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The coefficients of inbreeding revealed by ROH study among inbred individuals belonging to each type of the first cousin marriage: A preliminary report from North India. Genes Genomics 2023; 45:813-825. [PMID: 36807878 DOI: 10.1007/s13258-023-01367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Genome-wide runs of homozygosity (ROH) are appropriate to estimate genomic inbreeding, determine population history, unravel the genetic architecture of complex traits and disorders. OBJECTIVE The study sought to investigate and compare the actual proportion of homozygosity or autozygosity in the genomes of progeny of four subtypes of first cousin mating in humans, using both pedigree and genomic measures for autosomes and sex chromosomes. METHODS For this purpose, Illumina Global Screening Array-24 v1.0 BeadChip followed by cyto-ROH analysis through Illumina Genome Studio was used to characterise the homozygosity in five participants from North Indian state (Uttar Pradesh). PLINK v.1.9 software was used to estimate the genomic inbreeding coefficients viz. ROH-based inbreeding estimate (FROH) and homozygous loci-based inbreeding estimate (FHOM). RESULTS A total of 133 ROH segments were detected with maximum number and genomic coverage in Matrilateral Parallel (MP) type and minimum in outbred individual. ROH pattern revealed that MP type has a higher degree of homozygosity than other subtypes. The comparison of FROH, FHOM, and pedigree-based inbreeding estimate (FPED) showed some difference in theoretical and realised proportion of homozygosity for sex-chromosomal loci but not for autosome for each type of consanguinity. CONCLUSIONS This is the very first study to compare and estimate the pattern of homozygosity among the kindreds of first cousin unions. However, a greater number of individuals from each type of marriage is required for statistical inference of no difference between theoretical and realized homozygosity among different degrees of inbreeding prevalent in humans worldwide.
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Yasmin T, Andres EM, Ashraf K, Basra MAR, Raza MH. Genome-wide analysis of runs of homozygosity in Pakistani controls with no history of speech or language-related developmental phenotypes. Ann Hum Biol 2023; 50:100-107. [PMID: 36786444 PMCID: PMC10284496 DOI: 10.1080/03014460.2023.2180087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND Runs of homozygosity (ROHs) analysis of controls provide a convenient resource to minimize the association of false positive results of disease-associated ROHs and genetic variants for simple and complex disorders in individuals from the same population. Evidence for the value of ROHs to speech or language-related traits is restricted due to the absence of population-matched behaviourally defined controls and limited family-based studies. AIM This study aims to identify common ROHs in the Pakistani population, focussing on the total length and frequency of ROHs of variable sizes, shared ROHs, and their genomic distribution. SUBJECTS AND METHODS We performed homozygosity analysis (in PLINK) of 86 individuals (39 males, 47 females) with no history of speech or language-related phenotypes (controls) who had been genotyped with the Illumina Infinium QC Array-24. RESULTS ROHs of 1-<4 megabases (Mb) were frequent in unrelated individuals. We observed ROHs over 20 Mb among six individuals. Over 30 percent of the identified ROHs were shared among several individuals, indicating consanguinity's effect on the Pakistani population. CONCLUSION Our findings serve as a foundation for family-based genetic studies of consanguineous families with speech or language-related disorders to ultimately narrow the homozygosity regions of interest to identify pathogenic variants.
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Affiliation(s)
- Tahira Yasmin
- Centre for Clinical and Nutritional Chemistry, School of Chemistry, University of The Punjab, Lahore, Pakistan
| | - Erin M. Andres
- Thompson Center for Autism & Neurodevelopment, University of Missouri, Columbia, MO, USA
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, 66045, USA
| | - Komal Ashraf
- Centre for Clinical and Nutritional Chemistry, School of Chemistry, University of The Punjab, Lahore, Pakistan
| | - Muhammad Asim Raza Basra
- Centre for Clinical and Nutritional Chemistry, School of Chemistry, University of The Punjab, Lahore, Pakistan
| | - Muhammad Hashim Raza
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, 66045, USA
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3
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Zhao J, Wei K, Chang C, Xu L, Jiang P, Guo S, Schrodi SJ, He D. DNA Methylation of T Lymphocytes as a Therapeutic Target: Implications for Rheumatoid Arthritis Etiology. Front Immunol 2022; 13:863703. [PMID: 35309322 PMCID: PMC8927780 DOI: 10.3389/fimmu.2022.863703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease that can cause joint damage and disability. Epigenetic variation, especially DNA methylation, has been shown to be involved in almost all the stages of the pathology of RA, from autoantibody production to various self-effector T cells and the defects of protective T cells that can lead to chronic inflammation and erosion of bones and joints. Given the critical role of T cells in the pathology of RA, the regulatory functions of DNA methylation in T cell biology remain unclear. In this review, we elaborate on the relationship between RA pathogenesis and DNA methylation in the context of different T cell populations. We summarize the relevant methylation events in T cell development, differentiation, and T cell-related genes in disease prediction and drug efficacy. Understanding the epigenetic regulation of T cells has the potential to profoundly translate preclinical results into clinical practice and provide a framework for the development of novel, individualized RA therapeutics.
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Affiliation(s)
- Jianan Zhao
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Kai Wei
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Cen Chang
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Lingxia Xu
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Ping Jiang
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Shicheng Guo
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, United States.,Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Steven J Schrodi
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, United States.,Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Dongyi He
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
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Sanglard LP, Huang Y, Gray KA, Linhares DCL, Dekkers JCM, Niederwerder MC, Fernando RL, Serão NVL. Further host-genomic characterization of total antibody response to PRRSV vaccination and its relationship with reproductive performance in commercial sows: genome-wide haplotype and zygosity analyses. Genet Sel Evol 2021; 53:91. [PMID: 34875996 PMCID: PMC8650375 DOI: 10.1186/s12711-021-00676-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Background The possibility of using antibody response (S/P ratio) to PRRSV vaccination measured in crossbred commercial gilts as a genetic indicator for reproductive performance in vaccinated crossbred sows has motivated further studies of the genomic basis of this trait. In this study, we investigated the association of haplotypes and runs of homozygosity (ROH) and heterozygosity (ROHet) with S/P ratio and their impact on reproductive performance. Results There was no association (P-value ≥ 0.18) of S/P ratio with the percentage of ROH or ROHet, or with the percentage of heterozygosity across the whole genome or in the major histocompatibility complex (MHC) region. However, specific ROH and ROHet regions were significantly associated (P-value ≤ 0.01) with S/P ratio on chromosomes 1, 4, 5, 7, 10, 11, 13, and 17 but not (P-value ≥ 0.10) with reproductive performance. With the haplotype-based genome-wide association study (GWAS), additional genomic regions associated with S/P ratio were identified on chromosomes 4, 7, and 9. These regions harbor immune-related genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. Four haplotypes at the identified region on chromosome 7 were also associated with multiple reproductive traits. A haplotype significantly associated with S/P ratio that is located in the MHC region may be in stronger linkage disequilibrium (LD) with the quantitative trait loci (QTL) than the previously identified single nucleotide polymorphism (SNP) (H3GA0020505) given the larger estimate of genetic variance explained by the haplotype than by the SNP. Conclusions Specific ROH and ROHet regions were significantly associated with S/P ratio. The haplotype-based GWAS identified novel QTL for S/P ratio on chromosomes 4, 7, and 9 and confirmed the presence of at least one QTL in the MHC region. The chromosome 7 region was also associated with reproductive performance. These results narrow the search for causal genes in this region and suggest SLA-DOB and TAP2 as potential candidate genes associated with S/P ratio on chromosome 7. These results provide additional opportunities for marker-assisted selection and genomic selection for S/P ratio as genetic indicator for litter size in commercial pig populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00676-5.
