1
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Rafique H, Safdar A, Ghani MU, Akbar A, Awan FI, Naeem Z, Amar A, Awan MF, Wajahat Ullah S, Shaikh RS. Exploring the diversity of CFTR gene mutations in cystic fibrosis individuals of South Asia. J Asthma 2024; 61:511-519. [PMID: 38153325 DOI: 10.1080/02770903.2023.2297365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/16/2023] [Indexed: 12/29/2023]
Abstract
OBJECTIVE Cystic fibrosis (CF) is an autosomal recessive disorder caused by mutations in the CFTR gene. This study aimed to identify the spectrum of CFTR variants reported in individuals with CF from South Asia (ISA). DATA SOURCES AND STUDY SELECTION We conducted a PubMed search for CFTR variants reported in ISA. Full text of original articles and case reports was read to compile data on reported variants. To gather additional data, we independently cross-referenced each variant with the CFTR Mutation Database and ClinVar. RESULTS Our investigation identified a total of 92 CFTR variants reported across 30 articles. The most frequently tested, and reported variant was ΔF508 with a global frequency of 69.74%. Notably, we found 14 pathogenic CFTR mutations shared among ISA, originating from more than one South Asian country: ΔF508, 1525-1 G > A, G542X, S549N, R117H, S549R, R709X, V456A, Y569D, L1077P, 1161delC, 1898 + 1 G > T, G551D, and 2184insA. CONCLUSION In summary, the higher prevalence of consanguinity and the limited availability of CF diagnostic resources in South Asia considerably contribute to the prevalence of genetic disorders like CF. The spectrum of CFTR mutations exhibits noticeable variations within South Asian and other populations. The inclusion of current study-enlisted CFTR gene variants is highly recommended for CF disease genetic testing in South Asia which may aid in achieving a precise diagnosis, enhancing disease management, and discovering drugs for currently untreatable genetic variants. It is also imperative to conduct a comprehensive study in this region, especially in previously unexplored countries such as Nepal, Bhutan, Maldives, and Bangladesh.
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Affiliation(s)
- Hassan Rafique
- Precision Genomics Research Lab, Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Anum Safdar
- Precision Genomics Research Lab, Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Usman Ghani
- Precision Genomics Research Lab, Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ali Akbar
- Sandwell and West Birmingham Hospitals, NHS TRUST, Birmingham, United Kingdom
| | - Farheena Iqbal Awan
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Zartashay Naeem
- Precision Genomics Research Lab, Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ali Amar
- Department of Allied Health Sciences, University of Health Sciences, Kala Shah Kaku, Pakistan
| | | | - Syed Wajahat Ullah
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Rehan Sadiq Shaikh
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
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2
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Martiniano SL, Wu R, Farrell PM, Ren CL, Sontag MK, Elbert A, McColley SA. Late Diagnosis in the Era of Universal Newborn Screening Negatively Affects Short- and Long-Term Growth and Health Outcomes in Infants with Cystic Fibrosis. J Pediatr 2023; 262:113595. [PMID: 37406853 DOI: 10.1016/j.jpeds.2023.113595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/19/2023] [Accepted: 06/26/2023] [Indexed: 07/07/2023]
Abstract
Newborn screening for cystic fibrosis was fully implemented in the US by 2010, but delays in timeliness of evaluation for infants with positive newborn screening tests persist. Through evaluation of national patient registry data, we determined that late initiation of cystic fibrosis care is associated with poorer long-term nutritional outcomes.
