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Merc MD, Kotnik U, Peterlin B, Lovrecic L. Further exploration of cardiac channelopathy and cardiomyopathy genes in stillbirth. Prenat Diagn 2024; 44:1062-1072. [PMID: 38813989 DOI: 10.1002/pd.6616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/09/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
OBJECTIVE To explore genetic variation including whole genome copy number variation and sequence analysis of 98 genes associated with pediatric or adult cardiomyopathies, cardiac channelopathies, and sudden death in an unexplained intrauterine fetal death cohort. METHODS The study population included 55 stillbirth cases that remained unexplained after thorough postmortem examination, excluding maternal, fetal, and placental causes of stillbirth. Molecular karyotyping was performed in 55 cases and the trio exome sequencing approach was applied in 19 cases. RESULTS The analysis revealed six rare variants with predicted effects on protein function in six genes (CASQ2, DSC2, KCNE1, LDB3, MYH6, and SCN5A) previously reported in cases of stillbirth or severe early onset pediatric cardiac related phenotypes. When applying strict American College of Genetics and Genomics classification guidelines, these are still variants of uncertain significance. CONCLUSIONS Several potentially stillbirth-related genetic variants were detected in our cohort, adding to the growing literature on cardiac phenotype gene variation in stillbirth. However, the mechanisms of action, gene-gene interaction, and contribution of the uterine environment are still to be deciphered. In order to advance our knowledge of the genetics of unexplained fetal death, there is an evident need for international collaboration and field standardization.
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Affiliation(s)
- Maja Dolanc Merc
- Division of Gynecology and Obstetrics, Department of Perinatology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Urška Kotnik
- Clinical Institute for Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute for Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Luca Lovrecic
- Clinical Institute for Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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2
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Kovanda A, Lukežič T, Maver A, Vokač Križaj H, Čižek Sajko M, Šelb J, Rijavec M, Bidovec-Stojković U, Bitežnik B, Rituper B, Korošec P, Peterlin B. Genomic Landscape of Susceptibility to Severe COVID-19 in the Slovenian Population. Int J Mol Sci 2024; 25:7674. [PMID: 39062917 PMCID: PMC11277002 DOI: 10.3390/ijms25147674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Determining the genetic contribution of susceptibility to severe SARS-CoV-2 infection outcomes is important for public health measures and individualized treatment. Through intense research on this topic, several hundred genes have been implicated as possibly contributing to the severe infection phenotype(s); however, the findings are complex and appear to be population-dependent. We aimed to determine the contribution of human rare genetic variants associated with a severe outcome of SARS-CoV-2 infections and their burden in the Slovenian population. A panel of 517 genes associated with severe SARS-CoV-2 infection were obtained by combining an extensive review of the literature, target genes identified by the COVID-19 Host Genetic Initiative, and the curated Research COVID-19 associated genes from PanelApp, England Genomics. Whole genome sequencing was performed using PCR-free WGS on DNA from 60 patients hospitalized due to severe COVID-19 disease, and the identified rare genomic variants were analyzed and classified according to the ACMG criteria. Background prevalence in the general Slovenian population was determined by comparison with sequencing data from 8025 individuals included in the Slovenian genomic database (SGDB). Results show that several rare pathogenic/likely pathogenic genomic variants in genes CFTR, MASP2, MEFV, TNFRSF13B, and RNASEL likely contribute to the severe infection outcomes in our patient cohort. These results represent an insight into the Slovenian genomic diversity associated with a severe COVID-19 outcome.
