Nishika Karbhari
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Previous Organizations / Institutes
The organizations / institutes from the scholar's other articles in the past ten years
Research Subjects
Nishika Karbhari has a total of 53 co-authors. Here are the top co-authors by number of shared publications:
- Cory M. Pfeifer
University of Arizona College of Medicine, Phoenix, USA
2 shared publications - Jian Li Campian
Department of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA
2 shared publications - Justin Tang
Department of Biomedical Science, University of Guelph, Guelph, ON N1G 2W1, Canada
2 shared publications - Ugur Sener
Department of Neurology, Mayo Clinic, Rochester, MN, United States of America
2 shared publications - Abhinav Nellore
Computational Biology Program, Oregon Health & Science University , Portland, OR 97239, USA
1 shared publication - Adam C. Yopp
Division of Surgical Oncology, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, USA
1 shared publication
Latest Publications
- Open Access
- 15 September 2026
- Published by Wiley in Brain Pathology
Circumscribed Meningeal Melanocytic Neoplasms: CNS WHO Grade, Molecular Profile, and Clinical Outcomes
Circumscribed meningeal melanocytic neoplasms (CMMNs) represent a spectrum of rare central nervous system (CNS) tumors. Knowledge of their clinical behavior and molecular correlates remains limited. In this single‐institution retrospective study, we analyzed 31 patients (14 male, 17 female; median age, 59 years) diagnosed with CMMN between 2004 and 2025. In this patient cohort, based on the current World Health Organization Central Nervous System Tumor Classification (WHO CNS5) criteria, the majority of cases (18, 58.1%) fell into the intermediate‐grade melanocytic tumor (IMT) category based on histology, with either increased mitotic activity, CNS invasion, or both; 7 (22.6%) were melanocytomas, 5 (16.1%) melanomas, and 1 (3.2%) indeterminate case because of limited tissue. By next‐generation sequencing, mutations were identified in GNAQ/GNA11 in 21/24 cases, BAP1 in 5/23 (2 IMT, 3 melanoma), EIF1AX in 9/21 (1 melanocytoma, 8 IMT), and SF3B1 in 3/23 (2 IMT, 1 melanoma). Primary sites were spinal (20), posterior fossa (6), and supratentorial (5). During follow‐up, progression was observed in 5/6 melanocytomas, 9/13 IMTs, and 4/5 melanomas, suggesting a high frequency of progression across all groups. Two‐year progression‐free survival was 83.3% (95% confidence interval [CI], 53.5%–100.0%) for melanocytoma, 55.9% (95% CI, 26.7%–85.2%) for IMT, and 25.0% (95% CI, 0.0%–67.4%) for melanoma. Five‐year overall survival (OS) was 80.0% (95% CI, 44.9%–100.0%) for melanocytoma, 65.3% (95% CI, 37.0%–93.6%) for IMT, and 0.0% for melanoma. OS was significantly worse in melanoma compared with melanocytoma ( p = 0.002). BAP1 mutation correlated with worse OS (hazard ratio 8.73, p = 0.006). Upfront maximal safe resection appeared to be associated with improved outcomes in selected patients, whereas radiotherapy and systemic therapy did not demonstrate clear additional benefit in this cohort. In summary, our study shows that all CMMNs, irrespective of grade, have a high propensity to recur and melanoma histology and BAP1 mutation are associated with significantly worse OS.
