Whole-exome sequencing in adult ETP-ALL reveals a high rate of DNMT3A mutations

Key Points Exome sequencing of adult ETP-ALL reveals new recurrent mutations; in particular, DNMT3A is frequently mutated in adult ETP-ALL. More than 60% of all adult patients with ETP-ALL harbor a mutation that could potentially be targeted by a specific therapy.

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Gene alterations in epigenetic modifiers and JAK-STAT signaling are frequent in breast implant-associated ALCL.

Blood ◽

10.1182/blood.2019001904 ◽

2019 ◽

Cited By ~ 7

Author(s):

Camille Laurent ◽

Alina Nicolae ◽

Cécile Laurent ◽

Fabien Le Bras ◽

Corinne Haioun ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Breast Implant ◽

Epigenetic Modifiers ◽

Whole Exome ◽

Key Points ◽

Recurrent Mutations ◽

Epigenetic Regulators ◽

Gene Alterations ◽

Stat Pathway

Key Points An accumulation of alterations in epigenetic modifiers and genes in the JAK/STAT pathway likely drives BI-ALCL oncogenesis. Whole exome sequencing of a large series of BI-ALCL demonstrates recurrent mutations in epigenetic regulators.

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Whole-exome sequencing reveals a novel homozygous mutation in the COQ8B gene associated with nephrotic syndrome

Scientific Reports ◽

10.1038/s41598-021-92023-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mohd Fareed ◽

Vikas Makkar ◽

Ravi Angral ◽

Mohammad Afzal ◽

Gurdarshan Singh

Keyword(s):

Nephrotic Syndrome ◽

Disease Management ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Homozygous Mutation ◽

Consanguineous Family ◽

Clinical Prognosis ◽

Whole Exome ◽

Recurrent Mutations ◽

Ckd Stage

AbstractNephrotic syndrome arising from monogenic mutations differs substantially from acquired ones in their clinical prognosis, progression, and disease management. Several pathogenic mutations in the COQ8B gene are known to cause nephrotic syndrome. Here, we used the whole-exome sequencing (WES) technology to decipher the genetic cause of nephrotic syndrome (CKD stage-V) in a large affected consanguineous family. Our study exposed a novel missense homozygous mutation NC_000019.9:g.41209497C > T; NM_024876.4:c.748G > A; NP_079152.3:p.(Asp250Asn) in the 9th exon of the COQ8B gene, co-segregated well with the disease phenotype. Our study provides the first insight into this homozygous condition, which has not been previously reported in 1000Genome, ClinVar, ExAC, and genomAD databases. In addition to the pathogenic COQ8B variant, the WES data also revealed some novel and recurrent mutations in the GLA, NUP107, COQ2, COQ6, COQ7 and COQ9 genes. The novel variants observed in this study have been submitted to the ClinVar database and are publicly available online with the accessions: SCV001451361.1, SCV001451725.1 and SCV001451724.1. Based on the patient's clinical history and genomic data with in silico validation, we conclude that pathogenic mutation in the COQ8B gene was causing kidney failure in an autosomal recessive manner. We recommend WES technology for genetic testing in such a consanguineous family to not only prevent the future generation, but early detection can help in disease management and therapeutic interventions.

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Whole‐Exome Sequencing of a Saudi Epilepsy Cohort Reveals Association Signals in Known and Potentially Novel Loci

10.21203/rs.3.rs-915593/v1 ◽

2021 ◽

Author(s):

Amein Kadhem AlAli ◽

Abdulrahman Al-Enazi ◽

Ahmed Ammar ◽

Mahmoud Hajj ◽

Cyril Cyrus ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Rare Variants ◽

High Rate ◽

Variants Of Unknown Significance ◽

Pathogenic Variants ◽

Whole Exome ◽

Novel Variants ◽

Unknown Significance ◽

Rare Genetic Variants

Abstract Background Epilepsy, a serious chronic neurological condition effecting up to 100 million people globally, has clear genetic underpinnings including common and rare variants. In Saudi Arabia the prevalence of epilepsy is high and caused mainly by perinatal and genetic factors. No whole-exome sequencing (WES) studies have been performed to date in Saudi Arabian Epilepsy cohorts. This offers a unique opportunity for the discovery of rare genetic variants impacting this disease as there is a high rate of consanguinity amongst large tribal pedigrees. Results We performed WES on 144 individuals diagnosed with epilepsy, to interrogate known Epilepsy related genes for known and functional novel variants. We also used an American College of Medical Genetics (ACMG) guideline based variant prioritization approach in an attempt to discover putative causative variants. We identified a 32 potentially causative pathogenic variants across 30 different genes in 44/144 (30%) of these Saudi Epilepsy individuals. We also identified 232 variants of unknown significance (VUS) across 101 different genes in 133/144 (92%) subjects. Strong enrichment of variants of likely pathogenicity were observed in previously described epilepsy-associated loci, and a number of putative pathogenic variants in novel loci are also observed. Conclusion Several putative pathogenic variants known to be epilepsy-related loci were identified for the first time in our population, in addition to several potential new loci have been identified which may be prioritized for further investigation.

