Determine the impact of hybrid capture-based comprehensive genomic profiling (CGP) on the treatment strategies in patients with solid tumors: A national, multicenter, retrospective study.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e13646-e13646
Author(s):  
Umut Disel ◽  
Fatih Kose ◽  
Ahmet Bilici ◽  
Mustafa Özgüroğlu ◽  
Sezer Saglam ◽  
...  
Keyword(s):  
Solid Tumors ◽  
Treatment Strategies ◽  
Treatment Decision ◽  
Final Analysis ◽  
Diagnostic Methods ◽  
Driver Mutations ◽  
Genomic Profiling ◽  
Hybrid Capture ◽  
Comprehensive Genomic Profiling ◽  
The Impact

e13646 Background: Most of the frequent cancers present a large number of very rare targetable genomic alterations. Moreover, some oncogenic drivers are shared across several diseases, and their targeting could improve outcome. We think that testing a large number of genes across all tumor types could improve outcomes in patients with “hard-to-treat” advanced cancers. The most important factor for the cancer patient to benefit from precision medicine therapy is the detection of the targeted driver mutations. The objective of this study is to determine clinical advantages of hybrid capture based comprehensive genomic profiling over classical diagnostic methods in the treatment strategies of patients with advanced stage diverse solid tumors in Turkey. Methods: This study was designed as a national, multicenter, descriptive, non-drug, retrospective cohort study. Study data were collected from medical files of patients. Besides, a survey was conducted to investigate the impact of CGP results on the treatment decisions of the clinicians. Results: The study included the data of 118 patients (55; %46.6 female, 63; %53.4 male). The mean period between the diagnosis and CGP analysis was 748 days. For either due to progression (97; 75.2%) or intolerance to therapy (12; 9.3%), the treatment of some cases was discontinued after CGP analysis. The results of the electronic survey for the clinicians indicated that the 57;48.3% of the clinicians change their treatment approach based on the results of the CGP analysis, of these 24; 42.1% preferred on-label treatments,3; 5.3% clinical trials and the 30; 52.6% preferred off-label treatments. 59;69.8% of the clinicians declared that their patients can reach to the revised treatment. 48;42.1% of the clinicians expressed that CGP support was very important in the last treatment decision. This is the interim descriptive statistics of the study. Conclusions: This is the preliminary results of the study. Conclusions will be done after the final analysis of the study

The impact of comprehensive genomic profiling in the management of patients with metastatic solid tumors in a developing country.

2016 ◽  
Vol 34 (15_suppl) ◽  
pp. e18038-e18038
Author(s):  
Pablo M. Barrios ◽  
Marcio Debiasi ◽  
Carolina Cauduro ◽  
Fábio Herrmann ◽  
Gabriela Marchese ◽  
...  
Keyword(s):  
Solid Tumors ◽  
Developing Country ◽  
Genomic Profiling ◽  
Comprehensive Genomic Profiling ◽  
The Impact

scholarly journals Comprehensive genomic profiling of 30,000 consecutive solid tumors

2020 ◽  
Author(s):  
Scott A. Tomlins ◽  
Daniel H. Hovelson ◽  
Jennifer M. Suga ◽  
Daniel M. Anderson ◽  
Han A. Koh ◽  
...  
Keyword(s):  
Solid Tumors ◽  
Real World ◽  
Tumor Tissue ◽  
Tissue Sample ◽  
Treatment Selection ◽  
Genomic Profiling ◽  
Tissue Samples ◽  
Comprehensive Genomic Profiling ◽  
Prostate Carcinomas ◽  
The Impact

