scholarly journals Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing

2021 ◽  
Vol 22 (19) ◽  
pp. 10400
Author(s):  
H. Busra Cagirici ◽  
Bala Ani Akpinar ◽  
Taner Z. Sen ◽  
Hikmet Budak
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Variant Calling ◽  
High Sensitivity ◽  
Whole Exome ◽  
The Impact ◽  
Multiple Reference ◽  
Reference Genomes ◽  
Selection Of ◽  
Variant Identification

The highly challenging hexaploid wheat (Triticum aestivum) genome is becoming ever more accessible due to the continued development of multiple reference genomes, a factor which aids in the plight to better understand variation in important traits. Although the process of variant calling is relatively straightforward, selection of the best combination of the computational tools for read alignment and variant calling stages of the analysis and efficient filtering of the false variant calls are not always easy tasks. Previous studies have analyzed the impact of methods on the quality metrics in diploid organisms. Given that variant identification in wheat largely relies on accurate mining of exome data, there is a critical need to better understand how different methods affect the analysis of whole exome sequencing (WES) data in polyploid species. This study aims to address this by performing whole exome sequencing of 48 wheat cultivars and assessing the performance of various variant calling pipelines at their suggested settings. The results show that all the pipelines require filtering to eliminate false-positive calls. The high consensus among the reference SNPs called by the best-performing pipelines suggests that filtering provides accurate and reproducible results. This study also provides detailed comparisons for high sensitivity and precision at individual and population levels for the raw and filtered SNP calls.

scholarly journals IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples

2016 ◽  
Vol 23 (4) ◽  
pp. 721-730 ◽  
Author(s):  
Jennifer Hintzsche ◽  
Jihye Kim ◽  
Vinod Yadav ◽  
Carol Amato ◽  
Steven E Robinson ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Impact Analysis ◽  
Resistance Mutation ◽  
Braf Inhibitor ◽  
Egfr Mutations ◽  
Analysis Pipeline ◽  
Whole Exome ◽  
The Impact ◽  
Inhibitor Treatment

Abstract Objective Currently, there is a disconnect between finding a patient’s relevant molecular profile and predicting actionable therapeutics. Here we develop and implement the Integrating Molecular Profiles with Actionable Therapeutics (IMPACT) analysis pipeline, linking variants detected from whole-exome sequencing (WES) to actionable therapeutics. Methods and materials The IMPACT pipeline contains 4 analytical modules: detecting somatic variants, calling copy number alterations, predicting drugs against deleterious variants, and analyzing tumor heterogeneity. We tested the IMPACT pipeline on whole-exome sequencing data in The Cancer Genome Atlas (TCGA) lung adenocarcinoma samples with known EGFR mutations. We also used IMPACT to analyze melanoma patient tumor samples before treatment, after BRAF-inhibitor treatment, and after BRAF- and MEK-inhibitor treatment. Results IMPACT Food and Drug Administration (FDA) correctly identified known EGFR mutations in the TCGA lung adenocarcinoma samples. IMPACT linked these EGFR mutations to the appropriate FDA-approved EGFR inhibitors. For the melanoma patient samples, we identified NRAS p.Q61K as an acquired resistance mutation to BRAF-inhibitor treatment. We also identified CDKN2A deletion as a novel acquired resistance mutation to BRAFi/MEKi inhibition. The IMPACT analysis pipeline predicts these somatic variants to actionable therapeutics. We observed the clonal dynamic in the tumor samples after various treatments. We showed that IMPACT not only helped in successful prioritization of clinically relevant variants but also linked these variations to possible targeted therapies. Conclusion IMPACT provides a new bioinformatics strategy to delineate candidate somatic variants and actionable therapies. This approach can be applied to other patient tumor samples to discover effective drug targets for personalized medicine. IMPACT is publicly available at http://tanlab.ucdenver.edu/IMPACT.

scholarly journals Analysis of whole exome sequencing in severe mental illness hints at selection of brain development and immune related genes

2021 ◽  
Author(s):  
Jayant Mahadevan ◽  
Ajai Kumar Pathak ◽  
Alekhya Vemula ◽  
Ravi Kumar Nadella ◽  
Biju Viswanath ◽  
...  
Keyword(s):  
Mental Illness ◽  
Severe Mental Illness ◽  
Positive Selection ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Association Studies ◽  
Psychiatric Disease ◽  
Genome Wide Association Studies ◽  
Whole Exome ◽  
Selection Of