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367 TOWARDS PERSONALIZED INDUCTION THERAPY FOR ESOPHAGEAL ADENOCARCINOMA: ORGANOIDS DERIVED FROM ENDOSCOPIC BIOPSY RECAPITULATE THE PRE-TREATMENT TUMOR

Diseases of the Esophagus ◽

10.1093/dote/doaa087.86 ◽

2020 ◽

Vol 33 (Supplement_1) ◽

Author(s):

M Derouet ◽

J Allen ◽

G Wilson ◽

C Ng ◽

N Radulovich ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Esophageal Adenocarcinoma ◽

Induction Therapy ◽

Drug Testing ◽

Endoscopic Biopsy ◽

Patient Specific ◽

Endoscopic Biopsies ◽

Whole Exome ◽

Recurrent Mutations

Abstract Esophageal adenocarcinoma has few known recurrent mutations and therefore robust, reliable and reproducible patient-specific models are needed for personalized treatment. Patient-derived organoid culture is a strategy that may allow for the personalized study of esophageal adenocarcinoma and the development of personalized induction therapy. Methods We developed a protocol to establish EAC organoids from endoscopic biopsies of treatment naïve esophageal adenocarcinomas. Organoids were then characterized using histology and whole exome sequencing. Organoids were then exposed to clinically used chemotherapy and response assessed. Results Our success rate for establishing the endoscopic organoid was 60%. Histologic characterization (we used p53 and cytokeratin7 as markers) and molecular characterization of organoids by whole exome sequencing demonstrated recapitulation of the tumors’ histology and genomic (60% of the mutations were shared between the organoids and the endoscopic biopsies) characteristics. Drug testing using clinically appropriate chemotherapeutics and targeted therapeutics showed an overlap between the patient’s tumor response and the corresponding organoids’ response. Conclusion In conclusion, organoids can be successfully cultured from endoscopic biopsies of esophageal adenocarcinoma and recapitulate the originating tumor. This model demonstrates promise as a tool to better personalize therapy for esophageal adenocarcinoma patients.

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Somatic activating ARAF mutations in Langerhans cell histiocytosis

Blood ◽

10.1182/blood-2013-06-511139 ◽

2014 ◽

Vol 123 (20) ◽

pp. 3152-3155 ◽

Cited By ~ 111

Author(s):

David S. Nelson ◽

Willemijn Quispel ◽

Gayane Badalian-Very ◽

Astrid G. S. van Halteren ◽

Cor van den Bos ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Langerhans Cell Histiocytosis ◽

Langerhans Cell ◽

Braf V600e ◽

Novel Mutations ◽

Whole Exome ◽

Key Points ◽

Inhibitor Treatment

Key Points Whole exome sequencing reveals novel mutations in ARAF that activate the kinase and are inhibitable by vemurafenib in a patient with LCH. Requiring the presence of BRAF V600E in LCH to qualify for rat fibrosarcoma inhibitor treatment may be overly exclusionary.

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A novel mutation in the F5 gene (factor V Amsterdam) associated with bleeding independent of factor V procoagulant function

Blood ◽

10.1182/blood-2014-08-592733 ◽

2015 ◽

Vol 125 (11) ◽

pp. 1822-1825 ◽

Cited By ~ 29

Author(s):

Marisa L. R. Cunha ◽

Kamran Bakhtiari ◽

Jorge Peter ◽

J. Arnoud Marquart ◽

Joost C. M. Meijers ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Novel Mutation ◽

Bleeding Disorder ◽

Factor V ◽

East Texas ◽

Gain Of Function ◽

Whole Exome ◽

Key Points

Key Points A novel gain-of-function mutation in factor V leading to increased levels of TFPI and bleeding was identified by whole exome sequencing. Factor V Amsterdam (F5 C2588G) resembles the mutation (F5 A2350G) leading to East Texas bleeding disorder.

