51 results on '"Isaac Kinde"'
Search Results
2. Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy
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Simeon U Springer, Chung-Hsin Chen, Maria Del Carmen Rodriguez Pena, Lu Li, Christopher Douville, Yuxuan Wang, Joshua David Cohen, Diana Taheri, Natalie Silliman, Joy Schaefer, Janine Ptak, Lisa Dobbyn, Maria Papoli, Isaac Kinde, Bahman Afsari, Aline C Tregnago, Stephania M Bezerra, Christopher VandenBussche, Kazutoshi Fujita, Dilek Ertoy, Isabela W Cunha, Lijia Yu, Trinity J Bivalacqua, Arthur P Grollman, Luis A Diaz, Rachel Karchin, Ludmila Danilova, Chao-Yuan Huang, Chia-Tung Shun, Robert J Turesky, Byeong Hwa Yun, Thomas A Rosenquist, Yeong-Shiau Pu, Ralph H Hruban, Cristian Tomasetti, Nickolas Papadopoulos, Ken W Kinzler, Bert Vogelstein, Kathleen G Dickman, and George J Netto
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liquid biopsy ,cancer ,urine ,bladder ,renal pelvis ,ureter ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Current non-invasive approaches for detection of urothelial cancers are suboptimal. We developed a test to detect urothelial neoplasms using DNA recovered from cells shed into urine. UroSEEK incorporates massive parallel sequencing assays for mutations in 11 genes and copy number changes on 39 chromosome arms. In 570 patients at risk for bladder cancer (BC), UroSEEK was positive in 83% of those who developed BC. Combined with cytology, UroSEEK detected 95% of patients who developed BC. Of 56 patients with upper tract urothelial cancer, 75% tested positive by UroSEEK, including 79% of those with non-invasive tumors. UroSEEK detected genetic abnormalities in 68% of urines obtained from BC patients under surveillance who demonstrated clinical evidence of recurrence. The advantages of UroSEEK over cytology were evident in low-grade BCs; UroSEEK detected 67% of cases whereas cytology detected none. These results establish the foundation for a new non-invasive approach for detection of urothelial cancer.
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- 2018
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3. Diagnostic potential of tumor DNA from ovarian cyst fluid
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Yuxuan Wang, Karin Sundfeldt, Constantina Mateoiu, Ie-Ming Shih, Robert J Kurman, Joy Schaefer, Natalie Silliman, Isaac Kinde, Simeon Springer, Michael Foote, Björg Kristjansdottir, Nathan James, Kenneth W Kinzler, Nickolas Papadopoulos, Luis A Diaz, and Bert Vogelstein
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biomarker ,tumor DNA ,ovarian cancer ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
We determined whether the mutations found in ovarian cancers could be identified in the patients' ovarian cyst fluids. Tumor-specific mutations were detectable in the cyst fluids of 19 of 23 (83%) borderline tumors, 10 of 13 (77%) type I cancers, and 18 of 18 (100%) type II cancers. In contrast, no mutations were found in the cyst fluids of 18 patients with benign tumors or non-neoplastic cysts. Though large, prospective studies are needed to demonstrate the safety and clinical utility of this approach, our results suggest that the genetic evaluation of cyst fluids might be able to inform the management of the large number of women with these lesions.
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- 2016
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4. FAST-SeqS: a simple and efficient method for the detection of aneuploidy by massively parallel sequencing.
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Isaac Kinde, Nickolas Papadopoulos, Kenneth W Kinzler, and Bert Vogelstein
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Medicine ,Science - Abstract
Massively parallel sequencing of cell-free, maternal plasma DNA was recently demonstrated to be a safe and effective screening method for fetal chromosomal aneuploidies. Here, we report an improved sequencing method achieving significantly increased throughput and decreased cost by replacing laborious sequencing library preparation steps with PCR employing a single primer pair designed to amplify a discrete subset of repeated regions. Using this approach, samples containing as little as 4% trisomy 21 DNA could be readily distinguished from euploid samples.
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- 2012
- Full Text
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5. Supplementary Table 1 from TERT Promoter Mutations Occur Early in Urothelial Neoplasia and Are Biomarkers of Early Disease and Disease Recurrence in Urine
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George J. Netto, Nickolas Papadopoulos, Bert Vogelstein, Kenneth W. Kinzler, Luis A. Diaz, Yuxuan Wang, Simeon Springer, Mohamad Allaf, Trinity Bivalacqua, Mark Schoenberg, Ralph H. Hruban, Sheila F. Faraj, Enrico Munari, and Isaac Kinde
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PDF file - 8K, Table S1. TERT promoter mutation status in 59 pTa and 17 carcinoma in situ (CIS) patients.
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- 2023
6. Feasibility of blood testing combined with PET-CT to screen for cancer and guide intervention
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Ralph H. Hruban, Kathleen Sheridan, Christoph Lengauer, Andrew Warren, Cristian Tomasetti, Leonardo N. Hagmann, Aalpen A. Patel, Ashley Honushefsky, Christian S. Adonizio, Elliot K. Fishman, Prianka Bhattacharya, Joseph Vadakara, Zachary M. Salvati, Christopher D. Still, Bobbi Urban, Joshua D. Cohen, Anne Marie Lennon, Adam H. Buchanan, Lisa Kann, Chetan Bettegowda, Julie I. Woods, David L. Diehl, Nirav Malani, Rosemary Leeming, David H. Ledbetter, Nickolas Papadopoulos, Hee Jung Hwang, Kamel Lahouel, Isaac Kinde, Fred Sanfilippo, Alison P. Klein, Carroll Walter, Alex Parker, Kenneth W. Kinzler, Shibin Zhou, David D. K. Rolston, Christopher Douville, Dillenia Rosica, Bert Vogelstein, and Ariella Cohain
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medicine.medical_specialty ,MEDLINE ,Disease ,Article ,Cohort Studies ,Fluorodeoxyglucose F18 ,Intervention (counseling) ,Neoplasms ,Positron Emission Tomography Computed Tomography ,medicine ,Mass Screening ,Humans ,Clinical care ,Blood testing ,Early Detection of Cancer ,Aged ,PET-CT ,Hematologic Tests ,Multidisciplinary ,business.industry ,Cancer ,medicine.disease ,Feasibility Studies ,Female ,Radiology ,business ,Cohort study - Abstract
A real-time trial of a cancer blood test Cancers diagnosed early are often more responsive to treatment. Blood tests that detect molecular markers of cancer have successfully identified individuals already known to have the disease. Lennon et al. conducted an exploratory study that more closely reflects the way in which such blood tests would be used in the future. They evaluated the feasibility and safety of incorporating a multicancer blood test into the routine clinical care of 10,000 women with no history of cancer. Over a 12-month period, the blood test detected 26 cancers of different types. A combination of the blood test and positron emission tomography–computed tomography (PET-CT) imaging led to surgical removal of nine of these cancers. Use of the blood test did not result in a large number of futile follow-up procedures. Science , this issue p. eabb9601
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- 2020
7. Detection of aneuploidy in patients with cancer through amplification of long interspersed nucleotide elements (LINEs)
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Bert Vogelstein, Christopher Douville, Joshua D. Cohen, Nickolas Papadopoulos, Anne Marie Lennon, Isaac Kinde, Ralph H. Hruban, Rachel Karchin, Kenneth W. Kinzler, and Simeon Springer
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0301 basic medicine ,Aneuploidy ,Biology ,Genome ,03 medical and health sciences ,Neoplasms ,medicine ,Humans ,Genetic Predisposition to Disease ,Liquid biopsy ,Allele ,Chromosome Aberrations ,Genetics ,Multidisciplinary ,fungi ,food and beverages ,High-Throughput Nucleotide Sequencing ,Chromosome ,Microsatellite instability ,Cancer ,Biological Sciences ,Amplicon ,medicine.disease ,Long Interspersed Nucleotide Elements ,030104 developmental biology ,Nucleic Acid Amplification Techniques - Abstract
Aneuploidy is a feature of most cancer cells, and a myriad of approaches have been developed to detect it in clinical samples. We previously described primers that could be used to amplify ∼38,000 unique long interspersed nucleotide elements (LINEs) from throughout the genome. Here we have developed an approach to evaluate the sequencing data obtained from these amplicons. This approach, called Within-Sample AneupLoidy DetectiOn (WALDO), employs supervised machine learning to detect the small changes in multiple chromosome arms that are often present in cancers. We used WALDO to search for chromosome arm gains and losses in 1,677 tumors and in 1,522 liquid biopsies of blood from cancer patients or normal individuals. Aneuploidy was detected in 95% of cancer biopsies and in 22% of liquid biopsies. Using single-nucleotide polymorphisms within the amplified LINEs, WALDO concomitantly assesses allelic imbalances, microsatellite instability, and sample identification. WALDO can be used on samples containing only a few nanograms of DNA and as little as 1% neoplastic content and has a variety of applications in cancer diagnostics and forensic science.
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- 2018
8. Serial circulating tumour DNA analysis during multimodality treatment of locally advanced rectal cancer: a prospective biomarker study
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Natallie Silliman, Suzanne Kosmider, Bert Volgestein, Desmond Yip, Hany Elsaleh, Madhu Sudan Singh, David Goldstein, Yuxuan Wang, Matthew Burge, Carolyn Bampton, Iain Skinner, Timothy J. Price, Christos S. Karapetis, Matthew Croxford, Jeanne Tie, Cristian Tomasetti, Ian T. Jones, Lu Li, Andrew Haydon, Rachel Wong, Michael Christie, David Rangiah, Joshua D. Cohen, Mary J Schaefer, Margaret Lee, Nickolas Papadopoulos, Peter Gibbs, Ben Tran, Kenneth W. Kinzler, Koen Simons, Jeanne Ptak, Isaac Kinde, Ian Faragher, and Lisa Dobbyn
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Diagnostic Imaging ,Male ,0301 basic medicine ,Oncology ,medicine.medical_specialty ,Colorectal cancer ,medicine.medical_treatment ,Article ,Circulating Tumor DNA ,03 medical and health sciences ,0302 clinical medicine ,Risk Factors ,Internal medicine ,Biomarkers, Tumor ,medicine ,Adjuvant therapy ,Humans ,Combined Modality Therapy ,Prospective Studies ,Registries ,Prospective cohort study ,Survival analysis ,Neoplasm Staging ,Chemotherapy ,Rectal Neoplasms ,business.industry ,Australia ,Gastroenterology ,Middle Aged ,medicine.disease ,Survival Analysis ,030104 developmental biology ,Mutation ,Biomarker (medicine) ,Female ,030211 gastroenterology & hepatology ,Neoplasm Recurrence, Local ,business ,Chemoradiotherapy - Abstract
ObjectiveFor patients with locally advanced rectal cancer (LARC), adjuvant chemotherapy selection following surgery remains a major clinical dilemma. Here, we investigated the ability of circulating tumour DNA (ctDNA) to improve risk stratification in patients with LARC.DesignWe enrolled patients with LARC (T3/T4 and/or N+) planned for neoadjuvant chemoradiotherapy. Plasma samples were collected pretreatment, postchemoradiotherapy and 4–10 weeks after surgery. Somatic mutations in individual patient’s tumour were identified via massively parallel sequencing of 15 genes commonly mutated in colorectal cancer. We then designed personalised assays to quantify ctDNA in plasma samples. Patients received adjuvant therapy at clinician discretion, blinded to the ctDNA results.ResultsWe analysed 462 serial plasma samples from 159 patients. ctDNA was detectable in 77%, 8.3% and 12% of pretreatment, postchemoradiotherapy and postsurgery plasma samples. Significantly worse recurrence-free survival was seen if ctDNA was detectable after chemoradiotherapy (HR 6.6; PConclusionPostoperative ctDNA analysis stratifies patients with LARC into subsets that are either at very high or at low risk of recurrence, independent of conventional clinicopathological risk factors. ctDNA analysis could potentially be used to guide patient selection for adjuvant chemotherapy.
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- 2018
9. Correction: Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy
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Ralph H. Hruban, Janine Ptak, Cristian Tomasetti, Diana Taheri, Stephania M. Bezerra, Christopher Douville, Isabela Werneck da Cunha, Maria Del Carmen Rodriguez Pena, Maria Papoli, Isaac Kinde, Chia-Tung Shun, Lijia Yu, Yeong-Shiau Pu, Byeong Hwa Yun, Luis A. Diaz, Bert Vogelstein, Christopher J. VandenBussche, Rachel Karchin, Kenneth W. Kinzler, Lu Li, Joy Schaefer, Arthur P. Grollman, Aline C. Tregnago, Thomas A. Rosenquist, Robert J. Turesky, Bahman Afsari, Nickolas Papadopoulos, Kathleen G. Dickman, Kazutoshi Fujita, Trinity J. Bivalacqua, Chung-Hsin Chen, Natalie Silliman, George J. Netto, Joshua D. Cohen, Simeon Springer, Ludmila Danilova, Yuxuan Wang, Dilek Ertoy, Lisa Dobbyn, and Chao-Yuan Huang
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Adult ,Male ,0301 basic medicine ,Adolescent ,QH301-705.5 ,Science ,Aneuploidy ,Gene mutation ,Sensitivity and Specificity ,General Biochemistry, Genetics and Molecular Biology ,Young Adult ,03 medical and health sciences ,0302 clinical medicine ,Gene expression ,Humans ,Urothelial cancer ,Medicine ,Genetic Testing ,Cancer biology ,Biology (General) ,Child ,Telomerase ,Early Detection of Cancer ,Cancer Biology ,Aged ,Aged, 80 and over ,Carcinoma, Transitional Cell ,General Immunology and Microbiology ,business.industry ,General Neuroscience ,Non invasive ,Correction ,General Medicine ,Middle Aged ,Chromosomes and Gene Expression ,medicine.disease ,030104 developmental biology ,Urinary Bladder Neoplasms ,Child, Preschool ,030220 oncology & carcinogenesis ,Mutation ,Cancer research ,Female ,business - Abstract
Current non-invasive approaches for detection of urothelial cancers are suboptimal. We developed a test to detect urothelial neoplasms using DNA recovered from cells shed into urine. UroSEEK incorporates massive parallel sequencing assays for mutations in 11 genes and copy number changes on 39 chromosome arms. In 570 patients at risk for bladder cancer (BC), UroSEEK was positive in 83% of those who developed BC. Combined with cytology, UroSEEK detected 95% of patients who developed BC. Of 56 patients with upper tract urothelial cancer, 75% tested positive by UroSEEK, including 79% of those with non-invasive tumors. UroSEEK detected genetic abnormalities in 68% of urines obtained from BC patients under surveillance who demonstrated clinical evidence of recurrence. The advantages of UroSEEK over cytology were evident in low-grade BCs; UroSEEK detected 67% of cases whereas cytology detected none. These results establish the foundation for a new non-invasive approach for detection of urothelial cancer.
