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Romdhane L, Kefi S, Mezzi N, Abassi N, Jmel H, Romdhane S, Shan J, Chouchane L, Abdelhak S. Ethnic and functional differentiation of copy number polymorphisms in Tunisian and HapMap population unveils insights on genome organizational plasticity. Sci Rep 2024; 14:4654. [PMID: 38409353 PMCID: PMC10897484 DOI: 10.1038/s41598-024-54749-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024] Open
Abstract
Admixture mapping has been useful in identifying genetic variations linked to phenotypes, adaptation and diseases. Copy number variations (CNVs) represents genomic structural variants spanning large regions of chromosomes reaching several megabases. In this investigation, the "Canary" algorithm was applied to 102 Tunisian samples and 991 individuals from eleven HapMap III populations to genotype 1279 copy number polymorphisms (CNPs). In this present work, we investigate the Tunisian population structure using the CNP makers previously identified among Tunisian. The study revealed that Sub-Saharan African populations exhibited the highest diversity with the highest proportions of allelic CNPs. Among all the African populations, Tunisia showed the least diversity. Individual ancestry proportions computed using STRUCTURE analysis revealed a major European component among Tunisians with lesser contribution from Sub-Saharan Africa and Asia. Population structure analysis indicated the genetic proximity with Europeans and noticeable distance from the Sub-Saharan African and East Asian clusters. Seven genes harbouring Tunisian high-frequent CNPs were identified known to be associated with 9 Mendelian diseases and/or phenotypes. Functional annotation of genes under selection highlighted a noteworthy enrichment of biological processes to receptor pathway and activity as well as glutathione metabolism. Additionally, pathways of potential concern for health such as drug metabolism, infectious diseases and cancers exhibited significant enrichment. The distinctive genetic makeup of the Tunisians might have been influenced by various factors including natural selection and genetic drift, resulting in the development of distinct genetic variations playing roles in specific biological processes. Our research provides a justification for focusing on the exclusive genome organization of this population and uncovers previously overlooked elements of the genome.
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Affiliation(s)
- Lilia Romdhane
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.
- Department of Biology, Faculty of Sciences of Bizerte, University of Carthage, Zarzouna, Tunisia.
| | - Sameh Kefi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nessrine Mezzi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Najla Abassi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Haifa Jmel
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Safa Romdhane
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Jingxuan Shan
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Education City-Qatar Foundation, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Education City-Qatar Foundation, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Sonia Abdelhak
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
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Li Z, Sun Q, Shi Y. Somatic structural variations in pediatric brain tumors. Minerva Pediatr (Torino) 2022; 74:358-364. [DOI: 10.23736/s2724-5276.17.04830-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Han JY, Jang W, Park J, Kim M, Kim Y, Lee IG. Diagnostic approach with genetic tests for global developmental delay and/or intellectual disability: Single tertiary center experience. Ann Hum Genet 2018; 83:115-123. [PMID: 30402882 DOI: 10.1111/ahg.12294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 01/24/2023]
Abstract
The child with global developmental delay (GDD)/intellectual disability (ID) is deserving of the appropriate evaluation available for improving the health and well-being of patients and their families. To better elucidate the diagnostic approach of genetic tests for patients with GDD and/or ID, we evaluated the results in a cohort of 75 patients with clinical features of GDD and/or ID who were referred for diagnostic workup. A total of 75 children were investigated for GDD or ID in the pediatric neurology department. Ten patients (13%, 10/75) with a clinically recognizable syndrome were diagnosed by single-gene analysis. Next, chromosomal microarray was performed as a first-tier test, and 25 patients (33%, 25/75) showed structural abnormalities. Then, two fragile X syndrome (3%, 2/75) were confirmed by FMR1 gene fragment analysis. Thirty-eight remaining patients received a gene panel by next-generation sequencing. Eight patients were found to have an underlying genetic etiology: CHD8, ZDHHC9, MBD5, CACNA1H, SMARCB1, FOXP1, NSD1, and PAX6. As a result, 45 patients (60%, 45/75) had been diagnosed by genetic tests. Among 30 undiagnosed patients, brain structural abnormalities related to GDD/ID were observed in eight patients (11%, 8/75). However, in 22 patients (29%, 22/75), the causes of GDD/ID remained uncertain. A genetic diagnostic approach of GDD/ID by sequential molecular analysis can help in the planning of treatment, assigning the risk of occurrence in siblings, and providing emotional relief for the family.
