Smriti Malasi
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View article: Figure S3 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S3 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Supplemental Figure 3: Somatic lesions targeting chromatin regulators in ASCP genomes. CNV profiles of flow sorted aneuploid populations from: A) A129 with homozygous deletion of CDKN2A and SMARCA4. The X and Y axes in the CGH plots repres…
View article: Figure S1 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S1 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Histology and IHC analyses of ASCP tissues. Hematoxylin and Eosin (H&E) staining and IHC expression of cytokeratins 5 and 6 (CK5/6), and of TP63 for five ASCP cases. Adenosquamous content is consistent with WHO histology and diagnosis.
View article: Table S1 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Table S1 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Types of ASCP Specimen
View article: Figure S7 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S7 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Whole genome CNV landscape of PDX models profiled by ATAC-seq. A) ASCPs PAX139, PAX217, and PAX265. Vertical arrows highlight CDK6 amplicons and horizontal arrows highlight CDKN2A homozygous deletions. B) PDACs PAX295, PAX297, and PAX300. …
View article: Figure S8 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S8 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
IHC analysis of RORC in ASCP PDXs and metastases. A) PAX265; B) PAX139; C) 9R liver metastases; D) Summary of RORC staining in PDAC and ASCP primary PDXs, and in metastatic lesions (+ low predominately cytosolic, ++ medium cytosolic and nu…
View article: Figure S2 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S2 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
A-B) DNA content histograms and genomic profiles of flow sorted diploid only ASCP biopsies. A) female (two copies of chromosome X) and; B) male (one copy of chromosome X) diploid only ASCP biopsies. In both cases the 4.0N fractions were <6…
View article: Figure S8 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S8 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
IHC analysis of RORC in ASCP PDXs and metastases. A) PAX265; B) PAX139; C) 9R liver metastases; D) Summary of RORC staining in PDAC and ASCP primary PDXs, and in metastatic lesions (+ low predominately cytosolic, ++ medium cytosolic and nu…
View article: Figure S4 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S4 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Somatic mutations and homozygous deletions targeting chromatin regulators in ASCP genomes. IGV views of A) TP53Y205S and MSL2C44W in 3.8N population sorted from primary tumor 9R. B) KRASG12D and KANSL1Q396X in flow sorted tumor fraction in…
View article: Figure S3 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S3 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Supplemental Figure 3: Somatic lesions targeting chromatin regulators in ASCP genomes. CNV profiles of flow sorted aneuploid populations from: A) A129 with homozygous deletion of CDKN2A and SMARCA4. The X and Y axes in the CGH plots repres…
View article: Figure S7 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S7 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Whole genome CNV landscape of PDX models profiled by ATAC-seq. A) ASCPs PAX139, PAX217, and PAX265. Vertical arrows highlight CDK6 amplicons and horizontal arrows highlight CDKN2A homozygous deletions. B) PDACs PAX295, PAX297, and PAX300. …
View article: Figure S6 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S6 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
High level amplicons in ASCP genomes. The CNV profiles of A) A90 and B) PENN 040 included focal high level (log2 ratio >2.0) amplicons that targeted the MPL and the FRS2 loci respectively. The X and Y axes in the CGH plots represent chromo…
View article: Figure S5 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S5 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Focal amplicons in ASCP genomes. The CNV profiles of A) A129 and B) PAX232 included focal high level (log2 ratio >2) amplicons that targeted the TLK2 and the ASH2L loci respectively. The X and Y axes in the CGH plots represent chromosome a…
View article: Figure S1 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S1 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Histology and IHC analyses of ASCP tissues. Hematoxylin and Eosin (H&E) staining and IHC expression of cytokeratins 5 and 6 (CK5/6), and of TP63 for five ASCP cases. Adenosquamous content is consistent with WHO histology and diagnosis.