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Affiliation(s)
- Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadeja Lukežič
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Hana Vokač Križaj
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Mojca Čižek Sajko
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Julij Šelb
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
| | - Matija Rijavec
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
| | | | - Barbara Bitežnik
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
| | - Boštjan Rituper
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
| | - Peter Korošec
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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3
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SoRelle JA, Funke BH, Eno CC, Ji J, Santani A, Bayrak-Toydemir P, Wachsmann M, Wain KE, Mao R. Slice Testing-Considerations from Ordering to Reporting: A Joint Report of the Association for Molecular Pathology, College of American Pathologists, and National Society of Genetic Counselors. J Mol Diagn 2024; 26:159-167. [PMID: 38103592 DOI: 10.1016/j.jmoldx.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 10/09/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
As the number of genes associated with various germline disorders continues to grow, it is becoming more difficult for clinical laboratories to maintain separate assays for interrogating disease-focused gene panels. One solution to this challenge is termed slice testing, where capture backbone is used to analyze data specific to a set of genes, and for this article, we will focus on exome. A key advantage to this strategy is greater flexibility by adding genes as they become associated with disease or the ability to accommodate specific provider requests. Here, we provide expert consensus recommendations and results from an Association for Molecular Pathology-sponsored survey of clinical laboratories performing exome sequencing to compare a slice testing approach with traditional static gene panels and comprehensive exome analysis. We explore specific considerations for slices, including gene selection, analytic performance, coverage, quality, and interpretation. Our goal is to provide comprehensive guidance for clinical laboratories interested in designing and using slice tests as a diagnostic.
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Affiliation(s)
- Jeffrey A SoRelle
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Birgit H Funke
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Sema4, Stamford, Connecticut; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Celeste C Eno
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Academic Pathology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jianling Ji
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, University of Southern California, Los Angeles, California
| | - Avni Santani
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Pinar Bayrak-Toydemir
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Utah, Salt Lake City, Utah; ARUP Laboratories, Salt Lake City, Utah
| | - Megan Wachsmann
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas; VA North Texas Health Care System, Dallas, Texas
| | - Karen E Wain
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; GeneDx, LLC, Gaithersburg, Maryland
| | - Rong Mao
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Utah, Salt Lake City, Utah; ARUP Laboratories, Salt Lake City, Utah.
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4
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Rački V, Bergant G, Papić E, Kovanda A, Hero M, Rožmarić G, Starčević Čizmarević N, Ristić S, Ostojić S, Kapović M, Maver A, Peterlin B, Vuletić V. GiOPARK Project: The Genetic Study of Parkinson's Disease in the Croatian Population. Genes (Basel) 2024; 15:255. [PMID: 38397244 PMCID: PMC10888376 DOI: 10.3390/genes15020255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Parkinson's disease is a neurological disorder that affects motor function, autonomic functions, and cognitive abilities. It is likely that both genetic and environmental factors, along with age, contribute to the cause. However, there is no comprehensive guideline for genetic testing for Parkinson's disease, and more research is needed to understand genetic variations in different populations. There has been no research on the genetic background of Parkinson's disease in Croatia so far. Therefore, with the GiOPARK project, we aimed to investigate the genetic variants responsible for Parkinson's disease in 153 Croatian patients with early onset, familial onset, and sporadic late-onset using whole-exome sequencing, along with multiplex ligation-dependent probe amplification and Sanger sequencing in select patients. We found causative variants in 7.84% of the patients, with GBA being the most common gene (4.58%), followed by PRKN (1.96%), ITM2B (0.65%), and MAPT (0.65%). Moreover, variants of uncertain significance were identified in 26.14% of the patients. The causative variants were found in all three subgroups, indicating that genetic factors play a role in all the analyzed Parkinson's disease subtypes. This study emphasizes the need for more inclusive research and improved guidelines to better understand the genetic basis of Parkinson's disease and facilitate more effective clinical management.
