Whole-exome sequencing and clonal evolution of brain metastases in low-grade early-stage endometroid endometrial adenocarcinoma

2020 ◽  
Vol 159 ◽  
pp. 222-223
Author(s):  
K. Dessources ◽  
A.D.C. Paula ◽  
P. Cybulska ◽  
F. Pareja ◽  
A. Stylianou ◽  
...  
Keyword(s):  
Brain Metastases ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Early Stage ◽  
Clonal Evolution ◽  
Endometrial Adenocarcinoma ◽  
Low Grade ◽  
Whole Exome

P-047: Clonal evolution in multiple myeloma evaluated by Whole Exome Sequencing

2021 ◽  
Vol 21 ◽  
pp. S64
Author(s):  
Ritu Gupta ◽  
Gurvinder Kaur ◽  
Akanksha Farswan ◽  
Lingaraja Jena ◽  
Anubha Gupta ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Clonal Evolution ◽  
Whole Exome

scholarly journals Whole Exome Sequencing of Simultaneous Primary Multifocal Lung Cancer (SMPLC): Case Report and Bioinformatics Analysis

2020 ◽  
Author(s):  
Donglin Zhu ◽  
Minghong Shen ◽  
Jinghuan Lv
Keyword(s):  
Lung Cancer ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Bioinformatics Analysis ◽  
Clonal Evolution ◽  
Evolutionary Relationship ◽  
Primary Lung Cancer ◽  
The Cancer Genome Atlas ◽  
Control Group ◽  
Whole Exome

Abstract Background: To understand the molecular mechanism of synchronous multifocal lung cancer (SMLC) is of great significance for the differential diagnosis of intrapulmonary metastasis (IM) and synchronous multiple primary lung cancer (SMPLC). Recently, next-generation sequencing (NGS) has become a useful tool for understanding SMLC. Case presentation: In this study, two lesions of a 61-year-old man with lung cancer were detected by whole exome sequencing (WES) and the correlation between different lesions was analyzed at the molecular level. Lesion 1 was adenocarcinoma and lesion 2 was squamous cell carcinoma. Gene mutation and copy number variation (CNV) are different in the two lesions. The genome of lesion 2 is more unstable. The clonal evolution analysis showed that there was no obvious evolutionary relationship between the two lesions, and both lesions were independent double primary lesions. Bioinformatics analysis revealed that the alternate genes of the two lesions were inconsistent in function and pathway. PCA analysis was performed using the Cancer Genome Atlas (TCGA) database and the GTEx database, and it was found that the changed genes in these two lesions were significantly separated from the control group, and the changes of TP53 and EGFR genes in the TCGA database were further described. Conclusions: These results indicate that NGS may provide new ideas for SMLC classification.

scholarly journals Whole-Exome Sequencing-Based Mutational Profiling of Hepatitis B Virus-Related Early-Stage Hepatocellular Carcinoma

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Hao Zhan ◽  
Jiahao Jiang ◽  
Qiman Sun ◽  
Aiwu Ke ◽  
Jinwu Hu ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Axon Guidance ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Early Stage ◽  
Genetic Characteristics ◽  
Whole Exome ◽  
B Virus

Background. Hepatocellular carcinoma (HCC) ranks as the third leading cause of cancer-related mortality in China with increasing incidence. This study is designed to explore early genetic changes implicated in HCC tumorigenesis and progression by whole-exome sequencing. Methods. We firstly sequenced the whole exomes of 5 paired hepatitis B virus-related early-stage HCC and peripheral blood samples, followed by gene ontological analysis and pathway analysis of the single-nucleotide variants discovered. Then, the mutations of high frequency were further confirmed by Sanger sequencing. Results. We identified a mutational signature of dominant T:A>A:T transversion in early HCC and significantly enriched pathways including ECM-receptor interaction, axon guidance, and focal adhesion and enriched biological processes containing cell adhesion, axon guidance, and regulation of pH. Eight genes, including MUC16, UNC79, USH2A, DNAH17, PTPN13, TENM4, PCLO, and PDE1C, were frequently mutated. Conclusions. This study reveals a mutational profile and a distinct mutation signature of T:A>A:T transversion in early-stage HCC with HBV infection, which will enrich our understanding of genetic characteristics of the early-stage HCC.

