Academic literature on the topic 'Whole Exon Sequencing'
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Journal articles on the topic "Whole Exon Sequencing"
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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 (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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Glotov, Oleg S., Natalya A. Zhuchenko, Maria S. Balashova, et al. "The Benefits of Whole-Exome Sequencing in the Differential Diagnosis of Hypophosphatasia." International Journal of Molecular Sciences 25, no. 21 (2024): 11728. http://dx.doi.org/10.3390/ijms252111728.
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Hypophosphatasia (HPP) is a rare inherited disorder characterized by the decreased activity of tissue-nonspecific alkaline phosphatase (TNSALP), caused by mutations in the ALPL gene. The aim of this study was to conduct differential diagnostics in HPP patients using whole-exome sequencing (WES). The medical records of HPP patients and the genetic testing of the ALPL gene were reviewed. Seven patients were recruited and underwent WES using the Illumina or MGI sequencing platforms. All of the exome samples were matched onto a GRCh38.p13 reference genome assembly by using the Genome Analysis ToolKit (GATK) and the BWA MEM read aligner. We present the clinical and molecular findings of the seven patients referred for genetic analyses due to a clinical and biochemical suspicion of HPP. In two patients out of three (with identified heterozygous variants in the ALPL gene), we also identified c.682T>A in exon 3 of the WNT10A gene and c.3470del in exon 23 of the SMC1A gene variants for the first time. In four patients, variants in the ALPL gene were not detected, but WES allowed us to identify for the first time rare variants (c.5651A>C in exon 36 of the TRIO gene, c.880T>G in exon 6 of the TRPV4 gene, c.32078-1G>T in intron 159 of the TTN gene, c.47720_47721del in exon 235 of the TTN gene, and c.1946G>A in exon 15 of the SLC5A1 gene) and to conduct differential diagnostics with HPP. Using WES, for the first time, we demonstrate the possibility of early differential diagnostics in HPP patients with other rare genetic diseases.
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Kunii, M., H. Doi, S. Kubota, et al. "Genetic analysis of adult leukoencephalopathy patients using whole exon sequencing." Journal of the Neurological Sciences 381 (October 2017): 455. http://dx.doi.org/10.1016/j.jns.2017.08.3493.
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Li, Li-Yan, Zhao-Yun Liu, Hui Liu, Chun-Yan Liu, Zong-Hong Shao, and Rong Fu. "Deep sequencing of whole genome exon in paroxysmal nocturnal hemoglobinuria." American Journal of Hematology 92, no. 4 (2017): E51—E53. http://dx.doi.org/10.1002/ajh.24655.
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Hsu, Ting-Chang, Shelley Nakaya, and Arthur Thompson. "Severe haemophilia B due to a 6 kb factor IX gene deletion including exon 4: Non-homologous recombination associated with a shortened transcript from whole blood." Thrombosis and Haemostasis 97, no. 02 (2007): 176–80. http://dx.doi.org/10.1160/th06-10-0592.
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SummaryIn genotyping a severe hemophilia B subject, exons 1–3 and 5–8 were normal. Exon 4 did not amplify, suggesting a partial gene deletion. Previously, a French family with an exon 4 deletion had severe haemophilia B with a circulating, dysfunctional factor IX protein missing its first growth factor-like domain; breakpoints were not analyzed. Using a 5’ primer for exon 3 and a 3’ primer for exon 5 fragments, the subject’s factor IX gene amplified a 5 kb fragment whereas 11 kb was predicted, indicating a 6 kb deletion. Restriction endonucleases localized the 3’ intron 4 deletion breakpoint to 1.2 kb 5’ to exon 5. Sequencing through the breakpoints revealed a 5,969 bp deletion that included exon 4 and was accompanied by a 13 bp duplication inserted near the 3’ breakpoint site. Haemophilia was familial; on testing, his mother was confirmed as a heterozygous carrier, whereas his sister was homozygous for the normal, larger fragments. As exons 4 and 5 of the factor IX gene are in frame, this deletion should produce a shortened transcript, missing 114 bp (38 codons from the first growth factor-like domain). Reverse transcription of mRNA prepared from whole blood and PCR identified the shorter cDNA fragment. Western blotting demonstrated a smaller factor IX protein.