Evolutionary trends may underlie some aspects of the risk for common, non-communicable disorders, including psychiatric disease. We analyzed whole exome sequencing data from 80 unique individuals from India coming from families with two or more individuals with severe mental illness. We used Population Branch Statistics (PBS) to identify variants and genes under positive selection and identified 75 genes as candidates for positive selection. Of these, 20 were previously associated with Schizophrenia, Alzheimers disease and cognitive abilities in genome wide association studies. We then checked whether any of these 75 genes were involved in common biological pathways or related to specific cellular or molecular functions. We found that immune related pathways and functions related to innate immunity such as antigen binding were over-represented. We also evaluated for the presence of Neanderthal introgressed segments in these genes and found Neanderthal introgression in a single gene out of the 75 candidate genes. However, the introgression pattern indicates the region is unlikely to be the source for selection. Our findings hint at how selection pressures in individuals from families with a history of severe mental illness may diverge from the general population. Further, it also provides insights into the genetic architecture of severe mental illness, such as schizophrenia and its link to immune factors.

scholarly journals Novel metrics to measure coverage in whole exome sequencing datasets reveal local and global non-uniformity

2016 ◽  
Author(s):  
Qingyu Wang ◽  
Cooduvalli S. Shashikant ◽  
Matthew Jensen ◽  
Naomi S. Altman ◽  
Santhosh Girirajan
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Gc Content ◽  
Variant Calling ◽  
Segmental Duplications ◽  
Repeat Elements ◽  
Whole Exome ◽  
Detailed Assessment ◽  
Major Shortcoming ◽  
Low Coverage

ABSTRACTWhole Exome Sequencing (WES) is a powerful clinical diagnostic tool for discovering the genetic basis of many diseases. A major shortcoming of WES is uneven coverage of sequence reads over the exome targets contributing to many low coverage regions, which hinders accurate variant calling. In this study, we devised two novel metrics, Cohort Coverage Sparseness (CCS) and Unevenness (UE) Scores for a detailed assessment of the distribution of coverage of sequence reads. Employing these metrics we revealed non-uniformity of coverage and low coverage regions in the WES data generated by three different platforms. This non-uniformity of coverage is both local (coverage of a given exon across different platforms) and global (coverage of all exons across the genome in the given platform). The low coverage regions encompassing functionally important genes were often associated with high GC content, repeat elements and segmental duplications. While a majority of the problems associated with WES are due to the limitations of the capture methods, further refinements in WES technologies have the potential to enhance its clinical applications.

scholarly journals Deaminase associated single nucleotide variants in blood and saliva-derived exomes from healthy subjects

2019 ◽  
Author(s):  
Nathan E. Hall ◽  
Jared Mamrot ◽  
Christopher M.A. Frampton ◽  
Prue Read ◽  
Edward J. Steele ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Healthy Subjects ◽  
Intraclass Correlation ◽  
Correlation Coefficients ◽  
Healthy Individuals ◽  
Intraclass Correlation Coefficients ◽  
Whole Exome ◽  
The Impact ◽  
Group 1

AbstractBackgroundDeaminases play an important role in shaping inherited and somatic variants. Disease related SNVs are associated with deaminase mutagenesis and genome instability. Here, we investigate the reproducibility and variance of whole exome SNV calls in blood and saliva of healthy subjects and analyze variants associated with AID, ADAR, APOBEC3G and APOBEC3B deaminase sequence motifs.MethodsSamples from twenty-four healthy Caucasian volunteers, allocated into two groups, underwent whole exome sequencing. Group 1 (n=12) analysis involved one blood and four saliva replicates. A single saliva sample was sequenced for Group 2 subjects (n=12). Overall, a total of 72 whole exome datasets were analyzed. Biological (Group 1 & 2) and technical (Group 1) variance of SNV calls and deaminase metrics were calculated and analyzed using intraclass correlation coefficients. Candidate somatic SNVs were identified and evaluated.ResultsWe report high blood-saliva concordance in germline SNVs from whole exome sequencing. Concordant SNVs, found in all subject replicates, accounted for 97% of SNVs located within the protein coding sequence of genes. Discordant SNVs have a 30% overlap with variants that fail gnomAD quality filters and are less likely to be found in dbSNP. SNV calls and deaminase-associated metrics were found to be reproducible and robust (intraclass correlation coefficients >0.95). No somatic SNVs were conclusively identified when comparing blood and saliva samples.ConclusionsSaliva and blood both provide high quality sources of DNA for whole exome sequencing, with no difference in ability to resolve SNVs and deaminase-associated metrics. We did not identify somatic SNVs when comparing blood and saliva of healthy individuals, and we conclude that more specialized investigative methods are required to comprehensively assess the impact of deaminase activity on genome stability in healthy individuals.

scholarly journals Categorized Genetic Analysis in Childhood-Onset Cardiomyopathy

