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Article ; Online: High-Grade, Nonsarcomatoid Chromophobe Renal Cell Carcinoma: A Series of 22 Cases With Novel Molecular Features on a Subset.

Baraban, Ezra G / Elias, Roy / Lin, Ming-Tseh / Ged, Yasser / Zhu, Jing / Pallavajjala, Aparna / Singla, Nirmish / Lotan, Tamara L / Argani, Pedram / Eshleman, James R / Epstein, Jonathan I

Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc

2024 Volume 37, Issue 5, Page(s) 100472

Abstract: Chromophobe renal cell carcinoma (ChRCC) is the third most common subtype of renal cell carcinoma and typically exhibits indolent behavior, though a rare subset can exhibit high-grade morphologic features and is associated with a poor prognosis. Although ...

Abstract	Chromophobe renal cell carcinoma (ChRCC) is the third most common subtype of renal cell carcinoma and typically exhibits indolent behavior, though a rare subset can exhibit high-grade morphologic features and is associated with a poor prognosis. Although there are limited data on the molecular characteristics of metastatic and sarcomatoid ChRCC, the molecular features of high-grade, nonsarcomatoid ChRCC remain unexplored. Herein, we characterize 22 cases of ChRCC with high-grade, nonsarcomatoid components. High-grade ChRCC frequently demonstrated advanced stage at diagnosis (64% ≥pT3a or N1), with regions of extrarenal extension, nodal metastases, and vascular invasion consisting solely of high-grade ChRCC morphologically. We performed spatially guided panel-based DNA sequencing on 11 cases comparing high-grade and low-grade regions (n = 22 samples). We identified recurring somatic alterations emblematic of ChRCC, including deletions of chromosomes 1, 2, 6, 10, 13, 17, and 21 in 91% (10/11) of cases and recurring mutations in TP53 (81.8%, n = 9/11) and PTEN (36.4%, n = 4/11). Notably, although PTEN and TP53 alterations were found in both high-grade and low-grade regions, private mutations were identified in 3 cases, indicating convergent evolution. Finally, we identified recurring RB1 mutations in 27% (n = 3) of high-grade regions leading to selective protein loss by immunohistochemistry not observed in adjacent low-grade regions. This finding was confirmed in The Cancer Genome Atlas cohort where 2 of 66 cases contained RB1 mutations and demonstrated unequivocal high-grade, nonsarcomatoid morphology. We also detected multiple chromosomal gains confined to the high-grade regions, consistent with imbalanced chromosome duplication. These findings broaden our understanding of the molecular pathogenesis of ChRCC and suggest that subclonal RB1 mutations can drive the evolution to high-grade, nonsarcomatoid ChRCC.
Language	English
Publishing date	2024-03-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	645073-8
ISSN	1530-0285 ; 0893-3952
ISSN (online)	1530-0285
ISSN	0893-3952
DOI	10.1016/j.modpat.2024.100472
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Zs.A 2450: Show issues

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Article: HER2 amplification by next-generation sequencing to identify HER2-positive invasive breast cancer with negative HER2 immunohistochemistry.

Morsberger, Laura / Pallavajjala, Aparna / Long, Patty / Hardy, Melanie / Park, Rebecca / Parish, Rebecca / Nozari, Azin / Zou, Ying S

Cancer cell international

2022 Volume 22, Issue 1, Page(s) 350

Abstract: Background: Human epidermal growth factor receptor 2 (HER2) positive breast carcinomas due to HER2 amplification are associated with aggressive behavior and a poor prognosis. Anti-HER2-targeted therapies are widely used to treat HER2-positive breast ... ...