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Affiliation(s)
- Ji Yoon Han
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Woori Jang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - In Goo Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Valgaeren H, Koppen C, Van Camp G. A new perspective on the genetics of keratoconus: why have we not been more successful? Ophthalmic Genet 2017; 39:158-174. [DOI: 10.1080/13816810.2017.1393831] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hanne Valgaeren
- Department of Biomedical Sciences, Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Antwerp, Belgium
| | - Carina Koppen
- Department of Ophthalmology, Antwerp University Hospital, Edegem, Belgium
- Department of Ophthalmology, Visual Optics and Visual Rehabilitation, University of Antwerp, Antwerp, Belgium
| | - Guy Van Camp
- Department of Biomedical Sciences, Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Antwerp, Belgium
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Validation of quantitative PCR-based assays for detection of gene copy number aberrations in formalin-fixed, paraffin embedded solid tumor samples. Cancer Genet 2017; 212-213:24-31. [PMID: 28449808 DOI: 10.1016/j.cancergen.2017.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/27/2017] [Accepted: 03/02/2017] [Indexed: 01/04/2023]
Abstract
Gene copy number changes are important somatic alterations in cancers. A number of high throughput methods, such as next generation sequencing, are capable of detecting copy number aberrations, but their use can be challenging and cost prohibitive for screening a small number of markers. Furthermore, detection of CNAs by high throughput platforms needs confirmation by an orthogonal technique, especially in cases with low level CNAs. Here, we have validated TaqMan based quantitative PCR (qPCR) assays to detect CNAs in genes of high clinical importance in formalin-fixed, paraffin-embedded (FFPE) samples. A cohort of 22 tumors of various types that harbor 67 CNAs in 13 genes was assessed. The abnormalities in these tumors were detected by using a NGS-based 50 gene hotspot panel on Ion Torrent PGM and molecular inversion probe (MIP) array. The CNAs included ERBB2 (n = 6), PDGFRA (n = 6), KIT (n = 7), NRAS (n = 3), PIK3CA (n = 6), MYC (n = 7), MET (n = 4), FLT3 (n = 6), FGFR3 (n = 3), FGFR2 (n = 3), EGFR (n = 7), KRAS (n = 6) and FGFR1 (n = 5). Different amounts of input DNA were tested and 5 ng FFPE DNA was found to be adequate without limiting detection sensitivity. All 22 (100%) positive tumor samples revealed by MIP array were confirmed by real time qPCR and 17 of 22 (77.2%) samples tested by NGS were confirmed. The limit of detection of the qPCR assay was determined by serial dilution of SKBR3 cell line DNA (with amplified ERBB2) and showed an ability to detect 3 copies consistently up to 0.75% dilution. The ability to use low input of FFPE DNA, high sensitivity, and short turnaround time makes qPCR a valuable and economically viable platform for detecting single gene CNAs as well as for confirmation of CNAs detected by high throughput screening assays.
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Mehrotra M. PCR-Based Detection of DNA Copy Number Variation. Methods Mol Biol 2016; 1392:27-32. [PMID: 26843043 DOI: 10.1007/978-1-4939-3360-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Copy number variations are important polymorphisms that can influence gene expression within and close to the rearranged region, and results in phenotypic variation. Techniques that detect abnormalities in DNA copy number are therefore useful for studying the associations between DNA aberrations and disease phenotype and for locating critical genes. PCR-based detection of copy number of target gene using TaqMan copy number assay offers a reliable method to measure copy number variation in human genome.
