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Challapalli A, Ratnayake G, McGrane J, Frazer R, Gupta S, Parslow D, Kingdon S, Lydon A, Sharma A, Tuthill M, McCusker C, Ford V, Ferrera A, Malik J, Boh Z, Jones E, T.R. Geldart, Nelmes S, Brown J, Bahl A. 1463P Patterns of care and outcomes of metastatic renal cell carcinoma (mRCC) patients (pts) with bone metastases (BM): A UK multicenter review. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Ratnayake G, Challapalli A, McGrane J, Frazer R, Gupta S, Parslow D, Kingdon S, Lydon A, Sharma A, Tuthill M, McCartney T, Jabbar R, Charnley N, Malik J, Abhi D, Chau C, Geldart T, Halstead A, Anuforom U, Bahl A. 1457P A UK multicentre retrospective review of metastatic renal cell carcinoma (mRCC) patients (pts) outcomes with brain metastases (BM) in the modern era. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Yizhak K, Aguet F, Kim J, Hess JM, Kübler K, Grimsby J, Frazer R, Zhang H, Haradhvala NJ, Rosebrock D, Livitz D, Li X, Arich-Landkof E, Shoresh N, Stewart C, Segrè AV, Branton PA, Polak P, Ardlie KG, Getz G. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science 2019; 364:364/6444/eaaw0726. [PMID: 31171663 DOI: 10.1126/science.aaw0726] [Citation(s) in RCA: 295] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/02/2019] [Indexed: 02/06/2023]
Abstract
How somatic mutations accumulate in normal cells is poorly understood. A comprehensive analysis of RNA sequencing data from ~6700 samples across 29 normal tissues revealed multiple somatic variants, demonstrating that macroscopic clones can be found in many normal tissues. We found that sun-exposed skin, esophagus, and lung have a higher mutation burden than other tested tissues, which suggests that environmental factors can promote somatic mosaicism. Mutation burden was associated with both age and tissue-specific cell proliferation rate, highlighting that mutations accumulate over both time and number of cell divisions. Finally, normal tissues were found to harbor mutations in known cancer genes and hotspots. This study provides a broad view of macroscopic clonal expansion in human tissues, thus serving as a foundation for associating clonal expansion with environmental factors, aging, and risk of disease.
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Affiliation(s)
- Keren Yizhak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julian M Hess
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kirsten Kübler
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Jonna Grimsby
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Hailei Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas J Haradhvala
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Xiao Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eila Arich-Landkof
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Noam Shoresh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ayellet V Segrè
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Philip A Branton
- Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, National Cancer Institute, Bethesda, MD, USA
| | - Paz Polak
- Oncological Sciences, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | | | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
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Maruvka YE, Frazer R, Grimsby J, Cibulskis C, Adalsteinsson V, Corcoran R, Getz G. Abstract 2677: MSIClass–Identification and classification of microsatellite unstable using cell-free DNA from ultra-low-pass sequencing. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The acquisition of mismatch repair deficiency is common in many tumor types. A unique subtype of mismatch repair deficient tumors, called tumors with microsatellite instability (MSI), has been recently approved for treatment with PD-1\PD-L1 blockade immunotherapy. Therefore, developing a quick, inexpensive, and easy-to-implement technique for classifying tumors as MSI is of utmost importance. Here, we describe such a method using next-generation sequencing data, and show that it can detect MSI from cell-free DNA (cfDNA), even when there is low fraction of tumor DNA in the cfDNA.
We first analyzed the unique mutational features of MSI vs. microsatellite stable (MSS) tumors. Using our SignatureAnalyzer tool, we analyzed the signatures of the different insertions and deletions within microsatellite loci (MS-indels), and found that MSI tumors harbor elevated MS-indels of certain types, which we further validated using whole genome sequencing data from The Cancer Genome Atlas.
We next used this information to develop a method (MSIClass) that analyzes the WGS data of a given sample by capturing the features unique to MSI tumors. This method assigns each sample a score based on aggregating information from all MS loci simultaneously; since MSIClass is a sample-based tool, it can call the MSI status of tumor samples that have no patient-matched normal sample. We further demonstrate that MSIClass requires minimal genomic information; indeed, sequencing coverage as low as 0.05x (current sequencing cost of ~$2/sample) is sufficient for accurate classification by MSIClass.
Using in silico and in vitro DNA mixing we show that MSIClass can accurately identify MSI cases in very low purity cases, at 0.1% tumor DNA (using 0.5x sequencing coverage). We show that MSIClass, applied on cfDNA, could accurately classify 29 colon cases – 22 MSS and 7 MSI cases, 3 of which are early stage disease and with low tumor content.
