Genome resequencing and bioinformatic analysis of SNP containing candidate genes in the autoimmune vitiligo Smyth line chicken model

LARC patients were sorted according to their radio-responsiveness and patient-derived organoids were established from the respective cancer tissues. Expression profiles for each group were obtained using RNA-seq. Biological and bioinformatic analysis approaches were used in deciphering genes and pathways that participate in the radio-resistance of LARC. Thirty candidate genes encoding proteins involved in radio-responsiveness–related pathways, including the immune system, DNA repair and cell-cycle control, were identified. Interestingly, one of the candidate genes, cathepsin E (CTSE), exhibited differential methylation at the promoter region that was inversely correlated with the radio-resistance of patient-derived organoids, suggesting that methylation status could contribute to radio-responsiveness. On the basis of these results, we plan to pursue development of a gene chip for diagnosing the radio-responsiveness of LARC patients, with the hope that our efforts will ultimately improve the prognosis of LARC patients.

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MO039IDENTIFICATION OF A RECURRENT SYNONYMOUS GENETIC VARIANT IN NPHP3 LEADING TO NEPHRONOPHTHISIS AND CONGENITAL HEPATIC FIBROSIS

Nephrology Dialysis Transplantation ◽

10.1093/ndt/gfab080.0011 ◽

2021 ◽

Vol 36 (Supplement_1) ◽

Author(s):

Eric Olinger ◽

Intisar Al Alawi ◽

Elisa Molinari ◽

Eissa Ali Faqeih ◽

Mohamed Al Hamed ◽

...

Keyword(s):

Candidate Genes ◽

Rna Splicing ◽

Donor Site ◽

Saudi Arabian ◽

Bioinformatic Analysis ◽

Initial Assessment ◽

Splice Donor Site ◽

Uk Biobank ◽

Pathogenic Variants ◽

Exon 20

Abstract Background and Aims Whole exome sequencing (WES) is becoming part of routine clinical and diagnostic practice and has been extensively applied in research studies as well as for diagnostic utility to detect various novel genes and variants. Filtering of variants and scoring variants in terms of pathogenicity still represents a major challenge and may explain why ∼50% of patients remain without diagnosis after initial assessment. Method In this study, we performed WES to determine the genetic cause of a hepato-renal ciliopathy syndrome in a genetically unsolved consanguineous family from Oman with 2 affected children. For variants filtering and annotation Qiagen Clinical Insight tool was used. Database searches for identical alleles in patients with similar phenotypes were performed using Genomics England, UK Biobank and a Saudi Arabian cohort. RNA studies were used to confirm a splicing defect. This research was made possible through access to the data and findings generated by the 100,000 Genomes Project and from UK Biobank, a major biomedical database. Results Initial bioinformatic analysis of WES data from 2 affected sibs excluded obvious pathogenic variants in known genes associated with primary ciliopathy syndromes with liver and kidney phenotypes. However, by manual curation of variants in candidate genes, a rare homozygous synonymous allele in NPHP3 was identified (c.2805C>T; p.(Gly935Gly)), mid-exon 20 and within a region of shared homozygosity on chromosome 3. Correct segregation was confirmed via Sanger sequencing in the parents and the 2 affected sibs. The variant was rare in gnomAD (2/251374 alleles) and was found heterozygously in just one individual within the UK Biobank cohort of 200,000 exomes. Using various in silico tools, the allele was shown to activate a cryptic splice donor site in the middle of exon 20. RT-PCR with sequencing of parental whole blood RNA confirmed alternative splicing leading to frameshift p.Gly935GlyfsTer47. The identical homozygous allele was identified in 2 additional unsolved families within the Genomics England 100,000 Genomes Project and in 1 Saudi Arabian family with similar hepato-renal phenotypes. Conclusion This study shows that automated filtering of WES data may exclude synonymous variants which are pathogenic, especially if they are mid-exon. Here we identified a recurrent synonymous NPHP3 variant leading to a splice defect as the cause of a hepato-renal ciliopathy phenotype in four families. In unsolved cases, rare synonymous alleles in candidate genes need to be reassessed for impact on RNA splicing and possible pathogenicity.

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The Population Structure and Selection Signal Analysis of Shenxian Pigs Based on Genome Resequencing Technology

10.21203/rs.3.rs-244687/v1 ◽

2021 ◽

Author(s):

Diao Liu ◽

Chunlian Lu ◽

Shang Li ◽

Mengyu Jia ◽

Yutao Miao ◽

...

Keyword(s):

Candidate Genes ◽

Meat Quality ◽

Genetic Relationships ◽

Animal Husbandry ◽

Hebei Province ◽

Whole Genome ◽

Genome Resequencing ◽

Large White ◽

Bioinformatics Analyses ◽

Pig Breeds

Abstract Shenxian pigs are the only local black pig of Hebei Province, and were listed in the Genetics of Livestock and Poultry Resources of China in 2016. This breed of pig is considered to be a valuable local pig germplasm genetic resource in China. When compared with other introduced pig breeds, the Shenxian pig breed is characterized with early sexual maturity, short oestrus intervals, large litter sizes, and good meat quality, which are all of good research significance. However, the Shenxian pig variety was previously declared extinct in 2004 due to the introduction of a large number of foreign pig breeds. In order to preserve and study the Shenxian pig breed, the Hebei Zhengnong Animal Husbandry Co., Ltd. was established in Hebei Province for the purpose of preserving the purified Shenxian pig strain. In the present study, in order to understand the genetic variations of Shenxian pigs, identify selected regions related to superior traits, and accelerate the breeding processes of Shenxian pigs, the whole genome of the Shenxian pigs was resequenced and compared with that of large white pigs. The goal was to explore the germplasm characteristics of Shenxian pigs.The results obtained in this research investigation revealed that the genetic relationships of the Shenxian pig breed were complex, and that sub-populations could be identified within the general population. A total of 23M SNP sites were obtained by whole genome resequencing, and 1,509 selected sites were obtained via bioinformatics analyses. It was determined after annotation that a total of 19 genes were enriched in three items of bioengineering, molecular function, and cell composition.During this research investigation, the aforementioned 19 genes were subjected to GO and KEGG analyses. Subsequently, the candidate genes related to cell proliferation were obtained (DMTF1 and WDR5), which were considered to possibly be related to the slow growth and development of Shenxian pigs. In addition, the candidate genes related to lactation were obtained (CSN2 and CSN3). However, no genes related to meat quality traits were successfully screened.

