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Ariyaratne S, Whittaker P, James SL, Botchu R. Comparison of patterns and rates of cement leakage in percutaneous sacroplasty for sacral insufficiency fractures versus neoplasia. Skeletal Radiol 2024; 53:93-98. [PMID: 37301797 DOI: 10.1007/s00256-023-04386-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/04/2023] [Accepted: 06/04/2023] [Indexed: 06/12/2023]
Abstract
OBJECTIVE Percutaneous sacroplasty is a minimally invasive procedure which utilises injection of bone cement into the sacrum for stabilisation of osteoporotic sacral insufficiency fractures (SIF) and neoplastic lesions to relieve pain and improve function. While effective, cement leakage is an important complication associated with the procedure. This study aims to compare the incidence and patterns of the cement leakages following sacroplasty for SIF versus neoplasia and discuss the various patterns of cement leakage and their implications. MATERIALS AND METHODS This retrospective study analysed 57 patients who underwent percutaneous sacroplasty at a tertiary orthopaedic hospital. Patients were divided into 2 groups of SIF (n=46) and neoplastic lesions (n=11) based on their indication for sacroplasty. Pre- and post-procedural CT fluoroscopy was used to assess for cement leakage. The incidence and patterns of cement leakage were both compared among the two groups. A Fisher's exact test was used for statistical analysis. RESULTS Eleven (19%) patients had cement leakage on post-procedural imaging. The most common sites of cement leakage were into the presacral region (6), followed by sacroiliac joints (4), sacral foramina (3) and posterior sacral (1). There was a statistically significant higher incidence of leakage in the neoplastic group in comparison to SIF group (P-value <0.05). The incidence of cement leakage in the neoplastic group was 45% (n = 5/11) versus SIF 13% (n=6/46). CONCLUSION There was a statistically significant higher incidence of cement leak in sacroplasties conducted for the treatment of neoplastic lesions compared to those with sacral insufficiency fracture.
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Bourke M, Patterson L, Di Nardo F, Whittaker P, Verma A. Active video games and weight management in overweight children and adolescents-systematic review and meta-analysis. J Public Health (Oxf) 2023; 45:935-946. [PMID: 37496202 PMCID: PMC10788842 DOI: 10.1093/pubmed/fdad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/24/2023] [Accepted: 06/27/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND The prevalence of childhood obesity has been increasing for several decades. Active video games (AVG) may be an effective intervention to help manage this rising health crisis. The aim of this review is to evaluate whether AVG are effective at reducing weight or improving body composition in overweight youths. METHOD Medline, Embase, SportDiscus, ASSIA, CINAHL Plus, CENTRAL, CDSR and PsychINFO databases were searched for studies assessing quantitative or qualitative impact of AVG in overweight adolescents published in English. Three authors screened the results using inclusion/exclusion criteria. RESULTS A total of 12 studies met the inclusion criteria; 11 reported a significant decrease in at least one weight outcome. Results from seven randomized controlled trials were pooled by meta-analysis, which compared with controls subjects in AVG groups demonstrated greater body mass index (BMI) Z-score reduction (mean difference: -0.09 (-0.12, -0.05) I2 = 34%, P < 0.0001). The mean weight reduction (-2.66 Kg (-5.67, +0.35) I2 = 0%, P = 0.08) and BMI (-2.29 (-4.81, +0.22) I2 = 49%, P = 0.07) were greater in AVG groups but results did not reach statistical significance. CONCLUSIONS BMI Z-score was significantly reduced in the AVG group and the majority of included studies reported significant results in at least one weight outcome, suggesting AVG can be used to reduce weight or improve body composition in overweight youths. Further studies investigating the long-term sustainability of this change in body composition are needed.
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Colazo M, Whittaker P, Macmillan K, Bignell D, Boender G, de Carvalho Guimaraes R, Mapletoft R. Evaluation of a modified GnRH-based timed-AI protocol associated with estrus detection in beef heifers inseminated with sex-selected or conventional semen. Theriogenology 2018; 118:90-95. [DOI: 10.1016/j.theriogenology.2018.05.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 05/24/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022]
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Bode K, Hindricks G, Ten Berg J, Whittaker P. P2569Anticoagulation plus antiplatelet therapy for atrial fibrillation: Cost-Utility of combination therapy with non-Vitamin K oral anticoagulants versus Warfarin. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy565.p2569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Jones DA, Whittaker P, Rathod KS, Richards AJ, Andiapen M, Antoniou S, Mathur A, Ahluwalia A. P2564Sodium nitrite-mediated cardioprotection in primary percutaneous coronary intervention for ST-elevation myocardial infarction: a cost-effectiveness analysis. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy565.p2564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Lennerz C, Barman M, Sopher M, Tantawy M, Kolb C, Whittaker P. P399Colchicine for prevention of atrial fibrillation after open-heart surgery: a systematic review and meta-analysis. Europace 2018. [DOI: 10.1093/europace/euy015.210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Helguera IL, Whittaker P, Behrouzi A, Mapletoft RJ, Colazo MG. Effect of initial GnRH and time of insemination on reproductive performance in cyclic and acyclic beef heifers subjected to a 5-d Co-synch plus progesterone protocol. Theriogenology 2017; 106:39-45. [PMID: 29035836 DOI: 10.1016/j.theriogenology.2017.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/02/2017] [Accepted: 10/02/2017] [Indexed: 10/18/2022]
Abstract
