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Bhandari A, Dunham A, Bassily E, Mohanty BD, Wu R. First Description of Novel End-Organ Effects by Speed Modulation Using the Aortix™ Device. Case Rep Cardiol 2024; 2024:7430212. [PMID: 38695013 PMCID: PMC11062771 DOI: 10.1155/2024/7430212] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 05/04/2024] Open
Abstract
Aortix™ is a novel percutaneous mechanical circulatory support device designed to facilitate diuresis in patients with cardiorenal syndrome. We describe for the first time the development of end-organ hypoperfusion from excess blood acceleration at the nominal setting and demonstrate through temporal-perfusion marker curves, the potential for speed modulation to optimize results. This will inform future device development and investigation of patient-specific device titration.
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Affiliation(s)
| | | | | | | | - Robby Wu
- University of South Florida, Tampa, FL, USA
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2
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Noom MJ, Dunham A, DuCoin CG. Resolution of Roemheld Syndrome After Hiatal Hernia Repair and LINX Placement: Case Review. Cureus 2023; 15:e37429. [PMID: 37182025 PMCID: PMC10173368 DOI: 10.7759/cureus.37429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Roemheld syndrome, also known as gastrocardiac syndrome, was first studied as a relationship between gastrointestinal and cardiovascular symptoms through the vagus nerve. Several hypotheses have attempted to explain the pathophysiology of Roemheld syndrome, but the underlying process remains unclear. We present a clinically diagnosed case of Roemheld syndrome in a patient with a hiatal hernia whose gastrointestinal and cardiac symptoms were successfully treated with robotic assisted hernia repair, esophagogastroduodenoscopy (EGD), and LINX magnetic sphincter augmentation. Our case is a 60-year-old male with a history of esophageal stricture and hiatal hernia who presented with complaints of gastroesophageal reflux disease (GERD) and related arrhythmias for five years. The patient did not have a history of cardiovascular disease other than hypertension. The cause of the hypertension was assumed to be primary, as workup for possible pheochromocytoma was negative. Cardiac work-up revealed arrhythmias that were characterized as supraventricular tachycardia with intermittent pre-ventricular contractions (PVC); however, testing was unable to determine a cause for the arrhythmias. High-resolution manometry showed low pressure in the lower esophageal sphincter with normal esophageal motility. Further evaluation included a 96-hour Bravo test and DeMeester score of 31 was recorded, confirming mild GERD; however, EGD was unremarkable. Surgeons elected to perform a robotic assisted hiatal hernia repair, EGD, and magnetic sphincter augmentation. Four months following surgery, the patient denied symptoms of GERD or episodes of palpitation and subsequently weaned off proton pump inhibitors with continual lack of symptoms. GERD is a common complaint among the primary care setting; however, ventricular dysrhythmias among this population and a clinical diagnosis of Roemheld syndrome is unique. One hypothesis may be that protrusion of the stomach into the chest cavity may exacerbate current reflux, and the anatomical relationship between a herniated fundus and anterior vagal nerve may cause direct physical stimulation that is a more potent risk factor for the development of arrythmias. However, Roemheld Syndrome is a unique diagnosis, and the pathophysiology is still yet to be understood.
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Affiliation(s)
- Madison J Noom
- Surgery, University of South Florida Morsani College of Medicine, Tampa, USA
| | - Alden Dunham
- Surgery, University of South Florida Morsani College of Medicine, Tampa, USA
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Abdul-Rahman T, Dunham A, Huang H, Bukhari SMA, Mehta A, Awuah WA, Ede-Imafidon D, Cantu-Herrera E, Talukder S, Joshi A, Sundlof DW, Gupta R. Chemotherapy Induced Cardiotoxicity: A State of the Art Review on General Mechanisms, Prevention, Treatment and Recent Advances in Novel Therapeutics. Curr Probl Cardiol 2023; 48:101591. [PMID: 36621516 DOI: 10.1016/j.cpcardiol.2023.101591] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 01/03/2023] [Indexed: 01/08/2023]
Abstract
As medicine advances to employ sophisticated anticancer agents to treat a vast array of oncological conditions, it is worth considering side effects associated with several chemotherapeutics. One adverse effect observed with several classes of chemotherapy agents is cardiotoxicity which leads to reduced ejection fraction (EF), cardiac arrhythmias, hypertension and Ischemia/myocardial infarction that can significantly impact the quality of life and patient outcomes. Research into possible mechanisms has elucidated several mechanisms, such as ROS generation, calcium overload and apoptosis. However, there is a relative scarcity of literature detailing the relationship between the exact mechanism of cardiotoxicity for each anticancer agent and observed clinical effects. This review comprehensively describes cardiotoxicity associated with various classes of anticancer agents and possible mechanisms. Further research exploring possible mechanisms for cardiotoxicity observed with anticancer agents could provide valuable insight into susceptibility for developing symptoms and management guidelines. Chemotherapeutics are associated with several side effects. Several classes of chemotherapy agents cause cardiotoxicity leading to a reduced ejection fraction (EF), cardiac arrhythmias, hypertension, and Ischemia/myocardial infarction. Research into possible mechanisms has elucidated several mechanisms, such as ROS generation, calcium overload, and apoptosis. However, there is a relative scarcity of literature detailing the relationship between the exact mechanism of cardiotoxicity for each anticancer agent and observed clinical effects. This review describes cardiotoxicity associated with various classes of anticancer agents and possible mechanisms. Further research exploring mechanisms for cardiotoxicity observed with anticancer agents could provide insight that will guide management.