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Affiliation(s)
- Leticia P Sanglard
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Yijian Huang
- Smithfield Premium Genetic, Rose Hill, NC, 28458, USA
| | - Kent A Gray
- Smithfield Premium Genetic, Rose Hill, NC, 28458, USA
| | - Daniel C L Linhares
- Department of Veterinary Diagnostic & Production Animal Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Megan C Niederwerder
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, 66506, USA
| | - Rohan L Fernando
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Nick V L Serão
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
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Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle. BMC Genomics 2021; 22:678. [PMID: 34548021 PMCID: PMC8454143 DOI: 10.1186/s12864-021-07992-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle. RESULTS We detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher's exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle. CONCLUSIONS Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.
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Ben-Yosef N, Frampton M, Schiff ER, Daher S, Abu Baker F, Safadi R, Israeli E, Segal AW, Levine AP. Genetic analysis of four consanguineous multiplex families with inflammatory bowel disease. Gastroenterol Rep (Oxf) 2021; 9:521-532. [PMID: 34925849 PMCID: PMC8677555 DOI: 10.1093/gastro/goab007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/03/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
Background Family studies support a genetic predisposition to inflammatory bowel diseases (IBD), but known genetic variants only partially explain the disease heritability. Families with multiple affected individuals potentially harbour rare and high-impact causal variants. Long regions of homozygosity due to recent inbreeding may increase the risk of individuals bearing homozygous loss-of-function variants. This study aimed to identify rare and homozygous genetic variants contributing to IBD. Methods Four families with known consanguinity and multiple cases of IBD were recruited. In a family-specific analysis, we utilised homozygosity mapping complemented by whole-exome sequencing. Results We detected a single region of homozygosity shared by Crohn's disease cases from a family of Druze ancestry, spanning 2.6 Mb containing the NOD2 gene. Whole-exome sequencing did not identify any potentially damaging variants within the region, suggesting that non-coding variation may be involved. In addition, affected individuals in the families harboured several rare and potentially damaging homozygous variants in genes with a role in autophagy and innate immunity including LRRK1, WHAMM, DENND3, and C5. Conclusion This study examined the potential contribution of rare, high-impact homozygous variants in consanguineous families with IBD. While the analysis was not designed to achieve statistical significance, our findings highlight genes or loci that warrant further research. Non-coding variants affecting NOD2 may be of importance in Druze patients with Crohn's disease.
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Affiliation(s)
- Noam Ben-Yosef
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
- Institute of Gastroenterology and Liver disease, Hadassah Medical Center, Jerusalem, Israel
| | - Matthew Frampton
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
| | - Elena R Schiff
- Institute of Ophthalmology, Moorfields Eye Hospital, University College London, London, UK
| | - Saleh Daher
- Institute of Gastroenterology and Liver disease, Hadassah Medical Center, Jerusalem, Israel
| | - Fadi Abu Baker
- Institue of Gastroenterology and Hepatology, Hillel Yaffe Medical Center, Hadera, Israel
| | - Rifaat Safadi
- Institute of Gastroenterology and Liver disease, Hadassah Medical Center, Jerusalem, Israel
| | - Eran Israeli
- Institute of Gastroenterology and Liver disease, E. Wolfson Medical Center, Holon, Israel
| | - Anthony W Segal
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
| | - Adam P Levine
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
- Department of Pathology, University College London, London, UK
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Yang HC, Chen CW, Lin YT, Chu SK. Genetic ancestry plays a central role in population pharmacogenomics. Commun Biol 2021; 4:171. [PMID: 33547344 PMCID: PMC7864978 DOI: 10.1038/s42003-021-01681-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
Recent studies have pointed out the essential role of genetic ancestry in population pharmacogenetics. In this study, we analyzed the whole-genome sequencing data from The 1000 Genomes Project (Phase 3) and the pharmacogenetic information from Drug Bank, PharmGKB, PharmaADME, and Biotransformation. Here we show that ancestry-informative markers are enriched in pharmacogenetic loci, suggesting that trans-ancestry differentiation must be carefully considered in population pharmacogenetics studies. Ancestry-informative pharmacogenetic loci are located in both protein-coding and non-protein-coding regions, illustrating that a whole-genome analysis is necessary for an unbiased examination over pharmacogenetic loci. Finally, those ancestry-informative pharmacogenetic loci that target multiple drugs are often a functional variant, which reflects their importance in biological functions and pathways. In summary, we develop an efficient algorithm for an ultrahigh-dimensional principal component analysis. We create genetic catalogs of ancestry-informative markers and genes. We explore pharmacogenetic patterns and establish a high-accuracy prediction panel of genetic ancestry. Moreover, we construct a genetic ancestry pharmacogenomic database Genetic Ancestry PhD (http://hcyang.stat.sinica.edu.tw/databases/genetic_ancestry_phd/). Hsin-Chou Yang et al. examine population structure in several genomic databases and identify that pharmacogenetic loci are enriched for markers of genetic ancestry. Their results suggest that genetic ancestry must be carefully considered in population pharmacogenetics studies.