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Whole Exome Sequencing Reveals Spectrum of Gene Mutations in Pediatric AML

Blood ◽

10.1182/blood.v120.21.124.124 ◽

2012 ◽

Vol 120 (21) ◽

pp. 124-124

Author(s):

Norio Shiba ◽

Kenichi Yoshida ◽

Yusuke Okuno ◽

Yuichi Shiraishi ◽

Yasunobu Nagata ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Conflicts Of Interest ◽

Massively Parallel Sequencing ◽

Gene Mutations ◽

Pediatric Leukemia ◽

Protein Coding ◽

Whole Exome ◽

Recurrent Mutations ◽

Pediatric Aml

Abstract Abstract 124 Background Pediatric acute myeloid leukemia (AML) comprises ∼20% of pediatric leukemia, representing one of the major therapeutic challenges in pediatric oncology with the current overall survival remains to be ∼60%. As for the molecular pathogenesis of pediatric AML, it has been well established that gene fusions generated by recurrent chromosomal translocations, including t(15;17), t(8;21), inv(16) and t(9;11), play critical roles in leukemogenesis. However, they are not sufficient for leukemogenesis, indicating apparent need of additional genetic hits, and approximately 20% of pediatric AML cases lack any detectable chromosomal abnormalities (normal karyotype AML). Currently, a number of gene mutations have been implicated in the pathogenesis of both adult and pediatric AML, including mutations of RAS, KIT and FLT3, and more recently, a new class of mutational targets have been reported in adult AML, including CEBPA, NPM1, DNMT3A, IDH1/2, TET2 and EZH2. However, mutations of the latter class of gene targets seem to be rare in pediatric AML cases, whereas other abnormalities such as a NUP98-NSD1 fusion are barely found in adult cases, indicating the discrete pathogenesis between both AML at least in their subsets. Meanwhile, the recent development of massively parallel sequencing technologies has provided a new opportunity to discover genetic changes across the entire genomes or protein-coding sequences in human cancers at a single-nucleotide level, which could be successfully applied to the genetic analysis of pediatric AML to obtain a better understanding of its pathogenesis. Methods In order to reveal a complete registry of gene mutations and other genetic lesions, we performed whole exome sequencing of paired tumor-normal specimens from 23 pediatric AML cases using Illumina HiSeq 2000. Although incapable of detecting non-coding mutations and gene rearrangements, the whole-exome approach is a well-established strategy for obtaining comprehensive spectrum of protein-coding mutations. Recurrently mutated genes were further examined for mutations in an extended cohort of 200 pediatric AML samples, using deep sequencing, in which the prevalence and relative allele frequencies of mutations were investigated. Results Whole-exome sequencing of paired tumor-normal DNA from 23 patients were analyzed with a mean coverage of more than x120, and 90 % of the target sequences were analyzed at more than x20 depth on average. A total of 237 somatic mutations or 10.3 mutations per sample were identified. Many of the recurrent mutations identified in this study involved previously reported targets in adult AML, such as FLT3, CEBPA, KIT, CBL, NRAS, WT1, MLL3, BCOR, BCORL1, EZH2, and major cohesin components including XXX and ZZZ. On the other hand, several genes were newly identified in the current study, including BRAF, CUL2 and COL4A5, which were validated for the clinical significance in an extended cohort of 200 pediatric cases. Discussion Whole exome sequencing unmasked a complexity of gene mutations in pediatric AML genomes. Our results indicated that a subset of pediatric AML represents a discrete entity that could be discriminated from the adult counterpart, in terms of the spectrum of gene mutations. Disclosures: No relevant conflicts of interest to declare.

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Mutations of the SF3B1 splicing Factor in Chronic Lymphocytic Leukemia: Association with Progression and Fludarabine-Refractoriness

Blood ◽

10.1182/blood.v118.21.464.464 ◽

2011 ◽

Vol 118 (21) ◽

pp. 464-464

Author(s):

Davide Rossi ◽

Alessio Bruscaggin ◽

Valeria Spina ◽

Silvia Rasi ◽

Hossein Khiabanian ◽

...