AbstractPurposeTissue-based comprehensive genomic profiling (CGP) is increasingly utilized for treatment selection in patients with advanced solid tumors, however real-world tissue availability may limit widespread implementation. Here we established real-world CGP tissue availability and assessed CGP performance on consecutively received samples.Patients and MethodPost-hoc, non-prespecified analysis of 32,048 consecutive tumor tissue samples received for StrataNGS, a multiplex PCR based-CGP (PCR-CGP) test, as part of an ongoing observational trial (NCT03061305). Tumor tissue sample characteristics and PCR-CGP performance were assessed across all tested tumor samples, including exception samples not meeting minimum input requirements (<20% tumor content [TC], <2mm2 tumor surface area [TSA], DNA or RNA yield <1ng/ul, or specimen age >5yrs). Tests reporting at least one prioritized alteration or meeting all sequencing QC metrics (and ≥20% TC) were considered successful. For prostate carcinoma and lung adenocarcinoma, tests reporting at least one actionable/informative alteration or those meeting all sequencing QC metrics (and ≥20% TC) were considered actionable.ResultsPCR-CGP was attempted in 31,165 of 32,048 (97.2%) consecutively received solid tumor tissue samples. Among the 31,165 tested samples, 10.7% had low (<20%) tumor content (TC) and 58.4% were small (<25mm2 TSA), highlighting the challenging nature of samples received for CGP. Of the 31,101 samples evaluable for input requirements, 8,079 (26.0%) were exceptions not meeting requirements. However, 94.2% of the 31,101 tested samples were successfully reported, including 80.6% of exception samples. Importantly, 80.6% of 1,344 tested prostate carcinomas and 87.8% of 1,144 tested lung adenocarcinomas yielded results informing treatment selection.ConclusionMost real-world tumor tissue samples from patients with advanced cancer desiring CGP are limited, requiring optimized CGP approaches to produce meaningful results. An optimized PCR-CGP test, coupled with an inclusive exception testing policy, delivered reportable results for >94% of samples, potentially expanding the proportion of CGP-testable patients, and thus the impact of biomarker-guided targeted and immunotherapies.

scholarly journals Systematic Literature Review on Burden of Clostridioides difficile Infection in India

2021 ◽  
Vol 14 ◽  
pp. 2632010X2110138
Author(s):  
Canna J Ghia ◽  
Shaumil Waghela ◽  
Gautam S Rambhad
Keyword(s):  
Risk Factors ◽  
Multiple Testing ◽  
Final Analysis ◽  
Antibiotic Usage ◽  
Diagnostic Methods ◽  
North India ◽  
Enzyme Linked Immunosorbent Assay ◽  
Chi Square ◽  
Clostridioides Difficile ◽  
The Impact

Background: Owing to limited diagnostic facilities and surveillance protocols, there is a paucity on the prevalence data of Clostridioides difficile infections (CDIs) in developing countries such as India. Objective: The aims of these studies are (1) to determine the prevalence of CDI in India, (2) to understand the risk factors of CDI, and (3) to determine the impact of different diagnostic methods on reported CDI rates. Method: A systematic literature search was conducted using PubMed and Google Scholar database to identify Indian studies reporting the prevalence of CDI. A total of 31 studies, published between 1990 and 2020 were included in the final analysis. A chi-square test was used to determine statistically significant association between prevalence rates, accuracy of different diagnosis methods, and antibiotic usage rates of CDI. Results: The prevalence of CDI was in the range of 3.4% to 18%, and the difference between regional prevalence of CDI was statistically significant ( P < .001). The use of antibiotics, hospital stay, comorbidities, recent surgery, and the use of proton-pump inhibitors was considered as risk factors for the development of CDI. Compared to other regions, the rate of antibiotic usage was significantly higher in North India ( P < .001). Among different diagnostic methods, C. difficile detection was significantly higher with enzyme-linked immunosorbent assay (18.02%) versus other multiple testing methods used ( P < .001). Conclusion: There is a significant burden of CDI across the country. Further surveillance studies are required to monitor changes in prevalence of CDI, risk factors, and accuracy of diagnosis methods for a better understanding of the disease burden in India.

scholarly journals Identifying Opportunities and Challenges for Patients With Sarcoma as a Result of Comprehensive Genomic Profiling of Sarcoma Specimens

