Whole-genome sequencing identifies functional noncoding variation in SEMA3C that cosegregates with dyslexia in a multigenerational family

AbstractDyslexia is a common heritable developmental disorder involving impaired reading abilities. Its genetic underpinnings are thought to be complex and heterogeneous, involving common and rare genetic variation. Multigenerational families segregating apparent monogenic forms of language-related disorders can provide useful entrypoints into biological pathways. In the present study, we performed a genome-wide linkage scan in a three-generational family in which dyslexia affects 14 of its 30 members and seems to be transmitted with an autosomal dominant pattern of inheritance. We identified a locus on chromosome 7q21.11 which cosegregated with dyslexia status, with the exception of two cases of phenocopy (LOD = 2.83). Whole-genome sequencing of key individuals enabled the assessment of coding and noncoding variation in the family. Two rare single-nucleotide variants (rs144517871 and rs143835534) within the first intron of the SEMA3C gene cosegregated with the 7q21.11 risk haplotype. In silico characterization of these two variants predicted effects on gene regulation, which we functionally validated for rs144517871 in human cell lines using luciferase reporter assays. SEMA3C encodes a secreted protein that acts as a guidance cue in several processes, including cortical neuronal migration and cellular polarization. We hypothesize that these intronic variants could have a cis-regulatory effect on SEMA3C expression, making a contribution to dyslexia susceptibility in this family.

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Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

10.1101/316976 ◽

2018 ◽

Cited By ~ 4

Author(s):

Maxime Garcia ◽

Szilveszter Juhos ◽

Malin Larsson ◽

Pall I. Olason ◽

Marcel Martin ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Open Source ◽

Genome Sequencing ◽

Development Project ◽

Whole Genome ◽

Sequencing Analysis ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Insertion And Deletion ◽

Sample Heterogeneity

AbstractSummaryWhole-genome sequencing (WGS) is a cornerstone of precision medicine, but portable and reproducible open-source workflows for WGS analyses of germline and somatic variants are lacking. We present Sarek, a modular, comprehensive, and easy-to-install workflow, combining a range of software for the identification and annotation of single-nucleotide variants (SNVs), insertion and deletion variants (indels), structural variants, tumor sample heterogeneity, and karyotyping from germline or paired tumor/normal samples. Sarek is implemented in a bioinformatics workflow language (Nextflow) with Docker and Singularity compatible containers, ensuring easy deployment and full reproducibility at any Linux based compute cluster or cloud computing environment. Sarek supports the human reference genomes GRCh37 and GRCh38, and can readily be used both as a core production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups.AvailabilitySource code and instructions for local installation are available at GitHub (https://github.com/SciLifeLab/Sarek) under the MIT open-source license, and we invite the research community to contribute additional functionality as a collaborative open-source development project.

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Fine Mapping Using Whole-Genome Sequencing Confirms Anti-Müllerian Hormone as a Major Gene for Sex Determination in Farmed Nile Tilapia (Oreochromis niloticus L.)

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400297 ◽

2019 ◽

Vol 9 (10) ◽

pp. 3213-3223 ◽

Cited By ~ 8

Author(s):

Giovanna Cáceres ◽

María E. López ◽

María I. Cádiz ◽

Grazyella M. Yoshida ◽

Ana Jedlicki ◽

...

Keyword(s):

Sex Determination ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Oreochromis Niloticus ◽

Nile Tilapia ◽

Major Gene ◽

Whole Genome ◽

Important Species ◽

Genome Wide ◽

A Genome

Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Intensive production promotes the use of monosex animals, due to an important dimorphism that favors male growth. Currently, the main mechanism to obtain all-male populations is the use of hormones in feeding during larval and fry phases. Identifying genomic regions associated with sex determination in Nile tilapia is a research topic of great interest. The objective of this study was to identify genomic variants associated with sex determination in three commercial populations of Nile tilapia. Whole-genome sequencing of 326 individuals was performed, and a total of 2.4 million high-quality bi-allelic single nucleotide polymorphisms (SNPs) were identified after quality control. A genome-wide association study (GWAS) was conducted to identify markers associated with the binary sex trait (males = 1; females = 0). A mixed logistic regression GWAS model was fitted and a genome-wide significant signal comprising 36 SNPs, spanning a genomic region of 536 kb in chromosome 23 was identified. Ten out of these 36 genetic variants intercept the anti-Müllerian (Amh) hormone gene. Other significant SNPs were located in the neighboring Amh gene region. This gene has been strongly associated with sex determination in several vertebrate species, playing an essential role in the differentiation of male and female reproductive tissue in early stages of development. This finding provides useful information to better understand the genetic mechanisms underlying sex determination in Nile tilapia.

