Analysis of the Coding Genome of Follicular Lymphoma Identifies Multiple Novel Recurrently Mutated Genes

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 147-147
Author(s):  
Sami Malek ◽  
Yifeng Li ◽  
Hongxiu Li ◽  
Peter Ouillette ◽  
Sian Jones ◽  
...  
Keyword(s):  
B Cells ◽  
Follicular Lymphoma ◽  
Genetic Basis ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Read Length ◽  
Personal Genome ◽  
Sequencing Data ◽  
Structural Genomic ◽  
Frequent Mutations

Abstract Abstract 147 Introduction: Follicular lymphoma (FL) constitutes the second most common non-Hodgkin's lymphoma in the Western world. FL carries characteristic recurrent structural genomic aberrations. However despite recent advances, knowledge regarding the coding genome in FL is still evolving and currently incomplete. Methods: To further our understanding of the genetic basis of Follicular Lymphoma (FL), we used solution exon capture of sheared and processed genomic DNA isolated from FACS-sorted lymphomatous B-cells and paired CD3+ T-cells isolated from eleven cases of FL and one case of DLBCL transformed from prior FL followed by paired-end (96 base pair read length per side) massively parallel sequencing. Data from three independent HiSeq2000-based runs were pooled to maximize coverage. The sequence data were characterized by excellent technical QC parameters including a depth of coverage range of 43–73 and with 90% of bases in the target region covered by at least 10 reads. Data were subsequently analyzed using a validated bioinformatics pipelines (Personal Genome Diagnostics Inc., Baltimore, Maryland) serving as the primary data source to nominate candidate mutated genes. To complement the next gen sequencing data, we analyzed the 12 FL cases that constituted the discovery cohort for next generation sequencing for acquired genomic copy number aberrations (aCNA/LOH) and acquired uniparental disomy (aUPD) using SNP 6.0 array profiling. Data for paired DNA samples (sorted FL B-cells versus CD3 cells) were analyzed using dChip-based visual and algorithmic data analysis methods. Results: The bioinformatics pipeline nominated between 13 and 86 (mean of 47) somatically mutated genes per FL case; of these, 480 represented distinct genes. Importantly, 32 genes were nominated to be mutated in ≥2 out of 12 cases and all these candidate recurrent gene mutations and various other genes for a total of N=122 genes were subjected to Sanger sequence validation. Overall, we validated 68 genes as mutated in at least 1/12 FL discovery set cases. These included frequent mutations in MLL2 (8/12), CREBBP (7/12) and BCL2 (5/12). In addition, we identified 19 novel recurrently mutated genes (≥2 out of 12 FL cases with mutations). From these 19 genes and functionally related genes we selected 10 genes for a complete mutation analysis in a total 57 FL cases. Within the group of recurrently mutated genes we have identified a gene involved in apoptosis threshold regulation as well as multiple novel genes involved in B-cell transcriptional control. Further, we identify frequent mutations in the linker Histone genes HIST1H1 B-E. Finally, through incorporation of SNP array profiling data, we identify multiple candidate target genes for frequent aUPD in FL and further a list of single mutated genes (PTEN, A20, ARID1A, VAV1, TLR2 and TLR8 and others) that can be directly implicated in the pathogenesis of afflicted FL cases. Conclusion: This large genomic profiling study identifies 19 novel recurrently mutated genes in FL, including an apoptosis regulator, transcription factors and linker histones, thereby substantially broadening our understanding of the genetic basis of FL. Disclosures: Lebovic: Genentech: Speakers Bureau.

scholarly journals CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes

2019 ◽  
Author(s):  
Vinicius da Silva ◽  
Marcel Ramos ◽  
Martien Groenen ◽  
Richard Crooijmans ◽  
Anna Johansson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Association Analysis ◽  
Snp Array ◽  
Genomic Variation ◽  
Next Generation Sequencing Data ◽  
Major Type ◽  
Production Traits ◽  
Sequencing Data ◽  
Structural Genomic ◽  
Downstream Analysis

Abstract Summary Copy number variation (CNV) is a major type of structural genomic variation that is increasingly studied across different species for association with diseases and production traits. Established protocols for experimental detection and computational inference of CNVs from SNP array and next-generation sequencing data are available. We present the CNVRanger R/Bioconductor package which implements a comprehensive toolbox for structured downstream analysis of CNVs. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and genome-wide association analysis with gene expression and quantitative phenotypes. Availability and implementation http://bioconductor.org/packages/CNVRanger.