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- 2018
10. High prevalence of TERT promoter mutations in micropapillary urothelial carcinoma
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Isabela Werneck da Cunha, George J. Netto, Bert Vogelstein, Isaac Kinde, Nickolas Papadopoulos, Maria Angelica Mendoza Rodriguez, Kazutoshi Fujita, Doreen Nguyen, Matthew T. Olson, Morgan L. Cowan, Simeon Springer, Kenneth W. Kinzler, Yuxuan Wang, Bernardo F.P. Ricardo, Christopher J. VandenBussche, Diana Taheri, Dilek Ertoy, Trinity J. Bivalacqua, and Gunes Guner
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Male ,0301 basic medicine ,Telomerase ,Somatic cell ,Biology ,medicine.disease_cause ,Article ,Pathology and Forensic Medicine ,03 medical and health sciences ,0302 clinical medicine ,immune system diseases ,Biomarkers, Tumor ,Prevalence ,medicine ,Humans ,Telomerase reverse transcriptase ,Promoter Regions, Genetic ,Molecular Biology ,Gene ,Aged ,Upper urinary tract ,Aged, 80 and over ,Carcinoma, Transitional Cell ,Mutation ,Histology ,Cell Biology ,General Medicine ,Middle Aged ,Carcinoma, Papillary ,030104 developmental biology ,Urinary Bladder Neoplasms ,030220 oncology & carcinogenesis ,Cancer research ,Female ,Carcinogenesis - Abstract
Somatic activating mutations in the promoter of the telomerase reverse transcriptase (TERT) gene are the most common genetic alterations in urothelial carcinoma (UC) of the bladder and upper urinary tract. Little is known, however, about TERT-mutation status in the relatively uncommon but clinically aggressive micropapillary (MPC) variant. We evaluated the presence of TERT promoter mutations in MPC of the bladder and upper urinary tract. A retrospective search of our archives for MPC and UC with micropapillary features (2005–2014) was performed. All slides were reviewed to confirm the histologic diagnosis. Thirty-three specimens from 31 patients had FFPE blocks available for DNA analysis and were included in the study. Intratumoral areas of non-micropapillary histology were also evaluated when present. Samples were analyzed with Safe-SeqS, a sequencing error reduction technology, and sequenced using the Illumina MiSeq platform. TERT promoter mutations were detected in all specimens with pure MPC (18 of 18) and UC with focal micropapillary features (15 of 15). Similar to conventional UC, the predominant mutations identified occurred at positions −124 (C228T) (85 %) and −146 (C250T) (12 %) bp upstream of the TERT ATG start site. In heterogeneous tumors with focal variant histology, intratumoral concordant mutations were found in variant (MPC and non-MPC) and corresponding conventional UC. We found TERT promoter mutations, commonly found in conventional UC, to be frequently present in MPC. Our finding of concordant intratumoral mutational alterations in cases with focal variant histology lends support to the common oncogenesis origin of UC and its variant histology.
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- 2016
11. Detection of TERT promoter mutations in primary adenocarcinoma of the urinary bladder
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George J. Netto, Isabela Werneck da Cunha, Maria Angelica Mendoza Rodriguez, Diana Taheri, Nickolas Papadopoulos, Kazutoshi Fujita, Christopher J. VandenBussche, Dilek Ertoy, Bert Vogelstein, Kenneth W. Kinzler, Yuxuan Wang, Doreen Nguyen, Morgan L. Cowan, Gunes Guner, Maria Del Carmen Rodriguez Pena, Isaac Kinde, Simeon Springer, Mathew T. Olson, and Trinity J. Bivalacqua
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Adult ,Male ,0301 basic medicine ,congenital, hereditary, and neonatal diseases and abnormalities ,Pathology ,medicine.medical_specialty ,medicine.medical_treatment ,DNA Mutational Analysis ,Urine ,Adenocarcinoma ,Biology ,medicine.disease_cause ,Article ,Pathology and Forensic Medicine ,Cystectomy ,03 medical and health sciences ,0302 clinical medicine ,Biomarkers, Tumor ,medicine ,Humans ,Telomerase reverse transcriptase ,Promoter Regions, Genetic ,Telomerase ,Aged ,Retrospective Studies ,Mutation ,Bladder cancer ,Urinary bladder ,Not Otherwise Specified ,Middle Aged ,medicine.disease ,030104 developmental biology ,medicine.anatomical_structure ,Urinary Bladder Neoplasms ,030220 oncology & carcinogenesis ,Baltimore ,Cancer research ,Female - Abstract
TERT promoter mutations (TERT-mut) have been detected in 60% to 80% of urothelial carcinomas. A molecular urine-based screening assay for the detection of TERT-mut is currently being pursued by our group and others. A small but significant number of bladder carcinomas are adenocarcinoma. The current study assesses the incidence of TERT-mut in primary adenocarcinomas of urinary bladder. A retrospective search of our institutional pathology records identified 23 cystectomy specimens with a diagnosis of adenocarcinoma (2000–2014). All slides were reviewed by a senior urologic pathologist to confirm tumor type and select a representative formalin-fixed, paraffin-embedded block for mutational analysis. Adequate material for DNA testing was available in 14 cases (7 enteric type and 7 not otherwise specified). TERT-mut sequencing analysis was performed using previously described SafeSeq technique. Overall, 28.5% of primary adenocarcinoma harbored TERT-mut. Interestingly, 57% of nonenteric adenocarcinomas were mutation positive, whereas none of the enteric-type tumors harbored mutations. Similar to urothelial carcinoma, we found a relatively higher rate of TERT-mut among nonenteric-type adenocarcinomas further supporting the potential utility of TERT-mut urine-based screening assay for bladder cancer.
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- 2016
12. Lavage of the Uterine Cavity for Molecular Detection of Müllerian Duct Carcinomas: A Proof-of-Concept Study
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Florian Heitz, Paul Speiser, Jalid Sehouli, Robert Zeillinger, Nickolas Papadopoulos, Els Van Nieuwenhuysen, Elisabeth Maritschnegg, Yuxuan Wang, Nina Pecha, Bert Vogelstein, Luis Diaz, Isaac Kinde, Ignace Vergote, Reinhard Horvat, and Kenneth W. Kinzler
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Adult ,Cancer Research ,Pathology ,medicine.medical_specialty ,Mullerian Ducts ,Therapeutic irrigation ,Pilot Projects ,Polymerase Chain Reaction ,Proto-Oncogene Proteins p21(ras) ,Carcinoma ,medicine ,Humans ,Therapeutic Irrigation ,Survival rate ,Early Detection of Cancer ,Aged ,Ovarian Neoplasms ,Gynecologic Cancer ,Massive parallel sequencing ,business.industry ,Endometrial cancer ,Gync9 ,Uterus ,ORIGINAL REPORTS ,Middle Aged ,medicine.disease ,Gync16 ,Endometrial Neoplasms ,medicine.anatomical_structure ,Oncology ,Mutation ,Neoplasms, Unknown Primary ,Female ,Uterine cavity ,business ,Ovarian cancer - Abstract
Purpose Type II ovarian cancer (OC) and endometrial cancer (EC) are generally diagnosed at an advanced stage, translating into a poor survival rate. There is increasing evidence that Müllerian duct cancers may exfoliate cells. We have established an approach for lavage of the uterine cavity to detect shed cancer cells. Patients and Methods Lavage of the uterine cavity was used to obtain samples from 65 patients, including 30 with OC, five with EC, three with other malignancies, and 27 with benign lesions involving gynecologic organs. These samples, as well as corresponding tumor tissue, were examined for the presence of somatic mutations using massively parallel sequencing (next-generation sequencing) and, in a subset, singleplex analysis. Results The lavage technique could be applied successfully, and sufficient amounts of DNA were obtained in all patients. Mutations, mainly in TP53, were identified in 18 (60%) of 30 lavage samples of patients with OC using next-generation sequencing. Singleplex analysis of mutations previously determined in corresponding tumor tissue led to further identification of six patients. Taken together, in 24 (80%) of 30 patients with OC, specific mutations could be identified. This also included one patient with occult OC. All five analyzed lavage specimens from patients with EC harbored mutations. Eight (29.6%) of 27 patients with benign lesions tested positive for mutations, six (75%) as a result of mutations in the KRAS gene. Conclusion This study proved that tumor cells from ovarian neoplasms are shed and can be collected via lavage of the uterine cavity. Detection of OC and EC and even clinically occult OC was achieved, making it a potential tool of significant promise for early diagnosis.
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- 2015
13. A Combination of Molecular Markers and Clinical Features Improve the Classification of Pancreatic Cysts
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Volkan Adsay, Herbert J. Zeh, David S. Klimstra, Oscar W. Cummings, Jean Murphy, Bert Vogelstein, John L. Cameron, Jorge Paulino, Marco Dal Molin, Giuseppe Zamboni, Carlos Fernandez-del Castillo, Tyler M. Tomita, Song Cheol Kim, Michele T. Yip-Schneider, Nita Ahuja, Janine Ptak, Anne Marie Lennon, Siva P. Raman, C. Max Schmidt, Justin Geoghegan, Christopher L. Wolfgang, Kenji Yamao, Noushin Niknafs, Isaac Kinde, Mari Mino-Kenudson, Giuseppe Malleo, Jeanin E. van Hooft, Rachel Karchin, Kenneth W. Kinzler, Yuxuan Wang, Niall Swan, Seung-Mo Hong, James R. Eshleman, Christopher Douville, William R. Brugge, Lisa Dobbyn, Sun Whe Kim, Schalk Van der Merwe, Wooil Kwon, Mark A. Schattner, Matthew J. Weiss, Nickolas Papadopoulos, Barish H. Edil, Yuchen Jiao, Kenzo Hirose, Aldo Scarpa, Susuma Hijioka, Marcia I. Canto, Martin A. Makary, Shinichi Yachida, Roberto Salvia, Simeon Springer, Luis A. Diaz, Amanda L. Blackford, Aatur D. Singhi, David L. Masica, Nobuyoshi Hiraoka, Michael Goggins, Meredith E. Pittman, Satoshi Nara, Ki Byung Song, Randall E. Brand, Massimo Falconi, Peter J. Allen, Ralph H. Hruban, Jin-Young Jang, Richard D. Schulick, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, CCA -Cancer Center Amsterdam, Gastroenterology and Hepatology, Springer, Simeon, Wang, Yuxuan, Dal Molin, Marco, Masica David, L, Jiao, Yuchen, Kinde, Isaac, Blackford, Amanda, Raman Siva, P, Wolfgang Christopher, L, Tomita, Tyler, Niknafs, Noushin, Douville, Christopher, Ptak, Janine, Dobbyn, Lisa, Allen Peter, J, Klimstra David, S, Schattner Mark, A, Schmidt C., Max, Yip Schneider, Michele, Cummings Oscar, W, Brand Randall, E, Zeh Herbert, J, Singhi Aatur, D, Scarpa, Aldo, Salvia, Roberto, Malleo, Giuseppe, Zamboni, Giuseppe, Falconi, Massimo, Jang Jin, Young, Kim Sun, Whe, Kwon, Wooil, Hong Seung, Mo, Song Ki, Byung, Kim Song, Cheol, Swan, Niall, Murphy, Jean, Geoghegan, Justin, Brugge, William, Fernandez Del Castillo, Carlo, Mino Kenudson, Mari, Schulick, Richard, Edil Barish, H, Adsay, Volkan, Paulino, Jorge, van Hooft, Jeanin, Yachida, Shinichi, Nara, Satoshi, Hiraoka, Nobuyoshi, Yamao, Kenji, Hijioka, Susuma, van der Merwe, Schalk, Goggins, Michael, Canto Marcia, Irene, Ahuja, Nita, Hirose, Kenzo, Makary, Martin, Weiss Matthew, J, Cameron, John, Pittman, Meredith, Eshleman James, R, Diaz Luis A., Jr, Papadopoulos, Nickola, Kinzler Kenneth, W, Karchin, Rachel, Hruban Ralph, H, Vogelstein, Bert, and Lennon Anne, Marie
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Adult ,Male ,Pathology ,medicine.medical_specialty ,diagnosis ,medicine.disease_cause ,Article ,chemistry.chemical_compound ,Predictive Value of Tests ,CDKN2A ,Molecular marker ,Biomarkers, Tumor ,GNAS complex locus ,medicine ,Humans ,Genetic Predisposition to Disease ,Cyst ,molecular ,Genetic Testing ,Pancreas ,neoplasms ,IPMN ,pancreatic cyst ,Retrospective Studies ,Hepatology ,biology ,Intraductal papillary mucinous neoplasm ,Gastroenterology ,Middle Aged ,Prognosis ,medicine.disease ,Phenotype ,medicine.anatomical_structure ,chemistry ,Mutation ,biology.protein ,Female ,KRAS ,Pancreatic Cyst ,Pancreatic cysts ,Algorithms - Abstract
Background & Aims The management of pancreatic cysts poses challenges to both patients and their physicians. We investigated whether a combination of molecular markers and clinical information could improve the classification of pancreatic cysts and management of patients. Methods We performed a multi-center, retrospective study of 130 patients with resected pancreatic cystic neoplasms (12 serous cystadenomas, 10 solid pseudopapillary neoplasms, 12 mucinous cystic neoplasms, and 96 intraductal papillary mucinous neoplasms). Cyst fluid was analyzed to identify subtle mutations in genes known to be mutated in pancreatic cysts ( BRAF , CDKN2A , CTNNB1 , GNAS , KRAS , NRAS , PIK3CA , RNF43 , SMAD4 , TP53 , and VHL ); to identify loss of heterozygozity at CDKN2A , RNF43 , SMAD4 , TP53 , and VHL tumor suppressor loci; and to identify aneuploidy. The analyses were performed using specialized technologies for implementing and interpreting massively parallel sequencing data acquisition. An algorithm was used to select markers that could classify cyst type and grade. The accuracy of the molecular markers was compared with that of clinical markers and a combination of molecular and clinical markers. Results We identified molecular markers and clinical features that classified cyst type with 90%−100% sensitivity and 92%−98% specificity. The molecular marker panel correctly identified 67 of the 74 patients who did not require surgery and could, therefore, reduce the number of unnecessary operations by 91%. Conclusions We identified a panel of molecular markers and clinical features that show promise for the accurate classification of cystic neoplasms of the pancreas and identification of cysts that require surgery.
