Here the authors present BRIDGE, which matches non-overlapping sequence reads with their cognate DNA templates.
- Justin I. Yoo
- , Patrick S. Daugherty
- & Michelle A. O’Malley
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Article
| Open AccessGenome-wide rare variant analysis for thousands of phenotypes in over 70,000 exomes from two cohorts
Population-based association analyses of rare genetic variants with complex traits are limited by the availability of data from sufficiently large cohorts. Here, Cirulli et al. report gene-based collapsing analysis of exomes from 49,960 participants of the UK Biobank and 21,866 participants of the Healthy Nevada Project over a total of 4377 traits.
- Elizabeth T. Cirulli
- , Simon White
- & Nicole L. Washington
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Article
| Open AccessTranscriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain
Non-human primates share many features with humans and are an important animal model in neuroscience. Here, the authors present a comprehensive transcriptomic and open chromatin atlas of the rhesus macaque brain.
- Senlin Yin
- , Keying Lu
- & Yang Yu
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Article
| Open AccessIdentification of recurrent FHL2-GLI2 oncogenic fusion in sclerosing stromal tumors of the ovary
Little is known about the genetics of sclerosing stromal tumor of the ovary, a rare type of sex cord-stromal tumor. Here, the authors use sequencing strategies to show that in a cohort of 26 tumor samples 65% carry a FHL2-GLI2 fusion gene and demonstrate in vitro that the fusion gene has oncogenic properties.
- Sarah H. Kim
- , Arnaud Da Cruz Paula
- & Britta Weigelt
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Article
| Open AccessGraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs
Structural variants may be omitted in sequence analysis despite their importance in genome variation and phenotypic impact. Here the authors present GraphTyper2, which uses pangenome graphs to genotype structural variants using short-reads and can be applied in large-scale sequencing studies.
- Hannes P. Eggertsson
- , Snaedis Kristmundsdottir
- & Pall Melsted
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Article
| Open AccessCUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples
Genomics DNA library preparation from formalin-fixed paraffin-embedded tissues is challenging. Here the authors describe CUTseq that uses restriction enzymes and in vitro amplification to barcode samples for reduced representation genome sequencing.
- Xiaolu Zhang
- , Silvano Garnerone
- & Nicola Crosetto
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Article
| Open AccessDe novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes
Large whole-exome sequencing studies have suggested that the genetic architecture of syndromic congenital heart disease (CHD) is different from sporadic forms. Here, Watkins et al. estimate the relative contribution of damaging recessive and de novo genotypes to CHD in 2391 trios and find them to be associated with different gene functions.
- W. Scott Watkins
- , E. Javier Hernandez
- & Martin Tristani-Firouzi
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Article
| Open AccessSaturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution
Interpreting genetic variation in the noncoding genome remains challenging, with functional effects difficult to predict. Here, the authors perform saturation mutagenesis combined with massively parallel reporter assays for 20 disease-associated regulatory elements, quantifying the effects of over 30,000 variants.
- Martin Kircher
- , Chenling Xiong
- & Nadav Ahituv
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Article
| Open AccessFDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science
To be able to use infectious disease next generation sequencing as a diagnostic tool, appropriate reference datasets are required. Here, Sichtig et al. describe FDA-ARGOS, a reference database for high-quality microbial reference genomes, and demonstrate its utility on the example of two use cases.
- Heike Sichtig
- , Timothy Minogue
- & Uwe Scherf
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Article
| Open AccessAMPA receptor GluA2 subunit defects are a cause of neurodevelopmental disorders
Genetic variants in ionotropic glutamate receptors have been implicated in neurodevelopmental disorders. Here, the authors report heterozygous de novo mutations in the GRIA2 gene in 28 individuals with intellectual disability and neurodevelopmental abnormalities associated with reduced Ca2+ transport and AMPAR currents.”
- Vincenzo Salpietro
- , Christine L. Dixon
- & Henry Houlden
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Article
| Open AccessA genome-wide scan statistic framework for whole-genome sequence data analysis
Whole-genome sequencing data reveals a large number of variants for testing their associations with phenotypic traits and diseases. Here, the authors develop WGScan, a statistical method for detecting the existence and estimating the locations of the association signal at genome-wide scale.
- Zihuai He
- , Bin Xu
- & Iuliana Ionita-Laza