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Affiliation(s)
- Stacey L Martiniano
- University of Colorado School of Medicine, Aurora, CO; Breathing Institute, Children's Hospital Colorado, Aurora, CO.
| | - Runyu Wu
- Cystic Fibrosis Foundation, Bethesda, MD
| | - Philip M Farrell
- University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI
| | - Clement L Ren
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Children's Hospital of Philadelphia, Division of Pulmonary and Sleep Medicine, Philadelphia, PA
| | - Marci K Sontag
- Center for Public Health Innovation, CI International, Littleton, CO
| | | | - Susanna A McColley
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL; Northwestern University Feinberg School of Medicine, Chicago, IL
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3
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Andreou SH, Davies JC. Cystic fibrosis to CFSPID: Burden of care vs need and rational approach to weaning therapies. Paediatr Respir Rev 2023; 47:27-29. [PMID: 37487798 DOI: 10.1016/j.prrv.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023]
Abstract
We present a case of a 10-year-old boy initially diagnosed with CF based on NBS guidelines. However, as CF genetics knowledge has advanced, he has been reclassified as CFSPID based on normal investigations and excellent general clinical status, in line with updated CFSPID guidelines. This case highlights the significance of reviewing CF diagnoses according to the latest understanding of CFTR mutation phenotypes, as well as the patient's clinical status. In order to identify opportunities to save patients from burdensome CF treatment and management, we review current CFSPID guidelines, emphasizing care tailored to each individual case.
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Affiliation(s)
| | - J C Davies
- Royal Brompton Hospital, Sydney St, London SW3 6NP, United Kingdom
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4
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Kleinfelder K, Villella VR, Hristodor AM, Laudanna C, Castaldo G, Amato F, Melotti P, Sorio C. Theratyping of the Rare CFTR Genotype A559T in Rectal Organoids and Nasal Cells Reveals a Relevant Response to Elexacaftor (VX-445) and Tezacaftor (VX-661) Combination. Int J Mol Sci 2023; 24:10358. [PMID: 37373505 DOI: 10.3390/ijms241210358] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Despite the promising results of new CFTR targeting drugs designed for the recovery of F508del- and class III variants activity, none of them have been approved for individuals with selected rare mutations, because uncharacterized CFTR variants lack information associated with the ability of these compounds in recovering their molecular defects. Here we used both rectal organoids (colonoids) and primary nasal brushed cells (hNEC) derived from a CF patient homozygous for A559T (c.1675G>A) variant to evaluate the responsiveness of this pathogenic variant to available CFTR targeted drugs that include VX-770, VX-809, VX-661 and VX-661 combined with VX-445. A559T is a rare mutation, found in African-Americans people with CF (PwCF) with only 85 patients registered in the CFTR2 database. At present, there is no treatment approved by FDA (U.S. Food and Drug Administration) for this genotype. Short-circuit current (Isc) measurements indicate that A559T-CFTR presents a minimal function. The acute addition of VX-770 following CFTR activation by forskolin had no significant increment of baseline level of anion transport in both colonoids and nasal cells. However, the combined treatment, VX-661-VX-445, significantly increases the chloride secretion in A559T-colonoids monolayers and hNEC, reaching approximately 10% of WT-CFTR function. These results were confirmed by forskolin-induced swelling assay and by western blotting in rectal organoids. Overall, our data show a relevant response to VX-661-VX-445 in rectal organoids and hNEC with CFTR genotype A559T/A559T. This could provide a strong rationale for treating patients carrying this variant with VX-661-VX-445-VX-770 combination.