2020 ◽  
Vol 13 (5) ◽  
pp. 504-514
Author(s):  
Zuhair N. Al-Hassnan ◽  
Abdulrahman Almesned ◽  
Sahar Tulbah ◽  
Ali Alakhfash ◽  
Faten Alhadeq ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genome Sequencing ◽  
Founder Mutation ◽  
Genetic Test ◽  
Whole Genome ◽  
Childhood Onset ◽  
Whole Exome ◽  
The Impact

Background: Childhood-onset cardiomyopathy is a heterogeneous group of conditions the cause of which is largely unknown. The influence of consanguinity on the genetics of cardiomyopathy has not been addressed at a large scale. Methods: To unravel the genetic cause of childhood-onset cardiomyopathy in a consanguineous population, a categorized approach was adopted. Cases with childhood-onset cardiomyopathy were consecutively recruited. Based on the likelihood of founder mutation and on the clinical diagnosis, genetic test was categorized to either (1) targeted genetic test with targeted mutation test, single-gene test, or multigene panel for Noonan syndrome, or (2) untargeted genetic test with whole-exome sequencing or whole-genome sequencing. Several bioinformatics tools were used to filter the variants. Results: Two-hundred five unrelated probands with various forms of cardiomyopathy were evaluated. The median age of presentation was 10 months. In 30.2% (n=62), targeted genetic test had a yield of 82.7% compared with 33.6% for whole-exome sequencing/whole-genome sequencing (n=143) giving an overall yield of 53.7%. Strikingly, 96.4% of the variants were homozygous, 9% of which were found in 4 dominant genes. Homozygous variants were also detected in 7 novel candidates ( ACACB, AASDH, CASZ1, FLII, RHBDF1, RPL3L, ULK1 ). Conclusions: Our work demonstrates the impact of consanguinity on the genetics of childhood-onset cardiomyopathy, the value of adopting a categorized population-sensitive genetic approach, and the opportunity of uncovering novel genes. Our data suggest that if a founder mutation is not suspected, adopting whole-exome sequencing/whole-genome sequencing as a first-line test should be considered.

scholarly journals CopyDetective: Detection threshold–aware copy number variant calling in whole-exome sequencing data

GigaScience ◽  
2020 ◽  
Vol 9 (11) ◽  
Author(s):  
Sarah Sandmann ◽  
Marius Wöste ◽  
Aniek O de Graaf ◽  
Birgit Burkhardt ◽  
Joop H Jansen ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Copy Number ◽  
Detection Threshold ◽  
Variant Calling ◽  
Superior Performance ◽  
Quality Analysis ◽  
Data Set ◽  
Detection Thresholds ◽  
Whole Exome

Abstract Background Copy number variants (CNVs) are known to play an important role in the development and progression of several diseases. However, detection of CNVs with whole-exome sequencing (WES) experiments is challenging. Usually, additional experiments have to be performed. Findings We developed a novel algorithm for somatic CNV calling in matched WES data called “CopyDetective". Different from other approaches, CNV calling with CopyDetective consists of a 2-step procedure: first, quality analysis is performed, determining individual detection thresholds for every sample. Second, actual CNV calling on the basis of the previously determined thresholds is performed. Our algorithm evaluates the change in variant allele frequency of polymorphisms and reports the fraction of affected cells for every CNV. Analyzing 4 WES data sets (n = 100) we observed superior performance of CopyDetective compared with ExomeCNV, VarScan2, ControlFREEC, ExomeDepth, and CNV-seq. Conclusions Individual detection thresholds reveal that not every WES data set is equally apt for CNV calling. Initial quality analyses, determining individual detection thresholds—as realized by CopyDetective—can and should be performed prior to actual variant calling.

Postmortem Whole Exome Sequencing Identifies Novel EIF2B3 Mutation With Prenatal Phenotype in 2 Siblings

2017 ◽  
Vol 32 (10) ◽  
pp. 867-870 ◽  
Author(s):  
Hannah Song ◽  
Sina Haeri ◽  
Hannes Vogel ◽  
Marjo van der Knaap ◽  
Keith Van Haren
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Clinical Care ◽  
Mutation Screening ◽  
Medical Decision ◽  
Homozygous Mutation ◽  
Vitro Fertilization ◽  
Whole Exome ◽  
The Impact