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Affiliation(s)
| | - Alden Dunham
- University of South Florida Morsani College of Medicine, FL
| | - Helen Huang
- Royal College of Surgeons in Ireland, University of Medicine and Health Science, Dublin, Ireland
| | | | - Aashna Mehta
- University of Debrecen-Faculty of Medicine, Debrecen, Hungary
| | - Wireko A Awuah
- Sumy State University, Toufik's World Medical Association, Ukraine
| | | | - Emiliano Cantu-Herrera
- Department of Clinical Sciences, Division of Health Sciences, University of Monterrey, San Pedro Garza García, Nuevo León, México
| | | | - Amogh Joshi
- Department of Cardiology, Lehigh Valley Health Network, Allentown, PA
| | - Deborah W Sundlof
- Department of Cardiology, Lehigh Valley Health Network, Allentown, PA
| | - Rahul Gupta
- Department of Cardiology, Lehigh Valley Health Network, Allentown, PA.
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Stevenson A, Archer SK, Schultz JA, Dunham A, Marliave JB, Martone P, Harley CDG. Warming and acidification threaten glass sponge Aphrocallistes vastus pumping and reef formation. Sci Rep 2020; 10:8176. [PMID: 32424237 PMCID: PMC7235243 DOI: 10.1038/s41598-020-65220-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/30/2020] [Indexed: 11/09/2022] Open
Abstract
The glass sponge Aphrocallistes vastus contributes to the formation of large reefs unique to the Northeast Pacific Ocean. These habitats have tremendous filtration capacity that facilitates flow of carbon between trophic levels. Their sensitivity and resilience to climate change, and thus persistence in the Anthropocene, is unknown. Here we show that ocean acidification and warming, alone and in combination have significant adverse effects on pumping capacity, contribute to irreversible tissue withdrawal, and weaken skeletal strength and stiffness of A. vastus. Within one month sponges exposed to warming (including combined treatment) ceased pumping (50–60%) and exhibited tissue withdrawal (10–25%). Thermal and acidification stress significantly reduced skeletal stiffness, and warming weakened it, potentially curtailing reef formation. Environmental data suggests conditions causing irreversible damage are possible in the field at +0.5 °C above current conditions, indicating that ongoing climate change is a serious and immediate threat to A. vastus, reef dependent communities, and potentially other glass sponges.
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Affiliation(s)
- A Stevenson
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada. .,Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, British Columbia, Canada. .,Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany.
| | - S K Archer
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, British Columbia, V9T 6N7, Canada.,Louisiana Universities Marine Consortium, 8124 Highway 56, Chauvin, Louisiana, 70344, USA
| | - J A Schultz
- Ocean Wise Research Institute, PO Box 3232, Vancouver, British Columbia, V6B3X8, Canada
| | - A Dunham
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, British Columbia, V9T 6N7, Canada
| | - J B Marliave
- Ocean Wise Research Institute, PO Box 3232, Vancouver, British Columbia, V6B3X8, Canada
| | - P Martone
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - C D G Harley
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.,Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, British Columbia, Canada
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Hubert P, Mahoney M, Dunham A, Shanley E, Duffy V. Assessing Liking of Physical Activity Behaviors in College Females. J Acad Nutr Diet 2019. [DOI: 10.1016/j.jand.2019.06.241] [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: 10/26/2022]
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Bencheikh L, Nguyen KA, Chadebech P, Kiger L, Bodivit G, Jouard A, Pakdaman S, Adypagavane S, Audureau E, Tebbakha K, Hebert N, Pirenne F, Sowemimo-Coker S, Dunham A, Bartolucci P. S906 PRECLINICAL EVALUATION OF THE PRESERVATION OF RED BLOOD CELL CONCENTRATES IN HYPOXIA BY HYPOXIC STORAGE TECHNOLOGY FOR TRANSFUSION IN SICKLE CELL DISEASE. Hemasphere 2019. [DOI: 10.1097/01.hs9.0000561904.90219.03] [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: 11/25/2022] Open
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Dunham A, Archer SK, Davies SC, Burke LA, Mossman J, Pegg JR, Archer E. Assessing condition and ecological role of deep-water biogenic habitats: Glass sponge reefs in the Salish Sea. Mar Environ Res 2018; 141:88-99. [PMID: 30115533 DOI: 10.1016/j.marenvres.2018.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