View article: Table S2 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Table S2 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Evidence-based variant categorization
View article: Table S2 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Table S2 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Evidence-based variant categorization
View article: Data from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Data from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Adenosquamous cancer of the pancreas (ASCP) is a subtype of pancreatic cancer that has a worse prognosis and greater metastatic potential than the more common pancreatic ductal adenocarcinoma (PDAC) subtype. To distinguish the genomic land…
View article: Figure S5 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S5 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Focal amplicons in ASCP genomes. The CNV profiles of A) A129 and B) PAX232 included focal high level (log2 ratio >2) amplicons that targeted the TLK2 and the ASH2L loci respectively. The X and Y axes in the CGH plots represent chromosome a…
View article: Table S1 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Table S1 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Types of ASCP Specimen
View article: Figure S4 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S4 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Somatic mutations and homozygous deletions targeting chromatin regulators in ASCP genomes. IGV views of A) TP53Y205S and MSL2C44W in 3.8N population sorted from primary tumor 9R. B) KRASG12D and KANSL1Q396X in flow sorted tumor fraction in…
View article: Figure S6 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S6 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
High level amplicons in ASCP genomes. The CNV profiles of A) A90 and B) PENN 040 included focal high level (log2 ratio >2.0) amplicons that targeted the MPL and the FRS2 loci respectively. The X and Y axes in the CGH plots represent chromo…
View article: Figure S2 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Figure S2 from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
A-B) DNA content histograms and genomic profiles of flow sorted diploid only ASCP biopsies. A) female (two copies of chromosome X) and; B) male (one copy of chromosome X) diploid only ASCP biopsies. In both cases the 4.0N fractions were <6…
View article: Data from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Data from Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Adenosquamous cancer of the pancreas (ASCP) is a subtype of pancreatic cancer that has a worse prognosis and greater metastatic potential than the more common pancreatic ductal adenocarcinoma (PDAC) subtype. To distinguish the genomic land…
View article: PDJ amplicon in triple negative breast cancer
PDJ amplicon in triple negative breast cancer Open
Amplification of chromosome 9p24.1 targeting PD-L1 , PD-L2 , and JAK2 (PDJ amplicon) is present in subsets of triple negative breast cancers (TNBCs) and is associated with poor clinical outcomes. However, the prevalence of PDJ+ TNBCs varie…
View article: Unique evolutionary trajectories of breast cancers with distinct genomic and spatial heterogeneity
Unique evolutionary trajectories of breast cancers with distinct genomic and spatial heterogeneity Open
Breast cancers exhibit intratumoral heterogeneity associated with disease progression and therapeutic resistance. To define the sources and the extent of heterogeneity, we performed an in-depth analysis of the genomic architecture of three…
View article: Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas
Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas Open
Adenosquamous cancer of the pancreas (ASCP) is a subtype of pancreatic cancer that has a worse prognosis and greater metastatic potential than the more common pancreatic ductal adenocarcinoma (PDAC) subtype. To distinguish the genomic land…
View article: Unique genomic and neoepitope landscapes across tumors: a study across time, tissues, and space within a single lynch syndrome patient
Unique genomic and neoepitope landscapes across tumors: a study across time, tissues, and space within a single lynch syndrome patient Open
Lynch syndrome (LS) arises in patients with pathogenic germline variants in DNA mismatch repair genes. LS is the most common inherited cancer predisposition condition and confers an elevated lifetime risk of multiple cancers notably colore…
View article: Enhanced DNA repair and genomic stability identify a novel HIV‐related diffuse large B‐cell lymphoma signature
Enhanced DNA repair and genomic stability identify a novel HIV‐related diffuse large B‐cell lymphoma signature Open
Diffuse large B‐cell lymphoma (DLBCL) is up to 17‐fold more likely to occur, follows a more aggressive clinical course and frequently presents at advanced stages in HIV infected (+) individuals compared to HIV negative (−) individuals. How…
View article: Clonal analyses of refractory testicular germ cell tumors
Clonal analyses of refractory testicular germ cell tumors Open
Testicular germ cell tumors (TGCTs) are unique amongst solid tumors in terms of the high cure rates using chemotherapy for metastatic disease. Nevertheless, TGCTs still kill approximately 400 men per year, at a median age of 30 years, in t…
View article: Clinical study of genomic drivers in pancreatic ductal adenocarcinoma
Clinical study of genomic drivers in pancreatic ductal adenocarcinoma Open
We provide a clinically relevant framework for genomic drivers of PDA and for advancing novel treatments.