Recurrent STAT6 Mutations In Follicular Lymphoma

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 503-503 ◽  
Author(s):  
Sami Malek ◽  
Mark S. Kaminski ◽  
Hongxiu Li ◽  
Peter Ouillette ◽  
Sian Jones ◽  
...  
Keyword(s):  
Dna Binding ◽  
Follicular Lymphoma ◽  
Massively Parallel Sequencing ◽  
B Cell Lymphoma ◽  
Binding Domain ◽  
Read Length ◽  
Single Amino Acid ◽  
Primary Data ◽  
Dna Binding Domain ◽  
Structural Genomic

Abstract Introduction Follicular lymphoma (FL) constitutes the second most common non-Hodgkin’s lymphoma in the Western world. FL carries characteristic recurrent structural genomic aberrations. However despite recent advances, knowledge regarding the coding genome in FL is still evolving and is currently incomplete. Methods To further our understanding of the genetic basis of follicular lymphoma (FL), we used solution exon capture of sheared and processed genomic DNA isolated from FACS-sorted lymphomatous B-cells and paired CD3+ T-cells isolated from twenty three cases of FL and one case of DLBCL (which was transformed from prior FL), followed by paired-end (96-101 base pair read length per side) massively parallel sequencing. The sequence data were characterized by a mean depth of coverage of 41, and 90% of bases in the target region were covered by at least 10 reads. Bioinformatics pipelines developed by our bioinformatics core served as the primary data source to nominate candidate mutated genes in downstream data analysis. Results The bioinformatics pipeline nominated 711 distinct candidate mutations in 24 FL cases. Sanger sequence validation confirmed 39 recurrently (≥ 2 FL cases) mutated genes. Genes with confirmed mutations in ≥ 2 FL cases in the discovery cohort were subsequently selectively expanded into a combined FL validation cohort of 114 cases. In addition to frequent mutations in MLL2, CREBBP, BCL2, TNFRSF14, EZH2, OCT2, ARID1A, IRF8 and MEF2B, we here report novel mutations in STAT6 in FL. STAT6 mutations were identified in 11% (12/114) of FL and predominantly affected the DNA binding domain (DBD; comprising STAT6 amino acids 268-430). Two FL cases each carried two distinct STAT6 mutations, presumably targeting both alleles. Of interest, the majority of FL-associated STAT6 mutations affected a single amino acid codon (codon 419), resulting in the STAT6 mutants p.419D>D/G or p.419D>D/H. These FL-associated STAT6 mutations are distinct from mutations previously described in primary mediastinal B-cell lymphoma (PMBCL). Given the involvement of STAT6 in signal transduction pathways activated by multiple cell surface receptors, as well as the recently described involvement of STAT6 in antiviral innate immunity (involving an interaction between the STAT6 DBD and the protein STING), we are currently exploring functional consequences of the novel STAT6 mutations in FL and cell line models. Conclusion We report identification of somatic mutations in STAT6 in 11% of FL. These mutations predominantly affected the STAT6 DNA binding domain. We identify a novel STAT6 mutation hotspot in STAT6 codon 419 (p.419D>D/G or p.419D>D/H). Disclosures: Lebovic: Genentech: Speakers Bureau; Allos/Spectrum: Speakers Bureau; Celgene: Speakers Bureau; Onyx: Speakers Bureau.

scholarly journals Systematic analysis of the frequently amplified 2p15-p16.1 locus reveals PAPOLG as a potential proto-oncogene in follicular and transformed follicular lymphoma

2019 ◽  
pp. 124-132
Author(s):  
Deniz KURŞUN ◽  
Can KÜÇÜK
Keyword(s):  
B Cells ◽  
Follicular Lymphoma ◽  
Snp Array ◽  
Systematic Analysis ◽  
Non Hodgkin Lymphoma ◽  
Expression Of Genes ◽  
Histological Transformation ◽  
Significant Difference ◽  
The Relationship ◽  
Transformed Follicular Lymphoma