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Mi, Jingyi, Padmini Parthasarathy, Benjamin J. Halliday, et al. "Deletion of Exon 1 in AMER1 in Osteopathia Striata with Cranial Sclerosis." Genes 11, no. 12 (2020): 1439. http://dx.doi.org/10.3390/genes11121439.
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Osteopathia striata with cranial sclerosis (OSCS) is an X-linked dominant condition characterised by metaphyseal striations, macrocephaly, cleft palate, and developmental delay in affected females. Males have a more severe phenotype with multi-organ malformations, and rarely survive. To date, only frameshift and nonsense variants in exon 2, the single coding exon of AMER1, or whole gene deletions have been reported to cause OSCS. In this study, we describe two families with phenotypic features typical of OSCS. Exome sequencing and multiplex ligation-dependent probe amplification (MLPA) did not identify pathogenic variants in AMER1. Therefore, genome sequencing was employed which identified two deletions containing the non-coding exon 1 of AMER1 in the families. These families highlight the importance of considering variants or deletions of upstream non-coding exons in conditions such as OSCS, noting that often such exons are not captured on probe or enrichment-based platforms because of their high G/C content.
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Mao, Qijiang, Haoqi Pan, Boqiang Liu, et al. "Whole-exon sequencing insights into pancreatic synovial sarcoma: a case report." Gland Surgery 10, no. 5 (2021): 1812–18. http://dx.doi.org/10.21037/gs-20-680.
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Mahamdallie, Shazia, Elise Ruark, Shawn Yost, et al. "The ICR96 exon CNV validation series: a resource for orthogonal assessment of exon CNV calling in NGS data." Wellcome Open Research 2 (May 26, 2017): 35. http://dx.doi.org/10.12688/wellcomeopenres.11689.1.
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Detection of deletions and duplications of whole exons (exon CNVs) is a key requirement of genetic testing. Accurate detection of this variant type has proved very challenging in targeted next-generation sequencing (NGS) data, particularly if only a single exon is involved. Many different NGS exon CNV calling methods have been developed over the last five years. Such methods are usually evaluated using simulated and/or in-house data due to a lack of publicly-available datasets with orthogonally generated results. This hinders tool comparisons, transparency and reproducibility. To provide a community resource for assessment of exon CNV calling methods in targeted NGS data, we here present the ICR96 exon CNV validation series. The dataset includes high-quality sequencing data from a targeted NGS assay (the TruSight Cancer Panel) together with Multiplex Ligation-dependent Probe Amplification (MLPA) results for 96 independent samples. 66 samples contain at least one validated exon CNV and 30 samples have validated negative results for exon CNVs in 26 genes. The dataset includes 46 exon CNVs in BRCA1, BRCA2, TP53, MLH1, MSH2, MSH6, PMS2, EPCAM or PTEN, giving excellent representation of the cancer predisposition genes most frequently tested in clinical practice. Moreover, the validated exon CNVs include 25 single exon CNVs, the most difficult type of exon CNV to detect. The FASTQ files for the ICR96 exon CNV validation series can be accessed through the European-Genome phenome Archive (EGA) under the accession number EGAS00001002428.
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Leong, Matthew, Xiaomo Li Li, Jacob Mercer, et al. "Identification of a novel class of early exon ALK rearrangements across two pan tumor sequencing databases." Journal of Clinical Oncology 41, no. 16_suppl (2023): e15105-e15105. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.e15105.
