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de la Morena-Barrio B, Palomo Á, Padilla J, Martín-Fernández L, Rojo-Carrillo JJ, Cifuentes R, Bravo-Pérez C, Garrido-Rodríguez P, Miñano A, Rubio AM, Pagán J, Llamas M, Vicente V, Vidal F, Lozano ML, Corral J, de la Morena-Barrio ME. Impact of genetic structural variants in factor XI deficiency: identification, accurate characterization, and inferred mechanism by long-read sequencing. J Thromb Haemost 2023; 21:1779-1788. [PMID: 36940803 DOI: 10.1016/j.jtha.2023.03.009] [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: 12/23/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/23/2023]
Abstract
BACKGROUND Congenital factor XI (FXI) deficiency is a probably underestimated coagulopathy that confers antithrombotic protection. Characterization of genetic defects in F11 is mainly focused on the identification of single-nucleotide variants and small insertion/deletions because they represent up to 99% of the alterations accounting for factor deficiency, with only 3 gross gene defects of structural variants (SVs) having been described. OBJECTIVES To identify and characterize the SVs affecting F11. METHODS The study was performed in 93 unrelated subjects with FXI deficiency recruited in Spanish hospitals over a period of 25 years (1997-2022). F11 was analyzed by next-generation sequencing, multiplex ligand probe amplification, and long-read sequencing. RESULTS Our study identified 30 different genetic variants. Interestingly, we found 3 SVs, all heterozygous: a complex duplication affecting exons 8 and 9, a tandem duplication of exon 14, and a large deletion affecting the whole gene. Nucleotide resolution obtained by long-read sequencing revealed Alu repetitive elements involved in all breakpoints. The large deletion was probably generated de novo in the paternal allele during gametogenesis, and despite affecting 30 additional genes, no syndromic features were described. CONCLUSION SVs may account for a high proportion of F11 genetic defects implicated in the molecular pathology of congenital FXI deficiency. These SVs, likely caused by a nonallelic homologous recombination involving repetitive elements, are heterogeneous in both type and length and may be de novo. These data support the inclusion of methods to detect SVs in this disorder, with long-read-based methods being the most appropriate because they detect all SVs and achieve adequate nucleotide resolution.
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Affiliation(s)
- Belén de la Morena-Barrio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Ángeles Palomo
- Servicio de Hematología y Hemoterapia del centro Materno-Infantil del Hospital Regional Universitario Carlos de Haya, Málaga, Spain
| | - José Padilla
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Laura Martín-Fernández
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain; Medicina Transfusional. Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan José Rojo-Carrillo
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Rosa Cifuentes
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Carlos Bravo-Pérez
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Pedro Garrido-Rodríguez
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Antonia Miñano
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Ana María Rubio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Javier Pagán
- Servicio de Medicina Interna, Hospital Universitario Morales Meseguer, Murcia, Spain
| | - María Llamas
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Vicente Vicente
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Francisco Vidal
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain; Medicina Transfusional. Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
| | - María Luisa Lozano
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Javier Corral
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain.
| | - María Eugenia de la Morena-Barrio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain.
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Zlotogora J, Harel T, Meiner V. Explanations for the discrepancy between variant frequency and homozygous disease occurrence: Lessons from Ashkenazi Jewish data. Eur J Med Genet 2023; 66:104765. [PMID: 37028505 DOI: 10.1016/j.ejmg.2023.104765] [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: 09/05/2022] [Revised: 12/28/2022] [Accepted: 04/03/2023] [Indexed: 04/09/2023]
Abstract
Ample data on recessive disorders among Ashkenazi Jews has been gathered and published through the years. The opportunity to integrate molecular records analyzed in actual affected individuals with data derived from population-documented frequencies enables to compare these figures. We reviewed assumed pathogenic variants reported among patients in the Israeli medical genetic database (IMGD) with a carrier frequency of 1% or more among Ashkenazi Jews in gnomAD. Among the 60 assumed pathogenic variants recorded in IMGD, 15 (25%) had either a disease incidence considerably lower than expected by the calculated carrier frequency (12 variants), or the variant was not characterized in Ashkenazi Jewish patients (three variants). Possible explanations for the rarity or absence of affected individuals despite high carrier frequency include embryonic lethality, clinical variability, and incomplete and age-related penetrance, in addition to the existence of additional assumed pathogenic variants on the founder haplotype, hypomorphic variants or digenic inheritance. The discrepancy in actual versus expected number of patients calls for caution upon designing and choosing targeted genes and recessive mutations for carrier screening.