- 15 September 2026
- Published by Wiley in Brain Pathology
Open AccessCircumscribed Meningeal Melanocytic Neoplasms: CNS WHO Grade, Molecular Profile, and Clinical Outcomes
Circumscribed meningeal melanocytic neoplasms (CMMNs) represent a spectrum of rare central nervous system (CNS) tumors. Knowledge of their clinical behavior and molecular correlates remains limited. In this single‐institution retrospective study, we analyzed 31 patients (14 male, 17 female; median age, 59 years) diagnosed with CMMN between 2004 and 2025. In this patient cohort, based on the current World Health Organization Central Nervous System Tumor Classification (WHO CNS5) criteria, the majority of cases (18, 58.1%) fell into the intermediate‐grade melanocytic tumor (IMT) category based on histology, with either increased mitotic activity, CNS invasion, or both; 7 (22.6%) were melanocytomas, 5 (16.1%) melanomas, and 1 (3.2%) indeterminate case because of limited tissue. By next‐generation sequencing, mutations were identified in GNAQ/GNA11 in 21/24 cases, BAP1 in 5/23 (2 IMT, 3 melanoma), EIF1AX in 9/21 (1 melanocytoma, 8 IMT), and SF3B1 in 3/23 (2 IMT, 1 melanoma). Primary sites were spinal (20), posterior fossa (6), and supratentorial (5). During follow‐up, progression was observed in 5/6 melanocytomas, 9/13 IMTs, and 4/5 melanomas, suggesting a high frequency of progression across all groups. Two‐year progression‐free survival was 83.3% (95% confidence interval [CI], 53.5%–100.0%) for melanocytoma, 55.9% (95% CI, 26.7%–85.2%) for IMT, and 25.0% (95% CI, 0.0%–67.4%) for melanoma. Five‐year overall survival (OS) was 80.0% (95% CI, 44.9%–100.0%) for melanocytoma, 65.3% (95% CI, 37.0%–93.6%) for IMT, and 0.0% for melanoma. OS was significantly worse in melanoma compared with melanocytoma ( p = 0.002). BAP1 mutation correlated with worse OS (hazard ratio 8.73, p = 0.006). Upfront maximal safe resection appeared to be associated with improved outcomes in selected patients, whereas radiotherapy and systemic therapy did not demonstrate clear additional benefit in this cohort. In summary, our study shows that all CMMNs, irrespective of grade, have a high propensity to recur and melanoma histology and BAP1 mutation are associated with significantly worse OS.
- Open Access
Immunotherapy for High-Grade Gliomas
Background: High-grade gliomas (HGGs), particularly glioblastoma (GBM), are associated with exceptionally high mortality and inevitable recurrence. In considering novel treatment options for these devastating diseases, immunotherapies represent promising candidates. Immunotherapies have demonstrated efficacy for several advanced tumors outside the central nervous system, highlighting a potential role for these agents in treating HGGs. However, multiple challenges to immunotherapy efficacy have tempered therapeutic benefit in practice, including local and systemic immunosuppression, intratumoral heterogeneity, and various mechanisms of intrinsic and acquired resistance. In the past 30 years, diverse immunotherapeutic subclasses have been assessed for benefit against HGGs. Methods: We performed a PubMed search for randomized clinical trials performed within the last 30 years evaluating the following immunotherapy agents for high-grade gliomas: immune checkpoint inhibitors, vaccines, oncologic viruses, cytokines, and CAR T-cells. The present review offers a critical analysis of key pre-clinical and clinical trials that have shaped the immunotherapy landscape for high-grade gliomas over the past two decades. Results/Conclusions: Across the different immunotherapeutic methods and modalities explored thus far, a recurring theme emerges: while therapeutic strategies with a compelling conceptual basis are continually under development and even demonstrate a benefit in preclinical and early-phase trials, larger and later-phase trials consistently fail to produce concordantly significant outcomes. To date, no large-scale clinical trial has demonstrated a benefit of sufficient consequence to change practice. Continued critical appraisal of the strengths and pitfalls of prior investigative work, optimization of treatment development and delivery, and innovative approaches to combination therapy design will collectively be integral to future therapeutic advancement.
Open AccessImmunotherapy for High-Grade Gliomas
Background: High-grade gliomas (HGGs), particularly glioblastoma (GBM), are associated with exceptionally high mortality and inevitable recurrence. In considering novel treatment options for these devastating diseases, immunotherapies represent promising candidates. Immunotherapies have demonstrated efficacy for several advanced tumors outside the central nervous system, highlighting a potential role for these agents in treating HGGs. However, multiple challenges to immunotherapy efficacy have tempered therapeutic benefit in practice, including local and systemic immunosuppression, intratumoral heterogeneity, and various mechanisms of intrinsic and acquired resistance. In the past 30 years, diverse immunotherapeutic subclasses have been assessed for benefit against HGGs. Methods: We performed a PubMed search for randomized clinical trials performed within the last 30 years evaluating the following immunotherapy agents for high-grade gliomas: immune checkpoint inhibitors, vaccines, oncologic viruses, cytokines, and CAR T-cells. The present review offers a critical analysis of key pre-clinical and clinical trials that have shaped the immunotherapy landscape for high-grade gliomas over the past two decades. Results/Conclusions: Across the different immunotherapeutic methods and modalities explored thus far, a recurring theme emerges: while therapeutic strategies with a compelling conceptual basis are continually under development and even demonstrate a benefit in preclinical and early-phase trials, larger and later-phase trials consistently fail to produce concordantly significant outcomes. To date, no large-scale clinical trial has demonstrated a benefit of sufficient consequence to change practice. Continued critical appraisal of the strengths and pitfalls of prior investigative work, optimization of treatment development and delivery, and innovative approaches to combination therapy design will collectively be integral to future therapeutic advancement.