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Affiliation(s)
- Valentino Rački
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Gaber Bergant
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Eliša Papić
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Mario Hero
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Gloria Rožmarić
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Nada Starčević Čizmarević
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Smiljana Ristić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Saša Ostojić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Miljenko Kapović
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Vladimira Vuletić
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
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5
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Vaseghi P, Habibi L, Neidich JA, Cao Y, Fattahi N, Rashidi-Nezhad R, Salehnezhad T, Dalili H, Rahimi Sharbaf F, Zarkesh MR, Malekian M, Mokhberdezfuli M, Mehrtash A, Ardeshirdavani A, Kariminejad R, Ghorbansabagh V, Sadeghimoghadam P, Naddaf A, Esmaeilnia Shirvany T, Mosayebi Z, Sahebdel B, Golshahi F, Shirazi M, Shamel S, Moeini R, Heidari A, Daneshmand MA, Ghasemi R, Akrami SM, Rashidi-Nezhad A. Towards solving the genetic diagnosis odyssey in Iranian patients with congenital anomalies. Eur J Hum Genet 2024:10.1038/s41431-024-01533-x. [PMID: 38278869 DOI: 10.1038/s41431-024-01533-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 11/23/2023] [Accepted: 12/12/2023] [Indexed: 01/28/2024] Open
Abstract
Understanding the underlying causes of congenital anomalies (CAs) can be a complex diagnostic journey. We aimed to assess the efficiency of exome sequencing (ES) and chromosomal microarray analysis (CMA) in patients with CAs among a population with a high fraction of consanguineous marriage. Depending on the patient's symptoms and family history, karyotype/Quantitative Fluorescence- Polymerase Chain Reaction (QF-PCR) (n = 84), CMA (n = 81), ES (n = 79) or combined CMA and ES (n = 24) were performed on 168 probands (66 prenatal and 102 postnatal) with CAs. Twelve (14.28%) probands were diagnosed by karyotype/QF-PCR and seven (8.64%) others were diagnosed by CMA. ES findings were conclusive in 39 (49.36%) families, and 61.90% of them were novel variants. Also, 64.28% of these variants were identified in genes that follow recessive inheritance in CAs. The diagnostic rate (DR) of ES was significantly higher than that of CMA in children from consanguineous families (P = 0·0001). The highest DR by CMA was obtained in the non-consanguineous postnatal subgroup and by ES in the consanguineous prenatal subgroup. In a population that is highly consanguineous, our results suggest that ES may have a higher diagnostic yield than CMA and should be considered as the first-tier test in the evaluation of patients with congenital anomalies.
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Affiliation(s)
- Parisa Vaseghi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Photo Healing and Regeneration, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran
| | - Laleh Habibi
- Ronash Medical Genetics Laboratory, Tehran, Iran
| | - Julie A Neidich
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yang Cao
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Neda Fattahi
- Ronash Medical Genetics Laboratory, Tehran, Iran
| | | | | | - Hossein Dalili
- Breastfeeding Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Rahimi Sharbaf
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zarkesh
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | | | - Mahdieh Mokhberdezfuli
- Ronash Medical Genetics Laboratory, Tehran, Iran
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | | | - Vafa Ghorbansabagh
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Parvane Sadeghimoghadam
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Naddaf
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Tahereh Esmaeilnia Shirvany
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ziba Mosayebi
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrokh Sahebdel
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Golshahi
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahboobeh Shirazi
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Shirin Shamel
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | - Roksana Moeini
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | | | | | - Reza Ghasemi
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Seyed Mohammad Akrami
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ali Rashidi-Nezhad
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
- Genetics Ward, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran.
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6
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Vodnjov N, Toplišek J, Maver A, Čuturilo G, Jaklič H, Teran N, Višnjar T, Škrjanec Pušenjak M, Hodžić A, Miljanović O, Peterlin B, Writzl K. A novel splice-site FHOD3 founder variant is a common cause of hypertrophic cardiomyopathy in the population of the Balkans-A cohort study. PLoS One 2023; 18:e0294969. [PMID: 38051749 DOI: 10.1371/journal.pone.0294969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/11/2023] [Indexed: 12/07/2023] Open
Abstract
Founder variants in sarcomere protein genes account for a significant proportion of disease-causing variants in patients with hypertrophic cardiomyopathy (HCM). However, information on founder variants in non-sarcomeric protein genes, such as FHOD3, which have only recently been associated with HCM, remains scarce. In this study, we conducted a retrospective analysis of exome sequencing data of 134 probands with HCM for recurrent pathogenic variants. We discovered a novel likely pathogenic variant c.1646+2T>C in FHOD3 in heterozygous state in eight probands with HCM and confirmed its presence in seven additional relatives. Individuals with this variant had a wide range of ages at onset of the disease (4-63 years). No adverse cardiac events were observed. Haplotype analysis revealed that the individuals with this variant shared a genomic region of approximately 5 Mbp surrounding the variant, confirming the founder effect of the variant. FHOD3 c.1646+2T>C is estimated to have arisen 58 generations ago (95% CI: 45-81) in a common ancestor living on the Balkans. A founder FHOD3 c.1646+2T>C variant is the second most common genetic variant in our cohort of patients with HCM, occurring in 16% of probands with a known genetic cause of HCM, which represents a substantially higher proportion than the currently estimated 0.5-2% for causal FHOD3 variants. Our study broadens the understanding of the genetic causes of HCM and may improve the diagnosis of this condition, particularly in patients from the Balkans.
