A review of SNP heritability estimation methods

Tang, Mingsheng; Wang, Tong; Xue-fen, Zhang

doi:10.1093/bib/bbac067

Cited by 28 publications

(18 citation statements)

References 66 publications

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“…SNPs are among the high‐risk alterations associated with cancer occurrence. 295 85% of SNP are annotated in noncoding regions and related to disease development. These abnormalities could influence the expression and function of lncRNA downstream targets.…”

Section: Lncrnas and Circrnas In Neuroblastomamentioning

confidence: 99%

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LncRNAs and CircRNAs in cancer

Yin

Lin

et al. 2022

MedComm

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It is well known that noncoding RNAs (ncRNAs) cannot encode proteins, but they can play important regulatory roles in tumors by combining with proteins, RNAs, and DNAs. As more and more studies reveal the important roles and underlying mechanisms of long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) in cancer, their huge application potential in cancer therapy cannot be ignored. For example, lncRNAs can be involved in tumor‐related signal transduction pathways, cell cycle control, DNA damage, epigenetic regulation, and microRNA control. A group of studies confirmed that abnormal expression of lncRNAs can affect cancer progression. Furthermore, as covalently closed continuous circular ncRNAs, many recent studies have shown that circRNAs have regulatory effects and other important biological significances in cancer. Interestingly, circRNAs were found to have translational functions. This has greatly attracted people's attention to circRNAs research. In this review, we introduce the important roles of lncRNAs and circRNAs in some representative cancers, respectively. Furthermore, we focus on the biological functions and important clinical therapeutic implications of lnRNAs and circRNAs in neuroblastoma. Our review also focuses on providing rationale and relevant references for novel biomarkers for neuroblastoma diagnosis, prognosis, and treatment.

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Section: Lncrnas and Circrnas In Neuroblastomamentioning

confidence: 99%

“…SNPs are among the high‐risk alterations associated with cancer occurrence 295 . 85% of SNP are annotated in noncoding regions and related to disease development.…”

Section: Lncrnas and Circrnas In Neuroblastomamentioning

confidence: 99%

LncRNAs and CircRNAs in cancer

Yin

Lin

et al. 2022

MedComm

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“…For comparison, we also conducted the univariate GWAS of each of the amygdala nuclei. The SNP-based heritability, representing the phenotypic variance that arises due to the genetics, was also estimated [16]. Second, we discovered gene-level and gene-set associations, explored the functional mechanisms of the significant SNPs, and performed association lookups within the NHGRI-EBI GWAS catalog [17].…”

Section: Introductionmentioning

confidence: 99%

The genetic architecture of human amygdala volumes and their overlap with common brain disorders

et al. 2023

Transl Psychiatry

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The amygdala is a crucial interconnecting structure in the brain that performs several regulatory functions, yet its genetic architectures and involvement in brain disorders remain largely unknown. We carried out the first multivariate genome-wide association study (GWAS) of amygdala subfield volumes in 27,866 UK Biobank individuals. The whole amygdala was segmented into nine nuclei groups using Bayesian amygdala segmentation. The post-GWAS analysis allowed us to identify causal genetic variants in phenotypes at the SNP, locus, and gene levels, as well as genetic overlap with brain health-related traits. We further generalized our GWAS in Adolescent Brain Cognitive Development (ABCD) cohort. The multivariate GWAS identified 98 independent significant variants within 32 genomic loci associated (P < 5 × 10−8) with amygdala volume and its nine nuclei. The univariate GWAS identified significant hits for eight of the ten volumes, tagging 14 independent genomic loci. Overall, 13 of the 14 loci identified in the univariate GWAS were replicated in the multivariate GWAS. The generalization in ABCD cohort supported the GWAS results with the 12q23.2 (RNA gene RP11-210L7.1) being discovered. All of these imaging phenotypes are heritable, with heritability ranging from 15% to 27%. Gene-based analyses revealed pathways relating to cell differentiation/development and ion transporter/homeostasis, with the astrocytes found to be significantly enriched. Pleiotropy analyses revealed shared variants with neurological and psychiatric disorders under the conjFDR threshold of 0.05. These findings advance our understanding of the complex genetic architectures of amygdala and their relevance in neurological and psychiatric disorders.

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“…SNP mainly refers to DNA sequence polymorphism at the genome level, which is the most ideal marker for DNA inheritance and molecular breeding ( Kruglyak, 1997 ). It can be used to establish a variety of analytic models to estimate the degree of heritable variation and phenotypes, thus, it can be used as the biomarker for biological breeding process ( Tang et al, 2022 ). Yao et al (2022) have found the key SNPs in genes of melatonin synthesis in Holstein dairy cows.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis for the melatonin trait associated genes and SNPs in dairy goat (Capra hircus) as the molecular breeding markers

et al. 2023

Front. Genet.

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Previous studies have reported that the endogenous melatonin level is positively associated with the quality and yield of milk of cows. In the current study, a total of 34,921 SNPs involving 1,177 genes were identified in dairy goats by using the whole genome resequencing bulked segregant analysis (BSA) analysis. These SNPs have been used to match the melatonin levels of the dairy goats. Among them, 3 SNPs has been identified to significantly correlate with melatonin levels. These 3 SNPs include CC genotype 147316, GG genotype 147379 and CC genotype 1389193 which all locate in the exon regions of ASMT and MT2 genes. Dairy goats with these SNPs have approximately 5-fold-higher melatonin levels in milk and serum than the average melatonin level detected in the current goat population. If the melatonin level impacts the milk production in goats as in cows, the results strongly suggest that these 3 SNPs can serve as the molecular markers to select the goats having the improved milk quality and yield. This is a goal of our future study.

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A review of SNP heritability estimation methods

Cited by 28 publications

References 66 publications

LncRNAs and CircRNAs in cancer

LncRNAs and CircRNAs in cancer

The genetic architecture of human amygdala volumes and their overlap with common brain disorders

Genome-wide analysis for the melatonin trait associated genes and SNPs in dairy goat (Capra hircus) as the molecular breeding markers

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