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- 2015
14. Targeted sequencing of plasmacytoid urothelial carcinoma reveals frequent TERT promoter mutations
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Yuxuan Wang, Maria Angelica Mendoza Rodriguez, Maria Del Carmen Rodriguez Pena, Isabela Werneck da Cunha, Kenneth W. Kinzler, Kazutoshi Fujita, Trinity J. Bivalacqua, Gunes Guner, Doreen N. Palsgrove, George J. Netto, Isaac Kinde, Morgan L. Cowan, Dilek Ertoy, Diana Taheri, Nickolas Papadopoulos, Bert Vogelstein, Bernardo F.P. Ricardo, and Simeon Springer
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0301 basic medicine ,Male ,Urologic Neoplasms ,Biology ,medicine.disease_cause ,Proto-Oncogene Mas ,Article ,Pathology and Forensic Medicine ,CDH1 ,03 medical and health sciences ,0302 clinical medicine ,Mutation Rate ,medicine ,Humans ,Telomerase reverse transcriptase ,Liquid biopsy ,Promoter Regions, Genetic ,Gene ,Telomerase ,Aged ,Retrospective Studies ,Aged, 80 and over ,Mutation ,Carcinoma, Transitional Cell ,Bladder cancer ,Signet ring cell ,Middle Aged ,medicine.disease ,030104 developmental biology ,030220 oncology & carcinogenesis ,Cancer research ,biology.protein ,Female ,KRAS ,Urothelium - Abstract
Summary Activating mutations in the promoter of the telomerase reverse transcriptase (TERT) gene are the most common genetic alterations in urothelial carcinoma (UC) of the bladder and upper urinary tract. Although the cadherin 1 (CDH1) gene is commonly mutated in the clinically aggressive plasmacytoid variant of urothelial carcinoma (PUC), little is known about their TERT promoter mutation status. A retrospective search of our archives for PUC and UC with plasmacytoid and/or signet ring cell features (2007-2014) was performed. Ten specimens from 10 patients had archived material available for DNA analysis and were included in the study. Intratumoral areas of nonplasmacytoid histology were also evaluated when present. Samples were analyzed for TERT promoter mutations with Safe-SeqS, a sequencing error-reduction technology, and sequenced using a targeted panel of the 10 most commonly mutated genes in bladder cancer on the Illumina MiSeq platform. TERT promoter mutations were detected in specimens with pure and focal plasmacytoid features (6/10). Similar to conventional UC, the predominant mutation identified was g.1295228C>T. In heterogeneous tumors with focal variant histology, concordant mutations were found in plasmacytoid and corresponding conventional, glandular, or sarcomatoid areas. Co-occurring mutations in tumor protein p53 (TP53, 2 cases) and kirsten rat sarcoma (KRAS) viral proto-oncogene (1 case) were also detected. TERT promoter mutations are frequently present in PUC, which provides further evidence that TERT promoter mutations are common events in bladder cancer, regardless of histologic subtype, and supports their inclusion in any liquid biopsy assay for bladder cancer.
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- 2018
15. Evaluation of liquid from the Papanicolaou test and other liquid biopsies for the detection of endometrial and ovarian cancers
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Douglas A. Levine, Christopher Douville, Edward J. Tanner, Lisa Dobbyn, Lili Fu, Nickolas Papadopoulos, Ana M. Angarita, Kris Jardon, Jocelyne Arseneau, Rachel Karchin, Kenneth W. Kinzler, Karin Sundfelt, Ludmila Danilova, Maria Popoli, Ie Ming Shih, Tian Li Wang, Natalie Silliman, Yuxuan Wang, Robert J. Kurman, Isaac Kinde, Bert Vogelstein, Amanda N. Fader, Joy Schaefer, Maria Lycke, Bahman Afsari, Xing Zeng, Joshua D. Cohen, Lu Li, Susanne K. Kjaer, Luis A. Diaz, Ralph H. Hruban, Cristian Tomasetti, Ting Tai Yen, Janine Ptak, Kirsten Marie Jochumsen, Lucy Gilbert, and Simeon Springer
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0301 basic medicine ,Adult ,medicine.medical_specialty ,Adolescent ,Aneuploidy ,Papanicolaou stain ,Malignancy ,Gastroenterology ,Article ,03 medical and health sciences ,Young Adult ,0302 clinical medicine ,Internal medicine ,medicine ,Humans ,Stage (cooking) ,Aged ,Retrospective Studies ,Ovarian Neoplasms ,Vaginal Smears ,030102 biochemistry & molecular biology ,business.industry ,Endometrial cancer ,Liquid Biopsy ,Obstetrics and Gynecology ,Cancer ,General Medicine ,Papanicolaou Test ,Middle Aged ,medicine.disease ,Endometrial Neoplasms ,030104 developmental biology ,030220 oncology & carcinogenesis ,Female ,Ovarian cancer ,business - Abstract
We report the detection of endometrial and ovarian cancers based on genetic analyses of DNA recovered from the fluids obtained during a routine Papanicolaou (Pap) test. The new test, called PapSEEK, incorporates assays for mutations in 18 genes as well as an assay for aneuploidy. In Pap brush samples from 382 endometrial cancer patients, 81% [95% confidence interval (CI), 77 to 85%] were positive, including 78% of patients with early-stage disease. The sensitivity in 245 ovarian cancer patients was 33% (95% CI, 27 to 39%), including 34% of patients with early-stage disease. In contrast, only 1.4% of 714 women without cancer had positive Pap brush samples (specificity, ~99%). Next, we showed that intrauterine sampling with a Tao brush increased the detection of malignancy over endocervical sampling with a Pap brush: 93% of 123 (95% CI, 87 to 97%) patients with endometrial cancer and 45% of 51 (95% CI, 31 to 60%) patients with ovarian cancer were positive, whereas none of the samples from 125 women without cancer were positive (specificity, 100%). Finally, in 83 ovarian cancer patients in whom plasma was available, circulating tumor DNA was found in 43% of patients (95% CI, 33 to 55%). When plasma and Pap brush samples were both tested, the sensitivity for ovarian cancer increased to 63% (95% CI, 51 to 73%). These results demonstrate the potential of mutation-based diagnostics to detect gynecologic cancers at a stage when they are more likely to be curable.
- Published
- 2018
16. Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy
- Author
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Ralph H. Hruban, Cristian Tomasetti, Christopher J. VandenBussche, Isabela Werneck da Cunha, Joshua D. Cohen, Byeong Hwa Yun, Kathleen G. Dickman, Maria Papoli, Chia-Tung Shun, Diana Taheri, Simeon Springer, Ludmila Danilova, Kazutoshi Fujita, Luis A. Diaz, Joy Schaefer, Natalie Silliman, Lijia Yu, George J. Netto, Maria Del Carmen Rodriguez Pena, Janine Ptak, Lu Li, Bert Vogelstein, Isaac Kinde, Aline C. Tregnago, Arthur P. Grollman, Bahman Afsari, Stephania M. Bezerra, Nickolas Papadopoulos, Trinity J. Bivalacqua, Yuxuan Wang, Thomas A. Rosenquist, Robert J. Turesky, Chung-Hsin Chen, Rachel Karchin, Kenneth W. Kinzler, Christopher Douville, Chao-Yuan Huang, Yeong-Shiau Pu, Dilek Ertoy, and Lisa Dobbyn
- Subjects
0301 basic medicine ,renal pelvis ,QH301-705.5 ,Science ,Aneuploidy ,Gene mutation ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Cytology ,Medicine ,cancer ,Liquid biopsy ,Biology (General) ,bladder ,Cancer Biology ,Massive parallel sequencing ,Bladder cancer ,General Immunology and Microbiology ,liquid biopsy ,business.industry ,General Neuroscience ,Cancer ,General Medicine ,medicine.disease ,urine ,3. Good health ,030104 developmental biology ,medicine.anatomical_structure ,Genes and Chromosomes ,030220 oncology & carcinogenesis ,ureter ,Cancer research ,business ,Renal pelvis ,Research Article ,Human - Abstract
Current non-invasive approaches for detection of urothelial cancers are suboptimal. We developed a test to detect urothelial neoplasms using DNA recovered from cells shed into urine. UroSEEK incorporates massive parallel sequencing assays for mutations in 11 genes and copy number changes on 39 chromosome arms. In 570 patients at risk for bladder cancer (BC), UroSEEK was positive in 83% of those who developed BC. Combined with cytology, UroSEEK detected 95% of patients who developed BC. Of 56 patients with upper tract urothelial cancer, 75% tested positive by UroSEEK, including 79% of those with non-invasive tumors. UroSEEK detected genetic abnormalities in 68% of urines obtained from BC patients under surveillance who demonstrated clinical evidence of recurrence. The advantages of UroSEEK over cytology were evident in low-grade BCs; UroSEEK detected 67% of cases whereas cytology detected none. These results establish the foundation for a new non-invasive approach for detection of urothelial cancer.
- Published
- 2018
17. Non-invasive detection of bladder cancer through the analysis of driver gene mutations and aneuploidy
- Author
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Simeon Springer, Maria Del Carmen Rodriguez Pena, Lu Li, Christopher Douville, Yuxuan Wang, Josh Cohen, Diana Taheri, Bahman Afsari, Natalie Silliman, Joy Schaeffer, Janine Ptak, Lisa Dobbyn, Maria Papoli, Isaac Kinde, Aline C. Tregnago, Stephania M. Bezerra, Christopher VandenBussche, Kazutoshi Fujita, Dilek Ertoy, Isabela W. Cunha, Lijia Yu, Mark Schoenberg, Trinity J. Bivalacqua, Kathleen G. Dickman, Arthur P. Grollman, Luis A. Diaz, Rachel Karchin, Ralph Hruban, Cristian Tomasetti, Nickolas Papadopoulos, Kenneth W. Kinzler, Bert Vogelstein, and George J. Netto
- Subjects
0303 health sciences ,medicine.medical_specialty ,Bladder cancer ,business.industry ,Aneuploidy ,Chromosome ,Urine ,Gene mutation ,medicine.disease ,Gastroenterology ,3. Good health ,03 medical and health sciences ,0302 clinical medicine ,030220 oncology & carcinogenesis ,Internal medicine ,Cytology ,medicine ,Dysuria ,Microscopic hematuria ,medicine.symptom ,business ,030304 developmental biology - Abstract
Current non-invasive approaches for bladder cancer (BC) detection are suboptimal. We report the development of non-invasive molecular test for BC using DNA recovered from cells shed into urine. This “UroSEEK” test incorporates assays for mutations in 11 genes and copy number changes on 39 chromosome arms. We first evaluated 570 urine samples from patients at risk for BC (microscopic hematuria or dysuria). UroSEEK was positive in 83% of patients that developed BC, but in only 7% of patients who did not develop BC. Combined with cytology, 95% of patients that developed BC were positive. We then evaluated 322 urine samples from patients soon after their BCs had been surgically resected. UroSEEK detected abnormalities in 66% of the urine samples from these patients, sometimes up to 4 years prior to clinical evidence of residual neoplasia, while cytology was positive in only 25% of such urine samples. The advantages of UroSEEK over cytology were particularly evident in low-grade tumors, wherein cytology detected none while UroSEEK detected 67% of 49 cases. These results establish the foundation for a new, non-invasive approach to the detection of BC in patients at risk for initial or recurrent disease.
- Published
- 2017
18. Non-invasive detection of upper tract urothelial carcinomas through the analysis of driver gene mutations and aneuploidy in urine
- Author
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Chia-Tung Shun, Rachel Karchin, Kenneth W. Kinzler, Lu Li, Yeong-Shiau Pu, Arthur P. Grollman, Simeon Springer, Ralph H. Hruban, Christopher Douville, Byeong Hwa Yun, Cristian Tomasetti, Bert Vogelstein, Thomas A. Rosenquist, Chung-Hsin Chen, Robert J. Turesky, Ludmila Danilova, Josh Cohen, Natalie Silliman, Janine Ptak, Georges Jabboure Netto, Yuxuan Wang, Lisa Dobbyn, Chao-Yuan Huang, Kathleen G. Dickman, Maria Papoli, Joy Schaeffer, Nickolas Papadopoulos, Isaac Kinde, and Bahman Afsari
- Subjects
Genetics ,0303 health sciences ,Pathology ,medicine.medical_specialty ,medicine.diagnostic_test ,Urinary system ,Aristolochic acid ,Aneuploidy ,Urine ,Biology ,Gene mutation ,medicine.disease ,3. Good health ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Ureter ,medicine.anatomical_structure ,chemistry ,030220 oncology & carcinogenesis ,medicine ,Renal pelvis ,030304 developmental biology ,Urine cytology - Abstract
Upper tract urothelial carcinomas (UTUC) of the renal pelvis or ureter can be difficult to detect and challenging to diagnose. Here, we report the development and application of a non-invasive test for UTUC based on molecular analyses of DNA recovered from cells shed into the urine. The test, called UroSEEK, incorporates assays for mutations in eleven genes frequently mutated in urologic malignancies and for allelic imbalances on 39 chromosome arms. At least one genetic abnormality was detected in 75% of urinary cell samples from 56 UTUC patients but in only 0.5% of 188 samples from healthy individuals. The assay was considerably more sensitive than urine cytology, the current standard-of-care. UroSEEK therefore has the potential to be used for screening or to aid in diagnosis in patients at increased risk for UTUC, such as those exposed to herbal remedies containing the carcinogen aristolochic acid.