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e15105 Background: ALK-rearrangements are a powerful and highly prevalent driver in cancer biology. The advent of potent tyrosine kinase inhibitors has led to the development of numerous laboratory tests and FDA approved therapies for the detection and treatment of ALK-positive cancers. The vast majority of reported ALK rearrangements involve exon 20 with fusions involving exons 17-19 occasionally reported. While less common, ALK-rearrangements occurring earlier in the ALK gene have not been well characterized. This is largely because most clinically available biomarker testing is only optimized for detection of rearrangements involving the common regions. To this end, we aimed to investigate the prevalence of early exon ALK rearrangements (eALKr). Methods: Two pathology databases, including the Tempus deidentified database, were retrospectively queried to characterize eALKr, which were defined as any rearrangement that involved ALK exons 1-16. Demographic information and tumor type were recorded. Identification of eALKr was performed via targeted amplicon-based RNA sequencing, targeted hybrid capture DNA sequencing and whole transcriptome sequencing. Select specimens with early ALK fusions were also evaluated for ALK detection using available FDA-approved methods (immunohistochemistry [IHC] and fluorescent in-situ hybridization [FISH]). Results: Out of the specimens that underwent NGS testing in the two databases, the prevalence of eALKr was 0.05% (73/143,959) across the databases and 10.3% (73/709) for all tumors with ALK rearrangements. Across the 73 rearrangements, there were 58 unique 5’ partner genes of which 46 were only identified once. eALK rearrangements were identified in all exons from exons 1 to 16 except for exon 13, with exon 4 being the most common. Prostatic, breast and ovarian serous carcinoma were the most common tumor types (Table 1). In three cases IHC and FISH were unreliable due to the early rearrangement location (0/3 IHC positive, 1/3 FISH positive). FISH was negative for samples with rearrangements in exon 2 and 4 and showed an atypical (deletion) pattern with a rearrangement involving exon 12. Conclusions: A non-trivial number of eALKr were detected within two database using next generation sequencing (0.05% of total cancer cases; 10.3% of ALK fusion cases). These novel eALK rearrangements were predominantly in tumor types not normally associated with ALK fusions. FDA approved testing modalities are only optimized to detect common ALK rearrangements, which in part may be a reason why eALK-rearrangements are poorly characterized, with limited prevalence and treatment data available. [Table: see text]
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Clarke, Stanley R., Adrianna Vlachos, Jens Lichtenberg, et al. "Whole Genome Sequencing of Diamond Blackfan Anemia Syndrome Patients Detects Mutations That Alter mRNA Splicing." Blood 138, Supplement 1 (2021): 863. http://dx.doi.org/10.1182/blood-2021-145622.
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Abstract Diamond Blackfan anemia syndrome (DBAS) is a rare, heritable bone marrow failure syndrome characterized by severe macrocytic anemia, congenital anomalies and predisposition to cancer, most often diagnosed during infancy. More than 98% of DBAS patients with a molecular diagnosis have mutations in a gene encoding one of the ~80 ribosomal proteins (RP) leading to haploinsufficiency. A molecular diagnosis in a patient with DBAS is critical for a definitive diagnosis, the identification of compatible related transplant donors, and developing reproductive strategies for families. Targeted sequencing of RP genes, single nucleotide polymorphism comparative genome hybridization (SNP array) to detect >30 kb deletions (Farrar et al. Blood. 2011) and exome sequencing (WES) (Ulrisch et al. Am J Hum Genet. 2018) has identified RP mutations in ~80% of patients, leaving ~20% of patients with DBAS without a molecular diagnosis. Targeted sequencing and WES focus on only coding sequences. We hypothesized that remaining 20% of DBAS mutations were in the non-coding regions of RP genes, such as promoters or introns. To test this hypothesis, we collected DNA with informed consent for whole genome sequencing (WGS) analysis from 14 patients with no molecular diagnosis after targeted sequencing, SNP array or WES. On average, we aligned ~3.2x10 7 paired end reads of 250 base pairs for each patient (~65X coverage). We focused our analysis on the sequences in and around the RP genes. To identify deletions, we used a suite of detection tools: DELLY, GRIDSS, MANTA, and LUMPY. More than 90% of deletions identified by any 2 of these tools were confirmed by PCR. We identified 5 deletions in the introns of RP genes, ranging from 11 to 467 base pairs in length, which we hypothesized disrupted splicing of the nascent RNA transcript. To