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Affiliation(s)
- Nina Vodnjov
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Janez Toplišek
- Department of Cardiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Goran Čuturilo
- Department of Medical Genetics, University Children's Hospital, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Helena Jaklič
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Nataša Teran
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Tanja Višnjar
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Maruša Škrjanec Pušenjak
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Alenka Hodžić
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | | | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- European Reference Network for Rare, Low Prevalence, or Complex Diseases of the Heart (ERN GUARD-Heart)
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7
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Tesi B, Boileau C, Boycott KM, Canaud G, Caulfield M, Choukair D, Hill S, Spielmann M, Wedell A, Wirta V, Nordgren A, Lindstrand A. Precision medicine in rare diseases: What is next? J Intern Med 2023; 294:397-412. [PMID: 37211972 DOI: 10.1111/joim.13655] [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: 05/23/2023]
Abstract
Molecular diagnostics is a cornerstone of modern precision medicine, broadly understood as tailoring an individual's treatment, follow-up, and care based on molecular data. In rare diseases (RDs), molecular diagnoses reveal valuable information about the cause of symptoms, disease progression, familial risk, and in certain cases, unlock access to targeted therapies. Due to decreasing DNA sequencing costs, genome sequencing (GS) is emerging as the primary method for precision diagnostics in RDs. Several ongoing European initiatives for precision medicine have chosen GS as their method of choice. Recent research supports the role for GS as first-line genetic investigation in individuals with suspected RD, due to its improved diagnostic yield compared to other methods. Moreover, GS can detect a broad range of genetic aberrations including those in noncoding regions, producing comprehensive data that can be periodically reanalyzed for years to come when further evidence emerges. Indeed, targeted drug development and repurposing of medicines can be accelerated as more individuals with RDs receive a molecular diagnosis. Multidisciplinary teams in which clinical specialists collaborate with geneticists, genomics education of professionals and the public, and dialogue with patient advocacy groups are essential elements for the integration of precision medicine into clinical practice worldwide. It is also paramount that large research projects share genetic data and leverage novel technologies to fully diagnose individuals with RDs. In conclusion, GS increases diagnostic yields and is a crucial step toward precision medicine for RDs. Its clinical implementation will enable better patient management, unlock targeted therapies, and guide the development of innovative treatments.
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Affiliation(s)
- Bianca Tesi
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Catherine Boileau
- Département de Génétique, APHP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Guillaume Canaud
- INSERM U1151, Unité de médecine translationnelle et thérapies ciblées, Hôpital Necker-Enfants Malades, Université Paris Cité, AP-HP, Paris, France
| | - Mark Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Sue Hill
- Chief Scientific Officer, NHS England, London, UK
| | - Malte Spielmann
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Maassen W, Legger G, Kul Cinar O, van Daele P, Gattorno M, Bader-Meunier B, Wouters C, Briggs T, Johansson L, van der Velde J, Swertz M, Omoyinmi E, Hoppenreijs E, Belot A, Eleftheriou D, Caorsi R, Aeschlimann F, Boursier G, Brogan P, Haimel M, van Gijn M. Curation and expansion of the Human Phenotype Ontology for systemic autoinflammatory diseases improves phenotype-driven disease-matching. Front Immunol 2023; 14:1215869. [PMID: 37781402 PMCID: PMC10536149 DOI: 10.3389/fimmu.2023.1215869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/09/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Accurate and standardized phenotypic descriptions are essential in diagnosing rare diseases and discovering new diseases, and the Human Phenotype Ontology (HPO) system was developed to provide a rich collection of hierarchical phenotypic descriptions. However, although the HPO terms for inborn errors of immunity have been improved and curated, it has not been investigated whether this curation improves the diagnosis of systemic autoinflammatory disease (SAID) patients. Here, we aimed to study if improved HPO annotation for SAIDs enhanced SAID identification and to demonstrate the potential of phenotype-driven genome diagnostics using curated HPO terms for SAIDs. Methods We collected HPO terms from 98 genetically confirmed SAID patients across eight different European SAID expertise centers and used the LIRICAL (Likelihood Ratio Interpretation of Clinical Abnormalities) computational algorithm to estimate the effect of HPO curation on the prioritization of the correct SAID for each patient. Results Our results show that the percentage of correct diagnoses increased from 66% to 86% and that the number of diagnoses with the highest ranking increased from 38 to 45. In a further pilot study, curation also improved HPO-based whole-exome sequencing (WES) analysis, diagnosing 10/12 patients before and 12/12 after curation. In addition, the average number of candidate diseases that needed to be interpreted decreased from 35 to 2. Discussion This study demonstrates that curation of HPO terms can increase identification of the correct diagnosis, emphasizing the high potential of HPO-based genome diagnostics for SAIDs.