- Published
- 2017
19. Circulating tumor DNA as an early marker of therapeutic response in patients with metastatic colorectal cancer
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Nick Papadopoulos, Kenneth W. Kinzler, Mark Tacey, J. Roebert, Ben Tran, Robert L. Strausberg, Isaac Kinde, Jayesh Desai, MacDonald J. Christie, Peter Gibbs, Rachel Wong, Luis A. Diaz, Yuxuan Wang, Hui-Li Wong, Jeanne Tie, Christos S. Karapetis, Bert Vogelstein, and Madhu Sudan Singh
- Subjects
Male ,Oncology ,medicine.medical_specialty ,Organoplatinum Compounds ,Bevacizumab ,Colorectal cancer ,Irinotecan ,Disease-Free Survival ,Carcinoembryonic antigen ,Internal medicine ,Antineoplastic Combined Chemotherapy Protocols ,Biomarkers, Tumor ,Carcinoma ,medicine ,Humans ,Prospective Studies ,Aged ,biology ,business.industry ,Cancer ,DNA ,Hematology ,Middle Aged ,medicine.disease ,Oxaliplatin ,Response Evaluation Criteria in Solid Tumors ,Mutation ,biology.protein ,Camptothecin ,Female ,Colorectal Neoplasms ,business ,medicine.drug - Abstract
Early indicators of treatment response in metastatic colorectal cancer (mCRC) could conceivably be used to optimize treatment. We explored early changes in circulating tumor DNA (ctDNA) levels as a marker of therapeutic efficacy.This prospective study involved 53 mCRC patients receiving standard first-line chemotherapy. Both ctDNA and CEA were assessed in plasma collected before treatment, 3 days after treatment and before cycle 2. Computed tomography (CT) scans were carried out at baseline and 8-10 weeks and were centrally assessed using RECIST v1.1 criteria. Tumors were sequenced using a panel of 15 genes frequently mutated in mCRC to identify candidate mutations for ctDNA analysis. For each patient, one tumor mutation was selected to assess the presence and the level of ctDNA in plasma samples using a digital genomic assay termed Safe-SeqS.Candidate mutations for ctDNA analysis were identified in 52 (98.1%) of the tumors. These patient-specific candidate tissue mutations were detectable in the cell-free DNA from the plasma of 48 of these 52 patients (concordance 92.3%). Significant reductions in ctDNA (median 5.7-fold; P0.001) levels were observed before cycle 2, which correlated with CT responses at 8-10 weeks (odds ratio = 5.25 with a 10-fold ctDNA reduction; P = 0.016). Major reductions (≥10-fold) versus lesser reductions in ctDNA precycle 2 were associated with a trend for increased progression-free survival (median 14.7 versus 8.1 months; HR = 1.87; P = 0.266).ctDNA is detectable in a high proportion of treatment naïve mCRC patients. Early changes in ctDNA during first-line chemotherapy predict the later radiologic response.
- Published
- 2015
20. Detection of tumor-derived DNA in cerebrospinal fluid of patients with primary tumors of the brain and spinal cord
- Author
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Alfredo Quiñones-Hinojosa, Jon D. Weingart, Daniel M. Sciubba, Kaisorn L. Chaichana, Yuxuan Wang, Isaac Kinde, Daniele Rigamonti, Nickolas Papadopoulos, Nishant Agrawal, Matthias Holdhoff, Alessandro Olivi, Sueli Mieko Oba-Shinjo, K. Wyatt McMahon, Michael Lim, George I. Jallo, Chetan Bettegowda, Simeon Springer, Suely Kazue Nagahashi Marie, Gary L. Gallia, Kenneth W. Kinzler, Ming Zhang, Henry Brem, Lisa Dobbyn, Luis A. Diaz, Mari L. Groves, Jean Paul Wolinsky, Xiaobu Ye, Greg J. Riggins, Janine Ptak, Ziya L. Gokaslan, and Bert Vogelstein
- Subjects
Adult ,Male ,Pathology ,medicine.medical_specialty ,Adolescent ,Settore MED/27 - NEUROCHIRURGIA ,DNA Mutational Analysis ,Spinal Cord Neoplasm ,Central nervous system ,CSF-tDNA ,Biology ,medicine.disease_cause ,Cerebrospinal fluid ,80 and over ,medicine ,Humans ,Spinal Cord Neoplasms ,Preschool ,Child ,Aged ,Demography ,Aged, 80 and over ,Mutation ,Genome ,Multidisciplinary ,medicine.diagnostic_test ,Brain Neoplasms ,Genome, Human ,CNS tumors ,Magnetic resonance imaging ,Biomarker ,DNA ,DNA, Neoplasm ,Exons ,Middle Aged ,Biological Sciences ,Spinal cord ,Magnetic Resonance Imaging ,medicine.anatomical_structure ,Child, Preschool ,Multivariate Analysis ,Neoplasm ,Biomarker (medicine) ,Female ,Human genome ,Human - Abstract
Cell-free DNA shed by cancer cells has been shown to be a rich source of putative tumor-specific biomarkers. Because cell-free DNA from brain and spinal cord tumors cannot usually be detected in the blood, we studied whether the cerebrospinal fluid (CSF) that bathes the CNS is enriched for tumor DNA, here termed CSF-tDNA. We analyzed 35 primary CNS malignancies and found at least one mutation in each tumor using targeted or genome-wide sequencing. Using these patient-specific mutations as biomarkers, we identified detectable levels of CSF-tDNA in 74% [95% confidence interval (95% CI) = 57-88%] of cases. All medulloblastomas, ependymomas, and high-grade gliomas that abutted a CSF space were detectable (100% of 21 cases; 95% CI = 88-100%), whereas no CSF-tDNA was detected in patients whose tumors were not directly adjacent to a CSF reservoir (P0.0001, Fisher's exact test). These results suggest that CSF-tDNA could be useful for the management of patients with primary tumors of the brain or spinal cord.
- Published
- 2015
21. Detection of Somatic TP53 Mutations in Tampons of Patients With High-Grade Serous Ovarian Cancer
- Author
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Richard B. S. Roden, Warner K. Huh, Charles N. Landen, Britt K. Erickson, Kenneth W. Kinzler, Zachary C. Dobbin, Luis A. Diaz, Isaac Kinde, Michael G. Conner, Nickolas Papadopoulos, Ronald D. Alvarez, Yuxuan Wang, Bert Vogelstein, and J. Martin
- Subjects
Adult ,Oncology ,medicine.medical_specialty ,endocrine system diseases ,Somatic cell ,DNA Mutational Analysis ,Pilot Projects ,Gynecologic oncology ,Tp53 mutation ,Predictive Value of Tests ,Internal medicine ,Biomarkers, Tumor ,medicine ,Serous ovarian cancer ,Humans ,Menstrual Hygiene Products ,Cystadenocarcinoma ,Early Detection of Cancer ,Aged ,Ovarian Neoplasms ,Gynecology ,business.industry ,Obstetrics and Gynecology ,Middle Aged ,medicine.disease ,Cystadenocarcinoma, Serous ,Clinical trial ,medicine.anatomical_structure ,Predictive value of tests ,Vagina ,Female ,Neoplasm Grading ,Tumor Suppressor Protein p53 ,business - Abstract
To investigate whether tumor cells could be detected in the vagina of women with serous ovarian cancer through TP53 analysis of DNA samples collected by placement of a vaginal tampon.Women undergoing surgery for a pelvic mass were identified in the gynecologic oncology clinic. They placed a vaginal tampon before surgery, which was removed in the operating room. Cells were isolated and DNA was extracted from both the cells trapped within the tampon and the primary tumor. In patients with serous carcinoma, the DNA was interrogated for the presence of TP53 mutations using a method capable of detecting rare mutant alleles in a mixture of mutant and wild-type DNA.Thirty-three patients were enrolled. Eight patients with advanced serous ovarian cancer were included for analysis. Three had a prior tubal ligation. TP53 mutations were identified in all eight tumor samples. Analysis of the DNA from the tampons revealed mutations in three of the five patients with intact tubes (sensitivity 60%) and in none of the three patients with tubal ligation. In all three participants with mutation detected in the tampon specimen, the tumor and the vaginal DNA harbored the exact same TP53 mutation. The fraction of DNA derived from exfoliated tumor cells ranged from 0.01% to 0.07%.In this pilot study, DNA derived from tumor was detected in the vaginas of 60% of patients with ovarian cancer with intact fallopian tubes. With further development, this approach may hold promise for the early detection of this deadly disease.
- Published
- 2014
22. Prognostic Potential of Circulating Tumor DNA Measurement in Postoperative Surveillance of Nonmetastatic Colorectal Cancer
- Author
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Jeanne Tie, Lisa Dobbyn, Nickolas Papadopoulos, Louise Olsson, Cristian Tomasetti, Natalie Silliman, Yuxuan Wang, Joy Schaefer, Isaac Kinde, Maria Popoli, Lu Li, Bert Vogelstein, Joshua D. Cohen, Peter Gibbs, Janine Ptak, and Kenneth W. Kinzler
- Subjects
Surgical resection ,Cancer Research ,medicine.medical_specialty ,biology ,Colorectal cancer ,Adjuvant chemotherapy ,business.industry ,Disease ,medicine.disease ,Gastroenterology ,Computed tomographic ,03 medical and health sciences ,0302 clinical medicine ,Carcinoembryonic antigen ,Oncology ,Circulating tumor DNA ,030220 oncology & carcinogenesis ,Internal medicine ,medicine ,biology.protein ,In patient ,030212 general & internal medicine ,business ,Original Investigation - Abstract
Importance For patients with resected, nonmetastatic colorectal cancer (CRC), the optimal surveillance protocol remains unclear. Objective To evaluate whether serial circulating tumor DNA (ctDNA) levels detected disease recurrence earlier, compared with conventional postoperative surveillance, in patients with resected CRC. Design, Setting, and Participants This study included patients (n = 58) with stage I, II, or III CRC who underwent radical surgical resection at 4 Swedish hospitals from February 2, 2007, to May 8, 2013. Eighteen patients received adjuvant chemotherapy at the discretion of their clinicians, who were blinded to the ctDNA results. Blood samples were collected at 1 month after the surgical procedure and every 3 to 6 months thereafter for ctDNA analysis. Patients were followed up until metachronous metastases were detected, or for a median of 49 months. Data analysis was performed from March 1, 2009, to June 23, 2018. Main Outcomes and Measures Sensitivity and timing of ctDNA positivity were compared with those of conventional surveillance modalities (computed tomographic scans and serum carcinoembryonic antigen tests) for the detection of disease recurrence. Results This study included 319 blood samples from 58 patients, with a median (range) age of 69 (47-83) years and 34 males (59%). The recurrence rate among patients with positive ctDNA levels was 77% (10 of 13 patients). Positive ctDNA preceded radiologic and clinical evidence of recurrence by a median of 3 months. Of the 45 patients with negative ctDNA throughout follow-up, none (0%; 95% CI, 0%-7.9%) experienced a relapse, with a median follow-up of 49 months. However, 3 (6%; 95% CI, 1.3%-17%) of the 48 patients without relapse had a positive ctDNA result, which subsequently fell to undetectable levels during follow-up. Conclusion and Relevance Although these findings need to be validated in a larger, prospective trial, they suggest that ctDNA analysis could complement conventional surveillance strategies as a triage test to stratify patients with resected CRC on the basis of risk of disease recurrence.
- Published
- 2019
23. Exomic analysis of myxoid liposarcomas, synovial sarcomas, and osteosarcomas
- Author
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Kenneth W. Kinzler, Yuchen Jiao, Fredrik Mertens, Nils Mandahl, Nickolas Papadopoulos, Ralph H. Hruban, Tong-Chuan He, Isaac Kinde, Ji-An Wu, Bert Vogelstein, Luis A. Diaz, Jinyong Luo, Heejung Hwang, Laura D. Wood, and Christine G. Joseph
- Subjects
Cancer Research ,Mutation ,Gene mutation ,Liposarcoma ,Biology ,medicine.disease ,medicine.disease_cause ,Loss of heterozygosity ,SETD2 ,Genetics ,medicine ,Cancer research ,Sarcoma ,neoplasms ,Exome ,Exome sequencing - Abstract
Bone and soft tissue sarcomas are a group of histologically heterogeneous and relatively uncommon tumors. To explore their genetic origins, we sequenced the exomes of 13 osteosarcomas, eight myxoid liposarcomas (MLPS), and seven synovial sarcomas (SYN). These tumors had few genetic alterations (median of 10.8). Nevertheless, clear examples of driver gene mutations were observed, including canonical mutations in TP53, PIK3CA, SETD2, AKT1, and subclonal mutation in FBXW7. Of particular interest were mutations in H3F3A, encoding the variant histone H3.3. Mutations in this gene have only been previously observed in gliomas. Loss of heterozygosity of exomic regions was extensive in osteosarcomas but rare in SYN and MLPS. These results provide intriguing nucleotide-level information on these relatively uncommon neoplasms and highlight pathways that help explain their pathogenesis.
- Published
- 2013
24. Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing
- Author
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Isaac Kinde, Kenneth W. Kinzler, Margaret L. Hoang, Cristian Tomasetti, Thomas A. Rosenquist, Nickolas Papadopoulos, Arthur P. Grollman, K. Wyatt McMahon, and Bert Vogelstein
- Subjects
0301 basic medicine ,Adult ,Male ,Adolescent ,Genomics ,Biology ,medicine.disease_cause ,Genome ,DNA, Mitochondrial ,DNA sequencing ,03 medical and health sciences ,Young Adult ,Germline mutation ,medicine ,Humans ,Child ,Aged ,Genetics ,Aged, 80 and over ,Cell Nucleus ,Mutation ,Multidisciplinary ,Massive parallel sequencing ,Genome, Human ,Point mutation ,High-Throughput Nucleotide Sequencing ,Biological Sciences ,Middle Aged ,030104 developmental biology ,Child, Preschool ,Human genome ,Female - Abstract
We present the bottleneck sequencing system (BotSeqS), a next-generation sequencing method that simultaneously quantifies rare somatic point mutations across the mitochondrial and nuclear genomes. BotSeqS combines molecular barcoding with a simple dilution step immediately before library amplification. We use BotSeqS to show age- and tissue-dependent accumulations of rare mutations and demonstrate that somatic mutational burden in normal human tissues can vary by several orders of magnitude, depending on biologic and environmental factors. We further show major differences between the mutational patterns of the mitochondrial and nuclear genomes in normal tissues. Lastly, the mutation spectra of normal tissues were different from each other, but similar to those of the cancers that arose in them. This technology can provide insights into the number and nature of genetic alterations in normal tissues and can be used to address a variety of fundamental questions about the genomes of diseased tissues.