This study evaluated the effect of initial GnRH and timing of AI in a 5-d Co-synch plus CIDR (device containing 1.38 g of progesterone) protocol on pregnancy per AI (P/AI) and pregnancy loss in beef heifers. A secondary objective was to determine if the effect of initial GnRH on reproductive performance was influenced by cyclicity. Crossbred beef heifers (n = 1068; 301-514 kg of body weight, and 13-15 mo of age) at three locations were assigned to either a 5-d Co-synch plus CIDR protocol with (CIDR5G) or without (CIDR5NG) an initial injection of 100 μg of GnRH at CIDR insertion (Day 0). All heifers received a single dose of 500 μg of cloprostenol at CIDR removal (Day 5) and were divided into two groups to receive GnRH and TAI at either 66 or 72 h (Day 8) after CIDR removal. All heifers were inseminated by one technician with frozen-thawed semen from 1 of 4 sires available commercially. Transrectal ultrasonography was performed on Day 0 to determine cyclicity (presence of CL) and normalcy of the reproductive track, and 27 d after TAI to determine pregnancy status. Non-pregnant heifers (n = 470) were assigned to either a CIDR5G or a CIDR5NG protocol with TAI at 72 h after CIDR removal. Twelve days after second AI, heifers were exposure to bulls for 20 d and pregnancy diagnoses were performed approximately 30 d after second TAI and 60 d after bulls were removed to diagnose bull pregnancies and determine pregnancy loss rate. The percentage of acyclic heifers was 20.3%. Overall P/AI after first TAI was 55.6% (594/1068) and did not differ between CIDR5G and CIDR5NG (56.1 vs. 55.1%), or between TAI66 and TAI72 (55.8 vs. 55.4%). However, cyclic heifers were more likely to become pregnant than acyclic ones (59.3 vs. 41.2%; P < 0.01). Moreover, acyclic heifers subjected to the CIDR5NG had fewer P/AI than those subjected to CIDR5G (P < 0.01). Overall P/AI after resynchronization was 55.1% and did not differ between CIDR5G and CIDR5NG (51.3 vs. 59.0%). Overall pregnancy loss after first and second TAI were 3.0% (18/594) and 3.9% (8/205), respectively. When pregnancy loss data were combined, synchronization protocol (4.1 vs. 2.3% for CIDR5NG and CIDR5G; P = 0.01), cyclicity (5.8 vs. 2.9% for acyclic and cyclic; P = 0.03) and the interaction between synchronization protocol and cyclicity (P = 0.04) were significant. The overall cumulative pregnancy at the end of the breeding season was 94.2% (1006/1068); acyclic heifers were less likely to be pregnant at the end of the breeding season (88.4 vs. 95.8%; P < 0.01). In summary, the initial GnRH administration in a 5-d Co-synch plus CIDR protocol that includes a single PGF treatment is necessary in acyclic beef heifers to optimize P/AI, but not in cyclic heifers. Moreover, omission of initial GnRH was associated to greater pregnancy losses, particularly in acyclic heifers. Timing of AI did not affect P/AI.
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Whittaker P, Kantor P, De Palma R, Jones D. 1207Optimal extent and timing of percutaneous intervention for STEMI in multi-vessel disease: a meta-analysis of randomized controlled trials of complete revascularization vs culprit-vessel only therapy. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx502.1207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Tse G, Gong M, Wong W, Letsas K, Vassiliou V, To O, Chan Y, Yan B, Li G, Whittaker P, Wu W, Xia Y, Yan G, Lui K, Liu T. P5338Tpeak-Tend/QT ratio for arrhythmic risk stratification: a meta-analysis. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx493.p5338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Tse G, Gong M, Chan C, Chan YS, Yan B, Li G, Whittaker P, Wong SH, Lui KO, Wu WKK, Wong WT, Liu T. P945Total cosine R-to-T for predicting ventricular arrhythmic and mortality outcomes: a systematic review and meta-analysis. Europace 2017. [DOI: 10.1093/ehjci/eux151.127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Welsh S, Fife K, Matakidou A, Mullin J, Machin A, Qian W, Ingleson V, Dalchau KM, Whittaker P, Warren A, Priest AN, Zaccagna F, Barrett T, Gallagher FA, Riddick A, Armitage JN, Eisen TGQ. A phase II clinical study evaluating the efficacy and safety of neoadjuvant and adjuvant sunitinib in previously untreated patients with metastatic renal cell carcinoma (mRCC)(NeoSun). J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.e16087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e16087 Background: Sunitinib improves clinical outcomes in patients (pts) with mRCC. The single arm phase II NeoSun trial was designed to investigate its added value to nephrectomy, and to explore translational biological and imaging biomarkers. Methods: Pts with mRCC, scheduled for nephrectomy, no prior systemic therapy were recruited to receive 50mg OD sunitinib for 12 days, then post-surgery on a 4 week-on, 2 week-off, repeating 6 week cycle until disease progression. Diffusion-weighted, BOLD and dynamic contrast enhanced MR imaging (DW-MRI, DCE-MRI) and research blood sample collection were performed at baseline and end of 12 days. CT Imaging was performed at baseline, pre- and post-surgery, and then every 2 cycles. The primary endpoint was objective response rate (RECIST). Secondary endpoints included changes in diffusion DW-MRI, DCE- MRI of the tumour following 12 days suntinib, overall survival (OS), progression-free survival (PFS), response duration, surgical morbidity/mortality, and toxicity. Results: 14 pts received pre-surgery sunitinib, 71% (10/14) took the planned 12 doses. All 14 underwent total nephrectomy, and 13 recommenced sunitinib post-operatively. The mean number of post-surgery cycles was 11 (range 2 – 22). 58.3% (7/12) of pts achieved confirmed response (95% CI: 27.7 - 84.8%).91.7% (11/12) achieved objective clinical benefit (95% CI: 61.5 - 99.8%). Median OS is 33.7m and median PFS is 15.7m. Amongst those achieving PR/CR, median response duration is 8.7m. No unexpected surgical or sunitinib-related toxicities or complications were observed and the mean number of days from surgery to hospital discharge was 5.9 (range 3.0 – 17.0).There was a trend forOS to be better in pts with high baseline plasma VEGF-A (p = 0.06) or VEGF-C (p = 0.02) expression. A larger % tumour volume reduction after 12 days treatment is correlated with a smaller baseline % necrosis (coefficient = -0.51, p = 0.03). Conclusions: Sunitinib is effective and safe when given before and after nephrectomy to previously untreated pts with mRCC. Neoadjuvant studies such as NeoSun can safely explore translational biological and imaging endpoints. Clinical trial information: 2005-004502-82.
