publication . Article . 2019

Studying the effects of haplotype partitioning methods on the RA-associated genomic results from the North American Rheumatoid Arthritis Consortium (NARAC) dataset

Saad, Mohamed N.; Mabrouk, Mai S.; Eldeib, Ayman M.; Shaker, Olfat G.;
Open Access
  • Published: 01 Jul 2019 Journal: Journal of Advanced Research, volume 18, pages 113-126 (issn: 2090-1232, Copyright policy)
  • Publisher: Elsevier BV
Abstract
Graphical abstract
Subjects
ACM Computing Classification System: ComputingMethodologies_COMPUTERGRAPHICS
free text keywords: Multidisciplinary, Haplotype, Human genome, Linkage disequilibrium, Single-nucleotide polymorphism, SNP, Computational biology, Bonferroni correction, symbols.namesake, symbols, Polymorphism (computer science), Genome-wide association study, Chromatography, Medicine, business.industry, business, Medicine (General), R5-920, Science (General), Q1-390, Original Article, Confidence interval test, Four-gamete test, NARAC, Rheumatoid arthritis, Solid spine of linkage disequilibrium
Funded by
NIH| Genetic Analysis of Common Diseases: An Evaluation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| NARAC The Genetics of Rheumatoid Arthritis
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AR044422-10
  • Funding stream: NATIONAL INSTITUTE OF ARTHRITIS AND MUSCULOSKELETAL AND SKIN DISEASES
147 references, page 1 of 10

Saad, M.N., Mabrouk, M.S., Eldeib, A.M., Shaker, O.G.. Identification of rheumatoid arthritis biomarkers based on single nucleotide polymorphisms and haplotype blocks: a systematic review and meta-analysis. J Adv Res. 2016; 7 (1): 1-16 [OpenAIRE] [PubMed]

Saad, M.N., Mabrouk, M.S., Eldeib, A.M., Shaker, O.G.. 7th Cairo international biomedical engineering conference. 2014: 75-78

Saad, M.N., Mabrouk, M.S., Eldeib, A.M., Shaker, O.G.. Effect of MTHFR, TGFβ1, and TNFB polymorphisms on osteoporosis in rheumatoid arthritis patients. Gene. 2015; 568 (2): 124-128 [OpenAIRE] [PubMed]

Saad, M.N., Mabrouk, M.S., Eldeib, A.M., Shaker, O.G.. Genetic case-control study for eight polymorphisms associated with rheumatoid arthritis. PLoS One. 2015; 10 (7): e0131960 [OpenAIRE] [PubMed]

Alonso, N., Lucas, G., Hysi, P.. Big data challenges in bone research: genome-wide association studies and next-generation sequencing. BoneKEy Rep. 2015; 4: 635 [OpenAIRE] [PubMed]

Clark, A.G.. The role of haplotypes in candidate gene studies. Genet Epidemiol. 2004; 27 (4): 321-333 [PubMed]

Su, S.C., Kuo, C.C., Chen, T.. Single nucleotide polymorphism data analysis – state-of-the-art review on this emerging field from a signal processing viewpoint. IEEE Signal Process Mag. 2007; 24 (1): 75-82

Kim, S.A., Yoo, Y.J.. Effects of single nucleotide polymorphism marker density on haplotype block partition. Genomics Inform. 2016; 14 (4): 196-204 [OpenAIRE] [PubMed]

Ruyssen-Witrand, A., Constantin, A., Cambon-Thomsen, A., Thomsen, M.. New insights into the genetics of immune responses in rheumatoid arthritis. Tissue Antigens. 2012; 80 (2): 105-118 [OpenAIRE] [PubMed]

Lauzon, D., Kanzki, B., Dupuy, V., April, A., Phillips, M.S., Tremblay, J.. In: 2016 IEEE 1st international conference on connected health: applications, systems and engineering technologies (CHASE). 2016

Peise, E., Fabregat-Traver, D., Bientinesi, P.. High performance solutions for big-data GWAS. Parallel Comput. 2015; 42: 75-87

Balding, D.J.. A tutorial on statistical methods for population association studies. Nat Rev Genet. 2006; 7 (10): 781-791 [OpenAIRE] [PubMed]

Amos, C.I., Chen, W.V., Seldin, M.F., Remmers, E.F., Taylor, K.E., Criswell, L.A.. Data for Genetic Analysis Workshop 16 Problem 1, association analysis of rheumatoid arthritis data. BMC Proc. 2009; 3 (Suppl 7): S2 [OpenAIRE]

Yuan, T.-A., Yourk, V., Farhat, A., Ziogas, A., Meyskens, F.L., Anton-Culver, H.. A case-control study of the genetic variability in reactive oxygen species—metabolizing enzymes in melanoma risk. Int J Mol Sci. 2018; 19 (1): 242-260

Ballard, D.H., Cho, J., Zhao, H.. Comparisons of multi-marker association methods to detect association between a candidate region and disease. Genetic Epidemiol: Official Publ Int Genet Epidemiol Soc. 2010; 34 (3): 201-212

