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Hirai S, Suzuki M, Sakurai Y, Nakano S, Minowa K, Eguchi H, Okazaki Y, Shimizu T. The Coexistence of TRPV6 Variants With Other Pancreatitis-Associated Genes Affects Pediatric-Onset Pancreatitis. J Pediatr Gastroenterol Nutr 2023; 76:483-488. [PMID: 36599151 DOI: 10.1097/mpg.0000000000003700] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVES Recently, a genetic risk for chronic pancreatitis (CP) was found to be conferred by pathogenic variants in the transient receptor potential cation channel, subfamily V, member 6 ( TRPV6 ). Interestingly, 20%-57% of patients with functionally defective TRPV6 variants have other susceptibility genes such as cationic trypsinogen, serine protease inhibitor Kazal type 1, chymotrypsin C, cystic fibrosis transmembrane conductance regulator, and carboxypeptidase A1. In this study, we focused on pediatric patients with acute recurrent pancreatitis or CP with at least 1 variant in these 5 genes and investigated the presence of coexisting TRPV6 mutations. METHODS Ninety Japanese pediatric patients (median age at first onset, 8.0 years) who had at least 1 variant of these 5 genes were enrolled in this study. DNA samples were extracted for analysis from peripheral blood leukocytes. Coding regions of TRPV6 were screened by Sanger sequencing. RESULTS Regardless of functional defects or non-defects in TRPV6 variants, 14 of the 90 patients (15.6%) were trans-heterozygous for TRPV6 variants [p.A18S (n = 3), p.C197R (n = 3), p.I223T (n = 3), p.D324N (n = 4), p.M418V (n = 3), p.V540F (n = 1), p.A606T (n = 1), and p.M721T (n = 3)] and the 5 susceptibility genes noted above. Of these variants, p.D324N, p.V540F, and p.A606T are associated with pancreatitis. Three patients had the ancestral haplotype [p.C197R + p.M418V + p.M721T]. CONCLUSIONS Overall, 4 of 90 patients (4.4%) had the coexistence of clearly pathogenic TRPV6 variants with pancreatitis-associated variants. The cumulative accumulation of these genetic factors may contribute to the development of pancreatitis at a young age.
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Affiliation(s)
- Saeko Hirai
- From the Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mitsuyoshi Suzuki
- the Department of Pediatrics, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Yumiko Sakurai
- the Department of Pediatrics, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Satoshi Nakano
- the Department of Pediatrics, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Kei Minowa
- the Department of Pediatrics, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Hidetake Eguchi
- the Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Yasushi Okazaki
- the Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Toshiaki Shimizu
- From the Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Fujita S, Nishizawa H, Miyashita Y, Imada T, Yamaguchi T, Murano T, Bujo H, Asano Y, Kozawa J, Maeda N, Shimomura I. Genetic assessment using whole-exome sequencing for a young hypertriglyceridemic patient with repeated acute pancreatitis. Endocr J 2022; 69:1101-1108. [PMID: 35387941 DOI: 10.1507/endocrj.ej22-0024] [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] [Indexed: 11/23/2022] Open
Abstract
Hypertriglyceridemia is caused not only by environmental factors but also by genetic factors. Severe hypertriglyceridemia is prone to complications of acute pancreatitis. Here, we report a whole-exome sequencing (WES) analysis for a young hypertriglyceridemic patient with recurrent acute pancreatitis and the patient's mother. A 28-year-old hypertriglyceridemic female was admitted to our hospital. At 23 years old, a health checkup clarified her hypertriglyceridemia. At the age of 26 and 27, she had repeated acute pancreatitis with severe hypertriglyceridemia (serum triglyceride level were 3,888 mg/dL and 12,080 mg/dL, respectively). The patient's BMI was 29.0 kg/m2, and blood samples under fibrate medication showed triglyceride 451 mg/dL and HbA1c 7.2%. Type V dyslipidemia became more apparent at postprandial state. The WES analysis showed that the patients had two heterozygous variants in Apolipoprotein A5 (APOA5) gene (p.G185C and p.V153M), a heterozygous variant in Apolipoprotein E (APOE) gene (p.R176C), three heterozygous variants in Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene (p.T1220I, p.R1453W and p.V470M). On the other hand, her mother, who had moderate hypertriglyceridemia without acute pancreatitis, had a heterozygous variant in APOA5 gene (p.G185C) and two heterozygous variants in CFTR gene (p.T1220I and p.V470M). These results suggest that the more severe pathology of the patient than her mother might be due to the possible compound heterozygous APOA5 variants, the heterozygous APOE variant, and the possible compound heterozygous CFTR variants. In this case, WES analyses were useful to evaluate not only the causative genes of hypertriglyceridemia (APOA5 and APOE) but also the genes involved in the development of acute pancreatitis (CFTR) simultaneously.
