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scoreInvHap: Inversion genotyping for genome-wide association studies.

PLoS genetics

Ruiz-Arenas C, Cáceres A, López-Sánchez M, Tolosana I, Pérez-Jurado L, González JR.
PMID: 31269027
PLoS Genet. 2019 Jul 03;15(7):e1008203. doi: 10.1371/journal.pgen.1008203. eCollection 2019 Jul.

Polymorphic inversions contribute to adaptation and phenotypic variation. However, large multi-centric association studies of inversions remain challenging. We present scoreInvHap, a method to genotype inversions from SNP data for genome-wide association studies (GWASs), overcoming important limitations of current methods...

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Ruiz-Arenas C, Cáceres A, López-Sánchez M, et al. scoreInvHap: Inversion genotyping for genome-wide association studies. PLoS Genet. 2019;15(7):e1008203doi: 10.1371/journal.pgen.1008203.
Ruiz-Arenas, C., Cáceres, A., López-Sánchez, M., Tolosana, I., Pérez-Jurado, L., & González, J. R. (2019). scoreInvHap: Inversion genotyping for genome-wide association studies. PLoS genetics, 15(7), e1008203. https://doi.org/10.1371/journal.pgen.1008203
Ruiz-Arenas, Carlos, et al. "scoreInvHap: Inversion genotyping for genome-wide association studies." PLoS genetics vol. 15,7 (2019): e1008203. doi: https://doi.org/10.1371/journal.pgen.1008203
Ruiz-Arenas C, Cáceres A, López-Sánchez M, Tolosana I, Pérez-Jurado L, González JR. scoreInvHap: Inversion genotyping for genome-wide association studies. PLoS Genet. 2019 Jul 03;15(7):e1008203. doi: 10.1371/journal.pgen.1008203. eCollection 2019 Jul. PMID: 31269027; PMCID: PMC6608898.
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Multi-omics study for interpretation of genome-wide association study.

Journal of human genetics

Akiyama M.
PMID: 32948838
J Hum Genet. 2021 Jan;66(1):3-10. doi: 10.1038/s10038-020-00842-5. Epub 2020 Sep 18.

Genome-wide association studies (GWASs) have identified thousands of genetic loci associated with complex traits, including a wide variety of diseases. Despite the successful identification of associated loci, interpreting GWAS findings remains challenging and requires other biological resources. Omics, including...

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Akiyama M. Multi-omics study for interpretation of genome-wide association study. J Hum Genet. 2020;66(1):3-10doi: 10.1038/s10038-020-00842-5.
Akiyama, M. (2021). Multi-omics study for interpretation of genome-wide association study. Journal of human genetics, 66(1), 3-10. https://doi.org/10.1038/s10038-020-00842-5
Akiyama, Masato. "Multi-omics study for interpretation of genome-wide association study." Journal of human genetics vol. 66,1 (2021): 3-10. doi: https://doi.org/10.1038/s10038-020-00842-5
Akiyama M. Multi-omics study for interpretation of genome-wide association study. J Hum Genet. 2021 Jan;66(1):3-10. doi: 10.1038/s10038-020-00842-5. Epub 2020 Sep 18. PMID: 32948838.
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The fog of genetics: what is known, unknown and unknowable in the genetics of complex traits and diseases.

EMBO reports

de Magalhães JP, Wang J.
PMID: 31633864
EMBO Rep. 2019 Nov 05;20(11):e48054. doi: 10.15252/embr.201948054. Epub 2019 Oct 21.

A major task for genetics is searching for genetic variants associated with disease. But we may well be missing a large number of "unknown unknown" alleles in the "fog of genetics".

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de Magalhães JP, Wang J. The fog of genetics: what is known, unknown and unknowable in the genetics of complex traits and diseases. EMBO Rep. 2019;20(11):e48054doi: 10.15252/embr.201948054.
de Magalhães, J. P., & Wang, J. (2019). The fog of genetics: what is known, unknown and unknowable in the genetics of complex traits and diseases. EMBO reports, 20(11), e48054. https://doi.org/10.15252/embr.201948054
de Magalhães, João Pedro, and Wang, Jingwei. "The fog of genetics: what is known, unknown and unknowable in the genetics of complex traits and diseases." EMBO reports vol. 20,11 (2019): e48054. doi: https://doi.org/10.15252/embr.201948054
de Magalhães JP, Wang J. The fog of genetics: what is known, unknown and unknowable in the genetics of complex traits and diseases. EMBO Rep. 2019 Nov 05;20(11):e48054. doi: 10.15252/embr.201948054. Epub 2019 Oct 21. PMID: 31633864; PMCID: PMC6831998.
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Clinical use of current polygenic risk scores may exacerbate health disparities.

