scholarly journals Prognostic Impact of Subclonal TP53 Aberrations in Chronic Lymphocytic Leukemia Validated By a Robust Targeted Next Generation Sequencing Assay

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4380-4380
Author(s):  
Christian Brieghel ◽  
Christina Westmose Yde ◽  
Caspar da Cunha-Bang ◽  
Savvas Kinalis ◽  
Lone Bredo Pedersen ◽  
...  
Keyword(s):  
Overall Survival ◽  
Lymphocytic Leukemia ◽  
Prognostic Impact ◽  
Mutation Status ◽  
Tp53 Mutations ◽  
Targeted Next Generation Sequencing ◽  
Kaplan Meier ◽  
Significant Difference ◽  
Generation Sequencing ◽  
Allelic Burden

Abstract Introduction/background: Clonal TP53 aberrations (del(17p) and/or TP53 mutations) in patients with chronic lymphocytic leukemia (CLL) correlates with a poor prognosis. Similar outcome has been demonstrated for patients with subclonal TP53 aberrations (Rossi, Blood, 2014). In order to guide novel targeted therapies approved in frontline treatment of TP53 aberrated (TP53+) CLL, development and clinical validation of robust assays for subclonal TP53 aberrations is warranted. Methods: DNA extracted from peripheral blood of CLL patients were diluted 1:5 in DNA derived from a cell line containing a known, but rare TP53 point mutation. TP53 exons 2-10 were PCR amplified from undiluted and diluted DNA in parallel using Phusion proofreading DNA polymerase and subsequently sequenced by targeted Next Generation Sequencing (tNGS) on Illumina MiSeq and HiSeq 2500. Sensitivity and specificity of the assay was tested by serial dilution of patient samples with known TP53 insertions, deletions or substitutions. Consecutive biobanked samples from CLL patients at a single institution were used for validation of the clinical impact of subclonal TP53 aberrations. Nucleotide variants were called by CLC Biomedical Genomics Workbench 3.0. An algorithm for detection of true mutations was developed based on comparison of the diluted and undiluted samples analyzed in parallel. Overall survival (OS) was analyzed using Kaplan-Meier. Results: The sensitivity and specificity of the assay was validated by detection of all 8 known TP53 aberrations in serial dilutions with the threshold of the assay established at 0.2% allelic burden. Known mutations were still detectable at 0.02% at the highest dilution. A test sample of patients with known del(17p) demonstrated TP53 mutations in 6 out of 7 patients (5 clonal and 1 subclonal TP53+) in accordance with previously reported frequencies of TP53 mutations among patients with del(17p). In total, 92 samples from 46 consecutive patients were analyzed. With a median coverage of 93,272 reads (98% above 20,688 reads, range: 5,153-720,025), 27 TP53 aberrations were found in 10 (22%) of the patients. Twenty-six (96%) mutations were subclonal with a median allelic burden of 0.9% (range: 0.2-97.5%). Seven patients had a single aberration. In two previously treated patients, 8 and 10 subclonal aberrations were detected. One patient with a known del(17p) also had subclonal TP53 mutations. Three patients had solely subclonal mutations below 1% allelic burden. Considered the hot spot region of TP53 in CLL, exons 4-8 harbored 93% of the detected mutations. The median (IQR) survival for TP53+ patients and patients with wild type TP53 (wt-TP53) was 37.5 (range: 2-106) and 104 (range: 9-113) months, respectively. In Kaplan-Meier analyses, TP53+ patients had a significantly poorer OS versus patients with wt-TP53 (p=0.00002, Figure 1). The two TP53+ long-term survivors both had an allelic burden below 1%, and the only other TP53+ patient with less than 1% allelic burden survived for 53 months, indicating that the prognostic impact of very low allelic burden TP53 aberrations needs further investigation. Conclusion: We have developed a robust assay for TP53 aberrations with a sensitivity of 0.2% allelic burden based on an algorithm including a dilution step. In an initial test cohort of 46 patients, 10 patients demonstrated TP53 mutations as low as 0.2% allelic burden that significantly affected OS. Validation of the clinical impact of subclonal TP53 aberrations is ongoing based on our consecutive biobank with 600+ patients. Establishment of a new cut-off for clinical treatment decisions based on subclonal TP53 aberrations is warranted. Figure 1 Overall survival in 46 consecutive CLL patients based on TP53 mutation status shows significant difference (p=0.00002) between patients withwild type TP53 (wt-TP53) and TP53 mutations (TP53+) as low as 0.2% allelic burden. Figure 1. Overall survival in 46 consecutive CLL patients based on TP53 mutation status shows significant difference (p=0.00002) between patients withwild type TP53 (wt-TP53) and TP53 mutations (TP53+) as low as 0.2% allelic burden. Disclosures Niemann: Gilead: Consultancy; Abbvie: Consultancy; Roche: Consultancy; Janssen: Consultancy.