- Published
- 2016
25. Diagnostic potential of tumor DNA from ovarian cyst fluid
- Author
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Isaac Kinde, Simeon Springer, Natalie Silliman, Michael B. Foote, Joy Schaefer, Constantina Mateoiu, Luis A. Diaz, Karin Sundfeldt, Robert J. Kurman, Kenneth W. Kinzler, Bert Vogelstein, Ie Ming Shih, Nickolas Papadopoulos, Nathan T. James, Björg Kristjansdottir, and Yuxuan Wang
- Subjects
0301 basic medicine ,Pathology ,medicine.medical_specialty ,QH301-705.5 ,Science ,Biology ,medicine.disease_cause ,General Biochemistry, Genetics and Molecular Biology ,Diagnosis, Differential ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,None ,medicine ,Humans ,Cyst ,Prospective Studies ,Biology (General) ,Human Biology and Medicine ,Prospective cohort study ,Cancer Biology ,Ovarian Neoplasms ,Mutation ,Ovarian cyst ,General Immunology and Microbiology ,Cyst Fluid ,General Neuroscience ,DNA ,General Medicine ,medicine.disease ,humanities ,3. Good health ,Ovarian Cysts ,ovarian cancer ,030104 developmental biology ,chemistry ,030220 oncology & carcinogenesis ,Medicine ,biomarker ,Biomarker (medicine) ,Female ,tumor DNA ,Differential diagnosis ,Ovarian cancer ,Research Article - Abstract
We determined whether the mutations found in ovarian cancers could be identified in the patients' ovarian cyst fluids. Tumor-specific mutations were detectable in the cyst fluids of 19 of 23 (83%) borderline tumors, 10 of 13 (77%) type I cancers, and 18 of 18 (100%) type II cancers. In contrast, no mutations were found in the cyst fluids of 18 patients with benign tumors or non-neoplastic cysts. Though large, prospective studies are needed to demonstrate the safety and clinical utility of this approach, our results suggest that the genetic evaluation of cyst fluids might be able to inform the management of the large number of women with these lesions. DOI: http://dx.doi.org/10.7554/eLife.15175.001, eLife digest More than a third of women develop ovarian cysts during their lifetimes. The vast majority of these cysts are harmless, but a small number are caused by ovarian cancers. These cancers often produce no symptoms until the disease has spread throughout the abdomen or to other organs, so many women go undiagnosed until their chances of being successfully treated are low. Currently, there is no reliable way to determine whether an ovarian cyst is cancerous without performing surgery. As a result, many women undergo unnecessary, invasive surgeries for harmless ovarian cysts. Tumors shed cells and cell fragments into any fluid that surrounds them. Fluids from cysts in the pancreas, kidney, and thyroid are routinely examined to identify whether they contain cancerous cells. Now, Wang, Sundfeldt et al. show that ovarian cancers also shed DNA into the surrounding cyst fluid. Furthermore, mutations found in this DNA can provide valuable information about whether the cysts are cancerous. The study was performed by extracting DNA from the fluid in ovarian cysts that had been surgically removed from 77 women. Of these cysts, 10 were harmless cysts, 12 were benign tumors, 31 were invasive cancers, and 24 were so-called borderline tumors, which fall somewhere between the benign tumors and invasive cancers. Only cysts associated with the borderline tumors and invasive cancers need to be surgically removed. Here, Wang, Sundfeldt et al. report that DNA mutations that are characteristic of ovarian cancers were found in 87% of the cysts associated with borderline tumors and invasive cancers. In contrast, these mutations were not found in any of the cysts that do not require surgery. Fluid can be extracted from an ovarian cyst with a needle during an outpatient visit. Therefore, the results presented by Wang, Sundfeldt et al. suggest a relatively straightforward way of testing the DNA from ovarian cysts before deciding whether surgery is really necessary. First, however, larger studies that follow women with cysts over time will be necessary to confirm that this type of testing is effective and safe. DOI: http://dx.doi.org/10.7554/eLife.15175.002
- Published
- 2016
26. Author response: Diagnostic potential of tumor DNA from ovarian cyst fluid
- Author
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Michael B. Foote, Isaac Kinde, Natalie Silliman, Bert Vogelstein, Nathan T. James, Ie Ming Shih, Constantina Mateoiu, Yuxuan Wang, Karin Sundfeldt, Björg Kristjansdottir, Robert J. Kurman, Luis A. Diaz, Nickolas Papadopoulos, Kenneth W. Kinzler, Simeon Springer, and Joy Schaefer
- Subjects
chemistry.chemical_compound ,Pathology ,medicine.medical_specialty ,chemistry ,Ovarian cyst fluid ,business.industry ,medicine ,business ,DNA - Published
- 2016
27. Circulating tumor DNA analysis detects minimal residual disease and predicts recurrence in patients with stage II colon cancer
- Author
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Yuxuan Wang, Nickolas Papadopoulos, Iain Skinner, Jayesh Desai, Timothy J. Price, Hui-Li Wong, Robert L. Strausberg, Isaac Kinde, Bert Vogelstein, Jeanne Tie, Rachel Wong, Ben Tran, Ian T. Jones, Mark Tacey, Lu Li, Andrew Haydon, Malcolm Steel, Michael Christie, Luis A. Diaz, Kenneth W. Kinzler, Theresa M. Hayes, Suzanne Kosmider, Natalie Silliman, Peter Gibbs, Cristian Tomasetti, and Simeon Springer
- Subjects
0301 basic medicine ,Oncology ,medicine.medical_specialty ,Neoplasm, Residual ,Colorectal cancer ,medicine.medical_treatment ,Disease-Free Survival ,Article ,Circulating Tumor DNA ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,Medicine ,Neoplasm ,Humans ,Prospective Studies ,Prospective cohort study ,Neoplasm Staging ,Proportional Hazards Models ,Chemotherapy ,Proportional hazards model ,business.industry ,General Medicine ,medicine.disease ,Minimal residual disease ,030104 developmental biology ,Fluorouracil ,030220 oncology & carcinogenesis ,Colonic Neoplasms ,Lymph ,Neoplasm Recurrence, Local ,business ,medicine.drug - Abstract
Detection of circulating tumor DNA (ctDNA) after resection of stage II colon cancer may identify patients at the highest risk of recurrence and help inform adjuvant treatment decisions. We used massively parallel sequencing–based assays to evaluate the ability of ctDNA to detect minimal residual disease in 1046 plasma samples from a prospective cohort of 230 patients with resected stage II colon cancer. In patients not treated with adjuvant chemotherapy, ctDNA was detected postoperatively in 14 of 178 (7.9%) patients, 11 (79%) of whom had recurred at a median follow-up of 27 months; recurrence occurred in only 16 (9.8 %) of 164 patients with negative ctDNA [hazard ratio (HR), 18; 95% confidence interval (CI), 7.9 to 40; P < 0.001]. In patients treated with chemotherapy, the presence of ctDNA after completion of chemotherapy was also associated with an inferior recurrence-free survival (HR, 11; 95% CI, 1.8 to 68; P = 0.001). ctDNA detection after stage II colon cancer resection provides direct evidence of residual disease and identifies patients at very high risk of recurrence.
- Published
- 2016
28. High prevalence of TERT promoter mutations in primary squamous cell carcinoma of the urinary bladder
- Author
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George J. Netto, Maria Angelica Mendoza Rodriguez, Nickolas Papadopoulos, Bert Vogelstein, Dilek Ertoy, Isaac Kinde, Doreen Nguyen, Matthew T. Olson, Christopher J. VandenBussche, Kenneth W. Kinzler, Diana Taheri, Isabela Werneck da Cunha, Yuxuan Wang, Kazutoshi Fujita, Morgan L. Cowan, Gunes Guner, Trinity J. Bivalacqua, and Simeon Springer
- Subjects
0301 basic medicine ,Male ,medicine.medical_specialty ,Pathology ,congenital, hereditary, and neonatal diseases and abnormalities ,medicine.medical_treatment ,DNA Mutational Analysis ,Biology ,medicine.disease_cause ,Article ,Pathology and Forensic Medicine ,Surgical pathology ,Cystectomy ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Humans ,Promoter Regions, Genetic ,Telomerase ,Aged ,Retrospective Studies ,Aged, 80 and over ,Urinary bladder ,Bladder cancer ,Anatomical pathology ,Middle Aged ,medicine.disease ,030104 developmental biology ,medicine.anatomical_structure ,Urinary Bladder Neoplasms ,Cytopathology ,030220 oncology & carcinogenesis ,Mutation ,Carcinoma, Squamous Cell ,Female ,Hematopathology ,Carcinogenesis - Abstract
TERT promoter mutations (TERT-mut) are detectable in the majority of urothelial carcinomas. The detection of TERT-mut in urine is under investigation as a potential urine-based molecular-screening assay for bladder cancer. A small but significant number of bladder carcinomas are pure squamous cell carcinoma. We sought to assess the incidence of TERT-mut in squamous cell carcinoma of the urinary bladder. A retrospective search of the institutional pathology archives yielded 15 cystectomy specimens performed for squamous cell carcinoma (2000–2014). Histologic slides were reviewed by a senior urologic pathologist to confirm the diagnosis and select a representative formalin-fixed paraffin-embedded tissue block for mutational analysis. All cases yielded adequate material for DNA analysis. Sequencing for TERT-mut was performed using previously described SafeSeq technique. We detected TERT-mut in 12/15 (80%) of bladder squamous cell carcinomas. TERT promoter mutations, commonly found in conventional urothelial carcinoma, are also highly prevalent in urinary bladder squamous cell carcinoma suggesting a common tumorigenesis and potential utility as a molecular urine-based-screening assay.
- Published
- 2016
29. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers
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Kelly S. Oliner, J. Randolph Hecht, Jordan Berlin, Jian Wu, Martin A. Nowak, Kenneth W. Kinzler, Ivana Bozic, Luis A. Diaz, Richard Thomas Williams, Benjamin L. Allen, Isaac Kinde, Johannes G. Reiter, and Bert Vogelstein
- Subjects
0303 health sciences ,Multidisciplinary ,ABL ,Mutant ,Wild type ,Drug resistance ,Biology ,medicine.disease_cause ,Molecular biology ,Article ,3. Good health ,Blockade ,03 medical and health sciences ,0302 clinical medicine ,030220 oncology & carcinogenesis ,medicine ,Cancer research ,Panitumumab ,KRAS ,Gene ,030304 developmental biology ,medicine.drug - Abstract
Colorectal tumors that are wild-type (WT) for KRAS are often sensitive to EGFR blockade, but almost always develop resistance within several months of initiating therapy1,2. The mechanisms underlying this acquired resistance to anti-EGFR antibodies are largely unknown. This situation stands in marked contrast to that of small molecule targeted agents, such as inhibitors of ABL, EGFR, BRAF, and MEK, in which mutations in the genes encoding the protein targets render the tumors resistant to the effects of the drugs3–6. The simplest hypothesis to account for the development of resistance to EGFR blockade are that rare cells with KRAS mutations pre-exist at low levels in tumors with ostensibly WT KRAS genes. Though this hypothesis would seem readily testable, there is no evidence in pre-clinical models to support it, nor is there data from patients. To test this hypothesis, we determined whether mutant KRAS DNA could be detected in the circulation of 28 patients receiving monotherapy with panitumumab, a therapeutic anti-EGFR antibody. We found that nine of 24 (38%) patients whose tumors were initially KRAS WT developed detectable mutations in KRAS in their sera, three of which developed multiple different KRAS mutations. The appearance of these mutations was very consistent, generally occurring between five to six months following treatment. Mathematical modeling indicated that the mutations were present in expanded subclones prior to the initiation of panitumumab. These results suggest that the emergence of KRAS mutations is a mediator of acquired resistance to EGFR blockade and that these mutations can be detected in a non-invasive manner. Moreover, they explain why solid tumors develop resistance to targeted therapies in a highly reproducible fashion.
- Published
- 2012
30. Detection and quantification of rare mutations with massively parallel sequencing
- Author
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Kenneth W. Kinzler, Isaac Kinde, Nick Papadopoulos, Bert Vogelstein, and Jian Wu
- Subjects
DNA Mutational Analysis ,Molecular Sequence Data ,Biology ,medicine.disease_cause ,Polymerase Chain Reaction ,Genome ,law.invention ,Massively parallel signature sequencing ,law ,medicine ,Humans ,beta Catenin ,Polymerase chain reaction ,Polymerase ,Genetics ,Mutation ,Multidisciplinary ,Massive parallel sequencing ,Base Sequence ,Models, Genetic ,Oligonucleotide ,Reproducibility of Results ,Biological Sciences ,biology.protein - Abstract
The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Although massively parallel sequencing instruments are in principle well suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. The keys to this approach, called the Safe - Seq uencing S ystem (“Safe-SeqS”), are ( i ) assignment of a unique identifier (UID) to each template molecule, ( ii ) amplification of each uniquely tagged template molecule to create UID families, and ( iii ) redundant sequencing of the amplification products. PCR fragments with the same UID are considered mutant (“supermutants”) only if ≥95% of them contain the identical mutation. We illustrate the utility of this approach for determining the fidelity of a polymerase, the accuracy of oligonucleotides synthesized in vitro, and the prevalence of mutations in the nuclear and mitochondrial genomes of normal cells.