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Affiliation(s)
- Shingo Fujita
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Hitoshi Nishizawa
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Yohei Miyashita
- Department of Legal Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Tasuku Imada
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Takashi Yamaguchi
- Center of Diabetes, Endocrinology and Metabolism, Toho University Sakura Medical Center, Chiba 285-8741, Japan
| | - Takeyoshi Murano
- Clinical Laboratory Program, Faculty of Science, Toho University, Chiba 274-8510, Japan
| | - Hideaki Bujo
- Department of Clinical-Laboratory and Experimental-Research Medicine, Toho University Sakura Medical Center, Chiba 285-8741, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Junji Kozawa
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Department of Diabetes Care Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Norikazu Maeda
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Department of Metabolism and Atherosclerosis, Graduate School of Medicine Osaka University, Osaka 565-0871, Japan
| | - Iichiro Shimomura
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
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Molina Romero M, Yoldi Chaure A, Gañán Parra M, Navas Bastida P, del Pico Sánchez JL, Vaquero Argüelles Á, de la Fuente Vaquero P, Ramírez López JP, Castilla Alcalá JA. Probability of high-risk genetic matching with oocyte and semen donors: complete gene analysis or genotyping test? J Assist Reprod Genet 2022; 39:341-355. [PMID: 35091964 PMCID: PMC8956772 DOI: 10.1007/s10815-021-02381-0] [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: 03/29/2021] [Accepted: 12/17/2021] [Indexed: 02/03/2023] Open
Abstract
PURPOSE To estimate the probability of high-risk genetic matching when assisted reproductive techniques (ART) are applied with double gamete donation, following an NGS carrier test based on a complete study of the genes concerned. We then determine the results that would have been obtained if the genotyping tests most widely used in Spanish gamete banks had been applied. METHODS In this descriptive observational study, 1818 gamete donors were characterised by NGS. The pathogenic variants detected were analysed to estimate the probability of high-risk genetic matching and to determine the results that would have been obtained if the three most commonly used genotyping tests in ART had been applied. RESULTS The probability of high-risk genetic matching with gamete donation, screened by NGS and complete gene analysis, was 5.5%, versus the 0.6-2.7% that would have been obtained with the genotyping test. A total of 1741 variants were detected, including 607 different variants, of which only 22.6% would have been detected by all three genotyping tests considered and 44.7% of which would not have been detected by any of these tests. CONCLUSION Our study highlights the considerable heterogeneity of the genotyping tests, which present significant differences in their ability to detect pathogenic variants. The complete study of the genes by NGS considerably reduces reproductive risks when genetic matching is performed with gamete donors. Accordingly, we recommend that carrier screening in gamete donors be carried out using NGS and a complete study with nontargeted analysis of the variants of the screened genes.
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Affiliation(s)
- Marta Molina Romero
- CEIFER Biobanco - NextClinics, Calle Maestro Bretón, 1, 18004 Granada, Spain
| | | | | | | | | | | | | | | | - José Antonio Castilla Alcalá
- CEIFER Biobanco - NextClinics, Calle Maestro Bretón, 1, 18004 Granada, Spain ,U. Reproducción, UGC Obstetricia y Ginecología, HU Virgen de Las Nieves, Granada, Spain ,Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
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4
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Umair M, Ahmad F, Ahmad S, Alam Q, Rehan M, Alqosaibi AI, Alnamshan MM, Rafeeq MM, Haque S, Sain ZM, Ismail M, Alfadhel M. A Novel Homozygous Missense Mutation in the Zinc Finger DNA Binding Domain of GLI1 Causes Recessive Post-Axial Polydactyly. Front Genet 2021; 12:746949. [PMID: 34721536 PMCID: PMC8554680 DOI: 10.3389/fgene.2021.746949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/14/2021] [Indexed: 12/25/2022] Open
Abstract
Background: Polydactyly is a prevalent digit abnormality characterized by having extra digits/toes. Mutations in eleven known genes have been associated to cause nonsyndromic polydactyly: GLI3, GLI1, ZRS regulating LMBR1, IQCE, ZNF141, PITX1, MIPOL1, FAM92A, STKLD1, KIAA0825, and DACH1. Method: A single affected family member (IV-4) was subjected to whole-exome sequencing (WES) to identify the causal gene. Bi-directional Sanger sequencing was performed to segregate the identified variant within the family. In silico analysis was performed to investigate the effect of the variant on DNA binding properties. Results: whole-exome sequencing identified a bi-allelic missense variant (c.1010C > T; p. Ser337Leu) in exon nine of GLI1 gene located on chromosome 12q13.3. With the use of Sanger sequencing, the identified variant segregated perfectly with the disease phenotype. Furthermore, in silico analysis of this DNA binding protein revealed that the variant weakened the DNA binding interaction, resulting in indecorous GLI1 function. Conclusion: Herein, we report a novel variant in GLI1 gene, causing autosomal recessive post-axial polydactyly type A (PAPA) type 8. This confirms the critical role of GLI1 in digit development and might help in genotype-phenotype correlation in the future.