Prognostic Impact of Molecular Mutations in Acute Myeloid Leukemia (AML) and Myelodysplastic Syndromes (MDS) on Allogeneic Hematopoietic Cell Transplant (HCT) Outcomes: Adverse Impact of TET2 Mutations

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 740-740 ◽  
Author(s):  
Betty K. Hamilton ◽  
Navneet S. Majhail ◽  
Cassandra M Hirsch ◽  
Bartlomiej Przychodzen ◽  
Lisa A. Rybicki ◽  
...  
Keyword(s):  
Overall Survival ◽  
Prognostic Impact ◽  
Cell Transplant ◽  
Complex Karyotype ◽  
Monosomy 7 ◽  
Mutation Status ◽  
Tp53 Mutations ◽  
Allogeneic Hct ◽  
Molecular Abnormalities ◽  
Tet2 Mutation

Abstract AML and MDS are heterogeneous myeloid neoplasms with variable biologic and clinical outcomes. Although allogeneic HCT is the only potentially curative therapy for high risk AML and MDS, survival after transplant remains poor, and identifying who benefits is challenging. We hypothesized that next-generation sequencing (NGS) mutational analyses can predict outcome in MDS and AML patients undergoing allogeneic HCT. We performed multi-amplicon targeted pre-HCT NGS using a somatic panel of the 60 most commonly mutated genes in myeloid neoplasias as previously determined by whole exome sequencing, on 123 patients with AML (N=64, 52%) and MDS (N=59, 48%) who subsequently underwent HCT. Median age at transplant was 53 years (range, 20-73). 21 (17%) patients had complex karyotype, 10 (8%) with monosomy 7, 48 (39%) normal, and 48 (39%) with other or unknown cytogenetic abnormalities. 45 (37%) patients were in a complete remission (CR) prior to transplant, while 78 (63%) were in less than a CR; with CR as defined by International Working Group criteria for MDS, or <5% blasts for AML. The majority of patients received myeloablative conditioning (N=83, 68%), and 40 (33%) received a reduced-intensity preparative regimen. Donor source was matched sibling (N=52, 42%), matched unrelated (N=56, 46%), cord-blood (N=12, 10%), and haplo-identical (N=3, 2%). Median follow up was 35 months (range 5-178). Mutations were analyzed individually and by molecular pathway. 88 (72%) patients had at least one mutation, most frequently in STAG2 (10.2%), TET2 (9.8%), ASXL1 (8.1%), and RUNX1 (8.1%). TP53 mutations were more common in MDS patients compared to AML (10% versus 1.6%, P=0.05). NRAS (P=0.019) and TP53 (P=0.022)mutations were more commonly associated with complex karyotype. Mutations in BCOR (P=0.048) and TP53 (P=0.047)were associated with less than CR, while TET2 (P=0.03)mutations were associated with CR prior to HCT. In univariable analyses, the presence of complex karyotype was associated with shorter overall (OS) and relapse-free survival (RFS) (hazard ratio [HR] 2.4; P=0.002 and HR 3.1; P<0.001). Mutations in TET2 (HR 2.1; P=0.042) and EZH2 (HR 2.3; P=0.048), or presence of any mutation in the histone modification pathway (ASXL1, EZH2, KDM6A, SUZ12); (HR 1.7; P=0.039) was associated with poor OS. The presence of any mutation in the DEAD box RNA-helicase family genes (DHX29, DDX54, DDX41) was associated with poor RFS (HR 3.1; P=0.009). Nothing except complex karyotype was specifically associated with higher relapse. Unlike in previous reports, TP53 mutations were not found to be significantly associated with poor OS or RFS, though these cases (N=7) were limited. In multivariable analyses, adjusting for clinical variables, complex karyotype remained significantly associated with poor OS (HR 2.7; P<0.001) and RFS (HR 3.9; P<0.001). TET2 also remained independently associated with poor OS (HR 2.4; P=0.022). Presence of any of the DNA methylation mutations (TET2, DNMT3A, IDH1, IDH2) was associated with poor RFS (HR 1.7; P=0.05). 3-year OS was 23% in patients with a complex karyotype versus 48% in patients without (P=0.002); and 14% in patients with a TET2 mutation and 46% without (P=0.042) (Figure 1). Molecular abnormalities are important variables in determining outcome after allogeneic HCT. We demonstrate that TET2 mutations in AML and MDS predict for poor survival after HCT. Ongoing serial mutational analyses in an extended cohort of patients will enhance our understanding of the role of NGS in informing care decisions for patients undergoing allogeneic HCT for AML and MDS. Figure 1. Overall Survival by TET2 mutation status Figure 1. Overall Survival by TET2 mutation status Disclosures Majhail: Gamida Cell Ltd.: Consultancy; Anthem Inc.: Consultancy. Sekeres:Celgene Corporation: Membership on an entity's Board of Directors or advisory committees.

Research on the Characteristics of IGHV Gene In Chronic Lymphocytic Leukemia of China.