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Bodea C, Neale B, Ripke S, Daly M, Devlin B, Roeder K, Barclay M, Peyrin-Biroulet L, Chamaillard M, Colombel JF, Cottone M, Croft A, D’Incà R, Halfvarson J, Hanigan K, Henderson P, Hugot JP, Karban A, Kennedy N, Khan M, Lémann M, Levine A, Massey D, Milla M, Montgomery G, Ng S, Oikonomou I, Peeters H, Proctor D, Rahier JF, Roberts R, Rutgeerts P, Seibold F, Stronati L, Taylor K, Törkvist L, Ublick K, Van Limbergen J, Van Gossum A, Vatn M, Zhang H, Zhang W, Andrews J, Bampton P, Barclay M, Florin T, Gearry R, Krishnaprasad K, Lawrance I, Mahy G, Montgomery G, Radford-Smith G, Roberts R, Simms L, Amininijad L, Cleynen I, Dewit O, Franchimont D, Georges M, Laukens D, Peeters H, Rahier JF, Rutgeerts P, Theatre E, Van Gossum A, Vermeire S, Aumais G, Baidoo L, Barrie A, Beck K, Bernard EJ, Binion D, Bitton A, Brant S, Cho J, Cohen A, Croitoru K, Daly M, Datta L, Deslandres C, Duerr R, Dutridge D, Ferguson J, Fultz J, Goyette P, Greenberg G, Haritunians T, Jobin G, Katz S, Lahaie R, McGovern D, Nelson L, Ng S, Ning K, Oikonomou I, Paré P, Proctor D, Regueiro M, Rioux J, Ruggiero E, Schumm L, Schwartz M, Scott R, Sharma Y, Silverberg M, Spears D, Steinhart A, Stempak J, Swoger J, Tsagarelis C, Zhang W, Zhang C, Zhao H, Aerts J, Ahmad T, Arbury H, Attwood A, Auton A, Ball S, Balmforth A, Barnes C, Barrett J, Barroso I, Barton A, Bennett A, Bhaskar S, Blaszczyk K, Bowes J, Brand O, Braund P, Bredin F, Breen G, Brown M, Bruce I, Bull J, Burren O, Burton J, Byrnes J, Caesar S, Cardin N, Clee C, Coffey A, Connell J, Conrad D, Cooper J, Dominiczak A, Downes K, Drummond H, Dudakia D, Dunham A, Ebbs B, Eccles D, Edkins S, Edwards C, Elliot A, Emery P, Evans D, Evans G, Eyre S, Farmer A, Ferrier N, Flynn E, Forbes A, Forty L, Franklyn J, Frayling T, Freathy R, Giannoulatou E, Gibbs P, Gilbert P, Gordon-Smith K, Gray E, Green E, Groves C, Grozeva D, Gwilliam R, Hall A, Hammond N, Hardy M, Harrison P, Hassanali N, Hebaishi H, Hines S, Hinks A, Hitman G, Hocking L, Holmes C, Howard E, Howard P, Howson J, Hughes D, Hunt S, Isaacs J, Jain M, Jewell D, Johnson T, Jolley J, Jones I, Jones L, Kirov G, Langford C, Lango-Allen H, Lathrop G, Lee J, Lee K, Lees C, Lewis K, Lindgren C, Maisuria-Armer M, Maller J, Mansfield J, Marchini J, Martin P, Massey D, McArdle W, McGuffin P, McLay K, McVean G, Mentzer A, Mimmack M, Morgan A, Morris A, Mowat C, Munroe P, Myers S, Newman W, Nimmo E, O’Donovan M, Onipinla A, Ovington N, Owen M, Palin K, Palotie A, Parnell K, Pearson R, Pernet D, Perry J, Phillips A, Plagnol V, Prescott N, Prokopenko I, Quail M, Rafelt S, Rayner N, Reid D, Renwick A, Ring S, Robertson N, Robson S, Russell E, St Clair D, Sambrook J, Sanderson J, Sawcer S, Schuilenburg H, Scott C, Scott R, Seal S, Shaw-Hawkins S, Shields B, Simmonds M, Smyth D, Somaskantharajah E, Spanova K, Steer S, Stephens J, Stevens H, Stirrups K, Stone M, Strachan D, Su Z, Symmons D, Thompson J, Thomson W, Tobin M, Travers M, Turnbull C, Vukcevic D, Wain L, Walker M, Walker N, Wallace C, Warren-Perry M, Watkins N, Webster J, Weedon M, Wilson A, Woodburn M, Wordsworth B, Yau C, Young A, Zeggini E, Brown M, Burton P, Caulfield M, Compston A, Farrall M, Gough S, Hall A, Hattersley A, Hill A, Mathew C, Pembrey M, Satsangi J, Stratton M, Worthington J, Hurles M, Duncanson A, Ouwehand W, Parkes M, Rahman N, Todd J, Samani N, Kwiatkowski D, McCarthy M, Craddock N, Deloukas P, Donnelly P, Blackwell J, Bramon E, Casas J, Corvin A, Jankowski J, Markus H, Palmer C, Plomin R, Rautanen A, Trembath R, Viswanathan A, Wood N, Spencer C, Band G, Bellenguez C, Freeman C, Hellenthal G, Giannoulatou E, Pirinen M, Pearson R, Strange A, Blackburn H, Bumpstead S, Dronov S, Gillman M, Jayakumar A, McCann O, Liddle J, Potter S, Ravindrarajah R, Ricketts M, Waller M, Weston P, Widaa S, Whittaker P. A Method to Exploit the Structure of Genetic Ancestry Space to Enhance Case-Control Studies. Am J Hum Genet 2016; 98:857-868. [PMID: 27087321 DOI: 10.1016/j.ajhg.2016.02.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/29/2016] [Indexed: 02/08/2023] Open
Abstract
