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Belkadi, Aziz, Alexandre Bolze, Yuval Itan, Aurélie Cobat, Quentin B. Vincent, Alexander Antipenko, Lei Shang, Bertrand Boisson, Jean-Laurent Casanova, and Laurent Abel. "Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants." Proceedings of the National Academy of Sciences 112, no. 17 (March 31, 2015): 5473–78. http://dx.doi.org/10.1073/pnas.1418631112.
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We compared whole-exome sequencing (WES) and whole-genome sequencing (WGS) in six unrelated individuals. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and 13,325, respectively, for WES, and 84,968 and 12,702, respectively, for WGS. For both SNVs and indels, the distributions of coverage depth, genotype quality, and minor read ratio were more uniform for WGS than for WES. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called by both platforms. A mean of 105 coding HQ SNVs and 32 indels was identified exclusively by WES whereas 692 HQ SNVs and 105 indels were identified exclusively by WGS. We Sanger-sequenced a random selection of these exclusive variants. For SNVs, the proportion of false-positive variants was higher for WES (78%) than for WGS (17%). The estimated mean number of real coding SNVs (656 variants, ∼3% of all coding HQ SNVs) identified by WGS and missed by WES was greater than the number of SNVs identified by WES and missed by WGS (26 variants). For indels, the proportions of false-positive variants were similar for WES (44%) and WGS (46%). Finally, WES was not reliable for the detection of copy-number variations, almost all of which extended beyond the targeted regions. Although currently more expensive, WGS is more powerful than WES for detecting potential disease-causing mutations within WES regions, particularly those due to SNVs.
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Suspitsin, Evgeny N., Vladislav I. Tyurin, Evgeny N. Imyanitov, and Anna P. Sokolenko. "Whole exome sequencing: principles and diagnostic capabilities." Pediatrician (St. Petersburg) 7, no. 4 (December 15, 2016): 142–46. http://dx.doi.org/10.17816/ped74142-146.
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Diagnostics of genetic diseases in clinical routine often presents a challenge. In particular, most of hereditary diseases are exceptionally rare and therefore unfamiliar to practicing physicians. Furthermore, even if the diagnosis of a particular genetic condition appears convincing on the level of clinical evidence, the causative mutation often remains unknown due to limitations in DNA testing procedures. Recently developed high-throughput sequencing technologies (Next Generation Sequencing, NGS; synonym: massive parallel sequencing) provide a breakthrough in medical genetics. While in the past genetic testing was limited to a single gene or, at best, to a small number of genes, NGS is compatible with a large-scale DNA analysis. One of the most popular applications of NGS is whole exome sequencing (WES), which allows simultaneous reading of coding sequences (exons) of all known genes. Although this technology exists only for a few years, its use has already led to discovery of the causes of more than 150 genetic syndromes. Furthermore, WES may be recommended for the use in clinical routine for selected patients with orphan disease, especially for the families with multiple affected relative. It is likely that WES will become a powerful screening tool in the near future. This review discusses general principles of WES as well as the applications of this technology in medicine.
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Zeng, Xiaofang, Tianyu Lian, Jianhui Lin, Suqi Li, Haikuo Zheng, Chunyan Cheng, Jue Ye, Zhicheng Jing, Xiaojian Wang, and Wei Huang. "Whole-exome sequencing improves genetic testing accuracy in pulmonary artery hypertension." Pulmonary Circulation 8, no. 2 (February 26, 2018): 204589401876368. http://dx.doi.org/10.1177/2045894018763682.
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Sanger sequencing, the traditional “gold standard” for mutation detection, has been wildly used in genetic testing of pulmonary artery hypertension (PAH). However, with the advent of whole-exome sequencing (WES), few studies have compared the accuracy of WES and Sanger sequencing in routine genetic testing of PAH. PAH individuals were enrolled from Fu Wai Hospital and Shanghai Pulmonary Hospital. WES was used to analyze DNA samples from 120 PAH patients whose bone morphogenetic protein receptor type 2 (BMPR2) mutation statuses had been previously studied using Sanger sequencing. The Sanger sequencing and WES agreement was 98.3% (118/120) with near-perfect agreement (κ coefficient = 0.848). There was no significant difference between the two methods on the McNemar–Bowker test ( P > 0.05). Twenty-one BMPR2 mutation carriers and 99 non-carriers were detected by Sanger sequencing. Among the 21 BMPR2 carriers detected by Sanger sequencing, one variant (c.1040 T > A) was not found by WES. Among the 99 BMPR2 non-carriers, WES detected an extra mutation carrier (c.76 + 1 G > C) missed by Sanger sequencing. Both false-positive and false-negative results were highly conserved and were re-analyzed by Sanger sequencing. WES improved the accuracy of Sanger sequencing and detected 1% (1/99) false-positive and 4.8% (1/21) false-negative results of Sanger sequencing. No false-positive and false-negative results of WES were identified in our analysis. WES is non-inferior to Sanger sequencing and may play a more important role in genetic testing of PAH patients in the future.
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Hintzsche, Jennifer D., William A. Robinson, and Aik Choon Tan. "A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data." International Journal of Genomics 2016 (2016): 1–16. http://dx.doi.org/10.1155/2016/7983236.
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Whole Exome Sequencing (WES) is the application of the next-generation technology to determine the variations in the exome and is becoming a standard approach in studying genetic variants in diseases. Understanding the exomes of individuals at single base resolution allows the identification of actionable mutations for disease treatment and management. WES technologies have shifted the bottleneck in experimental data production to computationally intensive informatics-based data analysis. Novel computational tools and methods have been developed to analyze and interpret WES data. Here, we review some of the current tools that are being used to analyze WES data. These tools range from the alignment of raw sequencing reads all the way to linking variants to actionable therapeutics. Strengths and weaknesses of each tool are discussed for the purpose of helping researchers make more informative decisions on selecting the best tools to analyze their WES data.
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Fennessy, Paul, and Marianne Griffin. "OP64 Implementation Of Whole Exome Sequencing For Rare Diseases." International Journal of Technology Assessment in Health Care 35, S1 (2019): 16. http://dx.doi.org/10.1017/s0266462319001259.
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IntroductionThe Victorian Department of Health and Human Services provided AUD 25 million (i.e. USD 17.3 million) over four years to determine the place of whole exome sequencing (WES) for patients attending public genetics clinics. Comparative analysis of WES and ‘usual care’ determined that WES increased diagnosis rate (from 14 to 58 percent), changed clinical management in one third of patients and identified relatives and couples at high risk of recurrence in future pregnancies. Translating this into routine care requires co-design with clinical and laboratory stakeholders.MethodsVictoria's clinical and laboratory genetics service system uses a ‘hub and spoke’ model. Representatives from these were invited to join a ‘Clinical Adoption Group’ (CAG) to oversight implementation of new government funding (AUD 2 million (i.e. USD 1.4 million) per year) to ensure statewide access to, and funding of, WES for children with rare undiagnosed genetic conditions. The CAG developed terms of reference, ‘traffic light’ evidence-based eligibility criteria, a pricing model and reporting mechanism, and recommended funding for sequencing, curation, curator training and multidisciplinary team (MDT) meetings to support implementation.ResultsFunding was distributed across hub and spoke sites reflecting clinical and laboratory demand and workforce requirements. All cases demonstrated clinical utility and were reviewed at MDT meetings. To date, 37 percent of patients have received a diagnosis changing management, with equity of access between metropolitan and regional areas demonstrated. Eligibility criteria are reviewed as new evidence is published to ensure new evidence is incorporated, although curation capacity limits turn-around-times.ConclusionsCo-designing a statewide and evidence-based clinical model has resulted in sector (i.e. clinician and laboratory) buy-in and supported broad access to funded WES. In addition, the sector has developed a better understanding of how evidence informs policy and funding decisions, which has resulted in delivering equitable WES that provides early diagnosis leading to changed clinical management and cessation of unnecessary interventions.
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Zhang, Rong, Holger Thiele, Peter Bartmann, Alina C. Hilger, Christoph Berg, Ulrike Herberg, Dietrich Klingmüller, Peter Nürnberg, Michael Ludwig, and Heiko Reutter. "Whole-Exome Sequencing in Nine Monozygotic Discordant Twins." Twin Research and Human Genetics 19, no. 1 (December 18, 2015): 60–65. http://dx.doi.org/10.1017/thg.2015.93.
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By definition, monozygotic (MZ) twins carry an identical set of genetic information. The observation of early post-twinning mutational events was shown to cause phenotypic discordance among MZ twin pairs. These mutational events comprise genomic alterations at different scales, ranging from single nucleotide changes to larger copy-number variations (CNVs) of varying sizes, as well as epigenetic changes. Here, we performed whole-exome sequencing (WES) in nine discordant MZ twins to identify somatic mutational events in the affected twin that might exert a dominant negative effect. Five of these MZ twin pairs were discordant for congenital heart defects (CHD), two for endocrine disorders, one for omphalocele, and one for congenital diaphragmatic hernia (CDH). Analysis of WES data from all nine MZ twin pairs using the de novo probability tool DeNovoGear detected only one apparent de novo variation in TMPRSS13 in one of the CHD-affected twins. Analysis of WES data from all nine MZ twin pairs by using standard filter criteria without the de novo probability tool DeNovoGear revealed a total of 6,657 variations in which both the twin pairs differed. After filtering for variations only present in the affected twins and absent in in-house controls, 722 variations remained. Visual inspection for read quality decreased this number to 12, present only in the affected twin. However, Sanger sequencing of the overall 13 variations failed to confirm the variation in the affected twin. These results suggest that somatic mutational events in coding regions do not seem to play a major role in the phenotypic expression of MZ discordant twin pairs.
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Pastore, Matthew, Rachel Schrader, Emily Sites, Dennis Bartholomew, Chang-Yong Tsao, Kevin Flanigan, and Megan Waldrop. "Diagnostic Utility of Whole Exome Sequencing in the Neuromuscular Clinic." Neuropediatrics 50, no. 02 (January 21, 2019): 096–102. http://dx.doi.org/10.1055/s-0039-1677734.
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AbstractNext-generation sequencing is a powerful diagnostic tool, yet it has proven inadequate to establish a diagnosis in all cases of congenital hypotonia or childhood onset weakness. We sought to describe the impact of whole exome sequencing (WES), which has only recently become widely available clinically, on molecular diagnosis in the Nationwide Children's Hospital Neuromuscular clinics. We reviewed records of all patients in our clinic with pediatric onset of symptoms who had WES done since 2013. Patients were included if clinical suspicion was high for a neuromuscular disease. Clinical WES was performed in 30 families, representing 31 patients, all of whom were seen for hypotonia, weakness, or gait disturbance. Probands had between 2 and 12 genetic diagnostic tests prior to obtaining WES. A genetic diagnosis was established in 11 families (37%), and in 12 patients (39%), with mutations in 10 different genes. Five of these genes have only been associated with disease since 2013, and were not previously represented on clinically available disease gene panels. Our results confirm the utility of WES in the clinical setting, particularly for genetically heterogeneous syndromes. The availability of WES can provide an end to the diagnostic odyssey for parents and allow for expansion of phenotypes.
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Rahmani, E. S., Н. Azarpara, M. Karimipoor, and Н. Rahimi. "Whole exome analysis of primary immunodeficiency." Vavilov Journal of Genetics and Breeding 22, no. 5 (August 10, 2018): 620–26. http://dx.doi.org/10.18699/vj18.403.
