Kanika Arora
A5012795135- Cancer Genomics and Diagnostics
- Genetic factors in colorectal cancer
- Genomics and Rare Diseases
- Pancreatic and Hepatic Oncology Research
- DNA Repair Mechanisms
- BRCA gene mutations in cancer
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- Insect Resistance and Genetics
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- Protein Degradation and Inhibitors
- Prostate Cancer Treatment and Research
- Cancer-related molecular mechanisms research
- Acute Myeloid Leukemia Research
- Colorectal Cancer Treatments and Studies
- Global Cancer Incidence and Screening
- Glioma Diagnosis and Treatment
- Genomics and Chromatin Dynamics
- Endometrial and Cervical Cancer Treatments
- Cervical Cancer and HPV Research
- Cancer-related gene regulation
- Chemical Reactions and Isotopes
- Genetic Associations and Epidemiology
- Magnetic Field Sensors Techniques
Memorial Sloan Kettering Cancer Center
2016-2025
Molecular Oncology (United States)
2021-2025
University of Waterloo
2025
Beaumont Hospital, Royal Oak
2025
Kettering University
2022-2024
Graphic Era University
2024
Institute of Nano Science and Technology
2021-2024
Sanjay Gandhi Post Graduate Institute of Medical Sciences
2023-2024
Stanford University
2022-2023
Henry Ford Health System
2020-2023
Pancreatic cancer is the most lethal common solid malignancy. Systemic therapies are often ineffective, and predictive biomarkers to guide treatment urgently needed. We generated a pancreatic patient-derived organoid (PDO) library that recapitulates mutational spectrum transcriptional subtypes of primary cancer. New driver oncogenes were nominated transcriptomic analyses revealed unique clusters. PDOs exhibited heterogeneous responses standard-of-care chemotherapeutics investigational...
Purpose Owing to its exquisite chemotherapy sensitivity, most patients with metastatic germ cell tumors (GCTs) are cured cisplatin-based chemotherapy. However, up 30% of advanced GCT exhibit cisplatin resistance, which requires intensive salvage treatment, and have a 50% risk cancer-related death. To identify genetic basis for we performed whole-exome targeted sequencing cisplatin-sensitive cisplatin-resistant GCTs. Methods Men who received cisplatin-containing regimen had available tumor...
Women of sub-Saharan African descent have disproportionately higher incidence triple-negative breast cancer (TNBC) and TNBC-specific mortality across all populations. Population studies show racial differences in TNBC biology, including prevalence basal-like quadruple-negative subtypes Americans (AA). However, previous investigations relied on self-reported race (SRR) primarily U.S. Due to heterogeneous genetic admixture biological consequences social determinants, the true association...
Reliable detection of somatic variations is critical importance in cancer research. Here we present Lancet, an accurate and sensitive variant caller, which detects SNVs indels by jointly analyzing reads from tumor matched normal samples using colored de Bruijn graphs. We demonstrate, through extensive experimental comparison on synthetic real whole-genome sequencing datasets, that Lancet has better accuracy, especially for indel detection, than widely used callers, such as MuTect, MuTect2,...
RNAi shows potential as an agricultural technology for insect control, yet, a relatively low number of robust lethal targets have been demonstrated to control insects interest. In the current study, selection target genes from iBeetle (Tribolium castaneum) screen were used demonstrate efficacy orthologous in economically important coleopteran pests Diabrotica virgifera and Meligethes aeneus. Transcript orthologs 50 selected analyzed D. v. diet-based bioassays; 21 these showed mortality 36...
Abstract Accurate ancestry inference is critical for identifying genetic contributors of cancer disparities among populations. Although methods to infer have historically relied upon genome-wide markers, the adaptation targeted clinical sequencing panels presents an opportunity incorporate into routine diagnostic workflows. We show that global ancestral contributions and admixture continental populations can be quantitatively inferred using markers captured by MSK-IMPACT panel. In a...
Abstract Although the incidence of endometrial carcinoma (EC) is similar in Black and White women, racial disparities are stark, with highest mortality rates observed among patients. Here, analysis 1,882 prospectively sequenced ECs using a clinical FDA-authorized tumor–normal panel revealed significantly higher prevalence high-risk histologic molecular EC subtypes self-identified (n = 259) compared 1,623) Clinically actionable alterations, including high tumor mutational...
Importance Although differences in the prevalence of key cancer-specific somatic mutations as a function genetic ancestry among patients with cancer has been well-established, few studies have addressed practical clinical implications these for growing number biomarker-driven treatments. Objective To determine if approval precision oncology therapies benefited from various ancestral backgrounds equally over time. Design, Setting, and Participants A retrospective analysis samples solid...
Sequencing of matched tumor and normal samples is the standard study design for reliable detection somatic alterations. However, even very low levels cross-sample contamination significantly impact calling mutations, because contaminant germline variants can be incorrectly interpreted as somatic. There are currently no sequence-only based methods that reliably estimate in samples, which frequently display copy number changes. As a solution, we developed Conpair, tool sample swaps...
Waterlogging causes yield penalty in maize-growing countries of subtropical regions. Transcriptome analysis the roots a tolerant inbred HKI1105 using RNA sequencing revealed 21,364 differentially expressed genes (DEGs) under waterlogged stress condition. These DEGs are known to regulate important pathways including energy-production, programmed cell death (PCD), aerenchyma formation, and ethylene responsiveness. High up-regulation invertase (49-fold) hexokinase (36-fold) explained ATP...
Cancer genomes from patients with African (AFR) ancestry have been poorly studied in clinical research. We leverage two large genomic cohorts to investigate the relationship between alterations and AFR six common cancers. Cross-cancer type associations, such as an enrichment of MYC amplification lung, breast, prostate cancers, depletion BRAF are observed colorectal pancreatic There differences actionable alterations, KRAS G12C EGFR L858R, ROS1 fusion lung Interestingly, cancer, mutations...
To test the performance of a new sequencing platform, develop an updated somatic calling pipeline and establish reference for future benchmarking experiments, we performed whole-genome 3 common cancer cell lines (COLO-829, HCC-1143 HCC-1187) along with their matched normal to great depths (up 278x coverage) on both Illumina HiSeqX NovaSeq instruments. Somatic was generally consistent between two platforms despite minor differences at read level. We designed implemented novel analysis...
Background Germline risk assessment is increasing as part of cancer care; however, disparities in subsequent genetic counseling are unknown. Methods Pan‐cancer patients were prospectively consented to tumor‐normal sequencing via custom next generation panel (Memorial Sloan Kettering‐Integrated Mutation Profiling Actionable Cancer Targets) inclusive germline analysis ≥76 genes from January 2015 through December 2019 (97.5% research nonbillable) with protocol for genetics referral. Rates...
Abstract While the genomes of normal tissues undergo dynamic changes over time, little is understood about temporal-spatial dynamics in premalignant that progress to cancer compared those remain cancer-free. Here we use whole genome sequencing contrast genomic alterations 427 longitudinal samples from 40 patients with stable Barrett’s esophagus who progressed esophageal adenocarcinoma (ESAD). We show same somatic mutational processes are active tissue regardless outcome, high levels...
Abstract Understanding the molecular and phenotypic profile of colorectal cancer (CRC) in West Africa is vital to addressing regions rising burden disease. Tissue from unselected Nigerian patients was analyzed with a multigene, next-generation sequencing assay. The rate microsatellite instability significantly higher among CRC (28.1%) than Cancer Genome Atlas (TCGA, 14.2%) Memorial Sloan Kettering Center (MSKCC, 8.5%, P < 0.001). In microsatellite-stable cases, tumors are less likely have...