One goal of human genetics is to understand the genetic basis of disease, a challenge for diseases of complex inheritance because risk alleles are few relative to the vast set of benign variants. Risk variants are often sought by association studies in which allele frequencies in case subjects are contrasted with those from population-based samples used as control subjects. In an ideal world we would know population-level allele frequencies, releasing researchers to focus on case subjects. We argue this ideal is possible, at least theoretically, and we outline a path to achieving it in reality. If such a resource were to exist, it would yield ample savings and would facilitate the effective use of data repositories by removing administrative and technical barriers. We call this concept the Universal Control Repository Network (UNICORN), a means to perform association analyses without necessitating direct access to individual-level control data. Our approach to UNICORN uses existing genetic resources and various statistical tools to analyze these data, including hierarchical clustering with spectral analysis of ancestry; and empirical Bayesian analysis along with Gaussian spatial processes to estimate ancestry-specific allele frequencies. We demonstrate our approach using tens of thousands of control subjects from studies of Crohn disease, showing how it controls false positives, provides power similar to that achieved when all control data are directly accessible, and enhances power when control data are limiting or even imperfectly matched ancestrally. These results highlight how UNICORN can enable reliable, powerful, and convenient genetic association analyses without access to the individual-level data.
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López-Helguera I, Whittaker P, Behrouzi A, Colazo MG. 12 INITIAL GONADOTROPIN-RELEASING HORMONE TREATMENT INCREASED PREGNANCY PER TIMED INSEMINATION ONLY IN ACYCLIC BEEF HEIFERS SUBJECTED TO A 5-DAY CO-SYNCH PROTOCOL. Reprod Fertil Dev 2016. [DOI: 10.1071/rdv28n2ab12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We have shown that inclusion of initial gonadotropin-releasing hormone (GnRH) in a 5-day Co-synch protocol is unnecessary to achieve acceptable pregnancy rates in dairy heifers (2011 Theriogenology 76, 578). This study determined the efficacy of a modified (without initial GnRH) 5-day Co-synch protocol for timed AI (TAI) and the effect of interval from progesterone device removal to TAI on pregnancy per TAI (P/TAI) in acyclic and cyclic beef heifers. Heifers (n = 1062; 302 to 515 kg of body weight, and 13 to 15 months of age) at 2 locations were assigned to either a 5-day Co-synch protocol with (control) or without (modified) an initial injection of 100 μg of GnRH (Fertagyl; Merck Animal Health, Kenilworth, NJ, USA) at progesterone device (CIDR; Zoetis Animal Health, Florham Park, NJ) insertion (Day 0). All heifers received a single dose of 500 μg of cloprostenol (Estrumate; Merck Animal Health) at CIDR removal (Day 5) and were divided into 2 groups to receive GnRH and simultaneously TAI at either 66 or 72 h (Day 8) after CIDR removal. All heifers were inseminated by one technician with frozen-thawed semen from 1 of 4 commercially available sires. Ovarian ultrasonography was performed on Day 0 to determine cyclicity (presence of corpus luteum) and normalcy of the reproductive track, and on Day 35 (27 days after TAI) to determine pregnancy status. Data were analysed using the PROC GLIMMIX in SAS (SAS Institute Inc., Cary, NC, USA). The CIDR retention rate was 98%; P/TAI in heifers that lost the CIDR was 39%. Pregnancy per TAI [least squares means (n)] did not differ (P > 0.05) among sires [48 (235), 51 (318), 52 (274), and 53% (235)], location [57 (330) v. 53% (732)], timing of TAI [52 (533) v. 50% (529) for 66 and 72 h], or treatment groups [48 (525) v. 53% (537) for control and modified groups]. A total of 226 (21%) heifers were acyclic; P/TAI was lower in acyclic heifers compared with that in those cyclic (P < 0.01; 43 v. 59%). Administration of GnRH at CIDR insertion increased P/TAI in acyclic heifers (P < 0.01; 50 v. 35% for control and modified groups) but did not affect P/TAI in those that were cyclic at initiation of protocol (P > 0.05; 57 v. 62% for control and modified groups). In conclusion, timing of TAI did not affect fertility. However, administration of initial GnRH increased P/TAI by 15 percentiles in acyclic females, but as previously shown in Holstein heifers, initial GnRH was unnecessary to achieve acceptable P/TAI in cyclic beef heifers subjected to a 5-days Co-synch protocol.