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The human primary immunodeficiency diseases (PIDs) refer to a rare heterogeneous group of single-gene inherited disorders causing malfunctions in the immune system, and thus the affected patients have a predisposition to severe life-threatening infections. The heterogeneous nature of PIDs, which involves at list 300 different genes, makes diagnosis of the disease a complex issue. Although studies revealed that six million people have a kind of PID, but due to a complex diagnosis procedure many affected individuals have not gotten a correct diagnosis. However, thanks to advancing in the DNA sequencing method and availability of sophisticated sequencers molecular characterization of genetic disorders have been revolutionized. The whole exome sequencing (WES) method can help clinicians detect Mendelian disease and other complex genetic disorders. The presented study used WES to investigate two infants with symptoms of primary immunodeficiency including hemophagocytic lymphohistiocytosis (HLH) and severe combined immunodeficiency (SCID). It has been shown that the HLH patient had a mutation in the UNC13D gene (NM_199242.2:c.627delT), and the SCID patient had a mutation in the RAG1 gene (NM_000448.2:c.322C>G). It has been demonstrated that WES is a fast and cost-effective method facilitating genetic diagnosis in PID sufferers.
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Ouchi, K., S. Takahashi, K. Tatsuno, A. Hayashi, S. Yamamoto, H. Ueda, M. Inoue, H. Nakano, H. Aburatani, and C. Ishioka. "Whole-Exome Sequencing (WES) Using Formalin-Fixed Paraffin Embedded (FFPE) Tissue." Annals of Oncology 24 (November 2013): ix93. http://dx.doi.org/10.1093/annonc/mdt460.132.
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Lopez, S., C. Han, G. Altwerger, G. Menderes, L. Zammataro, S. Bellone, A. Bianchi, et al. "Whole exome sequencing (WES) reveals novel therapeutic targets in cervical cancer." Gynecologic Oncology 154 (June 2019): 61–62. http://dx.doi.org/10.1016/j.ygyno.2019.04.146.
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Oh, Sehyun, Ludwig Geistlinger, Marcel Ramos, Martin Morgan, Levi Waldron, and Markus Riester. "Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data." JCO Clinical Cancer Informatics, no. 4 (September 2020): 321–35. http://dx.doi.org/10.1200/cci.19.00130.
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PURPOSE Allele-specific copy number alteration (CNA) analysis is essential to study the functional impact of single-nucleotide variants (SNVs) and the process of tumorigenesis. However, controversy over whether it can be performed with sufficient accuracy in data without matched normal profiles and a lack of open-source implementations have limited its application in clinical research and diagnosis. METHODS We benchmark allele-specific CNA analysis performance of whole-exome sequencing (WES) data against gold standard whole-genome SNP6 microarray data and against WES data sets with matched normal samples. We provide a workflow based on the open-source PureCN R/Bioconductor package in conjunction with widely used variant-calling and copy number segmentation algorithms for allele-specific CNA analysis from WES without matched normals. This workflow further classifies SNVs by somatic status and then uses this information to infer somatic mutational signatures and tumor mutational burden (TMB). RESULTS Application of our workflow to tumor-only WES data produces tumor purity and ploidy estimates that are highly concordant with estimates from SNP6 microarray data and matched normal WES data. The presence of cancer type–specific somatic mutational signatures was inferred with high accuracy. We also demonstrate high concordance of TMB between our tumor-only workflow and matched normal pipelines. CONCLUSION The proposed workflow provides, to our knowledge, the only open-source option with demonstrated high accuracy for comprehensive allele-specific CNA analysis and SNV classification of tumor-only WES. An implementation of the workflow is available on the Terra Cloud platform of the Broad Institute (Cambridge, MA).
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Ebili, Henry O., Adedeji OJ Agboola, and Emad Rakha. "MSI-WES: a simple approach for microsatellite instability testing using whole exome sequencing." Future Oncology 17, no. 27 (September 2021): 3595–606. http://dx.doi.org/10.2217/fon-2021-0132.
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Aim: To demonstrate that MSI-WES is an accurate testing method for microsatellite instability (MSI). Materials & methods: Microsatellite-based indels were counted in the variant call-formatted whole exome sequencing (WES) data of 441 gastric cancer cases using Unix-based algorithms, and the counts expressed as a fraction of the genome sequenced to obtain next-generation sequencing-based MSI indices. Results: The next-generation sequencing-based MSI indices showed a near-perfect concordance with PCR-based MSI status, and moderate to good correlations with the molecular targets of MSI index, MLH1 expression and MLH1 methylation status, at a level comparable to the strengths of correlation between PCR-based MSI status and molecular targets of MSI index/ MLH1 expression and methylation. Conclusion: MSI-WES is a valid, adequate and sensitive approach for testing MSI in cancer.
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Muthaffar, OY. "The utility of whole exome sequencing in diagnosing pediatric neurological disorders." Balkan Journal of Medical Genetics 23, no. 2 (November 1, 2020): 17–24. http://dx.doi.org/10.2478/bjmg-2020-0028.
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Abstract Pediatric neurological disorders have a wide spectrum of clinical presentations and can be challenging to diagnose. Whole exome sequencing (WES) is increasingly becoming an integral diagnostic tool in medicine. It is cost-effective and has high diagnostic yield, especially in consanguineous populations. This study aims to review WES results and its value in diagnosing neurological disorders. A retrospective chart review was performed for WES results between the period of January 2018 to November 2019. Whole exome sequencing was requested for children with unexplained neurological signs and symptoms such as epilepsy, developmental delay, visual impairment, spasticity, hypotonia and magnetic resonance imaging (MRI) brain changes. It was conducted for children in a pediatric neurology clinic of a tertiary center at Jeddah, Saudi Arabia. Twenty-six children with undiagnosed neurological conditions were identified and underwent WES diagnosis. Nineteen patients (73.0%) of the cohort were diagnosed with pathogenic variants, likely pathogenic variants or variants of unknown significance (VUS). Consanguinity was positive in 18 families of the cohort (69.0%). Seven patients showed homozygous mutations. Five patients had heterozygous mutations. There were six patients with VUS and six patients had negative WES results. Whole exome sequencing showed a high diagnostic rate in this group of children with variable neurological disorders.
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Park, Su-Jung, Narae Lee, Seong-Hee Jeong, Mun-Hui Jeong, Shin-Yun Byun, and Kyung-Hee Park. "Genetic Aspects of Small for Gestational Age Infants Using Targeted-Exome Sequencing and Whole-Exome Sequencing: A Single Center Study." Journal of Clinical Medicine 11, no. 13 (June 27, 2022): 3710. http://dx.doi.org/10.3390/jcm11133710.
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Background: The etiology of small for gestational age (SGA) is multifactorial and includes maternal/uterine-placental factors, fetal epigenetics, and genetic abnormalities. We evaluated the genetic causes and diagnostic effectiveness of targeted-panel sequencing (TES) or whole-exome sequencing (WES) in SGA infants without a known cause. Methods: A prospective study was conducted on newborn infants born with a birth weight of less than the 10th percentile for gestational age between January 2019 and December 2020 at the Pusan National University Hospital. We excluded infants with known causes of SGA, including maternal causes or major congenital anomalies or infections. SGA infants without a known etiology underwent genetic evaluation, including karyotyping, chromosomal microarray (CMA), and TES/WES. Results: During the study period, 82 SGA infants were born at our hospital. Among them, 61 patients were excluded. A total of 21 patients underwent karyotyping and chromosomal CMA, and aberrations were detected in two patients, including one chromosomal anomaly and one copy number variation. Nineteen patients with normal karyotype and CMA findings underwent TES or WES, which identified three pathogenic or likely pathogenic single-gene mutations, namely LHX3, TLK2, and MED13L. Conclusions: In SGA infants without known risk factors, the prevalence of genetic causes was 22% (5/21). The diagnostic yield of TES or WES in SGA infants with normal karyotype and CMA was 15.7% (3/19). TES or WES was quite helpful in identifying the etiology in SGA infants without a known cause.
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Bryant, Dean, Will Tapper, Nicola J. Weston-Bell, Arnold Bolomsky, Li Song, Shengtao Xu, Andrew R. Collins, Niklas Zojer, and Surinder Singh Sahota. "Single Cell Whole Exome Sequencing in an Index Case of Amp1q21 Multiple Myeloma to Define Intraclonal Variation." Blood 128, no. 22 (December 2, 2016): 5651. http://dx.doi.org/10.1182/blood.v128.22.5651.5651.
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Abstract Introduction Multiple myeloma (MM) is a largely incurable plasma cell malignancy characterised by marked genomic heterogeneity, in which chromosome 1q21 amplification (amp1q21) associates with poor prognosis. Genomic analysis using next generation sequencing has identified recurrent mutations, but no universal acquired somatic mutation(s) have emerged in MM, suggesting that understanding pathways of survival will require analysis of individual tumours in distinct disease subsets. To compound complexity of the problem, intraclonal variation (ICV), known as a major driver mechanism in cancer plasticity, in which clonal competitor cells undergo selection during disease evolution and progression by Darwinian principles, will need to be fully mapped at the genome level. Identifying the true level of ICV in a tumour will thus require analysis at the level of whole exome sequencing (WES) in single cells (SCs). In this study, we sought to establish WES methodology able to identify ICV in SCs in an index case of amp1q21 MM. Methods Cell selection and sequencing CD138+ tumour cells and CD3+ T-cells were isolated from a presentation case of amp1q21 MM as bulk populations to high purity (>97%). Single MM cells and normal T cells were individually isolated and used for single cell (SC) whole exome sequencing (WES). Whole genome amplification (WGA) was performed by multiple displacement amplification (Qiagen REPLI-g Mini kit), and exome capture was performed using Agilent SureSelect. Libraries were then 90 bp paired end sequenced on an Illumina HiSeq2000 (BGI, China). Data analysis Data was produced for bulk (1000 cells) MM and bulk germline T cells, twenty MM SCs and five T cell SCs. Raw data was aligned to hg19 reference sequence using NovoAlignMPI (v3.02.03). Variant calling was performed using SAMtools (v1.2.1) and VarScan (v2.3.6) and variants were annotated using ANNOVAR. High confidence variants were called in the bulk tumour WES by pairwise comparison with bulk germline WES. Variant lists were also cross-searched against various variant databases (CG46, 1000 genomes, dbSNP, esp650 and in-house database) in order to exclude variants that occur in the general population. Multiple quality control measures were employed to reduce the number of false positive calls. Results and Discussion Data and bioinformatics pipelines are of a high quality SC WES generated raw data reads that were similar to bulk WES of 1000 cells, with comparable mapping to Agilent SureSelect target exome (69-76% SC vs. 70% bulk) and mean fold coverage (56.8-59.1x vs. 59.7x bulk). On average, 82% of the exome was covered sufficiently for somatic variant (SV) calling (often considered as ≥ 5x), which was higher than seminal published SC WES studies (70-80%) (Hou et al., Cell, 2012; Xu et al., Cell, 2012). We identified 33 potentially deleterious SVs in the bulk tumour exome with high confidence bioinformatics, 21 of which were also identified in one or more SC exomes. The variants identified include suspected deleterious mutations in genes involved in MAPK pathway, plasma cell differentiation, and those with known roles in B cell malignancies. To confirm SV calls, randomly selected variants were validated by conventional Sanger sequencing, and of 15/15 variants in the bulk WES and of 55/55 variants in SCs, to obtain 100% concordance. Intraclonal variation in MM Significantly, ICV was apparent from the SC exome variant data. Total variant counts varied considerably among SCs and most variant positions had at least several cells where no evidence of the variant existed. Bulk WES lacks crucial information We identified an additional 23 variants that were present in 2+ SC exomes, but absent in the bulk MM tumour exomes. Of these, 30% (7 variants) were examined for validation, and were amplifiable in at least one cell to deliver 100% concordance with variant calls. These variants are of significant interest as they reveal a marked occurrence of subclonal mutations in the MM tumour population that are not identified by bulk exome sequencing. They indicate that the mutational status of the MM genome may be substantially underestimated by analysis at the bulk tumour population level. Conclusion In this work we establish the feasibility of SC WES as a method for defining intraclonal genetic variation in MM. Disclosures No relevant conflicts of interest to declare.