Abstract	Background: Human epidermal growth factor receptor 2 (HER2) positive breast carcinomas due to HER2 amplification are associated with aggressive behavior and a poor prognosis. Anti-HER2-targeted therapies are widely used to treat HER2-positive breast carcinomas with excellent outcomes. Accurate identification of HER2 amplification status in breast carcinomas is of important diagnostic and treatment value. Currently, HER2 amplification status is routinely determined by immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH) testing. This study will review our past HER2 data to determine and characterize discordant results between HER2 IHC and FISH. It will also determine a potential impact of HER2 amplification status by next-generation sequencing (NGS) on these patients. Methods: We reviewed a total of 4884 breast carcinomas with coexisting HER2 IHC and HER2 FISH performed at our institution from 2010 to 2022. 57 cases also had a Next-Generation-Sequencing-based (NGS) gene panel performed. Given the advances in biostatic analysis pipelines, NGS methods were utilized to provide results on HER2 amplification status along with somatic mutations. Results: While the majority (ranging from 98.5% with IHC score of 0 and 93.1% with IHC score of 1 +) of 4884 breast carcinomas had concordant results from HER2 IHC and HER2 FISH testing, a small percentage of patients (ranging from 1.5% in those with IHC score of 0, to 6.9% with IHC score of 1 +) had discordant results, with negative HER2 IHC and positive HER2 FISH results. These patients could be reported as HER2-negative breast carcinomas if only HER2 IHC testing has been performed according to a current cost-effective HER2 test strategy. 57 patients had HER2 amplification status determined by NGS, and all patients had concordant results between HER2 NGS and FISH tests. A HER2-amplified breast carcinoma by NGS had a negative IHC and a positive HER2 FISH result. This case was classified as a HER2-positive breast carcinoma, had anti-HER2-targeted therapy, and achieved a complete clinical response. Conclusions: A small percentage of HER2-positive breast carcinomas are unidentified because of a negative HER2 IHC based on our current cost-effective HER2 test strategy. It is not feasible and affordable in routine clinical practice to perform HER2 FISH for the cases with negative HER2 IHC (IHC score 0 and 1 +). Therefore, NGS assays capable of simultaneously detecting both somatic mutations and HER2 amplification could provide a more comprehensive genetic profiling for breast carcinomas in a clinical setting. Identification of HER2 amplification by NGS in HER2-positive breast carcinomas with negative HER2 IHC results is important since these cases are concealed by our current cost-effective HER2 test strategy with IHC first (for all cases) and FISH reflex (only for cases with IHC score of 2 +), and would offer the opportunity for potentially beneficial anti-HER2-targeted therapies for these patients.
Language	English
Publishing date	2022-11-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2091573-1
ISSN	1475-2867
ISSN	1475-2867
DOI	10.1186/s12935-022-02761-1
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Article ; Online: Optimizing Insertion and Deletion Detection Using Next-Generation Sequencing in the Clinical Laboratory.

Craven, Kelly E / Fischer, Catherine G / Jiang, LiQun / Pallavajjala, Aparna / Lin, Ming-Tseh / Eshleman, James R

The Journal of molecular diagnostics : JMD

2022 Volume 24, Issue 12, Page(s) 1217–1231

Abstract: Detection of insertions and deletions (InDels) by short-read next-generation sequencing (NGS) technology can be challenging because of frequent misaligned reads. A systematic analysis of short InDels (1 to 30 bases) and fms-related receptor tyrosine ... ...

Abstract	Detection of insertions and deletions (InDels) by short-read next-generation sequencing (NGS) technology can be challenging because of frequent misaligned reads. A systematic analysis of short InDels (1 to 30 bases) and fms-related receptor tyrosine kinase 3 (FLT3) internal tandem duplications (ITDs; 6 to 183 bases) from 46 clinical cases of solid or hematologic malignancy processed with a clinical NGS assay identified misaligned reads in every case, ranging from 3% to 100% of reads with the InDel showing mismapped bases. Mismaps also increased with InDel size. As a consequence, the clinical NGS bioinformatics pipeline undercalled the variant allele frequency by 1% to 84%, incorrectly called simultaneous single-base substitutions along with InDels, or did not report an FLT3 ITD that had been detected by capillary electrophoresis. To improve the ability of the pipeline to better detect and quantify InDels, we utilized a software program called Assembly-Based ReAligner (ABRA2) to more accurately remap reads. ABRA2 was able to correct 41% to 100% of the reads with mismapped bases and led to absolute increases in the variant allele frequency from 1% to 61% along with correction of all of the single-base substitutions except for two cases. ABRA2 could also detect multiple FLT3 ITD clones except for one 183-base ITD. Our analysis has found that ABRA2 performs well on short InDels as well as FLT3 ITDs that are <100 bases.
MeSH term(s)	Humans ; Computational Biology/methods ; fms-Like Tyrosine Kinase 3/genetics ; High-Throughput Nucleotide Sequencing/methods ; INDEL Mutation ; Leukemia, Myeloid, Acute/genetics ; Software
Chemical Substances	fms-Like Tyrosine Kinase 3 (EC 2.7.10.1)
Language	English
Publishing date	2022-09-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2022.08.006
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Zs.A 5146: Show issues

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Article ; Online: Cell-free DNA measurable residual disease as a predictor of postallogeneic hematopoietic cell transplant outcomes.