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Contributions of de novo variants to systemic lupus erythematosus

European Journal of Human Genetics ◽

10.1038/s41431-020-0698-5 ◽

2020 ◽

Vol 29 (1) ◽

pp. 184-193 ◽

Cited By ~ 1

Author(s):

Jonas Carlsson Almlöf ◽

Sara Nystedt ◽

Aikaterini Mechtidou ◽

Dag Leonard ◽

Maija-Leena Eloranta ◽

...

Keyword(s):

Systemic Lupus Erythematosus ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Lupus Erythematosus ◽

De Novo ◽

Whole Genome ◽

Gene Promoters ◽

Single Nucleotide Variants ◽

Systemic Lupus ◽

Promoter Regions

AbstractBy performing whole-genome sequencing in a Swedish cohort of 71 parent-offspring trios, in which the child in each family is affected by systemic lupus erythematosus (SLE, OMIM 152700), we investigated the contribution of de novo variants to risk of SLE. We found de novo single nucleotide variants (SNVs) to be significantly enriched in gene promoters in SLE patients compared with healthy controls at a level corresponding to 26 de novo promoter SNVs more in each patient than expected. We identified 12 de novo SNVs in promoter regions of genes that have been previously implicated in SLE, or that have functions that could be of relevance to SLE. Furthermore, we detected three missense de novo SNVs, five de novo insertion-deletions, and three de novo structural variants with potential to affect the expression of genes that are relevant for SLE. Based on enrichment analysis, disease-affecting de novo SNVs are expected to occur in one-third of SLE patients. This study shows that de novo variants in promoters commonly contribute to the genetic risk of SLE. The fact that de novo SNVs in SLE were enriched to promoter regions highlights the importance of using whole-genome sequencing for identification of de novo variants.

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The Genetic Diversification of a Single Bluetongue Virus Strain Using an In Vitro Model of Alternating-Host Transmission

Viruses ◽

10.3390/v12091038 ◽

2020 ◽

Vol 12 (9) ◽

pp. 1038 ◽

Cited By ~ 1

Author(s):

Jennifer H. Kopanke ◽

Justin S. Lee ◽

Mark D. Stenglein ◽

Christie E. Mayo

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetic Stability ◽

Bluetongue Virus ◽

Genomic Structure ◽

Field Isolate ◽

Viral Population ◽

Whole Genome ◽

Single Nucleotide Variants

Bluetongue virus (BTV) is an arbovirus that has been associated with dramatic epizootics in both wild and domestic ruminants in recent decades. As a segmented, double-stranded RNA virus, BTV can evolve via several mechanisms due to its genomic structure. However, the effect of BTV’s alternating-host transmission cycle on the virus’s genetic diversification remains poorly understood. Whole genome sequencing approaches offer a platform for investigating the effect of host-alternation across all ten segments of BTV’s genome. To understand the role of alternating hosts in BTV’s genetic diversification, a field isolate was passaged under three different conditions: (i) serial passages in Culicoides sonorensis cells, (ii) serial passages in bovine pulmonary artery endothelial cells, or (iii) alternating passages between insect and bovine cells. Aliquots of virus were sequenced, and single nucleotide variants were identified. Measures of viral population genetics were used to quantify the genetic diversification that occurred. Two consensus variants in segments 5 and 10 occurred in virus from all three conditions. While variants arose across all passages, measures of genetic diversity remained largely similar across cell culture conditions. Despite passage in a relaxed in vitro system, we found that this BTV isolate exhibited genetic stability across passages and conditions. Our findings underscore the valuable role that whole genome sequencing may play in improving understanding of viral evolution and highlight the genetic stability of BTV.

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Local Ancestry Prediction with PyLAE

10.1101/2020.11.13.380105 ◽

2020 ◽

Author(s):

Alexander Smetanin ◽

Nikita Moshkov ◽

Tatiana V. Tatarinova

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Computational Efficiency ◽

Source Code ◽

High Density ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Local Ancestry ◽

A Genome

AbstractSummaryWe developed PyLAE - a new tool for determining local ancestry along a genome using whole-genome sequencing data or high-density genotyping experiments. PyLAE can process an arbitrarily large number of ancestral populations (with or without an informative prior). Since PyLAE does not involve estimation of many parameters, it can process thousands of genomes within a day. Computational efficiency, straightforward presentation of results, and an ease of installation makes PyLAE a useful tool to study admixed populations.Availability and implementationThe source code and installation manual are available at https://github.com/smetam/pylae.

