My research is focused on precision medicine - specifically using high-throughput techniques like next-generation sequencing, to characterize the cancer genome and identify clinically relevant biomarkers/ therapeutic targets for drug discovery. As a leukemia survivor, I owe my recovery to a precision medicine drug, and so precision medicine has become both a professional and personal calling. Address: Los Angeles, CA
Supplementary Figures S1-2, Tables S1-3. Figure S1. Comparison of the number of high confidence, ... more Supplementary Figures S1-2, Tables S1-3. Figure S1. Comparison of the number of high confidence, non-synonymous somatic point mutations/indels and high level copy number alterations (CNAs) by tumor grade. Figure S2. Copy number plots of representative benign and borderline phyllodes tumors. Table S2: Somatic non-synonymous mutations identified in FFPE phyllodes tumors subjected to targeted next generation sequencing. Table S3: Detailed information about identified somatic non-synonymous mutations.
Annals of oncology : official journal of the European Society for Medical Oncology / ESMO, Jan 3, 2015
Comprehensive molecular profiling led to the recognition of multiple prostate cancer (PCa) molecu... more Comprehensive molecular profiling led to the recognition of multiple prostate cancer (PCa) molecular subtypes and driving alterations, but translating these findings to clinical practice is challenging. We developed a formalin fixed paraffin embedded (FFPE) tissue compatible integrative assay for PCa molecular subtyping and interrogation of relevant genetic/transcriptomic alterations (MiPC). We applied MiPC, which combines capture based next generation sequencing and quantitative reverse transcription PCR (qRT-PCR), to 53 FFPE PCa specimens representing cases not well represented in frozen tissue cohorts, including 8 paired primary tumor and lymph node metastases. Results were validated using multiplexed PCR based NGS and Sanger sequencing. We identified known and novel potential driving, somatic mutations and copy number alterations, including a novel BRAF T599_V600insHT mutation and CYP11B2 amplification in a patient treated with ketoconazole (a potent CYP11B2 inhibitor). qRT-PCR ...
Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers... more Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible withā¦
Phyllodes tumors are rare fibroepithelial tumors with variable clinical behavior accounting for a... more Phyllodes tumors are rare fibroepithelial tumors with variable clinical behavior accounting for a small subset of all breast neoplasms, yet little is known about the genetic alterations that drive tumor initiation and/or progression. Here targeted next generation sequencing (NGS) was used to identify somatic alterations in formalin fixed paraffin embedded (FFPE) patient specimens from malignant, borderline and benign cases. NGS revealed mutations in mediator complex subunit 12 (MED12) affecting the G44 hotspot residue in the majority (67%) of cases spanning all three histological grades. In addition, loss-of-function mutations in p53 (TP53) as well as deleterious mutations in the tumor suppressors retinoblastoma (RB1) and neurofibromin 1 (NF1) were identified exclusively in malignant tumors. High-level copy number alterations (CNAs) were nearly exclusively confined to malignant tumors, including potentially clinically actionable gene amplifications in IGF1R and EGFR. Taken together,...
Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers... more Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible withā¦
Bladder urothelial carcinoma is typically a disease of older individuals and rarely occurs below ... more Bladder urothelial carcinoma is typically a disease of older individuals and rarely occurs below the age of 40 years.
Supplementary Figures S1-2, Tables S1-3. Figure S1. Comparison of the number of high confidence, ... more Supplementary Figures S1-2, Tables S1-3. Figure S1. Comparison of the number of high confidence, non-synonymous somatic point mutations/indels and high level copy number alterations (CNAs) by tumor grade. Figure S2. Copy number plots of representative benign and borderline phyllodes tumors. Table S2: Somatic non-synonymous mutations identified in FFPE phyllodes tumors subjected to targeted next generation sequencing. Table S3: Detailed information about identified somatic non-synonymous mutations.
Annals of oncology : official journal of the European Society for Medical Oncology / ESMO, Jan 3, 2015
Comprehensive molecular profiling led to the recognition of multiple prostate cancer (PCa) molecu... more Comprehensive molecular profiling led to the recognition of multiple prostate cancer (PCa) molecular subtypes and driving alterations, but translating these findings to clinical practice is challenging. We developed a formalin fixed paraffin embedded (FFPE) tissue compatible integrative assay for PCa molecular subtyping and interrogation of relevant genetic/transcriptomic alterations (MiPC). We applied MiPC, which combines capture based next generation sequencing and quantitative reverse transcription PCR (qRT-PCR), to 53 FFPE PCa specimens representing cases not well represented in frozen tissue cohorts, including 8 paired primary tumor and lymph node metastases. Results were validated using multiplexed PCR based NGS and Sanger sequencing. We identified known and novel potential driving, somatic mutations and copy number alterations, including a novel BRAF T599_V600insHT mutation and CYP11B2 amplification in a patient treated with ketoconazole (a potent CYP11B2 inhibitor). qRT-PCR ...
Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers... more Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible withā¦
Phyllodes tumors are rare fibroepithelial tumors with variable clinical behavior accounting for a... more Phyllodes tumors are rare fibroepithelial tumors with variable clinical behavior accounting for a small subset of all breast neoplasms, yet little is known about the genetic alterations that drive tumor initiation and/or progression. Here targeted next generation sequencing (NGS) was used to identify somatic alterations in formalin fixed paraffin embedded (FFPE) patient specimens from malignant, borderline and benign cases. NGS revealed mutations in mediator complex subunit 12 (MED12) affecting the G44 hotspot residue in the majority (67%) of cases spanning all three histological grades. In addition, loss-of-function mutations in p53 (TP53) as well as deleterious mutations in the tumor suppressors retinoblastoma (RB1) and neurofibromin 1 (NF1) were identified exclusively in malignant tumors. High-level copy number alterations (CNAs) were nearly exclusively confined to malignant tumors, including potentially clinically actionable gene amplifications in IGF1R and EGFR. Taken together,...
Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers... more Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible withā¦
Bladder urothelial carcinoma is typically a disease of older individuals and rarely occurs below ... more Bladder urothelial carcinoma is typically a disease of older individuals and rarely occurs below the age of 40 years.
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