Pasca, Sergiu / Guo, Matthew Z / Wang, Shiyu / Stokvis, Kristin / Shedeck, Audra / Pallavajjala, Aparna / Shams, Cynthia / Pallavajjala, Roshni / DeZern, Amy E / Varadhan, Ravi / Gocke, Christopher D / Jones, Richard J / Gondek, Lukasz P

Blood advances

2023 Volume 7, Issue 16, Page(s) 4660–4670

Abstract: The measurable residual disease (MRD) assessment provides an attractive predictor of allogeneic hematopoietic cell transplnat (alloHCT) outcomes. Cell-free DNA (cfDNA) has been applied to diagnosis, early detection, and disease burden monitoring in ... ...

Abstract	The measurable residual disease (MRD) assessment provides an attractive predictor of allogeneic hematopoietic cell transplnat (alloHCT) outcomes. Cell-free DNA (cfDNA) has been applied to diagnosis, early detection, and disease burden monitoring in various tumors, but its utility as an MRD test in myeloid malignancies has not been systematically evaluated. We sought to determine the differential sensitivity between bone marrow (BM) and cfDNA MRD and to assess the effect of cfDNA MRD on alloHCT outcomes. The technical and clinical validation cohorts, including 82 patients participating in clinical trials (Bone Marrow Transplant Clinical Trials Network-0201 and 0402), were used. Ultradeep error-corrected targeted sequencing was performed on plasma and BM-derived DNA. We demonstrated that 94.6% (range, 93.9-95.3) of cfDNA was derived from hematopoietic tissue. The mutant allele fraction was congruent between BM and cfDNA (rho = 0.8; P < .0001); however, cfDNA seemed to be more sensitive in detecting clones with a variant allele frequency (VAF) of <0.26%. cfDNA-MRD clearance by day 90 after alloHCT (D90) was associated with improved relapse-free survival (RFS, median survival not reached vs 5.5 months; P < .0001) and overall survival (OS, median survival not reached vs 7.3 months; P < .0001) when compared with patients with persistent MRD. Irrespective of pre-alloHCT MRD, D90 cfDNA MRD was associated with inferior 2-year OS (16.7% vs 84.8%; P < .0001) and RFS (16.7% vs 80.7%; P < .0001). cfDNA seems to be an accurate, minimally invasive alternative to BM aspirates in MRD assessment and confers important prognostic implications in patients with myeloid malignancies undergoing alloHCT.
MeSH term(s)	Humans ; Hematopoietic Stem Cell Transplantation ; Alleles ; Allogeneic Cells ; Cell-Free Nucleic Acids ; Clone Cells ; Neoplasm, Residual/diagnosis
Chemical Substances	Cell-Free Nucleic Acids
Language	English
Publishing date	2023-05-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2915908-8
ISSN	2473-9537 ; 2473-9529
ISSN (online)	2473-9537
ISSN	2473-9529
DOI	10.1182/bloodadvances.2023010416
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Zs.A 7153: Show issues

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Article ; Online: Validation of Long Mononucleotide Repeat Markers for Detection of Microsatellite Instability.

Lin, John H / Chen, Suping / Pallavajjala, Aparna / Guedes, Liana B / Lotan, Tamara L / Bacher, Jeffery W / Eshleman, James R

The Journal of molecular diagnostics : JMD

2021 Volume 24, Issue 2, Page(s) 144–157

Abstract: Mismatch repair deficiency (dMMR) predicts response to immune checkpoint inhibitor therapy in solid tumors. Long mononucleotide repeat (LMR) markers may improve the interpretation of microsatellite instability (MSI) assays. Our cohorts included mismatch ... ...