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Affiliation(s)
- Karina Kleinfelder
- Cystic Fibrosis Laboratory "D. Lissandrini", Department of Medicine, Division of General Pathology, University of Verona, 37134 Verona, Italy
| | - Valeria Rachela Villella
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80138 Napoli, Italy
- CEINGE-Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy
| | - Anca Manuela Hristodor
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria Integrata Verona, 37126 Verona, Italy
| | - Carlo Laudanna
- Cystic Fibrosis Laboratory "D. Lissandrini", Department of Medicine, Division of General Pathology, University of Verona, 37134 Verona, Italy
| | - Giuseppe Castaldo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80138 Napoli, Italy
- CEINGE-Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy
| | - Felice Amato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80138 Napoli, Italy
| | - Paola Melotti
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria Integrata Verona, 37126 Verona, Italy
| | - Claudio Sorio
- Cystic Fibrosis Laboratory "D. Lissandrini", Department of Medicine, Division of General Pathology, University of Verona, 37134 Verona, Italy
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5
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Farra C, Awwad J, Hamadeh L, Khoueiry P, Halawi Z, Yazbeck N, Daher R, Souaid M, Hamdar L, Yammine T, Yunis K. CFTR mutational screening by next-generation sequencing reveals novel variants and a high carrier rate in a Middle Eastern population. Ann Hum Genet 2021; 86:80-86. [PMID: 34888852 DOI: 10.1111/ahg.12450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 11/28/2022]
Abstract
Cystic fibrosis is the most common life-limiting autosomal recessive disease in western countries with an incidence of 1:2500 in United States and 1:1000 in some European countries. Similar incidences were noted for the Middle East with variations from 1 in 2560 to 1 in 15,876 according to the degree of consanguinity. This is a preliminary systematic study that aims to assess the incidence and carrier rate of cystic fibrosis in the Middle Eastern Lebanese population; known for a high frequency of consanguinity. One hundred thirteen DNA samples were collected from neonatal blood cards obtained from newborns to healthy unrelated families with no previous history of Cystic fibrosis. Screening for Cystic Fibrosis-causing pathogenic variants was performed using next generation sequencing, and 17 different single nucleotide variants were detected, including six pathogenic and likely pathogenic. 5.5%-7% newborns were found to be carriers of a variant strongly suggestive of pathogenicity and comparable to published literature worldwide. This pilot analysis highlights the challenging interpretation of CFTR variants in a country underrepresented by large ethnic population analyses, and stresses the importance of premarital screening programs for Cystic fibrosis.
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Affiliation(s)
- Chantal Farra
- Department of Pediatrics, American University of Beirut Medical Center, Beirut, Lebanon.,Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon.,Medical Genetics Unit, Saint Joseph University, Beirut, Lebanon
| | - Johnny Awwad
- Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Lama Hamadeh
- Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, American University of Beirut Medical Center, Beirut, Lebanon
| | - Zeina Halawi
- Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Nadine Yazbeck
- Department of Pediatrics, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rose Daher
- Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Mirna Souaid
- Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon.,Medical Genetics Unit, Saint Joseph University, Beirut, Lebanon
| | - Layal Hamdar
- Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Tony Yammine
- Medical Genetics Unit, Saint Joseph University, Beirut, Lebanon
| | - Khalid Yunis
- Department of Pediatrics, American University of Beirut Medical Center, Beirut, Lebanon
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6
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Abstract
Because CFTR gene studies now represent one of the most frequent genetic analyses routinely performed worldwide, the number of rare CFTR variants identified in various clinical situations, regularly increases. To provide appropriate diagnosis and prognosis to CF patients as well as appropriate genetic counseling to families, the clinical impact and the phenotypic spectrum of variants identified by diagnostic techniques need to be characterized. Three complementary locus specific databases, called CFTR1, CFTR2 and CFTR-France were developed to address these issues. Besides, the growing knowledge of the CF pathophysiology and the technical evolution in molecular biology allowed to identify candidate modifier genes, regulatory loci, epigenetic profiles and trans-regulators that could help to refine genotype-phenotype correlations at the individual level. These different factors may contribute to the large phenotypic variability between patients with CF, even when they carry identical CFTR variants, regarding lung function, meconium ileus susceptibility or the risk for developing CFTR-related diabetes and liver disease. Finally, the availability of new therapies that target the CFTR protein for numbers of CF patients led to the identification of 'good' and 'poor' responders, thus raising questions of pharmacogenetics factors that may influence treatment efficiency as a novel feature of the complexity of CF patients' management. © 2020 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.
