Searching for new genes and loci involved in cleft lip and palate in the Polish population – genome-wide association study

2016 ◽  
Vol 83 (3) ◽  
pp. 265-268 ◽  
Author(s):  
Adrianna Mostowska ◽  
Kamil K. Hozyasz ◽  
Piotr Wójcicki ◽  
Barbara Biedziak ◽  
Joanna Wesoły ◽  
...  
Keyword(s):  
Association Study ◽  
Cleft Lip ◽  
Genome Wide Association Study ◽  
Cleft Lip And Palate ◽  
Genome Wide Association ◽  
Polish Population ◽  
Orofacial Clefts ◽  
New Genes ◽  
Genome Wide ◽  
History Of

The project “Searching for new genes and loci involved in cleft lip and palate in the Polish population – genome-wide association study” is a case-control study in a group of unrelated subjects with non-syndromic cleft lip with or without cleft palate (NSCL/P) and healthy individuals with no family history of clefting or other congenital disorders. The overall goal of this grant proposal is to identify novel genetic factors, which can play a significant role in the pathogenesis of orofacial clefts in the Polish population. To accomplish the proposed aim, a two stage genome-wide association study will be performed. In the first stage, Illumina's HumanOmni Express BeadChips arrays will be used to genotype over 700,000 polymorphisms in NSCL/P patients and controls. In the second stage, SNPs showing the most compelling association with the risk of orofacial clefts will be tested in an independent sample set using standard genotyping methods. This research project is expected to be completed in July 2015.

Family-based genome-wide association study in Patagonia confirms the association of theDMDlocus and cleft lip and palate

2015 ◽  
Vol 123 (5) ◽  
pp. 381-384 ◽  
Author(s):  
Renata F. Fonseca ◽  
Flávia M. de Carvalho ◽  
Fernando A. Poletta ◽  
David Montaner ◽  
Joaquin Dopazo ◽  
...  
Keyword(s):  
Association Study ◽  
Cleft Lip ◽  
Genome Wide Association Study ◽  
Cleft Lip And Palate ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Family Based

A genome‐wide association study identifies new genes associated with developmental dysplasia of the hip

2019 ◽  
Vol 95 (3) ◽  
pp. 345-355 ◽  
Author(s):  
Wenjin Yan ◽  
Zheng Hao ◽  
Shuyan Tang ◽  
Jin Dai ◽  
Liming Zheng ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Developmental Dysplasia ◽  
Genome Wide Association ◽  
New Genes ◽  
Genome Wide ◽  
A Genome ◽  
Dysplasia Of The Hip

scholarly journals Genome-wide Association Study of Non-syndromic Orofacial Clefts in a Multiethnic Sample of Families and Controls Identifies Novel Regions

2020 ◽  
Author(s):  
Nandita Mukhopadhyay ◽  
Eleanor Feingold ◽  
Lina Moreno-Uribe ◽  
George Wehby ◽  
Luz Consuelo Valencia-Ramirez ◽  
...  
Keyword(s):  
Native American ◽  
Cleft Lip ◽  
Genome Wide Association Study ◽  
Population Level ◽  
Allele Frequencies ◽  
Genome Wide Association ◽  
South American ◽  
Orofacial Clefts ◽  
Public Health Burden ◽  
Genome Wide

AbstractOrofacial clefts (OFCs) are among the most prevalent craniofacial birth defects worldwide and create a significant public health burden. The majority of OFCs are non-syndromic and vary in prevalence by ethnicity. Africans have the lowest prevalence of OFCs (∼ 1/2,500), Asians have the highest prevalence (∼1/500), European and Latin Americans lie somewhere in the middle (∼1/800 and 1/900 respectively). Thus, ethnicity appears to be a major determinant of the risk of developing OFC. The Pittsburgh Orofacial Clefts Multiethnic study was designed to explore this ethnic variance, comprising a large number of families and individuals (∼12,000 individuals) from multiple populations worldwide: US and Europe, Asians, mixed Native American/Caucasians, and Africans. In this current study, we analyzed 2,915 OFC cases, 6,044 unaffected individuals related to the OFC cases, and 2,685 controls with no personal or family history of OFC. Participants were grouped by their ancestry into African, Asian, European, and Central and South American subsets, and genome-wide association run on the combined sample as well as the four ancestry-based groups. We observed 22 associations to cleft lip with or without cleft palate at 18 distinct loci with p-values < 1e-06, including 10 with genome-wide significance (< 5e-08), in the combined sample and within ancestry groups. Three loci - 2p12 (rs62164740, p=6.27e-07), 10q22.2 (rs150952246, p=3.14e-07), and 10q24.32 (rs118107597, p=8.21e-07) are novel. Nine were in or near known OFC loci - PAX7, IRF6, FAM49A, DCAF4L2, 8q24.21, NTN1, WNT3-WNT9B, TANC2, and RHPN2. The majority of the associations were observed only in the combined sample, European, and Central and South American groups. We investigated whether the observed differences in association strength were a) purely due to sample sizes, b) due to systematic allele frequency difference at the population level, or (c) due to the fact certain OFC-causing variants confer different amounts of risk depending on ancestral origin, by comparing effect sizes to observed allele frequencies of the effect allele in our ancestry-based groups. While some of the associations differ due to systematic differences in allele frequencies between groups, others show variation in effect size despite similar frequencies across ancestry groups.

scholarly journals Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate

2009 ◽  
Vol 42 (1) ◽  
pp. 24-26 ◽  
Author(s):  
Elisabeth Mangold ◽  
Kerstin U Ludwig ◽  
Stefanie Birnbaum ◽  
Carlotta Baluardo ◽  
Melissa Ferrian ◽  
...  
Keyword(s):  
Cleft Palate ◽  
Association Study ◽  
Cleft Lip ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Susceptibility Loci ◽  
Genome Wide

scholarly journals Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jianping Yu ◽  
Chaolei Liu ◽  
Hai Lin ◽  
Bin Zhang ◽  
Xiaoxia Li ◽  
...  
Keyword(s):  
Association Study ◽  
Transcriptome Analysis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Growth Responses ◽  
Cd Stress ◽  
New Genes ◽  
Genome Wide ◽  
A Genome ◽  
Natural Variations

Abstract Background Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity. Results In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs. Conclusion The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

scholarly journals The identification of 14 new genes for meat quality traits in chicken using a genome-wide association study

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 458 ◽  
Author(s):  
Yanfa Sun ◽  
Guiping Zhao ◽  
Ranran Liu ◽  
Maiqing Zheng ◽  
Yaodong Hu ◽  
...  
Keyword(s):  
Association Study ◽  
Meat Quality ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Quality Traits ◽  
Meat Quality Traits ◽  
New Genes ◽  
Genome Wide ◽  
A Genome
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