Nature genetics

Martin AR, Kanai M, Kamatani Y, Okada Y, Neale BM, Daly MJ.
PMID: 30926966
Nat Genet. 2019 Apr;51(4):584-591. doi: 10.1038/s41588-019-0379-x. Epub 2019 Mar 29.

Polygenic risk scores (PRS) are poised to improve biomedical outcomes via precision medicine. However, the major ethical and scientific challenge surrounding clinical implementation of PRS is that those available today are several times more accurate in individuals of European...

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Martin AR, Kanai M, Kamatani Y, et al. Clinical use of current polygenic risk scores may exacerbate health disparities. Nat Genet. 2019;51(4):584-591doi: 10.1038/s41588-019-0379-x.
Martin, A. R., Kanai, M., Kamatani, Y., Okada, Y., Neale, B. M., & Daly, M. J. (2019). Clinical use of current polygenic risk scores may exacerbate health disparities. Nature genetics, 51(4), 584-591. https://doi.org/10.1038/s41588-019-0379-x
Martin, Alicia R, et al. "Clinical use of current polygenic risk scores may exacerbate health disparities." Nature genetics vol. 51,4 (2019): 584-591. doi: https://doi.org/10.1038/s41588-019-0379-x
Martin AR, Kanai M, Kamatani Y, Okada Y, Neale BM, Daly MJ. Clinical use of current polygenic risk scores may exacerbate health disparities. Nat Genet. 2019 Apr;51(4):584-591. doi: 10.1038/s41588-019-0379-x. Epub 2019 Mar 29. PMID: 30926966; PMCID: PMC6563838.
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Towards practical privacy-preserving genome-wide association study.

BMC bioinformatics

Bonte C, Makri E, Ardeshirdavani A, Simm J, Moreau Y, Vercauteren F.
PMID: 30572817
BMC Bioinformatics. 2018 Dec 20;19(1):537. doi: 10.1186/s12859-018-2541-3.

BACKGROUND: The deployment of Genome-wide association studies (GWASs) requires genomic information of a large population to produce reliable results. This raises significant privacy concerns, making people hesitate to contribute their genetic information to such studies.RESULTS: We propose two provably...

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Bonte C, Makri E, Ardeshirdavani A, et al. Towards practical privacy-preserving genome-wide association study. BMC Bioinformatics. 2018;19(1):537doi: 10.1186/s12859-018-2541-3.
Bonte, C., Makri, E., Ardeshirdavani, A., Simm, J., Moreau, Y., & Vercauteren, F. (2018). Towards practical privacy-preserving genome-wide association study. BMC bioinformatics, 19(1), 537. https://doi.org/10.1186/s12859-018-2541-3
Bonte, Charlotte, et al. "Towards practical privacy-preserving genome-wide association study." BMC bioinformatics vol. 19,1 (2018): 537. doi: https://doi.org/10.1186/s12859-018-2541-3
Bonte C, Makri E, Ardeshirdavani A, Simm J, Moreau Y, Vercauteren F. Towards practical privacy-preserving genome-wide association study. BMC Bioinformatics. 2018 Dec 20;19(1):537. doi: 10.1186/s12859-018-2541-3. PMID: 30572817; PMCID: PMC6302495.
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Genetic background and transplantation outcomes: insights from genome-wide association studies.

Current opinion in organ transplantation

Zanoni F, Kiryluk K.
PMID: 31815792
Curr Opin Organ Transplant. 2020 Feb;25(1):35-41. doi: 10.1097/MOT.0000000000000718.

PURPOSE OF REVIEW: The current review summarizes recent advances in the genetic studies of transplantation outcomes, including new genome-wide association studies for acute rejection, allograft survival, pharmacogenomics, and common transplant comorbidities.RECENT FINDINGS: Genetic studies of kidney transplantation outcomes have...

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Zanoni F, Kiryluk K. Genetic background and transplantation outcomes: insights from genome-wide association studies. Curr Opin Organ Transplant. 2020;25(1):35-41doi: 10.1097/MOT.0000000000000718.
Zanoni, F., & Kiryluk, K. (2020). Genetic background and transplantation outcomes: insights from genome-wide association studies. Current opinion in organ transplantation, 25(1), 35-41. https://doi.org/10.1097/MOT.0000000000000718
Zanoni, Francesca, and Kiryluk, Krzysztof. "Genetic background and transplantation outcomes: insights from genome-wide association studies." Current opinion in organ transplantation vol. 25,1 (2020): 35-41. doi: https://doi.org/10.1097/MOT.0000000000000718
Zanoni F, Kiryluk K. Genetic background and transplantation outcomes: insights from genome-wide association studies. Curr Opin Organ Transplant. 2020 Feb;25(1):35-41. doi: 10.1097/MOT.0000000000000718. PMID: 31815792; PMCID: PMC7521467.
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A current snapshot of common genomic variants contribution in psychiatric disorders.