- Top Cited PapersOpen Access
Therapeutic Targets in Glioblastoma: Molecular Pathways, Emerging Strategies, and Future Directions
Glioblastoma (GBM) is the most aggressive primary brain tumor in adults, characterized by rapid growth, invasive infiltration into surrounding brain tissue, and resistance to conventional therapies. Despite advancements in surgery, radiotherapy, and chemotherapy, median survival remains approximately 15 months, underscoring the urgent need for innovative treatments. Key considerations informing treatment development include oncogenic genetic and epigenetic alterations that may dually serve as therapeutic targets and facilitate treatment resistance. Various immunotherapeutic strategies have been explored and continue to be refined for their anti-tumor potential. Technical aspects of drug delivery and blood–brain barrier (BBB) penetration have been addressed through novel vehicles and techniques including the incorporation of nanotechnology. Molecular profiling has emerged as an important tool to individualize treatment where applicable, and to identify patient populations with the most drug sensitivity. The goal of this review is to describe the spectrum of potential GBM therapeutic targets, and to provide an overview of key trial outcomes. Altogether, the progress of clinical and preclinical work must be critically evaluated in order to develop therapies for GBM with the strongest therapeutic efficacy.
Top Cited PapersOpen AccessTherapeutic Targets in Glioblastoma: Molecular Pathways, Emerging Strategies, and Future Directions
Glioblastoma (GBM) is the most aggressive primary brain tumor in adults, characterized by rapid growth, invasive infiltration into surrounding brain tissue, and resistance to conventional therapies. Despite advancements in surgery, radiotherapy, and chemotherapy, median survival remains approximately 15 months, underscoring the urgent need for innovative treatments. Key considerations informing treatment development include oncogenic genetic and epigenetic alterations that may dually serve as therapeutic targets and facilitate treatment resistance. Various immunotherapeutic strategies have been explored and continue to be refined for their anti-tumor potential. Technical aspects of drug delivery and blood–brain barrier (BBB) penetration have been addressed through novel vehicles and techniques including the incorporation of nanotechnology. Molecular profiling has emerged as an important tool to individualize treatment where applicable, and to identify patient populations with the most drug sensitivity. The goal of this review is to describe the spectrum of potential GBM therapeutic targets, and to provide an overview of key trial outcomes. Altogether, the progress of clinical and preclinical work must be critically evaluated in order to develop therapies for GBM with the strongest therapeutic efficacy.
- Open Access
- 18 February 2025
- Published by MDPI AG in Preprints.org
Therapeutic Targets in Glioblastoma: Molecular Pathways, Emerging Strategies, and Future Directions
Glioblastoma (GBM) is the most aggressive primary brain tumor in adults, characterized by rapid growth, invasive infiltration into surrounding brain tissue, and resistance to conventional therapies. Despite advancements in surgery, radiotherapy, and chemotherapy, median survival remains approximately 15 months, underscoring the urgent need for innovative treatments. Key considerations informing treatment development include oncogenic genetic and epigenetic alterations that may dually serve as therapeutic targets and facilitate treatment resistance. Various immunotherapeutic strategies have been explored and continue to be refined for their anti-tumor potential. Technical aspects of drug delivery and blood-brain barrier (BBB) penetration have been addressed through novel vehicles and techniques including the incorporation of nanotechnology. Molecular profiling has emerged as an important tool to individualize treatment where applicable, and to identify patient populations with the most drug sensitivity. The goal of this review is to describe the spectrum of potential GBM therapeutic targets, and to provide an overview of key trial outcomes. Altogether, the progress of clinical and preclinical work must be critically evaluated in order to develop therapies for GBM with the strongest therapeutic efficacy.