test this, we created minigenes in which we replaced exon 2 of a gamma globin gene with either the WT or mutant RP exon. All wild type exons spliced normally. A 467 base pair deletion in RPL27 exon 3 was sufficient to prevent the correct splicing of that intron. Examination of the eCLIP data for RNA binding proteins revealed that spliceosome complex proteins (including SF3B1, SF3B4 and EFTUD2) and Dead-box RNA helicases bind in the deleted region. A 28 base pair deletion in exon 3 of RPL6 removes a polypyrimidine tract that is a critical part of the 3' splice junction consensus sequence, which we presume is also deleterious. The other 3 intronic deletions did not disrupt splicing. We also identified 2 causative point mutations. A point mutation 5 bases into intron 1 of the RPS26 gene changes a base in the 5' splice donor consensus sequence, which activated a cryptic splice donor in the 5' untranslated region. This aberrant splice removes the ATG initiation codon causing an untranslatable RNA. In another patient, we identified a mutation in exon 1 of the RPS27 gene, judged to be a benign amino acid change. This mutation disrupted splicing.by activating a cryptic splice donor site in the 5' untranslated region which removes the ATG initiation codon and causes a frame shift. We were referred two patients with possible duplications of the RPL35a gene. To identify duplications, we employed MinION long read single molecule sequencing. We had an average read length of ~ 6-10kb with the longest read being 1.3Mb. Overall coverage was >85X. We used minimap2 to align the reads to the reference human genome and used SNIFFLES to call the variants. One patient was the parent of DBAS-affected patient with no history of anemia. In this patient, we identified a duplication of 400 kb that included the entire RPL35a region along with genes on either side. We conclude that this duplication is not likely to cause DBA. The second patient was diagnosed with DBAS. In this patient, we identified a duplication of 4 kb including exons 1 and 2 of RPL35a We conclude that this duplication disrupts the RPL35a gene and is a likely cause of DBA. Whole genome sequencing of 15 DBAS patients identified 5 likely causative mutations in RP genes, confirming that most genetically undiagnosed cases of DBAS will involve known genes encoding RP. We conclude that the pipeline for obtaining a molecular diagnosis for DBAS from targeted sequencing, SNP array, and exome sequencing to whole genome sequencing. Disclosures Vlachos: Novartis: Membership on an entity's Board of Directors or advisory committees. Lipton: Celgene: Membership on an entity's Board of Directors or advisory committees.
Dissertations / Theses on the topic "Whole Exon Sequencing"
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Tessoulin, Benoît. "Identification par séquençage de l'exome de la dérégulation des voies de signalisation dans le myélome multiple et leurs conséquences fonctionnelles, notamment sur la voie p53." Thesis, Nantes, 2018. http://www.theses.fr/2018NANT1027/document.
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Au sein des hémopathies malignes B, les plasmocytoses malignes (myélome multiple [MM) et leucémie à plasmocyte [PCLI) occupent une place particulière par leur biologie et leurs aspects cliniques. Biologiquement, elles présentent une forte proportion d’anomalies oncogéniques· (RAS, c-MYC) et de fréquentes altérations de la voie p53 (CDKN2ADel, TP53Del/Mut) qui conduisent, cliniquement, à l’inefficacité des traitements cytostatiques conventionnels. Des lignées cellulaires de MM (HMCls) qui recouvrent en partie la diversité des patients ont été générées depuis 50 ans. Nous avons caractérisé l’exome complet de 33 lignées cellulaires humaines de MM. Les mutations faux-sens sont les plus fréquentes (92%). les HMCLs portent entre 307 et 916 mutant par HMCL, TP53 étant le gène le plus altéré (67%). Des pertes bi-alléliques des voies du cycle cellulaire (CDKN2C, RB1), de la voie NFkB (TRAF3, BIRC2) et de la voie p53 (TP53, CDKN2A) sont fréquentes. La fréquence des mutations/délétion est semblable à celle des patients ( DIS3, PRDM1, KRAS), ou majorée (TP53, CDKN2C, NRAS, PRKD2). la voie MAPK est lá plus altérée (82% des HMCls), principalement par des mutants de RAS: peu décrites, les HMCLs présentent des altérations des voies épigénétiques (73%), de l’ anémie de Fanconi (54%) et très peu d’anonalies directes de la machinerie apoptotique. Nous avons mis en relation les données dexpression, de mutation/délétion et de réponse aux traitements et démontré que l’efficacité de plusieurs traitements est indépendante des mutations. Finalement, le développement de stratégies prenant en compte ces altérations peu décrites dans le MM (Fanconi, Epigenetique) sont nécessaires<br>Among B CeH malignancies, plasma-cell the NFKB pathway (TRAF3, BIRC2) and the p53 malignancies (multiple myeloma [MM] and plasma