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7
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Luo S, Feng J, Zhang Y, Yang X, Ma G, Hu T, Xi Y, Tu X, Wang C, Zhang H, Zou Z, Zhang Y. Mutation analysis of the cystic fibrosis transmembrane conductance regulator gene in Chinese congenital absence of vas deferens patients. Gene 2020; 765:145045. [PMID: 32777524 DOI: 10.1016/j.gene.2020.145045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
Abstract
To find the variant spectrum of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, and evaluate its frequent variants in Chinese congenital absence of vas deferens (CAVD) patients. A total of 276 patients with azoospermia and CAVD (aged from 21 to 44 years old) were investigated from May 2013 to September 2019 in the Third Affiliated Hospital of Sun Yat-sen University. Additionally, 50 healthy, unrelated volunteers were recruited as controls (aged from 21 to 46 years old). The 5'-UTR, exons and their flanking side of the CFTR gene were sequenced by high-throughput sequencing technology. The results were compared with those retrieved from the Ensembl Genome Browser. In addition, all 13 novel variants were further confirmed independently by Sanger sequencing and evaluated in the bioinformatics web servers. A schematic of the variant spectrum of the CFTR gene, including 13 novel variants (12 in CAVD patients, one in the control group), is shown, and the frequent variants in Chinese CAVD patients were 5 T (27.54%), c.-8G > C (7.25%), p.Q1352H (5.98%), and p.I556V (3.08%). 5 T was found to be the most frequent variant. p.Q1352H had a significantly high allelic frequency in CAVD patients (P < 0.05). c.-8G > C and p.I556V had high allelic frequencies but showed no difference between patients and controls (P > 0.05). p.Q1352H is the most common and important missense variant in Chinese patients with CAVD, while the pathological effects of C.-8G > C and p.I556V may be weak after evaluation.
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Affiliation(s)
- Shaoge Luo
- Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-sen University, No. 600, Tianhe Road, Guangzhou 510630, China
| | - Jiarong Feng
- Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-sen University, No. 600, Tianhe Road, Guangzhou 510630, China
| | - Yanan Zhang
- Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-sen University, No. 600, Tianhe Road, Guangzhou 510630, China
| | - Xiaojian Yang
- Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-sen University, No. 600, Tianhe Road, Guangzhou 510630, China
| | - Gongchao Ma
- Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-sen University, No. 600, Tianhe Road, Guangzhou 510630, China
| | - Tengfei Hu
- Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-sen University, No. 600, Tianhe Road, Guangzhou 510630, China
| | - Yu Xi
- Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-sen University, No. 600, Tianhe Road, Guangzhou 510630, China
| | - Xuchong Tu
- Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-sen University, No. 600, Tianhe Road, Guangzhou 510630, China
| | - Chunlin Wang
- Department of Andrology, Ruikang Hospital Affiliated to Guangxi University of Traditional Chinese Medicine, No.10, Huadong Road, Nanning 530011, China
| | - Hui Zhang
- Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-sen University, No. 600, Tianhe Road, Guangzhou 510630, China
| | - Zijun Zou
- Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-sen University, No. 600, Tianhe Road, Guangzhou 510630, China
| | - Yan Zhang
- Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-sen University, No. 600, Tianhe Road, Guangzhou 510630, China.
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8
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Bienvenu T, Lopez M, Girodon E. Molecular Diagnosis and Genetic Counseling of Cystic Fibrosis and Related Disorders: New Challenges. Genes (Basel) 2020; 11:E619. [PMID: 32512765 PMCID: PMC7349214 DOI: 10.3390/genes11060619] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 11/16/2022] Open
Abstract
Identification of the cystic fibrosis transmembrane conductance regulator (CFTR) gene and its numerous variants opened the way to fantastic breakthroughs in diagnosis, research and treatment of cystic fibrosis (CF). The current and future challenges of molecular diagnosis of CF and CFTR-related disorders and of genetic counseling are here reviewed. Technological advances have enabled to make a diagnosis of CF with a sensitivity of 99% by using next generation sequencing in a single step. The detection of heretofore unidentified variants and ethnic-specific variants remains challenging, especially for newborn screening (NBS), CF carrier testing and genotype-guided therapy. Among the criteria for assessing the impact of variants, population genetics data are insufficiently taken into account and the penetrance of CF associated with CFTR variants remains poorly known. The huge diversity of diagnostic and genetic counseling indications for CFTR studies makes assessment of variant disease-liability critical. This is especially discussed in the perspective of wide genome analyses for NBS and CF carrier screening in the general population, as future challenges.