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Affiliation(s)
- Hsin-Chou Yang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan. .,Institute of Statistics, National Cheng Kung University, Tainan, Taiwan. .,Institute of Public Health, National Yang-Ming University, Taipei, Taiwan.
| | - Chia-Wei Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Yu-Ting Lin
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Shih-Kai Chu
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
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Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle. Animals (Basel) 2020; 10:ani10081425. [PMID: 32824035 PMCID: PMC7460448 DOI: 10.3390/ani10081425] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of ROH leading to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of homozygosity and their association with important traits in Chinese Wagyu beef cattle. We identified a total of 29,271 ROH segments from 462 animals. Within each animal, an average number of ROH was 63.36 while an average length was 62.19 Mb. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events across all individuals. Of these, nine regions containing 154 candidate genes, were significantly associated with six traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, and carcass length; p < 0.01). Moreover, we found 26 consensus ROH regions with frequencies exceeding 10%, and several regions overlapped with QTLs, which are associated with body weight, calving ease, and stillbirth. Among them, we observed 41 candidate genes, including BCKDHB, MAB21L1, SLC2A13, FGFR3, FGFRL1, CPLX1, CTNNA1, CORT, CTNNBIP1, and NMNAT1, which have been previously reported to be related to body conformation, meat quality, susceptibility, and reproductive traits. In summary, we assessed genome-wide autozygosity patterns and inbreeding levels in Chinese Wagyu beef cattle. Our study identified many candidate regions and genes overlapped with ROH for several important traits, which could be unitized to assist the design of a selection mating strategy in beef cattle.
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Wang Z, Lu X, Yao X, Liu X, Zhao L, Chang S, Zhang T, Niu B, Wang L. Relationship between HLA-DPA1 genetic polymorphism and anembryonic pregnancy. Mol Genet Genomic Med 2020; 8:e1046. [PMID: 31785132 PMCID: PMC6978238 DOI: 10.1002/mgg3.1046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/05/2019] [Accepted: 10/11/2019] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Human leukocyte antigen (HLA)-DP is an HLA class II molecule. Overexpression of HLA class II molecules in placental trophoblast cells may induce pregnancy loss. However, the association between HLA-DP and pregnancy loss remains unclear. HLA-DPA1 is an HLA-DP peptide chain. The objective of this study was to assess the association between HLA-DPA1 genetic polymorphism and anembryonic pregnancy, a type of early pregnancy loss, in the Chinese population. METHODS A case-control study was designed to compare the frequencies of HLA-DPA1 gene polymorphisms in an anembryonic pregnancy group and a control group. Sixty-eight cases and 122 controls were recruited. Statistical analysis was performed to assess the correlation between single-nucleotide polymorphisms (SNPs) and anembryonic pregnancy susceptibility. MassARRAY high-throughput DNA analysis was used to analyze 19 HLA-DPA1 SNPs. To explore how HLA-DPA1 polymorphism could affect anembryonic pregnancy, HLA-DPA1 serum levels were analyzed by ELISA. RESULTS Homozygous typing of rs1431403 (CC and TT) significantly increased the risk of anembryonic pregnancy in the case group (ORCC = 3.13, 95% CI: 1.50-6.53; ORTT = 2.96, 95% CI: 1.31-6.66; ORCC+TT = 3.06, 95% CI: 1.62-5.78). In samples with high HLA-DPA1 levels (≥1,500 pg/ml), the homozygous rs1431403 genotypes (nCC = 21, 43.8%; nTT = 20, 57.1%) were observed more frequently than were heterozygous genotypes. CONCLUSION HLA-DPA1 rs1431403 may be a risk factor for anembryonic pregnancy in the Chinese population. Homozygous rs1431403 genotypes (CC and TT) may increase the risk of anembryonic pregnancy by aberrantly increasing the HLA-DPA1 levels.
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Affiliation(s)
- Zhendong Wang
- Laboratory of Biochemistry and Molecular BiologyShanxi Medical UniversityShanxiChina
| | - Xiaolin Lu
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingP.R. China
| | - Xiuying Yao
- Department of Obstetrics and GynecologyPLA General Hospital 263th Clinical DepartmentBeijingChina
| | - Xinli Liu
- Department of Obstetrics and GynecologyPLA General Hospital 263th Clinical DepartmentBeijingChina
| | - Linlin Zhao
- Department of Obstetrics and GynecologyPLA General Hospital 263th Clinical DepartmentBeijingChina
| | - Shaoyan Chang
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingP.R. China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingP.R. China
| | - Bo Niu
- Laboratory of Biochemistry and Molecular BiologyShanxi Medical UniversityShanxiChina
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingP.R. China
| | - Li Wang
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingP.R. China
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10
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Went M, Sud A, Li N, Johnson DC, Mitchell JS, Kaiser M, Houlston RS. Regions of homozygosity as risk factors for multiple myeloma. Ann Hum Genet 2019; 83:231-238. [PMID: 30768683 PMCID: PMC6563058 DOI: 10.1111/ahg.12304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 11/30/2018] [Accepted: 01/31/2019] [Indexed: 11/29/2022]
Abstract
Genomic regions of homozygosity (ROH), detectable in outbred populations, have been implicated as determinants of inherited risk. To examine whether ROH is associated with risk of multiple myeloma (MM), we performed whole-genome homozygosity analysis using single-nucleotide polymorphism genotype data from 2,282 MM cases and 5,197 controls, with replication in an additional 878 MM cases and 7,083 controls. Globally, the distribution of ROH between cases and controls was not significantly different. However, one ROH at chromosome 9q21, harboring the B-cell transcription factor gene KLF9, showed evidence of a consistent association and may therefore warrant further investigation as a candidate risk factor for MM. Overall, our analysis provides little support for a homozygosity signature being a significant factor in MM risk.
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Affiliation(s)
- Molly Went
- Division of Genetics and EpidemiologyThe Institute of Cancer ResearchLondonUK
- Division of Molecular PathologyThe Institute of Cancer ResearchLondonUK
| | - Amit Sud
- Division of Genetics and EpidemiologyThe Institute of Cancer ResearchLondonUK
| | - Ni Li
- Division of Genetics and EpidemiologyThe Institute of Cancer ResearchLondonUK
| | - David C. Johnson
- Division of Molecular PathologyThe Institute of Cancer ResearchLondonUK
| | | | - Martin Kaiser
- Division of Molecular PathologyThe Institute of Cancer ResearchLondonUK
| | - Richard S. Houlston
- Division of Genetics and EpidemiologyThe Institute of Cancer ResearchLondonUK
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11
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Skryabin NA, Vasilyev SA, Nikitina TV, Zhigalina DI, Savchenko RR, Babushkina NP, Lopatkina ME, Kashevarova AA, Lebedev IN. Runs of homozygosity in spontaneous abortions from families with recurrent pregnancy loss. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recurrent pregnancy loss (RPL) is a severe reproductive pathology with a significant component of unexplained etiology. Extended homozygous regions as a possible etiological factor for RPL were sought in the genomes of embryos. Twenty-two paired first-trimester spontaneously aborted embryos from eleven women with recurrent miscarriage were analyzed. All embryos had normal karyotypes according to metaphase karyotyping and conventional comparative genomic hybridization. SurePrint G3 Human CGH + SNP 4 × 180K microarrays (Agilent Technologies) were used to search for homozygous regions. As a result, 39 runs of homozygosity (ROH) were identified in extraembryonic tissues of 15 abortuses. Verification of recurrent homozygous regions was performed by Sanger sequencing. The presence of occasional heterozygous SNPs was shown in 25 extended ROHs, which may indicate that they did not arise de novo but were inherited from parents. In the course of inheritance in a series of generations, they may accumulate mutations, leading to heterozygosity for several sites in the initially homozygous population-specific regions. Homozygotization of recessive mutations is one of the putative mechanisms of the influence of such inherited ROHs on RPL development. The high frequency of extended ROHs detected in the present study may point to a role of inbreeding in RPL etiology. Homozygous regions may also occur due to uniparental disomy, and abnormalities of genomic imprinting may be another mechanism responsible for the pathological manifestation of ROHs in embryogenesis. Indeed, five predicted imprinted genes were identified within ROHs according to the Geneimprint database: OBSCN, HIST3H2BB, LMX1B, CELF4, and FAM59A. This work reports the first finding of a high frequency of extended ROHs in spontaneously aborted embryos with normal karyotypes from families with RPL.