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Identification of Pathogenic Structural Variants in Rare Disease Patients through Genome Sequencing

10.1101/627661 ◽

2019 ◽

Cited By ~ 2

Author(s):

James M. Holt ◽

Camille L. Birch ◽

Donna M. Brown ◽

Manavalan Gajapathy ◽

Nadiya Sosonkina ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Rare Disease ◽

Genome Sequencing ◽

Genomic Analysis ◽

Whole Genome ◽

Structural Variants ◽

Single Nucleotide Variants ◽

Standard Clinical Practice ◽

Wide Range ◽

Genetic Features

AbstractPurposeClinical whole genome sequencing is becoming more common for determining the molecular diagnosis of rare disease. However, standard clinical practice often focuses on small variants such as single nucleotide variants and small insertions/deletions. This leaves a wide range of larger “structural variants” that are not commonly analyzed in patients.MethodsWe developed a pipeline for processing structural variants for patients who received whole genome sequencing through the Undiagnosed Diseases Network (UDN). This pipeline called structural variants, stored them in an internal database, and filtered the variants based on internal frequencies and external annotations. The remaining variants were manually inspected and then interesting findings were reported as research variants to clinical sites in the UDN.ResultsOf 477 analyzed UDN cases, 286 cases (≈ 60%) received at least one structural variant as a research finding. The variants in 16 cases (≈ 4%) are considered “Certain” or “Highly likely” molecularly diagnosed and another 4 cases are currently in review. Of those 20 cases, at least 13 were identified originally through our pipeline with one finding leading to identification of a new disease. As part of this paper, we have also released the collection of variant calls identified in our cohort along with heterozygous and homozygous call counts. This data is available at https://github.com/HudsonAlpha/UDN_SV_export.ConclusionStructural variants are key genetic features that should be analyzed during routine clinical genomic analysis. For our UDN patients, structural variants helped solve ≈ 4% of the total number of cases (≈ 13% of all genome sequencing solves), a success rate we expect to improve with better tools and greater understanding of the human genome.

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Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani

10.1101/2021.06.28.450143 ◽

2021 ◽

Author(s):

Severin Einspanier ◽

Tamara Susanto ◽

Nicole Metz ◽

Pieter J. Wolters ◽

Vivianne G.A.A. Vleeshouwers ◽

...

Keyword(s):

Genetic Diversity ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Fungicide Resistance ◽

Early Blight ◽

Management Strategies ◽

Resistance Management ◽

Alternaria Solani ◽

Whole Genome ◽

A Genome

Early blight of potato is caused by the fungal pathogen Alternaria solani and is an increasing problem worldwide. The primary strategy to control the disease is applying fungicides such as succinate dehydrogenase inhibitors (SDHI). SDHI-resistant strains, showing reduced sensitivity to treatments, appeared in Germany in 2013, five years after introduction of SDHIs. Two primary mutations in the Sdh complex (SdhB-H278Y and SdhC-H134R) have been frequently found throughout Europe. How these resistances arose and spread, and whether they are linked to other genomic features, remains unknown. We performed whole-genome sequencing for A. solani isolates from potato fields across Europe (Germany, Sweden, Belgium, and Serbia) to better understand the pathogen's genetic diversity in general and understand the development and spread of the genetic mutations that lead to SDHI resistance. We used ancestry analysis and phylogenetics to determine the genetic background of 48 isolates. The isolates can be grouped into 7 genotypes. These genotypes do not show a geographical pattern but appear spread throughout Europe. The Sdh mutations appear in different genetic backgrounds, suggesting they arose independently, and the observed admixtures might indicate a higher adaptive potential in the fungus than previously thought. Our research gives insights into the genetic diversity of A. solani on a genome level. The mixed occurrence of different genotypes and apparent admixture in the populations indicate higher genomic complexity than anticipated. The conclusion that SDHI tolerance arose multiple times independently has important implications for future fungicide resistance management strategies. These should not solely focus on preventing the spread of isolates between locations but also on limiting population size and the selective pressure posed by fungicides in a given field to avoid the rise of new mutations in other genetic backgrounds.