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Gileles-Hillel, Alex, Hagar Mor-Shaked, David Shoseyov, Joel Reiter, Reuven Tsabari, Avigdor Hevroni, Malena Cohen-Cymberknoh, et al. "Whole-exome sequencing accuracy in the diagnosis of primary ciliary dyskinesia." ERJ Open Research 6, no. 4 (October 2020): 00213–2020. http://dx.doi.org/10.1183/23120541.00213-2020.
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The diagnosis of primary ciliary dyskinesia (PCD) relies on clinical features and sophisticated studies. The detection of bi-allelic disease-causing variants confirms the diagnosis. However, a standardised genetic panel is not widely available and new disease-causing genes are continuously identified.To assess the accuracy of untargeted whole-exome sequencing (WES) as a diagnostic tool for PCD, patients with symptoms highly suggestive of PCD were consecutively included. Patients underwent measurement of nasal nitric oxide (nNO) levels, ciliary transmission electron microscopy analysis (TEM) and WES. A confirmed PCD diagnosis in symptomatic patients was defined as a recognised ciliary ultrastructural defect on TEM and/or two pathogenic variants in a known PCD-causing gene.Forty-eight patients (46% male) were enrolled, with a median age of 10.0 years (range 1.0–37 years). In 36 patients (75%) a diagnosis of PCD was confirmed, of which 14 (39%) patients had normal TEM. A standalone untargeted WES had a diagnostic yield of 94%, identifying bi-allelic variants in 11 known PCD-causing genes in 34 subjects. A nNO<77 nL·min was nonspecific when including patients younger than 5 years (area under the receiver operating characteristic curve (AUC) 0.75, 95% CI 0.60–0.90). Consecutive WES considerably improved the diagnostic accuracy of nNO in young children (AUC 0.97, 95% CI 0.93–1). Finally, WES established an alternative diagnosis in four patients.In patients with clinically suspected PCD and low nNO levels, WES is a simple, beneficial and accurate next step to confirm the diagnosis of PCD or suggest an alternative diagnosis, especially in preschool-aged children in whom nNO is less specific.
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Yadava, Stacy M., and Elena Ashkinadze. "125: Whole exome sequencing (WES) in prenatal diagnosis for carefully selected cases." American Journal of Obstetrics and Gynecology 216, no. 1 (January 2017): S87—S88. http://dx.doi.org/10.1016/j.ajog.2016.11.029.
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Middelburg, P., G. Monroe, K. van Gassen, A. Hovels, N. Knoers, T. Vrijenhoek, and G. Frederix. "Impact of Whole Exome Sequencing (WES) on Costs and Medical Decision-Making." Value in Health 19, no. 7 (November 2016): A705—A706. http://dx.doi.org/10.1016/j.jval.2016.09.2060.
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Murdock, David R., Frank X. Donovan, Settara C. Chandrasekharappa, Nicole Banks, Carolyn Bondy, Maximilian Muenke, and Paul Kruszka. "Whole-Exome Sequencing for Diagnosis of Turner Syndrome: Toward Next-Generation Sequencing and Newborn Screening." Journal of Clinical Endocrinology & Metabolism 102, no. 5 (January 24, 2017): 1529–37. http://dx.doi.org/10.1210/jc.2016-3414.
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Abstract Context: Turner syndrome (TS) is due to a complete or partial loss of an X chromosome in female patients and is not currently part of newborn screening (NBS). Diagnosis is often delayed, resulting in missed crucial diagnostic and therapeutic opportunities. Objectives: This study sought to determine if whole-exome sequencing (WES) as part of a potential NBS program could be used to diagnose TS. Design, Setting, Patients: Karyotype, chromosomal microarray, and WES were performed on blood samples from women with TS (n = 27) enrolled in the Personalized Genomic Research study at the National Institutes of Health. Female control subjects (n = 37) and male subjects (n = 27) also underwent WES. Copy number variation was evaluated using EXCAVATOR2 and B allele frequency was calculated from informative single nucleotide polymorphisms. Simulated WES data were generated for detection of low-level mosaicism and complex structural chromosome abnormalities. Results: We detected monosomy for chromosome X in all 27 TS samples, including 1 mosaic for 45,X/46,XX and another with previously unreported material on chromosome Y. Sensitivity and specificity were both 100% for the diagnosis of TS with no false-positive or false-negative results. Using simulated WES data, we detected isochromosome Xq and low-level mosaicism as low as 5%. Conclusion: We present an accurate method of diagnosing TS using WES, including cases with low-level mosaicism, isochromosome Xq, and cryptic Y-chromosome material. Given the potential use of next-generation sequencing for NBS in many different diseases and syndromes, we propose WES can be used as a screening test for TS in newborns.
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Shim, Ye Jee, Jung-Sook Ha, Young-Rok Do, and Heung Sik Kim. "Whole-Exome Sequencing in Korean Children with Acute Lymphoblastic Leukemia." Blood 126, no. 23 (December 3, 2015): 4994. http://dx.doi.org/10.1182/blood.v126.23.4994.4994.
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Abstract Purpose: Next-generation sequencing methods recently have been applied for leukemia patients to discover genetic variants. In this study, we conducted whole-exome sequencing (WES) in Korean acute lymphoblastic leukemia (ALL) children to identify putative genetic drivers of leukemia. Methods: Four Korean ALL children were included for WES. For two of them, we also conducted WES after remission, considered as germline control. The characteristics of subjects and the diagnostic information are described in Table 1. Genomic DNA was extracted from the subject¡¯s bone marrow aspirates at diagnosis of leukemia and/or after remission. Whole-exome was captured by SureSelect Human All Exon V4 (Agilent Technologies, California, USA). Sequencing was performed using HiSeq2000 (Illumina, California, USA). Variants in dbSNP135 and TIARA database were excluded. Variants with minor allele frequencies > 0.5% of 1000g were filtered out. Functional variants (gain of stop codon, frameshifts and nonsynonymous SNVs) were selected as pathogenic mutations and were scanned for the 571 cancer gene set using ¡°Cancer gene Census¡± in COSMIC website. The finally selected variants were verified by PROVEAN, SIFT and PolyPhen-2. This research was approved by The Institutional Review Board in Keimyung University Dongsan Medical Center (Approval No., 2015-05-029-002). Results: After comparison between WES at diagnosis and WES after remission, p.W112C in PAX5 in patient 1 andp.G315C in KMT2C, p.T311P in NOTCH1, p.G11A in HOXD13 in patient 2 were considered as pathogenic, respectively. In patient 3 and 4, p.R293C in FNBP1, p.R254H in PCSK7, p.E11Q in TP53, p.R806Q in MYO5A, p.R108G in PPFIBP1, p.C1785R in RNF213, and p.A963P in WRN were suspected as putative drivers of leukemia. The respective variants are shown in Table 2. Conclusions: This is the first attempt of WES in Korean children with leukemia. WES is a valuable method to identify genomics of childhood ALL. Table 1. Characteristics and diagnostic information of four Korean acute lymphoblastic leukemia children. No. Diagnosis BMblast Karyotype Hemavision FISH Immunophenotype WESAt diagnosis WESAfter remission 1 B-ALL 88.4% 44,XX,der(2)t(2;?),-4,-9,der(9)t(2;9),der(16)t(9;16)(q13;q12) Negative . CD10, D19, CD20, CD22, cCD22,cCD79a, CD34, CD45 Yes Yes 2 Pre B-ALL 95.0% No mitosis t(1;19)(q23;p13) . CD38, CD138, CD10, CD19, CD22,cCD79a, HLA-DR, CD45 Yes Yes 3 B-ALL 88.6% 46,XX Negative . CD10, CD19, CD22, cCD79a, CD34,TdT, HLA-DR, CD45, CD38 Yes No 4 B-ALL 94.3% Hypotriploidywith structural abnormality/46,XY Negative Trisomy 5, 11, 12Tetrasomy 21 CD10, CD19, CD22, cCD79a, CD34,TdT, HLA-DR Yes No Table 2. Identified putative genetic drivers in four Korean acute lymphoblastic leukemia children by whole-exome sequencing. No. Gene Chr:Position Variant PROVEAN (score) SIFT (score) Polyphen-2 (score) Germline or somatic 1 PAX5 9:37015068 exon3:c.G336T:p.W112C Deleterious (-11.12) Damaging (0.000) Probably damaging (0.998) Somatic 2 KMT2C 7:151970859 exon7:c.G943T:p.G315C Deleterious (-7.05) Damaging (0.001) Probably damaging (1.000) Somatic NOTCH1 9:139413211 exon6:c.A931C:p.T311P Deleterious (-4.82) Damaging (0.012) Benign (0.033) Somatic HOXD13 2:176957650 exon1:c.G32C:p.G11A Neutral (-0.88) Tolerated (0.118) Possibly damaging (0.953) Somatic 3 FNBP1 9:132687349 exon9:c.C877T:p.R293C Deleterious (-6.03) Damaging (0.001) Probably damaging (1.000) Somatic PCSK7 11:117097881 exon5:c.G761A:p.R254H Deleterious (-3.30) Damaging (0.007) Probably damaging (0.991) Somatic 4 TP53 17:7579882 exon2:c.G31C:p.E11Q Neutral (0.42) Damaging (0.000) Probably damaging (0.996) Germline/somatic MYO5A 15:52668547 exon19:c.G2417A:p.R806Q Deleterious (-3.12) Damaging (0.003) Possibly damaging (0.575) Somatic PPFIBP1 12:27799046 exon5:c.C322G:p.R108G Deleterious (-5.76) Damaging (0.000) Probably damaging (1.000) Somatic RNF213 17:78313373 exon27:c.T5353C:p.C1785R Deleterious (-10.45) Damaging (0.000) Probably damaging (1.000) Somatic WRN 8:30989942 exon24:c.G2887C:p.A963P Deleterious (-3.90) Damaging (0.003) Probably damaging (0.988) Germline Disclosures No relevant conflicts of interest to declare.
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Zhou, Jia, Ziying Yang, Jun Sun, Lipei Liu, Xinyao Zhou, Fengxia Liu, Ya Xing, et al. "Whole Genome Sequencing in the Evaluation of Fetal Structural Anomalies: A Parallel Test with Chromosomal Microarray Plus Whole Exome Sequencing." Genes 12, no. 3 (March 6, 2021): 376. http://dx.doi.org/10.3390/genes12030376.