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Affiliation(s)
- Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Science, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Farooq Ahmad
- Department of Chemistry, Women University Swabi, Swabi, Pakistan
| | - Saeed Ahmad
- Consultant Orthopedic Surgeon, Capital Hospital Islamabad, Islamabad, Pakistan
| | - Qamre Alam
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Science, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Mohd Rehan
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amany I Alqosaibi
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mashael M Alnamshan
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abduaziz University, Jeddah, Saudi Arabia
| | - Shahnaz Haque
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abduaziz University, Jeddah, Saudi Arabia
| | - Ziaullah M Sain
- Department of Microbiology, Faculty of Medicine, Rabigh, King Abduaziz University, Jeddah, Saudi Arabia
| | - Muhammad Ismail
- Department of Chemistry, Women University Swabi, Swabi, Pakistan
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Science, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia.,Genetics and Precision Medicine department (GPM), King Abdullah Specialized Children's Hospital (KASCH), King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
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Carriers of cystic fibrosis among sperm donors: complete CFTR gene analysis versus CFTR genotyping. Fertil Steril 2020; 114:524-534. [PMID: 32773111 DOI: 10.1016/j.fertnstert.2020.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To determine the frequency of cystic fibrosis (CF) carriers among sperm donors in Spain studied through a complete analysis of the CFTR gene and to compare the results with those that would have been obtained by the 4 genotyping panels of the CFTR gene most commonly used as a carrier test in the context of assisted reproduction in our country. DESIGN Descriptive observational study. SETTING Private center. PATIENTS Nine hundred thirty-five sperm donors, from January 2014 to June 2019. INTERVENTION None. MAIN OUTCOME MEASURE Presence of pathogenic variants in the CFTR gene. RESULTS 17% of the donors were carriers of at least 1 pathogenic variant in CFTR, with 39 different pathogenic variants detected. Only 4 of these 39 variants (10.27%) would have been detected by the 4 genotyping tests considered, and 22 variants (56.41%) would not have been detected by any of the genotyping tests. The pathogenic variants of the CFTR gene included in the different genotyping tests analyzed vary widely, and <50% are common to all of them. CONCLUSIONS Although the was not based in the general population, these results show that the use of genotyping tests is associated with a high reproductive risk, because the rate of detection of CF carriers was lower when these panels were applied, in comparison with the complete study of the CFTR gene. We recommend that complete sequencing of the CFTR gene by next-generation sequencing be performed as a screening method for CF in sperm donors.
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Masamune A, Kotani H, Sörgel FL, Chen JM, Hamada S, Sakaguchi R, Masson E, Nakano E, Kakuta Y, Niihori T, Funayama R, Shirota M, Hirano T, Kawamoto T, Hosokoshi A, Kume K, Unger L, Ewers M, Laumen H, Bugert P, Mori MX, Tsvilovskyy V, Weißgerber P, Kriebs U, Fecher-Trost C, Freichel M, Diakopoulos KN, Berninger A, Lesina M, Ishii K, Itoi T, Ikeura T, Okazaki K, Kaune T, Rosendahl J, Nagasaki M, Uezono Y, Algül H, Nakayama K, Matsubara Y, Aoki Y, Férec C, Mori Y, Witt H, Shimosegawa T. Variants That Affect Function of Calcium Channel TRPV6 Are Associated With Early-Onset Chronic Pancreatitis. Gastroenterology 2020; 158:1626-1641.e8. [PMID: 31930989 DOI: 10.1053/j.gastro.2020.01.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 12/09/2019] [Accepted: 01/02/2020] [Indexed: 01/21/2023]
Abstract
BACKGROUND & AIMS Changes in pancreatic calcium levels affect secretion and might be involved in development of chronic pancreatitis (CP). We investigated the association of CP with the transient receptor potential cation channel subfamily V member 6 gene (TRPV6), which encodes a Ca2+-selective ion channel, in an international cohort of patients and in mice. METHODS We performed whole-exome DNA sequencing from a patient with idiopathic CP and from his parents, who did not have CP. We validated our findings by sequencing DNA from 300 patients with CP (not associated with alcohol consumption) and 1070 persons from the general population in Japan (control individuals). In replication studies, we sequenced DNA from patients with early-onset CP (20 years or younger) not associated with alcohol consumption from France (n = 470) and Germany (n = 410). We expressed TRPV6 variants in HEK293 cells and measured their activity using Ca2+ imaging assays. CP was induced by repeated injections of cerulein in TRPV6mut/mut mice. RESULTS We identified the variants c.629C>T (p.A210V) and c.970G>A (p.D324N) in TRPV6 in the index patient. Variants that affected function of the TRPV6 product were found in 13 of 300 patients (4.3%) and 1 of 1070 control individuals (0.1%) from Japan (odds ratio [OR], 48.4; 95% confidence interval [CI], 6.3-371.7; P = 2.4 × 10-8). Twelve of 124 patients (9.7%) with early-onset CP had such variants. In the replication set from Europe, 18 patients with CP (2.0%) carried variants that affected the function of the TRPV6 product compared with 0 control individuals (P = 6.2 × 10-8). Variants that did not affect the function of the TRPV6 product (p.I223T and p.D324N) were overrepresented in Japanese patients vs control individuals (OR, 10.9; 95% CI, 4.5-25.9; P = 7.4 × 10-9 for p.I223T and P = .01 for p.D324N), whereas the p.L299Q was overrepresented in European patients vs control individuals (OR, 3.0; 95% CI, 1.9-4.8; P = 1.2 × 10-5). TRPV6mut/mut mice given cerulein developed more severe pancreatitis than control mice, as shown by increased levels of pancreatic enzymes, histologic alterations, and pancreatic fibrosis. CONCLUSIONS We found that patients with early-onset CP not associated with alcohol consumption carry variants in TRPV6 that affect the function of its product, perhaps by altering Ca2+ balance in pancreatic cells. TRPV6 regulates Ca2+ homeostasis and pancreatic inflammation.