Transformed follicular lymphoma (tFL) originates from histological transformation of follicular lymphoma (FL), which is the most common indolent non-Hodgkin lymphoma. High-resolution genomic copy-number analysis previously identified frequent amplification of the 2p15-p16.1 locus in FL and tFL cases. The genes (i.e. BCL11A, PAPOLG, PUS10, and USP34) in this amplified locus have not been systematically investigated to date in terms of their role in FL pathogenesis or transformation to tFL. Here we investigated the relationship between amplification and expression of genes in 2p15-p16.1 as well as their expression after histological transformation. NCBI GEO SNP array and gene expression profile (GEP) data of tFL cases were analyzed to evaluate the relationship between amplification and mRNA expression. Moreover, transcript levels of these four genes in FL cases were compared with those of patient-matched tFL cases and normal B-cells. Amplification of the 2p15-p16.1 locus is associated with increased transcription of BCL11A and PAPOLG in tFL cases, of which the latter showed increased expression after histological transformation. Compared with the level in normal B-cells, PAPOLG was significantly overexpressed in FL cases, but expression levels of the other three genes did not show any significant difference. Altogether these results suggest that PAPOLG may be the most critical gene in terms of transformation to tFL.

Whole Exome Sequencing Defines the Genetic Differences Between Pediatric and Adult Follicular Lymphoma

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3636-3636
Author(s):  
Sarah Lynn Ondrejka ◽  
Elaine S Jaffe ◽  
Shunyou Gong ◽  
Deepthi Rajagopalan ◽  
Cassandra Love ◽  
...  
Keyword(s):  
B Cells ◽  
Follicular Lymphoma ◽  
B Cell ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Germinal Center ◽  
Genetic Basis ◽  
Whole Exome ◽  
Germinal Center B Cell ◽  
Germinal Center B Cells

Abstract Follicular lymphoma (FL) is the most common low grade lymphoma in adults, but uncommon in children. While the two diseases are similar in morphology and immunophenotype, pediatric-type FLs manifest higher grade histology with most cases being localized and curable with standard therapy. Pediatric-type FLs are thought arise from germinal center B cells and typically demonstrate higher expression of the germinal center B cell markers BCL6 and CD10. While the genetic basis of adult FL has been studied previously, the genetic basis of pediatric-type FL remains largely unknown. In this study, we sought to define the gene coding mutations occurring in pediatric FL and compared them to those of 48 adult FLs, as well as other adult lymphomas derived from germinal center B cells including 88 GCB DLBCLs and 67 cases of BL that we, and others, have published previously. We obtained a total of 32 pediatric-type FLs along with paired normal tissue. The median age wa 8 years with 62% male patients. We performed whole-exome sequencing for these cases using the Agilent solution-based system of exon capture, which uses RNA baits to target all protein coding genes (CCDS database), as well as ~700 human miRNAs from miRBase (v13). In all, we generated over 6 GB of sequencing data using high throughput sequencing on the Illumina platform. Using bioinformatics approaches that we have described previously, we identified 26 candidate cancer genes that were recurrently somatically mutated in pediatric FL. We found that the genes mutated in pediatric FLs were from three predominant ontologies/pathways. These included DNA damage repair (40%, ATM, RB1), chromatin modification (34%, SETD2, SMARCA4 and TET2) and alternative splicing (12%, SF3B1). We also noted IRF4 translocations and TNFRSF14 mutations in 10% of the cases as has been described previously. We further compared pediatric FLs to other germinal center B cell derived lymphomas and, in particular, FLs occurring in adults. We found that the mutations that characterize adult FLs including MLL2, CREBBP, and GNA13 were absent in pediatric FLs. There was only one pediatric FL case with an EZH2 mutation, which otherwise occur commonly in germinal center B cell derived lymphomas. Thus, pediatric FLs are genetically unlike both adult FLs and other germinal center B cell derived lymphomas. Our data provide new clues to the distinctive genetic basis of these tumors and their clinical behavior. Disclosures No relevant conflicts of interest to declare.

scholarly journals Regions of acquired uniparental disomy at diagnosis of follicular lymphoma are associated with both overall survival and risk of transformation

Blood ◽  
2009 ◽  
Vol 113 (10) ◽  
pp. 2298-2301 ◽  
Author(s):  
Derville O'Shea ◽  
Ciarán O'Riain ◽  
Manu Gupta ◽  
Rachel Waters ◽  
Youwen Yang ◽  
...  
Keyword(s):  
Overall Survival ◽  
Multivariate Analysis ◽  
Follicular Lymphoma ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Progression Free Survival ◽  
Array Analysis ◽  
Free Survival ◽  
Genetic Abnormalities ◽  
Snp Array Analysis

