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Reyna J, Fetter K, Ignacio R, Marandi CCA, Rao N, Jiang Z, Figueroa DS, Bhattacharyya S, Ay F. Loop Catalog: a comprehensive HiChIP database of human and mouse samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591349. [PMID: 38746164 PMCID: PMC11092438 DOI: 10.1101/2024.04.26.591349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
HiChIP enables cost-effective and high-resolution profiling of regulatory and structural loops. To leverage the increasing number of publicly available HiChIP datasets from diverse cell lines and primary cells, we developed the Loop Catalog (https://loopcatalog.lji.org), a web-based database featuring HiChIP loop calls for 1319 samples across 133 studies and 44 high-resolution Hi-C loop calls. We demonstrate its utility in interpreting fine-mapped GWAS variants (SNP-to-gene linking), in identifying enriched sequence motifs and motif pairs at loop anchors, and in network-level analysis of loops connecting regulatory elements (community detection). Our comprehensive catalog, spanning over 4M unique 5kb loops, along with the accompanying analysis modalities constitutes an important resource for studies in gene regulation and genome organization.
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Affiliation(s)
- Joaquin Reyna
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Bioinformatics and Systems Biology Graduate Program University of California, San Diego, La Jolla, CA 92093 USA
| | - Kyra Fetter
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Romeo Ignacio
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
| | - Cemil Can Ali Marandi
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Bioinformatics and Systems Biology Graduate Program University of California, San Diego, La Jolla, CA 92093 USA
| | - Nikhil Rao
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Zichen Jiang
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Department of Mathematics, University of California San Diego, La Jolla, CA 92093 USA
| | - Daniela Salgado Figueroa
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Bioinformatics and Systems Biology Graduate Program University of California, San Diego, La Jolla, CA 92093 USA
| | - Sourya Bhattacharyya
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
| | - Ferhat Ay
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Bioinformatics and Systems Biology Graduate Program University of California, San Diego, La Jolla, CA 92093 USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA
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Brlek P, Bulić L, Bračić M, Projić P, Škaro V, Shah N, Shah P, Primorac D. Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives. Cells 2024; 13:504. [PMID: 38534348 DOI: 10.3390/cells13060504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The integration of whole genome sequencing (WGS) into all aspects of modern medicine represents the next step in the evolution of healthcare. Using this technology, scientists and physicians can observe the entire human genome comprehensively, generating a plethora of new sequencing data. Modern computational analysis entails advanced algorithms for variant detection, as well as complex models for classification. Data science and machine learning play a crucial role in the processing and interpretation of results, using enormous databases and statistics to discover new and support current genotype-phenotype correlations. In clinical practice, this technology has greatly enabled the development of personalized medicine, approaching each patient individually and in accordance with their genetic and biochemical profile. The most propulsive areas include rare disease genomics, oncogenomics, pharmacogenomics, neonatal screening, and infectious disease genomics. Another crucial application of WGS lies in the field of multi-omics, working towards the complete integration of human biomolecular data. Further technological development of sequencing technologies has led to the birth of third and fourth-generation sequencing, which include long-read sequencing, single-cell genomics, and nanopore sequencing. These technologies, alongside their continued implementation into medical research and practice, show great promise for the future of the field of medicine.
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Affiliation(s)
- Petar Brlek
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Luka Bulić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Matea Bračić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Petar Projić
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
| | | | - Nidhi Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Parth Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Dragan Primorac
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Split, 21000 Split, Croatia
- Eberly College of Science, The Pennsylvania State University, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- REGIOMED Kliniken, 96450 Coburg, Germany
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- National Forensic Sciences University, Gujarat 382007, India
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Ben-Zvi I, Karasik D, Ackert-Bicknell CL. Zebrafish as a Model for Osteoporosis: Functional Validations of Genome-Wide Association Studies. Curr Osteoporos Rep 2023; 21:650-659. [PMID: 37971665 DOI: 10.1007/s11914-023-00831-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/02/2023] [Indexed: 11/19/2023]
Abstract
PURPOSE OF REVIEW GWAS, as a largely correlational analysis, requires in vitro or in vivo validation. Zebrafish (Danio rerio) have many advantages for studying the genetics of human diseases. Since gene editing in zebrafish has been highly valuable for studying embryonic skeletal developmental processes that are prenatally or perinatally lethal in mammalian models, we are reviewing pros and cons of this model. RECENT FINDINGS The true power for the use of zebrafish is the ease by which the genome can be edited, especially using the CRISPR/Cas9 system. Gene editing, followed by phenotyping, for complex traits such as BMD, is beneficial, but the major physiological differences between the fish and mammals must be considered. Like mammals, zebrafish do have main bone cells; thus, both in vivo stem cell analyses and in vivo imaging are doable. Yet, the "long" bones of fish are peculiar, and their bone cavities do not contain bone marrow. Partial duplication of the zebrafish genome should be taken into account. Overall, small fish toolkit can provide unmatched opportunities for genetic modifications and morphological investigation as a follow-up to human-first discovery.