These results demonstrate that MSIClass is an inexpensive MSI test that can be applied in various cases: bulk sequencing where a matched normal is not available, cases of very low purity tumors, and even using cfDNA from blood in cases a biopsy is not available or possible. Finally, this methodology can be the basis for monitoring minimal residual disease, and potential be used for early detection of MSI tumors.
Citation Format: Yosef E. Maruvka, Ruslana Frazer, Jonna Grimsby, Carrie Cibulskis, Viktor Adalsteinsson, Ryan Corcoran, Gad Getz. MSIClass–Identification and classification of microsatellite unstable using cell-free DNA from ultra-low-pass sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2677.
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Barrington C, Frazer R, Higgins E, Shore A. The role of tumour marker testing in earlier diagnosis of cancer. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx440.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Allcock E, Spencer E, Frazer R, Applegate G, Buckenmaier C. Continuous Transversus Abdominis Plane (TAP) Block Catheters in a Combat Surgical Environment. Pain Med 2010; 11:1426-9. [DOI: 10.1111/j.1526-4637.2010.00894.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Socinski M, Halle J, Morris D, Limentani S, Frazer R, Rosenman J. Phase I trial of induction and concurrent chemotherapy with dose-escalated thoracic conformal radiation therapy (TCRT) to 78 Gy and beyond in unresectable stage III A/B non small cell lung cancer (NSCLC). Int J Radiat Oncol Biol Phys 2002. [DOI: 10.1016/s0360-3016(02)03570-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Duncan C, Li H, Dykhuizen R, Frazer R, Johnston P, MacKnight G, Smith L, Lamza K, McKenzie H, Batt L, Kelly D, Golden M, Benjamin N, Leifert C. Protection against oral and gastrointestinal diseases: importance of dietary nitrate intake, oral nitrate reduction and enterosalivary nitrate circulation. Comp Biochem Physiol A Physiol 1997; 118:939-48. [PMID: 9505412 DOI: 10.1016/s0300-9629(97)00023-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the last 20 years, dietary nitrate has been implicated in the formation of methemoglobin and carcinogenic nitrosamines in humans. This has led to restrictions of nitrate and nitrite levels in food and drinking water. However, there is no epidemiological evidence for an increased risk of gastric and intestinal cancer in population groups with high dietary vegetable or nitrate intake. A reevaluation of our currently very negative perception of dietary nitrates comes from recent research into the metabolism and enterosalivary circulation of nitrate in mammals. These studies showed that nitrate is converted to nitrite in the oral cavity that then "fuels" an important mammalian resistance mechanism against infectious diseases. Moreover, there is now evidence that the conversion of nitrate into oxides of nitrogen prevents the formation carcinogenic nitrosamines.
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Affiliation(s)
- C Duncan
- Department of Plant & Soil Science, University of Aberdeen, Scotland, U.K
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Dykhuizen RS, Frazer R, Duncan C, Smith CC, Golden M, Benjamin N, Leifert C. Antimicrobial effect of acidified nitrite on gut pathogens: importance of dietary nitrate in host defense. Antimicrob Agents Chemother 1996; 40:1422-5. [PMID: 8726013 PMCID: PMC163343 DOI: 10.1128/aac.40.6.1422] [Citation(s) in RCA: 130] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Dietary intake of nitrate generates salivary nitrite, which is acidified in the stomach, leading to a number of reactive intermediates of nitrogen, among which are the potentially carcinogenic N-nitrosamines. Acidified nitrite, however, also has antimicrobial activity which coincides with the formation of nitric oxide. The present study examines the antimicrobial effect in vitro of acidified nitrite on Salmonella enteritidis, Salmonella typhimurium, Yersinia enterocolitica, Shigella sonnei, and Escherichia coli O157. First-order regression plots showed a linear inverse relationship of log-transformed proton and nitrite concentrations with MICs and MBCs after 30 min, 2 h, and 24 h of exposure (P < 0.001 for all antibacterial activities). Susceptibility to the acidified nitrate solutions ranked as follows: Y. enterocolitica > S. enteritidis > S. typhimurium = Shigella sonnei > E. coli O157 (P < 0.05). Addition of SCN-, but not that of CI-, increased the antibacterial activity (paired t testing, P < 0.001). Generation of salivary nitrite from dietary nitrate may provide significant protection against gut pathogens in humans.
