Gordon Saksena
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View article: Characterization of IGHV subgroups and their prognostic relevance in CLL
Characterization of IGHV subgroups and their prognostic relevance in CLL Open
Introduction: Immunoglobulin heavy chain variable region (IGHV) somatic hypermutation (SHM) status is a strong prognostic marker in CLL. Previous studies in the chemoimmunotherapy era reported inferior outcome linked to specific IGHV stere…
View article: Supplementary Figure 14 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Figure 14 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 340K, Hierarchical clustering of copy-number profiles
View article: Supplementary Figures 1-13 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Figures 1-13 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 1MB, Supplemental Figures 1-13 - Figure S1. Average levels of focal amplification and deletion along the chromosome arm; Figure S2. Patterns of chromosomal instability differ across adenocarcinomas of the gastrointestinal tract …
View article: Supplementary Legends for Figures 1-14, and Tables 1-6 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Legends for Figures 1-14, and Tables 1-6 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 103K
View article: Supplementary Methods from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Methods from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 99K
View article: Data from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Data from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
A more detailed understanding of the somatic genetic events that drive gastrointestinal adenocarcinomas is necessary to improve diagnosis and therapy. Using data from high-density genomic profiling arrays, we conducted an analysis of somat…
View article: Supplementary Note 3 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Note 3 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 64K, Analysis of SNP6.0 Data Only
View article: Supplementary Note 3 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Note 3 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 64K, Analysis of SNP6.0 Data Only
View article: Supplementary Tables 1-6 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Tables 1-6 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 134K
View article: Supplementary Note 2 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Note 2 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 88K, Description of Sample Validation
View article: Supplementary Note 1 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Note 1 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 50K, Description of Combining SNP6.0 and 250K Platforms
View article: Supplementary Note 1 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Note 1 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 50K, Description of Combining SNP6.0 and 250K Platforms
View article: Supplementary Note 2 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Note 2 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 88K, Description of Sample Validation
View article: Supplementary Methods from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Methods from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 99K
View article: Supplementary Tables 1-6 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Tables 1-6 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 134K
View article: Data from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Data from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
A more detailed understanding of the somatic genetic events that drive gastrointestinal adenocarcinomas is necessary to improve diagnosis and therapy. Using data from high-density genomic profiling arrays, we conducted an analysis of somat…
View article: Supplementary Legends for Figures 1-14, and Tables 1-6 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Legends for Figures 1-14, and Tables 1-6 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 103K
View article: Supplementary Figures 1-13 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Figures 1-13 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 1MB, Supplemental Figures 1-13 - Figure S1. Average levels of focal amplification and deletion along the chromosome arm; Figure S2. Patterns of chromosomal instability differ across adenocarcinomas of the gastrointestinal tract …
View article: Supplementary Figure 14 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis
Supplementary Figure 14 from Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis Open
PDF file - 340K, Hierarchical clustering of copy-number profiles
View article: Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes
Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes Open
View article: Author Correction: Integrative pathway enrichment analysis of multivariate omics data
Author Correction: Integrative pathway enrichment analysis of multivariate omics data Open
View article: Pirtobrutinib targets BTK C481S in ibrutinib-resistant CLL but second-site BTK mutations lead to resistance
Pirtobrutinib targets BTK C481S in ibrutinib-resistant CLL but second-site BTK mutations lead to resistance Open
Covalent inhibitors of Bruton tyrosine kinase (BTK) have transformed the therapy of chronic lymphocytic leukemia (CLL), but continuous therapy has been complicated by the development of resistance. The most common resistance mechanism in p…
View article: Tangent normalization for somatic copy-number inference in cancer genome analysis
Tangent normalization for somatic copy-number inference in cancer genome analysis Open
Motivation Somatic copy-number alterations (SCNAs) play an important role in cancer development. Systematic noise in sequencing and array data present a significant challenge to the inference of SCNAs for cancer genome analyses. As part of…
View article: Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples Open
View article: Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion
Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion Open
Prior studies have identified recurrent oncogenic mutations in colorectal adenocarcinoma1 and have surveyed exons of protein-coding genes for mutations in 11 affected individuals2,3. Here we report whole-genome sequencing from nine individ…
View article: Prognostically relevant gene signatures of high-grade serous ovarian carcinoma
Prognostically relevant gene signatures of high-grade serous ovarian carcinoma Open
Because of the high risk of recurrence in high-grade serous ovarian carcinoma (HGS-OvCa), the development of outcome predictors could be valuable for patient stratification. Using the catalog of The Cancer Genome Atlas (TCGA), we developed…
View article: The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma
The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma Open
We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) based on multidimensional and comprehensive characterization, including mitochondrial DNA (mtDNA) and whole genome sequencing. The re…
View article: Framework for quality assessment of whole genome cancer sequences
Framework for quality assessment of whole genome cancer sequences Open
View article: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples Open
View article: Publisher Correction: Butler enables rapid cloud-based analysis of thousands of human genomes
Publisher Correction: Butler enables rapid cloud-based analysis of thousands of human genomes Open