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| 1 | Improving genomic predictions by correction of genotypes from genotyping by sequencing in livestock populations显示文摘Background: Genotyping by sequencing(GBS) is a robust method to genotype markers. Many factors can influence the genotyping quality. One is that heterozygous genotypes could be wrongly genotyped as homozygotes,dependent on the genotyping depths. In this study, a method correcting this type of genotyping error was demonstrated. The efficiency of this correction method and its effect on genomic prediction were assessed using simulated data of livestock populations.Results: Chip array(Chip) and four depths of GBS data was simulated. After quality control(call rate ≥ 0.8 and MAF ≥ 0.01), the remaining number of Chip and GBS SNPs were both approximately 7,000, averaged over 10 replicates. GBS genotypes were corrected with the proposed method. The reliability of genomic prediction was calculated using GBS, corrected GBS(GBSc), true genotypes for the GBS loci(GBSr) and Chip data. The results showed that GBSc had higher rates of correct genotype calls and higher correlations with true genotypes than GBS. For genomic prediction, using Chip data resulted in the highest reliability. As the depth increased to 10, the prediction reliabilities using GBS and GBSc data approached those using true GBS data. The reliabilities of genomic prediction using GBSc data were 0.604, 0.672, 0.684 and 0.704 after genomic correction, with the improved values of 0.013, 0.009, 0.006 and 0.001 at depth = 2, 4, 5 and 10, respectively.Conclusions: The current study showed that a correction method for GBS data increased the genotype accuracies and, consequently, improved genomic predictions. These results suggest that a correction of GBS genotype is necessary, especially for the GBS data with low depths. | Xiao Wang Mogens SandΦ Lund Peipei Ma Luc Janss Haja N.Kadarmideen Guosheng Su | 2019 | Journal of Animal Science and Biotechnology2019，10，2： | 4 |
| 2 | Toxoplasmosis of the central nervous system in the acquired immunodeficiency syndrome显示文摘 | Porter SB Sande MA | 1993 | N Engl J Med1993，2，： | 1 |
| 3 | The microbial etiology and antimicrobial therapy of adults with acute community acpuired sinusitis: a fifteen - year experience at University of virginia and review of other selected studies显示文摘 | Gwaltney JM Scheld WM Sande MA | 1992 | J Allergy Clinimmunol1992，90，： | 1 |
| 4 | Long-term treatment of rectovaginal fistulas in Crohn′s disease:response to infliximab in the ACCENT Ⅱ Study显示文摘 | Sands BE Blank MA Patel K | | 0，，10： | 1 |
| 5 | Soft tissueextension increases the risk of local recurrence after curettage with adjuvants for giant-cell tumor of the long bones: a retrospective study of 93 patients 显示文摘 | van der Heijden L van de Sande MA Dijkstra R | 2012 | Acta Orthopaedica2012，83，： | 1 |
| 6 | Self-restriction of medications due to cost in seniors without prescription coverage:A national survey显示文摘 | Steinman MA Sands LP Covinsky KE | 2001 | J Gen Intern Med2001，16，12： | 1 |
| 7 | Update in infectious diseases显示文摘 | Sande MA Ronald AR | 2004 | AM Inter Med2004，140，4： | 1 |
| 8 | Infections with Cryptococcus neoformans in the acquired immunodeficiency syndrome显示文摘 | Chuck SL Sande MA | 1989 | Br Engl J Med1989，321，12： | 1 |
| 9 | Risk of atrial fibrillation, stroke, and death after radiofrequency catheter ablation of typical atrial flutter显示文摘 | Javier García Seara Sergio Raposeiras Roubin Francisco Gude Sampedro Vanessa Balboa Barreiro José Martínez Sande Moisés Rodriguez Ma?ero Pilar Cabans Grandio Belen Alvarez José González Juanatey | 2014 | Clinical Research in Cardiology2014，，7： | 1 |
| 10 | Family history:an opportunity for early interventions and improved control of hypertension,obesity and diabetes 显示文摘 | Van der sande MA Walraven GE Milligan PJ | 2001 | Bull World Health Organ2001，79，4： | 1 |
| 11 | Intercalary allograft reconstructions following resection of primary bone tumors: a nationwide multicenter study 显示文摘 | Bus MP Dijkstra PD van de Sande MA | 2014 | J Bone Joint Surg Am2014，96，4： | 1 |
| 12 | Soft tissue extension increases the risk of local recurrence after curettage with adjuvants for giant-cell tumor of the long bones: A retro- spective study of 93 patients显示文摘 | L van der Heijden MA van de Sande PD Dijkstra | 2012 | Acta Orthop2012，83，4： | 1 |
| 13 | Severe respiratory syncytial virus infection in early life is associated with increased type 2 cytokine production in Gambian children显示文摘 | van der Sande MA Kidd IM Goetghebuer T | 2002 | Clin Exp Allergy2002，32，10： | 1 |
| 14 | Long-term treatment of rectovaginal fistulas in Crohn' s disease: response to infliximab in the ACCENT II Study 显示文摘 | Sands BE Blank MA Patel K ACCENT II Study | 2004 | Clin Gastroenterol Hepatol2004，2，10： | 1 |
| 15 | Antibiotic prescribing for adults with colds, upper respiratory tract infections, and bronchitis by ambulatory care physicians显示文摘 | Gonzales R Steiner JF Sande MA | 1997 | JAMA1997，278，： | 1 |
| 16 | Current diagnosis and treatment in infectious diseases显示文摘 | Wilson WR Sande MA | | 0，，05： | 1 |
| 17 | Long-term treatment of rectova- gina fistulas in Crohn's disease response to infliximab in the AC- CENT lI Study 显示文摘 | Sands BE Blank MA Patel K | 2004 | Clin Gastroenterol Hepato12004，2，10： | 1 |
| 18 | Antibiotic prescribing for colds,upper respiratory tract infections,and bronchitis by ambulatory care physicians显示文摘 | Gonzales R Steiner JF Sande MA | 1997 | JAMA1997，278，11： | 1 |
| 19 | Use of fluorescence imaging to investigate the structure and function of intestinal M cells 显示文摘 | Buda A Sands C Jepson MA | 2005 | Adv Drug Deliv Rev2005，57，1： | 1 |
| 20 | Pathogenesis of bacterial meningitis: contributions by experimental models in rabbits 显示文摘 | Tauber MG Sande MA | 1984 | Infection1984，12，1： | 1 |
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