cell pathway (TP53, CDKN2A). Frequency of leukemia [PCL]) harbor particular biological and mutations/deletions in HMCLs were either similar to clinical insights. Biologically, they present with both a that of patients (e.g. DIS3, PRDM1, KRAS), or highly high frequency of oncogenic abnormalities (RAS, e- increased (e.g. TP53, CDKN2C, NRAS, PRKD2). MYC) and a high frequency of p53 pathway MAPK was the most altered pathway (82% of abnormalities (CDKN2Adel, TP53 del/mut). Those two HMCLs), mainly by RAS mutants. Surprisingly, latter leading to chemo-resistance to conventional HMCLs displayed alterations in epigenetic (73%) and cytostatic drugs. Human myeloma cell lines (HMCLs) Fanconi anemia (54%) and few alterations in are widely used for their representation of primary apoptotic machinery. We further identified mutually myeloma cells as they cover patient diversity, exclusive and associated mutations/deletions in afthough not fully. We performed whole-exon genes involved in the MAPK and p53 pathways as sequencing of 33 HMCLs, which were established well as in chromatin regulator/modifier genes. over the last 50 years. Missense mutations were the Finally, by combining the gene expression profile, most frequent mutations {92%). HMCLs harbored gene mutation. gene deletion and drug response, we between 307 and 916 mutations per sample, with demonstrated that several targeted drugs overcome TP53 being the most mutated gene (67%). Recurrent or bypass some mutations bi-allelic losses were found in genes involved in cell cycle regulation (RB1. CDKN2C)
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Quenez, Olivier. "Optimisation de la détection et de l'interpretation des variations génomiques issues de données d'exomes pour les études cas-contrôles." Electronic Thesis or Diss., Normandie, 2023. http://www.theses.fr/2023NORMR071.
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Au cours des 20 dernières années, l'évolution des nouvelles technologies a révélé la grande variabilitéde notre génome depuis la simple substitution jusqu'aux réarrangements chromosomiques. Lestechnologies de séquençage à haut débit ont particulièrement amélioré l’identification etl’interprétation des variations de petite taille tout en offrant l’opportunité d’explorer les variations destructure avec une résolution supérieure à celle disponible grâce aux analyses pangénomiques surpuces. Néanmoins, l’identification des variations de structure, et plus particulièrement des variationsdu nombre de copies (CNV) à partir de données de séquençage par capture, a été sous exploitée etpeu évaluée. Notre objectif principal était de mettre en place un pipeline bioinformatique basé sur laprofondeur de lecture pour l’identification des CNV, puis de l’appliquer à une études cas-témoinsd’exome dans le cadre de la recherche sur la maladie d’Alzheimer.La maladie d’Alzheimer (MA) est la maladie neurodégénérative la plus fréquente. Les facteursgénétiques individuels jouent un rôle important dans son déterminisme et de multiples facteurs derisque ont été identifiés, essentiellement des substitutions et petites insertions/délétions. Pourtant,des variations de structure ont déjà été identifiées dans des formes monogéniques de MA, comme lesduplications complètes du gène APP. Les CNV restent très peu étudiés dans la MA et nous avonssouhaité appliquer une approche cas-témoins à partir de données massives d’exomes pour détecterdes CNV contribuant au risque de MA.Dans un premier temps, nous avons établi une stratégie d'analyse basée sur le logiciel CANOES afin dedétecter les CNV à partir de données de NGS issues d’une capture (panel, exomes). Cette approche aété validée à travers deux grands jeux de données de panels et d’exomes comparés à des techniquesindépendantes. Dans le premier jeu de données (panels), la sensibilité et la spécificité étaient de 100%et nous obtenons une sensibilité de 87,25 % et une valeur prédictive positive de 88,5% sur la détectionde CNV sur les données de séquençage d'exomes.Par la suite, nous avons appliqué cette approche aux données d’exomes issues des consortium ADES(Alzheimer Disease Exome Sequencing) et ADSP (Alzheimer Disease Sequencing Project), regroupant,après un contrôle qualité extensif développé dans le cadre de ces travaux, 22 094 individus répartisentre 4077 formes précoces de MA, 8458 formes tardives et 9559 témoins. Nous avons mis au pointdes analyses au niveau des transcrits et appliqué une méthode statistique basée sur les dosagesappliquée aux formes précoces et aux témoins. Nous avons pu identifier plusieurs potentiels nouveauxfacteurs de risque dont la région du chr22q11.21, déjà impliquée dans les troubles duneurodéveloppement (p=3,8x10-4). De plus, nous avons identifié des délétions très rares dans lesgènes ABCA1 et ABCA7 dont les variations perte de fonction sont connues comme facteurs de risquede MA depuis peu, et nous avons réalisé une analyse