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Affiliation(s)
- Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Unit 72, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
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Genotyping of common SIRPB1 copy number variant using Paralogue Ratio Test coupled to MALDI-MS quantification. Mol Cell Probes 2015; 29:517-521. [PMID: 26239731 DOI: 10.1016/j.mcp.2015.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/15/2015] [Accepted: 07/27/2015] [Indexed: 11/23/2022]
Abstract
Copy number variant (CNV) regions have been proven to have a significant impact on gene expression. Some of them have been also found to be associated to different human diseases. CNV genotyping is often prone to error and cross-validation with independent methods is frequently required. The platform of choice depends on whether it is a genome-wide discovery screening or a candidate CNV study, the cohort size and the number of CNVs included in the assay and, finally, the budget available. Here we illustrate a affordable approach to determine the CNV genotype using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and based on the quantitative determination of single nucleotide duplicated mismatches (SNDM) mapping the CNV region and a paralogue genomic region that is used as a two-copy reference. We have genotyped nsv436327, a common CNV mapping SIRPB1 intron 1 that has been associated to human personality behavior. SIRP cluster region was subjected to several ancestral duplication events what makes SIRPB1 CNV genotyping technically challenging. We designed three sets of primer pairs that amplified paralogue regions inside and outside the CNV, containing three SNDMs. Post-PCR extension analyses of sequencing oligonucleotides mapping immediately upstream each SNDM allowed us to quantify using MALDI-MS the proportion of PCR products derived from the CNV region versus the external reference. In contrast to other approaches, setting up this genotyping method requires an affordable investment.
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Helsmoortel C, Vandeweyer G, Ordoukhanian P, Van Nieuwerburgh F, Van der Aa N, Kooy RF. Challenges and opportunities in the investigation of unexplained intellectual disability using family-based whole-exome sequencing. Clin Genet 2014; 88:140-8. [PMID: 25081361 DOI: 10.1111/cge.12470] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/22/2014] [Accepted: 07/25/2014] [Indexed: 12/25/2022]
Abstract
Intellectual disability (ID), characterized by an intellectual performance of at least 2 SD (standard deviations) below average is a frequent, lifelong disorder with a prevalence of 2-3%. Today, only for at most half of patients a diagnosis is made. Knowing the cause of the ID is important for patients and their relatives, as it allows for appropriate medical care, prognosis on further development of the disorder, familial counselling or access to support groups. Whole-exome sequencing (WES) now offers the possibility to identify the genetic cause for patients for which all previously available genetic tests, including karyotyping, specific gene analysis, or microarray analysis did not reveal causative abnormalities. However, data analysis of WES experiments is challenging. Here we present an analysis workflow implementable in any laboratory, requiring no bioinformatics knowledge. We demonstrated its feasibility on a cohort of 10 patients, in which we found a conclusive diagnosis in 3 and a likely diagnosis in 2 more patients. Of the three conclusive diagnoses, one was a clinically suspected mutation missed by Sanger sequencing, and one was an atypical presentation of a known monogenic disorder, highlighting two essential strengths of WES-based diagnostics.
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Affiliation(s)
- C Helsmoortel
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - G Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Center Antwerpen (Biomina), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - P Ordoukhanian
- Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA, USA
| | - F Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - N Van der Aa
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Department of Medical Genetics, University Hospital Antwerp, Antwerp, Belgium
| | - R F Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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Vandeweyer G, Van Laer L, Loeys B, Van den Bulcke T, Kooy RF. VariantDB: a flexible annotation and filtering portal for next generation sequencing data. Genome Med 2014; 6:74. [PMID: 25352915 PMCID: PMC4210545 DOI: 10.1186/s13073-014-0074-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/15/2014] [Indexed: 12/30/2022] Open
Abstract
Interpretation of the multitude of variants obtained from next generation sequencing (NGS) is labor intensive and complex. Web-based interfaces such as Galaxy streamline the generation of variant lists but lack flexibility in the downstream annotation and filtering that are necessary to identify causative variants in medical genomics. To this end, we built VariantDB, a web-based interactive annotation and filtering platform that automatically annotates variants with allele frequencies, functional impact, pathogenicity predictions and pathway information. VariantDB allows filtering by all annotations, under dominant, recessive or de novo inheritance models and is freely available at http://www.biomina.be/app/variantdb/.