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Affiliation(s)
- Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Hiroshi Kotani
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Franziska Lena Sörgel
- Else Kröner-Fresenius-Zentrum für Ernährungsmedizin, Paediatric Nutritional Medicine, Technische Universität München, Freising, Germany
| | - Jian-Min Chen
- Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, France
| | - Shin Hamada
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Reiko Sakaguchi
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
| | - Emmanuelle Masson
- Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, France; CHU Brest, Service de Génétique, Brest, France
| | - Eriko Nakano
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ryo Funayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Matsuyuki Shirota
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tatsuya Hirano
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Tetsuya Kawamoto
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Atsuki Hosokoshi
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kiyoshi Kume
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Lara Unger
- Else Kröner-Fresenius-Zentrum für Ernährungsmedizin, Paediatric Nutritional Medicine, Technische Universität München, Freising, Germany
| | - Maren Ewers
- Else Kröner-Fresenius-Zentrum für Ernährungsmedizin, Paediatric Nutritional Medicine, Technische Universität München, Freising, Germany
| | - Helmut Laumen
- Else Kröner-Fresenius-Zentrum für Ernährungsmedizin, Paediatric Nutritional Medicine, Technische Universität München, Freising, Germany
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, German Red Cross Blood Service of Baden-Württemberg-Hessen, Mannheim, Germany
| | - Masayuki X Mori
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Volodymyr Tsvilovskyy
- Pharmakologisches Institut, Universität Heidelberg, Heidelberg, Germany; German Center for Cardiovascular Research, partner site Heidelberg, Germany
| | - Petra Weißgerber
- Experimentelle und Klinische Pharmakologie und Toxikologie, Universität des Saarlandes, Homburg, Germany
| | - Ulrich Kriebs
- Pharmakologisches Institut, Universität Heidelberg, Heidelberg, Germany; German Center for Cardiovascular Research, partner site Heidelberg, Germany
| | - Claudia Fecher-Trost
- Experimentelle und Klinische Pharmakologie und Toxikologie, Universität des Saarlandes, Homburg, Germany
| | - Marc Freichel
- Pharmakologisches Institut, Universität Heidelberg, Heidelberg, Germany; German Center for Cardiovascular Research, partner site Heidelberg, Germany
| | - Kalliope N Diakopoulos
- Mildred Scheel Chair of Tumor Metabolism and Comprehensive Cancer Center Munich at the Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Alexandra Berninger
- Mildred Scheel Chair of Tumor Metabolism and Comprehensive Cancer Center Munich at the Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Marina Lesina
- Mildred Scheel Chair of Tumor Metabolism and Comprehensive Cancer Center Munich at the Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Kentaro Ishii
- Department of Gastroenterology and Hepatology, Tokyo Medical University, Tokyo, Japan
| | - Takao Itoi
- Department of Gastroenterology and Hepatology, Tokyo Medical University, Tokyo, Japan
| | - Tsukasa Ikeura
- Department of Gastroenterology and Hepatology, Kansai Medical University, Hirakata, Japan
| | - Kazuichi Okazaki
- Department of Gastroenterology and Hepatology, Kansai Medical University, Hirakata, Japan
| | - Tom Kaune
- Department of Internal Medicine I, Martin Luther University, Halle (Saale), Germany
| | - Jonas Rosendahl
- Department of Internal Medicine I, Martin Luther University, Halle (Saale), Germany
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yasuhito Uezono
- Cancer Pathophysiology Division, National Cancer Center Research Institute, Tokyo, Japan
| | - Hana Algül
- Mildred Scheel Chair of Tumor Metabolism and Comprehensive Cancer Center Munich at the Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Keiko Nakayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Yoko Aoki
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Claude Férec
- Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, France; CHU Brest, Service de Génétique, Brest, France
| | - Yasuo Mori
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Heiko Witt
- Else Kröner-Fresenius-Zentrum für Ernährungsmedizin, Paediatric Nutritional Medicine, Technische Universität München, Freising, Germany
| | - Tooru Shimosegawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
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7
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Leung ML, Watson DJ, Vaccaro CN, Mafra F, Wenocur A, Wang T, Hakonarson H, Santani A. Evaluating sequence data quality from the Swift Accel-Amplicon CFTR Panel. Sci Data 2020; 7:8. [PMID: 31913291 PMCID: PMC6949293 DOI: 10.1038/s41597-019-0339-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/21/2019] [Indexed: 11/26/2022] Open
Abstract
Cystic fibrosis (CF) is one of the most common genetic diseases worldwide with high carrier frequencies across different ethnicities. Next generation sequencing of the cystic fibrosis transmembrane conductance regulator (CFTR) gene has proven to be an effective screening tool to determine carrier status with high detection rates. Here, we evaluate the performance of the Swift Biosciences Accel-Amplicon CFTR Capture Panel using CFTR-positive DNA samples. This assay is a one-day protocol that allows for one-tube reaction of 87 amplicons that span all coding regions, 5' and 3'UTR, as well as four intronic regions. In this study, we provide the FASTQ, BAM, and VCF files on seven unique CFTR-positive samples and one normal control sample (14 samples processed including repeated samples). This method generated sequencing data with high coverage and near 100% on-target reads. We found that coverage depth was correlated with the GC content of each exon. This dataset is instrumental for clinical laboratories that are evaluating this technology as part of their carrier screening program.