Objective: We describe 2 male siblings with a severe, prenatal phenotype of vanishing white matter disease and the impact of whole exome sequencing on their diagnosis and clinical care. Methods: The 2 children underwent detailed clinical characterization, through clinical and laboratory testing, as well as prenatal and postnatal imaging. Biobanked blood from the 2 siblings was submitted for whole exome sequencing at Baylor Laboratories. Results: Both male children had abnormal prenatal neuroimaging and suffered precipitous, fatal neurologic decline. Neuropathologic findings included subependymal pseudocysts, microcalcifications, and profound lack of brain myelin and sparing of peripheral nerve myelin. A novel homozygous mutation in the EIF2B3 gene (c.97A>G [p.Lys33Glu]) was found in both children; both parents were heterozygous carriers. The family subsequently conceived a healthy child via in vitro fertilization with preimplantation mutation screening. Conclusion: These histories expand the prenatal phenotype of eIF2b-related disorders and poignantly illustrate the impact that unbiased genomic sequencing can have on the diagnosis and medical decision making for families affected by childhood neurodegenerative disorders.

scholarly journals A MT-TL1 variant identified by whole exome sequencing in an individual with intellectual disability, epilepsy, and spastic tetraparesis

2021 ◽  
Author(s):  
Elke de Boer ◽  
◽  
Charlotte W. Ockeloen ◽  
Leslie Matalonga ◽  
Rita Horvath ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Variant Calling ◽  
Maternal Line ◽  
Feeding Difficulties ◽  
Severe Intellectual Disability ◽  
Whole Exome ◽  
Mtdna Variants ◽  
Spastic Tetraparesis

AbstractThe genetic etiology of intellectual disability remains elusive in almost half of all affected individuals. Within the Solve-RD consortium, systematic re-analysis of whole exome sequencing (WES) data from unresolved cases with (syndromic) intellectual disability (n = 1,472 probands) was performed. This re-analysis included variant calling of mitochondrial DNA (mtDNA) variants, although mtDNA is not specifically targeted in WES. We identified a functionally relevant mtDNA variant in MT-TL1 (NC_012920.1:m.3291T > C; NC_012920.1:n.62T > C), at a heteroplasmy level of 22% in whole blood, in a 23-year-old male with severe intellectual disability, epilepsy, episodic headaches with emesis, spastic tetraparesis, brain abnormalities, and feeding difficulties. Targeted validation in blood and urine supported pathogenicity, with heteroplasmy levels of 23% and 58% in index, and 4% and 17% in mother, respectively. Interestingly, not all phenotypic features observed in the index have been previously linked to this MT-TL1 variant, suggesting either broadening of the m.3291T > C-associated phenotype, or presence of a co-occurring disorder. Hence, our case highlights the importance of underappreciated mtDNA variants identifiable from WES data, especially for cases with atypical mitochondrial phenotypes and their relatives in the maternal line.

scholarly journals Whole Exome Sequencing Identifies a Novel COL1A1 Missense Mutation Causing Dentinogenesis Imperfecta Type I Without Skeletal Abnormalities

2021 ◽  
Author(s):  
Yuting Zeng ◽  
Yuhua Pan ◽  
Jiayao Mo ◽  
Zhiting Ling ◽  
Lifang Jiang ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Missense Mutation ◽  
Whole Exome Sequencing ◽  
Blue Staining ◽  
Nanoindentation Test ◽  
Type I ◽  
Dentinogenesis Imperfecta ◽  
Whole Exome ◽  
Blue Sclerae ◽  
The Impact

Abstract Background：Osteogenesis imperfecta (OI) is a genetic disorder characterized by bone fragility, blue sclerae and dentinogenesis imperfecta (DGI), which are mainly caused by a mutation of the COL1A1 or COL1A2 genes that encode type I procollagen.Methods: The ultrastructure of dentin was analyzed by micro-CT, scanning electron microscopy, energy-dispersive spectroscopy analysis, nanoindentation test and Toluidine Blue Staining. Whole-exome sequencing (WES) was performed to identify the pathogenic gene. The function of the mutant COL1A1 was studied by real-time PCR, western blotting, subcellular localization. Functional analysis in dental pulp stem cells (DPSCs) was also performed to explore the impact of the identified mutation on this phenotype. Results: WES identified a missense mutation (c.1463G > C) in exon 22 of the COL1A1 gene. However, the cases reported herein only exhibited DGI-I in the clinical phenotype, there is no bone disease and any other common abnormal symptom caused by COL1A1 mutation. In addition, ultrastructural analysis of the tooth affected with non-syndromic DGI-I showed that the abnormal dentin was accompanied by disruption of odontoblast polarization, reduced numbers of odontoblasts, loss of dentinal tubules, and reduction in hardness and elasticity, suggesting severe developmental disturbance. What’s more, the odontoblast differentiation ability based on DPSCs that were isolated and cultured from the DGI-I patient was enhanced compared with those from an age-matched, healthy control.Conclusion: This study helped the family members to understand the disease progression and provided new insights into the phenotype-genotype association in collagen-associated diseases and improve clinical diagnosis of OI/DGI-I.

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