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Affiliation(s)
| | | | - Emmanuelle Girodon
- Molecular Genetics Laboratory, Cochin Hospital, APHP.Centre–Université de Paris, 75014 Paris, France; (T.B.); (M.L.)
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9
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Zeiger AM, McGarry ME, Mak ACY, Medina V, Salazar S, Eng C, Liu AK, Oh SS, Nuckton TJ, Jain D, Blackwell TW, Kang HM, Abecasis G, Oñate LC, Seibold MA, Burchard EG, Rodriguez-Santana J. Identification of CFTR variants in Latino patients with cystic fibrosis from the Dominican Republic and Puerto Rico. Pediatr Pulmonol 2020; 55:533-540. [PMID: 31665830 PMCID: PMC7571374 DOI: 10.1002/ppul.24549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/28/2019] [Indexed: 11/09/2022]
Abstract
BACKGROUND In cystic fibrosis (CF), the spectrum and frequency of CFTR variants differ by geography and race/ethnicity. CFTR variants in White patients are well-described compared with Latino patients. No studies of CFTR variants have been done in patients with CF in the Dominican Republic or Puerto Rico. METHODS CFTR was sequenced in 61 Dominican Republican patients and 21 Puerto Rican patients with CF and greater than 60 mmol/L sweat chloride. The spectrum of CFTR variants was identified and the proportion of patients with 0, 1, or 2 CFTR variants identified was determined. The functional effects of identified CFTR variants were investigated using clinical annotation databases and computational prediction tools. RESULTS Our study found 10% of Dominican patients had two CFTR variants identified compared with 81% of Puerto Rican patients. No CFTR variants were identified in 69% of Dominican patients and 10% of Puerto Rican patients. In Dominican patients, there were 19 identified CFTR variants, accounting for 25 out of 122 disease alleles (20%). In Puerto Rican patients, there were 16 identified CFTR variants, accounting for 36 out of 42 disease alleles (86%) in Puerto Rican patients. Thirty CFTR variants were identified overall. The most frequent variants for Dominican patients were p.Phe508del and p.Ala559Thr and for Puerto Rican patients were p.Phe508del, p.Arg1066Cys, p.Arg334Trp, and p.I507del. CONCLUSIONS In this first description of the CFTR variants in patients with CF from the Dominican Republic and Puerto Rico, there was a low detection rate of two CFTR variants after full sequencing with the majority of patients from the Dominican Republic without identified variants.