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Affiliation(s)
- Marco L Leung
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
| | - Deborah J Watson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Courtney N Vaccaro
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Fernanda Mafra
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Adam Wenocur
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Tiancheng Wang
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Avni Santani
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
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8
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The CFTR gene variants in Japanese children with idiopathic pancreatitis. Hum Genome Var 2019; 6:17. [PMID: 30992994 PMCID: PMC6459923 DOI: 10.1038/s41439-019-0049-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 12/15/2022] Open
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) gene has been reported as one of the pancreatitis susceptibility genes. Although many variants of CFTR have been reported in Caucasian patients, there are few data in Japanese patients. We aimed to survey CFTR variants in Japanese children with idiopathic pancreatitis. Twenty-eight Japanese paediatric patients with idiopathic pancreatitis were enroled, who were not previously diagnosed by genetic analysis of PRSS1 and SPINK1. The entire CFTR gene was sequenced in the patients by combining LA-PCR and next-generation sequencing analysis. To determine a splice-affecting variant, CFTR expression was investigated in the nasal epithelial cells by RT-PCR. One (3.6%) and 15 (53.6%) of 28 patients had pathogenic and functionally affected variants in the CFTR gene, respectively. Two variants, p.Arg352Gln and p.Arg1453Trp, were found more frequently in the patients compared with one in Japanese healthy controls (p = 0.0078 and 0.044, respectively). We confirmed skipping of exon 10 in the nasal epithelial cells in one patient having a splice-affecting variant (c.1210-12 T(5)) in intron 9. Functionally affected variants of the CFTR gene are not so rare in Japanese paediatric patients with idiopathic pancreatitis. Surveying CFTR gene variants in a Japanese sample could help identify pancreatitis risk in these children. Mutations in a cystic fibrosis-related gene could help identify Japanese children at risk of developing pancreatic inflammation. Tadashi Kaname, of Tokyo’s National Center for Child Health and Development, and colleagues sequenced the cystic fibrosis transmembrane conductance regulator gene (CFTR) in 28 Japanese children with pancreatitis of unknown origin. The gene is involved in the development of cystic fibrosis and has been reported to be associated with pancreatitis but little is known about its role in idiopathic pancreatitis in Asian populations. The team found CFTR gene mutations in 16 out of the 28 children. Cystic fibrosis is uncommon among Japanese, so CFTR mutations were also thought to be rare. The study suggests, however, that mutations might not be so rare in Japanese children with idiopathic pancreatitis and could help identify those at risk of developing the condition.
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Ivanov M, Matsvay A, Glazova O, Krasovskiy S, Usacheva M, Amelina E, Chernyak A, Ivanov M, Musienko S, Prodanov T, Kovalenko S, Baranova A, Khafizov K. Targeted sequencing reveals complex, phenotype-correlated genotypes in cystic fibrosis. BMC Med Genomics 2018; 11:13. [PMID: 29504914 PMCID: PMC5836842 DOI: 10.1186/s12920-018-0328-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Cystic fibrosis (CF) is one of the most common life-threatening genetic disorders. Around 2000 variants in the CFTR gene have been identified, with some proportion known to be pathogenic and 300 disease-causing mutations have been characterized in detail by CFTR2 database, which complicates its analysis with conventional methods. Methods We conducted next-generation sequencing (NGS) in a cohort of 89 adult patients negative for p.Phe508del homozygosity. Complete clinical and demographic information were available for 84 patients. Results By combining MLPA with NGS, we identified disease-causing alleles in all the CF patients. Importantly, in 10% of cases, standard bioinformatics pipelines were inefficient in identifying causative mutations. Class IV-V mutations were observed in 38 (45%) cases, predominantly ones with pancreatic sufficient CF disease; rest of the patients had Class I-III mutations. Diabetes was seen only in patients homozygous for class I-III mutations. We found that 12% of the patients were heterozygous for more than two pathogenic CFTR mutations. Two patients were observed with p.[Arg1070Gln, Ser466*] complex allele which was associated with milder pulmonary obstructions (FVC 107 and 109% versus 67%, CI 95%: 63-72%; FEV 90 and 111% versus 47%, CI 95%: 37-48%). For the first time p.[Phe508del, Leu467Phe] complex allele was reported, observed in four patients (5%). Conclusion NGS can be a more information-gaining technology compared to standard methods. Combined with its equivalent diagnostic performance, it can therefore be implemented in the clinical practice, although careful validation is still required. Electronic supplementary material The online version of this article (10.1186/s12920-018-0328-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maxim Ivanov
- Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, Dolgoprudny, Moscow Region, Russian Federation, 141700. .,Atlas Biomed Group, Moscow, Russian Federation, 121069.