This study was supported by Alberta Agriculture and Forestry, Intervet Canada Corp., and collaborative beef producers.
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Hauck YL, Kelly G, Dragovic M, Butt J, Whittaker P, Badcock JC. Australian midwives knowledge, attitude and perceived learning needs around perinatal mental health. Midwifery 2015; 31:247-55. [DOI: 10.1016/j.midw.2014.09.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 08/26/2014] [Accepted: 09/04/2014] [Indexed: 12/01/2022]
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Corrie P, Qian W, Jodrell D, Lao-Sirieix S, Whittaker P, Gopinathan A, Chhabra A, Dalchau K, Basu B, Hardy R, Valle J. Scheduling Nab-Paclitaxel with Gemcitabine (Siege): Randomised Phase Ii Trial to Investigate Two Different Schedules of Nab-Paclitaxel (Abx) Combined with Gemcitabine (Gem) As First Line Treatment for Metastatic Pancreatic Adenocarcinoma (Pdac). Ann Oncol 2014. [DOI: 10.1093/annonc/mdu334.132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Ripke S, O'Dushlaine C, Chambert K, Moran JL, Kähler AK, Akterin S, Bergen SE, Collins AL, Crowley JJ, Fromer M, Kim Y, Lee SH, Magnusson PKE, Sanchez N, Stahl EA, Williams S, Wray NR, Xia K, Bettella F, Borglum AD, Bulik-Sullivan BK, Cormican P, Craddock N, de Leeuw C, Durmishi N, Gill M, Golimbet V, Hamshere ML, Holmans P, Hougaard DM, Kendler KS, Lin K, Morris DW, Mors O, Mortensen PB, Neale BM, O'Neill FA, Owen MJ, Milovancevic MP, Posthuma D, Powell J, Richards AL, Riley BP, Ruderfer D, Rujescu D, Sigurdsson E, Silagadze T, Smit AB, Stefansson H, Steinberg S, Suvisaari J, Tosato S, Verhage M, Walters JT, Levinson DF, Gejman PV, Kendler KS, Laurent C, Mowry BJ, O'Donovan MC, Owen MJ, Pulver AE, Riley BP, Schwab SG, Wildenauer DB, Dudbridge F, Holmans P, Shi J, Albus M, Alexander M, Campion D, Cohen D, Dikeos D, Duan J, Eichhammer P, Godard S, Hansen M, Lerer FB, Liang KY, Maier W, Mallet J, Nertney DA, Nestadt G, Norton N, O'Neill FA, Papadimitriou GN, Ribble R, Sanders AR, Silverman JM, Walsh D, Williams NM, Wormley B, Arranz MJ, Bakker S, Bender S, Bramon E, Collier D, Crespo-Facorro B, Hall J, Iyegbe C, Jablensky A, Kahn RS, Kalaydjieva L, Lawrie S, Lewis CM, Lin K, Linszen DH, Mata I, McIntosh A, Murray RM, Ophoff RA, Powell J, Rujescu D, Van Os J, Walshe M, Weisbrod M, Wiersma D, Donnelly P, Barroso I, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin AP, Deloukas P, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CNA, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Spencer CCA, Band G, Bellenguez C, Freeman C, Hellenthal G, Giannoulatou E, Pirinen M, Pearson RD, Strange A, Su Z, Vukcevic D, Donnelly P, Langford C, Hunt SE, Edkins S, Gwilliam R, Blackburn H, Bumpstead SJ, Dronov S, Gillman M, Gray E, Hammond N, Jayakumar A, McCann OT, Liddle J, Potter SC, Ravindrarajah R, Ricketts M, Tashakkori-Ghanbaria A, Waller MJ, Weston P, Widaa S, Whittaker P, Barroso I, Deloukas P, Mathew CG, Blackwell JM, Brown MA, Corvin AP, McCarthy MI, Spencer CCA, Bramon E, Corvin AP, O'Donovan MC, Stefansson K, Scolnick E, Purcell S, McCarroll SA, Sklar P, Hultman CM, Sullivan PF. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat Genet 2013; 45:1150-9. [PMID: 23974872 PMCID: PMC3827979 DOI: 10.1038/ng.2742] [Citation(s) in RCA: 1139] [Impact Index Per Article: 103.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 08/01/2013] [Indexed: 12/11/2022]
Abstract
Schizophrenia is an idiopathic mental disorder with a heritable component and a substantial public health impact. We conducted a multi-stage genome-wide association study (GWAS) for schizophrenia beginning with a Swedish national sample (5,001 cases and 6,243 controls) followed by meta-analysis with previous schizophrenia GWAS (8,832 cases and 12,067 controls) and finally by replication of SNPs in 168 genomic regions in independent samples (7,413 cases, 19,762 controls and 581 parent-offspring trios). We identified 22 loci associated at genome-wide significance; 13 of these are new, and 1 was previously implicated in bipolar disorder. Examination of candidate genes at these loci suggests the involvement of neuronal calcium signaling. We estimate that 8,300 independent, mostly common SNPs (95% credible interval of 6,300-10,200 SNPs) contribute to risk for schizophrenia and that these collectively account for at least 32% of the variance in liability. Common genetic variation has an important role in the etiology of schizophrenia, and larger studies will allow more detailed understanding of this disorder.