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Whole genome sequencing (WGS) is a powerful tool for postnatal genetic diagnosis, but relevant clinical studies in the field of prenatal diagnosis are limited. The present study aimed to prospectively evaluate the utility of WGS compared with chromosomal microarray (CMA) and whole exome sequencing (WES) in the prenatal diagnosis of fetal structural anomalies. We performed trio WGS (≈40-fold) in parallel with CMA in 111 fetuses with structural or growth anomalies, and sequentially performed WES when CMA was negative (CMA plus WES). In comparison, WGS not only detected all pathogenic genetic variants in 22 diagnosed cases identified by CMA plus WES, yielding a diagnostic rate of 19.8% (22/110), but also provided additional and clinically significant information, including a case of balanced translocations and a case of intrauterine infection, which might not be detectable by CMA or WES. WGS also required less DNA (100 ng) as input and could provide a rapid turnaround time (TAT, 18 ± 6 days) compared with that (31 ± 8 days) of the CMA plus WES. Our results showed that WGS provided more comprehensive and precise genetic information with a rapid TAT and less DNA required than CMA plus WES, which enables it as an alternative prenatal diagnosis test for fetal structural anomalies.
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Batu, Ezgi Deniz, Can Koşukcu, Ekim Taşkıran, Sezgin Sahin, Sema Akman, Betül Sözeri, Erbil Ünsal, et al. "Whole Exome Sequencing in Early-onset Systemic Lupus Erythematosus." Journal of Rheumatology 45, no. 12 (July 15, 2018): 1671–79. http://dx.doi.org/10.3899/jrheum.171358.
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Objective.Systemic lupus erythematosus (SLE) is a multisystem autoimmune disorder. Early-onset, familial, and/or syndromic SLE may reveal monogenic pathologies. The aim of this study was to examine genetic associations in patients with early-onset or familial SLE.Methods.We enrolled 7 SLE cases (from different families) with disease onset ≤ 5 years of age and family history consistent with an autosomal recessive inheritance. Whole exome sequencing (WES) was performed in 6 index cases. Suspected variants were confirmed by Sanger sequencing. We did not perform WES in 1 patient who had features similar to the first 3 cases; only the exons of C1QA, C1QB, and C1QC were screened with Sanger sequencing.Results.We demonstrated 2 novel and 3 previously reported variants in genes associated with SLE: a homozygous non-sense alteration (c.622C>T/p.Gln208Ter) in C1QA in 2 patients; homozygous non-sense alteration (c.79C>T/p.Gln27Ter) in C1QC in 1 (novel variant); homozygous missense alteration (c.100G>A/p.Gly34Arg) in C1QC in 1; homozygous missense alteration (c.1945G>C/p.Ala649Pro) in C1S in 1 (novel variant); and homozygous frameshift alteration (c.289_290delAC/p.Thr97Ilefs*2) in DNASE1L3 in 1 patient. Further, in 1 patient, we determined a strong candidate variant in HDAC7 (histone decetylase 7).Conclusion.Five patients had homozygous alterations in genes coding early complement proteins. This may lead to decreased clearance of apoptotic bodies. One patient had DNASE1L3 variant, which functions in the clearance of self-antigens. In 1 patient, we determined a novel gene that may be important in SLE pathogenesis. We suggest that monogenic causes/associations should be sought in early-onset and/or familial SLE.
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Mann, Nina, Daniela A. Braun, Kassaundra Amann, Weizhen Tan, Shirlee Shril, Dervla M. Connaughton, Makiko Nakayama, et al. "Whole-Exome Sequencing Enables a Precision Medicine Approach for Kidney Transplant Recipients." Journal of the American Society of Nephrology 30, no. 2 (January 17, 2019): 201–15. http://dx.doi.org/10.1681/asn.2018060575.
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BackgroundWhole-exome sequencing (WES) finds a CKD-related mutation in approximately 20% of patients presenting with CKD before 25 years of age. Although provision of a molecular diagnosis could have important implications for clinical management, evidence is lacking on the diagnostic yield and clinical utility of WES for pediatric renal transplant recipients.MethodsTo determine the diagnostic yield of WES in pediatric kidney transplant recipients, we recruited 104 patients who had received a transplant at Boston Children’s Hospital from 2007 through 2017, performed WES, and analyzed results for likely deleterious variants in approximately 400 genes known to cause CKD.ResultsBy WES, we identified a genetic cause of CKD in 34 out of 104 (32.7%) transplant recipients. The likelihood of detecting a molecular genetic diagnosis was highest for patients with urinary stone disease (three out of three individuals), followed by renal cystic ciliopathies (seven out of nine individuals), steroid-resistant nephrotic syndrome (nine out of 21 individuals), congenital anomalies of the kidney and urinary tract (ten out of 55 individuals), and chronic glomerulonephritis (one out of seven individuals). WES also yielded a molecular diagnosis for four out of nine individuals with ESRD of unknown etiology. The WES-related molecular genetic diagnosis had implications for clinical care for five patients.ConclusionsNearly one third of pediatric renal transplant recipients had a genetic cause of their kidney disease identified by WES. Knowledge of this genetic information can help guide management of both transplant patients and potential living related donors.
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Basu, Gargi D., Kevin Drenner, Audrey Ozols, Candyce M. Bair, Tracey White, Janine R. LoBello, Thomas Royce, and Sunil Sharma. "Whole exome and transcriptome sequencing of colorectal and pancreatic cancer." Journal of Clinical Oncology 38, no. 15_suppl (May 20, 2020): e15666-e15666. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e15666.
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e15666 Background: Integration of Whole Exome Sequencing (WES) into clinical cancer therapeutics has revolutionized medicine in recent years. DNA sequencing alone may miss clinically actionable variants or identify aberrations that are not being transcribed. In this study we investigated the utility of integrating DNA and RNA sequencing in clinical samples. Methods: A cohort of 32 patient samples were analyzed by WES and RNA sequencing. Differential expression analysis was performed using a cohort of controls. Pathway analysis was performed using Ingenuity Pathway Analysis. WES and RNA analysis detected alterations including SNVs, indels, copy number events, fusions, alternate transcripts, TMB, MSI status and differential expression. Results: A total of 25 CRC (39-78yrs) and 7 pancreatic cancers (PCs) (51-91 yrs) were profiled by WES and RNA seq. A 66 yr old pt with neoplasm of rectosigmoid junction tumor was found to be KRAS wildtype and was treated with cetuximab plus FOLFIRI. Patient failed therapy after 2 yrs and sequencing revealed MET amplification which is a known mechanism of resistance to cetuximab treatment. Further, RNA expression analysis showed 44-fold increase in MET expression along with overexpression of AREG and EREG. Out of the 7 PCs, 3 cases that did not harbor KRAS mutation were found to harbor VTCN1/NRG1 fusion, FGFR1/G3BP2 fusion and BRAF V600E mutation respectively. A 50 year-old stage IV metastatic (met) PC pt was treated with standard of care regimens. Upon relapse the sample was found to harbor VTCN1/NRG1 fusion along with a TERT promoter mutation. RNA expression analysis revealed 54-fold increased expression of NRG1 which may lead to clinical trial enrollment. A 52 year-old male met Stage IV PC, was treated with rucaparib and irinotecan based on prior sequencing data. Upon relapse, the pt went on ATR inhibitor (BAY1895344) and progressed very quickly. Sequencing of the met lesion was found to harbor FGFR1/G3BP2 fusion which was also confirmed by RNA expression. A 55 year-old met pt with PC was treated with standard chemotherapy. Upon disease progression pt was sequenced and based on presence of BRAF V600E, pt was treated with trametinib and dabrafenib. Following disease progression on BRAF/MEKi, met sample was resequenced and RNA expression analysis found increased expression of MET, MACC1 and SMAD7 and 4-fold decrease in PTEN which could potentially cause resistance to BRAF/MEKi therapy. Conclusions: Our study highlights the utility of comprehensive testing integrating genomic and transcriptomic data, in identifying targeted therapy options for cancer patients.
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Oyama, Yu, Akira Honda, Kensuke Matsuda, Hideaki Mizuno, Kazuki Taoka, and Mineo Kurokawa. "Novel Recurrent Mutations in Eldheim-Chester Disease Patients Identified By Whole Exome Sequencing and Whole Genome Sequencing." Blood 138, Supplement 1 (November 5, 2021): 3123. http://dx.doi.org/10.1182/blood-2021-149864.
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Abstract Background: Erdheim-Chester disease (ECD) is a type of systemic, non-Langerhans histiocytic disorder characterized by diffuse organ damage with infiltration of CD68-positive, CD163-positive, and CD1a-negative histiocytes. Although most patients have mutations associated with the hyperactivation of the MAPK pathway, including BRAF, MAP2K1, and NRAS, the remaining have no known driver mutations. So far, there is no specific target of treatment for them. To elucidate novel driver mutations and establish new treatment strategies in these patients, we performed whole-exome sequencing (WES) and whole-genome sequencing (WGS) using patient samples with ECD. In addition, we performed WES with multi-organ lesions in a patient with ECD to reveal the mutational profiles of each organ lesion. Methods: We performed a nationwide survey and collected clinical samples of ECD in Japan. We collected 22 samples of ECD lesions from 15 adult patients. All cases were pathologically proved. Twenty of 22 samples were formalin-fixed and paraffin-embedded tissue (FFPE) and were examined by WES. For WGS, DNA was extracted from 2 raw samples of ECD lesions. In addition, we collected multi-organ lesions in 3 patients. One patient developed myelodysplastic syndrome (MDS) and subsequent acute myeloid leukemia (AML). Therefore, we also performed WES with each bone marrow (BM) sample to reveal the relationship between ECD and these myeloid malignancies. We used 6 samples of peripheral blood, 1 BM sample, 1 skin sample, and 1 oral mucosa sample as normal controls. Result: We detected known driver mutations in seven of 15 cases (47%). Among them, BRAF V600E was detected in 5 cases (8 samples), MAP2K1 C121S in 1 case (1 sample), and NRAS Q61R in 1 case (2 samples) by WES and WGS. A mean of 69 nonsynonymous mutations per patient was identified in normal-tumor analysis (range, 2-491) and 188 in tumor-only analysis (range, 17-3598) of WES, and 3134 in normal-tumor analysis (range, 2588-3680) of WGS. The median variant allele frequency (VAF) for the 11 samples with known activating kinase mutations identified by WES and WGS was 14.4% (range, 6.3-34.7). We could not detect known driver mutations in the other 8 cases (53%). Therefore, to reveal novel driver mutations, we focused on these 8 cases. Notably, EPHA2 P786L, MYBPC3 D798N, TDRD5 P115L, and TCEAL4 F17L mutations are recurrently found in 2 out of the 8 cases, suggesting new driver mutations are contained in these. The VAFs of EPHA2 P786L were 9.1% and 9.3%, MYBPC3 D798N 5.5% and 11.9%, TDRD5 P115L 10.2% and 18.7%, and TCEAL4 F17L 7.5% and 9.0% in each case. We also analyzed multiple organ samples of a case with BRAF V600E mutation (5 samples of ECD lesions, BM with MDS, BM with AML, and skin as normal control). Interestingly, BRAF V600E mutation was identified in 3 samples (bone lesion, heart, and intestine) but was not in other samples (kidney lesion, dura matter, BM tumor, BM with MDS, and BM with AML), suggesting mutational profiles are different depending on the organ of the lesion. Conclusion: Our nation-wide analysis revealed that no well-known driver mutations were found in more than half of the ECD cases. We identified EPHA2 P786L, MYBPC3 D798N, TDRD5 P115L, and TCEAL4 F17L mutations as candidates of novel driver mutations in ECD. To elucidate the role of these mutations in pathogenesis of ECD, further functional analyses are warranted. In addition, we revealed heterogeneity of mutational profile of multi lesions in an ECD patient with BRAF V600E mutation. It is noteworthy that mutational profiles might be different depending on the organ of the lesion. Disclosures Honda: Chugai Pharmaceutical: Other: Lecture fee; Ono Pharmaceutical: Other: Lecture fee; Nippon Shinyaku: Other: Lecture fee; Takeda Pharmaceutical: Other: Lecture fee; Otsuka Pharmaceutical: Other: Lecture fee; Jansen Pharmaceutical: Other: Lecture fee. Matsuda: Kyowa Kirin: Other: Lecture fee; Ono Pharmaceutical: Other: Lecture fee. Taoka: ONO PHARMACEUTICAL CO., LTD.: Other; Chugai Pharmaceutical Company: Other. Kurokawa: Teijin Limited: Research Funding, Speakers Bureau; Chugai Pharmaceutical Company: Research Funding, Speakers Bureau; Takeda Pharmaceutical Company Limited.: Research Funding, Speakers Bureau; ONO PHARMACEUTICAL CO., LTD.: Research Funding, Speakers Bureau; Otsuka Pharmaceutical Co., Ltd.: Research Funding, Speakers Bureau; Eisai Co., Ltd.: Research Funding, Speakers Bureau; Astellas Pharma Inc.: Research Funding, Speakers Bureau; MSD K.K.: Research Funding, Speakers Bureau; Nippon Shinyaku Co., Ltd.: Research Funding, Speakers Bureau; Daiichi Sankyo Company.: Research Funding, Speakers Bureau; Sumitomo Dainippon Pharma Co., Ltd.: Research Funding, Speakers Bureau; Kyowa Hakko Kirin Co., Ltd.: Research Funding, Speakers Bureau; AbbVie GK: Research Funding, Speakers Bureau; Pfizer Japan Inc.: Research Funding, Speakers Bureau.