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Affiliation(s)
- Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, 2650 Edegem, Antwerp Belgium ; Biomedical Informatics Research Center Antwerp, University and University Hospital of Antwerp, 2650 Edegem, Antwerp Belgium
| | - Lut Van Laer
- Department of Medical Genetics, University of Antwerp, 2650 Edegem, Antwerp Belgium ; Department of Medical Genetics, University Hospital of Antwerp, 2650 Edegem, Antwerp Belgium
| | - Bart Loeys
- Department of Medical Genetics, University of Antwerp, 2650 Edegem, Antwerp Belgium ; Department of Medical Genetics, University Hospital of Antwerp, 2650 Edegem, Antwerp Belgium
| | - Tim Van den Bulcke
- Biomedical Informatics Research Center Antwerp, University and University Hospital of Antwerp, 2650 Edegem, Antwerp Belgium
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, 2650 Edegem, Antwerp Belgium
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Boyd SD, Galli SJ, Schrijver I, Zehnder JL, Ashley EA, Merker JD. A Balanced Look at the Implications of Genomic (and Other "Omics") Testing for Disease Diagnosis and Clinical Care. Genes (Basel) 2014; 5:748-66. [PMID: 25257203 PMCID: PMC4198929 DOI: 10.3390/genes5030748] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/20/2014] [Accepted: 08/18/2014] [Indexed: 11/16/2022] Open
Abstract
The tremendous increase in DNA sequencing capacity arising from the commercialization of "next generation" instruments has opened the door to innumerable routes of investigation in basic and translational medical science. It enables very large data sets to be gathered, whose interpretation and conversion into useful knowledge is only beginning. A challenge for modern healthcare systems and academic medical centers is to apply these new methods for the diagnosis of disease and the management of patient care without unnecessary delay, but also with appropriate evaluation of the quality of data and interpretation, as well as the clinical value of the insights gained. Most critically, the standards applied for evaluating these new laboratory data and ensuring that the results and their significance are clearly communicated to patients and their caregivers should be at least as rigorous as those applied to other kinds of medical tests. Here, we present an overview of conceptual and practical issues to be considered in planning for the integration of genomic methods or, in principle, any other type of "omics" testing into clinical care.
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Affiliation(s)
- Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - Stephen J Galli
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - Iris Schrijver
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - James L Zehnder
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - Euan A Ashley
- Department of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Jason D Merker
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
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Confidence limits for genome DNA copy number variations in HR-CGH array measurements. Biomed Signal Process Control 2014. [DOI: 10.1016/j.bspc.2013.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Copy Number Studies in Noisy Samples. MICROARRAYS 2013; 2:284-303. [PMID: 27605193 PMCID: PMC5003442 DOI: 10.3390/microarrays2040284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 10/24/2013] [Accepted: 10/25/2013] [Indexed: 11/17/2022]
Abstract
System noise was analyzed in 77 Affymetrix 6.0 samples from a previous clinical study of copy number variation (CNV). Twenty-three samples were classified as eligible for CNV detection, 29 samples as ineligible and 25 were classified as being of intermediate quality. New software (“noise-free-cnv”) was developed to visualize the data and reduce system noise. Fresh DNA preparations were more likely to yield eligible samples (p < 0.001). Eligible samples had higher rates of successfully genotyped SNPs (p < 0.001) and lower variance of signal intensities (p < 0.001), yielded fewer CNV findings after Birdview analysis (p < 0.001), and showed a tendency to yield fewer PennCNV calls (p = 0.053). The noise-free-cnv software visualized trend patterns of noise in the signal intensities across the ordered SNPs, including a wave pattern of noise, being co-linear with the banding pattern of metaphase chromosomes, as well as system deviations of individual probe sets (per-SNP noise). Wave noise and per-SNP noise occurred independently and could be separately removed from the samples. We recommend a two-step procedure of CNV validation, including noise reduction and visual inspection of all CNV calls, prior to molecular validation of a selected number of putative CNVs.
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