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Identification of ATP2B4 Regulatory Element Containing Functional Genetic Variants Associated with Severe Malaria. Int J Mol Sci 2022; 23:ijms23094849. [PMID: 35563239 PMCID: PMC9101746 DOI: 10.3390/ijms23094849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 12/04/2022] Open
Abstract
Genome-wide association studies for severe malaria (SM) have identified 30 genetic variants mostly located in non-coding regions. Here, we aimed to identify potential causal genetic variants located in these loci and demonstrate their functional activity. We systematically investigated the regulatory effect of the SNPs in linkage disequilibrium (LD) with the malaria-associated genetic variants. Annotating and prioritizing genetic variants led to the identification of a regulatory region containing five ATP2B4 SNPs in LD with rs10900585. We found significant associations between SM and rs10900585 and our candidate SNPs (rs11240734, rs1541252, rs1541253, rs1541254, and rs1541255) in a Senegalese population. Then, we demonstrated that both individual SNPs and the combination of SNPs had regulatory effects. Moreover, CRISPR/Cas9-mediated deletion of this region decreased ATP2B4 transcript and protein levels and increased Ca2+ intracellular concentration in the K562 cell line. Our data demonstrate that severe malaria-associated genetic variants alter the expression of ATP2B4 encoding a plasma membrane calcium-transporting ATPase 4 (PMCA4) expressed on red blood cells. Altering the activity of this regulatory element affects the risk of SM, likely through calcium concentration effect on parasitaemia.
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Al Bkhetan Z, Chana G, Soon Ong C, Goudey B, Ramamohanarao K. eQTLHap: a tool for comprehensive eQTL analysis considering haplotypic and genotypic effects. Brief Bioinform 2021; 22:6214641. [PMID: 33834181 DOI: 10.1093/bib/bbab093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The high accuracy of recent haplotype phasing tools is enabling the integration of haplotype (or phase) information more widely in genetic investigations. One such possibility is phase-aware expression quantitative trait loci (eQTL) analysis, where haplotype-based analysis has the potential to detect associations that may otherwise be missed by standard SNP-based approaches. RESULTS We present eQTLHap, a novel method to investigate associations between gene expression and genetic variants, considering their haplotypic and genotypic effect. Using multiple simulations based on real data, we demonstrate that phase-aware eQTL analysis significantly outperforms typical SNP-based methods when the causal genetic architecture involves multiple SNPs. We show that phase-aware eQTL analysis is robust to phasing errors, showing only a minor impact ($<4\%$) on sensitivity. Applying eQTLHap to real GEUVADIS and GTEx datasets detects numerous novel eQTLs undetected by a single-SNP approach, with 22 eQTLs replicating across studies or tissue types, highlighting the utility of phase-aware eQTL analysis. AVAILABILITY AND IMPLEMENTATION https://github.com/ziadbkh/eQTLHap. CONTACT ziad.albkhetan@gmail.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Briefings in Bioinformatics online.
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Affiliation(s)
- Ziad Al Bkhetan
- School of Computing and Information Systems, The University of Melbourne, Parkville, 3010, Australia
| | - Gursharan Chana
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, 3010, Australia
| | | | - Benjamin Goudey
- School of Computing and Information Systems, The University of Melbourne, Parkville, 3010, Australia.,IBM Australia Research, Southgate, Victoria, Australia
| | - Kotagiri Ramamohanarao
- School of Computing and Information Systems, The University of Melbourne, Parkville, 3010, Australia
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Reichman RD, Gaynor SC, Monson ET, Gaine ME, Parsons MG, Zandi PP, Potash JB, Willour VL. Targeted sequencing of the LRRTM gene family in suicide attempters with bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 2020; 183:128-139. [PMID: 31854516 PMCID: PMC8380126 DOI: 10.1002/ajmg.b.32767] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/17/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022]
Abstract
Glutamatergic signaling is the primary excitatory neurotransmission pathway in the brain, and its relationship to neuropsychiatric disorders is of considerable interest. Our previous attempted suicide genome-wide association study, and numerous studies investigating gene expression, genetic variation, and DNA methylation have implicated aberrant glutamatergic signaling in suicide risk. The glutamatergic pathway gene LRRTM4 was an associated gene identified in our attempted suicide genome-wide association study, with association support seen primarily in females. Recent evidence has also shown that glutamatergic signaling is partly regulated by sex-related hormones. The LRRTM gene family encodes neuronal leucine-rich transmembrane proteins that localize to and promote glutamatergic synapse development. In this study, we sequenced the coding and regulatory regions of all four LRRTM gene members plus a large intronic region of LRRTM4 in 476 bipolar disorder suicide attempters and 473 bipolar disorder nonattempters. We identified two male-specific variants, one female- and five male-specific haplotypes significantly associated with attempted suicide in LRRTM4. Furthermore, variants within significant haplotypes may be brain expression quantitative trait loci for LRRTM4 and some of these variants overlap with predicted hormone response elements. Overall, these results provide supporting evidence for a sex-specific association of genetic variation in LRRTM4 with attempted suicide.