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 4609-4609
Author(s):  
Chun Qiao ◽  
Kourong Miao ◽  
Jianyong Li
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Heavy Chain ◽  
Conflicts Of Interest ◽  
Gene Families ◽  
Lymphocytic Leukemia ◽  
Chinese Patients ◽  
Prognostic Impact ◽  
Mutation Status ◽  
Ighv Gene ◽  
Significant Difference

Abstract Abstract 4609 Objective The usage, mutation status and prognostic impact of immunoglobulin heavy chain variable (IGHV) gene in Chinese patients with chronic lymphocytic leukemia (CLL) is unclear. We set out to define the characteristics of IGHV gene and its relevance to clinical and biological parameter in our patients. Methods IGHV gene mutations were detected by multiplex PCR in 202 Chinese CLL patients and the purified PCR amplification products were sequenced. IGHV somatic hypermutation status and gene usage were analyzed by IMGT/V-QUEST software. The association analysis between IGHV somatic mutation status and the clinical and biological features, including Binet staging, immunophenotype, cytogenetic aberrant, were also emphasized in this study. Results The results showed that 129 patients had mutated (M) IGHV, and the remaining 73 patients had unmutated (UM) IGHV according to the cutoff value of accordance rate 98%. The most frequent VH gene family was found to be VH3 (47.5%), followed by VH4 (34.7%), VH1 (11.4%), VH2 (2.5%), VH5(1.5%), VH7(1.5%) and VH6(0.9%) gene families, which was similar to other Asian populations. The overall survival (OS) time of UM IGHV group was significant shorter than M IGHV group (P=0.025). Significance was found in the expression of CD38 and ZAP-70 between patients with and without IGHV mutations (P<0.0001 and P=0.015, respectively). Binet staging was significantly different with IGHV mutation status (P<0.001). “Unmutated” sequences had significantly longer heavy chain complementarity-determining region 3 (HCDR3). Seven of these patients used VH1-69, which was similar to other Asia countries, but in striking contrast to those in Western countries, where VH1-69 was one of the most frequently used genes. FISH was performed in 117 cases, del(11q22) was considered as high risk factors, and 10(10/42, 23.8%) cases with UM IGHV gene. On the other hand, there were 7(7/75, 9.3%) cases with M IGHV gene (P=0.033). No significance was found in del(17p),del(13q),del(6q),add(12),IGH translocation between IGHV mutation and unmuatioan patients. A total of five stereotyped BCR were identified, IGHV3-21/IGHD3-9/IGHJ6, IGHV4-34/IGHD2-15/IGHJ6, IGHV1-3/IGHD6-19/IGHJ4, IGHV4-59/IGHD3-22/IGHJ6 and IGHV4-39/IGHD6-13/IGHJ5. Conclusions The usage of IGHV gene families indicates significant difference in Chinese CLL patients compared with Western patients, suggesting involvement of ethnic and/or environmental factors in CLL disease initiation. In the development course of CLL, BCR play an important role in the immunological recognition and selection. There are intimate relationships between mutation status of IGHV gene and prognosis. The usage of IGHV provides enlightment for the occurrence mechanism of CLL. Disclosures: No relevant conflicts of interest to declare.

Prognostic Impact of Biallelic Versus Monoallelic Deletion 13q and the Proportion of Cells with Deletion 13q within the CLL8 Trial of the German CLL Study Group (GCLLSG)

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2841-2841
Author(s):  
Dirk Winkler ◽  
Raymonde Busch ◽  
Andreas Buehler ◽  
Michael K. Wenger ◽  
Kirsten Fischer ◽  
...  
Keyword(s):  
Board Of Directors ◽  
Response Rates ◽  
Continuous Variable ◽  
Lymphocytic Leukemia ◽  
Prognostic Impact ◽  
Advisory Committees ◽  
Clone Size ◽  
Mutation Status ◽  
Significant Difference ◽  
Baseline Characteristics