Abstract Acquired homozygosity in the form of segmental acquired uniparental disomy (aUPD) has been described in follicular lymphoma (FL) and is usually due to mitotic recombination. SNP array analysis was performed with the use of the Affymetrix 10K 2.0 Gene-chip array on DNA from 185 diagnostic FL patients to assess the prognostic relevance of aUPD. Genetic abnormalities were detected in 118 (65%) of 182 patients. Number of abnormalities was predictive of outcome; more than 3 abnormalities was associated with inferior overall survival (OS; P < .03). Sites of recurrent aUPD were detected on 6p (n = 25), 16p (n = 22), 12q (n = 17), 1p36 (n = 14), 10q (n = 8), and 6q (n = 8). On multivariate analysis aUPD on 1p36 correlated with shorter OS (P = .05). aUPD on 16p was predictive of transformation (P = .03) and correlated with poorer progression-free survival (P = .02). aUPD is frequent at diagnosis of FL and affects probability of disease transformation and clinical outcome.

scholarly journals Characterisation of two unusual cases of haemoglobin Bart’s hydrops foetalis caused by –SEA and large novel α-globin gene cluster deletions

2021 ◽  
Vol 49 (2) ◽  
pp. 030006052199364
Author(s):  
Yunan Wang ◽  
Ying Xiong ◽  
Chang Liu ◽  
Jian Lu ◽  
Jicheng Wang ◽  
...  
Keyword(s):  
De Novo ◽  
Southern China ◽  
Globin Gene ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Maternal Cell ◽  
Suspension Array ◽  
Frequent Mutations ◽  
History Of ◽  
Hb Bart's

Background We describe 2 unusual haemoglobin (Hb) Bart’s hydrops cases that could not be explained by traditional factors. Case presentation: Two families with a diagnosis or history of foetal hydrops were enrolled. A suspension-array system was used to detect the 23 most frequent mutations in southern China. Multiplex ligation-dependent probe amplification (MLPA) was used to screen for possible deletions. Precise characterisation of the breakpoints of the novel variants and uniparental disomy analysis were performed using a single nucleotide polymorphism (SNP) array. Quantitative fluorescence PCR was used to eliminate maternal cell contamination and nonpaternity. In case 1, the suspension-array system indicated a maternal heterozygous (–SEA/) deletion, and the paternal sample was negative. The foetal hydrops was caused by the maternal (–SEA/) deletion and a de novo α-globin gene deletion (–193). In case 2, the paternal sample had a heterozygous (–SEA/) deletion, and MLPA and SNP array analysis revealed a large maternal deletion (–227) that encompassed the α-globin gene, which explained the history of Hb Bart’s foetal hydrops. Conclusions Our cases describe 2 new α0-thalassaemia deletions and illustrate the importance of using a combination of methods to detect rare types of α-thalassaemia.

aUPD in the Clonal Evolution of Follicular Lymphoma.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2065-2065
Author(s):  
Derville O’Shea ◽  
Sameena Iqbal ◽  
Emanuela Carlotti ◽  
Andrew Davies ◽  
Tracy Chaplin ◽  
...  
Keyword(s):  
Follicular Lymphoma ◽  
Mhc Class Ii ◽  
Clonal Evolution ◽  
Snp Array ◽  
Uniparental Disomy ◽  
B Cell Lymphoma ◽  
Selective Advantage ◽  
Mitotic Recombination ◽  
Lymphoma Cell ◽  
Early Event