| | - Alina Matsvay
- Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, Dolgoprudny, Moscow Region, Russian Federation, 141700.,Central Research Scientific Institute of Epidemiology, Moscow, Russian Federation, 111123
| | - Olga Glazova
- Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, Dolgoprudny, Moscow Region, Russian Federation, 141700
| | | | - Mariya Usacheva
- Federal Pulmonology Research Institute, Moscow, Russian Federation, 105077
| | - Elena Amelina
- Federal Pulmonology Research Institute, Moscow, Russian Federation, 105077
| | - Aleksandr Chernyak
- Federal Pulmonology Research Institute, Moscow, Russian Federation, 105077
| | - Mikhail Ivanov
- Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, Dolgoprudny, Moscow Region, Russian Federation, 141700
| | | | - Timofey Prodanov
- Department of Mathematics and Information Technology, St. Petersburg Academic University, St. Petersburg, Russian Federation, 195251
| | - Sergey Kovalenko
- The Institute of Molecular Biology and Biophysics, Novosibirsk, Russian Federation, 630117.,Novosibirsk State University, Novosibirsk, Russian Federation, 630090
| | - Ancha Baranova
- Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, Dolgoprudny, Moscow Region, Russian Federation, 141700.,Atlas Biomed Group, Moscow, Russian Federation, 121069.,Research Centre for Medical Genetics, Moscow, Russia.,Center for the Study of Chronic Metabolic Diseases, School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - Kamil Khafizov
- Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, Dolgoprudny, Moscow Region, Russian Federation, 141700.,Central Research Scientific Institute of Epidemiology, Moscow, Russian Federation, 111123
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Masamune A, Kikuta K, Hamada S, Nakano E, Kume K, Inui A, Shimizu T, Takeyama Y, Nio M, Shimosegawa T. Nationwide survey of hereditary pancreatitis in Japan. J Gastroenterol 2018; 53:152-160. [PMID: 28861620 DOI: 10.1007/s00535-017-1388-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 08/18/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Hereditary pancreatitis (HP) is a rare cause of chronic pancreatitis. We here report a nationwide survey to clarify the epidemiological, genetic, and clinical features of HP in Japan. METHODS Target subjects were patients with HP and their family members who had visited selected hospitals between 2005 and 2014. This study consisted of two-stage surveys; patients with HP were identified by the first questionnaire and their clinical features were assessed by the second questionnaire. RESULTS Two hundred seventy-one patients (153 males and 118 females) in 100 families diagnosed based on the Japanese criteria or 231 patients (131 males and 100 females) patients in 80 families based on the EUROPAC criteria were reported. Of the families undertaking genetic tests, 41% had the PRSS1 mutations (p.R122H 33%, p.N29I 8%) and 36% had the SPINK1 mutations (p.N34S 22%, c.194+2T>C 14%, p.P45S 1%). The mean age at symptom onset was 17.8 years. The cumulative rates of pancreatic exocrine insufficiency and diabetes mellitus were 16.1 and 5.5% at 20 years old, and 45.3 and 28.2% at 40 years, respectively. Forty-four percent of the patients underwent endoscopic treatment and/or surgery. The cumulative rate of pancreatic cancer diagnosis was 2.8% at 40 years old, 10.8% at 60 years, and 22.8% at 70 years. CONCLUSIONS HP was characterized by early disease onset, frequent development of pancreatic exocrine insufficiency and diabetes mellitus, requirement of endoscopic treatment and/or surgery, and increased risk of pancreatic cancer. PRSS1 and SPINK1 mutations serve as genetic background for HP in Japan.
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Affiliation(s)
- Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan.
| | - Kazuhiro Kikuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Shin Hamada
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Eriko Nakano
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Kiyoshi Kume
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Ayano Inui
- Department of Pediatric Hepatology and Gastroenterology, Eastern Yokohama Hospital, Yokohama, Japan
| | | | - Yoshifumi Takeyama
- Department of Surgery, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Masaki Nio
- Department of Pediatric Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tooru Shimosegawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
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Lucarelli M, Porcaro L, Biffignandi A, Costantino L, Giannone V, Alberti L, Bruno SM, Corbetta C, Torresani E, Colombo C, Seia M. A New Targeted CFTR Mutation Panel Based on Next-Generation Sequencing Technology. J Mol Diagn 2017; 19:788-800. [PMID: 28736296 DOI: 10.1016/j.jmoldx.2017.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 06/01/2017] [Accepted: 06/07/2017] [Indexed: 01/16/2023] Open
Abstract
Searching for mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) is a key step in the diagnosis of and neonatal and carrier screening for cystic fibrosis (CF), and it has implications for prognosis and personalized therapy. The large number of mutations and genetic and phenotypic variability make this search a complex task. Herein, we developed, validated, and tested a laboratory assay for an extended search for mutations in CFTR using a next-generation sequencing-based method, with a panel of 188 CFTR mutations customized for the Italian population. Overall, 1426 dried blood spots from neonatal screening, 402 genomic DNA samples from various origins, and 1138 genomic DNA samples from patients with CF were analyzed. The assay showed excellent analytical and diagnostic operative characteristics. We identified and experimentally validated 159 (of 188) CFTR mutations. The assay achieved detection rates of 95.0% and 95.6% in two large-scale case series of CF patients from central and northern Italy, respectively. These detection rates are among the highest reported so far with a genetic test for CF based on a mutation panel. This assay appears to be well suited for diagnostics, neonatal and carrier screening, and assisted reproduction, and it represents a considerable advantage in CF genetic counseling.
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Affiliation(s)
- Marco Lucarelli
- Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy; Pasteur Institute Cenci Bolognetti Foundation, Sapienza University, Rome, Italy.
| | - Luigi Porcaro
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alice Biffignandi
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lucy Costantino
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Giannone
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luisella Alberti
- Newborn Screening Laboratory, ASST Fatebenefratelli Sacco-PO Ospedale dei Bambini "V. Buzzi", Milan, Italy
| | - Sabina Maria Bruno
- Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Carlo Corbetta
- Newborn Screening Laboratory, ASST Fatebenefratelli Sacco-PO Ospedale dei Bambini "V. Buzzi", Milan, Italy
| | - Erminio Torresani
- Unit of Microbiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Carla Colombo
- Cystic Fibrosis Centre, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Manuela Seia
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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Masamune A, Nakano E, Niihori T, Hamada S, Nagasaki M, Aoki Y, Shimosegawa T. Variants in the UBR1 gene are not associated with chronic pancreatitis in Japan. Pancreatology 2016; 16:814-8. [PMID: 27397733 DOI: 10.1016/j.pan.2016.06.662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND/OBJECTIVES The UBR1 gene encodes the enzyme ubiquitin-protein ligase E3 component n-recognin 1. Loss-of-function mutations in the UBR1 gene cause Johanson-Blizzard syndrome, which involves pancreatic exocrine insufficiency. No previous studies have examined an association of UBR1 variants with pancreatitis, in part due to the large size of the gene. This study aimed to clarify whether UBR1 variants are associated with chronic pancreatitis (CP) by the application of targeted next generation sequencing. METHODS Exon sequences of the UBR1 gene from 389 Japanese patients with CP (188 idiopathic, 172 alcoholic, 20 hereditary, 9 familial) were captured by the HaloPlex target enrichment technology and subjected to next generation sequencing. RESULTS Ninety nine point two % of the coding regions of the UBR1 gene could be sequenced by ≥ 20 reads with a mean read depth of 595 and a median depth of 399. Fifteen non-synonymous variants including three novel ones [c.4514T > C (p.I1505T), c.4828C > G (p.H1610D) and c.4856A > T (p.D1619V)] and two synonymous variants were identified in the exonic regions. The frequency of any non-synonymous or synonymous variants was not different between the patients with CP and controls. CONCLUSIONS Variants in the UBR1 gene were not associated with CP in Japan.