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Lee, Eun-Ju, Daniel J. Dykas, Andrew D. Leavitt, Rodney M. Camire, Eduard Ebberink, Pablo García de Frutos, Kavitha Gnanasambandan, et al. "Whole-exome sequencing in evaluation of patients with venous thromboembolism." Blood Advances 1, no. 16 (June 29, 2017): 1224–37. http://dx.doi.org/10.1182/bloodadvances.2017005249.
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Key Points Using WES, we designed an extended thrombophilia panel consisting of 55 genes of significance to thrombosis. The extended thrombophilia panel identified multiple novel genetic variants with predicted roles in thrombosis or thrombophilia.
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Park, Heetae, Kazuyoshi Hosomichi, Yong-Il Kim, Atsushi Tajima, and Tetsutaro Yamaguchi. "Exploring the Genetic Basis of Dens Evaginatus Using Whole-Exome Sequencing." Applied Sciences 12, no. 18 (September 6, 2022): 8962. http://dx.doi.org/10.3390/app12188962.
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Dens evaginatus (DE) is a dental abnormality characterized by tubercles on the occlusal surfaces of teeth and is associated with the risk of pulpal inflammation due to fractures. The cause of DE remains unclear, as limited data are available to determine its etiology. The aim of this study was to investigate the genetic background of DE using whole-exome sequencing (WES). Saliva samples were collected from two patients of Family A and three patients of Family B, including an incident case of DE, and analyzed using WES. Rare variants were extracted from the WES data and filtered by family to extract candidate variants. Gene variants of TLR3 and MDC1 were identified as etiologic factors for DE. The variant MDC1 (c.3908C>T) was identified to be damaging, according to the scores from Polymorphism Phenotyping v2. Our findings contribute towards an understanding of the etiology of DE, which would facilitate improved treatment to prevent the risk of DE fractures and pulpal inflammation. Understanding the mechanism of DE development may also be helpful for developing regenerative medicine and gene therapy strategies.
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Kumar, Ashwini, Sadiksha Adhikari, Matti Kankainen, and Caroline A. Heckman. "Comparison of Structural and Short Variants Detected by Linked-Read and Whole-Exome Sequencing in Multiple Myeloma." Cancers 13, no. 6 (March 10, 2021): 1212. http://dx.doi.org/10.3390/cancers13061212.
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Linked-read sequencing was developed to aid the detection of large structural variants (SVs) from short-read sequencing efforts. We performed a systematic evaluation to determine if linked-read exome sequencing provides more comprehensive and clinically relevant information than whole-exome sequencing (WES) when applied to the same set of multiple myeloma patient samples. We report that linked-read sequencing detected a higher number of SVs (n = 18,455) than WES (n = 4065). However, linked-read predictions were dominated by inversions (92.4%), leading to poor detection of other types of SVs. In contrast, WES detected 56.3% deletions, 32.6% insertions, 6.7% translocations, 3.3% duplications and 1.2% inversions. Surprisingly, the quantitative performance assessment suggested a higher performance for WES (AUC = 0.791) compared to linked-read sequencing (AUC = 0.766) for detecting clinically validated cytogenetic alterations. We also found that linked-read sequencing detected more short variants (n = 704) compared to WES (n = 109). WES detected somatic mutations in all MM-related genes while linked-read sequencing failed to detect certain mutations. The comparison of somatic mutations detected using linked-read, WES and RNA-seq revealed that WES and RNA-seq detected more mutations than linked-read sequencing. These data indicate that WES outperforms and is more efficient than linked-read sequencing for detecting clinically relevant SVs and MM-specific short variants.
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Sampson, Juliana, Nihar Sheth, Vishal N. Koparde, Allison Scalora, Myrna G. Serrano, Vladimir Lee, Maximillian Jamison-Lee, et al. "Whole Exome Sequencing To Estimate Alloreactivity Potential Between Donors and Recipients In Stem Cell Transplantation." Blood 122, no. 21 (November 15, 2013): 150. http://dx.doi.org/10.1182/blood.v122.21.150.150.
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Abstract Graft versus host disease (GVHD) continues to afflict allogeneic hematopoietic stem cell transplant (SCT) recipients despite HLA matching at the molecular level. This is largely a consequence of minor histocompatibility antigen (mHA) variation between the donors and recipients resulting in alloreactivity. To determine the extent of potential antigenic variation at a molecular level, whole exome sequencing (WES) was performed on DNA samples from nine HLA-matched donor-recipient (D-R) pairs to catalogue the sequence variation. TruSeq exome enriched libraries were prepared using Illumina HiSeq 2000 platform. All exomes had at least 28X coverage; single nucleotide polymorphism (SNP) calling was performed using Genome Analysis Toolkit v1.6. Donor and recipient samples were compared with each other and reference human genome using ANNOVAR. SNP between donors and recipients were coded as either synonymous (S) or nonsynonymous (NS); and either NS conservative (NSc), or non-conservative (NSnc). Further, SNPs were analyzed with respect to graft versus host (GVH) or host vs. graft (HVG) vector. First, the recipient exomes were compared with the actual HLA matched and ‘simulated’ non-HLA matched donors; in this analysis, the major histocompatibility region demonstrated a 4-10 fold difference between the actual and simulated D-R pairs, unlike the whole exome, where similar sequence variation was observed between individuals regardless of HLA matching. For the actual D-R pairs the mean difference across the exome was 13,423 SNP, of which an average 6,445 were NS. Normalized for the number of nucleotide positions sequenced in the whole exome, the S- and NS-SNP scores were approximately equal, and NSnc-SNP were consistently > NSc-SNP (Figure 1). Further, in unrelated donor (URD) SCT, difference scores were approximately twice as large as in matched related donor recipients. GVHD was seen in 3/5 URD SCT with an alloreactivity score >0.1 NSnc-SNP/kilobase pair (Figure 1). Importantly the SNPs were equally distributed in GVH or HVG direction across the whole exome and the MHC locus in HLA matched pairs. When the location of the SNP was mapped onto the individual chromosomes, these were distributed across the entire genome with a small number of genes demonstrating frequent variation and others with a diminishing frequency. T cell receptor b sequencing was performed to determine T cell repertoire in donors, and recipients following SCT. Comparison of exome sequence variation between donor-recipient pairs and the proportion of unique to shared T cell clones and their frequency in recipients, suggested that post-transplant T cell repertoire reconstitution in the recipient may be influenced by exome sequence variation (Figure 2). In conclusion, WES reveals extensive nucleotide sequence variation in the exomes of HLA-matched donors and recipients indicating a large potential for alloreactivity in stem cell transplantation. By directly measuring this alloreactivity potential, in the future whole exome sequencing may aid in determining GVHD risk in HLA matched and mismatched D-R pairs. Disclosures: No relevant conflicts of interest to declare.
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Lee, Eun-Ju, Daniel Dykas, Allen Bale, Caroline Cromwell, Terri L. Parker, Stephanie Halene, Adrienne Burns, Xiaopan Yao, and Alfred I. Lee. "Whole Exome Sequencing in Evaluation of Thrombophilia: A Novel 33-Gene Panel." Blood 126, no. 23 (December 3, 2015): 3529. http://dx.doi.org/10.1182/blood.v126.23.3529.3529.