- Published
- 2011
31. Structure of the Antiviral Assembly Inhibitor CAP-1 Complex with the HIV-1 CA Protein
- Author
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Bruce R. Howard, Sampson K. Kyere, Chun Tang, Isaac Kinde, Christopher P. Hill, Wesley I. Sundquist, Michael F. Summers, Brian N. Kelly, and Howard Robinson
- Subjects
Conformational change ,Hydrogen bond ,Chemistry ,Viral protein ,Nuclear magnetic resonance spectroscopy ,Ring (chemistry) ,medicine.disease_cause ,Crystallography ,chemistry.chemical_compound ,Capsid ,Structural Biology ,Urea ,medicine ,Molecular Biology ,Two-dimensional nuclear magnetic resonance spectroscopy - Abstract
antiviral assembly inhibitor N-(3-chloro-4-methylphenyl)-N′-{2-[({5[(dimethylamino)-methyl]-2-furyl}-methyl)-sulfanyl]ethyl}-urea) (CAP-1) using a combination of NMR spectroscopy and X-ray crystallography. The protein undergoes a remarkable conformational change upon CAP-1 binding, in which Phe32 is displaced from its buried position in the protein core to open a deep hydrophobic cavity that serves as the ligand binding site. The aromatic ring of CAP-1 inserts into the cavity, with the urea NH groups forming hydrogen bonds with the backbone oxygen of Val59 and the dimethylamonium group interacting with the side-chains of Glu28 and Glu29. Elements that could be exploited to improve binding affinity are apparent in the structure. The displacement of Phe32 by CAP-1 appears to be facilitated by a strained main-chain conformation, which suggests a potential role for a Phe32 conformational switch during normal capsid assembly.
- Published
- 2007
32. Entropic switch regulates myristate exposure in the HIV-1 matrix protein
- Author
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Erin Loeliger, Paz Luncsford, Michael F. Summers, Chun Tang, Dorothy Beckett, and Isaac Kinde
- Subjects
Models, Molecular ,Conformational change ,Multidisciplinary ,Viral matrix protein ,HIV Antigens ,Protein Conformation ,Gene Products, gag ,myr ,Myristic acid ,Trimer ,Biology ,Myristic Acid ,gag Gene Products, Human Immunodeficiency Virus ,Viral Proteins ,chemistry.chemical_compound ,Protein structure ,chemistry ,Biochemistry ,Commentary ,Biophysics ,Thermodynamics ,Lipid raft ,Myristoylation - Abstract
The myristoylated matrix protein (myr-MA) of HIV functions as a regulator of intracellular localization, targeting the Gag precursor polyprotein to lipid rafts in the plasma membrane during virus assembly and dissociating from the membrane during infectivity for nuclear targeting of the preintegration complex. Membrane release is triggered by proteolytic cleavage of Gag, and it has, until now, been believed that proteolysis induces a conformational change in myr-MA that sequesters the myristyl group. NMR studies reported here reveal that myr-MA adopts myr-exposed [myr(e)] and -sequestered [myr(s)] states, as anticipated. Unexpectedly, the tertiary structures of the protein in both states are very similar, with the sequestered myristyl group occupying a cavity that requires only minor conformational adjustments for insertion. In addition, myristate exposure is coupled with trimerization, with the myristyl group sequestered in the monomer and exposed in the trimer ( K assoc = 2.5 ± 0.6 × 10 8 M –2 ). The equilibrium constant is shifted ≈20-fold toward the trimeric, myristate-exposed species in a Gag-like construct that includes the capsid domain, indicating that exposure is enhanced by Gag subdomains that promote self-association. Our findings indicate that the HIV-1 myristyl switch is regulated not by mechanically induced conformational changes, as observed for other myristyl switches, but instead by entropic modulation of a preexisting equilibrium.
- Published
- 2003
33. The potential of circulating tumor DNA (ctDNA) to guide adjuvant chemotherapy decision making in locally advanced rectal cancer (LARC)
- Author
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Rachel Wong, Peter Gibbs, Isaac Kinde, Lu Li, Kenneth W. Kinzler, Joshua D. Cohen, Margaret Lee, David Goldstein, Suzanne Kosmider, Bert Vogelstein, Desmond Yip, Hany Elsaleh, Madhu Sudan Singh, Jeanne Tie, Luis A. Diaz, Nickolas Papadopoulos, Cristian Tomasetti, Matthew Burge, Ben Tran, and Yuxuan Wang
- Subjects
0301 basic medicine ,Oncology ,Cancer Research ,medicine.medical_specialty ,business.industry ,Adjuvant chemotherapy ,Colorectal cancer ,Locally advanced ,Routine practice ,medicine.disease ,Surgery ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Circulating tumor DNA ,030220 oncology & carcinogenesis ,Internal medicine ,medicine ,business - Abstract
3521 Background: The optimal approach to adjuvant chemotherapy for rectal cancer is keenly debated. Routine practice and clinical guidelines vary widely. After pre-operative chemoradiation (CRT), a pathologic complete response (pCR) or nodal involvement (pN+) are prognostic markers that can guide clinical decision-making, but markers that better define the patients (pts) that are likely or unlikely to benefit from chemotherapy are urgently needed. We investigated the potential role of ctDNA as a biomarker to guide therapy. Methods: We conducted a prospective, multi-centre study in pts with LARC (T3/T4 and/or N+) planned for CRT and curative resection. Serial plasma samples were collected pre-CRT, post-CRT, and 4-10 weeks after surgery. Somatic mutations in individual pts’ tumor were identified via sequencing of 15 genes commonly mutated in colorectal cancers. We then designed personalized assays to quantify ctDNA in plasma samples. Pts received adjuvant therapy at clinician discretion. Results: 200 pts were enrolled between Apr-2012 and Dec-2015. Median age was 62 years (range 28-86), 67% were male and 159 pts had pre-CRT and post-op ctDNA samples available for analysis. Of these, 122 (77%) pts had detectable ctDNA prior to therapy. After surgery, 19 pts had detectable ctDNA and 11 of these 19 (58%) have recurred during a median follow up of 22 months. Recurrence occurred in only 12 of 140 (8.6%) with negative ctDNA (HR 12, p < 0.001). One hundred and two (64%) pts received adjuvant chemotherapy. Post-op ctDNA detection was predictive of recurrence irrespective of adjuvant chemotherapy (chemo: HR 10, p < 0.001; no chemo: HR 16, p < 0.001). Thirty-four pts (21%) achieved a pCR, 43 (27%) had pN+ disease. pCR (vs non-pCR) was associated with a trend for lower recurrence risk (HR 0.31, p = 0.089) and pN+ (vs pN0) with a higher recurrence risk (HR 4.2, p < 0.001). ctDNA detection remained predictive of recurrence among pts with a pCR (HR 14, p = 0.014) or with pN+ disease (HR 11, p < 0.001). Conclusions: Post-op ctDNA analysis stratifies pts with LARC into very high and low risk groups. ctDNA analysis remains strongly predictive of recurrence among pts with both lower risk (pCR) and higher risk (pN+) disease.
- Published
- 2017
34. Association of the Autoimmune Disease Scleroderma with an Immunologic Response to Cancer
- Author
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Livia Casciola-Rosen, Andrea Fava, Ami A. Shah, Nickolas Papadopoulos, Christopher J. Thoburn, Bert Vogelstein, Isaac Kinde, Francesco Boin, Christine G. Joseph, Yuchen Jiao, Andrew D. Skora, Kenneth W. Kinzler, Fredrick M. Wigley, Antony Rosen, and Erika Darrah
- Subjects
CD4-Positive T-Lymphocytes ,Cellular immunity ,Mutation, Missense ,Autoimmunity ,Biology ,medicine.disease_cause ,Polymorphism, Single Nucleotide ,Autoantigens ,Article ,Autoimmune Diseases ,Immune system ,Antigen ,Neoplasms ,medicine ,Humans ,Alleles ,Autoantibodies ,Autoimmune disease ,Multidisciplinary ,Scleroderma, Systemic ,Autoantibody ,RNA Polymerase III ,medicine.disease ,Acquired immune system ,Connective tissue disease ,Genetic Loci ,Immunology - Abstract
Cancer Immunosurveillance Gone Bad? A subset of patients who develop scleroderma, a debilitating autoimmune disease, have an elevated risk of developing cancer. These patients harbor autoantibodies to RPC1, an RNA polymerase subunit encoded by the POLR3A gene. Joseph et al. (p. 152 , published online December 5; see the Perspective by Teng and Smyth ) explored whether the RPC1 autoantibodies target a “foreign” antigen derived from a mutated POLR3A gene. Sequence analysis revealed that POLR3A mutations were present in tumors from six of eight patients with RPC1 autoantibodies but in no tumors from eight control patients who lacked RPC1 autoantibodies. Cell culture data suggested that the POLR3A mutations triggered cellular and humoral immune responses in the patients. These results provide support for the “immunosurveillance” hypothesis, which posits the continual eradication of nascent tumor cells via immune responses.
- Published
- 2013
35. Evaluation of DNA from the Papanicolaou Test to Detect Ovarian and Endometrial Cancers
- Author
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Nishant Agrawal, Jian Wu, Chetan Bettegowda, Robert J. Kurman, James R. Eshleman, Robert L. Giuntoli, Yuxuan Wang, Fanny Dao, Jesus Paula Carvalho, Douglas A. Levine, Isaac Kinde, Ie Ming Shih, Suely Kazue Nagahashi Marie, Luis A. Diaz, Richard B.S. Roden, Kenneth W. Kinzler, Nickolas Papadopoulos, and Bert Vogelstein
- Subjects
Oncology ,medicine.medical_specialty ,Papanicolaou stain ,Article ,Internal medicine ,Genotype ,Humans ,Medicine ,Pelvic examination ,Cervix ,Ovarian Neoplasms ,Vaginal Smears ,Cervical cancer ,Massive parallel sequencing ,medicine.diagnostic_test ,business.industry ,DNA, Neoplasm ,General Medicine ,Papanicolaou Test ,medicine.disease ,Endometrial Neoplasms ,medicine.anatomical_structure ,Mutation ,Smear Specimen ,Female ,business - Abstract
Papanicolaou (Pap) smears have revolutionized the management of patients with cervical cancers by permitting the detection of early, surgically curable tumors and their precursors. In recent years, the traditional Pap smear has been replaced by a liquid-based method, which allows not only cytologic evaluation but also collection of DNA for detection of human papillomavirus, the causative agent of cervical cancer. We reasoned that this routinely collected DNA could be exploited to detect somatic mutations present in rare tumor cells that accumulate in the cervix once shed from endometrial or ovarian cancers. A panel of genes that are commonly mutated in endometrial and ovarian cancers was assembled with new whole-exome sequencing data from 22 endometrial cancers and previously published data on other tumor types. We used this panel to search for mutations in 24 endometrial and 22 ovarian cancers and identified mutations in all 46 samples. With a sensitive massively parallel sequencing method, we were able to identify the same mutations in the DNA from liquid Pap smear specimens in 100% of endometrial cancers (24 of 24) and in 41% of ovarian cancers (9 of 22). Prompted by these findings, we developed a sequence-based method to query mutations in 12 genes in a single liquid Pap smear specimen without previous knowledge of the tumor's genotype. When applied to 14 samples selected from the positive cases described above, the expected tumor-specific mutations were identified. These results demonstrate that DNA from most endometrial and a fraction of ovarian cancers can be detected in a standard liquid-based Pap smear specimen obtained during routine pelvic examination. Although improvements need to be made before applying this test in a routine clinical manner, it represents a promising step toward a broadly applicable screening methodology for the early detection of gynecologic malignancies.
- Published
- 2013
36. Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing
- Author
-
Giovanni Parmigiani, Nickolas Papadopoulos, David Craig, John D. Carpten, Kenneth W. Kinzler, Luis A. Diaz, Rebecca J. Leary, Isaac Kinde, Victor E. Velculescu, Joyce O'Shaughnessy, Bert Vogelstein, and Mark Sausen
- Subjects
DNA Copy Number Variations ,Chromosomal Alterations ,Breast Neoplasms ,Biology ,Bioinformatics ,Sensitivity and Specificity ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Breast cancer ,Neoplasms ,medicine ,Humans ,Gene ,030304 developmental biology ,Chromosome Aberrations ,Gene Rearrangement ,Whole genome sequencing ,0303 health sciences ,Massive parallel sequencing ,Genome, Human ,Cancer ,Sequence Analysis, DNA ,General Medicine ,medicine.disease ,3. Good health ,chemistry ,030220 oncology & carcinogenesis ,Colonic Neoplasms ,Cancer research ,biology.protein ,Female ,Cyclin-dependent kinase 6 ,DNA - Abstract
Clinical management of cancer patients could be improved through the development of noninvasive approaches for the detection of incipient, residual, and recurrent tumors. We describe an approach to directly identify tumor-derived chromosomal alterations through analysis of circulating cell-free DNA from cancer patients. Whole-genome analyses of DNA from the plasma of 10 colorectal and breast cancer patients and 10 healthy individuals with massively parallel sequencing identified, in all patients, structural alterations that were not present in plasma DNA from healthy subjects. Detected alterations comprised chromosomal copy number changes and rearrangements, including amplification of cancer driver genes such as ERBB2 and CDK6. The level of circulating tumor DNA in the cancer patients ranged from 1.4 to 47.9%. The sensitivity and specificity of this approach are dependent on the amount of sequence data obtained and are derived from the fact that most cancers harbor multiple chromosomal alterations, each of which is unlikely to be present in normal cells. Given that chromosomal abnormalities are present in nearly all human cancers, this approach represents a useful method for the noninvasive detection of human tumors that is not dependent on the availability of tumor biopsies.