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Affiliation(s)
- R S Dykhuizen
- Infection Unit, Aberdeen Royal Infirmary, United Kingdom
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Frazer R. ICN reports on nursing shortages and death-in-childbirth rates. Nurs Stand 1991; 5:9. [PMID: 1906338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Boyd JS, Dinsmore WW, Frazer R, Maw RD, Horner T. Assessing the role of the HIV-CHEK kit. Int J STD AIDS 1990; 1:292. [PMID: 2088543 DOI: 10.1177/095646249000100417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Mika L, Buhler C, Thomas F, Kralova O, Frazer R, Stamper D. The development of air medical services in Czechoslovakia. J Air Med Transp 1990; 9:22-3, 25-6. [PMID: 10105613 DOI: 10.1016/s1046-9095(05)80406-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The Czechoslovakian system of centralized dispatch of all emergency medical services prevents competition between ground ambulances and air medical services. Although this program is less than two years old, remarkable progress has pushed Czechoslovakia to the forefront of modern-day air medical transport. However, the future of Czechoslovakian air medical transport will require the acquisition of better-performing EMS helicopters and accessibility to medical equipment using Western technology. As with all current United States helicopter EMS systems, Czechoslovakia will face many of the financial considerations required in funding this extensive and elaborate project.
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Frazer R. Briggs went wrong in not recognising the nurse was capable of change. Nurs Stand (1984) 1984:5. [PMID: 6569337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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Frazer R. Should not be the only type of care in the future. Nurs Stand (1984) 1984:5. [PMID: 6566986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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Frazer R. "I only wanted them cleaned and checked.". Dentalpractice 1981; 2:68-9. [PMID: 6949741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Davidson EC, Morris JA, O'Grady JP, Hendrickx AG, Anderson J, Kaback M, Frazer R. Sampling the fetoplacental circulation. III. Combined laparoscopy-fetoscopy in the pregnant macaque for hemoglobin identification. Am J Obstet Gynecol 1978; 132:833-44. [PMID: 153713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To demonstrate increased technical experience with fetoscopy and fetal blood sampling, two groups of macaques were compared to control animals. Group 2 had a perinatal mortality rate that was not significantly different from that of the control group. A 2.7 mm. Hopkins rod lens endoscope encased in an eccentric cannula, 3.8 mm. outside diameter, was used. When compared to the earlier test group (Group 1), the later test group (Group 2) showed greater adequacy of the fetal blood sample for laboratory analysis (P less than 0.01). Anthropometric and hematologic data collected at term births compared favorably in test and control groups, with the exception of the white blood cell count, which was significantly lower with fetoscopy (P less than 0.01). This is the first report of experimental fetoscopy with the use of a control group to provide precise data to aid in clarification of the ethical issues yet unresolved in this technology.
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Morris JA, Davidson EC, Maidman JE, Arce JJ, Brown JE, Frazer R. Sampling the fetoplacental circulation. II. Combined laparoscopy-fetoscopy in the pregnant ovine. Am J Obstet Gynecol 1977; 128:279-86. [PMID: 140606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Induction of pneumoperitoneum, laparoscopy, and intrauterine endoscopy (fetoscopy) were successfully accompished in 23 pregnant sheep at 45 to 60 days' gestational age. The fetoscope, a conventional 2.7 mm. Hopkins straightforward wide-angle telescope (Stortz 27018A) encased in a prototype 3.1 mm. eccentric cannula, incorporates a 25 gauge needle channel. Multiple pregnancy was encountered in 11 animals. Forty-two separate fetoscopic trials were accomplished; a fetoplacental blood sample was obtained in 52 per cent of the trials. A mean interval of 19 +/- 9 days (+/- S.D., range 6 to 37 days) was allowed between fetoscopy trials. Fetal deaths occurred in nine animals (39 per cent). We believe that laparoscopy permits preselection of the proposed fetoscopy puncture site and will permit the operator to thereby avoid the placenta and/or uterine vessels.
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Abstract
Intrauterine endoscopy (fetoscopy) was successfully accomplished in 26 specially prepared pregnant sheep at 85 to 110 days' gestational age, with the use of a conventional 2.7 mm. Hopkins straightforward wide-angle telescope (Stortz 27018A) encased in a prototype 3.1 mm. eccentric cannula which incorporates a 25 gauge needle channel. Fetal blood was aspirated in 12 lambs. Twenty-five animals were followed throughout the remainder of pregnancy: nine (36 per cent) aborted within three days-three weeks after endoscopy. The pregnant ovine appeared to be a useful experimental animal model for the development of an intrauterine endoscopy technique.
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Wren BG, Frazer R. A commercial kit for urine testing. Med J Aust 1969; 1:547. [PMID: 5777914 DOI: 10.5694/j.1326-5377.1969.tb92278.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Joplin GF, Hill DW, Oakley NW, Kohner E, Frazer R. Yttrium 90 needle implantation in diabetes: correlation between degree of hypopituitarism and retinopathy response. Proc R Soc Med 1967; 60:149. [PMID: 6018838 PMCID: PMC1901561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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