- 18 February 2025
- Published by MDPI AG in Preprints.org
Open AccessTherapeutic Targets in Glioblastoma: Molecular Pathways, Emerging Strategies, and Future Directions
Glioblastoma (GBM) is the most aggressive primary brain tumor in adults, characterized by rapid growth, invasive infiltration into surrounding brain tissue, and resistance to conventional therapies. Despite advancements in surgery, radiotherapy, and chemotherapy, median survival remains approximately 15 months, underscoring the urgent need for innovative treatments. Key considerations informing treatment development include oncogenic genetic and epigenetic alterations that may dually serve as therapeutic targets and facilitate treatment resistance. Various immunotherapeutic strategies have been explored and continue to be refined for their anti-tumor potential. Technical aspects of drug delivery and blood-brain barrier (BBB) penetration have been addressed through novel vehicles and techniques including the incorporation of nanotechnology. Molecular profiling has emerged as an important tool to individualize treatment where applicable, and to identify patient populations with the most drug sensitivity. The goal of this review is to describe the spectrum of potential GBM therapeutic targets, and to provide an overview of key trial outcomes. Altogether, the progress of clinical and preclinical work must be critically evaluated in order to develop therapies for GBM with the strongest therapeutic efficacy.
- Open Access
Marine-Derived Therapeutics for the Management of Glioblastoma: A Case Series and Comprehensive Review of the Literature
Introduction: Glioblastoma is a fatal intracranial neoplasm that is refractory to treatment, with inevitable disease recurrence and progression to death. Marine-derived compounds, including those found in nutraceutical products, may provide therapeutic benefit in the setting of glioblastoma. We present two patient cases whose courses demonstrate a compelling role for marine-derived products in the management of glioblastoma. Cases: Case 1 describes a patient with MGMT promoter unmethylated glioblastoma who went on to complete standard of care chemoradiation along with concurrent use of a majority sea cucumber (MSC) blend known as SeaCare® (SeaCare, Torrington, CT, USA). Her survival of over 2 years significantly exceeds the recognized median survival time of glioblastoma. Case 2 describes a patient with a complicated course who experienced dramatic improvement after the initiation of the MSC blend, with an exceptional survival time of over 4 years post-diagnosis. Discussion: The mechanisms of marine-derived products that underlie these dramatic clinical effects are likely multifaceted but may hinge on the modification of the tumor immune microenvironment and suppression of tumorigenic effects. Specifically, the change in tumor-associated macrophages (TAMs) within the tumor microenvironment is central to this complex interplay. Conclusions: Ultimately, the use of marine products in the treatment of glioblastoma may present a novel and promising therapeutic strategy that warrants further investigation.
Open AccessMarine-Derived Therapeutics for the Management of Glioblastoma: A Case Series and Comprehensive Review of the Literature
Introduction: Glioblastoma is a fatal intracranial neoplasm that is refractory to treatment, with inevitable disease recurrence and progression to death. Marine-derived compounds, including those found in nutraceutical products, may provide therapeutic benefit in the setting of glioblastoma. We present two patient cases whose courses demonstrate a compelling role for marine-derived products in the management of glioblastoma. Cases: Case 1 describes a patient with MGMT promoter unmethylated glioblastoma who went on to complete standard of care chemoradiation along with concurrent use of a majority sea cucumber (MSC) blend known as SeaCare® (SeaCare, Torrington, CT, USA). Her survival of over 2 years significantly exceeds the recognized median survival time of glioblastoma. Case 2 describes a patient with a complicated course who experienced dramatic improvement after the initiation of the MSC blend, with an exceptional survival time of over 4 years post-diagnosis. Discussion: The mechanisms of marine-derived products that underlie these dramatic clinical effects are likely multifaceted but may hinge on the modification of the tumor immune microenvironment and suppression of tumorigenic effects. Specifically, the change in tumor-associated macrophages (TAMs) within the tumor microenvironment is central to this complex interplay. Conclusions: Ultimately, the use of marine products in the treatment of glioblastoma may present a novel and promising therapeutic strategy that warrants further investigation.