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Assessing reproducibility of inherited variants detected with short-read whole genome sequencing

Genome Biology ◽

10.1186/s13059-021-02569-8 ◽

2022 ◽

Vol 23 (1) ◽

Author(s):

Bohu Pan ◽

Luyao Ren ◽

Vitor Onuchic ◽

Meijian Guan ◽

Rebecca Kusko ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Precision Medicine ◽

Genome Sequencing ◽

Whole Genome ◽

Single Nucleotide Variants ◽

Short Read ◽

Sequencing Platforms ◽

The Impact ◽

Two Populations

Abstract Background Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically assessing reproducibility of inherited variants with WGS and impact of each step in the process is needed for understanding and improving quality of inherited variants from WGS. Results To dissect the impact of factors involved in detection of inherited variants with WGS, we sequence triplicates of eight DNA samples representing two populations on three short-read sequencing platforms using three library kits in six labs and call variants with 56 combinations of aligners and callers. We find that bioinformatics pipelines (callers and aligners) have a larger impact on variant reproducibility than WGS platform or library preparation. Single-nucleotide variants (SNVs), particularly outside difficult-to-map regions, are more reproducible than small insertions and deletions (indels), which are least reproducible when > 5 bp. Increasing sequencing coverage improves indel reproducibility but has limited impact on SNVs above 30×. Conclusions Our findings highlight sources of variability in variant detection and the need for improvement of bioinformatics pipelines in the era of precision medicine with WGS.

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AmpliCoV: Rapid Whole-Genome Sequencing Using Multiplex PCR Amplification and Real-Time Oxford Nanopore MinION Sequencing Enables Rapid Variant Identification of SARS-CoV-2

Frontiers in Microbiology ◽

10.3389/fmicb.2021.651151 ◽

2021 ◽

Vol 12 ◽

Author(s):

Annika Brinkmann ◽

Sophie-Luisa Ulm ◽

Steven Uddin ◽

Sophie Förster ◽

Dominique Seifert ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Real Time ◽

Genome Sequencing ◽

Phylogenetic Analyses ◽

Diagnostic Methods ◽

Virus Concentration ◽

Sequence Information ◽

Whole Genome ◽

Oxford Nanopore ◽

A Genome

Since the emergence of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in December 2019, the scientific community has been sharing data on epidemiology, diagnostic methods, and whole-genomic sequences almost in real time. The latter have already facilitated phylogenetic analyses, transmission chain tracking, protein modeling, the identification of possible therapeutic targets, timely risk assessment, and identification of novel variants. We have established and evaluated an amplification-based approach for whole-genome sequencing of SARS-CoV-2. It can be used on the miniature-sized and field-deployable sequencing device Oxford Nanopore MinION, with sequencing library preparation time of 10 min. We show that the generation of 50,000 total reads per sample is sufficient for a near complete coverage (>90%) of the SARS-CoV-2 genome directly from patient samples even if virus concentration is low (Ct 35, corresponding to approximately 5 genome copies per reaction). For patient samples with high viral load (Ct 18–24), generation of 50,000 reads in 1–2 h was shown to be sufficient for a genome coverage of >90%. Comparison to Illumina data reveals an accuracy that suffices to identify virus mutants. AmpliCoV can be applied whenever sequence information on SARS-CoV-2 is required rapidly, for instance for the identification of circulating virus mutants.

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Whole-genome sequencing suggests a role of MIF in the pathophysiology of TEMPI syndrome

Blood Advances ◽

10.1182/bloodadvances.2020003783 ◽

2021 ◽

Vol 5 (12) ◽

pp. 2563-2568

Author(s):

Chunyan Sun ◽

Jian Xu ◽

Bo Zhang ◽

Haifan Huang ◽

Lei Chen ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Plasma Cells ◽

Whole Genome ◽

Chromosome 2 ◽

Single Nucleotide Variants ◽

Intrapulmonary Shunting ◽

Complex Structural ◽

Fluid Collections

TEMPI syndrome (telangiectasias, elevated erythropoietin level and erythrocytosis, monoclonal gammopathy, perinephric fluid collections, and intrapulmonary shunting) is a newly defined multisystemic disease with its pathophysiology largely unknown. Here, we report the whole-genome sequencing (WGS) analysis on the tumor-normal paired cells from a patient with TEMPI syndrome. WGS revealed somatic nonsynonymous single-nucleotide variants, including SLC7A8, NRP2, and AQP7. Complex structural variants of chromosome 2 were found, particularly within regions where some putative oncogenes reside. Of potential clinical relevance, duplication of 22q11.23 was identified, and the expression of the located gene macrophage migration inhibitory factor (MIF) was significantly upregulated in 3 patients with TEMPI syndrome. Importantly, the level of serum MIF in one patient with TEMPI syndrome was significantly decreased in accordance with the downtrend of plasma cells, M-protein, hemoglobin, and erythropoietin and the improvement of telangiectasias, perinephric fluid collections, and intrapulmonary shunting after treatment with plasma cell–directed therapy. In conclusion, our study provides insights into the genomic landscape and suggests a role of MIF in the pathophysiology of TEMPI syndrome.

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