Abstract Abstract 2841 Introduction: Genomic aberrations are widely used markers to predict survival of patients with chronic lymphocytic leukemia (CLL). Deletion of 13q as sole abnormality (del 13q) has been associated with a favorable prognosis. However, whether the clinical impact of monoallelic del 13q (mono-del 13q) is different as compared to biallelic del 13q (bi-del 13q), remains controversial. Similarly, it is unsettled, if there is an impact of clone size on outcome of patients with del 13q. Methods: The prognostic impact of mono-del 13q and bi-del 13q, as well as the proportion of cells with del 13q prior therapy was studied in the CLL8 trial of the GCLLSG (1st line FC vs FCR). Pretherapeutic variables, response rates (ORR, CR), progression free survival (PFS), and overall survival (OS) were compared between the groups. Results: 224 patients with del 13q as single aberration were analyzed. 189 patients (84%) had a mono-del 13q, and 35 (16%) a bi-del 13q. B-symptoms were observed more frequently in patients with bi-del 13q (63% vs. 38%, P<.01). No significant differences were seen when comparing all other baseline characteristics between the two groups (Binet/Rai stage, ECOG, leukocyte count, sex, levels of thymidine kinase and ß2-mikroglobuline, IGHV mutation status, usage of V3-21 genes and TP53 mutation) and there was no significant difference in ORR (87% vs 89%) and CR (34% vs 37%) rates. However, PFS was significantly longer in patients with bi-del 13q (median not reached vs. 52 months, P=.04; Fig. 1a). When treated with FCR, patients with bi-del 13q had significantly higher CR rates than those with mono-del 13q (60% vs 47%), while there was no significant difference when treated with FC (25% vs 22%). Similarly, FCR resulted in longer PFS in patients with bi-del 13q as compared to mono-del 13q patients (P=.06). Interestingly, this difference was not observed for FC therapy. Regarding OS, there was a trend towards better outcome in patients with bi-del 13q when combining both treatment arms (P=.18, Fig. 1b). Comparison of treatment arms regarding OS was limited due to few events. However, it was of note that not a single death was observed in the group with bi-del 13q when treated with FCR. Interestingly, among bi-del 13q cases, PFS and OS was independent of the IGHV mutation status (P=.78 for PFS, P=.42 for OS). In contrast, patients with mono-del 13q with mutated IGHV genes had a significantly longer PFS and OS than those with unmutated IGHV genes (P<.01 for PFS, P<.01 for OS). Regarding the clone size of del 13q, there were no significant differences in response rates, PFS and OS in relation to the % of cells with del 13q. This was irrespective of using clone size as a continuous variable, using the median value as cut-point, or separating clone size into quartiles (percentile 25: 42%, median: 76%, percentile 75: 88% del 13q). Median clone sizes in patients achieving a CR, PR, SD or PD were 74% (N=77), 78% (N=119), 74% (N=14) and 70% (N=1), respectively. Median PFS in months was 66, 59, 57 and 39 in quartiles 1–4 (P=.44) and median OS was not reached in either quartile. Conclusion: Although most baseline characteristics were not significantly different when comparing mono-del 13q and bi-del 13q, the presence of a bi-del 13q was associated with significantly longer PFS and a trend towards longer OS after FC-based 1st line treatment in CLL. Bi-del 13q appeared to predict for higher CR rates and longer PFS with FCR as compared to FC treatment. For patients with bi-del 13q, PFS and OS were independent of IGHV mutation status. The size of the aberrant del 13q clone did not impact response rate, PFS or OS. Disclosures: Fischer: Hoffmann La Roche:. Hallek:Hoffmann-la Roche: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees. Stilgenbauer:Hoffmann La Roche: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Travel Grants.

Acquisition of TP53 Mutations in Chronic Lymphocytic Leukemia (CLL) Patients During the Course of Disease Is Associated with an Unmutated IGHV Status and Mutations in XPO1 and SF3B1

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1768-1768
Author(s):  
Vera Grossmann ◽  
Alexander Kohlmann ◽  
Susanne Schnittger ◽  
Sandra Weissmann ◽  
Frank Dicker ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Lymphocytic Leukemia ◽  
Discovery Cohort ◽  
Mutation Status ◽  
Course Of Disease ◽  
Tp53 Mutations ◽  
Equity Ownership ◽  
Generation Sequencing ◽  
First Diagnosis