Keyword(s):

Chronic Lymphocytic Leukemia ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Lymphocytic Leukemia ◽

Splicing Factor ◽

Potential Contribution ◽

Critical Component ◽

Newly Diagnosed ◽

Whole Exome ◽

Recurrent Mutations

Abstract Abstract 464 Fludarabine-refractoriness of chronic lymphocytic leukemia (CLL) is due to TP53 disruption in ∼40% of refractory cases, but in a sizeable fraction of patients the molecular basis of this aggressive clinical phenotype remains unclear. Our initial findings from whole exome sequencing of fludarabine-refractory CLL led to the identification of recurrent mutations of SF3B1, a critical component of the cell spliceosome, prompting further investigations of these alterations in a large CLL panel. The study population comprised 3 clinical cohorts representative of: i) fludarabine-refractory CLL (n=59), including cases (n=11) subjected to whole exome sequencing; ii) newly diagnosed and previously untreated CLL (n=301); and iii) clonally related RS (n=33). Tumor samples were obtained: i) for fludarabine-refractory CLL, immediately before starting the treatment to which the patient eventually failed to respond; ii) for newly diagnosed and previously untreated CLL, at disease presentation. All RS studies were performed on RS diagnostic biopsies. Mutation analysis of SF3B1 was performed on genomic DNA by a combination of Sanger sequencing and targeted next generation sequencing. SF3B1 was altered in 10/59 (17%) fludarabine-refractory CLL by missense mutations (n=9) or in-frame deletions (n=1) clustering in the HEAT3, HEAT4 and HEAT5 repeats of the SF3B1 protein. Two sites that are highly conserved inter-species (codon 662 and codon 700) were recurrently mutated in 3 and 5 cases, respectively. SF3B1 mutations were monoallelic, and were predicted to be functionally significant according to the PolyPhen-2 algorithm. Mutations occurred irrespective of IGHV mutation status, CD38 expression and ZAP70 expression. At the time of fludarabine-refractoriness, SF3B1 mutations were enriched in cases harboring a normal FISH karyotype (p=.008) and distributed in a mutually exclusive fashion with TP53 disruption (mutual information I =0.0609; p=.046). By combining SF3B1 mutations with other genetic lesions enriched in chemorefractory cases (TP53 disruption, NOTCH1 mutations, ATM deletion), fludarabine-refractory CLL appeared to be characterized by multiple molecular alterations that, to some extent, are mutually exclusive. We then compared the prevalence of mutations observed at the time of fludarabine-refractoriness to that observed in other disease phases. At diagnosis, SF3B1 mutations were rare (17/301; 5%), and showed a crude association with short treatment free survival (p<.001) and overall survival (p=.011). Remarkably, 5/17 (29%) CLL mutated at diagnosis were primary fludarabine-refractory patients. In CLL investigated at diagnosis, the hotspot distribution and molecular spectrum of SF3B1 mutations, as well as their mutual relationship with other genetic lesions, were similar to those observed in fludarabine-refractory CLL. SF3B1 mutations were restricted to 2/33 (6.0%) clonally-related RS. Across the different disease phases investigated, mutations were somatically acquired in all cases (n=18) for which germline DNA was available. These data document that mutations of SF3B1, a splicing factor that is a critical component of the spliceosome; i) recurrently associate with fludarabine-refractory CLL; ii) occur at a low rate at CLL presentation; iii) play a minor role in RS transformation, corroborating the notion that CLL histologic shift is molecularly distinct from chemorefractory progression without RS transformation. The identification of SF3B1 mutations points to the involvement of splicing regulation as a novel pathogenetic mechanism in CLL. The pathogenicity of SF3B1 mutations in CLL is strongly supported by clustering of these mutations in evolutionarily conserved hotspots localized within HEAT domains, which are tandemly arranged curlicue-like structures serving as flexible scaffolding on which other components can assemble. Also, the observation that SF3B1 regulates the alternative splicing program of genes controlling cell cycle progression and apoptosis points to a potential contribution of SF3B1 mutations in modulating tumor cell proliferation and survival. In addition to pathogenetic implications, SF3B1 mutations might also provide a therapeutic target for SF3B1 inhibitors, that are currently under pre-clinical development as anti-cancer drugs. Disclosures: No relevant conflicts of interest to declare.

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Whole Exome Sequencing In Relapsed Pediatric T-ALL: Progression Into Relapse Is Characterized By An Increased Number Of Somatic Mutations and a Conservation Of Mutations In Leukemogenic Driver Genes

Blood ◽

10.1182/blood.v122.21.228.228 ◽

2013 ◽

Vol 122 (21) ◽

pp. 228-228

Author(s):

Joachim Kunz ◽

Tobias Rausch ◽

Obul R Bandapalli ◽

Martina U. Muckenthaler ◽

Adrian M Stuetz ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Copy Number ◽

Lymphoblastic Leukemia ◽

Initial Diagnosis ◽

Driver Mutations ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Whole Exome ◽