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Affiliation(s)
- Willem Maassen
- Genomics Coordination Centre, Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Geertje Legger
- Department of Rheumatology and Clinical Immunology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Ovgu Kul Cinar
- Department of Paediatric Rheumatology, Great Ormond Street Hospital for Children National Health Service Trust, London, United Kingdom
| | - Paul van Daele
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, Netherlands
- Department of Immunology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Marco Gattorno
- UOC Reumatologia e Malattie Autoinfiammatorie, IRCCS Istituto Giannini Gaslini, Genoa, Italy
| | - Brigitte Bader-Meunier
- Department of Paediatric Immunology-Hematology and Rheumatology, Necker University Hospital - APHP, Paris, France
- Laboratory of Immunogenetics of Paediatric Autoimmune Diseases, UMR 1163, Imagine Institute, INSERM, Paris, France
| | - Carine Wouters
- Department of Pediatric Rheumatology, University Hospital Leuven, Leuven, Belgium
| | - Tracy Briggs
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University Hospitals National Health Service Foundation Trust, Manchester, United Kingdom
| | - Lennart Johansson
- Genomics Coordination Centre, Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Joeri van der Velde
- Genomics Coordination Centre, Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Morris Swertz
- Genomics Coordination Centre, Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Ebun Omoyinmi
- Department of Paediatric Rheumatology, Great Ormond Street Hospital for Children National Health Service Trust, London, United Kingdom
| | - Esther Hoppenreijs
- Department of Pediatric Rheumatology, Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alexandre Belot
- National Referee Centre for Rheumatic and AutoImmune and Systemic Diseases in Children (RAISE), Pediatric Nephrology, Rheumatology, Dermatology Unit, INSERM, Hospital of Mother and Child, Hospices Civils of Lyon, Lyon, France
- International Center of Infectiology Research (CIRI), University of Lyon, INSERM, Claude Bernard University, Lyon, France
| | - Despina Eleftheriou
- Department of Paediatric Rheumatology, Great Ormond Street Hospital for Children National Health Service Trust, London, United Kingdom
| | - Roberta Caorsi
- UOC Reumatologia e Malattie Autoinfiammatorie, IRCCS Istituto Giannini Gaslini, Genoa, Italy
| | - Florence Aeschlimann
- Department of Paediatric Immunology-Hematology and Rheumatology, Necker University Hospital - APHP, Paris, France
- Division of Pediatric Rheumatology, University Children’s Hospital Basel, Basel, Switzerland
| | - Guilaine Boursier
- Laboratory of Rare and Autoinflammatory Genetic Diseases and Reference Centre for Autoinflammatory Diseases and Amyloidosis (CEREMAIA), Department of Medical Genetics, Rare Diseases and Personalized Medicine, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Paul Brogan
- Inflammation and Rheumatology Section, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | | | - Marielle van Gijn
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
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Henry OJ, Stödberg T, Båtelson S, Rasi C, Stranneheim H, Wedell A. Individualised human phenotype ontology gene panels improve clinical whole exome and genome sequencing analytical efficacy in a cohort of developmental and epileptic encephalopathies. Mol Genet Genomic Med 2023; 11:e2167. [PMID: 36967109 PMCID: PMC10337286 DOI: 10.1002/mgg3.2167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/21/2023] [Accepted: 03/01/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND The majority of genetic epilepsies remain unsolved in terms of specific genotype. Phenotype-based genomic analyses have shown potential to strengthen genomic analysis in various ways, including improving analytical efficacy. METHODS We have tested a standardised phenotyping method termed 'Phenomodels' for integrating deep-phenotyping information with our in-house developed clinical whole exome/genome sequencing analytical pipeline. Phenomodels includes a user-friendly epilepsy phenotyping template and an objective measure for selecting which template terms to include in individualised Human Phenotype Ontology (HPO) gene panels. In a pilot study of 38 previously solved cases of developmental and epileptic encephalopathies, we compared the sensitivity and specificity of the individualised HPO gene panels with the clinical epilepsy gene panel. RESULTS The Phenomodels template showed high sensitivity for capturing relevant phenotypic information, where 37/38 individuals' HPO gene panels included the causative gene. The HPO gene panels also had far fewer variants to assess than the epilepsy gene panel. CONCLUSION We have demonstrated a viable approach for incorporating standardised phenotype information into clinical genomic analyses, which may enable more efficient analysis.
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Affiliation(s)
- Olivia J. Henry
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
| | - Tommy Stödberg
- Department of Women's and Children's HealthKarolinska InstitutetStockholmSweden
- Department of Pediatric NeurologyKarolinska University HospitalStockholmSweden
| | - Sofia Båtelson
- Department of Pediatric NeurologyKarolinska University HospitalStockholmSweden
| | - Chiara Rasi
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Henrik Stranneheim
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell BiologyKarolinska InstitutetStockholmSweden
- Centre for Inherited Metabolic DiseasesKarolinska University HospitalStockholmSweden
| | - Anna Wedell
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
- Centre for Inherited Metabolic DiseasesKarolinska University HospitalStockholmSweden
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Kotnik U, Maver A, Peterlin B, Lovrecic L. Assessment of pathogenic variation in gynecologic cancer genes in a national cohort. Sci Rep 2023; 13:5307. [PMID: 37002323 PMCID: PMC10066348 DOI: 10.1038/s41598-023-32397-8] [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: 12/06/2022] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Population-based estimates of pathogenic variation burden in gynecologic cancer predisposition genes are a prerequisite for the development of effective precision public health strategies. This study aims to reveal the burden of pathogenic variants in a comprehensive set of clinically relevant breast, ovarian, and endometrial cancer genes in a large population-based study. We performed a rigorous manual classification procedure to identify pathogenic variants in a panel of 17 gynecologic cancer predisposition genes in a cohort of 7091 individuals, representing 0.35% of the general population. The population burden of pathogenic variants in hereditary gynecologic cancer-related genes in our study was 2.14%. Pathogenic variants in genes ATM, BRCA1, and CDH1 are significantly enriched and the burden of pathogenic variants in CHEK2 is decreased in our population compared to the control population. We have identified a high burden of pathogenic variants in several gynecologic cancer-related genes in the Slovenian population, most importantly in the BRCA1 gene.
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Affiliation(s)
- Urška Kotnik
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia.
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Luca Lovrecic
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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11
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Kovanda A, Rački V, Bergant G, Georgiev D, Flisar D, Papić E, Brankovic M, Jankovic M, Svetel M, Teran N, Maver A, Kostic VS, Novakovic I, Pirtošek Z, Rakuša M, Vuletić V, Peterlin B. A multicenter study of genetic testing for Parkinson’s disease in the clinical setting. NPJ Parkinsons Dis 2022; 8:149. [PMCID: PMC9636217 DOI: 10.1038/s41531-022-00408-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
Parkinson’s disease (PD) guidelines lack clear criteria for genetic evaluation. We assessed the yield and rationale of genetic testing for PD in a routine clinical setting on a multicenter cohort of 149 early-onset and familial patients by exome sequencing and semi-quantitative multiplex ligation-dependent probe amplification of evidence-based PD-associated gene panel. We show that genetic testing for PD should be considered for both early-onset and familial patients alike, and a clinical yield of about 10% in the Caucasian population can be expected.