American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics

Santoro ML, Moretti PN, Pellegrino R, Gadelha A, Abílio VC, Hayashi MA, Belangero SI, Hakonarson H.
PMID: 27486013
Am J Med Genet B Neuropsychiatr Genet. 2016 Dec;171(8):997-1005. doi: 10.1002/ajmg.b.32475. Epub 2016 Aug 03.

In the past decade, numerous advances were achieved in psychiatric genetics. Particularly, the genome wide association studies (GWAS) have contributed to uncovering new genes and pathways associated to psychiatric disorders (PDs). At the same time, with increasing sample sizes...

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Santoro ML, Moretti PN, Pellegrino R, et al. A current snapshot of common genomic variants contribution in psychiatric disorders. Am J Med Genet B Neuropsychiatr Genet. 2016;171(8):997-1005doi: 10.1002/ajmg.b.32475.
Santoro, M. L., Moretti, P. N., Pellegrino, R., Gadelha, A., Abílio, V. C., Hayashi, M. A., Belangero, S. I., & Hakonarson, H. (2016). A current snapshot of common genomic variants contribution in psychiatric disorders. American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, 171(8), 997-1005. https://doi.org/10.1002/ajmg.b.32475
Santoro, Marcos L, et al. "A current snapshot of common genomic variants contribution in psychiatric disorders." American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics vol. 171,8 (2016): 997-1005. doi: https://doi.org/10.1002/ajmg.b.32475
Santoro ML, Moretti PN, Pellegrino R, Gadelha A, Abílio VC, Hayashi MA, Belangero SI, Hakonarson H. A current snapshot of common genomic variants contribution in psychiatric disorders. Am J Med Genet B Neuropsychiatr Genet. 2016 Dec;171(8):997-1005. doi: 10.1002/ajmg.b.32475. Epub 2016 Aug 03. PMID: 27486013.
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FOLD: a method to optimize power in meta-analysis of genetic association studies with overlapping subjects.

Bioinformatics (Oxford, England)

Kim EE, Lee S, Lee CH, Oh H, Song K, Han B.
PMID: 29036405
Bioinformatics. 2017 Dec 15;33(24):3947-3954. doi: 10.1093/bioinformatics/btx463.

MOTIVATION: In genetic association studies, meta-analyses are widely used to increase the statistical power by aggregating information from multiple studies. In meta-analyses, participating studies often share the same individuals due to the shared use of publicly available control data...

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Kim EE, Lee S, Lee CH, et al. FOLD: a method to optimize power in meta-analysis of genetic association studies with overlapping subjects. Bioinformatics. 2017;33(24):3947-3954doi: 10.1093/bioinformatics/btx463.
Kim, E. E., Lee, S., Lee, C. H., Oh, H., Song, K., & Han, B. (2017). FOLD: a method to optimize power in meta-analysis of genetic association studies with overlapping subjects. Bioinformatics (Oxford, England), 33(24), 3947-3954. https://doi.org/10.1093/bioinformatics/btx463
Kim, Emma E, et al. "FOLD: a method to optimize power in meta-analysis of genetic association studies with overlapping subjects." Bioinformatics (Oxford, England) vol. 33,24 (2017): 3947-3954. doi: https://doi.org/10.1093/bioinformatics/btx463
Kim EE, Lee S, Lee CH, Oh H, Song K, Han B. FOLD: a method to optimize power in meta-analysis of genetic association studies with overlapping subjects. Bioinformatics. 2017 Dec 15;33(24):3947-3954. doi: 10.1093/bioinformatics/btx463. PMID: 29036405; PMCID: PMC5860085.
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Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wide scale.

BMC research notes

Chen L, Qin ZS.
PMID: 29084591
BMC Res Notes. 2017 Oct 30;10(1):530. doi: 10.1186/s13104-017-2851-y.

OBJECTIVE: The majority of sequence variants identified by Genome-wide association studies (GWASs) fall outside of the protein-coding regions. Unlike coding variants, it is challenging to connect these noncoding variants to the pathophysiology of complex diseases/traits due to the lack...