Recurrent Mutations

Abstract Acute precursor T-lymphoblastic leukemia (T-ALL) remains a serious challenge in pediatric oncology, because relapses carry a particularly poor prognosis with high rates of induction failure and death despite generally excellent treatment responses of the initial disease. It is critical, therefore, to understand the molecular evolution of pediatric T-ALL and to elucidate the mechanisms leading to T-ALL relapse and to understand the differences in treatment response between the two phases of the disease. We have thus subjected DNA from bone marrow samples obtained at the time of initial diagnosis, remission and relapse of 14 patients to whole exome sequencing (WES). Eleven patients suffered from early relapse (duration of remission 6-19 months) and 3 patients from late relapse (duration of remission 29-46 months).The Agilent SureSelect Target Enrichment Kit was used to capture human exons for deep sequencing. The captured fragments were sequenced as 100 bp paired reads using an Illumina HiSeq2000 sequencing instrument. All sequenced DNA reads were preprocessed using Trimmomatic (Lohse et al., Nucl. Acids Res., 2012) to clip adapter contaminations and to trim reads for low quality bases. The remaining reads greater than 36bp were mapped to build hg19 of the human reference genome with Stampy (Lunter & Goodson, Genome Res. 2011), using default parameters. Following such preprocessing, the number of mapped reads was >95% for all samples. Single-nucleotide variants (SNVs) were called using SAMtools mpileup (Li et al., Bioinformatics, 2009). The number of exonic SNVs varied between 23,741 and 31,418 per sample. To facilitate a fast classification and identification of candidate driver mutations, all identified coding SNVs were comprehensively annotated using the ANNOVAR framework (Wang et al., Nat. Rev. Genet., 2010). To identify possible somatic driver mutations, candidate SNVs were filtered for non-synonymous, stopgain or stoploss SNVs, requiring an SNV quality greater or equal to 50, and requiring absence of segmental duplications. Leukemia-specific mutations were identified by filtering against the corresponding remission sample and validated by Sanger sequencing of the genomic DNA following PCR amplification. We identified on average 9.3 somatic single nucleotide variants (SNV) and 0.6 insertions and deletions (indels) per patient sample at the time of initial diagnosis and 21.7 SNVs and 0.3 indels in relapse. On average, 6.3 SNVs were detected both at the time of initial diagnosis and in relapse. These SNVs were thus defined as leukemia specific. Further to SNVs, we have also estimated the frequency of copy number variations (CNV) at low resolution. Apart from the deletions resulting from T-cell receptor rearrangement, we identified on average for each patient 0.7 copy number gains and 2.2 copy number losses at the time of initial diagnosis and 0.5 copy number gains and 2.4 copy number losses in relapse. We detected 24/27 copy number alterations both in initial diagnosis and in relapse. The most common CNV detected was the CDKN2A/B deletion on chromosome 9p. Nine genes were recurrently mutated in 2 or more patients thus indicating the functional leukemogenic potential of these SNVs in T-ALL. These recurrent mutations included known oncogenes (Notch1), tumor suppressor genes (FBXW7, PHF6, WT1) and genes conferring drug resistance (NT5C2). In several patients one gene (such as Notch 1, PHF6, WT1) carried different mutations either at the time of initial diagnosis and or in relapse, indicating that the major leukemic clone had been eradicated by primary treatment, but that a minor clone had persisted and expanded during relapse. The types of mutations did not differ significantly between mutations that were either already present at diagnosis or those that were newly acquired in relapse, indicating that the treatment did not cause specific genomic damage. We will further characterize the clonal evolution of T-ALL into relapse by targeted re-sequencing at high depth of genes with either relapse specific or initial-disease specific mutations. In conclusion, T-ALL relapse differs from primary disease by a higher number of leukemogenic SNVs without gross genomic instability resulting in large CNVs. Disclosures: No relevant conflicts of interest to declare.

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Whole-exome sequencing in relapsing chronic lymphocytic leukemia: clinical impact of recurrent RPS15 mutations

Blood ◽

10.1182/blood-2015-10-674572 ◽

2016 ◽

Vol 127 (8) ◽

pp. 1007-1016 ◽

Cited By ~ 76

Author(s):

Viktor Ljungström ◽

Diego Cortese ◽

Emma Young ◽

Tatjana Pandzic ◽

Larry Mansouri ◽

...

Keyword(s):

Chronic Lymphocytic Leukemia ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Poor Prognosis ◽

Clinical Impact ◽

Lymphocytic Leukemia ◽

Whole Exome ◽

Key Points ◽

Frequent Mutations

Key Points Whole-exome sequencing of CLL patients who relapsed after FCR treatment revealed frequent mutations in RPS15. RPS15 mutations are likely to be early clonal events and confer poor prognosis.

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