Biogenic habitats play important roles in shallow-water ecosystems, but their roles in deeper waters are less well-studied. We quantitatively assessed 19 glass sponge reefs in the Salish Sea for live reef-building sponge cover and biodiversity, explored potential drivers behind variation observed among reefs, and quantified individual and collective roles the reefs play in filtration and carbon removal. The reefs support diverse and abundant communities of invertebrates and fish, with 115 unique taxonomic groups observed. Sponge cover varied widely between reefs: percent live reef-building sponge cover ranged from 0.2 to 17.5% and proportion of live reef habitat category ranged from 0.2 to 92%. These differences were predominantly driven by the seabed terrain characteristics such as seafloor rugosity, curvature, and depth; human pressure measures explored in this study - density of anthropogenic objects and fishing footprint over the past 17 years - did not mask the natural influence of seabed terrain. The difference in sponge cover between the reefs led to wide variation in ecosystem function with individual reefs processing between 465 and 47,300 L/m2 per day. Collectively, each day the 19 reefs filter 1.04 × 1011 L of water which corresponds to 1% of the total water volume in Strait of Georgia and Howe Sound combined. The reefs remove up to 1 g of carbon per m2 per day, comparable to carbon sequestration rates reported for terrestrial old growth forests and to "blue carbon" sequestration rates by marine vegetation. Implications for sponge reef conservation and monitoring are discussed.
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Affiliation(s)
- A Dunham
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada; Fisheries and Aquaculture Department, Vancouver Island University, 900 Fifth Street, Nanaimo, BC, V9R 5S5, Canada.
| | - S K Archer
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - S C Davies
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - L A Burke
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - J Mossman
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - J R Pegg
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - E Archer
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
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Burlet E, HogenEsch H, Dunham A, Morefield G. Evaluation of the Potency, Neutralizing Antibody Response, and Stability of a Recombinant Fusion Protein Vaccine for Streptococcus pyogenes. AAPS J 2017; 19:875-881. [DOI: 10.1208/s12248-017-0069-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/25/2017] [Indexed: 11/30/2022]
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9
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Dunham A, Pegg JR, Carolsfeld W, Davies S, Murfitt I, Boutillier J. Effects of submarine power transmission cables on a glass sponge reef and associated megafaunal community. Mar Environ Res 2015; 107:50-60. [PMID: 25884466 DOI: 10.1016/j.marenvres.2015.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/12/2015] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
We examined the effects of submarine power transmission cable installation and operation on glass sponge reef condition and associated megafauna. Video and still imagery were collected using a Remotely Operated Vehicle twice a year for 4 years following cable installation. The effects of cables on glass sponges were assessed by comparing sponge cover along fixed transects and at marked index sites. Megafauna counts along transects were used to explore the effects on associated community. We found no evidence of cable movement across the sponge reef surface. Live sponge cover was found to be consistently lower along cable transects and at cable index sites compared to controls. Live sponge cover was the lowest (55 ± 1.1% decrease) at cable index sites 1.5 years after installation and recovered to 85 ± 30.6% of the original size over the following 2 years. Our data suggest 100% glass sponge mortality along the direct cable footprint and 15% mortality in the surrounding 1.5 m corridor 3.5 years after cable installation. Growth rate of a new glass sponge was 1 and 3 cm/year in first and second year, respectively, and appeared to be seasonal. We observed a diverse megafaunal community with representatives from 7 phyla and 14 classes. Total megafauna, spot prawn, and other Arthropoda abundances were slightly lower along cable transects although the effect of cable presence was not statistically significant. The following measures could be taken to reduce the amount of damage to glass sponge reefs and associated fauna: routing the cable around reefs, whenever possible, minimizing cable movement across the surface of the reef at installation and routine operation, and assessing potential damage to glass sponges prior to decommissioning.