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Affiliation(s)
- Andrew M Zeiger
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Meghan E McGarry
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Angel C Y Mak
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Vivian Medina
- Department of Pediatrics, Centro de Neumología Pediátrica, San Juan, Puerto Rico
| | - Sandra Salazar
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Amy K Liu
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Sam S Oh
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Thomas J Nuckton
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Thomas W Blackwell
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Hyun Min Kang
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Goncalo Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Leandra Cordero Oñate
- Department of Pediatrics, Neumología Pediátrica del Hospital Infantil Dr. Robert Reid Cabral, Santo Domingo, República Dominicana
| | - Max A Seibold
- Department of Pediatrics, National Jewish Health, Denver, Colorado
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, California.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California
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10
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Ruiz-Cabezas JC, Barros F, Sobrino B, García G, Burgos R, Farhat C, Castro A, Muñoz L, Zambrano AK, Martínez M, Montalván M, Paz-Y-Miño C. Mutational analysis of CFTR in the Ecuadorian population using next-generation sequencing. Gene 2019; 696:28-32. [PMID: 30763667 DOI: 10.1016/j.gene.2019.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/09/2019] [Accepted: 02/01/2019] [Indexed: 11/18/2022]
Abstract
The frequency distributions of cystic fibrosis variants are heterogeneous in Ecuador because of the genetic admixture of its population. The aim of this study was to identify disease-causing variants among Ecuadorian cystic fibrosis (CF) patients by next-generation sequencing (NGS) of the entire cystic fibrosis transmembrane conductance regulator (CFTR) gene. The results showed an approximation of the frequencies of pathogenic variants in the population under study and an optimal mutation panel for routine first-line CF molecular diagnosis. One hundred and forty-one patients with suspected CF from the 3 largest Ecuadorian cities (Guayaquil, Quito, and Cuenca) were studied. One hundred and seventy mutated alleles were detected in eighty-five individuals. Twenty-eight disease-causing variants were identified, with p.Phe508del and p.His609Arg being the most frequent (both 24.7%) followed by p.Gly85Glu (11.1%), p.Leu15Pro (9.4%), p.Asn1303Lys (4.1%), and p.Gly542* (2.3%). Together, these variants constituted 76.44% of the detected disease-causing variants. The following six novel potentially disease-associated variants were detected: 3 deletions (CFTR_dele10, CFTR_dele12, and c.2672delA), 1 nonsense variant (p.Cys491*), 1 missense variant (p.Trp496Arg), and 1 complex allele (p.[Gly253Arg;Gly451Val]). The remaining mutations occurred in isolation and were present in the databases.
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Affiliation(s)
- Juan Carlos Ruiz-Cabezas
- Universidad de Especialidades Espíritu Santo (UEES), Guayaquil, Ecuador; Instituto de Investigación Integral en Salud (ISAIN-UCSG), Universidad Católica de Santiago de Guayaquil, Guayaquil, Ecuador; Instituto Oncológico Nacional de la Sociedad de Lucha Contra el Cáncer (ION-SOLCA), Guayaquil, Ecuador.
| | - Francisco Barros
- Grupo de Medicina Xenómica - USC, CIBERER, Fundacion Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain
| | - Beatriz Sobrino
- Grupo de Medicina Xenómica - USC, CIBERER, Fundacion Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain
| | - Gustavo García
- Universidad de Especialidades Espíritu Santo (UEES), Guayaquil, Ecuador; Instituto Oncológico Nacional de la Sociedad de Lucha Contra el Cáncer (ION-SOLCA), Guayaquil, Ecuador; Escuela de Odontología, Universidad Católica de Santiago de Guayaquil, Guayaquil, Ecuador
| | - Ramiro Burgos
- Instituto Oncológico Nacional de la Sociedad de Lucha Contra el Cáncer (ION-SOLCA), Guayaquil, Ecuador
| | - Carlos Farhat
- Universidad de Especialidades Espíritu Santo (UEES), Guayaquil, Ecuador
| | - Antonella Castro
- Universidad de Especialidades Espíritu Santo (UEES), Guayaquil, Ecuador
| | - Lenin Muñoz
- Universidad de Especialidades Espíritu Santo (UEES), Guayaquil, Ecuador
| | - Ana Karina Zambrano
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud, Universidad UTE, Quito, Ecuador
| | | | - Martha Montalván
- Universidad de Especialidades Espíritu Santo (UEES), Guayaquil, Ecuador; Facultad de Ciencias Médicas, Universidad de Guayaquil, Ecuador; Facultad de Ciencias Médicas, Universidad Católica de Santiago de Guayaquil, Guayaquil, Ecuador
| | - César Paz-Y-Miño
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud, Universidad UTE, Quito, Ecuador
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