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Affiliation(s)
- N. A. Skryabin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, RAS
| | - S. A. Vasilyev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, RAS
| | - T. V. Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, RAS
| | - D. I. Zhigalina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, RAS
| | - R. R. Savchenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, RAS
| | - N. P. Babushkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, RAS
| | - M. E. Lopatkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, RAS
| | - A. A. Kashevarova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, RAS
| | - I. N. Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, RAS
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12
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Yang HC, Chen CW. Homozygosity disequilibrium associated with treatment response and its methylation regulation. BMC Proc 2018; 12:45. [PMID: 30263048 PMCID: PMC6156896 DOI: 10.1186/s12919-018-0150-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Homozygosity disequilibrium (HD), indicating a nonrandom pattern of sizable runs of homozygosity that deviates from a random allocation of homozygous and heterozygous genotypes in the genome, is an important phenomenon in population genomics and medical genomics. We performed the first genome-wide study investigating the roles of HD in pharmacogenomics and pharmacoepigenomics by analyzing GAW20 data. We inferred whole-genome profiles of homozygosity intensities and performed genome-wide homozygosity association analyses to identify regions of HD associated with triglyceride (TG) response to fenofibrate by using LOHAS (Loss-of-Heterozygosity Analysis Suite) software. The analysis identified a region of HD contained in MACROD2 at 20p12 to be significantly associated with TG response to fenofibrate. We also examined the common genetic component in TG and methylation responses to fenofibrate. The methylation response to fenofibrate was regarded as a methylation quantitative trait, and our methylation quantitative trait locus analysis identified a cis-acting regulation association with marginal significance between the homozygosity intensity of MACROD2 and the methylation response to fenofibrate. These findings may help delineate the genetic basis of pharmacogenomic and pharmacoepigenomic responses to fenofibrate intervention.
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Affiliation(s)
- Hsin-Chou Yang
- Institute of Statistical Science, Academia Sinica, No 128, Sec 2, Academia Rd, Nankang 115, Taipei, Taiwan
| | - Chia-Wei Chen
- Institute of Statistical Science, Academia Sinica, No 128, Sec 2, Academia Rd, Nankang 115, Taipei, Taiwan
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13
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Szpiech ZA, Blant A, Pemberton TJ. GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification. Bioinformatics 2018; 33:2059-2062. [PMID: 28205676 DOI: 10.1093/bioinformatics/btx102] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 02/15/2017] [Indexed: 12/14/2022] Open
Abstract
Summary Runs of homozygosity (ROH) are important genomic features that manifest when identical-by-descent haplotypes are inherited from parents. Their length distributions and genomic locations are informative about population history and they are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. Here, we present software implementing a model-based method ( Pemberton et al., 2012 ) for inferring ROH in genome-wide SNP datasets that incorporates population-specific parameters and a genotyping error rate as well as provides a length-based classification module to identify biologically interesting classes of ROH. Using simulations, we evaluate the performance of this method. Availability and Implementation GARLIC is written in C ++. Source code and pre-compiled binaries (Windows, OSX and Linux) are hosted on GitHub ( https://github.com/szpiech/garlic ) under the GNU General Public License version 3. Contact zachary.szpiech@ucsf.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California - San Francisco, San Francisco, CA 94158, USA
| | - Alexandra Blant
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Trevor J Pemberton
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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14
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Ceballos FC, Hazelhurst S, Ramsay M. Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data. BMC Genomics 2018; 19:106. [PMID: 29378520 PMCID: PMC5789638 DOI: 10.1186/s12864-018-4489-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/19/2018] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Runs of Homozygosity (ROH) are genomic regions where identical haplotypes are inherited from each parent. Since their first detection due to technological advances in the late 1990s, ROHs have been shedding light on human population history and deciphering the genetic basis of monogenic and complex traits and diseases. ROH studies have predominantly exploited SNP array data, but are gradually moving to whole genome sequence (WGS) data as it becomes available. WGS data, covering more genetic variability, can add value to ROH studies, but require additional considerations during analysis. RESULTS Using SNP array and low coverage WGS data from 1885 individuals from 20 world populations, our aims were to compare ROH from the two datasets and to establish software conditions to get comparable results, thus providing guidelines for combining disparate datasets in joint ROH analyses. By allowing heterozygous SNPs per window, using the PLINK homozygosity function and non-parametric analysis, we were able to obtain non-significant differences in number ROH, mean ROH size and total sum of ROH between data sets using the different technologies for almost all populations. CONCLUSIONS By allowing 3 heterozygous SNPs per ROH when dealing with WGS low coverage data, it is possible to establish meaningful comparisons between data using SNP array and WGS low coverage technologies.
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Affiliation(s)
- Francisco C Ceballos
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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15
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Ceballos FC, Joshi PK, Clark DW, Ramsay M, Wilson JF. Runs of homozygosity: windows into population history and trait architecture. Nat Rev Genet 2018; 19:220-234. [PMID: 29335644 DOI: 10.1038/nrg.2017.109] [Citation(s) in RCA: 361] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Long runs of homozygosity (ROH) arise when identical haplotypes are inherited from each parent and thus a long tract of genotypes is homozygous. Cousin marriage or inbreeding gives rise to such autozygosity; however, genome-wide data reveal that ROH are universally common in human genomes even among outbred individuals. The number and length of ROH reflect individual demographic history, while the homozygosity burden can be used to investigate the genetic architecture of complex disease. We discuss how to identify ROH in genome-wide microarray and sequence data, their distribution in human populations and their application to the understanding of inbreeding depression and disease risk.