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Affiliation(s)
- Rachel D. Reichman
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Sophia C. Gaynor
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Eric T. Monson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Marie E. Gaine
- Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Meredith G. Parsons
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Peter P. Zandi
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - James B. Potash
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Virginia L. Willour
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
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Al Bkhetan Z, Zobel J, Kowalczyk A, Verspoor K, Goudey B. Exploring effective approaches for haplotype block phasing. BMC Bioinformatics 2019; 20:540. [PMID: 31666002 PMCID: PMC6822470 DOI: 10.1186/s12859-019-3095-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/10/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Knowledge of phase, the specific allele sequence on each copy of homologous chromosomes, is increasingly recognized as critical for detecting certain classes of disease-associated mutations. One approach for detecting such mutations is through phased haplotype association analysis. While the accuracy of methods for phasing genotype data has been widely explored, there has been little attention given to phasing accuracy at haplotype block scale. Understanding the combined impact of the accuracy of phasing tool and the method used to determine haplotype blocks on the error rate within the determined blocks is essential to conduct accurate haplotype analyses. RESULTS We present a systematic study exploring the relationship between seven widely used phasing methods and two common methods for determining haplotype blocks. The evaluation focuses on the number of haplotype blocks that are incorrectly phased. Insights from these results are used to develop a haplotype estimator based on a consensus of three tools. The consensus estimator achieved the most accurate phasing in all applied tests. Individually, EAGLE2, BEAGLE and SHAPEIT2 alternate in being the best performing tool in different scenarios. Determining haplotype blocks based on linkage disequilibrium leads to more correctly phased blocks compared to a sliding window approach. We find that there is little difference between phasing sections of a genome (e.g. a gene) compared to phasing entire chromosomes. Finally, we show that the location of phasing error varies when the tools are applied to the same data several times, a finding that could be important for downstream analyses. CONCLUSIONS The choice of phasing and block determination algorithms and their interaction impacts the accuracy of phased haplotype blocks. This work provides guidance and evidence for the different design choices needed for analyses using haplotype blocks. The study highlights a number of issues that may have limited the replicability of previous haplotype analysis.
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Affiliation(s)
- Ziad Al Bkhetan
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia
| | - Justin Zobel
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia
| | - Adam Kowalczyk
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia.,Centre for Neural Engineering, University of Melbourne, Carlton, 3053, Australia.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, 00-662, Poland.,Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, 3010, Australia
| | - Karin Verspoor
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia.
| | - Benjamin Goudey
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, 3010, Australia.,IBM Australia - Research, Southgate, 3006, Australia
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Farashi S, Kryza T, Clements J, Batra J. Post-GWAS in prostate cancer: from genetic association to biological contribution. Nat Rev Cancer 2019; 19:46-59. [PMID: 30538273 DOI: 10.1038/s41568-018-0087-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) have been successful in deciphering the genetic component of predisposition to many human complex diseases including prostate cancer. Germline variants identified by GWAS progressively unravelled the substantial knowledge gap concerning prostate cancer heritability. With the beginning of the post-GWAS era, more and more studies reveal that, in addition to their value as risk markers, germline variants can exert active roles in prostate oncogenesis. Consequently, current research efforts focus on exploring the biological mechanisms underlying specific susceptibility loci known as causal variants by applying novel and precise analytical methods to available GWAS data. Results obtained from these post-GWAS analyses have highlighted the potential of exploiting prostate cancer risk-associated germline variants to identify new gene networks and signalling pathways involved in prostate tumorigenesis. In this Review, we describe the molecular basis of several important prostate cancer-causal variants with an emphasis on using post-GWAS analysis to gain insight into cancer aetiology. In addition to discussing the current status of post-GWAS studies, we also summarize the main molecular mechanisms of potential causal variants at prostate cancer risk loci and explore the major challenges in moving from association to functional studies and their implication in clinical translation.
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Affiliation(s)
- Samaneh Farashi
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Thomas Kryza
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Judith Clements
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jyotsna Batra
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia.
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