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Chen L, Qin ZS. Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wide scale. BMC Res Notes. 2017;10(1):530doi: 10.1186/s13104-017-2851-y.
Chen, L., & Qin, Z. S. (2017). Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wide scale. BMC research notes, 10(1), 530. https://doi.org/10.1186/s13104-017-2851-y
Chen, Li, and Qin, Zhaohui S. "Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wide scale." BMC research notes vol. 10,1 (2017): 530. doi: https://doi.org/10.1186/s13104-017-2851-y
Chen L, Qin ZS. Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wide scale. BMC Res Notes. 2017 Oct 30;10(1):530. doi: 10.1186/s13104-017-2851-y. PMID: 29084591; PMCID: PMC5663107.
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OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants.

Scientific reports

Boudellioua I, Kulmanov M, Schofield PN, Gkoutos GV, Hoehndorf R.
PMID: 30279426
Sci Rep. 2018 Oct 02;8(1):14681. doi: 10.1038/s41598-018-32876-3.

An increasing number of disorders have been identified for which two or more distinct alleles in two or more genes are required to either cause the disease or to significantly modify its onset, severity or phenotype. It is difficult...

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Boudellioua I, Kulmanov M, Schofield PN, et al. OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants. Sci Rep. 2018;8(1):14681doi: 10.1038/s41598-018-32876-3.
Boudellioua, I., Kulmanov, M., Schofield, P. N., Gkoutos, G. V., & Hoehndorf, R. (2018). OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants. Scientific reports, 8(1), 14681. https://doi.org/10.1038/s41598-018-32876-3
Boudellioua, Imane, et al. "OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants." Scientific reports vol. 8,1 (2018): 14681. doi: https://doi.org/10.1038/s41598-018-32876-3
Boudellioua I, Kulmanov M, Schofield PN, Gkoutos GV, Hoehndorf R. OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants. Sci Rep. 2018 Oct 02;8(1):14681. doi: 10.1038/s41598-018-32876-3. PMID: 30279426; PMCID: PMC6168481.
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[Genome-wide association approach].

Medecine sciences : M/S

Thomas G.
PMID: 19361411
Med Sci (Paris). 2009 Mar;25:42-4. doi: 10.1051/medsci/2009251s42.

The genome-wide association approach has been the most powerful and efficient study design thus far in identifying genetic variants that are associated with complex human diseases. This approach became feasible as the result of several key advancements in genetic...

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Thomas G. Application de la génétique multifactorielle. [Genome-wide association approach]. Med Sci (Paris). 2009;25:42-4doi: 10.1051/medsci/2009251s42.
Thomas, G. (2009). Application de la génétique multifactorielle. [Genome-wide association approach]. Medecine sciences : M/S, 2542-4. https://doi.org/10.1051/medsci/2009251s42
Thomas, Gilles. "Application de la génétique multifactorielle." [Genome-wide association approach]. Medecine sciences : M/S vol. 25 (2009): 42-4. doi: https://doi.org/10.1051/medsci/2009251s42
Thomas G. Application de la génétique multifactorielle. [Genome-wide association approach]. Med Sci (Paris). 2009 Mar;25:42-4. doi: 10.1051/medsci/2009251s42. French. PMID: 19361411.
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The variant call format provides efficient and robust storage of GWAS summary statistics.

Genome biology

Lyon MS, Andrews SJ, Elsworth B, Gaunt TR, Hemani G, Marcora E.
PMID: 33441155
Genome Biol. 2021 Jan 13;22(1):32. doi: 10.1186/s13059-020-02248-0.

GWAS summary statistics are fundamental for a variety of research applications yet no common storage format has been widely adopted. Existing tabular formats ambiguously or incompletely store information about genetic variants and associations, lack essential metadata and are typically...

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Lyon MS, Andrews SJ, Elsworth B, et al. The variant call format provides efficient and robust storage of GWAS summary statistics. Genome Biol. 2021;22(1):32doi: 10.1186/s13059-020-02248-0.
Lyon, M. S., Andrews, S. J., Elsworth, B., Gaunt, T. R., Hemani, G., & Marcora, E. (2021). The variant call format provides efficient and robust storage of GWAS summary statistics. Genome biology, 22(1), 32. https://doi.org/10.1186/s13059-020-02248-0
Lyon, Matthew S, et al. "The variant call format provides efficient and robust storage of GWAS summary statistics." Genome biology vol. 22,1 (2021): 32. doi: https://doi.org/10.1186/s13059-020-02248-0
Lyon MS, Andrews SJ, Elsworth B, Gaunt TR, Hemani G, Marcora E. The variant call format provides efficient and robust storage of GWAS summary statistics. Genome Biol. 2021 Jan 13;22(1):32. doi: 10.1186/s13059-020-02248-0. PMID: 33441155; PMCID: PMC7805039.
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Showing 97 to 108 of 108 entries