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Affiliation(s)
- Francisco C Ceballos
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa.,Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - David W Clark
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Braamfontein 2000, Johannesburg, South Africa
| | - James F Wilson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK.,Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
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16
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Blant A, Kwong M, Szpiech ZA, Pemberton TJ. Weighted likelihood inference of genomic autozygosity patterns in dense genotype data. BMC Genomics 2017; 18:928. [PMID: 29191164 PMCID: PMC5709839 DOI: 10.1186/s12864-017-4312-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/16/2017] [Indexed: 12/14/2022] Open
Abstract
Background Genomic regions of autozygosity (ROA) arise when an individual is homozygous for haplotypes inherited identical-by-descent from ancestors shared by both parents. Over the past decade, they have gained importance for understanding evolutionary history and the genetic basis of complex diseases and traits. However, methods to infer ROA in dense genotype data have not evolved in step with advances in genome technology that now enable us to rapidly create large high-resolution genotype datasets, limiting our ability to investigate their constituent ROA patterns. Methods We report a weighted likelihood approach for inferring ROA in dense genotype data that accounts for autocorrelation among genotyped positions and the possibilities of unobserved mutation and recombination events, and variability in the confidence of individual genotype calls in whole genome sequence (WGS) data. Results Forward-time genetic simulations under two demographic scenarios that reflect situations where inbreeding and its effect on fitness are of interest suggest this approach is better powered than existing state-of-the-art methods to infer ROA at marker densities consistent with WGS and popular microarray genotyping platforms used in human and non-human studies. Moreover, we present evidence that suggests this approach is able to distinguish ROA arising via consanguinity from ROA arising via endogamy. Using subsets of The 1000 Genomes Project Phase 3 data we show that, relative to WGS, intermediate and long ROA are captured robustly with popular microarray platforms, while detection of short ROA is more variable and improves with marker density. Worldwide ROA patterns inferred from WGS data are found to accord well with those previously reported on the basis of microarray genotype data. Finally, we highlight the potential of this approach to detect genomic regions enriched for autozygosity signals in one group relative to another based upon comparisons of per-individual autozygosity likelihoods instead of inferred ROA frequencies. Conclusions This weighted likelihood ROA inference approach can assist population- and disease-geneticists working with a wide variety of data types and species to explore ROA patterns and to identify genomic regions with differential ROA signals among groups, thereby advancing our understanding of evolutionary history and the role of recessive variation in phenotypic variation and disease. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4312-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra Blant
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Michelle Kwong
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Trevor J Pemberton
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
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17
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Abstract
Homozygosity disequilibrium (HD) describes a nonrandom pattern of sizable runs of homozygosity (ROH) that deviated from a random distribution of homozygotes and heterozygotes in the genome. In this study, we developed a double-weight local polynomial model for estimating homozygosity intensity. This new estimation method enables considering the local property and genetic information of homozygosity in the human genome when detecting regions of HD. By using this new method, we estimated whole-genome homozygosity intensities by analyzing real whole-genome sequencing data of 959 related individuals from 20 large pedigrees provided by Genetic Analysis Workshop 19 (GAW19). Through the analysis, we derived the distribution of HD in the human genome and provided evidence for the genetic component of natural variation in HD. Generalized estimating equation analysis for 855 related individuals was performed to identify regions of HD associated with diastolic blood pressure (DBP), systolic blood pressure, and hypertension (HTN), with concomitant adjustment for age and sex. We identified one DBP-associated and 2 HTN-associated regions of HD. We also studied the gene regulation of HD by analyzing the real whole-genome transcription data of 647 individuals. A set of gene expressions regulated by the DBP- and HTN-associated regions of HD was identified. Finally, we conducted simulation studies to evaluate the performance of our homozygosity association test. The results showed that the association test had a high power and that type 1 error was controlled. The methods have been integrated into our developed Loss-of-Heterozygosity Analysis Suite software, which can be downloaded at http://www.stat.sinica.edu.tw/hsinchou/genetics/loh/LOHAS.htm.
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Affiliation(s)
- Hsin-Chou Yang
- Institute of Statistical Science, Academia Sinica, Nankang 115, Taipei, Taiwan
| | - Yu-Ting Lin
- Institute of Statistical Science, Academia Sinica, Nankang 115, Taipei, Taiwan
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18
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Abstract
CONTEXT Inbreeding increases the level of homozygotes for autosomal recessive disorders and is the major objective in clinical studies. The prevalence of consanguinity and the degree of inbreeding vary from one population to another depending on ethnicity, religion, culture and geography. Global epidemiological studies have revealed that consanguineous unions have been significantly associated with increased susceptibility to various forms of inherited diseases. OBJECTIVE The study aimed to determine the role of consanguinity in human health and to highlight the associated risks for various diseases or disorders. METHODS PubMed and Google Scholar search engines were used to explore the published literature on consanguinity and its associated risks using the key words "consanguinity", "prevalence", "inbreeding depression", "coefficient of inbreeding", "child health", "mortality", "human health", "homozygosity" and "complex diseases" in different combinations. The studies were screened for eligibility on the basis of their epidemiological relevance. RESULTS This comprehensive assessment highlights the deleterious consequences in populations with a higher prevalence of consanguinity among different countries worldwide. CONCLUSIONS To avoid the inbreeding load there is the need to improve socioeconomic and educational status and to increase public awareness of reproductive health and anticipated deleterious effects. Pre-marital and pre-conception counselling of consanguineous populations should be an integral part of health policy to train people and make people aware of its harmful consequences. Furthermore, runs of homozygosity (ROH) and whole-exome sequencing (WES) are useful tools in exploring new genomic signatures for the cause of inbreeding depression.
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Affiliation(s)
- Mohd Fareed
- a Human Genetics and Toxicology Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences , Aligarh Muslim University , Aligarh , Uttar Pradesh , India.,b Centre for Biodiversity Studies, School of Biosciences and Biotechnology , Baba Ghulam Shah Badshah University , Rajouri , Jammu and Kashmir , India
| | - Mohammad Afzal
- a Human Genetics and Toxicology Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences , Aligarh Muslim University , Aligarh , Uttar Pradesh , India
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19
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König IR, Auerbach J, Gola D, Held E, Holzinger ER, Legault MA, Sun R, Tintle N, Yang HC. Machine learning and data mining in complex genomic data--a review on the lessons learned in Genetic Analysis Workshop 19. BMC Genet 2016; 17 Suppl 2:1. [PMID: 26866367 PMCID: PMC4895282 DOI: 10.1186/s12863-015-0315-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In the analysis of current genomic data, application of machine learning and data mining techniques has become more attractive given the rising complexity of the projects. As part of the Genetic Analysis Workshop 19, approaches from this domain were explored, mostly motivated from two starting points. First, assuming an underlying structure in the genomic data, data mining might identify this and thus improve downstream association analyses. Second, computational methods for machine learning need to be developed further to efficiently deal with the current wealth of data.In the course of discussing results and experiences from the machine learning and data mining approaches, six common messages were extracted. These depict the current state of these approaches in the application to complex genomic data. Although some challenges remain for future studies, important forward steps were taken in the integration of different data types and the evaluation of the evidence. Mining the data for underlying genetic or phenotypic structure and using this information in subsequent analyses proved to be extremely helpful and is likely to become of even greater use with more complex data sets.