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Evans DM, Spencer CCA, Pointon JJ, Su Z, Harvey D, Kochan G, Oppermann U, Opperman U, Dilthey A, Pirinen M, Stone MA, Appleton L, Moutsianas L, Moutsianis L, Leslie S, Wordsworth T, Kenna TJ, Karaderi T, Thomas GP, Ward MM, Weisman MH, Farrar C, Bradbury LA, Danoy P, Inman RD, Maksymowych W, Gladman D, Rahman P, Morgan A, Marzo-Ortega H, Bowness P, Gaffney K, Gaston JSH, Smith M, Bruges-Armas J, Couto AR, Sorrentino R, Paladini F, Ferreira MA, Xu H, Liu Y, Jiang L, Lopez-Larrea C, Díaz-Peña R, López-Vázquez A, Zayats T, Band G, Bellenguez C, Blackburn H, Blackwell JM, Bramon E, Bumpstead SJ, Casas JP, Corvin A, Craddock N, Deloukas P, Dronov S, Duncanson A, Edkins S, Freeman C, Gillman M, Gray E, Gwilliam R, Hammond N, Hunt SE, Jankowski J, Jayakumar A, Langford C, Liddle J, Markus HS, Mathew CG, McCann OT, McCarthy MI, Palmer CNA, Peltonen L, Plomin R, Potter SC, Rautanen A, Ravindrarajah R, Ricketts M, Samani N, Sawcer SJ, Strange A, Trembath RC, Viswanathan AC, Waller M, Weston P, Whittaker P, Widaa S, Wood NW, McVean G, Reveille JD, Wordsworth BP, Brown MA, Donnelly P. Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility. Nat Genet 2011; 43:761-7. [PMID: 21743469 PMCID: PMC3640413 DOI: 10.1038/ng.873] [Citation(s) in RCA: 661] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 06/03/2011] [Indexed: 02/07/2023]
Abstract
Ankylosing spondylitis is a common form of inflammatory arthritis predominantly affecting the spine and pelvis that occurs in approximately 5 out of 1,000 adults of European descent. Here we report the identification of three variants in the RUNX3, LTBR-TNFRSF1A and IL12B regions convincingly associated with ankylosing spondylitis (P < 5 × 10(-8) in the combined discovery and replication datasets) and a further four loci at PTGER4, TBKBP1, ANTXR2 and CARD9 that show strong association across all our datasets (P < 5 × 10(-6) overall, with support in each of the three datasets studied). We also show that polymorphisms of ERAP1, which encodes an endoplasmic reticulum aminopeptidase involved in peptide trimming before HLA class I presentation, only affect ankylosing spondylitis risk in HLA-B27-positive individuals. These findings provide strong evidence that HLA-B27 operates in ankylosing spondylitis through a mechanism involving aberrant processing of antigenic peptides.
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Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA, de Bakker PIW, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Yu F, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Gibbs RA, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, Nemesh J, Dermitzakis E, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Bonnen PE, Gibbs RA, Gonzaga-Jauregui C, Keinan A, Price AL, Yu F, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Schaffner SF, Zhang Q, Ghori MJR, McGinnis R, McLaren W, Pollack S, Price AL, Schaffner SF, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C, Brooks LD, McEwen JE. Integrating common and rare genetic variation in diverse human populations. Nature 2010; 467:52-8. [PMID: 20811451 DOI: 10.1038/nature09298] [Citation(s) in RCA: 2053] [Impact Index Per Article: 146.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 06/21/2010] [Indexed: 12/24/2022]
Abstract
Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of <or=5%, and demonstrated the feasibility of imputing newly discovered CNPs and SNPs. This expanded public resource of genome variants in global populations supports deeper interrogation of genomic variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.
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Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, Beyan H, Whittaker P, McCann OT, Finer S, Valdes AM, Leslie RD, Deloukas P, Spector TD. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res 2010; 20:434-9. [PMID: 20219945 DOI: 10.1101/gr.103101.109] [Citation(s) in RCA: 531] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
There is a growing realization that some aging-associated phenotypes/diseases have an epigenetic basis. Here, we report the first genome-scale study of epigenomic dynamics during normal human aging. We identify aging-associated differentially methylated regions (aDMRs) in whole blood in a discovery cohort, and then replicate these aDMRs in sorted CD4(+) T-cells and CD14(+) monocytes in an independent cohort, suggesting that aDMRs occur in precursor haematopoietic cells. Further replication of the aDMRs in buccal cells, representing a tissue that originates from a different germ layer compared with blood, demonstrates that the aDMR signature is a multitissue phenomenon. Moreover, we demonstrate that aging-associated DNA hypermethylation occurs predominantly at bivalent chromatin domain promoters. This same category of promoters, associated with key developmental genes, is frequently hypermethylated in cancers and in vitro cell culture, pointing to a novel mechanistic link between aberrant hypermethylation in cancer, aging, and cell culture.