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Affiliation(s)
- A Dunham
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada; Fisheries and Aquaculture Department, Vancouver Island University, 900 Fifth Street, Nanaimo, BC V9R 5S5, Canada.
| | - J R Pegg
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - W Carolsfeld
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - S Davies
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - I Murfitt
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - J Boutillier
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
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Sánchez E, Dunham A, Nowak D, Straton J, Doughty J. Enhanced image contrast with delocalized near-field excitation. Crystal Research and Technology 2014. [DOI: 10.1002/crat.201300325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- E. Sánchez
- Department of Physics; Portland State University; PO Box 751 Portland OR 97207 USA
| | - A. Dunham
- Department of Physics; Portland State University; PO Box 751 Portland OR 97207 USA
| | - D. Nowak
- Department of Physics; Portland State University; PO Box 751 Portland OR 97207 USA
| | - J. Straton
- Department of Physics; Portland State University; PO Box 751 Portland OR 97207 USA
| | - J. Doughty
- Department of Physics; Portland State University; PO Box 751 Portland OR 97207 USA
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Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D, Dunham A, Scott CE, Howe KL, Woodfine K, Spencer CCA, Jones MC, Gillson C, Searle S, Zhou Y, Kokocinski F, McDonald L, Evans R, Phillips K, Atkinson A, Cooper R, Jones C, Hall RE, Andrews TD, Lloyd C, Ainscough R, Almeida JP, Ambrose KD, Anderson F, Andrew RW, Ashwell RIS, Aubin K, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Beasley H, Bethel G, Bird CP, Bray-Allen S, Brown JY, Brown AJ, Bryant SP, Buckley D, Burford DC, Burrill WDH, Burton J, Bye J, Carder C, Chapman JC, Clark SY, Clarke G, Clee C, Clegg SM, Cobley V, Collier RE, Corby N, Coville GJ, Davies J, Deadman R, Dhami P, Dovey O, Dunn M, Earthrowl M, Ellington AG, Errington H, Faulkner LM, Frankish A, Frankland J, French L, Garner P, Garnett J, Gay L, Ghori MRJ, Gibson R, Gilby LM, Gillett W, Glithero RJ, Grafham DV, Gribble SM, Griffiths C, Griffiths-Jones S, Grocock R, Hammond S, Harrison ESI, Hart E, Haugen E, Heath PD, Holmes S, Holt K, Howden PJ, Hunt AR, Hunt SE, Hunter G, Isherwood J, James R, Johnson C, Johnson D, Joy A, Kay M, Kershaw JK, Kibukawa M, Kimberley AM, King A, Knights AJ, Lad H, Laird G, Langford CF, Lawlor S, Leongamornlert DA, Lloyd DM, Loveland J, Lovell J, Lush MJ, Lyne R, Martin S, Mashreghi-Mohammadi M, Matthews L, Matthews NSW, McLaren S, Milne S, Mistry S, oore MJFM, Nickerson T, O'Dell CN, Oliver K, Palmeiri A, Palmer SA, Pandian RD, Parker A, Patel D, Pearce AV, Peck AI, Pelan S, Phelps K, Phillimore BJ, Plumb R, Porter KM, Prigmore E, Rajan J, Raymond C, Rouse G, Saenphimmachak C, Sehra HK, Sheridan E, Shownkeen R, Sims S, Skuce CD, Smith M, Steward C, Subramanian S, Sycamore N, Tracey A, Tromans A, Van Helmond Z, Wall J. M. Wallis M, White S, Whitehead SL, Wilkinson JE, Willey DL, Williams H, Wilming L, Wray PW, Wu Z, Coulson A, Vaudin M, Sulston JE, Durbin R, Hubbard T, Wooster R, Dunham I, Carter NP, McVean G, Ross MT, Harrow J, Olson MV, Beck S, Rogers J, Bentley DR. Erratum: The DNA sequence and biological annotation of human chromosome 1. Nature 2006. [DOI: 10.1038/nature05152] [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: 11/09/2022]