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Affiliation(s)
- Inke R König
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.
| | - Jonathan Auerbach
- Department of Statistics, Columbia University, New York, NY, 10027, USA.
| | - Damian Gola
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.
| | - Elizabeth Held
- Department of Mathematics, Iowa State University, Ames, IA, 50011, USA.
| | - Emily R Holzinger
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 21224, USA.
| | - Marc-André Legault
- Université de Montréal, Faculty of Medicine, 2900 Chemin de la Tour, Montreal, QC, H3T 1N8, Canada.
| | - Rui Sun
- Division of Biostatistics, School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, Hong Kong SAR.
| | - Nathan Tintle
- Department of Mathematics, Statistics and Computer Science, Dordt College, Sioux Center, IA, 51250, USA.
| | - Hsin-Chou Yang
- Institute of Statistical Science, Academia Sinica, Nankang 115, Taipei, Taiwan.
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20
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Sud A, Cooke R, Swerdlow AJ, Houlston RS. Genome-wide homozygosity signature and risk of Hodgkin lymphoma. Sci Rep 2015; 5:14315. [PMID: 26391888 PMCID: PMC4585760 DOI: 10.1038/srep14315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/25/2015] [Indexed: 12/11/2022] Open
Abstract
Recent studies have reported that regions of homozygosity (ROH) in the genome are detectable in outbred populations and can be associated with an increased risk of malignancy. To examine whether homozygosity is associated with an increased risk of developing Hodgkin lymphoma (HL) we analysed 589 HL cases and 5,199 controls genotyped for 484,072 tag single nucleotide polymorphisms (SNPs). Across the genome the cumulative distribution of ROH was not significantly different between cases and controls. Seven ROH at 4q22.3, 4q32.2, 7p12.3-14.1, 7p22.2, 10p11.22-23, 19q13.12-2 and 19p13.2 were associated with HL risk at P < 0.01. Intriguingly 4q22.3 harbours an ROH to which the nuclear factor NF-kappa-B p105 subunit (NFKB1) maps (P = 0.002). The ROH at 19q13.12-2 has previously been implicated in B-cell precursor acute lymphoblastic leukaemia. Aside from these observations which require validation, it is unlikely that levels of measured homozygosity caused by autozygosity, uniparental isodisomy or hemizygosity play a major role in defining HL risk in predominantly outbred populations.
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Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Anthony J. Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
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21
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Butler JM, Sharif U, Ali M, McKibbin M, Thompson JP, Gale R, Yang YC, Inglehearn C, Paraoan L. A missense variant in CST3 exerts a recessive effect on susceptibility to age-related macular degeneration resembling its association with Alzheimer's disease. Hum Genet 2015; 134:705-15. [PMID: 25893795 PMCID: PMC4460273 DOI: 10.1007/s00439-015-1552-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/05/2015] [Indexed: 12/27/2022]
Abstract
Age-related macular degeneration (AMD) and Alzheimer's disease (AD) are degenerative, multifactorial diseases involving age-related accumulation of extracellular deposits linked to dysregulation of protein homeostasis. Here, we strengthen the evidence that an nsSNP (p.Ala25Thr) in the cysteine proteinase inhibitor cystatin C gene CST3, previously confirmed by meta-analysis to be associated with AD, is associated with exudative AMD. To our knowledge, this is the first report highlighting a genetic variant that increases the risk of developing both AD and AMD. Furthermore, we demonstrate that the risk associated with the mutant allele follows a recessive model for both diseases. We perform an AMD-CST3 case-control study genotyping 350 exudative AMD Caucasian individuals. Bringing together our data with the previously reported AMD-CST3 association study, the evidence of a recessive effect on AMD risk is strengthened (OR = 1.89, P = 0.005). This effect closely resembles the AD-CST3 recessive effect (OR = 1.73, P = 0.005) previously established by meta-analysis. This resemblance is substantiated by the high correlation between CST3 genotype and effect size across the two diseases (R(2) = 0.978). A recessive effect is in line with the known function of cystatin C, a potent enzyme inhibitor. Its potency means that, in heterozygous individuals, a single functional allele is sufficient to maintain its inhibitory function; only homozygous individuals will lack this form of proteolytic regulation. Our findings support the hypothesis that recessively acting variants account for some of the missing heritability of multifactorial diseases. Replacement therapy represents a translational opportunity for individuals homozygous for the mutant allele.
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Affiliation(s)
- Joe M. Butler
- />Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L69 3GA UK
| | - Umar Sharif
- />Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L69 3GA UK
| | - Manir Ali
- />Ophthalmology and Neuroscience, University of Leeds, Leeds, LS9 7TF UK
| | - Martin McKibbin
- />Ophthalmology Department, St James’s University Hospital, Leeds, LS9 7TF UK
| | - Joseph P. Thompson
- />Ophthalmology and Neuroscience, University of Leeds, Leeds, LS9 7TF UK
| | - Richard Gale
- />Ophthalmology Department, The York Hospital, York, YO31 8HE UK
| | - Yit C. Yang
- />Ophthalmology, The Royal Wolverhampton NHS Trust, Wolverhampton, WV10 0QP UK
| | - Chris Inglehearn
- />Ophthalmology and Neuroscience, University of Leeds, Leeds, LS9 7TF UK
| | - Luminita Paraoan
- />Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L69 3GA UK
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22
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Mukherjee S, Guha S, Ikeda M, Iwata N, Malhotra AK, Pe'er I, Darvasi A, Lencz T. Excess of homozygosity in the major histocompatibility complex in schizophrenia. Hum Mol Genet 2014; 23:6088-95. [PMID: 24943592 PMCID: PMC4204767 DOI: 10.1093/hmg/ddu308] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 04/11/2014] [Accepted: 06/12/2014] [Indexed: 01/20/2023] Open
Abstract
Genome-wide association studies (GWAS) in schizophrenia have focused on additive allelic effects to identify disease risk loci. In order to examine potential recessive effects, we applied a novel approach to identify regions of excess homozygosity in an ethnically homogenous cohort: 904 schizophrenia cases and 1640 controls drawn from the Ashkenazi Jewish (AJ) population. Genome-wide examination of runs of homozygosity identified an excess in cases localized to the major histocompatibility complex (MHC). To refine this signal, we used the recently developed GERMLINE algorithm to identify chromosomal segments shared identical-by-descent (IBD) and compared homozygosity at such segments in cases and controls. We found a significant excess of homozygosity in schizophrenia cases compared with controls in the MHC (P-value = 0.003). An independent replication cohort of 548 schizophrenia cases from Japan and 542 matched healthy controls demonstrated similar effects. The strongest case-control recessive effects (P = 8.81 × 10(-8)) were localized to a 53-kb region near HLA-A, in a segment encompassing three poorly annotated genes, TRIM10, TRIM15 and TRIM40. At the same time, an adjacent segment in the Class I MHC demonstrated clear additive effects on schizophrenia risk, demonstrating the complexity of association in the MHC and the ability of our IBD approach to refine localization of broad signals derived from conventional GWAS. In sum, homozygosity in the classical MHC region appears to convey significant risk for schizophrenia, consistent with the ecological literature suggesting that homozygosity at the MHC locus may be associated with vulnerability to disease.