conjointe des délétions et des variations pertede fonction de petite taille.En conclusion, nous avons montré que la détection de CNV issus de données d’exome est fiable et nousen avons mesuré les performances et les limites avant de les appliquer à un grand jeu de données afind’identifier de nouveaux mécanismes contribuant au développement de la maladie d’Alzheimer<br>Over the past 20 years, the evolution of new technologies has revealed the great variability of ourgenome, from simple substitutions to chromosomal rearrangements. High-throughput sequencing hasparticularly improved the identification and interpretation of small variations, while offering theopportunity to explore structural variations with a higher resolution than that available with genome-wide microarray analyses. Nevertheless, the identification of structural variations and more specificallycopy number variations (CNVs) from capture sequencing data, has been under exploited and underevaluated. Our main objective was to develop a read depth based bioinformatics pipeline for CNVidentification, and then apply it to a case-control exome study in Alzheimer’s disease research.Alzheimer’s disease (AD) is the most common neurodegenerative disorder. Individual genetic factorsplay an important role in its determinism, and multiple risk factors have been identified, mainlysubstitutions and small insertions/deletions. However, structural variations have already beenidentified in monogenic forms of AD, such as complete duplication of APP gene. CNVs remain largelyunstudied in AD, we set out to apply a case-control approach using massive exome data to detect CNVscontributing to AD risk.As a first step, we established an analysis strategy based on CANOES software to detect CNVs fromNGS data derived from a capture (gene panels, exomes). This approach was validated using 2 largegene panels and exome datasets, compared with independent targeted techniques. In the first dataset(gene panels), sensitivity and specificity were 100%, and we obtained a sensitivity of 87.25% and apredictive positive value of 88.5% for CNV detection in whole exome sequencing data.We then applied this approach to whole exome data from the ADES (Alzheimer Disease ExomeSequencing) and ADSP (Alzheimer Disease Sequencing Project) consortia, grouping, after extensivequality control developed as part of this work, 22,094 samples divided between 4077 early onset cases,8458 late onset and 9559 controls. We developed transcript-level analyses and applied a statisticalmethod based on dosage applied on early onset cases and controls. We were able to identify severalpotential new risk factors, including the 22q11.21 regions, already implicated in neurodevelopmentaldisorders (p=3,8x10-4). In addition, we identified rare deletions in ABCA1 and ABCA7 genes, whoseloss-of-function variations have recently been identified as risk factors for AD, and carried out a jointanalysis of deletions and small loss-of-function variations.In conclusion, we have shown that CNV detection from exome data is reliable, and we have measuredits performance and limitations before applying it to a large dataset to identify new mechanismscontributing to the development of Alzheimer's disease
Book chapters on the topic "Whole Exon Sequencing"
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Zhang, Bin, and Chencheng Xu. "Gene regulation via RNA isoform variations." In Beyond the Blueprint - Decoding the Elegance of Gene Expression [Working Title]. IntechOpen, 2024. http://dx.doi.org/10.5772/intechopen.1005044.
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The completion of the draft and complete human genome has revealed that there are only around 20,000 genes encoding proteins. Nonetheless, these genes can generate eight times more RNA transcript isoforms, while this number is still growing with the accumulation of high-throughput RNA sequencing (RNA-seq) data. In general, over 90% of genes generate various RNA isoforms emerging from variations at the 5′ and 3′ ends, as well as different exon combinations, known as alternative transcription start site (TSS), alternative polyadenylation (APA), and alternative splicing (AS). In this chapter, our focus will be on introducing the significance of these three types of isoform variations in gene regulation and their underlying molecular mechanisms. Additionally, we will highlight the historical, current, and prospective technological advancements in elucidating isoform regulations, from both the computational side such as deep-learning-based artificial intelligence, and the experimental aspect such as the long-read third-generation sequencing (TGS).
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Mastrangelo, Mario. "Clinical Approaches to Genetic Epilepsies in Children." In Updates on Pediatric Health and Diseases. BENTHAM SCIENCE PUBLISHERS, 2023. http://dx.doi.org/10.2174/9789815124187123020009.