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Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D, Dunham A, Scott CE, Howe KL, Woodfine K, Spencer CCA, Jones MC, Gillson C, Searle S, Zhou Y, Kokocinski F, McDonald L, Evans R, Phillips K, Atkinson A, Cooper R, Jones C, Hall RE, Andrews TD, Lloyd C, Ainscough R, Almeida JP, Ambrose KD, Anderson F, Andrew RW, Ashwell RIS, Aubin K, Babbage AK, Bagguley CL, Bailey J, Beasley H, Bethel G, Bird CP, Bray-Allen S, Brown JY, Brown AJ, Buckley D, Burton J, Bye J, Carder C, Chapman JC, Clark SY, Clarke G, Clee C, Cobley V, Collier RE, Corby N, Coville GJ, Davies J, Deadman R, Dunn M, Earthrowl M, Ellington AG, Errington H, Frankish A, Frankland J, French L, Garner P, Garnett J, Gay L, Ghori MRJ, Gibson R, Gilby LM, Gillett W, Glithero RJ, Grafham DV, Griffiths C, Griffiths-Jones S, Grocock R, Hammond S, Harrison ESI, Hart E, Haugen E, Heath PD, Holmes S, Holt K, Howden PJ, Hunt AR, Hunt SE, Hunter G, Isherwood J, James R, Johnson C, Johnson D, Joy A, Kay M, Kershaw JK, Kibukawa M, Kimberley AM, King A, Knights AJ, Lad H, Laird G, Lawlor S, Leongamornlert DA, Lloyd DM, Loveland J, Lovell J, Lush MJ, Lyne R, Martin S, Mashreghi-Mohammadi M, Matthews L, Matthews NSW, McLaren S, Milne S, Mistry S, Moore MJF, Nickerson T, O'Dell CN, Oliver K, Palmeiri A, Palmer SA, Parker A, Patel D, Pearce AV, Peck AI, Pelan S, Phelps K, Phillimore BJ, Plumb R, Rajan J, Raymond C, Rouse G, Saenphimmachak C, Sehra HK, Sheridan E, Shownkeen R, Sims S, Skuce CD, Smith M, Steward C, Subramanian S, Sycamore N, Tracey A, Tromans A, Van Helmond Z, Wall M, Wallis JM, White S, Whitehead SL, Wilkinson JE, Willey DL, Williams H, Wilming L, Wray PW, Wu Z, Coulson A, Vaudin M, Sulston JE, Durbin R, Hubbard T, Wooster R, Dunham I, Carter NP, McVean G, Ross MT, Harrow J, Olson MV, Beck S, Rogers J, Bentley DR, Banerjee R, Bryant SP, Burford DC, Burrill WDH, Clegg SM, Dhami P, Dovey O, Faulkner LM, Gribble SM, Langford CF, Pandian RD, Porter KM, Prigmore E. The DNA sequence and biological annotation of human chromosome 1. Nature 2006; 441:315-21. [PMID: 16710414 DOI: 10.1038/nature04727] [Citation(s) in RCA: 170] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2005] [Accepted: 03/13/2006] [Indexed: 11/08/2022]
Abstract
The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.
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Affiliation(s)
- S G Gregory
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
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Dunham A, Matthews LH, Burton J, Ashurst JL, Howe KL, Ashcroft KJ, Beare DM, Burford DC, Hunt SE, Griffiths-Jones S, Jones MC, Keenan SJ, Oliver K, Scott CE, Ainscough R, Almeida JP, Ambrose KD, Andrews DT, Ashwell RIS, Babbage AK, Bagguley CL, Bailey J, Bannerjee R, Barlow KF, Bates K, Beasley H, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burrill W, Carder C, Carter NP, Chapman JC, Clamp ME, Clark SY, Clarke G, Clee CM, Clegg SCM, Cobley V, Collins JE, Corby N, Coville GJ, Deloukas P, Dhami P, Dunham I, Dunn M, Earthrowl ME, Ellington AG, Faulkner L, Frankish AG, Frankland J, French L, Garner P, Garnett J, Gilbert JGR, Gilson CJ, Ghori J, Grafham DV, Gribble SM, Griffiths C, Hall RE, Hammond S, Harley JL, Hart EA, Heath PD, Howden PJ, Huckle EJ, Hunt PJ, Hunt AR, Johnson C, Johnson D, Kay M, Kimberley AM, King A, Laird GK, Langford CJ, Lawlor S, Leongamornlert DA, Lloyd DM, Lloyd C, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, McLaren SJ, McMurray A, Milne S, Moore MJF, Nickerson T, Palmer SA, Pearce AV, Peck AI, Pelan S, Phillimore B, Porter KM, Rice CM, Searle S, Sehra HK, Shownkeen R, Skuce CD, Smith M, Steward CA, Sycamore N, Tester J, Thomas DW, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Wilming L, Wray PW, Wright MW, Young L, Coulson A, Durbin R, Hubbard T, Sulston JE, Beck S, Bentley DR, Rogers J, Ross MT. The DNA sequence and analysis of human chromosome 13. Nature 2004; 428:522-8. [PMID: 15057823 PMCID: PMC2665288 DOI: 10.1038/nature02379] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Accepted: 01/27/2004] [Indexed: 12/14/2022]
Abstract
Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.