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Affiliation(s)
- Semanti Mukherjee
- The Zucker Hillside Hospital, Psychiatry Research, 75-59 263rd Street, Glen Oaks, NY 11004, USA, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA,
| | - Saurav Guha
- The Zucker Hillside Hospital, Psychiatry Research, 75-59 263rd Street, Glen Oaks, NY 11004, USA, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA
| | - Masashi Ikeda
- Fujita Health University School of Medicine, 1-98 Kutsukake-cho Dengakugakubo, Toyoake, Aichi 470-1192, Japan
| | - Nakao Iwata
- Fujita Health University School of Medicine, 1-98 Kutsukake-cho Dengakugakubo, Toyoake, Aichi 470-1192, Japan
| | - Anil K Malhotra
- The Zucker Hillside Hospital, Psychiatry Research, 75-59 263rd Street, Glen Oaks, NY 11004, USA, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA, Hofstra University School of Medicine, 500 Hofstra University, Hempstead, NY 11549, USA
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY 10027, USA and
| | - Ariel Darvasi
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Todd Lencz
- The Zucker Hillside Hospital, Psychiatry Research, 75-59 263rd Street, Glen Oaks, NY 11004, USA, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA, Hofstra University School of Medicine, 500 Hofstra University, Hempstead, NY 11549, USA,
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23
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Abstract
Homozygosity disequilibrium (HD), a nonrandom sizable run of homozygosity in the genome, may be related to the evolution of populations and may also confer susceptibility to disease. No studies have investigated HD using whole genome sequencing (WGS) analysis. In this study, we used an enhanced version of Loss-Of-Heterozygosity Analysis Suite (LOHAS) software to investigate HD through analysis of real and simulated WGS data sets provided by Genetic Analysis Workshop 18. Using a local polynomial model, we derived whole-genome profiles of homozygosity intensities for 959 individuals and characterized the patterns of HD. Generalized estimating equation analysis for 855 related samples was performed to examine the association between patterns of HD and 3 phenotypes of interest, namely diastolic blood pressure, systolic blood pressure, and hypertension status, with covariate adjustments for age and gender. We found that 4.48% of individuals in this study carried sizable runs of homozygosity (ROHs). Distributions of the length of ROHs were derived and revealed a familial aggregation of HD. Genome-wide homozygosity association analysis identified 5 and 3 ROHs associated with diastolic blood pressure and hypertension, respectively. These regions contain genes associated with calcium channels (CACNA1S), renin catalysis (REN), blood groups (ABO), apolipoprotein (APOA5), and cardiovascular diseases (RASGRP1). Simulation studies showed that our homozygosity association tests controlled type 1 error well and had a promising power. This study provides a useful analysis tool for studying HD and allows us to gain a deeper understanding of HD in the human genome.
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Affiliation(s)
- Hsin-Chou Yang
- Institute of Statistical Science, Academia Sinica, Nankang 115, Taipei, Taiwan
| | - Han-Wei Li
- Institute of Statistical Science, Academia Sinica, Nankang 115, Taipei, Taiwan
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24
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Runs of homozygosity and a cluster of vulvar cancer in young Australian Aboriginal women. Gynecol Oncol 2014; 133:421-6. [PMID: 24690477 DOI: 10.1016/j.ygyno.2014.03.566] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/20/2014] [Accepted: 03/23/2014] [Indexed: 11/20/2022]
Abstract
OBJECTIVE A cluster of vulvar cancer exists in young Aboriginal women living in remote communities in Arnhem Land, Australia. A genetic case-control study was undertaken involving 30 cases of invasive vulvar cancer and its precursor lesion, high-grade vulvar intraepithelial neoplasia (VIN), and 61 controls, matched for age and community of residence. It was hypothesized that this small, isolated population may exhibit increased autozygosity, implicating recessive effects as a possible mechanism for increased susceptibility to vulvar cancer. METHODS Genotyping data from saliva samples were used to identify runs of homozygosity (ROH) in order to calculate estimates of genome-wide homozygosity. RESULTS No evidence of an effect of genome-wide homozygosity on vulvar cancer and VIN in East Arnhem women was found, nor was any individual ROH found to be significantly associated with case status. This study found further evidence supporting an association between previous diagnosis of CIN and diagnosis of vulvar cancer or VIN, but found no association with any other medical history variable. CONCLUSIONS These findings do not eliminate the possibility of genetic risk factors being involved in this cancer cluster, but rather suggest that alternative analytical strategies and genetic models should be explored.