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Affiliation(s)
- Joël Zlotogora
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, 9112001, Israel.
| | - Tamar Harel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, 9112001, Israel; Department of Genetics, Hadassah Medical Organization, Jerusalem, 9112001, Israel
| | - Vardiella Meiner
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, 9112001, Israel; Department of Genetics, Hadassah Medical Organization, Jerusalem, 9112001, Israel
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Pshenichnikova OS, Surin VL, Sats NV, Yakovleva EV, Dimitrieva OS, Zozulya NI. Mutation Analysis of F11 Gene in Patients with FXI Deficiency in Russia. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422070134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Coller BS, Varon D. Uri Seligsohn, MD (1937-2022). J Thromb Haemost 2022; 20:1275-1279. [PMID: 35247294 DOI: 10.1111/jth.15688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 02/19/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Barry S Coller
- Allen and Frances Adler Laboratory of Blood and Vascular Biology, The Rockefeller University, New York, New York, USA
| | - David Varon
- Coagulation Unit, Tel Aviv Medical Center, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Archeogenetics of F11 p.Cys38Arg: a 5400-year-old mutation identified in different southwestern European countries. Blood 2019; 133:2618-2622. [PMID: 31043424 DOI: 10.1182/blood.2019000055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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Esteban J, de la Morena-Barrio ME, Salloum-Asfar S, Padilla J, Miñano A, Roldán V, Soria JM, Vidal F, Corral J, Vicente V. High incidence of FXI deficiency in a Spanish town caused by 11 different mutations and the first duplication of F11: Results from the Yecla study. Haemophilia 2017; 23:e488-e496. [PMID: 28960694 DOI: 10.1111/hae.13356] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2017] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Factor XI (FXI) deficiency is a rare disorder with molecular heterogeneity in Caucasians but relatively frequent and molecularly homogeneous in certain populations. AIM To characterize FXI deficiency in a Spanish town of 60 000 inhabitants. METHODS A total of 324 764 APTT tests were screened during 20 years. FXI was evaluated by FXI:C and by Western blot. Genetic analysis of F11 was performed by sequencing, multiplex ligation-dependent probe amplification and genotyping. RESULTS Our study identified 46 unrelated cases and 170 relatives with FXI deficiency carrying 12 different genetic defects. p.Cys56Arg, described as founder mutation in the French-Basque population, was identified in 109 subjects from 24 unrelated families. This mutation was also identified in 2% of the general population. p.Cys416Tyr, c.1693G>A and p.Pro538Leu were identified in 7, 6 and 2 unrelated families, respectively. NGS analysis of the whole F11 gene revealed a common haplotype for each of the four recurrent mutations, suggesting a founder effect. The analysis of plasma FXI of four p.Pro538Leu homozygous carriers revealed that this variant was not activated by FXIIa. We identified four mutations previously described in other Caucasian subjects with FXI deficiency (p.Lys536Asn; p.Thr322Ile, p.Arg268Cys and c.325G>A) and four new gene defects: p.(Cys599Tyr) potentially causing a functional deficiency, p.(Ile426Thr), p.(Ile592Thr) and the first worldwide duplication of 1653 bp involving exons 8 and 9. Bleeding was rare and mild. CONCLUSIONS Our population-cohort study supplies new evidences that FXI deficiency in Caucasians is more common than previously thought and confirmed the wide underlying genetic heterogeneity, caused by both recurrent and sporadic mutations.
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Affiliation(s)
- J Esteban
- Servicio de Hematología, Hospital Virgen del Castillo de Yecla, Murcia, Spain
| | - M E de la Morena-Barrio
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, IMIB-Arrixaca, Universidad de Murcia, CIBERER, Murcia, Spain
| | - S Salloum-Asfar
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, IMIB-Arrixaca, Universidad de Murcia, CIBERER, Murcia, Spain
| | - J Padilla
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, IMIB-Arrixaca, Universidad de Murcia, CIBERER, Murcia, Spain
| | - A Miñano
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, IMIB-Arrixaca, Universidad de Murcia, CIBERER, Murcia, Spain
| | - V Roldán
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, IMIB-Arrixaca, Universidad de Murcia, CIBERER, Murcia, Spain
| | - J M Soria
- IIB-Sant Pau, Unitat de Genòmica de Malalties Complexes, Barcelona, Spain
| | - F Vidal
- Coagulopaties congènites, Banc de Sang i Teixits, Barcelona, Spain.,Unitat de Diagnòstic i Teràpia Molecular, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain.,CIBER de Enfermedades Cardiovasculares, Spain
| | - J Corral
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, IMIB-Arrixaca, Universidad de Murcia, CIBERER, Murcia, Spain
| | - V Vicente
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, IMIB-Arrixaca, Universidad de Murcia, CIBERER, Murcia, Spain
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Ioscovich A, Fadeev D, Kenet G, Naamad M, Schtrechman G, Zimran A, Elstein D. Thromboelastography as a Surrogate Marker of Perisurgical Hemostasis in Gaucher Disease. Clin Appl Thromb Hemost 2016; 22:693-7. [DOI: 10.1177/1076029615578165] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Thromboelastography (TEG) has long been available for routine monitoring of perisurgical and postpartum hemostasis, especially at point of care. The purpose of this study is to retrospectively compare TEG parameters to concomitant standard clotting test results in an unselected cohort of patients with Gaucher disease to ascertain whether TEG values are specific and sensitive enough to substitute for classic coagulation tests for decision making. This remains a cogent concern because of high incidence of thrombocytopenia in patients with Gaucher disease. Thromboelastography values were compared to concomitant platelet counts, partial thromboplastin time, international normalization ratio, and plasma fibrinogen. Demographic characteristics were collected from patients’ files. There were 22 patients with Gaucher disease (2 children; 12.5%) for whom there were 24 TEG results at the same time as classic coagulation test results and 30% performed platelet function tests. The current study shows linear and/or monotonic relationships between platelet counts and several TEG values that were significant over a range of platelet counts including severe thrombocytopenia. The fibrinogen component, correlating only with the rate of clot lysis, played a lesser role. Based on these preliminary results albeit in a small cohort with only 1 case of hemorrhage, there is putative support for the intention to treat patients with Gaucher disease based on TEG results using the same TEG protocol as for other patients undergoing comparable procedures in our institution.