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Affiliation(s)
- A Dunham
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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14
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Guptill L, Wu CC, HogenEsch H, Slater LN, Glickman N, Dunham A, Syme H, Glickman L. Prevalence, risk factors, and genetic diversity of Bartonella henselae infections in pet cats in four regions of the United States. J Clin Microbiol 2004; 42:652-9. [PMID: 14766832 PMCID: PMC344466 DOI: 10.1128/jcm.42.2.652-659.2004] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [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: 11/20/2022] Open
Abstract
Blood was collected from a convenience sample of 271 pet cats aged 3 months to 2 years (mean age, 8 months, median and mode, 6 months) between May 1997 and September 1998 in four areas of the United States (southern California, Florida, metropolitan Chicago, and metropolitan Washington, D.C.). Sixty-five (24%) cats had Bartonella henselae bacteremia, and 138 (51%) cats were seropositive for B. henselae. Regional prevalences for bacteremia and seropositivity were highest in Florida (33% and 67%, respectively) and California (28% and 62%, respectively) and lowest in the Washington, D.C. (12% and 28%, respectively) and Chicago (6% and 12%, respectively) areas. No cats bacteremic with B. clarridgeiae were found. The 16S rRNA type was determined for 49 B. henselae isolates. Fourteen of 49 cats (28.6%) were infected with 16S rRNA type I, 32 (65.3%) with 16S rRNA type II, and three (6.1%) were coinfected with 16S rRNA types I and II. Flea infestation was a significant risk factor for B. henselae bacteremia (odds ratio = 2.82, 95% confidence interval, 1.1 to 7.3). Cats >or=13 months old were significantly less likely to be bacteremic than cats <or=6 months old (odds ratio = 0.18, 95% confidence interval, 0.05 to 0.61). Flea infestation, adoption from a shelter or as a stray cat, hunting, and being from Florida or California were significant risk factors for B. henselae seropositivity. DNA fingerprint was significantly associated with region (P = 0.03) and indoor/outdoor status of cats (P = 0.03).
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Affiliation(s)
- L Guptill
- Department of Veterinary Clinical Sciences, Pathobiology Center for Applied Ethology and Human-Animal Interaction, Purdue University, West Lafayette, Indiana 47907, USA.
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Neat MJ, Foot N, Jenner M, Goff L, Ashcroft K, Burford D, Dunham A, Norton A, Lister TA, Fitzgibbon J. Localisation of a novel region of recurrent amplification in follicular lymphoma to an approximately 6.8 Mb region of 13q32-33. Genes Chromosomes Cancer 2001; 32:236-43. [PMID: 11579463 DOI: 10.1002/gcc.1187] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [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: 11/09/2022] Open
Abstract
Follicular lymphoma (FL) is characterised by the presence of the t(14;18)(q32;q21) and represents approximately 25% of new cases of non-Hodgkin's lymphoma. While the t(14;18) is a well-documented rearrangement, the role of secondary cytogenetic abnormalities in the development and progression of these tumours remains unclear. Comparative genomic hybridisation was used to characterise changes in DNA copy number in tumour DNA from patients with this malignancy. The mean numbers of deletion and amplification events found in each of the 45 samples studied were 1.8 and 2.3, respectively. Regions of recurrent (>10% tumour samples) gain involved chromosomes 2p13-16 (16%), 7 (20%), 12 (16%), 13q21-33 (18%), 18 (27%), and X (36%) and frequent losses localised to 6q (29%) and 17p (20%). Amplification of chromosome 13 represents a novel finding in FL. The minimal amplified region was refined to a 6.8-Mb interval of 13q32-33 between the BAC clones 88K16 and 44H20 by fluorescence in situ hybridisation studies using metaphase chromosomes derived from tumour material. There are a number of reports in the literature suggesting that amplification of chromosome 13 also occurs in other human cancers. The location of the putative oncogene on 13q described here in follicular and transformed lymphoma may also be important in the evolution of many other malignancies.
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Affiliation(s)
- M J Neat
- ICRF Medical Oncology Unit, St. Bartholomew's Hospital, Charterhouse Square, London, UK.