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A genetic etiology is determined in more than 30% of all diagnosed cases of epilepsy with onset at the pediatric age. About 210 single disease-causing genes and 400 chromosomal imbalances are associated with epilepsy, and a presumed pathogenic role has been suggested for about 7000 different genes. Genetic epilepsies can be divided, according to the main correlated epileptogenic mechanisms, into the following groups: a) channelopathies, b) transportopathies, c) disorders of the intermediate metabolism, d) disorders of the neuronal cellular cycle and signaling, e) disorders of synaptic vesicles trafficking and release, f) disorders involving neuronal structural proteins, g) disorders of synaptic secreted proteins and h) chromosomopathies and pathogenic copy number variants. A careful diagnostic work-up should be focused on the exclusion of acquired causes of seizures, the analysis of family history, the definition of seizure semiology and epileptic syndromes, and the characterization of associated neurological and non-neurological manifestations. Traditional genetic techniques (karyotype, array CGH, and Sanger sequencing) remain useful for known epilepsy phenotypes (e.g. Dravet syndrome) and for various syndromes including neurodevelopmental impairment. Next-generation sequencing (NGS) includes different techniques (targeted gene panels and whole genome sequencing) that allow a simultaneous sequencing of exons belonging to a selected group of genes organized in panels or to the whole exome or genome. Advantages of NGS include: a) the identification of new disease-causing genes associated with epilepsy, b) an expansion of the known phenotypes associated with previously discovered disease-causing genes, c) an improvement of genetic counseling, d) a reduction of the times for the diagnosis, and e) a reduction of economic costs.
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Ivens, Alasdair c., and Peter F. R. Little. "Cosmid clones and their application to genome studies." In DNA Cloning 3. Oxford University PressOxford, 1995. http://dx.doi.org/10.1093/oso/9780199634835.003.0001.
Full textAbstract:
Abstract A 1000-fold range of DNA sizes may be cloned in the current range of cloning vectors: the ideal vector for genome mapping studies would be one that is easy to use while containing as much DNA as possible. Cosmids now occupy the middle ground: they have a significant capacity, thus reducing the number of steps required to clone an entire gene or region, combined with very simple methods for isolating inserted DNA in pure form. As a consequence, positional cloning strategies frequently involve the use of cosmids as a final cloning vector for reducing a yeast artificial chromosome (YAC) clone to manageably sized DNA fragments (1). Cosmids are units that are very likely to contain an entire gene, are easily mapped with respect to restriction sites, and are amenable to the application of a number of other functional assays, e.g. exon trapping (2, 3), genomic sequencing (4-6), and fingerprinting to generate contig maps (7, 8). As a result, the detailed information that can be obtained from a cosmid clone makes it the ideal medium for genome analysis. Indeed, several genome mapping studies (e.g, Caenorhabditis elegans (9), Escherichia coli (10)), have relied on physical DNA maps built around cosmid clones.
Conference papers on the topic "Whole Exon Sequencing"
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Wang, Y., S. Kuss-Duerkop, E. Decurtis, et al. "A Novel Two-tier Genotyping and Whole Exon Sequencing Testing Algorithm to Identify Alpha-1 Antitrypsin Deficiency (AATD)." In American Thoracic Society 2024 International Conference, May 17-22, 2024 - San Diego, CA. American Thoracic Society, 2024. http://dx.doi.org/10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a4288.
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Braga, Vinícius Lopes, Wladimir Bocca Vieira de Rezende Pinto, Bruno de Mattos Lombardi Badia, et al. "Spastic paraplegia type 73: expanding phenotype of the first two Brazilian families." In XIII Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1516-3180.552.