Abstract Abstract 1768 Background: In chronic lymphocytic leukemia (CLL), an association between TP53 mutations (TP53mut) and a poor prognosis has been reported. Two hypotheses are discussed regarding the occurrence of TP53mut during the course of disease: 1. TP53mut are already present at first diagnosis in a small subclone, which selectively grow despite treatment, and 2. TP53mut occur de novo during disease progression. Aim: Investigation of the acquisition of TP53mut in previously TP53wt CLL cases during the course of disease. Patient and Methods: The discovery cohort included 20 cases, which were selected based on negativity for TP53mut at first diagnosis and acquisition of TP53mut during follow-up (7 female, 13 male patients; median age: 60.7 yrs, range: 41.3–76.6 yrs). 16/20 patients were treated according to various regimens (including fludarabine and rituximab). TP53 analyses of the discovery cohort were performed by DHPLC and subsequent direct Sanger sequencing and, additionally, by 454 deep-sequencing analyses (454 Life Sciences, Branford, CT) enabling a higher sensitivity. Further, a comprehensive molecular characterization included in addition to TP53 the following markers: IGHV mutation status, NOTCH1, FBXW7, SF3B1, XPO1, and MYD88. All markers had been analyzed both at initial diagnosis and at the first follow-up time point that revealed an acquired TP53mut. A second cohort (n=326) was used for comparison of the mutation frequencies of IGHV, NOTCH1, FBXW7, SF3B1, XPO1, and MYD88. Results: Next-generation sequencing confirmed 18/20 cases as wild-type at first diagnosis (median coverage: 733-fold; range: 378-1, 369; sensitivity: <2.0%). However, in 2/20 cases deep-sequencing revealed a low-level clone of TP53 aberration (4.0% and 7.0%) that had not been detected by DHPLC and Sanger sequencing. Both patients with a detectable TP53mut at first diagnosis were excluded from further analyses. New TP53mut occurred at a median of 39.0 months after first diagnosis (range: 13.7–68.4 months). The patients harbored between 1 and 4 TP53mut (mean: 1.3) with a median mutation load of 18.0% (range: 2.0–93.0%). Of note, 15/18 patients had received therapy prior to the acquisition of the TP53mut. In addition, 13/17 (76.5%; n=1 no data available) cases showed a concomitant TP53 deletion detected by fluorescence in situ hybridization. Only 1/10 of these cases showed a TP53 deletion already at first diagnosis (no data available: n=3). Mutation frequencies of the NOTCH1 PEST domain, MYD88, FBXW7, XPO1, SF3B1 and the IGHV mutation status were compared between the discovery cohort and an independent cohort of 326 newly diagnosed CLL cases. Mutation frequencies in NOTCH1 PEST domain (2/18, 11.1% vs 45/326, 13.8%), MYD88 (1/18, 5.6% vs 6/326, 1.8%), and FBXW7 (0/18, 0% vs 8/326, 2.5%) were comparable between both cohorts, while mutations in XPO1 (4/18; 22.2% vs 14/326; 4.3%, P=0.010) and in SF3B1 (4/18; 22.2% vs 27/326 8.3%, P=0.067) were observed at significantly higher frequencies in the discovery cohort. Also an unmutated IGHV status was significantly more frequent in the discovery cohort compared to the unselected comparison cohort (16/18, 88.9% vs 196/326, 60.1%; P=0.01). Of note, in one case with a MYD88 mut and another case with a SF3B1 mut, these alterations were detected at first diagnosis, but disappeared during course of disease. In contrast, an XPO1 mutation was acquired during the course of disease in parallel to the TP53mut. In the remaining cases with SF3B1 (n=3), XPO1 (n=3), and NOTCH1 (n=2), mutations were observed both at first diagnosis and follow-up time point that revealed an acquired TP53mut. Conclusions: 1. A small fraction of CLL patients (2/20) harbored a subclone with TP53 mutations at first diagnosis which escaped detection by conventional laboratory assays (DHPLC and Sanger sequencing) and were only identified retrospectively by using a more sensitive next-generation sequencing assay. These subclones increased in size during the course of disease. 2. A subset of CLL patients acquired TP53mut during course of their disease. Thus, repeated TP53 mutation analyses are necessary for optimal treatment decisions. 3. An unmutated IGHV status and mutations in XPO1 and SF3B1 were more frequent in CLL patients who acquired TP53 mutations during the course of disease, suggesting that these are potential risk factors for the acquisition of TP53 mutations during disease progression. Disclosures: Grossmann: MLL Munich Leukemia Laboratory: Employment. Kohlmann:MLL Munich Leukemia Laboratory: Employment. Schnittger:MLL Munich Leukemia Laboratory: Equity Ownership. Weissmann:MLL Munich Leukemia Laboratory: Employment. Dicker:MLL Munich Leukemia Laboratory: Employment. Jeromin:MLL Munich Leukemia Laboratory: Employment. Boeck:MLL Munich Leukemia Laboratory: Employment. Alpermann:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Equity Ownership.

scholarly journals P04.16 TP53 mutations in codon 273 is predictive of overall survival in astrocytoma patients

2019 ◽  
Vol 21 (Supplement_3) ◽  
pp. iii32-iii32
Author(s):  
H Noor ◽  
R Rapkins ◽  
K McDonald
Keyword(s):  
Overall Survival ◽  
Tp53 Mutation ◽  
Progression Free Survival ◽  
Low Grade Glioma ◽  
Low Grade ◽  
Wild Type ◽  
Mutation Status ◽  
Free Survival ◽  
Tp53 Mutations ◽  
Fresh Frozen