Clonal Evolution in Chronic Myeloid Leukemia Progression Revelead by Whole-Exome Sequencing

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1415-1415
Author(s):  
Juliane Menezes ◽  
Francesco Acquadro ◽  
Gonzalo Gómez López ◽  
Sara Alvarez ◽  
Mercedes Trujillo ◽  
...  
Keyword(s):  
Chronic Myeloid Leukemia ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Myeloid Leukemia ◽  
Blast Crisis ◽  
Clonal Evolution ◽  
Chronic Phase ◽  
Rapid Expansion ◽  
Molecular Therapy ◽  
Whole Exome

Abstract Abstract 1415 Background: Chronic myeloid leukemia (CML) is one of the best examples of a disease that can be targeted by molecular therapy however, the success of new designed drugs is largely restricted to the chronic phase of the disease. If not cured at this stage, CML invariably progresses and transforms into an acute-type leukemia undegoing a blast crisis, that is characterized by a rapid expansion of myeloid or lymphoid differentiation-arrested blast cells leading to short median survival. To investigate the genetic changes associated with CML progression under tyrosin-kinase inhibitor treatment, and to determine whether clonal evolution contributes to blast crisis, we performed whole-exome sequencing of an individual patient at three different times of the CML progression: chronic phase (CP), complete hematological remission (CHR) and blast crisis (BC). Methods and Case Description: We collected genomic DNA from bone marrow cells (tumor DNA) at three disease evolution points and from epithelial cells (germline DNA). The sequence capture, enrichment and elution was performed according to manufacturer's instructions and protocols (SureSelect, Agilent). Each eluted-enriched DNA sample was sequenced on an Illumina GAIIX as paired-end 75b reads. The bioinformatics analysis of sequencing data was based on a pipeline which includes alignment, annotation, and filtering of the somatic variants, all linked to a coverage/depth statistical analysis. Validation of somatic mutations was done by capilary sequencing. The patient, a 65 year-old men, showed at diagnosis a classic CML with a 45,XY,t(9;22)(q34;q11.2),rob(13;14)(q10;q10)c [20]. He was treated with Imatinib (400 mg/day) achieving complete hematological and cytogenetic remission after 12 months of treatment. Real-time qRT-PCR demonstrated molecular response: BCR/ABL1 ratio decreased from 53% to 13% within the first year. Unfortunately, the disease progressed at month 14 to a blast crisis with a complex karyotype that did not respond to 2nd line treatment (Dasatinib + Idaurobinice-AraC) and the patient died of the disease 18 months after diagnosis. Results: After discarding the variants present in the matched normal DNA and in the dbSNP132 database, we obteined a total of 3123, 7678 and 3306 single nucleotide substitutions (SNSs) and small insertions and deletions (indels) for CP, CHR and BC, respectively. Next, we selected only those variants within coding regions that, passing depth and quality controls, were predicted to produce non-synonymous amino acid changes. This resulted in 27, 30 and 26 SNSs for CP, CHR and BC, respectively, (Fig. 1). Among those SNSs, we validated mutations in genes known to be involved in CML (such as ASXL1 and TP53) as well as in genes that have not been described so far in the disease (such as UBE2G2, ZEB2 and IKZF3). TP53 mutation (p.E286K) was found in the three phases of CML progression. However, ASXL1 (p.G679*), UBE2G2 (p.D35V), ZEB2 (p.L420R) and IKZF3 (p.E272K) were present only in the CP and BC-CML. On the other hand, only 7%, 42% and 6% of the mutated gene were exclusively found in CP, CHR and BC, respectively (Fig. 1). The evaluation of the number of mutated reads for each gene allowed us to study clonality and clonal evolution patters during CML progression. 93% of the selected SNSs that were present in the CP were also seen in BC (only 46% during CHR). In fact, the percentages of reads of the mutant alleles identified for the most relevant genes were the same (around 50%) both at CP and at BC. Conclusions: Whole-exome sequencing allowed to identify a large number of mutated genes, even at the chonic phase of CML, that harbour clear prognostic and predictive significance (TP53, IKZF3, absence of ABL1 mutations). The study of the mutation profile through the disease progression indicated that, at least in this patient, the number and the type of mutations were rather similar at CP and BC. Disclosures: No relevant conflicts of interest to declare.

scholarly journals CMET-15. WHOLE EXOME SEQUENCING OF BRAIN METASTASES FROM COLORECTAL PRIMARY CANCERS REVEALS CLINICALLY ACTIONABLE MUTATIONS

2018 ◽  
Vol 20 (suppl_6) ◽  
pp. vi56-vi56
Author(s):  
Matthew Strickland ◽  
Mia Bertalan ◽  
Benjamin Kuter ◽  
Tareq Juratli ◽  
Victoria Melchert ◽  
...  
Keyword(s):  
Brain Metastases ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome

scholarly journals Whole-Exome Sequencing Reveals New Potential Mutations Genes for Primary Mucosa-Associated Lymphoid Tissue Lymphoma Arising From the Kidney