- Published
- 2012
37. Abstract NG01: Accumulation of somatic mutations in normal and cancerous tissues with age
- Author
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Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Isaac Kinde, Thomas A. Rosenquist, Arthur P. Grollman, Margaret L. Hoang, and Cristian Tomasetti
- Subjects
Genetics ,Cancer Research ,Mutation ,Somatic cell ,Point mutation ,Normal tissue ,Cancer ,Biology ,medicine.disease_cause ,medicine.disease ,Genome ,Oncology ,medicine ,Carcinogenesis - Abstract
Fundamental theories in carcinogenesis and aging evoke the accumulation of rare somatic mutations in normal tissues over time. However, absence of a simple and systematic method to characterize somatic mutations in normal tissues precludes the understanding of their functional consequences. We present Bottleneck Sequencing System (BotSeqS), a next-generation sequencing method that quantitates rare somatic point mutations simultaneously across the mitochondrial and nuclear genomes. BotSeqS combines molecular barcoding with a simple dilution step immediately before library amplification. Using BotSeqS, we determine the mutation frequencies and spectra in normal brain, kidney, and colon from a total of 34 individuals ranging from < 1 to 98 years old. We show an age and tissue-dependent accumulation of rare point mutations and demonstrate that the somatic mutational burden in normal tissues can vary by several orders of magnitude depending on biological and environmental factors. For example, individuals with defects in the mismatch repair machinery or exposure to environmental carcinogens (smoking, aristolochic acid) show significant increases in mutational frequencies and altered mutational spectra compared to controls. We further show major differences between the mutational patterns of the mitochondrial and nuclear genomes in normal tissues. Lastly, we find that the mutational spectra of normal tissues were different from each other but similar to cancers from the same tissue type, suggesting that the differential mutational spectra observed in cancers are tissue-specific rather than cancer-specific. This technology can provide insights into the number and nature of genetic alterations in normal tissues and can be used to address a variety of fundamental questions about the genomes of diseased tissues. Citation Format: Margaret L. Hoang, Isaac Kinde, Cristian Tomasetti, Thomas Rosenquist, Arthur P. Grollman, Kenneth W. Kinzler, Bert Vogelstein, Nickolas Papadopoulos. Accumulation of somatic mutations in normal and cancerous tissues with age. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr NG01.
- Published
- 2016
38. The potential of circulating tumor DNA (ctDNA) to reshape the design of clinical trials testing adjuvant therapy in patients with early stage cancers
- Author
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Nickolas Papadopoulos, Rachel Wong, Peter Gibbs, Jayesh Desai, Bert Vogelstein, Michael Christie, Luis A. Diaz, Simeon Springer, Robert L. Strausberg, Isaac Kinde, Yuxuan Wang, Kenneth W. Kinzler, Desmond Yip, Cristian Tomasetti, Ben Tran, Lu Li, Andrew Haydon, Jeanne Tie, Theresa M. Hayes, and Suzanne Kosmider
- Subjects
Oncology ,Cancer Research ,medicine.medical_specialty ,business.industry ,medicine.medical_treatment ,macromolecular substances ,Surgery ,carbohydrates (lipids) ,Clinical trial ,stomatognathic diseases ,03 medical and health sciences ,0302 clinical medicine ,Circulating tumor DNA ,030220 oncology & carcinogenesis ,Internal medicine ,otorhinolaryngologic diseases ,medicine ,Adjuvant therapy ,bacteria ,030211 gastroenterology & hepatology ,In patient ,Stage (cooking) ,business ,Adjuvant - Abstract
3511Background: The conventional approach to testing the benefit of adjuvant therapies in patients (pts) with relatively favorable prognoses is to follow a large number of pts for long periods of t...
- Published
- 2016
39. Serial circulating tumor DNA (ctDNA) and recurrence risk in patients (pts) with resectable colorectal liver metastasis (CLM)
- Author
-
Nickolas Papadopoulos, Rachel Wong, Simeon Springer, Kenneth W. Kinzler, Kathryn M. Field, Yuxuan Wang, Jeanne Tie, Hui-Li Wong, Jenny Shannon, Matthew Burge, Dusan Kotasek, Michael Christie, Luis A. Diaz, Bert Vogelstein, Ben Tran, Suzanne Kosmider, Peter Gibbs, Robert L. Strausberg, Isaac Kinde, and Benjamin N. J. Thomson
- Subjects
0301 basic medicine ,Oncology ,Cancer Research ,medicine.medical_specialty ,Pathology ,Colorectal cancer ,business.industry ,food and beverages ,medicine.disease ,digestive system diseases ,Metastasis ,Resection ,Recurrence risk ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Circulating tumor DNA ,030220 oncology & carcinogenesis ,Internal medicine ,medicine ,In patient ,business - Abstract
e15131Background: In pts with metastatic colorectal cancer (mCRC), the resection of isolated CLM is potentially curative. Previous studies have shown that ctDNA can be detected in a high proportion...
- Published
- 2016
40. FAST-SeqS: a simple and efficient method for the detection of aneuploidy by massively parallel sequencing
- Author
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Nickolas Papadopoulos, Kenneth W. Kinzler, Isaac Kinde, and Bert Vogelstein
- Subjects
Genetic Screens ,Aneuploidy ,lcsh:Medicine ,Chromosome Disorders ,Trisomy ,Polymerase Chain Reaction ,law.invention ,Chromosomal Disorders ,0302 clinical medicine ,Pregnancy ,law ,Prenatal Diagnosis ,Genomic library ,lcsh:Science ,Polymerase chain reaction ,Genetics ,0303 health sciences ,Multidisciplinary ,Massive parallel sequencing ,Chromosome Biology ,High-Throughput Nucleotide Sequencing ,Genomics ,030220 oncology & carcinogenesis ,Female ,Research Article ,Biotechnology ,Adult ,Sequence analysis ,Genetic Counseling ,Biology ,DNA sequencing ,Molecular Genetics ,03 medical and health sciences ,Genomic Medicine ,medicine ,Humans ,Genetic Testing ,DNA Primers ,Gene Library ,030304 developmental biology ,Chromosome Aberrations ,lcsh:R ,Computational Biology ,Human Genetics ,DNA ,Sequence Analysis, DNA ,medicine.disease ,Pregnancy Complications ,Genetics of Disease ,lcsh:Q ,Down Syndrome ,Primer (molecular biology) - Abstract
Massively parallel sequencing of cell-free, maternal plasma DNA was recently demonstrated to be a safe and effective screening method for fetal chromosomal aneuploidies. Here, we report an improved sequencing method achieving significantly increased throughput and decreased cost by replacing laborious sequencing library preparation steps with PCR employing a single primer pair designed to amplify a discrete subset of repeated regions. Using this approach, samples containing as little as 4% trisomy 21 DNA could be readily distinguished from euploid samples.
- Published
- 2012
41. Testing the accuracy of mutation detection for the prevention of ovarian neoplasia: The TAMPON study
- Author
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Zachary C. Dobbin, J. Martin, Warner K. Huh, Richard B.S. Roden, Luis A. Diaz, Bert Vogelstein, Yuxuan Wang, Isaac Kinde, Britt K. Erickson, and Charles N. Landen
- Subjects
Gynecology ,medicine.medical_specialty ,Oncology ,business.industry ,OVARIAN NEOPLASIA ,medicine ,Obstetrics and Gynecology ,Mutation detection ,business - Published
- 2014
42. Development of personalized tumor biomarkers using massively parallel sequencing
- Author
-
Kerstin Schmidt, Clarence Lee, Francisco M. De La Vega, Rebecca J. Leary, Alena A. Antipova, Luis A. Diaz, Kevin McKernan, Kenneth W. Kinzler, Victor E. Velculescu, Cisilya Duncan, Isaac Kinde, Frank Diehl, Bert Vogelstein, and Christopher Clouser
- Subjects
Sequence analysis ,Molecular Sequence Data ,Computational biology ,Biology ,Bioinformatics ,Polymerase Chain Reaction ,Article ,Translocation, Genetic ,law.invention ,chemistry.chemical_compound ,law ,Neoplasms ,medicine ,Biomarkers, Tumor ,Humans ,Precision Medicine ,Polymerase chain reaction ,Gene Rearrangement ,Massive parallel sequencing ,Genome ,Base Sequence ,business.industry ,Breakpoint ,Cancer ,General Medicine ,Gene rearrangement ,Genomics ,DNA ,Sequence Analysis, DNA ,medicine.disease ,chemistry ,Personalized medicine ,business - Abstract
Clinical management of human cancer is dependent on the accurate monitoring of residual and recurrent tumors. The evaluation of patient-specific translocations in leukemias and lymphomas has revolutionized diagnostics for these diseases. We have developed a method, called personalized analysis of rearranged ends (PARE), which can identify translocations in solid tumors. Analysis of four colorectal and two breast cancers with massively parallel sequencing revealed an average of nine rearranged sequences (range, 4 to 15) per tumor. Polymerase chain reaction with primers spanning the breakpoints was able to detect mutant DNA molecules present at levels lower than 0.001% and readily identified mutated circulating DNA in patient plasma samples. This approach provides an exquisitely sensitive and broadly applicable approach for the development of personalized biomarkers to enhance the clinical management of cancer patients.
- Published
- 2010
43. 2777 Lavage of the uterine cavity for early and differential diagnosis of serous ovarian cancer
- Author
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Elisabeth Maritschnegg, Isaac Kinde, Luis Diaz, Yuxuan Wang, Reinhard Horvat, Kenneth W. Kinzler, Ignace Vergote, Nina Pecha, Bert Vogelstein, Nickolas Papadopoulos, Paul Speiser, R Zeillinger, and E. Van Nieuwenhuysen
- Subjects
Oncology ,Cancer Research ,medicine.medical_specialty ,Pathology ,medicine.anatomical_structure ,business.industry ,Internal medicine ,medicine ,Serous ovarian cancer ,Uterine cavity ,Differential diagnosis ,business - Published
- 2015
44. Circulating tumor DNA (ctDNA) in nonmetastatic colorectal cancer (CRC): Potential role as a screening tool
- Author
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Jeanne Tie, Nickolas Papadopoulos, Peter Gibbs, Kenneth W. Kinzler, Luis A. Diaz, Bert Vogelstein, Robert L. Strausberg, Isaac Kinde, Hany Elsaleh, Ben Tran, Madhu Sudan Singh, Yuxuan Wang, Malcolm Steel, and Natalie Turner
- Subjects
Oncology ,Cancer Research ,medicine.medical_specialty ,Crc screening ,Colorectal cancer ,business.industry ,Cancer ,medicine.disease ,Bioinformatics ,Cancer incidence ,Circulating tumor DNA ,Internal medicine ,medicine ,Screening tool ,Endoscopic screening ,Stage (cooking) ,business - Abstract
518 Background: CRC screening significantly reduces cancer incidence and mortality. Participation rates in screening, both stool based and endoscopic, are often low. The value and safety of endoscopic screening in older individuals is also uncertain. Preliminary data indicate ctDNA can be detected in a high proportion of patients with early stage CRC, suggesting promise as a screening test that should have broad community acceptance. Methods: Plasma samples were collected at diagnosis from 100 patients (pts) with newly diagnosed CRC. Surgical, clinicopathologic and outcome data were prospectively captured. All samples were sent to Johns Hopkins Kimmel Cancer Center, where tumors were sequenced using a panel of 15 genes frequently mutated in CRC to identify candidate mutations for ctDNA analysis. For each pt, one tumor mutation was selected to assess for ctDNA in plasma samples using the Safe-SeqS digital genomic assay. Results: Preliminary data is available on 68 pts. Median follow-up is 15.2 months. Candidate mutations for ctDNA analysis were identified in all cases, with a matching mutation detectable in the plasma cell-free DNA in 41 pts (60%). Median mutant allele fraction was 0.24% (range 0.11% - 8.39%). Tumor stage did not appear to have a major impact on the detection rate of ctDNA (Table), and ctDNA detection was independent of CEA levels. Five pts have recurred, all of whom had detectable ctDNA at diagnosis, whereas CEA was elevated in only 1 of these cases. Conclusions: Preliminary data suggests ctDNA is detectable at diagnosis in the majority of pts with non-metastatic CRC. The potential for ctDNA as a CRC screening tool, and as a prognostic marker for patients with early stage cancer, should be further explored. [Table: see text]
- Published
- 2015
45. Abstract 5606: Detection of circulating tumor DNA in early and late stage human malignancies
- Author
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Brandon Luber, Nishant Agrawal, Kenneth W. Kinzler, Hao Wang, Rebecca J. Leary, Bjarne Bartlett, Bert Vogelstein, Luis A. Diaz, Mark Sausen, Isaac Kinde, Nickolas Papadopoulos, and Chetan Bettegowda
- Subjects
Neuroblastoma RAS viral oncogene homolog ,Cancer Research ,Pathology ,medicine.medical_specialty ,business.industry ,Colorectal cancer ,Melanoma ,Cancer ,Gene mutation ,medicine.disease ,medicine.disease_cause ,Circulating tumor cell ,Oncology ,Pancreatic cancer ,Cancer research ,Medicine ,KRAS ,business - Abstract
The development of minimally-invasive methods to detect and monitor tumors continues to be a major challenge in oncology. We used digital PCR-based technologies to evaluate the ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types. We initially use targeted, exomic, or whole genome sequencing to identify sequence or structural alterations in tumor tissues of 410 patients using targeted, exomic, or whole genome sequencing. We found that at least one tumor-specific mutant molecule could be identified in 75% of patients with advanced ovarian, colorectal, bladder, gastroesophoageal, pancreatic, breast, melanoma, hepatocellular and head and neck cancers, but in less than 50% of primary brain, renal, prostate, or thyroid cancers. In patients with localized tumors, ctDNA was detected in 73%, 57%, 48% and 50% of patients with colorectal cancer, gastroesophageal cancer, pancreatic cancer, and breast adenocarcinoma, respectively. Circulating tumor DNA was often present in patients without detectable circulating tumor cells, suggesting that these two biomarkers are distinct entities. In a separate panel of 206 patients with metastatic colorectal cancers, we showed that the sensitivity of ctDNA for detection of clinically relevant KRAS gene mutations was 87.2% while and its specificity was 99.2%. Finally, we assessed whether ctDNA could provide clues into the mechanisms underlying resistance to epidermal growth factor receptor (EGFR) blockade in 24 patients who objectively responded to therapy but who subsequently relapsed. Twenty-three (96%) of these patients developed one or more mutations in genes involved in the mitogen-activated protein kinase (MAPK) pathway. Remarkably, nearly half (45%) of the observed mutations observed were in codon 61 of either the KRAS or NRAS gene. Taken together, these data suggest that ctDNA is a broadly applicable, sensitive, specific and robust biomarker that can be used for a variety of clinical and research purposes in patients with several multiple different types of cancer. Note: This abstract was not presented at the meeting. Citation Format: Chetan Bettegowda, Mark Sausen, Rebecca Leary, Isaac Kinde, Nishant Agrawal, Bjarne Bartlett, Hao Wang, Brandon Luber, Kenneth Kinzler, Bert Vogelstein, Nickolas Papadopoulos, Luis Diaz. Detection of circulating tumor DNA in early and late stage human malignancies. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5606. doi:10.1158/1538-7445.AM2014-5606
- Published
- 2014
46. Antiviral inhibition of the HIV-1 capsid protein
- Author
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Chun Tang, Mingjun Huang, Keith Mayo, Samson Kyere, Yongnian Sun, Erin Loeliger, Isaac Kinde, Eric Barklis, and Michael F. Summers
- Subjects
Models, Molecular ,Anti-HIV Agents ,Protein Conformation ,viruses ,medicine.medical_treatment ,Blotting, Western ,HIV Infections ,Biology ,Virus ,Protein structure ,Capsid ,Structural Biology ,Viral entry ,medicine ,Humans ,Binding site ,Furans ,Molecular Biology ,Infectivity ,Protease ,Binding Sites ,Sulfur Compounds ,Virulence ,Phenylurea Compounds ,Group-specific antigen ,Virology ,Microscopy, Electron ,HIV-1 - Abstract
During the assembly stage of the human immunodeficiency virus (HIV) replication cycle, several thousand copies of the viral Gag polyprotein associate at the cell membrane and bud to form an immature, non-infectious virion. Gag is subsequently cleaved by the protease, which liberates the capsid proteins for assembly into the polyprotein shell of the central core particle (or capsid) of the mature virus. Viral infectivity is critically dependent on capsid formation and stability, making the capsid protein a potentially attractive antiviral target. We have identified compounds that bind to an apical site on the N-terminal domain of the HIV-1 capsid protein and inhibit capsid assembly in vitro. One compound, N-(3-chloro-4-methylphenyl)-N'-[2-[([5-[(dimethylamino)-methyl]-2-furyl]-methyl)-sulfanyl]ethyl]urea) (CAP-1), is well tolerated in cell cultures, enabling in vivo antiviral and mechanistic studies. CAP-1 inhibits HIV-1 infectivity in a dose-dependent manner, but does not interfere with viral entry, reverse transcription, integration, proteolytic processing, or virus production, indicating a novel antiviral mechanism. Significantly, virus particles generated in the presence of CAP-1 exhibit heterogeneous sizes and abnormal core morphologies, consistent with inhibited CA-CA interactions during virus assembly and maturation. These findings lay the groundwork for the development of assembly inhibitors as a new class of therapeutic agents for the treatment of AIDS.