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Ghani M, Sato C, Lee JH, Reitz C, Moreno D, Mayeux R, St George-Hyslop P, Rogaeva E. Evidence of recessive Alzheimer disease loci in a Caribbean Hispanic data set: genome-wide survey of runs of homozygosity. JAMA Neurol 2013; 70:1261-7. [PMID: 23978990 PMCID: PMC3991012 DOI: 10.1001/jamaneurol.2013.3545] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
IMPORTANCE The search for novel Alzheimer disease (AD) genes or pathologic mutations within known AD loci is ongoing. The development of array technologies has helped to identify rare recessive mutations among long runs of homozygosity (ROHs), in which both parental alleles are identical. Caribbean Hispanics are known to have an elevated risk for AD and tend to have large families with evidence of inbreeding. OBJECTIVE To test the hypothesis that the late-onset AD in a Caribbean Hispanic population might be explained in part by the homozygosity of unknown loci that could harbor recessive AD risk haplotypes or pathologic mutations. DESIGN We used genome-wide array data to identify ROHs (>1 megabase) and conducted global burden and locus-specific ROH analyses. SETTING A whole-genome case-control ROH study. PARTICIPANTS A Caribbean Hispanic data set of 547 unrelated cases (48.8% with familial AD) and 542 controls collected from a population known to have a 3-fold higher risk of AD vs non-Hispanics in the same community. Based on a Structure program analysis, our data set consisted of African Hispanic (207 cases and 192 controls) and European Hispanic (329 cases and 326 controls) participants. EXPOSURE Alzheimer disease risk genes. MAIN OUTCOMES AND MEASURES We calculated the total and mean lengths of the ROHs per sample. Global burden measurements among autosomal chromosomes were investigated in cases vs controls. Pools of overlapping ROH segments (consensus regions) were identified, and the case to control ratio was calculated for each consensus region. We formulated the tested hypothesis before data collection. RESULTS In total, we identified 17 137 autosomal regions with ROHs. The mean length of the ROH per person was significantly greater in cases vs controls (P = .0039), and this association was stronger with familial AD (P = .0005). Among the European Hispanics, a consensus region at the EXOC4 locus was significantly associated with AD even after correction for multiple testing (empirical P value 1 [EMP1], .0001; EMP2, .002; 21 AD cases vs 2 controls). Among the African Hispanic subset, the most significant but nominal association was observed for CTNNA3, a well-known AD gene candidate (EMP1, .002; 10 AD cases vs 0 controls). CONCLUSIONS AND RELEVANCE Our results show that ROHs could significantly contribute to the etiology of AD. Future studies would require the analysis of larger, relatively inbred data sets that might reveal novel recessive AD genes. The next step is to conduct sequencing of top significant loci in a subset of samples with overlapping ROHs.
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Affiliation(s)
- Mahdi Ghani
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Christine Sato
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Joseph H Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Medicine, College of Physicians and Surgeons, Columbia University, New York, New York3Department of Epidemiolo
| | - Christiane Reitz
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Danielle Moreno
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Peter St George-Hyslop
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada4Department of Medicine, University of Toronto, Toronto, Ontario, Canada5Cambridge Institute for Medical Research and Department of Clinical Neuroscienc
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada4Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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Multiple sclerosis genetics is dead. Mult Scler Relat Disord 2013; 2:156-61. [DOI: 10.1016/j.msard.2012.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 11/24/2022]
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Ruyssen-Witrand A, Constantin A, Cambon-Thomsen A, Thomsen M. New insights into the genetics of immune responses in rheumatoid arthritis. ACTA ACUST UNITED AC 2013; 80:105-18. [PMID: 22835281 DOI: 10.1111/j.1399-0039.2012.01939.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Rheumatoid arthritis (RA) is a common autoimmune disease with a strong genetic component. Numerous aberrant immune responses have been described during the evolution of the disease. In later years, the appearance of anti-citrullinated protein antibodies (ACPAs) has become a hallmark for the diagnosis and prognosis of RA. The post-translational transformation of arginine residues of proteins and peptides into citrulline (citrullination) is a natural process in the body, but for unknown reasons autoreactivity towards citrullinated residues may develop in disposed individuals. ACPAs are often found years before clinical manifestations. ACPAs are present in about 70% of RA patients and constitute an important disease marker, distinguishing patient groups with different prognoses and different responses to various treatments. Inside the human leukocyte antigen (HLA) region, some HLA-DRB1 alleles are strongly associated with their production. Genome-wide association studies in large patient cohorts have defined a great number of single nucleotide polymorphisms (SNPs) outside of the HLA region that are associated with ACPA positive (ACPA+) RA. The SNPs are generally located close to or within genes involved in the immune response or signal transduction in immune cells. Some environmental factors such as tobacco smoking are also positively correlated with ACPA production. In this review, we will describe the genes and loci associated with ACPA+ RA or ACPA- RA and attempt to clarify their potential role in the development of the disease.
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Wang C, Xu Z, Jin G, Hu Z, Dai J, Ma H, Jiang Y, Hu L, Chu M, Cao S, Shen H. Genome-wide analysis of runs of homozygosity identifies new susceptibility regions of lung cancer in Han Chinese. J Biomed Res 2013; 27:208-14. [PMID: 23720676 PMCID: PMC3664727 DOI: 10.7555/jbr.27.20130017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 02/27/2013] [Accepted: 03/14/2013] [Indexed: 12/02/2022] Open
Abstract
Runs of homozygosity (ROHs) are a class of important but poorly studied genomic variations and may be involved in individual susceptibility to diseases. To better understand ROH and its relationship with lung cancer, we performed a genome-wide ROH analysis of a subset of a previous genome-wide case-control study (1,473 cases and 1,962 controls) in a Han Chinese population. ROHs were classified into two classes, based on lengths, intermediate and long ROHs, to evaluate their association with lung cancer risk using existing genome-wide single nucleotide polymorphism (SNP) data. We found that the overall level of intermediate ROHs was significantly associated with a decreased risk of lung cancer (odds ratio = 0.63; 95% confidence interval: 0.51-0.77; P = 4.78×10−6 ), while the long ROHs seemed to be a risk factor of lung cancer. We also identified one ROH region at 14q23.1 that was consistently associated with lung cancer risk in the study. These results indicated that ROHs may be a new class of variation which may be associated with lung cancer risk, and genetic variants at 14q23.1 may be involved in the development of lung cancer.
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Affiliation(s)
- Cheng Wang
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
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Freidin MB, Bragina EY, Saltykova IV, Deeva EV, Ogorodova LM, Puzyrev VP. Effect of additional disease (Comorbidity) on association of allergic rhinitis with KCNE4 gene rs12621643 variant. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413040054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Boonpeng H, Yusoff K. The utility of copy number variation (CNV) in studies of hypertension-related left ventricular hypertrophy (LVH): rationale, potential and challenges. Mol Cytogenet 2013; 6:8. [PMID: 23448375 PMCID: PMC3599593 DOI: 10.1186/1755-8166-6-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 01/03/2013] [Indexed: 01/08/2023] Open
Abstract
The ultimate goal of human genetics is to understand the role of genome variation in elucidating human traits and diseases. Besides single nucleotide polymorphism (SNP), copy number variation (CNV), defined as gains or losses of a DNA segment larger than 1 kb, has recently emerged as an important tool in understanding heritable source of human genomic differences. It has been shown to contribute to genetic susceptibility of various common and complex diseases. Despite a handful of publications, its role in cardiovascular diseases remains largely unknown. Here, we deliberate on the currently available technologies for CNV detection. The possible utility and the potential roles of CNV in exploring the mechanisms of cardiac remodeling in hypertension will also be addressed. Finally, we discuss the challenges for investigations of CNV in cardiovascular diseases and its possible implications in diagnosis of hypertension-related left ventricular hypertrophy (LVH).
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Affiliation(s)
- Hoh Boonpeng
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Jalan Hospital, Sungai, Buloh, 47000, Malaysia.
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