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Affiliation(s)
- Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Eriko Nakano
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tetsuya Niihori
- Division of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shin Hamada
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yoko Aoki
- Division of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tooru Shimosegawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
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Pagin A, Devos A, Figeac M, Truant M, Willoquaux C, Broly F, Lalau G. Applicability and Efficiency of NGS in Routine Diagnosis: In-Depth Performance Analysis of a Complete Workflow for CFTR Mutation Analysis. PLoS One 2016; 11:e0149426. [PMID: 26900683 PMCID: PMC4762772 DOI: 10.1371/journal.pone.0149426] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/31/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Actually, about 2000 sequence variations have been documented in the CFTR gene requiring extensive and multi-step genetic testing in the diagnosis of cystic fibrosis and CFTR-related disorders. We present a two phases study, with validation and performance monitoring, of a single experiment methodology based on multiplex PCR and high throughput sequencing that allows detection of all variants, including large rearrangements, affecting the coding regions plus three deep intronic loci. METHODS A total of 340 samples, including 257 patients and 83 previously characterized control samples, were sequenced in 17 MiSeq runs and analyzed with two bioinformatic pipelines in routine diagnostic conditions. We obtained 100% coverage for all the target regions in every tested sample. RESULTS We correctly identified all the 87 known variants in the control samples and successfully confirmed the 62 variants identified among the patients without observing false positive results. Large rearrangements were identified in 18/18 control samples. Only 17 patient samples showed false positive signals (6.6%), 12 of which showed a borderline result for a single amplicon. We also demonstrated the ability of the assay to detect allele specific dropout of amplicons when a sequence variation occurs at a primer binding site thus limiting the risk for false negative results. CONCLUSIONS We described here the first NGS workflow for CFTR routine analysis that demonstrated equivalent diagnostic performances compared to Sanger sequencing and multiplex ligation-dependent probe amplification. This study illustrates the advantages of NGS in term of scalability, workload reduction and cost-effectiveness in combination with an improvement of the overall data quality due to the simultaneous detection of SNVs and large rearrangements.
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Affiliation(s)
- Adrien Pagin
- Department of Toxicology and Genopathy, Biology Pathology Center, Lille University Hospital, Lille, France
| | - Aurore Devos
- Department of Toxicology and Genopathy, Biology Pathology Center, Lille University Hospital, Lille, France
| | - Martin Figeac
- Functional and Structural Genomic Platform, Lille, France
| | - Maryse Truant
- Department of Toxicology and Genopathy, Biology Pathology Center, Lille University Hospital, Lille, France
| | - Christelle Willoquaux
- Department of Toxicology and Genopathy, Biology Pathology Center, Lille University Hospital, Lille, France
| | - Franck Broly
- Department of Toxicology and Genopathy, Biology Pathology Center, Lille University Hospital, Lille, France
- University of Lille 2, Lille, France
| | - Guy Lalau
- Department of Toxicology and Genopathy, Biology Pathology Center, Lille University Hospital, Lille, France
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14
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Kondo S, Fujiki K, Ko SBH, Yamamoto A, Nakakuki M, Ito Y, Shcheynikov N, Kitagawa M, Naruse S, Ishiguro H. Functional characteristics of L1156F-CFTR associated with alcoholic chronic pancreatitis in Japanese. Am J Physiol Gastrointest Liver Physiol 2015; 309:G260-9. [PMID: 26089335 PMCID: PMC4537928 DOI: 10.1152/ajpgi.00015.2014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 06/09/2015] [Indexed: 01/31/2023]
Abstract
Although cystic fibrosis is rare in Japanese, measurement of sweat Cl(-) has suggested mild dysfunction of cystic fibrosis transmembrane conductance regulator (CFTR) in some patients with chronic pancreatitis. In the present study, we have investigated the association of CFTR variants and chronic pancreatitis in Japanese and the functional characteristics of a Japanese- and pancreatitis-specific CFTR variant, L1156F. Seventy patients with alcoholic chronic pancreatitis, 18 patients with idiopathic chronic pancreatitis, and 180 normal subjects participated. All exons and their boundaries and promoter region of the CFTR gene were sequenced. Human embryonic kidney-293 cells were transfected with three CFTR variants (M470V, L1156F, and M470V+L1156F), and the protein expression was examined. Xenopus laevis oocytes were injected with the CFTR variants, and bicarbonate (HCO3 (-)) transport activity was examined. CFPAC-1 cells were transfected with the CFTR variants and Cl(-)/HCO3 (-) exchange activity was examined. Six variants (E217G, I556V, M470V, L1156F, Q1352H, and R1453W) were identified in the coding region of the CFTR gene. Cystic fibrosis-causing mutations were not found. The allele frequencies of L1156F and Q1352H in alcoholic chronic pancreatitis (5.0 and 7.9%) were significantly (P < 0.01) higher than those in normal subjects (0.6 and 1.9%). L1156F was linked with a worldwide CFTR variant, M470V. Combination of M470V and L1156F significantly reduced CFTR expression to ∼60%, impaired CFTR-mediated HCO3 (-)/Cl(-) transport activity to 50-60%, and impaired CFTR-coupled Cl(-)/HCO3 (-) exchange activity to 20-30%. The data suggest that the Japanese-specific CFTR variant L1156F causes mild dysfunction of CFTR and increases the risk of alcoholic chronic pancreatitis in Japanese.