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Przyklenk K, Frelinger AL, Linden MD, Whittaker P, Li Y, Barnard MR, Adams J, Morgan M, Al-Shamma H, Michelson AD. Targeted inhibition of the serotonin 5HT2A receptor improves coronary patency in an in vivo model of recurrent thrombosis. J Thromb Haemost 2010; 8:331-40. [PMID: 19922435 PMCID: PMC2916638 DOI: 10.1111/j.1538-7836.2009.03693.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Release of serotonin and activation of serotonin 5HT2A receptors on platelet surfaces is a potent augmentative stimulus for platelet aggregation. However, earlier-generation serotonin receptor antagonists were not successfully exploited as antiplatelet agents, possibly owing to their lack of specificity for the 5HT2A receptor subtype. OBJECTIVE To assess whether targeted inhibition of the serotonin 5HT2A receptor attenuates recurrent thrombosis and improves coronary patency in an in vivo canine model mimicking unstable angina. METHODS In protocol 1, anesthetized dogs were pretreated with a novel, selective inverse agonist of the 5HT2A receptor (APD791) or saline. Recurrent coronary thrombosis was then initiated by coronary artery injury+stenosis, and coronary patency was monitored for 3 h. Protocol 2 was similar, except that: (i) treatment with APD791 or saline was begun 1 h after the onset of recurrent thrombosis; (ii) template bleeding time was measured; and (iii) blood samples were obtained for in vitro flow cytometric assessment of platelet responsiveness to serotonin. RESULTS APD791 attenuated recurrent thrombosis, irrespective of the time of treatment: in both protocols, flow-time area (index of coronary patency; normalized to baseline coronary flow) averaged 58-59% (P<0.01) following administration of APD791 vs. 21-28% in saline controls. Moreover, the in vivo antithrombotic effect of APD791 was not accompanied by increased bleeding, but was associated with significant and selective inhibition of serotonin-mediated platelet activation. CONCLUSION 5HT2A receptor inhibition with APD791, even when initiated after the onset of recurrent thrombosis, improves coronary patency in the in vivo canine model.
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Reveille JD, Sims AM, Danoy P, Evans DM, Leo P, Pointon JJ, Jin R, Zhou X, Bradbury LA, Appleton LH, Davis JC, Diekman L, Doan T, Dowling A, Duan R, Duncan EL, Farrar C, Hadler J, Harvey D, Karaderi T, Mogg R, Pomeroy E, Pryce K, Taylor J, Savage L, Deloukas P, Kumanduri V, Peltonen L, Ring SM, Whittaker P, Glazov E, Thomas GP, Maksymowych WP, Inman RD, Ward MM, Stone MA, Weisman MH, Wordsworth BP, Brown MA. Genome-wide association study of ankylosing spondylitis identifies non-MHC susceptibility loci. Nat Genet 2010; 42:123-7. [PMID: 20062062 PMCID: PMC3224997 DOI: 10.1038/ng.513] [Citation(s) in RCA: 470] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 11/30/2009] [Indexed: 02/07/2023]
Abstract
To identify susceptibility loci for ankylosing spondylitis, we undertook a genome-wide association study in 2,053 unrelated ankylosing spondylitis cases among people of European descent and 5,140 ethnically matched controls, with replication in an independent cohort of 898 ankylosing spondylitis cases and 1,518 controls. Cases were genotyped with Illumina HumHap370 genotyping chips. In addition to strong association with the major histocompatibility complex (MHC; P < 10(-800)), we found association with SNPs in two gene deserts at 2p15 (rs10865331; combined P = 1.9 x 10(-19)) and 21q22 (rs2242944; P = 8.3 x 10(-20)), as well as in the genes ANTXR2 (rs4333130; P = 9.3 x 10(-8)) and IL1R2 (rs2310173; P = 4.8 x 10(-7)). We also replicated previously reported associations at IL23R (rs11209026; P = 9.1 x 10(-14)) and ERAP1 (rs27434; P = 5.3 x 10(-12)). This study reports four genetic loci associated with ankylosing spondylitis risk and identifies a major role for the interleukin (IL)-23 and IL-1 cytokine pathways in disease susceptibility.
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Jallow M, Teo YY, Small KS, Rockett KA, Deloukas P, Clark TG, Kivinen K, Bojang KA, Conway DJ, Pinder M, Sirugo G, Sisay-Joof F, Usen S, Auburn S, Bumpstead SJ, Campino S, Coffey A, Dunham A, Fry AE, Green A, Gwilliam R, Hunt SE, Inouye M, Jeffreys AE, Mendy A, Palotie A, Potter S, Ragoussis J, Rogers J, Rowlands K, Somaskantharajah E, Whittaker P, Widden C, Donnelly P, Howie B, Marchini J, Morris A, SanJoaquin M, Achidi EA, Agbenyega T, Allen A, Amodu O, Corran P, Djimde A, Dolo A, Doumbo OK, Drakeley C, Dunstan S, Evans J, Farrar J, Fernando D, Hien TT, Horstmann RD, Ibrahim M, Karunaweera N, Kokwaro G, Koram KA, Lemnge M, Makani J, Marsh K, Michon P, Modiano D, Molyneux ME, Mueller I, Parker M, Peshu N, Plowe CV, Puijalon O, Reeder J, Reyburn H, Riley EM, Sakuntabhai A, Singhasivanon P, Sirima S, Tall A, Taylor TE, Thera M, Troye-Blomberg M, Williams TN, Wilson M, Kwiatkowski DP. Genome-wide and fine-resolution association analysis of malaria in West Africa. Nat Genet 2009; 41:657-65. [PMID: 19465909 PMCID: PMC2889040 DOI: 10.1038/ng.388] [Citation(s) in RCA: 277] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 04/27/2009] [Indexed: 11/08/2022]
Abstract
We report a genome-wide association (GWA) study of severe malaria in The Gambia. The initial GWA scan included 2,500 children genotyped on the Affymetrix 500K GeneChip, and a replication study included 3,400 children. We used this to examine the performance of GWA methods in Africa. We found considerable population stratification, and also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD). To investigate possible solutions to the problem of low LD, we focused on the HbS locus, sequencing this region of the genome in 62 Gambian individuals and then using these data to conduct multipoint imputation in the GWA samples. This increased the signal of association, from P = 4 × 10(-7) to P = 4 × 10(-14), with the peak of the signal located precisely at the HbS causal variant. Our findings provide proof of principle that fine-resolution multipoint imputation, based on population-specific sequencing data, can substantially boost authentic GWA signals and enable fine mapping of causal variants in African populations.