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Abstract Introduction: Venous thromboembolism (VTE) occurs with an incidence of 1-2 per 1000 individuals per year. Approximately 10-20% of patients with VTE have a heritable thrombophilia involving one of five known genes: Factor V, prothrombin (PT), antithrombin (AT), protein C (PC), and protein S (PS). Significant variability of laboratory functional assays as well as fluctuating plasma levels of AT, PC and PS lead not only to delay in initial thrombophilia screening but also to multiple rounds of costly testing. Whole exome sequencing (WES) is a potentially useful diagnostic tool for inherited thrombophilias as it avoids dependence on laboratory and situational variation in protein levels. We compiled a panel of 33 genes involved in thrombosis with a goal of investigating the diagnostic yield and cost of WES in comparison to traditional thrombophilia testing. Methods: Since January of 2014, we have been performing WES in patients with a personal and family history of VTE seen at Yale New Haven Hospital. Thus far, 18 such patients have had a complete WES analysis. Data regarding patient demographics, number and type of VTE events, family/surgical history, medical co-morbidities, and traditional laboratory testing for inherited thrombophilias was recorded. Costs of each test were determined based on the amount billed to insurance. WES focusing on 33 genes involved in thrombosis was performed and analyzed by the DNA Diagnostic Lab at the Yale School of Medicine. Positive WES testing was defined as identification of a pathogenic variant in a gene known to be associated with thrombophilia, found at a frequency consistent with frequency of the disease, and with evidence that the variant predisposes to thrombosis. Positive laboratory testing was defined as any test that led to an unequivocal diagnosis of Factor V Leiden, PT mutation, homozygous MTHFR mutation with hyperhomocysteinemia, or a deficiency in AT, PC, or PS. Results: All 18 patients (7 male, 11 female) were included in the final analysis. Median age at first VTE was 35.5 years (range, 14-78 years); median number of independent VTE events was 2 (range, 1-9). WES with our 33-gene thrombophilia panel was positive in 11 of 18 (61.1%) patients, while traditional laboratory testing was positive in only 2 of 16 (12.5%) cases (Table 1). There were no statistically significant differences in clinical characteristics between those patients with positive findings on WES versus those without. Identified variants included those in genes with well known roles in thrombosis (SERPINC1, PROS1, F5), and in genes with emerging data regarding thrombosis (HABP2, SERPINA10, SERPIND1). Two patients identified on WES as having PS deficiency, one with AT deficiency, and one with a non-Leiden Factor V mutation had laboratory testing that was either normal or uninterpretable. The total cost of WES at our institution was $1935.00; by comparison, among 16 patients who underwent laboratory testing, median cost of laboratory testing was $2892.70 (range, $406.90-$11419.80), and the cost of laboratory testing exceeded WES in 13 patients. Conclusions: WES using our 33-gene thrombophilia panel has higher diagnostic yield and is more cost effective than traditional thrombophilia testing. With increasing availability and declining cost, this thrombophilia gene panel has the potential to truly transform thrombophilia testing. Further investigation of the diagnostic power and phenotypic correlation of identified mutations is in progress. Table 1. Mutations detected by the 33 gene thrombophilia panel Gender Age (yrs) Lab testing result WES result M 40 Negative SERPINA10 (Q384R) heterozygous M 67 Negative SERPINC1 (S426W) heterozygous M 30 Negative PROS1 (Y234C) heterozygous F 34 Negative HABP2 (G508E) heterozygous F 56 APC resistance F5 (R506Q) heterozygous F 27 F2 20210 G>A heterozygous F2 20210G>A heterozygous; vWF P2063S heterozygous F 37 Negative SERPIND1 (R468C) heterozygous F 48 Negative F5 (T915S) heterozygous M 20 Negative PROS1 (P76L) heterozygous M 55 Negative SERPINA10 (21_23delCCT ) heterozygous F 78 Negative HABP2 (G534E) heterozygous F 49 Negative Negative F 41 Negative Negative M 32 Negative Negative F 64 Negative Negative M 42 Negative Negative F 51 Negative Negative F 28 Negative Negative Disclosures No relevant conflicts of interest to declare.
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Belkadi, Aziz, Vincent Pedergnana, Aurélie Cobat, Yuval Itan, Quentin B. Vincent, Avinash Abhyankar, Lei Shang, et al. "Whole-exome sequencing to analyze population structure, parental inbreeding, and familial linkage." Proceedings of the National Academy of Sciences 113, no. 24 (May 31, 2016): 6713–18. http://dx.doi.org/10.1073/pnas.1606460113.
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Principal component analysis (PCA), homozygosity rate estimations, and linkage studies in humans are classically conducted through genome-wide single-nucleotide variant arrays (GWSA). We compared whole-exome sequencing (WES) and GWSA for this purpose. We analyzed 110 subjects originating from different regions of the world, including North Africa and the Middle East, which are poorly covered by public databases and have high consanguinity rates. We tested and applied a number of quality control (QC) filters. Compared with GWSA, we found that WES provided an accurate prediction of population substructure using variants with a minor allele frequency > 2% (correlation = 0.89 with the PCA coordinates obtained by GWSA). WES also yielded highly reliable estimates of homozygosity rates using runs of homozygosity with a 1,000-kb window (correlation = 0.94 with the estimates provided by GWSA). Finally, homozygosity mapping analyses in 15 families including a single offspring with high homozygosity rates showed that WES provided 51% less genome-wide linkage information than GWSA overall but 97% more information for the coding regions. At the genome-wide scale, 76.3% of linked regions were found by both GWSA and WES, 17.7% were found by GWSA only, and 6.0% were found by WES only. For coding regions, the corresponding percentages were 83.5%, 7.4%, and 9.1%, respectively. With appropriate QC filters, WES can be used for PCA and adjustment for population substructure, estimating homozygosity rates in individuals, and powerful linkage analyses, particularly in coding regions.
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Zhang, Jianjun, Junya Fujimoto, Jianhua Zhang, Yu Cao, Chi-Wan Chow, Kathryn A. Gold, Curtis Gumbs, et al. "Intratumor heterogeneity (ITH) of lung adenocarcinomas defined by multiregion whole exome sequencing (WES)." Journal of Clinical Oncology 32, no. 15_suppl (May 20, 2014): 11032. http://dx.doi.org/10.1200/jco.2014.32.15_suppl.11032.
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Anh Linh, Duong, Nguyen Thi Kim Lien, Nguyen Van Tung, Nguyen Thi Van Anh, Nguyen Thi Phuong Mai, Ngo Manh Tien, Tran Thi My Hanh, and Nguyen Huy Hoang. "Whole-exome sequencing as a diagnostic tool for ipex syndrome." Academia Journal of Biology 44, no. 1 (March 30, 2022): 53–60. http://dx.doi.org/10.15625/2615-9023/16305.
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Immune dysregulation-Polyendocrinopathy-Enteropathy-X-linked (IPEX) syndrome is a life-threatening congenital autoimmune disorder caused by mutations in the forkhead box protein 3 (FOXP3) gene. Typical clinical manifestations of IPEX patients are early onset of intractable diarrhea, type 1 diabetes mellitus, and skin diseases. However, other autoimmune types such as severe food allergies, autoimmune cytopenias, autoimmune respiratory illness, and mesangial glomerulonephritis may complicate IPEX diagnosis. In this study, we report a Vietnamese 1-year-old boy with IPEX syndrome due to a hemizygous missense mutation, c.1190G>A (p.Arg397Gln), in exon 12 of the FOXP3 gene (NM_014009.4). The child had dermatitis, diarrhea, respiratory infections, and splenomegaly. The patient's serum routine test results were expected, except for white blood cells and neutrophils were higher than the normal, while IgA concentration was slightly below the normal range. However, he got no signal of diabetes or failure to thrive. Whole exome sequencing was applied to identify a genetic variant, and variant validation was examined using Sanger sequencing. The patient’s genetic mutation was inherited from his mother, an obligate carrier. His father had a normal genotype. This study is the first report of IPEX syndrome in a Vietnamese patient with a mutation in the FOXP3 gene detected by WES. This study provides further evidence for the role of mutations in the FOXP3 gene in patients with IPEX syndrome and demonstrates the need for genetic counselling and prenatal testing. Our results also show that WES sequencing is an effective tool in diagnosing genetic diseases.
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Adema, Vera, Laura Palomo, María Díez-Campelo, Mar Mallo, Leonor Arenillas, Elisa Luño, Albert Perez-Ladaga, et al. "Whole-Exome Sequencing in Myelodysplastic Syndromes with 5q Deletion." Blood 124, no. 21 (December 6, 2014): 4635. http://dx.doi.org/10.1182/blood.v124.21.4635.4635.
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Abstract INTRODUCTION Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal myeloid stem cell disorders that are highly prevalent in elderly populations. MDS are characterized by inefficient hematopoiesis, peripheral blood (PB) cytopenias, and increased risk of transformation to acute myeloid leukemia (AML; 20–30% of patients with MDS). Around 50% of MDS patients carry at least one karyotypic aberration. The interstitial deletion of the long arm of chromosome 5 ([del(5q)] is the most common aberration, accounting for almost 30% of abnormal MDS karyotype. Various studies supports a favorable prognosis of MDS with isolated del(5q) with an excellent response to lenalidomide treatment. In order to describe the molecular events associated with MDS and del(5q) we performed whole-exome sequencing (WES)(assessing 334,378 exons) of tumor-normal paired samples from 20 MDS patients to unravel the genetic basis of MDS with del(5q). The analysis is ongoing and the complete results will be presented in the meeting. METHODS A total of 50 samples from 20 patients with MDS, with del(5q) were collected. For each diagnostic sample, we performed Conventional G-banding cytogenetics and fluorescence in situ hybridization (FISH, to confirm or dismiss del(5q)) and SNP arrays with Cytoscan HD (Affymetrix). These samples included: 20 tumor samples at diagnosis, 20 control samples and 10 samples after diagnosis, during lenalidomide treatment (5) or at the moment of relapse (5) in order to compare the genetic status before and during the treatment. Genomic DNA from tumor cells was obtained from bone marrow (BM) samples or from PB granulocytes. As a source of constitutional DNA we used CD3+T cells from each patient by isolating by magnetic-activated cell sorting. WES targeted capture was carried out on 7μg of genomic DNA, using the SureSelect Human Exome Kit 51Mb version 4.Libraries were sequenced on an Illumina HiSeq2000. Sequencing data will be analyzed using an in-house bioinformatics pipeline as previously reported. RESULTS Our preliminary analysis of these 20 new patients by WES confirmed our previous analyses with mutations in well described genes as ASXL1, JAK2 and TET2, but not in genes RUNX1, SF3B1 and SRSF2. In those patients we found two patients with missense mutation in TP53, one of the patients had an isolated del(5q) and is receiving lenalidomide treatment, and the other one had a complex karyotype. According to our prior analyses, in which 249 non-silent somatic variants were detected, we look forward to validate these mutations in this new series of patients. CONCLUSIONS We envision to validate these previous results with the new sequencing data of more patients with MDS and del(5q). We expect to measure somatic mutations that vary in abundance after lenalidomide treatment, potentially identifying mutations associated with resistance or relapse. ACKNOWLEDGEMENTS: This work has been supported (in part) by a grants from Instituto de Salud Carlos III, Ministerio de Sanidad y Consumo, Spain (PI 11/02010); by Red Temática de Investigación Cooperativa en Cáncer (RTICC, FEDER) (RD07/0020/2004; RD12/0036/0044); 2014 SGR225 (GRE) Generalitat de Catalunya; Fundació Internacional Josep Carreras; Obra Social “la Caixa”; Sociedad Española de Hematología y Hemoterapia (SEHH)and Celgene Spain. FOOTNOTES Rafael Bejar and Francesc Sole contributed equally. Disclosures Díez-Campelo: Novartis, Celgene: Honoraria, Research Funding. Xicoy:Celgene: Honoraria. Cañizo:Celgene, Jansen-Cilag, Arry, Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding. sanchez-Garcia:Celgene: Honoraria, Research Funding. Bejar:Celgene: Membership on an entity's Board of Directors or advisory committees; Genoptix Medical Laboratory: Consultancy, Honoraria, Licensed IP, no royalties Patents & Royalties, Membership on an entity's Board of Directors or advisory committees. Sole:Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding.
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Quitmann, Christina M., Stephan Rust, Janine Reunert, Saskia Biskup, Barbara Fiedler, and Thorsten Marquardt. "Tubulin Folding Cofactor D Deficiency: Missing the Diagnosis With Whole Exome Sequencing." Child Neurology Open 8 (January 2021): 2329048X2110349. http://dx.doi.org/10.1177/2329048x211034969.
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Two siblings with an early onset of a neurodegenerative disease were presented with muscular hypotonia, secondary microcephaly, and severe developmental delay. Seizures were refractory to treatment but could be controlled with a ketogenic diet. Over the course of 5 years, whole exome sequencing (WES) was performed twice in both children. The first time the diagnosis was missed. The next one revealed compound heterozygous mutations in the gene coding for the tubulin folding cofactor D. Technical improvements in WES mandated a new investigation after a few years in children where the diagnosis has not been found.