2020 ◽  
pp. 176-182 ◽  
Author(s):  
Margaret A. Hay ◽  
Eric A. Severson ◽  
Vincent A. Miller ◽  
David A. Liebner ◽  
Jo-Anne Vergilio ◽  
...  
Keyword(s):  
Decision Making ◽  
Bone Biopsy ◽  
Clinical Care ◽  
Soft Tissue Sarcomas ◽  
Treatment Decision ◽  
Progression Free Survival ◽  
Tumor Location ◽  
Treatment Selection ◽  
Genomic Profiling ◽  
Comprehensive Genomic Profiling

PURPOSE Comprehensive genomic profiling (CGP) of sarcomas is rapidly being integrated into routine clinical care to help refine diagnosis and prognosis and determine treatment. However, little is known about barriers to successful CGP or its clinical utility in sarcoma. We set out to determine whether CGP alters physician treatment decision-making, and whether sarcoma subtypes influence the frequency of successful technical performance of CGP. METHODS A single-institution study evaluated profiling outcomes of 392 samples from patients with sarcoma, using a commercially available CGP panel. Of this group, 34 patients were evaluated prospectively (Decision Impact Trial) to evaluate the utility of CGP in physician decision-making. All cases were retrospectively analyzed to identify causes of CGP failure. RESULTS CGP successfully interrogated 75.3% (n = 295 of 392) of patients with sarcoma. Bone sarcomas had lower passing rates at 65.3% (n = 32 of 49) compared with soft tissue sarcomas at 76.7% (n = 263 of 343; P = .0008). Biopsy location also correlated with profiling efficiency. Bone biopsy specimens had a 52.8% (n = 19 of 36) passing rate versus lung (61.1%; n = 33 of 54) and abdomen (80.1%; n = 109 of 136) specimens. CGP altered physician treatment selection in 25% of evaluable patients (n = 7 of 28) and was associated with improved progression-free survival. CONCLUSION To our knowledge, this is the largest technical evaluation of the performance of CGP in sarcoma. CGP was effectively performed in the vast majority of sarcoma samples and altered physician treatment selection. Tumor location and tissue subtype were key determinants of profiling success and associated with preanalytic variables that affect DNA and RNA quality. These results support standardized biopsy collection protocols to improve profiling outcomes.

Targeted therapy for HER2 driven colorectal cancer.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 3583-3583 ◽  
Author(s):  
Jeffrey S. Ross ◽  
Siraj Mahamed Ali ◽  
Julia Andrea Elvin ◽  
Alexa Betzig Schrock ◽  
James Suh ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Clinical Trials ◽  
Genomic Profiling ◽  
Hybrid Capture ◽  
Mutational Burden ◽  
Precision Therapy ◽  
Comprehensive Genomic Profiling ◽  
Tumor Mutational Burden ◽  
Upper Gastrointestinal ◽  
Colonic Adenocarcinomas