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Affiliation(s)
- Shiho Kondo
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kotoyo Fujiki
- Department of Nutrition, Nagoya University of Arts and Sciences, Nisshin, Japan
| | - Shigeru B H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Akiko Yamamoto
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Miyuki Nakakuki
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasutomo Ito
- Division for Medical Research Engineering, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nikolay Shcheynikov
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, Maryland; and
| | - Motoji Kitagawa
- Department of Nutrition, Nagoya University of Arts and Sciences, Nisshin, Japan
| | | | - Hiroshi Ishiguro
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan;
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15
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Trujillano D, Weiss MER, Köster J, Papachristos EB, Werber M, Kandaswamy KK, Marais A, Eichler S, Creed J, Baysal E, Jaber IY, Mehaney DA, Farra C, Rolfs A. Validation of a semiconductor next-generation sequencing assay for the clinical genetic screening of CFTR. Mol Genet Genomic Med 2015; 3:396-403. [PMID: 26436105 PMCID: PMC4585447 DOI: 10.1002/mgg3.149] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/17/2015] [Accepted: 03/24/2015] [Indexed: 12/13/2022] Open
Abstract
Genetic testing for cystic fibrosis and CFTR-related disorders mostly relies on laborious molecular tools that use Sanger sequencing to scan for mutations in the CFTR gene. We have explored a more efficient genetic screening strategy based on next-generation sequencing (NGS) of the CFTR gene. We validated this approach in a cohort of 177 patients with previously known CFTR mutations and polymorphisms. Genomic DNA was amplified using the Ion AmpliSeq™ CFTR panel. The DNA libraries were pooled, barcoded, and sequenced using an Ion Torrent PGM sequencer. The combination of different robust bioinformatics tools allowed us to detect previously known pathogenic mutations and polymorphisms in the 177 samples, without detecting spurious pathogenic calls. In summary, the assay achieves a sensitivity of 94.45% (95% CI: 92% to 96.9%), with a specificity of detecting nonvariant sites from the CFTR reference sequence of 100% (95% CI: 100% to 100%), a positive predictive value of 100% (95% CI: 100% to 100%), and a negative predictive value of 99.99% (95% CI: 99.99% to 100%). In addition, we describe the observed allelic frequencies of 94 unique definitely and likely pathogenic, uncertain, and neutral CFTR variants, some of them not previously annotated in the public databases. Strikingly, a seven exon spanning deletion as well as several more technically challenging variants such as pathogenic poly-thymidine-guanine and poly-thymidine (poly-TG-T) tracts were also detected. Targeted NGS is ready to substitute classical molecular methods to perform genetic testing on the CFTR gene.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Erol Baysal
- Pathology and Genetics Department, Dubai Genetic and Thalassemia Center, Dubai Health Authority Dubai, United Arab Emirates
| | - Iqbal Yousuf Jaber
- Pathology and Genetics Department, Dubai Genetic and Thalassemia Center, Dubai Health Authority Dubai, United Arab Emirates
| | - Dina Ahmed Mehaney
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University Cairo, Egypt
| | - Chantal Farra
- Department of Pathology & Laboratory Medicine, American University of Beirut Medical Center Beirut, Lebanon
| | - Arndt Rolfs
- Centogene AG Rostock, Germany ; Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock Rostock, Germany
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van der Werf IM, Kooy RF, Vandeweyer G. A robust protocol to increase NimbleGen SeqCap EZ multiplexing capacity to 96 samples. PLoS One 2015; 10:e0123872. [PMID: 25875648 PMCID: PMC4397063 DOI: 10.1371/journal.pone.0123872] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/23/2015] [Indexed: 01/08/2023] Open
Abstract
Contemporary genetic studies frequently involve sequencing of a targeted gene panel, for instance consisting of a set of genes associated with a specific disease. The NimbleGen SeqCap EZ Choice kit is commonly used for the targeted enrichment of sequencing libraries comprising a target size up to 7 Mb. A major drawback of this commercially available method is the exclusive use of single-indexing, meaning that at most 24 samples can be multiplexed in a single reaction. In case of relatively small target sizes, this will lead to excessive amounts of data per sample. We present an extended version of the NimbleGen SeqCap EZ protocol which allows to robustly multiplex up to 96 samples. We achieved this by incorporating Illumina dual-indexing based custom adapters into the original protocol. To further extend the optimization of cost-efficient sequencing of custom target panels, we studied the effect of higher pre-enrichment pooling factors and show that pre-enrichment pooling of up to 12 samples does not affect the quality of the data. To facilitate evaluation of capture efficiency in custom design panels, we also provide a detailed reporting tool.
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Affiliation(s)
- Ilse M. van der Werf
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
- * E-mail:
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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