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Timpson NJ, Tobias JH, Richards JB, Soranzo N, Duncan EL, Sims AM, Whittaker P, Kumanduri V, Zhai G, Glaser B, Eisman J, Jones G, Nicholson G, Prince R, Seeman E, Spector TD, Brown MA, Peltonen L, Smith GD, Deloukas P, Evans DM. Common variants in the region around Osterix are associated with bone mineral density and growth in childhood. Hum Mol Genet 2009; 18:1510-7. [PMID: 19181680 PMCID: PMC2664147 DOI: 10.1093/hmg/ddp052] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 01/26/2009] [Accepted: 01/26/2009] [Indexed: 11/15/2022] Open
Abstract
Peak bone mass achieved in adolescence is a determinant of bone mass in later life. In order to identify genetic variants affecting bone mineral density (BMD), we performed a genome-wide association study of BMD and related traits in 1518 children from the Avon Longitudinal Study of Parents and Children (ALSPAC). We compared results with a scan of 134 adults with high or low hip BMD. We identified associations with BMD in an area of chromosome 12 containing the Osterix (SP7) locus, a transcription factor responsible for regulating osteoblast differentiation (ALSPAC: P = 5.8 x 10(-4); Australia: P = 3.7 x 10(-4)). This region has previously shown evidence of association with adult hip and lumbar spine BMD in an Icelandic population, as well as nominal association in a UK population. A meta-analysis of these existing studies revealed strong association between SNPs in the Osterix region and adult lumbar spine BMD (P = 9.9 x 10(-11)). In light of these findings, we genotyped a further 3692 individuals from ALSPAC who had whole body BMD and confirmed the association in children as well (P = 5.4 x 10(-5)). Moreover, all SNPs were related to height in ALSPAC children, but not weight or body mass index, and when height was included as a covariate in the regression equation, the association with total body BMD was attenuated. We conclude that genetic variants in the region of Osterix are associated with BMD in children and adults probably through primary effects on growth.
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McGinnis R, McLaren W, Ranganath V, Whittaker P, Hunt S, Deloukas P. Haplotype-based search for SNPs associated with differential type 1 diabetes risk among chromosomes carrying a specific HLA DRB1-DQA1-DQB1 haplotype. Diabetes Obes Metab 2009; 11 Suppl 1:8-16. [PMID: 19143810 PMCID: PMC2697815 DOI: 10.1111/j.1463-1326.2008.00998.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIM The aim of this study was to test chromosomes carrying the same DRB1-DQA1-DQB1 haplotype for single nucleotide polymorphisms (SNPs) in the major histocompatibility complex (MHC) that might mark subgroups of the haplotype with different risks for type 1 diabetes (T1D). METHODS Chromosomes from T1D children, their parents and non-diabetic siblings in families of the Type 1 Diabetes Genetics Consortium (T1DGC) were analysed by two haplotype-based methods: (i) logistic regression analysis restricted to phased chromosomes carrying the same DRB1-DQA1-DQB1 haplotype but differentiated by the two alleles at MHC SNPs, which were individually tested for association with T1D and (ii) homozygous parent transmission disequilibrium test (TDT) for biased transmission of a SNP allele to diabetic children from parents who are heterozygous at the SNP but homozygous for the specific DRB1-DQA1-DQB1 haplotype being evaluated. RESULTS A number of SNPs gave nominally significant (p < 0.05) evidence of marking two subsets of the 301-501-201 haplotype that might differ with respect to their diabetogenic potency. However, none of the SNPs achieved experiment-wide significance and hence may be false-positive associations. CONCLUSIONS We discuss limitations and possible deficiencies of our study suggesting further work that might yield more robust SNP associations marking two subgroups of a DRB1-DQA1-DQB1 haplotype with different T1D risks.
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Yngvadottir B, Xue Y, Searle S, Hunt S, Delgado M, Morrison J, Whittaker P, Deloukas P, Tyler-Smith C. A genome-wide survey of the prevalence and evolutionary forces acting on human nonsense SNPs. Am J Hum Genet 2009; 84:224-34. [PMID: 19200524 DOI: 10.1016/j.ajhg.2009.01.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 01/10/2009] [Accepted: 01/14/2009] [Indexed: 12/17/2022] Open
Abstract
Nonsense SNPs introduce premature termination codons into genes and can result in the absence of a gene product or in a truncated and potentially harmful protein, so they are often considered disadvantageous and are associated with disease susceptibility. As such, we might expect the disrupted allele to be rare and, in healthy people, observed only in a heterozygous state. However, some, like those in the CASP12 and ACTN3 genes, are known to be present at high frequencies and to occur often in a homozygous state and seem to have been advantageous in recent human evolution. To evaluate the selective forces acting on nonsense SNPs as a class, we have carried out a large-scale experimental survey of nonsense SNPs in the human genome by genotyping 805 of them (plus control synonymous SNPs) in 1,151 individuals from 56 worldwide populations. We identified 169 genes containing nonsense SNPs that were variable in our samples, of which 99 were found with both copies inactivated in at least one individual. We found that the sampled humans differ on average by 24 genes (out of about 20,000) because of these nonsense SNPs alone. As might be expected, nonsense SNPs as a class were found to be slightly disadvantageous over evolutionary timescales, but a few nevertheless showed signs of being possibly advantageous, as indicated by unusually high levels of population differentiation, long haplotypes, and/or high frequencies of derived alleles. This study underlines the extent of variation in gene content within humans and emphasizes the importance of understanding this type of variation.
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