Abstract BACKGROUND Tumour Protein 53 (TP53) is a tumour suppressor gene that is mutated in at least 50% of human malignancies. The prevalence of TP53 mutation is much higher in astrocytomas with reports of up to 75% TP53 mutant cases. Rare cases of TP53 mutation also exist in oligodendroglial tumours (10–13%). P53 pathway is therefore an important factor in low-grade glioma tumorigenesis. Although the prognostic impact of TP53 mutations has been studied previously, no concrete concordance were reached between the studies. In this study, we investigated the prognostic effects of TP53 mutation in astrocytoma and oligodendroglioma. MATERIAL AND METHODS A cohort of 65 matched primary and recurrent fresh frozen tumours were sequenced to identify hotspot exons of TP53 mutation. Exons 1 to 10 were sequenced and pathogenic mutations were mostly predominant between Exons 4 and 8. The cohort was further expanded with 78 low grade glioma fresh frozen tissues and hotspot exons were sequenced. Selecting only the primary tumour from 65 matched tumours, a total of 50 Astrocytoma cases and 51 oligodendroglioma cases were analysed for prognostic effects of TP53. Only pathogenic TP53 mutations confirmed through COSMIC and NCBI databases were included in the over survival and progression-free survival analysis. RESULTS 62% (31/50) of astrocytomas and 16% (8/51) of oligodendrogliomas harboured pathogenic TP53 mutations. Pathogenic hotspot mutations in codon 273 (c.817 C>T and c.818 G>A) was prevalent in astrocytoma with 58% (18/31) of tumours with these mutations. TP53 mutation status was maintained between primary and recurrent tumours in 93% of cases. In astrocytoma, overall survival of TP53 mutant patients was longer compared to TP53 wild-type patients (p<0.01) but was not significant after adjusting for age, gender, grade and IDH1 mutation status. In contrast, astrocytoma patients with specific TP53 mutation in codon 273 showed significantly better survival compared to other TP53 mutant and TP53 wild-type patients combined (p<0.01) in our multivariate analysis. Time to first recurrence (progression-free survival) of TP53 mutant patients was significantly longer than TP53 wild-type patients (p<0.01) after adjustments were made, while TP53 mutation in codon 273 was not prognostic for progression-free survival. In oligodendroglioma patients, TP53 mutations did not significantly affect overall survival and progression-free survival. CONCLUSION In agreement with others, TP53 mutation is more prevalent in Astrocytoma and mutations in codon 273 are significantly associated with longer survival.

Monoallelic TP53 inactivation is associated with poor prognosis in chronic lymphocytic leukemia: results from a detailed genetic characterization with long-term follow-up

Blood ◽  
2008 ◽  
Vol 112 (8) ◽  
pp. 3322-3329 ◽  
Author(s):  
Thorsten Zenz ◽  
Alexander Kröber ◽  
Katrin Scherer ◽  
Sonja Häbe ◽  
Andreas Bühler ◽  
...  
Keyword(s):  
Tp53 Mutation ◽  
Direct Sequencing ◽  
Clonal Evolution ◽  
Lymphocytic Leukemia ◽  
Prognostic Impact ◽  
Clone Size ◽  
Tp53 Mutations ◽  
Long Term Follow Up ◽  
Serial Samples

AbstractThe exact prognostic role of TP53 mutations (without 17p deletion) and any impact of the deletion without TP53 mutation in CLL are unclear. We studied 126 well-characterized CLL patients by direct sequencing and DHPLC to detect TP53 mutations (exons 2-11). Most patients with 17p deletions also had TP53 mutations (81%). Mutations in the absence of 17p deletions were found in 4.5%. We found a shorter survival for patients with TP53 mutation (n = 18; P = .002), which was more pronounced when analyzed from the time point of mutation detection (6.8 vs 69 months, P < .001). The survival was equally poor for patients with deletion 17p plus TP53 mutation (7.6 months, n = 13), TP53 mutation only (5.5 months, n = 5), and 17p deletion only (5.4 months, n = 3). The prognostic impact of TP53 mutation (HR 3.71) was shown to be independent of stage, VH status, and 11q and 17p deletion in multivariate analysis. Serial samples showed evidence of clonal evolution and increasing clone size during chemotherapy, suggesting that there may be patients where this treatment is potentially harmful. TP53 mutations are associated with poor sur-vival once they occur in CLL. The de-monstration of clonal evolution under selective pressure supports the biologic significance of TP53 mutations in CLL.

scholarly journals The genetic analysis of Chinese patients with clonal cytopenias using targeted next-generation sequencing

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Lijuan Zhang ◽  
YuYe Shi ◽  
Yue Chen ◽  
Shandong Tao ◽  
Wenting Shi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Myelodysplastic Syndromes ◽  
Rna Splicing ◽  
Myeloproliferative Neoplasms ◽  
Chinese Patients ◽  
Newly Diagnosed ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Significant Difference ◽  
Generation Sequencing

Abstract Background Clonal hematopoiesis (CH) can be found in various myeloid neoplasms (MN), such as myelodysplastic syndromes (MDS), myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN), also in pre-MDS conditions. Methods Cytogenetics is an independent prognostic factor in MDS, and fluorescence in-situ hybridization (FISH) can be used as an adjunct to karyotype analysis. In the past 5 years, only 35 of 100 newly diagnosed MDS and MDS/MPN patients were identified abnormalities, who underwent the FISH panel. In addition, we examined a cohort of 51 cytopenic patients suspected MDS or MDS/MPN with a 20-gene next generation sequencing (NGS), including 35 newly diagnosed MN patients and 16 clonal cytopenias of undetermined significance (CCUS) patients. Results Compared with the CCUS group, the MN group had higher male ratio (22/13 vs 10/6), cytogenetics abnormalities rate (41.4% vs 21.4%) and frequency of a series of mutations, such as ASXL1 (28.6% vs 25%), U2AF1 (25.7% vs 25%), RUNX1 (20% vs 0.0%); also, higher adverse mutations proportion (75% vs 85.2%), and double or multiple mutations (54.3% vs 43.75%). There were 7 MN patients and 4 CCUS patients who experienced cardio-cerebrovascular embolism events demonstrated a significant difference between the two groups (25% vs 20%). Ten of the 11 patients had somatic mutations, half had DNA methylation, while the other half had RNA splicing. Additionally, six patients had disease transformation, and four patients had mutated U2AF1, including two CCUS cases and two MDS-EB cases. Following up to January 2021, there was no significant difference in over survival between the CCUS and MN groups. Conclusion NGS facilitates the diagnosis of unexplained cytopenias. The monitoring and management of CCUS is necessary, also cardio-cerebrovascular embolism events in patients with CH need attention in the clinical practice.