Abstract	Mismatch repair deficiency (dMMR) predicts response to immune checkpoint inhibitor therapy in solid tumors. Long mononucleotide repeat (LMR) markers may improve the interpretation of microsatellite instability (MSI) assays. Our cohorts included mismatch repair (MMR) proficient and dMMR colorectal cancer (CRC) samples, MMR proficient and dMMR endometrial cancer (EC) samples, dMMR prostate cancer samples, MSI-high (MSI-H) samples of other cancer types, and MSI-low (MSI-L) samples of various cancer types. MMR status was determined by immunohistochemical staining and/or MSI Analysis System Version 1.2 (V1.2). The sensitivity and specificity of the LMR MSI panel for dMMR detection were both 100% in CRC. The sensitivity values of the MSI V1.2 and LMR MSI panels in EC were 88% and 98%, respectively, and the specificity values were both 100%. The sensitivity of the LMR panel was 75% in dMMR prostate cancer detected by immunohistochemistry. The 22 samples of other cancer types that were previously classified as MSI-H were also classified as MSI-H using the LMR MSI panel. For the 12 samples that were previously classified as MSI-L, 1 sample was classified as microsatellite stable using the LMR MSI panel, 8 as MSI-L, and 3 as MSI-H. The LMR MSI panel showed high concordance to the MSI V1.2 panel in CRC and greater sensitivity in EC. The LMR MSI panel improves dMMR detection in noncolorectal cancers.
MeSH term(s)	Colorectal Neoplasms/diagnosis ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/pathology ; DNA Mismatch Repair/genetics ; Humans ; Immunohistochemistry ; Male ; Microsatellite Instability ; Sensitivity and Specificity
Language	English
Publishing date	2021-12-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2021.10.011
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Zs.A 5146: Show issues

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Article ; Online: Identification of a novel KMT2A-SEPT14 fusion in acute myeloid leukemia.

Nguyen, Doreen / Haley, Lisa / Pallavajjala, Aparna / Gojo, Ivana / Ning, Yi

Leukemia & lymphoma

2017 Volume 59, Issue 1, Page(s) 265–267

MeSH term(s)	Acute Disease ; Aged ; Chromosomes, Human, Pair 11/genetics ; Chromosomes, Human, Pair 7/genetics ; High-Throughput Nucleotide Sequencing ; Histone-Lysine N-Methyltransferase/genetics ; Humans ; In Situ Hybridization, Fluorescence ; Karyotyping ; Leukemia, Myeloid/genetics ; Leukemia, Myeloid/pathology ; Male ; Myeloid-Lymphoid Leukemia Protein/genetics ; Oncogene Proteins, Fusion/genetics ; Septins/genetics ; Translocation, Genetic
Chemical Substances	KMT2A protein, human ; Oncogene Proteins, Fusion ; Myeloid-Lymphoid Leukemia Protein (149025-06-9) ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43) ; SEPTIN14 protein, human (EC 3.6.1.-) ; Septins (EC 3.6.1.-)
Language	English
Publishing date	2017-06-02
Publishing country	United States
Document type	Case Reports ; Letter
ZDB-ID	1042374-6
ISSN	1029-2403 ; 1042-8194
ISSN (online)	1029-2403
ISSN	1042-8194
DOI	10.1080/10428194.2017.1324163
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Zs.A 2997: Show issues

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Article ; Online: Utility of targeted next-generation sequencing assay to detect 1p/19q co-deletion in formalin-fixed paraffin-embedded glioma specimens.

Pallavajjala, Aparna / Haley, Lisa / Stinnett, Victoria / Adams, Emily / Pallavajjala, Roshni / Huang, Jialing / Morsberger, Laura / Hardy, Melanie / Long, Patty / Gocke, Christopher D / Eshleman, James R / Rodriguez, Fausto J / Zou, Ying S

Human pathology

2022 Volume 126, Page(s) 63–76

Abstract: Molecular classification of brain neoplasms is important for diagnosis, prognosis, and treatment outcome of histologically similar tumors. Oligodendroglioma is a glioma subtype characterized by 1p/19q co-deletion and IDH1/IDH2 mutations, which predict a ... ...