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Gene Set Subtraction Reveals 633 Candidate Genes for Bamboo Culm Wall Thickening

Forests ◽

10.3390/f11121331 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1331

Author(s):

Yaping Hu ◽

Jie Zhou ◽

Zhaoyan Yu ◽

Jiajia Li ◽

Jinfeng Cai ◽

...

Keyword(s):

Candidate Genes ◽

Reference Genome ◽

Wall Thickening ◽

Phyllostachys Edulis ◽

Genome Resequencing ◽

Bamboo Culm ◽

Gene Set ◽

Physiological Processes ◽

Culm Wall ◽

Whole Genome Resequencing

Abundant research has been conducted on the physiological, biochemical, and anatomical aspects of bamboo culm wall thickening, but its molecular mechanism has not yet been investigated. In this study, we performed whole-genome resequencing of Phyllostachys edulis ‘Pachyloen’, Phyllostachys nidularia f. farcta, Phyllostachys heteroclada f. solida with significantly thicker culm walls, and Schizostachyum dumetorum var. xinwuense with extremely thin culm walls. Moreover, we pioneered the innovative use of gene set subtraction to explore candidate genes that regulate bamboo culm wall thickening. A candidate gene set, containing 633 genes, was obtained by eliminating shared genes that help maintain physiological processes after alignment with the P. edulis reference genome. Starch and sucrose, oxidative phosphorylation, and ribosome were the three most important pathways enriched by differentially expressed genes. Although it cannot be used for hyperfine localization of bamboo wall thickness-regulatory genes, gene set reduction narrows down the range of candidate genes at minimal cost and provides new clues for the application of bioinformatics in plant research.

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Identification of ROBO1/2 and SCEL as candidate genes in Kallmann syndrome with emerging bioinformatic analysis

Endocrine ◽

10.1007/s12020-019-02010-y ◽

2019 ◽

Vol 67 (1) ◽

pp. 224-232

Author(s):

Zuobin Zhu ◽

Xiaoxiao Han ◽

Ying Li ◽

Conghui Han ◽

Mengqiong Deng ◽

...

Keyword(s):

Candidate Genes ◽

Bioinformatic Analysis ◽

Kallmann Syndrome

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Identification of candidate genes and mutations in QTL regions for chicken growth using bioinformatic analysis of NGS and SNP-chip data

Frontiers in Genetics ◽

10.3389/fgene.2013.00226 ◽

2013 ◽

Vol 4 ◽

Cited By ~ 20

Author(s):

Muhammad Ahsan ◽

Xidan Li ◽

Andreas E. Lundberg ◽

Marcin Kierczak ◽

Paul B. Siegel ◽

...

Keyword(s):

Candidate Genes ◽

Bioinformatic Analysis ◽

Chip Data ◽

Snp Chip

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Identification of candidate genes for an early-maturing soybean mutant by genome resequencing analysis

Molecular Genetics and Genomics ◽

10.1007/s00438-016-1183-2 ◽

2016 ◽

Vol 291 (4) ◽

pp. 1561-1571 ◽

Cited By ~ 14

Author(s):

Kyung Jun Lee ◽

Dong Sub Kim ◽

Jin-Baek Kim ◽

Sung-Hwan Jo ◽

Si-Yong Kang ◽

...

Keyword(s):

Candidate Genes ◽

Genome Resequencing ◽

Early Maturing

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Integrated in-depth bioinformatic analysis suggests RELCH/KIAA1468, LINC02341, and AKAP11 as candidate genes for ages at menarche and menopause

RESEARCH RESULTS IN BIOMEDICINE ◽

10.18413/2658-6533-2021-7-3-0-2 ◽

2021 ◽

Vol 7 (3) ◽

pp. 220-231

Author(s):

Volodymyr Dvornyk ◽

Keyword(s):

Lipid Metabolism ◽

Cell Survival ◽

Candidate Genes ◽

Bioinformatic Analysis ◽

Age At Menarche ◽

Biological Processes ◽

Genetic Associations ◽

Biological Mechanisms ◽

Natural Menopause ◽

Online Databases

Polymorphisms of the TNFRSF11A and TNFSF11 genes were reported for their association with age at menarche (AAM) and age at natural menopause (ANM). However, the biological mechanisms underlying this association remain largely unclear. The aim of the study: This study was to determine biological processes backing the observed genetic associations. Materials and methods: Fortyfour SNPs were analyzed using in silico approach and ten publicly available online databases and tools. Results: TNFRSF11A and TNFSF11 are highly pleiotropic genes that play a role in many metabolic processes. However, among that variety, lipid metabolism and cell survival and apoptosis seem the most biologically plausible mechanisms, through which these genes contribute to AAM and ANM. The analysis identified several mechanisms underlying the previously determined association of the TNFRSF11A and TNFSF11 genes with AAM and ANM and suggested RELCH/KIAA1468, LINC02341, and AKAP11 as new candidate genes for the traits.

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