scholarly journals Prognostic Impact of NOTCH1 Hotspot Mutation in TP53-Mutated Patients with Chronic Lymphocytic Leukemia

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 3283-3283
Author(s):  
Barbara Kantorova ◽  
Jitka Malcikova ◽  
Veronika Navrkalova ◽  
Jana Smardova ◽  
Kamila Brazdilova ◽  
...  
Keyword(s):  
Overall Survival ◽  
Chronic Lymphocytic Leukemia ◽  
Tp53 Mutation ◽  
Direct Sequencing ◽  
Lymphocytic Leukemia ◽  
The Other ◽  
Wild Type ◽  
Tp53 Mutations ◽  
Time To First Treatment ◽  
Hotspot Mutation

Abstract Introduction A presence of activating mutations in NOTCH1 gene has been recently associated with reduced survival and chemo-immunotherapy resistance in chronic lymphocytic leukemia (CLL). However, a prognostic significance of the NOTCH1 mutations with respect to TP53mutation status has not been fully explained yet. Methods An examined cohort included 409 patients with CLL enriched for high risk cases; in 121 patients consecutive samples were investigated. To determine the TP53 mutation status, a functional analysis of separated alleles in yeast (FASAY, exons 4-10) combined with direct sequencing was performed; the ambiguous cases were retested using an ultra-deep next generation sequencing (MiSeq platform; Illumina). The presence of NOTCH1 hotspot mutation (c.7544_7545delCT) was analyzed using direct sequencing complemented by allele-specific PCR in the selected samples. In several patients harboring concurrent NOTCH1 and TP53 mutations, single separated cancer cells were examined using multiplex PCR followed by direct sequencing. A correlation between mutation presence and patient overall survival, time to first treatment and other molecular and cytogenetic prognostic markers was assessed using Log-rank (Mantel-cox) test and Fisher's exact test, respectively. Results The NOTCH1 and TP53 mutations were detected in 16% (65/409) and 27% (110/409) of the examined patients, respectively; a coexistence of these mutations in the same blood samples was observed in 11% (19/175) of the mutated patients. The detected increased mutation frequency attributes to more unfavorable profile of the analyzed cohort; in the TP53-mutated patients missense substitutions predominated (75% of TP53 mutations). As expected, a significantly reduced overall survival in comparison to the wild-type cases (147 months) was observed in the NOTCH1-mutated (115 months; P = 0.0018), TP53-mutated (79 months; P < 0.0001) and NOTCH1-TP53-mutated patients (101 months; P = 0.0282). Since both NOTCH1 and TP53 mutations were strongly associated with an unmutated IGHV gene status (P < 0.0001 and P = 0.0007), we reanalyzed the IGHV-unmutated patients only and interestingly, the impact of simultaneous NOTCH1 and TP53 mutation presence on patient survival was missed in this case (P = 0.1478). On the other hand, in the NOTCH1 and/or TP53-mutated patients significantly reduced time to first treatment was identified as compared to the wild-type cases (41 months vs. 25 months in NOTCH1-mutated, P = 0.0075; 17 months in TP53-mutated, P < 0.0001; and 18 months in NOTCH1-TP53-mutated patients, P = 0.0003). The similar results were observed also in the subgroup of the IGHV-unmutated patients, with the exception of patients carrying sole NOTCH1 mutation (P = 0.2969). Moreover, in the NOTCH1-TP53-mutated patients an increased frequency of del(17p)(13.1) was found in comparison to the TP53-mutated patients only (72% vs. 56%); this cytogenetic defect was not detected in the patients with sole NOTCH1 mutation. Our results might indicate, that NOTCH1 mutation could preferentially co-selected with particular, less prognostic negative type of TP53 defects. Notably, in our cohort the NOTCH1 mutation predominated in the patients harboring truncating TP53 mutations localized in a C-terminal part of the TP53 gene behind the DNA-binding domain (P = 0.0128). Moreover, in one of the NOTCH1-TP53-mutated patients the analysis of separated cancer cells revealed a simultaneous presence of NOTCH1 mutation and TP53 in-frame deletion in the same CLL cell. In contrast, in the other examined NOTCH1-TP53-mutated patient the concurrent NOTCH1 mutation and TP53 missense substitution (with presumed negative impact on patient prognosis) were found in different CLL cells. Conclusions The parallel presence of NOTCH1 hotspot mutation might be detected in a significant proportion of TP53-mutated patients and it seems to be associated with less prognostic unfavorable TP53 mutations. Nevertheless, these preliminary data should be further confirmed in a large cohort of patients. This study was supported by projects VaVPI MSMT CR CZ.1.05/1.1.00/02.0068 of CEITEC, IGA MZ CR NT13493-4/2012, NT13519-4/2012 and CZ.1.07/2.3.00/30.0009. Disclosures Brychtova: Roche: Travel grants Other. Doubek:Roche: Travel grants Other.