147 references, page 1 of 10
Abstract
Graphical abstract
Subjects
ACM Computing Classification System: ComputingMethodologies_COMPUTERGRAPHICS
free text keywords: Multidisciplinary, Haplotype, Human genome, Linkage disequilibrium, Single-nucleotide polymorphism, SNP, Computational biology, Bonferroni correction, symbols.namesake, symbols, Polymorphism (computer science), Genome-wide association study, Chromatography, Medicine, business.industry, business, Medicine (General), R5-920, Science (General), Q1-390, Original Article, Confidence interval test, Four-gamete test, NARAC, Rheumatoid arthritis, Solid spine of linkage disequilibrium
Funded by
NIH| Genetic Analysis of Common Diseases: An Evaluation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| NARAC The Genetics of Rheumatoid Arthritis
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AR044422-10
  • Funding stream: NATIONAL INSTITUTE OF ARTHRITIS AND MUSCULOSKELETAL AND SKIN DISEASES
147 references, page 1 of 10

Saad, M.N., Mabrouk, M.S., Eldeib, A.M., Shaker, O.G.. Identification of rheumatoid arthritis biomarkers based on single nucleotide polymorphisms and haplotype blocks: a systematic review and meta-analysis. J Adv Res. 2016; 7 (1): 1-16 [OpenAIRE] [PubMed]

Saad, M.N., Mabrouk, M.S., Eldeib, A.M., Shaker, O.G.. 7th Cairo international biomedical engineering conference. 2014: 75-78

Saad, M.N., Mabrouk, M.S., Eldeib, A.M., Shaker, O.G.. Effect of MTHFR, TGFβ1, and TNFB polymorphisms on osteoporosis in rheumatoid arthritis patients. Gene. 2015; 568 (2): 124-128 [OpenAIRE] [PubMed]

Saad, M.N., Mabrouk, M.S., Eldeib, A.M., Shaker, O.G.. Genetic case-control study for eight polymorphisms associated with rheumatoid arthritis. PLoS One. 2015; 10 (7): e0131960 [OpenAIRE] [PubMed]

Alonso, N., Lucas, G., Hysi, P.. Big data challenges in bone research: genome-wide association studies and next-generation sequencing. BoneKEy Rep. 2015; 4: 635 [OpenAIRE] [PubMed]

Clark, A.G.. The role of haplotypes in candidate gene studies. Genet Epidemiol. 2004; 27 (4): 321-333 [PubMed]

Su, S.C., Kuo, C.C., Chen, T.. Single nucleotide polymorphism data analysis – state-of-the-art review on this emerging field from a signal processing viewpoint. IEEE Signal Process Mag. 2007; 24 (1): 75-82

Kim, S.A., Yoo, Y.J.. Effects of single nucleotide polymorphism marker density on haplotype block partition. Genomics Inform. 2016; 14 (4): 196-204 [OpenAIRE] [PubMed]

Ruyssen-Witrand, A., Constantin, A., Cambon-Thomsen, A., Thomsen, M.. New insights into the genetics of immune responses in rheumatoid arthritis. Tissue Antigens. 2012; 80 (2): 105-118 [OpenAIRE] [PubMed]

Lauzon, D., Kanzki, B., Dupuy, V., April, A., Phillips, M.S., Tremblay, J.. In: 2016 IEEE 1st international conference on connected health: applications, systems and engineering technologies (CHASE). 2016

Peise, E., Fabregat-Traver, D., Bientinesi, P.. High performance solutions for big-data GWAS. Parallel Comput. 2015; 42: 75-87

Balding, D.J.. A tutorial on statistical methods for population association studies. Nat Rev Genet. 2006; 7 (10): 781-791 [OpenAIRE] [PubMed]

Amos, C.I., Chen, W.V., Seldin, M.F., Remmers, E.F., Taylor, K.E., Criswell, L.A.. Data for Genetic Analysis Workshop 16 Problem 1, association analysis of rheumatoid arthritis data. BMC Proc. 2009; 3 (Suppl 7): S2 [OpenAIRE]

Yuan, T.-A., Yourk, V., Farhat, A., Ziogas, A., Meyskens, F.L., Anton-Culver, H.. A case-control study of the genetic variability in reactive oxygen species—metabolizing enzymes in melanoma risk. Int J Mol Sci. 2018; 19 (1): 242-260

Ballard, D.H., Cho, J., Zhao, H.. Comparisons of multi-marker association methods to detect association between a candidate region and disease. Genetic Epidemiol: Official Publ Int Genet Epidemiol Soc. 2010; 34 (3): 201-212

147 references, page 1 of 10
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publication . Article . 2019

Studying the effects of haplotype partitioning methods on the RA-associated genomic results from the North American Rheumatoid Arthritis Consortium (NARAC) dataset

Saad, Mohamed N.; Mabrouk, Mai S.; Eldeib, Ayman M.; Shaker, Olfat G.;