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Li, Ran, Yali Zheng, Yuqian Li, Rongbao Zhang, Fang Wang, Donghong Yang, Yanliang Ma, Xinlin Mu, Zhaolong Cao, and Zhancheng Gao. "Common Variable Immunodeficiency with Genetic Defects Identified by Whole Exome Sequencing." BioMed Research International 2018 (September 30, 2018): 1–7. http://dx.doi.org/10.1155/2018/3724630.
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Common variable immunodeficiency (CVID) belongs to the primary immunodeficiency disorders (PIDs), presenting a profound heterogeneity in phenotype and genotype, with monogenic or complex causes. Recurrent respiratory infections are the most common clinical manifestations. CVID patients can also develop various autoimmune and lymphoproliferative complications. Genetic testing such as whole exome sequencing (WES) can be utilized to investigate likely genetic defects, helping for better clinical management. We described the clinical phenotypes of three sporadic cases of CVID, who developed recurrent respiratory infections with different autoimmune and lymphoproliferative complications. WES was applied to screen disease-causing or disease-associated mutations. Two patients were identified to have monogenic disorders, with compound heterozygous mutations in LRBA for one patient and a frameshift insertion in NFKB1 for another. The third patient was identified to be a complex form of CVID. Two novel mutations were identified, respectively, in LRBA and NFKB1. A combination of clinical and genetic diagnosis can be more extensively utilized in the clinical practice due to the complexity and heterogeneity of CVID.
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Kim, Min-Jee, Mi-Sun Yum, Go Hun Seo, Yena Lee, Han Na Jang, Tae-Sung Ko, and Beom Hee Lee. "Clinical Application of Whole Exome Sequencing to Identify Rare but Remediable Neurologic Disorders." Journal of Clinical Medicine 9, no. 11 (November 20, 2020): 3724. http://dx.doi.org/10.3390/jcm9113724.
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Background: The aim of this study was to describe the application of whole exome sequencing (WES) in the accurate genetic diagnosis and personalized treatment of extremely rare neurogenetic disorders. Methods: From 2017 to 2019, children with neurodevelopmental symptoms were evaluated using WES in the pediatric neurology clinic and medical genetics center. The clinical presentation, laboratory findings including the genetic results from WES, and diagnosis-based treatment and outcomes of the four patients are discussed. Results: A total of 376 children with neurodevelopmental symptom were evaluated by WES, and four patients (1.1%) were diagnosed with treatable neurologic disorders. Patient 1 (Pt 1) showed global muscle hypotonia, dysmorphic facial features, and multiple anomalies beginning in the perinatal period. Pt 1 was diagnosed with congenital myasthenic syndrome 22 of PREPL deficiency. Pt 2 presented with hypotonia and developmental arrest and was diagnosed with autosomal recessive dopa-responsive dystonia due to TH deficiency. Pt 3, who suffered from intractable epilepsy and progressive cognitive decline, was diagnosed with epileptic encephalopathy 47 with a heterozygous FGF12 mutation. Pt 4 presented with motor delay and episodic ataxia and was diagnosed with episodic ataxia type II (heterozygous CACNA1A mutation). The patients’ major neurologic symptoms were remarkably relieved with pyridostigmine (Pt 1), levodopa (Pt 2), sodium channel blocker (Pt 3), and acetazolamide (Pt 4), and most patients regained developmental milestones in the follow-up period (0.4 to 3 years). Conclusions: The early application of WES helps in the identification of extremely rare genetic diseases, for which effective treatment modalities exist. Ultimately, WES resulted in optimal clinical outcomes of affected patients.
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Shevell, Lauren Marsh, Eun-Ju Lee, Rahul Dhodapkar, Daniel Dykas, Andreea Popa, Deqiong Ma, Noffar Bar, et al. "Whole Exome Sequencing and Extended Thrombophilia Testing in Patients with Venous Thromboembolism." Blood 132, Supplement 1 (November 29, 2018): 2506. http://dx.doi.org/10.1182/blood-2018-99-115529.
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Abstract Introduction: Venous thromboembolism (VTE), defined as deep venous thrombosis (DVT) and pulmonary embolism (PE), is a cause of significant morbidity and mortality worldwide, with an overall incidence of about 10,000,000 cases per year. The majority of VTEs are believed to be attributable to genetic factors. Yet, the five established heritable thrombophilias of factor V Leiden (FVL), prothrombin (PT) gene mutation, antithrombin (AT) deficiency, protein C (PC) deficiency, and protein S (PS) deficiency comprise only a small portion of VTEs, suggesting that further genetic factors contributing to VTE risk are unrecognized. In our previously published study, we performed whole exome sequencing (WES) in 64 patients with VTE and developed a 55-gene extended thrombophilia panel which identified 40 pathogenic or likely pathogenic variants or variants of uncertain significance (VUS) involving 22 different genes. Here, we present updated data from an expanded patient cohort. Methods: Blood was obtained from 101 patients with VTE. Genomic DNA was extracted and WES performed; mean coverage of the exome was 100x with 98% of the exome covered >/= 20 times. Variants were filtered for an allele frequency of 7% in the GnomAD database. A targeted analysis of the 55 genes in the extended thrombophilia panel was then performed. Variants in these genes were classified according to ACGM criteria as pathogenic, likely pathogenic, VUS, benign or likely benign. The number of patients with pathogenic or likely pathogenic variants and VUS in VTE patients was compared to a control population of 237 patients who had WES performed for reason other than VTE. The results of WES were also compared to those of traditional laboratory-based thrombophilia testing. Further, 17 VUS underwent in silico protein modeling to evaluate structural modifications. Results: Of the 101-patient study population, 46 were men and 55 women; 62% were Caucasian, 22% African American and 5% Hispanic; 15% had unprovoked VTE, 71% had provoked, 12% had both; and 55% had first degree family members with VTE. WES and extended thrombophilia testing identified a pathogenic or likely pathogenic variant or VUS in 69/101 (68%) VTE patients compared to 6/237 (2.5%) controls, a statistically significant difference (p-value <0.001). 86 patients underwent traditional laboratory-based thrombophilia testing; of these, 35 patients had a positive laboratory abnormality, with 31/35 (89%) also demonstrating a variant on WES. Among these 35 patients, in instances when laboratory-based thrombophilia testing did not correlate with WES, the abnormal lab was usually a borderline low PC or PS level that was not interpretable due to the clinical scenario (e.g. warfarin use). 51 patients had negative laboratory-based thrombophilia testing, of whom 30/50 (58%) had a variant on WES. A total of 72 genetic variants (26 previously published and 46 novel) were identified in 30 genes in the extended thrombophilia panel. 18 variants were categorized as pathogenic or likely pathogenic and 54 as VUS. 32 patients had pathogenic or likely pathogenic variants in one or more of the major thrombophilia genes, with FVL being the most common, and AT and PS deficiency being more common than PT gene mutation (FVL, n=15; PT gene mutation, n=3; AT deficiency, n=5; PC deficiency, n=3; PS deficiency, n=6). Of pathogenic variants in major thrombophilia genes, 15 were previously reported in literature, while 13 were novel. Of the 52 VUS, 17 were subjected to in silico analysis, including protein modeling, which suggested impaired protein folding in 14 variants. Conclusions: WES and extended thrombophilia testing reveal a high frequency of pathogenic or likely pathogenic variants or VUS in VTE patients compared to controls. These variants demonstrate good concordance with traditional laboratory-based thrombophilia testing. Several novel pathogenic or likely pathogenic variants were identified. In silico studies and protein modeling suggest that many VUS identified by this approach are likely to be deleterious to protein function. The results may underlie a strong genetic component to VTE. Next steps include further characterization of VUS using protein modeling, biochemical analysis, and epidemiological and familial studies to understand potential roles these variants may play in thrombosis. Table. Table. Disclosures Camire: Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Spark Therapeutics: Membership on an entity's Board of Directors or advisory committees; Bayer: Consultancy.
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Timms, Kirsten, Andrey Zharkikh, Michael Perry, Nicolai Birkbak, Zoltan Szallasi, Alexander Gutin, Andrea Richardson, and Jerry Lanchbury. "Comparison between whole exome sequencing (WES) and single nucleotide polymorphism (SNP)-based tumor mutation burden analysis." Journal of Clinical Oncology 37, no. 15_suppl (May 20, 2019): 2634. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.2634.
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2634 Background: Immune checkpoint inhibitors (ICI) block proteins which enable cancer cells to evade the immune system. Recent studies have shown that the higher the tumor mutation burden (TMB) the greater the likelihood of response to ICI therapy. Analysis of TMB has focused on WES of paired tumor and normal samples. This study tests the feasibility of measuring TMB from a SNP-based resequencing assay (myChoice HRD Plus). Methods: WES and myChoice HRD Plus were performed on matched tumor and normal DNA from 44 breast and 12 colon tumors. myChoice HRD Plus combines homologous recombination deficiency analysis with resequencing of 108 genes and microsatellite instability analysis. WES-based TMB was calculated by identifying all variants in paired samples, and subtracting germline variants. Two SNP-based TMB (SbTMB) methods were utilized to calculate TMB. The first used germline subtraction similar to the WES-based method. The second utilized an algorithm which removed background germline variants. Median sequence length to calculate TMB was 9.7 Mb for WES, 4.6 Mb for SbTMB (germline subtraction), and 1.9 Mb for SbTMB (algorithm). Results: Correlation coefficients for WES vs. SbTMB (germline subtraction) and SbTMB (algorithm) were 0.895 and 0.908, respectively. The two SbTMB methods had a correlation coefficient of 0.834. SbTMB measures of TMB were generally higher than WES-based TMB with a mean increase in score of 1.6 variants/Mb for SbTMB (germline subtraction; p = 4.6x10-6) and 1.5 variants/MB for SbTMB (algorithm; p = 1.2x10-5). No significant difference in magnitude of TMB score between the SbTMB measures was observed (0.04 variants/Mb; p = 0.88). Conclusions: SNP-based methods for calculating TMB produced highly concordant scores compared to WES-based methods. SbTMB assays produced elevated TMB scores, consistent with selective pressure against mutations in coding regions of genes, necessitating a higher score threshold for when using a SbTMB assay. This SbTMB analysis expands the utility of myChoice HRD Plus, and provides a method for calculation of TMB without sequencing a germline comparator.
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Tal-Ben Ishay, Rotem, Apurba Shil, Shirley Solomon, Noa Sadigurschi, Hadeel Abu-Kaf, Gal Meiri, Hagit Flusser, et al. "Diagnostic Yield and Economic Implications of Whole-Exome Sequencing for ASD Diagnosis in Israel." Genes 13, no. 1 (December 23, 2021): 36. http://dx.doi.org/10.3390/genes13010036.