2021 ◽  
Vol 10 ◽  
Author(s):  
Shuang Wen ◽  
Tianqing Liu ◽  
Hongshuo Zhang ◽  
Xu Zhou ◽  
Huidan Jin ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Tumor Cells ◽  
Whole Exome Sequencing ◽  
Lymphoid Tissue ◽  
Clinical Investigation ◽  
Driver Mutations ◽  
Low Grade ◽  
Driver Genes ◽  
Molecular Features ◽  
Whole Exome

Low-grade B cell lymphomas of mucosa-associated lymphoid tissue (MALT) lymphomas involving the kidney were extremely rare, genetic alteration or molecular features was not yet explored, which may lead to limited choices for postoperative adjuvant or targeted. Whole-exome sequencing based tumor mutation profiling was performed on the tumor sample from a 77-year-old female presenting with discomfort at the waist was pathologically diagnosed as MALT lymphomas in the right kidney. We identified 101 somatic SNVs, and the majority of the identified SNVs were located in CDS and intronic regions. A total of 190 gain counts of CNVs with a total size of 488,744,073 was also investigated. After filtering with the CGC database, seven predisposing genes (ARID4A, COL2A1, FANCL, ABL2, HSP90AB1, FANCA, and DIS3) were found in renal MALT specimen. Furthermore, we compared somatic variation with known driver genes and validated three mutational driver genes including ACSL3, PHOX2B, and ADCY1. Sanger sequencing of germline DNA revealed the presence of a mutant base T of PHOX2B and a mutant base C of ADCY1 in the sequence, which were discovered for the first time in MALT lymphomas involving the kidney. Moreover, immunohistochemical analysis revealed that tumor cells were positive for CD20, CD79a, PAX5, CD21, and CD23, and expression of CD3, CD5, and CD8 were observed in reactive T lymphocytes surrounding tumor cells. These findings illustrated that concurrent aberrant PHOX2B and ADCY1 signaling may be a catastrophic event resulting in disease progression and inhibition of the putative driver mutations may be alternative adjuvant therapy for MALT lymphoma in the kidney which warrants further clinical investigation.

scholarly journals Single Cell Whole Exome Sequencing in NPM1/Flt3 Positive Pediatric Acute Myeloid Leukemia

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1043-1043
Author(s):  
Christiane Walter ◽  
Winfried Hofmann ◽  
Katarina Reinhardt ◽  
Dirk Reinhardt ◽  
Nils von Neuhoff
Keyword(s):  
Acute Myeloid Leukemia ◽  
Single Cell ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Myeloid Leukemia ◽  
Single Cells ◽  
Clonal Evolution ◽  
Npm1 Mutation ◽  
Whole Exome ◽  
Acute Myeloid

Abstract Introduction: Acute myeloid leukemia (AML) is one of the most frequent forms of leukemia in children younger than 15 years. The detection of several mutations in a blast population of pediatric AML (pAML) is supposed to be caused by a clonal evolution from a leukemic stem cell (LSC) to leukemic blasts. LSC are believed to be more resistant to chemotherapy, to be able to survive during treatment and to be responsible for the emergence of a relapse due to the persistence in the bone marrow (BM) niche. Since LSC and potential leukemic subclones are only present in small subpopulations, it has been a major technical challenge to particular analyse only the specific population. To acquire a better understanding of the underlying mechanisms of mutagenesis, clonal evolution and leukemogenesis, the aim of this study was to establish methods that allow the analysis and detection of mutations in single cells of a subpopulation known to contain HSC as well as LSC (CD34+CD38-). We especially focused on a pAML subgroup with mutations in Nucleophosmin (NPM1) and/or fms related tyrosine kinase 3 (Flt3). Methods and Results: We established methods to perform single cell sorting, whole genome amplification (WGA) using multiple displacement amplification (MDA) technology (Qiagen) and subsequent whole exome sequencing. The sorting efficiency was checked as Hoechst stained cells were sorted onto glas slides with 48 defined spots and the presence of single cells was checked under an inverse fluorescent microscope. Subsequently, single CD34+CD38- patient derived cells were sorted into 0,5ml low binding tubes containing 4µl PBS followed by WGA and whole exome sequencing. The mutational status of the sorted single cells from three patients suffering from pAML was analysed and compared to mutations detected at initial diagnosis in DNA from a bulk of BM cells. WGA from single CD34+CD38-PI- cells resulted in an amount of 29 to 31.7µg DNA from each of five single cells. The quality of the amplified DNA was sufficient for whole exome sequencing. A 4bp insertion in exon 12 of NPM1 reflecting a common NPM1 mutation (MutA) initially detected from a bulk of cells was identified in amplified DNA from single cells using whole exome sequencing in 2/3 patients. Internal tandem duplications in Flt3 indicated by mismatches in the alignment could be detected in amplified DNA from single cells of two patients. The detected ITD resemble those initially detected in DNA from a bulk of BM cells. Discussion and Conclusion: Single cell sequencing provides a useful tool to amend the detection of genetic aberrations from a bulk of cells and to confirm the presence of specific mutations in single cells from small subpopulations. It therefore helps to get further insights into the clonal evolution in pAML. Disclosures No relevant conflicts of interest to declare.