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- 2003
47. DETECTION OF CIRCULATING TUMOR DNA IN EARLY AND LATE STAGE HUMAN MALIGNANCIES
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Nishant Agrawal, Brandon Luber, Isaac Kinde, Chetan Bettegowda, Kenneth W. Kinzler, Bjarne Bartlett, Hao Wang, Rebecca J. Leary, Mark Sausen, Nickolas Papadopoulos, and Bert Vogelstein
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Medulloblastoma ,Cancer Research ,Pathology ,medicine.medical_specialty ,Colorectal cancer ,Melanoma ,Cancer ,Biology ,medicine.disease ,abstracts ,Oncology ,Pancreatic cancer ,Glioma ,medicine ,Cancer research ,Biomarker (medicine) ,Neurology (clinical) ,Thyroid cancer - Abstract
BACKGROUND: The development of minimally-invasive methods to detect and monitor tumors continues to be a major challenge in oncology. We used digital PCR-based technologies to evaluate the ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types. In particular we studied the plasma of 14 medulloblastoma, 13 WHO grade 2-3 glioma and 14 WHO grade IV astrocytoma cases for levels of ctDNA. METHODS: The basis of our approach is to differentiate DNA shed by normal cells from DNA derived from tumor cells. In order to distinguish the two populations of cell-free DNA, we first identify a tumor-specific alteration. We then query for that exact mutation in matching plasma from the same patient to generate a personalized tumor biomarker. Only DNA derived from the tumor will harbor the genetic alteration. We initially use targeted, exomic, or whole genome sequencing to identify sequence or structural alterations in tumor tissues of 410 individuals. DNA was extracted from less than 5 ml of plasma in each case. The majority of plasma samples were queried for levels of ctDNA using a high fidelity next-generation sequencing approach coined Safe-SeqS. RESULTS: We found that at least one tumor-specific mutant molecule could be identified in 75% of patients with advanced ovarian, colorectal, bladder, gastroesophoageal, pancreatic, breast, melanoma, hepatocellular and head and neck cancers, but in less than 50% of primary brain, renal, prostate, or thyroid cancers. Approximately 40% of medulloblastoma and 10% of low or high grade glioma cases had detectable levels of ctDNA. In patients with localized non-CNS tumors, ctDNA was detected in 73%, 57%, 48% and 50% of patients with colorectal cancer, gastroesophageal cancer, pancreatic cancer, and breast adenocarcinoma, respectively. Finally, we assessed whether ctDNA could provide clues into the mechanisms underlying resistance to epidermal growth factor receptor (EGFR) blockade in 24 colorectal cancer patients who objectively responded to therapy but who subsequently relapsed. Twenty-three (96%) of these patients developed one or more mutations in genes involved in the mitogen-activated protein kinase (MAPK) pathway. CONCLUSIONS: Taken together, these data suggest that ctDNA is a sensitive, specific and robust biomarker that can be used for a variety of clinical and research purposes in patients with several multiple different types of cancer. For individuals with CNS neoplasms, alternate strategies may need to be developed in order to detect cell-free tumor derived DNA at levels that are clinically meaningful. ABSTRACT CATEGORY: Neuropathology & Tumor Biomarkers.
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- 2014
48. Circulating tumor DNA (ctDNA) as a marker of recurrence risk in stage II colon cancer (CC)
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Desmond Yip, Suzanne Kosmider, Bert Vogelstein, Peter Gibbs, Malcolm Steel, Iain Skinner, Robert L. Strausberg, Isaac Kinde, Craig Underhill, Rachel Wong, Jeanne Tie, Andrew Haydon, Michael Christie, Luis A. Diaz, Nickolas Papadopoulos, Kenneth W. Kinzler, Yuxuan Wang, and Hui-Li Wong
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Oncology ,Neuroblastoma RAS viral oncogene homolog ,Cancer Research ,medicine.medical_specialty ,Pathology ,business.industry ,medicine.medical_treatment ,Disease ,medicine.disease_cause ,Recurrence risk ,Circulating tumor DNA ,Internal medicine ,medicine ,KRAS ,business ,Prospective cohort study ,Adjuvant ,Stage ii colon cancer - Abstract
11015 Background: Markers that better define recurrence risk for patients (pts) with stage II CC are urgently required, potentially defining a subset that would most benefit from adjuvant chemotherapy (CTX) and intensive surveillance. An alternative strategy to standard analyses of the resected surgical specimen is to directly examine plasma for evidence of residual disease. Recently, ctDNA has shown promise as a blood biomarker in advanced colorectal cancer; here we explore the potential of this marker in stage II CC. Methods: In this prospective study, plasma samples are being collected at 4-10 weeks post-op in 250 stage II CC pts, with serial 3 monthly samples on a subset of 175 pts. Adjuvant CTX is at clinician discretion, blinded to ctDNA analysis. Surveillance includes 3 monthly CEA and 6 monthly CT imaging for 2 years. All samples were sent to Johns Hopkins Kimmel Cancer Center, where tumor tissue was analyzed for hotspot mutations in TP53, APC, KRAS, NRAS, BRAF, PIK3CA, CTNNB1, SMAD4, and FBXW7 us...
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- 2014
49. Massively parallel sequencing (MPS) of circulating DNA in patients with metastatic colorectal cancer (mCRC): Prognostic significance and early changes during chemotherapy (CT)
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Christos S. Karapetis, Hui-Li Wong, Kenneth W. Kinzler, Joseph McKendrick, Isaac Kinde, Justin Kelvin Roebert, Ben Tran, Madhu Sudan Singh, Jeanne Tie, Jayesh Desai, Peter Gibbs, and Bert Vogelstein
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Oncology ,Cancer Research ,medicine.medical_specialty ,Chemotherapy ,Massive parallel sequencing ,business.industry ,Colorectal cancer ,medicine.medical_treatment ,medicine.disease ,Bioinformatics ,Circulating tumor cell ,Internal medicine ,Medicine ,Circulating DNA ,In patient ,business ,Predictive biomarker - Abstract
11015 Background: Prognostic and predictive biomarkers in mCRC are urgently needed. Circulating tumor cells are a promising blood biomarker, but are detectable in only a minority of pts. Recently, analysis of circulating tumor DNA (ctDNA) has shown promise as a liquid biopsy, reflecting the evolving mutational status of the tumor. Here we explored baseline ctDNA as a prognostic marker, and early changes in ctDNA as a marker of CT response. Methods: Serial plasma samples and CEA were collected at baseline (D1), day 3 (D3) and cycle 2 day 1 (C2D1) from 40 mCRC pts receiving standard combination CT. Restaging scans performed at 8 weeks were centrally assessed using RECIST criteria. Samples were analyzed at Johns Hopkins Kimmel Cancer Center. Initially tumor tissue was analyzed for hotspot mutations in TP53, APC, KRAS, BRAF, PIK3CA and FBXW7. The same mutation was queried and quantified in plasma using a MPS platform (Safe-SeqS). Log-rank test was used to compare survival curves and Wilcoxon matched pairs test was used to compare paired plasma samples. Results: Preliminary data is available on 19 pts in this ongoing study. Using our initial panel at least 1 mutation was found in 16 of 19 (84.2%) tumors (7 KRAS, 3 TP53, 3 BRAF, 2 APC and 1 PIK3CA), with matching ctDNA found for each pt. For the remaining 3 cases a further panel of mutations is being analyzed. Median D1 cell free DNA (cfDNA) and ctDNA levels were 1.98 ng/ul (0.15 – 57.18) and 523 mutant fragments (frag)/ml (0.4 – 109,876), respectively. Pts with D1 cfDNA of ≥ 2.5 compared with < 2.5 had shorter median overall survival (OS; 6.9 v 12.2 months, p = 0.0086), with a trend for shorter progression-free survival (PFS; 3.6 v 8.2 months, p = 0.3477). A surge of ctDNA level from D1 to D3 was typically observed (median increase: 91.2 frag/ml, p = 0.0313), followed by a drop (median decrease from D1 to C2D1: 208.8 frag/ml, p = 0.0098). All pts with a decrease in ctDNA at C2D1 had a reduction in tumor size at 8 weeks. Conclusions: In all cases of mCRC where tumor mutation was identified, matching ctDNA was detected in plasma. Circulating DNA is a promising marker of prognosis. Early changes in DNA levels may be a useful marker of tumor response.
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- 2013
50. Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies
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Jian Wu, Clarence Lee, Silvio Veronese, Mark Sausen, Dung T. Le, Louise Olsson, Ralph H. Hruban, Gregory J. Riggins, Alessandro Olivi, Calogero Lauricella, Yuchen Jiao, Hartmut Juhl, Nickolas Papadopoulos, Evan J. Lipson, Victor E. Velculescu, Chetan Bettegowda, Hao Wang, Alberto Bardelli, Kerstin Schmidt, Matthias Holdhoff, Rebecca J. Leary, Nishant Agrawal, Isaac Kinde, Dan Theodorescu, Sueli Mieko Oba-Shinjo, Michael Goggins, Peter J. Allen, Michael Lim, Michael A. Choti, Timothy T. Harkins, Michael D. Hogarty, Seung-Mo Hong, Brandon Luber, Kenneth W. Kinzler, Christopher L. Wolfgang, Rhoda M. Alani, Peter Gibbs, Dongmei Xing, Nilofer S. Azad, Bjarne Bartlett, George J. Netto, Suely Kazue Nagahashi Marie, Giulia Siravegna, Gary L. Gallia, John L. Cameron, C. Max Schmidt, Bert Vogelstein, Yuxuan Wang, Luis A. Diaz, Leslie A. Fecher, Jenny J. Kim, Laura D. Wood, Jeanne Tie, Robert L. Giuntoli, Andrea Sartore-Bianchi, Jon D. Weingart, le-Ming Shih, Emmanuel S. Antonarakis, Salvatore Siena, Daniel A. Laheru, Kelly S. Oliner, Tian Li Wang, and Henry Brem
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Adult ,Male ,Oncology ,medicine.medical_specialty ,Colorectal cancer ,detection ,Gene mutation ,medicine.disease_cause ,Article ,Young Adult ,03 medical and health sciences ,0302 clinical medicine ,Circulating tumor cell ,Neoplasms ,Internal medicine ,Pancreatic cancer ,medicine ,Humans ,Neoplasm Metastasis ,Liquid biopsy ,Aged ,030304 developmental biology ,circulating tumor DNA ,Aged, 80 and over ,0303 health sciences ,business.industry ,Melanoma ,Cancer ,DNA, Neoplasm ,General Medicine ,Middle Aged ,CANCER ,medicine.disease ,3. Good health ,030220 oncology & carcinogenesis ,Female ,KRAS ,business - Abstract
The development of noninvasive methods to detect and monitor tumors continues to be a major challenge in oncology. We used digital polymerase chain reaction–based technologies to evaluate the ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types. We found that ctDNA was detectable in >75% of patients with advanced pancreatic, ovarian, colorectal, bladder, gastroesophageal, breast, melanoma, hepatocellular, and head and neck cancers, but in less than 50% of primary brain, renal, prostate, or thyroid cancers. In patients with localized tumors, ctDNA was detected in 73, 57, 48, and 50% of patients with colorectal cancer, gastroesophageal cancer, pancreatic cancer, and breast adenocarcinoma, respectively. ctDNA was often present in patients without detectable circulating tumor cells, suggesting that these two biomarkers are distinct entities. In a separate panel of 206 patients with metastatic colorectal cancers, we showed that the sensitivity of ctDNA for detection of clinically relevant KRAS gene mutations was 87.2% and its specificity was 99.2%. Finally, we assessed whether ctDNA could provide clues into the mechanisms underlying resistance to epidermal growth factor receptor blockade in 24 patients who objectively responded to therapy but subsequently relapsed. Twenty-three (96%) of these patients developed one or more mutations in genes involved in the mitogen-activated protein kinase pathway. Together, these data suggest that ctDNA is a broadly applicable, sensitive, and specific biomarker that can be used for a variety of clinical and research purposes in patients with multiple different types of cancer.
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