Abstract	Molecular classification of brain neoplasms is important for diagnosis, prognosis, and treatment outcome of histologically similar tumors. Oligodendroglioma is a glioma subtype characterized by 1p/19q co-deletion and IDH1/IDH2 mutations, which predict a good prognosis, responsiveness to therapy, and an improved overall survival compared to other adult gliomas. In a routine clinical setting, 1p/19q co-deletion is detected by interphase-FISH and SNP microarray, and somatic mutations are detected by targeted next-generation sequencing (NGS). The aim of this proof-of-principle study was to investigate the feasibility of using targeted NGS to simultaneously detect both 1p/19q co-deletion and somatic mutations. Among 247 consecutive patients with formalin-fixed paraffin-embedded brain tumors with various subtypes, NGS revealed 1p/19q co-deletion in 26 oligodendrogliomas and an IDH-wildtype astrocytoma, and partial loss across chromosomes 1p and 19q/whole-arm loss of 1p or 19q/copy neutral loss of heterozygosity in 11 nonoligodendrogliomas. For this 247 brain-tumor cohort, the overall sensitivity, specificity, and accuracy of detecting 1p/19q co-deletion by NGS in oligodendrogliomas were 96.2%, 99.6%, and 99.2%, respectively. The oligodendroglioma cohort had more mutations in IDH1/IDH2, CIC, FUBP1, and TERT, and fewer mutations in ATRX and TP53 than the nonoligodendroglioma cohort. This proof-of-concept study demonstrated that targeted NGS can simultaneously detect both 1p/19q co-deletion and somatic mutations, which can provide a more comprehensive genetic profiling for patients with gliomas using a single assay in a clinical setting.
MeSH term(s)	Brain Neoplasms/pathology ; Chromosome Aberrations ; Chromosome Deletion ; Chromosomes, Human, Pair 1/genetics ; Chromosomes, Human, Pair 19/genetics ; DNA-Binding Proteins/genetics ; Formaldehyde ; Glioma/genetics ; Glioma/pathology ; High-Throughput Nucleotide Sequencing ; Humans ; Isocitrate Dehydrogenase/genetics ; Mutation ; Oligodendroglioma/genetics ; Oligodendroglioma/pathology ; Paraffin Embedding ; RNA-Binding Proteins/genetics
Chemical Substances	DNA-Binding Proteins ; FUBP1 protein, human ; RNA-Binding Proteins ; Formaldehyde (1HG84L3525) ; Isocitrate Dehydrogenase (EC 1.1.1.41)
Language	English
Publishing date	2022-05-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	207657-3
ISSN	1532-8392 ; 0046-8177
ISSN (online)	1532-8392
ISSN	0046-8177
DOI	10.1016/j.humpath.2022.05.001
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Zs.A 722: Show issues

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Article ; Online: Clonal hematopoiesis in men living with HIV and association with subclinical atherosclerosis.

Wang, Shiyu / Pasca, Sergiu / Post, Wendy S / Langan, Susan / Pallavajjala, Aparna / Haley, Lisa / Gocke, Christopher D / Budoff, Matthew / Haberlen, Sabina / Brown, Todd T / Ambinder, Richard F / Margolick, Joseph B / Gondek, Lukasz P

AIDS (London, England)

2022 Volume 36, Issue 11, Page(s) 1521–1531

Abstract: Objectives: People with HIV (PWH) are at increased risk for premature cardiovascular disease (CVD). Clonal hematopoiesis is a common age-related condition that may be associated with increased CVD risk. The goal of this study was to determine the ... ...

Abstract	Objectives: People with HIV (PWH) are at increased risk for premature cardiovascular disease (CVD). Clonal hematopoiesis is a common age-related condition that may be associated with increased CVD risk. The goal of this study was to determine the prevalence of clonal hematopoiesis and its association with chronic inflammation and CVD in PWH. Design: Cross-sectional study utilizing archived specimens and data from 118 men (86 PWH and 32 HIV-uninfected) from the Baltimore-Washington DC center of the Multicenter AIDS Cohort Study (MACS) who had had coronary computed tomography angiography (CTA) and measurement of 34 serologic inflammatory biomarkers. Methods: Clonal hematopoiesis was assessed on peripheral blood mononuclear cells utilizing targeted error-corrected next generation sequencing (NGS) focused on 92 genes frequently mutated in hematologic malignancies. Clinical and laboratory data were obtained from the MACS database. Results: Clonal hematopoiesis with a variant allele frequency (VAF) greater than 1% was significantly more common in PWH [20/86 (23.3%)] than in HIV-uninfected men [2/32 (6.3%)] ( P = 0.035). PWH with clonal hematopoiesis (VAF > 1%) were more likely to have coronary artery stenosis of at least 50% than those without clonal hematopoiesis [6/20 (30%) vs. 6/64 (9%); P = 0.021]. Presence of clonal hematopoiesis was not significantly associated with serological inflammatory markers, except for significantly lower serum leptin levels; this was not significant after adjustment for abdominal or thigh subcutaneous fat area. Conclusion: Clonal hematopoiesis was more common in PWH and among PWH was associated with the extent of coronary artery disease. Larger studies are needed to further examine the biological and clinical consequences of clonal hematopoiesis in PWH.
MeSH term(s)	Acquired Immunodeficiency Syndrome/complications ; Atherosclerosis/complications ; Atherosclerosis/genetics ; Biomarkers ; Cohort Studies ; Coronary Stenosis ; Cross-Sectional Studies ; HIV Infections/complications ; Humans ; Leukocytes, Mononuclear ; Male
Chemical Substances	Biomarkers
Language	English
Publishing date	2022-07-21
Publishing country	England
Document type	Journal Article ; Multicenter Study ; Research Support, N.I.H., Extramural
ZDB-ID	639076-6
ISSN	1473-5571 ; 0269-9370 ; 1350-2840
ISSN (online)	1473-5571
ISSN	0269-9370 ; 1350-2840
DOI	10.1097/QAD.0000000000003280
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Zs.A 2228: Show issues