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Context: Hereditary spastic paraplegias (HSPs) represent an expanding group of neurodegenerative diseases characterized mainly by progressive spastic paraparesis of the lower limbs. More than 80 different genetic loci have been associated with HSPs. In 2015, heterozygous pathogenic variants in the CPT1C gene were first associated with SPG73, not yet described in Brazilian patients. Objective: We present clinical, neuroimaging and genetic features of three Brazilian patients with SPG73. Cases reports: We report one male and two female patients, age range 36 to 78 years old. Case 1 presented with a 4-year-history of spasticity, predominantly crural tetraplegia, bladder incontinence, dysphagia and dysphonia. Family history disclosed a sister with epilepsy. Whole-exome sequencing (WES) disclosed a heterozygosis variant c.863G>A (p.Arg288His) in exon 9 of the CPT1C. Cases 2 and 3 are first degree relatives (mother and son). Both presented with long-standing slowly progressive spastic paraplegia. Case 3 presented bladder incontinence, constipation, dysphagia and dysphonia at late stages. Cases 2 and 3 WES disclosed the heterozygosis variant c.196T>G (p.Phe66Val) in exon 4 of the CPT1C. Discussion: Previous literature described six patients from an Italian family with pure HSPs phenotype and the pathogenic variant c.109C>G (p.Arg3. 7Cys) in CPT1C gene. Another group described three patients associated with pure HSPs phenotype and the pathogenic variant (c.226C>T) in the CPT1C gene. All previous reported cases had benign clinical course and bulbar involvement was not described before. One of our cases presented with a de novo variant and rapidly progressive motor and bulbar compromise. Conclusion: our cases expand the current knowledge about SPG73, including a rapidly progressive phenotype with bulbar involvement and cognitive compromise at late stages of disease course.
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Chen, Jo-Pai, Jui-Ying Chang, and Ruey-Long Hong. "Abstract 4741: Exploring possible drug resistance and sensitivity mechanisms in treatment-refracotry betel-nuts related HNSCC cell line(TW2.6) by whole exon sequencing and molecular signaling for future drug combinations." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-4741.
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Antonarakis, E. "The Molecular Genetics of Hemophilia A Stylianos." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643980.
Full textAbstract:
Hemophilia A is a common X linked hereditary disorder of blood coagulation due to deficiency of factor 8. The gene for factor 8 has been cloned and characterized (Nature 312:326-342, 1984). It is divided into 26 exons and 25 introns and spans 186 kb of DNA. The CGNA is 9 kb and codes for 2351 amino acids. The first 19 amino acids comprise the secretory leader peptide and the mature excreted polypeptide consists of 2332 amino acids. The nucleotide sequence of the exons and the exon-intron junctions is known and the complete amino acid sequence has been deducedSeveral laboratories have used cloned factor 8 DNA sequences as probes to characterized mutations that are responsible for hemophilia A in certain pedigrees. These mutations have been characterized by restriction analysis, oligonucleotide hybridization, cloning and sequencing of DNA from appropriate patientsIn about 500 patients with hemophilia A examined, the molecular defect has been recognized in 39. Both gross alterations (mainly deletions) and point mutations of the factor 8 gene have been found.A total of 19 different deletions have been observed. No two unrelated pedigrees share the same exact deletion.The size of the deleted DNA varies from 1.5 kb to more than 210 kb. All but one of these deletions are associated with severe hemophilia A. A deletion of 6 kb that contains exon 22 only is associated with moderate hemophilia. Some deletions are present in patients with inhibitors to factor 8. No correlation of the size or the position of the deletions can be found with the presence of inhibitors to factor 8.A total of 20 point mutations have been characterized. All are recognized by restriction analysis and involve Taq I sites. All are mutations of CpG dinucleotides and generate nonsense or missence codons. Unrelated pedigrees have the same single nucleotide change because of independent origin of the same mutation. In many instances de novo occurrence of a point mutation has been observed. CpG dinucleotides are hot spots for mutation to TG or CA presumably because of spontaneous deamination of methylcytosine. Some point mutations are present in patients with inhibitors but no correlation of the site of mutation and inhibitor formation has been found. The nonsense mutations are present in patients with severe hemophilia A. A missense mutation (Arg Gin) in exon 26 was found in a patient with mild hemophilia while another Arg Gin mutation in exon 24 has been observed in a patient with severe disease. The creation of a donor splice site in IVS 4 of factor 8 gene has been observed in a patient with mild hemophilia.Few DNA polymorphisms within the factor 8 gene and two other closely linked polymorphisms have been used for carrier detection and prenatal diagnosis of hemophilia A. These DNA markers are useful in more than 90% of families at risk for hemophilia A.The author thanks Drs. Gitschier, Din, Olek, Pirastou, Lawn for communication of their data prior to publication.The hemophilia project at Johns Hopkins was supported by an Institutional grant and NIH grant to S.S.A. and Haig H. Kazazian, Jr.