- Open Access
- 30 March 2022
- Published by S. Karger AG in Case Reports in Oncology
- Vol. 15 (1) , 345-350
Venetoclax: A Novel Therapeutic Agent for CLL with CNS Involvement
Chronic lymphocytic leukemia (CLL) involves the proliferation of a clonal population of B cells within the bone marrow that classically spreads to the blood and lymphatic system. Central nervous system (CNS) manifestations of CLL occur rarely, and no gold standard treatment regimen has been designated to date. We report a case of CLL with CNS involvement in a 68-year-old woman who presented with a severe headache 4 years after initial diagnosis. She was started on ibrutinib, which failed to clear her CSF of malignancy. Venetoclax was then added, and this was successful in clearing her CSF. For its CNS penetration and efficacy in achieving CSF remission of CLL, we propose that venetoclax be considered as a treatment option for CLL meningitis.
- 30 March 2022
- Published by S. Karger AG in Case Reports in Oncology
- Vol. 15 (1) , 345-350
Open AccessVenetoclax: A Novel Therapeutic Agent for CLL with CNS Involvement
Chronic lymphocytic leukemia (CLL) involves the proliferation of a clonal population of B cells within the bone marrow that classically spreads to the blood and lymphatic system. Central nervous system (CNS) manifestations of CLL occur rarely, and no gold standard treatment regimen has been designated to date. We report a case of CLL with CNS involvement in a 68-year-old woman who presented with a severe headache 4 years after initial diagnosis. She was started on ibrutinib, which failed to clear her CSF of malignancy. Venetoclax was then added, and this was successful in clearing her CSF. For its CNS penetration and efficacy in achieving CSF remission of CLL, we propose that venetoclax be considered as a treatment option for CLL meningitis.
- 18 March 2021
- Published by American Society of Neuroradiology (ASNR) in American Journal of Neuroradiology
- Vol. 42 (6) , E35
Improving Access to Fast MRI for Emergent Shunt Evaluation
- 18 March 2021
- Published by American Society of Neuroradiology (ASNR) in American Journal of Neuroradiology
- Vol. 42 (6) , E35
Improving Access to Fast MRI for Emergent Shunt Evaluation
- Open Access
- 1 August 2020
- Published by Elsevier in Radiology Case Reports
- Vol. 15 (8) , 1285-1288
ACTA2 leukovasculopathy: A rare pediatric white matter disorder
- 1 August 2020
- Published by Elsevier in Radiology Case Reports
- Vol. 15 (8) , 1285-1288
Open AccessACTA2 leukovasculopathy: A rare pediatric white matter disorder
- Open Access
Effect of fragmentation of cancer care on treatment use and survival in hepatocellular carcinoma
Background: Fragmented cancer care (FC), or care received from multiple institutions, increases systemic health care costs and potentiates cancer care disparities. There is a paucity of data on mechanisms contributing to FC and the resulting effect on patient outcomes. This study characterized patient‐ and hospital‐level factors associated with FC, time to treatment (TTT), and overall survival (OS) in patients with hepatocellular carcinoma (HCC).Methods: Patients newly diagnosed with HCC from 2004 to 2015 and receiving treatment were identified in the Texas Cancer Registry. Patient‐ and hospital‐level factors were compared across 2 cohorts: an FC treatment group and a nonfragmented cancer care (NFC) treatment group. Covariate‐adjusted treatment use and OS were compared between the 2 treatment groups.Results: Among 4329 patients with HCC, 1185 (27.4%) received FC, and 3144 (72.6%) received NFC. Compared with NFC patients, FC patients had larger tumors (median size ≥4 cm, 52.6% vs 35.2%; P < .001), and a higher proportion had a regional/metastatic stage (35.9% vs 26.7%; P < .001). Among patients with localized disease, FC was associated with decreased odds of curative therapy (odds ratio, 0.83; 95% confidence interval [CI], 0.7‐0.9). FC was associated with worse OS (hazard ratio [HR], 1.14; 95% CI, 1.05‐1.24) and increased TTT (HR, 0.76; 95% CI, 0.7‐0.8). In the subset of patients with localized‐stage HCC who received curative therapy, FC was associated with worse OS (median survival, 67 vs 43 months; HR, 1.2; 95% CI, 1.0‐1.4) and increased TTT (HR, 0.74; 95% CI, 0.7‐0.8).Conclusions: FC patients were less likely to undergo curative therapy when they were diagnosed at an early stage. After covariate adjustment, newly diagnosed patients with HCC receiving FC had worse OS and increased TTT.