3583 Background: ERBB2 ( HER2) genomic alterations (GA) are evolving therapy taregets in metastatc coorectal cancer (mCRC). Methods: Hybrid capture based comprehensive genomic profiling (CGP) was performed on 8874 (9.6%) mCRC including both colonic adenocarcinomas (7587 cases; 85%) and rectal adenocarcinomas (1287 cases, 15%) Tumor mutational burden (TMB) was calculated from a minimum of 1.2 Mb of sequenced DNA. Results: ERBB2 amplifications or a short variant (SV) alterations or both were found in 433 (4.9%) of the total mCRC. 195 (45%) of the ERBB2 positive mCRC were female and 238 (55%) were male. Median age was 54 years (range 22 to 88 years). The most frequently co-altered genes were SV GA in TP53 (82%), APC (70%), KRAS (26%), SMAD4 (15%) and PIK3CA (13%). Clinically relevant GA significantly under-represented in ERBB2-altered CRC included significantly reduced GA in KRAS at 26% (p = 0.001) and BRAF at 4% (p = 0.003) as well as other kinases at 1% including EGFR, KIT, MET and RET. The frequency of TMB at > 10 mut/Mb (p < 0.0001), but at > 20 mut/Mb mCRC cases demonstrated virtually the same results regardless to ERBB2 status at a frequency of x%. The overall ERBB2 GA frequency at 5.3% in rectal mCRC is slightly higher than that seen in colonic mCRC at 4.9%, (p = 0.36). The frequency of TMB > 10 mut/Mb in ERBB2 WT mCRC is greater in the colonic mCRC than the rectal mCRC (p < 0.0001 for both comparisons). When > 20 mut/Mb is used as the cut-off, the greater frequency of TMB in colonic mCRC versus rectal mCRC remains significant (p < 0.0001). When the ERBB2altered mCRC cases are evaluated, the greater frequency of TMB > 10 mu/Mb in colonic mCRC versus rectal mCRC remains significant (p = 0.009), but the greater frequency in colonic verses rectal mCRC at the > 20 mut/Mb is not significant (p = 0.37). Conclusions: Although lower than observed in breast and upper gastrointestinal carcinomas where anti-HER2 therapies are approved indications, the frequency of ERBB2 GA in CRC at 4.9% is significant. Importantly, nearly half of CRC ERBB2 alterations are SVs, not detectable by routine IHC and FISH testing. However, the success of anti-HER2 therapies shown here and progress in on-going clinical trials indicates that targeting ERBB2 has potential to become an approved advance in precision therapy for mCRC patients.

PD-L1 genomic alterations (GA) in solid tumors and hematologic malignancies: A comprehensive genomic profiling (CGP) study.

2018 ◽  
Vol 36 (15_suppl) ◽  
pp. 12092-12092
Author(s):  
Laurie M. Gay ◽  
David Fabrizio ◽  
Garrett Michael Frampton ◽  
Lee A. Albacker ◽  
Ethan Sokol ◽  
...  
Keyword(s):  
Solid Tumors ◽  
Hematologic Malignancies ◽  
Genomic Profiling ◽  
Genomic Alterations ◽  
Comprehensive Genomic Profiling

Adenocarcinoma (ACB), urothelial carcinoma (UCB) and squamous cell carcinoma (SCCB) of the bladder: A Comprehensive Genomic Profiling (CGP) Study.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 4533-4533 ◽  
Author(s):  
Joseph Jacob ◽  
Gennady Bratslavsky ◽  
Oleg Shapiro ◽  
Nick Liu ◽  
Elizabeth Kate Ferry ◽  
...  
Keyword(s):  
High Status ◽  
Genomic Profiling ◽  
Dna Repair Genes ◽  
Genomic Profile ◽  
Hybrid Capture ◽  
Mutational Burden ◽  
Comprehensive Genomic Profiling ◽  
Tumor Mutational Burden ◽  
Tumor Types ◽  
Repair Genes

4533 Background: We performed a CGP to compare the genomic alterations (GA) in ABC, UBC and SCCB. Methods: 143 cases of ACB, 2,142 cases of UCB and 83 cases of SCCB were subjected to CGP using a hybrid-capture based assay. Tumor mutational burden (TMB) was determined on 1.1 Mbp of sequenced DNA and microsatellite instability (MSI) was determined on 114 loci. PD-L1 expression was determined by IHC. Results: ABC patients were younger and more often female than UBC and SCCB (P < 0.0001). UBC and SCCB had a higher GA/tumor than ABC (P = 0.01). Un-targetable GA were similar in all 3 groups involving TP53 and KRAS. APC GA were more frequent in ABC whereas TERT, CDKN2A/B and DNA-repair genes ( ARID1A and KDM6A) more frequently altered in UBC and SCCB. Targetable MTOR pathway GA ( PIK3CA, TSC1, PTEN) were more frequent in UBC and SCCB as were targetable kinase alterations ( FGFR3 and ERBB2). The UBC and SCCB had a significantly higher TMB than ABC (P < 0.0001) including mean TMB and TMB > 20 mut/Mb (P < 0.0001). CD274 (PD-L1) was amplified more frequently in SCCB than ACB or UBC (P < 0.0001). MSI high status was very uncommon in all tumor types. Conclusions: Deep sequencing reveals that ABC features a widely different genomic profile from UBC and SCCB. UBC has the highest frequencies of targetable kinase GA and high TMB. SCCB has the highest frequencies of IO efficacy predicting biomarkers including mean TMB and PD-L1 amp. Nonetheless, ABC does feature potential kinase targets such as FGFR3 and ERBB2. [Table: see text]