scholarly journals Impact of Treatment Facility Chracteristics on Patient (Pt) Outcomes in Acute Myeloid Leukemia (AML) Using Data from the National Cancer Database (NCDB)

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 22-22
Author(s):  
Allison Taylor ◽  
Kimberley Doucette ◽  
Bryan Chan ◽  
Xiaoyang Ma ◽  
Jaeil Ahn ◽  
...  
Keyword(s):  
Overall Survival ◽  
Hazard Analysis ◽  
Treatment Options ◽  
Academic Research ◽  
High Volume ◽  
Rank Test ◽  
Rural Residence ◽  
Integrated Network ◽  
Kaplan Meier ◽  
Significant Difference

Introduction The literature suggests a widespread reduction in the availability and accessibility of newer treatment options among marginalized groups in AML. Studies from large national databases point to lower socio-economic status, Hispanic and African American race, Medicare or no insurance, being unmarried, treatment at non-academic centers, and rural residence as negatively impacting overall survival (OS) and rates of chemotherapy utilization in AML patients (Patel et al. 2015, Jaco et al. 2017, Bhatt et al. 2018, Master et al. 2016). We hypothesized that facility affiliation and pt volume would also have important effects on time to treatment (TTT) and OS in AML, even when these socioeconomic disparities were accounted for. Methods For this retrospective analysis, we used NCDB data that included 124,988 pts over the age of 18 with AML between the years 2004-2016. Variables analyzed included facility types described as community cancer programs (CP), comprehensive community cancer programs (CCP), academic/research center cancer programs (AC) and integrated network cancer programs (IN), and volume of facilities defined as high volume (HV) and low volume (LV). HV facilities had case volumes of ≥ 99th percentile and all other facilities were classified as LV. Multivariate analyses (MVA) included demographic and socioeconomic covariables. We used Cox proportional hazard analysis for both TTT and OS MVA. The Kaplan-Meier method was used to estimate median TTT and OS, and the log rank test used to compare TTT and OS across predictor variables. Results The median age of AML patients was 63 yrs (range 18-90) with 54% males, and 86% Caucasian. Five percent of patients were treated at CP, 30% at CCP, 44% at AC, and 10% at IN. 21% at HV facilities and 79% at LV facilities. Median TTT in days at CP facilities was 7, compared to 5 days in CCP and AC facilities versus 4 days at IN (p&lt;0.0001). TTT was 5 days at HV facilities versus 4 days at LV facilities (p&lt;0.0001). Kaplan-Meier curves showed that TTT was similar between HV and LV facilities(figure 1). The median OS was 3.25 months in CP compared to 4.34 months at CCP, 5.06 months at IN and 9.53 months at AC (p&lt;0.0001). For facility volume, the median OS was 13.11 months in HV facilities compared to 6.93 months in LV facilities (p&lt;0.0001). When sex, race, age, Hispanic Origin, education, urban/rural residence, Charlson-Deyo Comorbidity score and Great Circle Distance were adjusted for in MVA (table 1), the OS was higher in AC versus CP facilities (hazard ratio [HR] of 0.90 (0.87-0.93, p&lt;0.0001), and there was no statistically significant difference with comparison of other facility types to CP. Similarly, there was a lower OS at LV versus HV facilities with a HR of 1.14 (1.12-1.16, p&lt;0.0001). CCP facilities had a shorter TTT compared to CP with a HR of 1.21 (1.17-1.26, p&lt;0.0001). AC had a shorter TTT than CP with a HR of 1.17 (1.13-1.22, p&lt;0.0001), and IN had a shorter TTT compared to CP with a HR of 1.29 (1.24-1.34, p&lt;0.0001). Additionally, TTT in the MVA for facility volume was shorter in LV facilities compared to HV facilities with HR of 1.05 (1.04-1.07, p&lt;0.0001) [table 1]. Conclusion When adjusting for various socioeconomic factors, we found that TTT was longest in CP compared to CCP, AC, and IN. Treatment at a LV facility resulted in a decreased overall survival. LV facilities may be less familiar with treatment regimens for AML, less likely to use novel treatment options, and be less familiar with the disease. We showed that treatment at an AC compared to CP, CCP and IN facilities improved survival. Given poor outcomes for AML, these results show the importance of going to AC and HV facilities with more experience in treating AML for improved outcomes. Disclosures Lai: Astellas: Speakers Bureau; Jazz: Speakers Bureau; Abbvie: Consultancy; Agios: Consultancy; Macrogenics: Consultancy.

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