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Affiliation(s)
- Anja Kovanda
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Valentino Rački
- grid.22939.330000 0001 2236 1630Department of Neurology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Gaber Bergant
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Dejan Georgiev
- grid.29524.380000 0004 0571 7705Department of Neurology, University Medical Centre Ljubljana, Ljubljana, Slovenia ,grid.8954.00000 0001 0721 6013Artificial Intelligence Lab, Faculty of Computer and Information Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Dušan Flisar
- grid.29524.380000 0004 0571 7705Department of Neurology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Eliša Papić
- grid.22939.330000 0001 2236 1630Department of Neurology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Marija Brankovic
- grid.7149.b0000 0001 2166 9385Neurology Clinic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Marina Svetel
- grid.7149.b0000 0001 2166 9385Neurology Clinic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Nataša Teran
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Vladimir S. Kostic
- grid.7149.b0000 0001 2166 9385Neurology Clinic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivana Novakovic
- grid.7149.b0000 0001 2166 9385Institute of Human Genetics and Neurology Clinic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Zvezdan Pirtošek
- grid.29524.380000 0004 0571 7705Department of Neurology, University Medical Centre Ljubljana, Ljubljana, Slovenia ,grid.8954.00000 0001 0721 6013Department of Neurology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Martin Rakuša
- grid.412415.70000 0001 0685 1285Department of Neurology, University Medical Centre Maribor, Maribor, Slovenia
| | - Vladimira Vuletić
- grid.22939.330000 0001 2236 1630Department of Neurology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Borut Peterlin
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
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12
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Dzinovic I, Winkelmann J, Zech M. Genetic intersection between dystonia and neurodevelopmental disorders: Insights from genomic sequencing. Parkinsonism Relat Disord 2022; 102:131-140. [DOI: 10.1016/j.parkreldis.2022.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 10/15/2022]
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Dzinovic I, Boesch S, Škorvánek M, Necpál J, Švantnerová J, Pavelekova P, Havránková P, Tsoma E, Indelicato E, Runkel E, Held V, Weise D, Janzarik W, Eckenweiler M, Berweck S, Mall V, Haslinger B, Jech R, Winkelmann J, Zech M. Genetic overlap between dystonia and other neurologic disorders: A study of 1,100 exomes. Parkinsonism Relat Disord 2022; 102:1-6. [PMID: 35872528 DOI: 10.1016/j.parkreldis.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/29/2022] [Accepted: 07/08/2022] [Indexed: 10/17/2022]
Abstract
INTRODUCTION Although shared genetic factors have been previously reported between dystonia and other neurologic conditions, no sequencing study exploring such links is available. In a large dystonic cohort, we aimed at analyzing the proportions of causative variants in genes associated with disease categories other than dystonia. METHODS Gene findings related to whole-exome sequencing-derived diagnoses in 1100 dystonia index cases were compared with expert-curated molecular testing panels for ataxia, parkinsonism, spastic paraplegia, neuropathy, epilepsy, and intellectual disability. RESULTS Among 220 diagnosed patients, 21% had variants in ataxia-linked genes; 15% in parkinsonism-linked genes; 15% in spastic-paraplegia-linked genes; 12% in neuropathy-linked genes; 32% in epilepsy-linked genes; and 65% in intellectual-disability-linked genes. Most diagnosed presentations (80%) were related to genes listed in ≥1 studied panel; 71% of the involved loci were found in the non-dystonia panels but not in an expert-curated gene list for dystonia. CONCLUSIONS Our study indicates a convergence in the genetics of dystonia and other neurologic phenotypes, informing diagnostic evaluation strategies and pathophysiological considerations.