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Affiliation(s)
- Inbar Ben-Zvi
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - David Karasik
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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Chumakova OS, Baulina NM. Advanced searching for hypertrophic cardiomyopathy heritability in real practice tomorrow. Front Cardiovasc Med 2023; 10:1236539. [PMID: 37583586 PMCID: PMC10425241 DOI: 10.3389/fcvm.2023.1236539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease associated with morbidity and mortality at any age. As studies in recent decades have shown, the genetic architecture of HCM is quite complex both in the entire population and in each patient. In the rapidly advancing era of gene therapy, we have to provide a detailed molecular diagnosis to our patients to give them the chance for better and more personalized treatment. In addition to emphasizing the importance of genetic testing in routine practice, this review aims to discuss the possibility to go a step further and create an expanded genetic panel that contains not only variants in core genes but also new candidate genes, including those located in deep intron regions, as well as structural variations. It also highlights the benefits of calculating polygenic risk scores based on a combination of rare and common genetic variants for each patient and of using non-genetic HCM markers, such as microRNAs that can enhance stratification of risk for HCM in unselected populations alongside rare genetic variants and clinical factors. While this review is focusing on HCM, the discussed issues are relevant to other cardiomyopathies.
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Affiliation(s)
- Olga S. Chumakova
- Laboratory of Functional Genomics of Cardiovascular Diseases, National Medical Research Centre of Cardiology Named After E.I. Chazov, Moscow, Russia
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Rosen J, Lee L, Abnousi A, Chen J, Wen J, Hu M, Li Y. HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets. Comput Struct Biotechnol J 2023; 21:931-939. [PMID: 38213897 PMCID: PMC10782010 DOI: 10.1016/j.csbj.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
High-throughput chromatin conformation capture technologies, such as Hi-C and Micro-C, have enabled genome-wide view of chromatin spatial organization. Most recently, Hi-C-derived enrichment-based technologies, including HiChIP and PLAC-seq, offer attractive alternatives due to their high signal-to-noise ratio and low cost. While a series of computational tools have been developed for Hi-C data, methods tailored for HiChIP and PLAC-seq data are still under development. Here we present HPTAD, a computational method to identify topologically associating domains (TADs) from HiChIP and PLAC-seq data. We performed comprehensive benchmark analysis to demonstrate its superior performance over existing TAD callers designed for Hi-C data. HPTAD is freely available at https://github.com/yunliUNC/HPTAD.
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Affiliation(s)
- Jonathan Rosen
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Lindsay Lee
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
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Ma Q, Yang Y, Liu Y. Associations between NKX2-5 gene polymorphisms and congenital heart disease in the Chinese Tibetan population. Am J Transl Res 2022; 14:8407-8415. [PMID: 36505279 PMCID: PMC9730064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/14/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND The pathogenesis of congenital heart disease (CHD) has not been fully elucidated, and this study considers the interaction between inheritance and the environment as the main cause of CHD. Previous studies have found that the incidence of CHD in the Tibetan plateau population is significantly higher than in low-altitude populations. Numerous reports have confirmed that NKX2-5 gene mutations can lead to coronary heart disease, but the relationship between NKX2-5 and Tibetan nationality has not yet been reported. OBJECTIVE To explore the relationship between NKX2-5 gene polymorphisms and CHD in Tibetan people. METHODS Blood samples were collected retrospectively from Tibetan patients diagnosed with CHD as well as healthy Tibetans, and the exons of NKX2-5 were sequenced. The MassARRAY technique was used to detect and genotype candidate tag single nucleotide polymorphisms (SNPs) in the non-coding regions of NKX2-5. RESULTS Exon sequencing revealed no difference in the coding regions of the NKX2-5 gene between the CHD and control groups. In the non-coding regions of NKX2-5, rs6882776 and rs2546741 differed significantly between the two groups. Strong linkage disequilibrium was found between the selected sites of NKX2-5. CONCLUSIONS The NKX2-5 exons do not associate with CHD in Tibetans. Rs6882776 and rs2546741 in the non-coding regions of NKX2-5 may protect against CHD in Tibetans. The NKX2-5 haplotype associated with CHD occurrence in the Tibetan population.
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Affiliation(s)
- Qiang Ma
- High Altitude Medical Research Center, Medical College of Qinghai University16 Kunlun Road, Xining 810001, Qinghai, China,Department of Pathology, Sunshine Union HospitalYingqian Road, Weifang 261000, Shandong, China
| | - Yingzhong Yang
- High Altitude Medical Research Center, Medical College of Qinghai University16 Kunlun Road, Xining 810001, Qinghai, China
| | - Yongnian Liu
- High Altitude Medical Research Center, Medical College of Qinghai University16 Kunlun Road, Xining 810001, Qinghai, China
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