Whole Exome Sequencing Reveals the Landscape of Clonal Evolution from MDS to AML Progression

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2596-2596
Author(s):  
Taehyung Simon Kim ◽  
Zhaolei Zhang ◽  
Marc Tyndel ◽  
Jae-Sook Ahn ◽  
Yeo-Kyeoung Kim ◽  
...  
Keyword(s):  
Time Series ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Research Funding ◽  
Clonal Evolution ◽  
Secondary Aml ◽  
Frame Shift ◽  
Whole Exome ◽  
Tier 1 ◽  
Splicing Machinery

Abstract BACKGROUND: Acute myeloid leukemia (AML) is a biologically heterogeneous disease that can be classified into three distinct categories. For example, AML can develop after a prior myeloid malignancy such as myelodysplastic syndrome (MDS). This is known as secondary AML. In previous studies, the genetic basis of secondary AML has been shown such as mutations in genes involved in splicing machinery. However, the progression from MDS to AML has not been studied extensively. In this study, we performed whole-exome sequencing on 26 patients at the time of MDS and AML to dissect the mutational profiles and clonal evolution from MDS to AML. METHODS: We reviewed the cryopreserved samples from 2003 October to 2013 June in Chonnam National University Hwasun Hospital. We only selected the patients who preserved paired sample at the time of MDS and AML. Germline and tumor samples at the time of MDS and AML were analyzed using whole exome sequencing (Agilent SureSelect v3, HiSeq 2000). Targeted sequencing for selected variants were performed to validate the result. RESULTS: Exome sequencing was performed as per the manufacturer's protocol using an Illumina HiSeq 2000 sequencer. DNA from T-cell was used as a control for variant calling in all 26 cases. Exome sequencing reads processing includes mapping to human genome hg19, marking PCR duplicates, realignment of indels, fixing mate information, and discard the reads with more than 1 mismatch to reduce the false positive rate. In the end, we have on-target-coverage of 72x. Lastly, 80% of target positions are mapped more than 30x. To detect variants that may have been filtered out due to our stringent criteria, we compiled a variant list consisting of all unique variants from all cases in this study as well as the unique variants from two other studies not already found in any of our cases, searched for these variants in each of the cases, and classified them into three tiers within each case: Tier 1. Variants that are statistically significant and meet our criteria in at least one of the MDS or sAML samples within each case. Tier 2. Variants that occur in Tier 1 from any other case with a minumum VAF of 10% in at least one of the MDS or sAML samples per each case. Tier 3. Reported variants from previous studies, which have a VAF of at least 10% in either MDS or sAML in each case. We identified the mean and median of 11.59 and 11 variants, respectively. In total, we identified 313 unique somatic mutations, consisting of 205 non-synonymous SNVs, 66 synonymous SNVs, 8 frame-shift deletions, 5 frame-shift insertion, 20 stop-gain mutation, 1 non-frameshift insertion, 4 non-frameshift deletion, and 8 splicing variants from 273 genes. Among them, 18 genes were recurrently mutated including U2AF1 and TP53. We are currently validating these variants using targeted deep sequencing with much higher coverage. Our pathway analyses confirm that 13/26 patients have mutations and 12/26 patients have mutations in pathways related to splicing machinery and/or epigenetics (total n=17). Our analyses confirm that 21/26 patients have at least 1 mutation in at least one of the pathways in 8 commonly mutated pathways related to AML. In addition, we found that variants in these pathways are mutually exclusive, which means that two mutations in same pathways are highly unlikely to occur in a single patient. Using such time series data, we have inferred clonal evolution of these cases. Our analyses postulate the hierarchy of mutated pathways in secondary AML as well as hierarchy of variants. CONCLUSION: In this study, we have performed the whole exome sequencing of 26 secondary AML patients at the time of MDS and AML. Our extensive analyses reveal the order of gene mutations, inferring the hierarchy of mutated pathways during the progression. Also, our study shows that time series analysis contrasting MDS and AML periods provides a much more comprehensive view of clonal structure and evolution. Disclosures Kim: Novartis Pharmaceuticals: Consultancy, Research Funding; Bristol-Myers Squibb: Consultancy, Research Funding.

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