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16
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Bentley DR, Deloukas P, Dunham A, French L, Gregory SG, Humphray SJ, Mungall AJ, Ross MT, Carter NP, Dunham I, Scott CE, Ashcroft KJ, Atkinson AL, Aubin K, Beare DM, Bethel G, Brady N, Brook JC, Burford DC, Burrill WD, Burrows C, Butler AP, Carder C, Catanese JJ, Clee CM, Clegg SM, Cobley V, Coffey AJ, Cole CG, Collins JE, Conquer JS, Cooper RA, Culley KM, Dawson E, Dearden FL, Durbin RM, de Jong PJ, Dhami PD, Earthrowl ME, Edwards CA, Evans RS, Gillson CJ, Ghori J, Green L, Gwilliam R, Halls KS, Hammond S, Harper GL, Heathcott RW, Holden JL, Holloway E, Hopkins BL, Howard PJ, Howell GR, Huckle EJ, Hughes J, Hunt PJ, Hunt SE, Izmajlowicz M, Jones CA, Joseph SS, Laird G, Langford CF, Lehvaslaiho MH, Leversha MA, McCann OT, McDonald LM, McDowall J, Maslen GL, Mistry D, Moschonas NK, Neocleous V, Pearson DM, Phillips KJ, Porter KM, Prathalingam SR, Ramsey YH, Ranby SA, Rice CM, Rogers J, Rogers LJ, Sarafidou T, Scott DJ, Sharp GJ, Shaw-Smith CJ, Smink LJ, Soderlund C, Sotheran EC, Steingruber HE, Sulston JE, Taylor A, Taylor RG, Thorpe AA, Tinsley E, Warry GL, Whittaker A, Whittaker P, Williams SH, Wilmer TE, Wooster R, Wright CL. The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X. Nature 2001; 409:942-3. [PMID: 11237015 DOI: 10.1038/35057165] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [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: 11/09/2022]
Abstract
We constructed maps for eight chromosomes (1, 6, 9, 10, 13, 20, X and (previously) 22), representing one-third of the genome, by building landmark maps, isolating bacterial clones and assembling contigs. By this approach, we could establish the long-range organization of the maps early in the project, and all contig extension, gap closure and problem-solving was simplified by containment within local regions. The maps currently represent more than 94% of the euchromatic (gene-containing) regions of these chromosomes in 176 contigs, and contain 96% of the chromosome-specific markers in the human gene map. By measuring the remaining gaps, we can assess chromosome length and coverage in sequenced clones.
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MESH Headings
- Chromosomes, Human, Pair 1
- Chromosomes, Human, Pair 10
- Chromosomes, Human, Pair 13
- Chromosomes, Human, Pair 20
- Chromosomes, Human, Pair 6
- Contig Mapping
- Genome, Human
- Humans
- X Chromosome
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17
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Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome. Nature 2001; 409:860-921. [PMID: 11237011 DOI: 10.1038/35057062] [Citation(s) in RCA: 14499] [Impact Index Per Article: 630.4] [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: 12/11/2022]
Abstract
The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
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Affiliation(s)
- E S Lander
- Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, MA 02142, USA.
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18
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McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, Gregory SG, Humphray SJ, French L, Evans RS, Bethel G, Whittaker A, Holden JL, McCann OT, Dunham A, Soderlund C, Scott CE, Bentley DR, Schuler G, Chen HC, Jang W, Green ED, Idol JR, Maduro VV, Montgomery KT, Lee E, Miller A, Emerling S, Gibbs R, Scherer S, Gorrell JH, Sodergren E, Clerc-Blankenburg K, Tabor P, Naylor S, Garcia D, de Jong PJ, Catanese JJ, Nowak N, Osoegawa K, Qin S, Rowen L, Madan A, Dors M, Hood L, Trask B, Friedman C, Massa H, Cheung VG, Kirsch IR, Reid T, Yonescu R, Weissenbach J, Bruls T, Heilig R, Branscomb E, Olsen A, Doggett N, Cheng JF, Hawkins T, Myers RM, Shang J, Ramirez L, Schmutz J, Velasquez O, Dixon K, Stone NE, Cox DR, Haussler D, Kent WJ, Furey T, Rogic S, Kennedy S, Jones S, Rosenthal A, Wen G, Schilhabel M, Gloeckner G, Nyakatura G, Siebert R, Schlegelberger B, Korenberg J, Chen XN, Fujiyama A, Hattori M, Toyoda A, Yada T, Park HS, Sakaki Y, Shimizu N, Asakawa S, Kawasaki K, Sasaki T, Shintani A, Shimizu A, Shibuya K, Kudoh J, Minoshima S, Ramser J, Seranski P, Hoff C, Poustka A, Reinhardt R, Lehrach H. A physical map of the human genome. Nature 2001; 409:934-41. [PMID: 11237014 DOI: 10.1038/35057157] [Citation(s) in RCA: 549] [Impact Index Per Article: 23.9] [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: 12/13/2022]
Abstract
The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.
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Affiliation(s)
- J D McPherson
- Washington University School of Medicine, Genome Sequencing Center, Department of Genetics, St. Louis, Missouri 63108, USA.
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19
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Abstract
Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human BAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 37 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation.
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Affiliation(s)
- C Soderlund
- Clemson University Genomic Institute, Clemson, South Carolina 29634-5808, USA.
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20
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Abstract
Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human BAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 37 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation.
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Affiliation(s)
- C Soderlund
- Clemson University Genomic Institute, Clemson, South Carolina 29634-5808, USA.