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Affiliation(s)
- Alexander Ioscovich
- Department of Anesthesiology, Perioperative Medicine & Pain Treatment, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Dmitri Fadeev
- Department of Anesthesiology, Perioperative Medicine & Pain Treatment, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Gili Kenet
- National Hemophilia Center, Sheba Medical Center, Tel Hashomer affiliated with the Sackler Medical School of the Tel Aviv University, Tel Aviv, Israel
| | - Mira Naamad
- Blood Bank, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Gal Schtrechman
- Department of Anesthesiology, Perioperative Medicine & Pain Treatment, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Ari Zimran
- Gaucher Clinic, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Deborah Elstein
- Gaucher Clinic, Shaare Zedek Medical Center, Jerusalem, Israel
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Baskovich B, Hiraki S, Upadhyay K, Meyer P, Carmi S, Barzilai N, Darvasi A, Ozelius L, Peter I, Cho JH, Atzmon G, Clark L, Lencz T, Pe’er I, Ostrer H, Oddoux C. Expanded genetic screening panel for the Ashkenazi Jewish population. Genet Med 2016; 18:522-8. [PMID: 26334176 PMCID: PMC4814352 DOI: 10.1038/gim.2015.123] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 07/22/2015] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Carrier screening programs that identify the presence of known mutations have been effective for reducing the incidence of autosomal recessive conditions in the Ashkenazi Jewish (AJ) population and other populations. Yet, these programs have not realized their full potential. Furthermore, many known autosomal recessive and dominant conditions are not screened for and the molecular basis of other conditions for which screening might be offered is unknown. METHODS Through literature review and annotation of full sequenced genomes from healthy individuals, we expanded the list of mutations. Mutations were identified in a sample of 128 fully sequenced AJ genomes that were filtered through clinical databases and curated manually for clinical validity and utility using the American College of Medical Genetics and Genomics scoring (ACMG) system. Other known mutations were identified through literature review. RESULTS A panel of 163 mutations was identified for 76 autosomal recessive, 24 autosomal dominant, and 3 X-linked disorders. CONCLUSION Screening for a broader range of disorders not only could further reduce the incidence of autosomal recessive disorders but also could offer the benefits of early or presymptomatic diagnosis.Genet Med 18 5, 522-528.
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Affiliation(s)
- Brett Baskovich
- Montefiore Medical Center, Department of Pathology, New York, NY
| | - Susan Hiraki
- Albert Einstein College of Medicine of Yeshiva University, New York, NY
| | - Kinnari Upadhyay
- Albert Einstein College of Medicine of Yeshiva University, New York, NY
| | - Philip Meyer
- Albert Einstein College of Medicine of Yeshiva University, New York, NY
| | - Shai Carmi
- Columbia University, Department of Computer Science, New York, NY
| | - Nir Barzilai
- Albert Einstein College of Medicine of Yeshiva University, New York, NY
| | - Ariel Darvasi
- Hebrew University of Jerusalem, Department of Genetics, Givat Ram, Jerusalem
| | - Laurie Ozelius
- Icahn School of Medicine at Mount Sinai School of Medicine, Department of Genetics, New York, NY
| | - Inga Peter
- Icahn School of Medicine at Mount Sinai School of Medicine, Department of Genetics, New York, NY
| | - Judy H. Cho
- Icahn School of Medicine at Mount Sinai School of Medicine, Department of Genetics, New York, NY
| | - Gil Atzmon
- Albert Einstein College of Medicine of Yeshiva University, New York, NY
- University of Haifa, Faculty of Natural Science, Israel
| | - Lorraine Clark
- Columbia University, Department of Pathology, New York, NY
| | - Todd Lencz
- Albert Einstein College of Medicine of Yeshiva University, New York, NY
| | - Itsik Pe’er
- The Feinstein Institute for Medical Research, Manhasset, NY
| | - Harry Ostrer
- Montefiore Medical Center, Department of Pathology, New York, NY
- Albert Einstein College of Medicine of Yeshiva University, New York, NY
| | - Carole Oddoux
- Montefiore Medical Center, Department of Pathology, New York, NY
- Albert Einstein College of Medicine of Yeshiva University, New York, NY
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