Abstract The use of Single Nucleotide Polymorphism (SNP) array profiling has uncovered extensive regions of acquired uniparental disomy (aUPD) in the cancer genome that go undetected using cytogenetics or array-CGH platforms. These regions usually arise by mitotic recombination and can render a cell homozygous for a pre-existing abnormality. SNP array analysis was performed using the Affymetrix 10K Gene-chip mapping array on DNA extracted from a series of Follicular Lymphoma (FL) lymph nodes biopsies from 42 patients, taken at time of diagnosis (n=20), progression (n=16) and transformation (t-FL) (n=32), and the t(14;18) positive lymphoma cell lines DoHH2 and RL 2261. Analysis was performed using the genome oriented laboratory file system, a software package designed to interpret SNP data. The criteria of > 96% homozygosity in at least 50 contiguous SNPs was found to detect no abnormalities in 24 normal remission bone marrows and was therefore adopted for the detection of abnormal runs of homozygosity. Abnormalities were detected in 53/68 primary specimens; these were non-random with recurring sites of aUPD on several chromosomes including 6p, 9p, 12q and 17p. This panel included 26 paired FL and t-FL samples; in 9 FL cases regions of homozygosity were identified which were not present in the subsequent t-FL sample, suggesting that t-FL may arise in a proportion of patients by a mechanism other than a process of direct clonal evolution. Homozygosity of 9p and 17p was seen primarily in the transformation samples and in three cases rendered the cell homozygous for a pre-existing mutation of either CDKN2A or TP53. Thus mutation precedes mitotic recombination which leads to the removal of the remaining wild-type allele. Nine out of 42 patients studied (21%) have aUPD of chromosome 6p. This appears to be an early event in lymphomagenesis as it was present in both FL and t-FL samples obtained from the same patient. The sites of mitotic recombination cluster in a region immediately proximal to the MHC complex at 6p21-12 in 8/9 cases. Mutations in CCND3, CDKN1A, and two translocation partners of BCL6: SRP20 and HIST1H4I, which are all located within or just distal of this cluster, were excluded by direct sequence analysis. Loss of MHC class II expression has been frequently observed in Diffuse Large B-cell lymphoma and a selective advantage gained by the lymphoma cell here would have implications in tumour surveillance. This study highlights the frequency of aUPD in follicular lymphoma and ongoing studies will elucidate the selective basis of a UPD at this location in the pathogenesis of lymphoma.

scholarly journals Use of SNP chips to detect rare pathogenic variants: retrospective, population based diagnostic evaluation

BMJ ◽  
2021 ◽  
pp. n214
Author(s):  
Weedon MN ◽  
Jackson L ◽  
Harrison JW ◽  
Ruth KS ◽  
Tyrrell J ◽  
...  
Keyword(s):  
Positive Predictive Value ◽  
Predictive Value ◽  
Population Based ◽  
Genome Project ◽  
Personal Genome ◽  
Uk Biobank ◽  
Sequencing Data ◽  
Snp Chip ◽  
Pathogenic Variants ◽  
The Uk

Abstract Objective To determine whether the sensitivity and specificity of SNP chips are adequate for detecting rare pathogenic variants in a clinically unselected population. Design Retrospective, population based diagnostic evaluation. Participants 49 908 people recruited to the UK Biobank with SNP chip and next generation sequencing data, and an additional 21 people who purchased consumer genetic tests and shared their data online via the Personal Genome Project. Main outcome measures Genotyping (that is, identification of the correct DNA base at a specific genomic location) using SNP chips versus sequencing, with results split by frequency of that genotype in the population. Rare pathogenic variants in the BRCA1 and BRCA2 genes were selected as an exemplar for detailed analysis of clinically actionable variants in the UK Biobank, and BRCA related cancers (breast, ovarian, prostate, and pancreatic) were assessed in participants through use of cancer registry data. Results Overall, genotyping using SNP chips performed well compared with sequencing; sensitivity, specificity, positive predictive value, and negative predictive value were all above 99% for 108 574 common variants directly genotyped on the SNP chips and sequenced in the UK Biobank. However, the likelihood of a true positive result decreased dramatically with decreasing variant frequency; for variants that are very rare in the population, with a frequency below 0.001% in UK Biobank, the positive predictive value was very low and only 16% of 4757 heterozygous genotypes from the SNP chips were confirmed with sequencing data. Results were similar for SNP chip data from the Personal Genome Project, and 20/21 individuals analysed had at least one false positive rare pathogenic variant that had been incorrectly genotyped. For pathogenic variants in the BRCA1 and BRCA2 genes, which are individually very rare, the overall performance metrics for the SNP chips versus sequencing in the UK Biobank were: sensitivity 34.6%, specificity 98.3%, positive predictive value 4.2%, and negative predictive value 99.9%. Rates of BRCA related cancers in UK Biobank participants with a positive SNP chip result were similar to those for age matched controls (odds ratio 1.31, 95% confidence interval 0.99 to 1.71) because the vast majority of variants were false positives, whereas sequence positive participants had a significantly increased risk (odds ratio 4.05, 2.72 to 6.03). Conclusions SNP chips are extremely unreliable for genotyping very rare pathogenic variants and should not be used to guide health decisions without validation.

Sign in / Sign up

Export Citation Format

Share Document