Open AccessEffect of fragmentation of cancer care on treatment use and survival in hepatocellular carcinoma
Background: Fragmented cancer care (FC), or care received from multiple institutions, increases systemic health care costs and potentiates cancer care disparities. There is a paucity of data on mechanisms contributing to FC and the resulting effect on patient outcomes. This study characterized patient‐ and hospital‐level factors associated with FC, time to treatment (TTT), and overall survival (OS) in patients with hepatocellular carcinoma (HCC).Methods: Patients newly diagnosed with HCC from 2004 to 2015 and receiving treatment were identified in the Texas Cancer Registry. Patient‐ and hospital‐level factors were compared across 2 cohorts: an FC treatment group and a nonfragmented cancer care (NFC) treatment group. Covariate‐adjusted treatment use and OS were compared between the 2 treatment groups.Results: Among 4329 patients with HCC, 1185 (27.4%) received FC, and 3144 (72.6%) received NFC. Compared with NFC patients, FC patients had larger tumors (median size ≥4 cm, 52.6% vs 35.2%; P < .001), and a higher proportion had a regional/metastatic stage (35.9% vs 26.7%; P < .001). Among patients with localized disease, FC was associated with decreased odds of curative therapy (odds ratio, 0.83; 95% confidence interval [CI], 0.7‐0.9). FC was associated with worse OS (hazard ratio [HR], 1.14; 95% CI, 1.05‐1.24) and increased TTT (HR, 0.76; 95% CI, 0.7‐0.8). In the subset of patients with localized‐stage HCC who received curative therapy, FC was associated with worse OS (median survival, 67 vs 43 months; HR, 1.2; 95% CI, 1.0‐1.4) and increased TTT (HR, 0.74; 95% CI, 0.7‐0.8).Conclusions: FC patients were less likely to undergo curative therapy when they were diagnosed at an early stage. After covariate adjustment, newly diagnosed patients with HCC receiving FC had worse OS and increased TTT.
- Open Access
- 30 December 2016
- Published by Springer Nature in Genome Biology
- Vol. 17 (1) , 1-14
Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0. We aligned 21,504 Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations. We found 56,861 junctions (18.6%) in at least 1000 samples that were not annotated, and their expression associated with tissue type. Junctions well expressed in individual samples tended to be annotated. Newer samples contributed few novel well-supported junctions, with the vast majority of detected junctions present in samples before 2013. We compiled junction data into a resource called intropolis available at http://intropolis.rail.bio . We used this resource to search for a recently validated isoform of the ALK gene and characterized the potential functional implications of unannotated junctions with publicly available TRAP-seq data. Considering only the variation contained in annotation may suffice if an investigator is interested only in well-expressed transcript isoforms. However, genes that are not generally well expressed and nonetheless present in a small but significant number of samples in the SRA are likelier to be incompletely annotated. The rate at which evidence for novel junctions has been added to the SRA has tapered dramatically, even to the point of an asymptote. Now is perhaps an appropriate time to update incomplete annotations to include splicing present in the now-stable snapshot provided by the SRA.
- 30 December 2016
- Published by Springer Nature in Genome Biology
- Vol. 17 (1) , 1-14
Open AccessHuman splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0. We aligned 21,504 Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations. We found 56,861 junctions (18.6%) in at least 1000 samples that were not annotated, and their expression associated with tissue type. Junctions well expressed in individual samples tended to be annotated. Newer samples contributed few novel well-supported junctions, with the vast majority of detected junctions present in samples before 2013. We compiled junction data into a resource called intropolis available at http://intropolis.rail.bio . We used this resource to search for a recently validated isoform of the ALK gene and characterized the potential functional implications of unannotated junctions with publicly available TRAP-seq data. Considering only the variation contained in annotation may suffice if an investigator is interested only in well-expressed transcript isoforms. However, genes that are not generally well expressed and nonetheless present in a small but significant number of samples in the SRA are likelier to be incompletely annotated. The rate at which evidence for novel junctions has been added to the SRA has tapered dramatically, even to the point of an asymptote. Now is perhaps an appropriate time to update incomplete annotations to include splicing present in the now-stable snapshot provided by the SRA.