Analysis of HER2 mutant bladder urothelial carcinomas reveals unique mutational signature.

2019 ◽  
Vol 37 (7_suppl) ◽  
pp. 460-460
Author(s):  
Luke Juckett ◽  
Russell Madison ◽  
Jon Chung ◽  
Alexa Betzig Schrock ◽  
Brian Alexander ◽  
...  
Keyword(s):  
Transitional Cell ◽  
Large Set ◽  
Genomic Profiling ◽  
Hybrid Capture ◽  
Mutational Signature ◽  
Mutational Burden ◽  
Urothelial Carcinomas ◽  
Comprehensive Genomic Profiling ◽  
Tumor Mutational Burden ◽  
Cancer Tumor

460 Background: Early work has described the presence of HER2 alterations in metastatic urothelial carcinomas (UC), particularly the micropapillary urothelial carcinoma (MPUC) subtype. We reviewed the genomic profiles of a large set of UC cases to further characterize HER2 altered UCs and how such alterations would suggest benefit from the expanding array of anit-HER2 therapeutics. Methods: Tissue from 2,150 UCs were assayed using hybrid capture-based comprehensive genomic profiling (CGP) of 186 to 315 genes plus introns from 14 to 28 genes commonly arranged in cancer. Tumor mutational burden (TMB) was determined on up to 1.1 Mbp of sequenced DNA. Results: Within the UC dataset 74.6% of cases were male (1603/2150), with a median TMB of 7 mut/Mb. 383 genomic alterations (GA) of HER2 were identified in 15.5% (334/2150) of cases which exhibited a median TMB of 8.7 mut/Mb (p < 1E-5) vs patients with wildtype HER2, median TMB of 7 mut/Mb. The most frequent HER2 alterations were amplification HER2amp (45.7%, 175/383), S310F (19.8%, 76/383), and S310Y (7/6%, 29/383). Patients harbouring a HER2amp, S310 (n = 105) exhibited a median TMB of 8.7 and 12.2 mut/Mb, respectively. 42 patients presented with multiple ( > 1) HER2 GA and exhibited a median TMB of 11.3 mut/Mb (p < 0.1) vs patients with single HER2 GA, median TMB of 12.3 mut/Mb. Of patients with multiple HER2 alterations, 57% (24/42) harbored a HER2amp. The most common co-occuring HER2 alteration pair was an amplification and extracellular S310X alteration (38.1%, 16/42). Of these 16, the median TMB was 19.5 mut/Mb (average 22.7 mut/Mb). Morphological assessments were performed on the 24 cases harbouring a HER2amp and an additional HER2 GA. 8 cases displayed MPUC features 44.4% (8/18; 6 cases histology unavailable); of these MPUC cases, 75% (6/8), harboured a HER2 amp and S310 extracellular mutation. Conclusions: CGP of bladder urothelial (transitional cell) carcinomas reveals subclasses of HER2 altered cases. Drawing on recent advances in targeting HER2 alterations in breast cancer, dual HER2 blockade (e.g. combinations of mAB/TKI/mAB+ADC) may be needed for HER2amp cases. For cases with both HER2amp and S310 GA, neratinib monotherapy may be the agent of choice and thus may be effective in MPUC.

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