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Article ; Online: Artificial Intelligence-Assisted Serial Analysis of Clinical Cancer Genomics Data Identifies Changing Treatment Recommendations and Therapeutic Targets.

Fischer, Catherine G / Pallavajjala, Aparna / Jiang, LiQun / Anagnostou, Valsamo / Tao, Jessica / Adams, Emily / Eshleman, James R / Gocke, Christopher D / Lin, Ming-Tseh / Platz, Elizabeth A / Xian, Rena R

Clinical cancer research : an official journal of the American Association for Cancer Research

2022 Volume 28, Issue 11, Page(s) 2361–2372

Abstract: Purpose: Given the pace of predictive biomarker and targeted therapy development, it is unknown whether repeat annotation of the same next-generation sequencing data can identify additional clinically actionable targets that could be therapeutically ... ...

Abstract	Purpose: Given the pace of predictive biomarker and targeted therapy development, it is unknown whether repeat annotation of the same next-generation sequencing data can identify additional clinically actionable targets that could be therapeutically leveraged. In this study, we sought to determine the predictive yield of serial reanalysis of clinical tumor sequencing data. Experimental design: Using artificial intelligence (AI)-assisted variant annotation, we retrospectively reanalyzed sequencing data from 2,219 patients with cancer from a single academic medical center at 3-month intervals totaling 9 months in 2020. The yield of serial reanalysis was assessed by the proportion of patients with improved strength of therapeutic recommendations. Results: A total of 1,775 patients (80%) had ≥1 potentially clinically actionable mutation at baseline, including 243 (11%) patients who had an alteration targeted by an FDA-approved drug for their cancer type. By month 9, the latter increased to 458 (21%) patients mainly due to a single pan-cancer agent directed against tumors with high tumor mutation burden. Within this timeframe, 67 new therapies became available and 45 were no longer available. Variant pathogenicity classifications also changed leading to changes in treatment recommendations for 124 patients (6%). Conclusions: Serial reannotation of tumor sequencing data improved the strength of treatment recommendations (based on level of evidence) in a mixed cancer cohort and showed substantial changes in available therapies and variant classifications. These results suggest a role for repeat analysis of tumor sequencing data in clinical practice, which can be streamlined with AI support.
MeSH term(s)	Artificial Intelligence ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/therapeutic use ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Mutation ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/pathology ; Retrospective Studies
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2022-04-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-21-4061
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Article: Germline

Braunstein, Evan M / Chen, Hang / Juarez, Felicia / Yang, Fanghan / Tao, Lindsay / Makhlin, Igor / Williams, Donna M / Chaturvedi, Shruti / Pallavajjala, Aparna / Karantanos, Theodoros / Martin, Renan / Wohler, Elizabeth / Sobreira, Nara / Gocke, Christopher D / Moliterno, Alison R

Cancers

2021 Volume 13, Issue 13

Abstract: Familial cases of myeloproliferative neoplasms (MPN) are relatively common, yet few inherited risk factors have been identified. Exome sequencing of a kindred with a familial cancer syndrome characterized by both MPN and melanoma produced a germline ... ...

Abstract	Familial cases of myeloproliferative neoplasms (MPN) are relatively common, yet few inherited risk factors have been identified. Exome sequencing of a kindred with a familial cancer syndrome characterized by both MPN and melanoma produced a germline variant in the
Language	English
Publishing date	2021-06-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers13133246
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