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21
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Steingruber HE, Dunham A, Coffey AJ, Clegg SM, Howell GR, Maslen GL, Scott CE, Gwilliam R, Hunt PJ, Sotheran EC, Huckle EJ, Hunt SE, Dhami P, Soderlund C, Leversha MA, Bentley DR, Ross MT. High-resolution landmark framework for the sequence-ready mapping of Xq23-q26.1. Genome Res 1999; 9:751-62. [PMID: 10447510 PMCID: PMC310799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
We have established a landmark framework map over 20-25 Mb of the long arm of the human X chromosome using yeast artificial chromosome (YAC) clones. The map has approximately one landmark per 45 kb of DNA and stretches from DXS7531 in proximal Xq23 to DXS895 in proximal Xq26, connecting to published framework maps on its proximal and distal sides. There are three gaps in the framework map resulting from the failure to obtain clone coverage from the YAC resources available. Estimates of the maximum sizes of these gaps have been obtained. The four YAC contigs have been positioned and oriented using somatic-cell hybrids and fluorescence in situ hybridization, and the largest is estimated to cover approximately 15 Mb of DNA. The framework map is being used to assemble a sequence-ready map in large-insert bacterial clones, as part of an international effort to complete the sequence of the X chromosome. PAC and BAC contigs currently cover 18 Mb of the region, and from these, 12 Mb of finished sequence is available.
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Affiliation(s)
- H E Steingruber
- The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, UK
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22
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Coffey AJ, Brooksbank RA, Brandau O, Oohashi T, Howell GR, Bye JM, Cahn AP, Durham J, Heath P, Wray P, Pavitt R, Wilkinson J, Leversha M, Huckle E, Shaw-Smith CJ, Dunham A, Rhodes S, Schuster V, Porta G, Yin L, Serafini P, Sylla B, Zollo M, Franco B, Bolino A, Seri M, Lanyi A, Davis JR, Webster D, Harris A, Lenoir G, de St Basile G, Jones A, Behloradsky BH, Achatz H, Murken J, Fassler R, Sumegi J, Romeo G, Vaudin M, Ross MT, Meindl A, Bentley DR. Host response to EBV infection in X-linked lymphoproliferative disease results from mutations in an SH2-domain encoding gene. Nat Genet 1998; 20:129-35. [PMID: 9771704 DOI: 10.1038/2424] [Citation(s) in RCA: 606] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
X-linked lymphoproliferative syndrome (XLP or Duncan disease) is characterized by extreme sensitivity to Epstein-Barr virus (EBV), resulting in a complex phenotype manifested by severe or fatal infectious mononucleosis, acquired hypogammaglobulinemia and malignant lymphoma. We have identified a gene, SH2D1A, that is mutated in XLP patients and encodes a novel protein composed of a single SH2 domain. SH2D1A is expressed in many tissues involved in the immune system. The identification of SH2D1A will allow the determination of its mechanism of action as a possible regulator of the EBV-induced immune response.
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Affiliation(s)
- A J Coffey
- The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.
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23
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Affiliation(s)
- J Silverstein
- Dept. Civil, Environmental & Architectural Engineering; University of Colorado, Boulder, USA
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24
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25
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Affiliation(s)
- A J Garrett
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, U.K
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26
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Dunham A. Premature menopause: three teenage cases. Br J Clin Pract 1987; 41:978-9. [PMID: 3505182] [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: 01/06/2023]
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27
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Abstract
Competition has become a popular prescription for the problem of rising health costs. One issue largely absent fom discussions of market systems and medicine, however, has been analysis of the implications for the poor. This paper explores the implications of proposals to use health maintenance organizations and vouchers to promote competition. We conclude that, as they stand, pro-competitive proposals could cause a significant deterioration in the position of the poor, especially if costs continue to rise, and that their effects are likely to be exacerbated by problems with implementation.
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Shurvell HF, Dunham A, Cyvin SJ, Brunvoll J. On the planarity of the NSi3 skeleton in the trisilylamine molecule. A normal coordinate analysis involving complex symmetry coordinates. CAN J CHEM 1979. [DOI: 10.1139/v79-284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Normal coordinate calculations have been carried out for the N(SiH3)3 molecule. A model with C3h symmetry was used, which is based on a planar NSi3 skeleton. The presence of complex numbers for the characters of degenerate irreducible representations of the point group C3h leads to an unusual problem when factoring the G and F matrices. A set of real degenerate symmetry coordinates for the E′ and E′′ species can be constructed, but these are not true symmetry coordinates under the C3h point group. However, they can be obtained from the genuine (complex) symmetry coordinates by a unitary transformation. For a degenerate species, this procedure leads to a and b blocks of the factored G and F matrices, which contain interaction terms. Consequently both blocks must be taken together when forming the secular equation, and subsequently the calculated frequencies appear as pairs of identical numbers.A valence force field that includes all reasonable interactions has been obtained and used to predict the wavenumbers of the 15N and d9 isotopic molecules. Details of the normal vibrations in the three molecules have been obtained from potential energy distributions. The results show reasonable agreement with the limited experimental data available for the isotopic molecules.
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