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Whole-exome sequencing (WES) is an effective approach to identify the susceptibility of genetic variants of autism spectrum disorder (ASD). The Israel Ministry of Health supports WES as an adjunct tool for ASD diagnosis, despite its unclear diagnostic yield and cost effectiveness. To address this knowledge gap, we applied WES to a population-based sample of 182 Bedouin and Jewish children with ASD from southern Israel, and assessed its yield in a gene panel of 205 genes robustly associated with ASD. We then compared the incremental cost-effectiveness ratios (ICERs) for an ASD diagnosis by WES, chromosomal microarray analysis (CMA), and CMA + WES. Overall, 32 ASD candidate variants were detected in 28 children, corresponding to an overall WES diagnostic yield of 15.4%. Interestingly, the diagnostic yield was significantly higher for the Bedouin children than for the Jewish children, i.e., 27.6% vs. 11.1% (p = 0.036). The most cost-effective means for genetic testing was the CMA alone, followed closely by the CMA + WES strategy (ICER = USD 117 and USD 124.8 per child). Yet, WES alone could become more cost effective than the other two approaches if there was to be a 25% increase in its yield or a 50% decrease in its cost. These findings suggest that WES should be recommended to facilitate ASD diagnosis in Israel, especially for highly consanguineous populations, such as the Bedouin.
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Bartha and Győrffy. "Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology." Cancers 11, no. 11 (November 4, 2019): 1725. http://dx.doi.org/10.3390/cancers11111725.
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Whole exome sequencing (WES) enables the analysis of all protein coding sequences in the human genome. This technology enables the investigation of cancer-related genetic aberrations that are predominantly located in the exonic regions. WES delivers high-throughput results at a reasonable price. Here, we review analysis tools enabling utilization of WES data in clinical and research settings. Technically, WES initially allows the detection of single nucleotide variants (SNVs) and copy number variations (CNVs), and data obtained through these methods can be combined and further utilized. Variant calling algorithms for SNVs range from standalone tools to machine learning-based combined pipelines. Tools for CNV detection compare the number of reads aligned to a dedicated segment. Both SNVs and CNVs help to identify mutations resulting in pharmacologically druggable alterations. The identification of homologous recombination deficiency enables the use of PARP inhibitors. Determining microsatellite instability and tumor mutation burden helps to select patients eligible for immunotherapy. To pave the way for clinical applications, we have to recognize some limitations of WES, including its restricted ability to detect CNVs, low coverage compared to targeted sequencing, and the missing consensus regarding references and minimal application requirements. Recently, Galaxy became the leading platform in non-command line-based WES data processing. The maturation of next-generation sequencing is reinforced by Food and Drug Administration (FDA)-approved methods for cancer screening, detection, and follow-up. WES is on the verge of becoming an affordable and sufficiently evolved technology for everyday clinical use.
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Iwama, Kazuhiro, Takeshi Mizuguchi, Eri Takeshita, Eiji Nakagawa, Tetsuya Okazaki, Yoshiko Nomura, Yoshitaka Iijima, et al. "Genetic landscape of Rett syndrome-like phenotypes revealed by whole exome sequencing." Journal of Medical Genetics 56, no. 6 (March 6, 2019): 396–407. http://dx.doi.org/10.1136/jmedgenet-2018-105775.
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BackgroundRett syndrome (RTT) is a characteristic neurological disease presenting with regressive loss of neurodevelopmental milestones. Typical RTT is generally caused by abnormality of methyl-CpG binding protein 2 (MECP2). Our objective to investigate the genetic landscape of MECP2-negative typical/atypical RTT and RTT-like phenotypes using whole exome sequencing (WES).MethodsWe performed WES on 77 MECP2-negative patients either with typical RTT (n=11), atypical RTT (n=22) or RTT-like phenotypes (n=44) incompatible with the RTT criteria.ResultsPathogenic or likely pathogenic single-nucleotide variants in 28 known genes were found in 39 of 77 (50.6%) patients. WES-based CNV analysis revealed pathogenic deletions involving six known genes (including MECP2) in 8 of 77 (10.4%) patients. Overall, diagnostic yield was 47 of 77 (61.0 %). Furthermore, strong candidate variants were found in four novel genes: a de novo variant in each of ATPase H+ transporting V0 subunit A1 (ATP6V0A1), ubiquitin-specific peptidase 8 (USP8) and microtubule-associated serine/threonine kinase 3 (MAST3), as well as biallelic variants in nuclear receptor corepressor 2 (NCOR2).ConclusionsOur study provides a new landscape including additional genetic variants contributing to RTT-like phenotypes, highlighting the importance of comprehensive genetic analysis.
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Yang, Kai, Ming Shen, Yousheng Yan, Ya Tan, Jing Zhang, Jue Wu, Guangming Yang, et al. "Genetic Analysis in Fetal Skeletal Dysplasias by Trio Whole-Exome Sequencing." BioMed Research International 2019 (May 14, 2019): 1–8. http://dx.doi.org/10.1155/2019/2492590.
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Skeletal dysplasias (SDs) comprise a series of severe congenital disorders that have strong clinical heterogeneity and usually attribute to diverse genetic variations. The pathogenesis of more than half of SDs remains unclear. Additionally, the clinical manifestations of fetal SDs are ambiguous, which poses a big challenge for accurate diagnosis. In this study, eight unrelated families with fetal SD were recruited and subjected to sequential tests including chromosomal karyotyping, chromosomal microarray analysis (CMA), and trio whole-exome sequencing (WES). Sanger sequencing and quantitative fluorescence PCR (QF-PCR) were performed as affirmative experiments. In six families, a total of six pathogenic/likely pathogenic variations were identified in four genes including SLC26A2, FGFR3, FLNB, and TMEM38B. These variations caused disorders following autosomal dominant or autosomal recessive inheritance patterns, respectively. The results provided reliable evidence for the subsequent genetic counseling and reproductive options to these families. With its advantage in variation calling and interpreting, trio WES is a promising strategy for the investigation of fetal SDs in cases with normal karyotyping and CMA results. It has considerable prospects to be utilized in prenatal diagnosis.
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Zhang, Yanfeng, Bingshan Li, Chun Li, Qiuyin Cai, Wei Zheng, and Jirong Long. "Improved Variant Calling Accuracy by Merging Replicates in Whole-Exome Sequencing Studies." BioMed Research International 2014 (2014): 1–7. http://dx.doi.org/10.1155/2014/319534.
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In large scale population-based whole-exome sequencing (WES) studies, there are some samples occasionally sequenced two or more times due to a variety of reasons. To investigate how to efficiently utilize these duplicated sequencing data, we conducted comprehensive evaluation of variant calling strategies. 92 samples subjected to WES twice were selected from a large population study. These 92 duplicated samples were divided into two groups: group H consisting of the higher sequencing depth for each subject and group L consisting of the lower depth for each subject. The merged samples for each subject were put in a third group M. Using the GATK multisample toolkit, we compared variant calling accuracy among three strategies. Hierarchical clustering analysis indicated that the two replicates for each subject showed high homogeneity. The comparative analyses on the basis of heterozygous-homozygous ratio (Hete/Homo), transition-transversion ratio (Ti/Tv), and overlapping rate with the 1000 Genomes Project consistently showed that the data quality of the SNPs detected from the M group was more accurate than that of SNPs detected from the H and L groups. These results suggested that merging homogeneous duplicated exomes instead of using one of them could improve variant calling accuracy.
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Cagirici, H. Busra, Bala Ani Akpinar, Taner Z. Sen, and Hikmet Budak. "Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing." International Journal of Molecular Sciences 22, no. 19 (September 27, 2021): 10400. http://dx.doi.org/10.3390/ijms221910400.
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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.
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Albino, Elinette, Simon Carlo, Cristel Chapel-Crespo, Alberto Santiago-Cornier, and Carmen Buxo. "360 Retrospective Evaluation of Whole-Exome Sequencing in Puerto Ricans with Neurogenetic Complex Traits." Journal of Clinical and Translational Science 6, s1 (April 2022): 67. http://dx.doi.org/10.1017/cts.2022.204.
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OBJECTIVES/GOALS: Assess the diagnostic yield and test utilization of WES in patients having complex traits. We aim to evaluate the use of the first genetic approach for the identification of primary variants that contribute to neurogenetic disease etiology and influence onset and progression in Puerto Ricans. METHODS/STUDY POPULATION: Prospective cohort of 45 Puerto Rican probands (19 months - 36 years old) with complex neurogenetic traits that underwent WES (2019 - 2021). WES was performed, including copy number variant analysis and mitochondrial genome sequencing. We evaluated several factors possibly influencing the rate of WES diagnosis including early age, consanguinity, and family history of neurogenetic diseases. In addition, we only evaluated probands rather than dyads/trios and the clinical phenotypes. Descriptive analysis was performed, including a catalog of all variants reported. Multivariate analysis was performed to estimate the statistical association between variants and phenotypes reported and adjusting for potential confounders (age, sex, family history, income, health insurance and zip code). RESULTS/ANTICIPATED RESULTS: Auspiciously, positive pathogenic findings altered the clinical management in 29% of the probands in this study. A likely genetic diagnosis was achieved in 53% of the probands including pathogenic, likely pathogenic and variants of uncertain significance. Intronic variants, copy number variants detection and mitochondrial genome was included in WES methodology. Despite these facts, a 47% of the reported WES were negative, which deserve re-analysis potentially genotype based. Multivariate analysis is expected to adjust for potential confounders to establish a genotype-phenotype correlations in neurogenetic complex traits in this Puerto Rican admixed population. DISCUSSION/SIGNIFICANCE: Clinical WES offers an alternative approach for identification of variants in patients with complex traits. WES is also applicable in genetically heterogeneous individuals when specific genetic tests are not available or unsuccessful. Variants reported contribute to understand complex neurogenetic disease in underrepresented Puerto Ricans.
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Barinotti, Alice, Massimo Radin, Irene Cecchi, Silvia Grazietta Foddai, Elena Rubini, Dario Roccatello, Savino Sciascia, and Elisa Menegatti. "Genetic Factors in Antiphospholipid Syndrome: Preliminary Experience with Whole Exome Sequencing." International Journal of Molecular Sciences 21, no. 24 (December 15, 2020): 9551. http://dx.doi.org/10.3390/ijms21249551.
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As in many autoimmune diseases, the pathogenesis of the antiphospholipid syndrome (APS) is the result of a complex interplay between predisposing genes and triggering environmental factors, leading to a loss of self-tolerance and immune-mediated tissue damage. While the first genetic studies in APS focused primarily on the human leukocytes antigen system (HLA) region, more recent data highlighted the role of other genes in APS susceptibility, including those involved in the immune response and in the hemostatic process. In order to join this intriguing debate, we analyzed the single-nucleotide polymorphisms (SNPs) derived from the whole exome sequencing (WES) of two siblings affected by APS and compared our findings with the available literature. We identified genes encoding proteins involved in the hemostatic process, the immune response, and the phospholipid metabolism (PLA2G6, HSPG2, BCL3, ZFAT, ATP2B2, CRTC3, and ADCY3) of potential interest when debating the pathogenesis of the syndrome. The study of the selected SNPs in a larger cohort of APS patients and the integration of WES results with the network-based approaches will help decipher the genetic risk factors involved in the diverse clinical features of APS.
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Qiu, Ping, Ling Pang, Gladys Arreaza, Maureen Maguire, Ken Chang, Matthew Marton, and Diane Levitan. "Data Interoperability of Whole Exome Sequencing (WES) Based Mutational Burden Estimates from Different Laboratories." International Journal of Molecular Sciences 17, no. 5 (April 29, 2016): 651. http://dx.doi.org/10.3390/ijms17050651.
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