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Affiliation(s)
- Ivana Dzinovic
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sylvia Boesch
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Matej Škorvánek
- Department of Neurology, P.J. Safarik University, Kosice, Slovak Republic; Department of Neurology, University Hospital of L. Pasteur, Kosice, Slovak Republic
| | - Ján Necpál
- Department of Neurology, Zvolen Hospital, Slovakia
| | - Jana Švantnerová
- Second Department of Neurology, Faculty of Medicine, Comenius University, University Hospital Bratislava, Bratislava, Slovakia
| | - Petra Pavelekova
- Department of Neurology, P.J. Safarik University, Kosice, Slovak Republic; Department of Neurology, University Hospital of L. Pasteur, Kosice, Slovak Republic
| | - Petra Havránková
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Eugenia Tsoma
- Regional Clinical Center of Neurosurgery and Neurology, Department of Family Medicine and Outpatient Care, Uzhhorod National University, Uzhhorod, Ukraine
| | | | - Eva Runkel
- Klinikum Aschaffenburg-Alzenau, Aschaffenburg, Germany
| | - Valentin Held
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - David Weise
- Klinik für Neurologie, Asklepios Fachklinikum Stadtroda, Stadtroda, Germany; Department of Neurology, University of Leipzig, Leipzig, Germany
| | - Wibke Janzarik
- Department of Neuropediatrics and Muscle Disorders, University Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Matthias Eckenweiler
- Department of Neuropediatrics and Muscle Disorders, University Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Steffen Berweck
- Ludwig Maximilian University of Munich, Munich, Germany; Hospital for Neuropediatrics and Neurological Rehabilitation, Centre of Epilepsy for Children and Adolescents, Schoen Klinik Vogtareuth, Vogtareuth, Germany
| | - Volker Mall
- Lehrstuhl für Sozialpädiatrie, Technische Universität München, Munich, Germany; kbo-Kinderzentrum München, Munich, Germany
| | - Bernhard Haslinger
- Department of Neurology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Robert Jech
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany; Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
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Višnjar T, Maver A, Writzl K, Maloku O, Bergant G, Jaklič H, Neubauer D, Fogolari F, Pečarič Meglič N, Peterlin B. Biallelic ATOH1 Gene Variant in Siblings With Pontocerebellar Hypoplasia, Developmental Delay, and Hearing Loss. Neurol Genet 2022; 8:e677. [PMID: 35518571 PMCID: PMC9067583 DOI: 10.1212/nxg.0000000000000677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/04/2022] [Indexed: 11/15/2022]
Abstract
Background and Objectives To report on the novel association of biallelic variant in atonal basic helix-loop-helix transcription factor 1 (ATOH1) gene and pontocerebellar hypoplasia (PCH), severe global developmental delay, intellectual disability, and hearing loss in a family with 2 affected siblings. Methods A detailed clinical assessment and exome sequencing of peripheral blood sample were performed. Segregation analysis with Sanger sequencing and structural modeling of the variant was performed to support the pathogenicity of the variant. Results A homozygous missense variant (NM_005172.1:c.481C>G) in the ATOH1 gene was identified in the proband and his affected sister. The segregation analysis subsequently confirmed its segregation with an apparently recessive PCH in this family. ATOH1 encodes for the atonal basic helix-loop-helix (bHLH) transcription factor 1, a core transcription factor in the developing cerebellum, brainstem, and dorsal spinal cord, and in the ear. The identified variant results in the p.(Arg161Gly) amino acid substitution in the evolutionarily conserved DNA-binding bHLH domain of the ATOH1 protein. Biallelic missense variants in this domain were previously reported to result in disordered cerebellar development and hearing loss in animal models. In silico homology modeling revealed that p.Arg161Gly in ATOH1 protein probably disrupts a salt bridge with DNA backbone phosphate and increases the flexibility of the bHLH helix-both of which together affect the binding capability of the bHLH domain to the DNA. Discussion Based on the sequencing results and evidence from structural modeling of the identified variant, as well as with previous reports of ATOH1 gene disruption, we conclude that ATOH1 may represent a novel candidate gene associated with the phenotype of PCH, global developmental delay, and hearing loss in humans.
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Affiliation(s)
- Tanja Višnjar
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Aleš Maver
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Karin Writzl
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Ornela Maloku
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Gaber Bergant
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Helena Jaklič
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - David Neubauer
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Federico Fogolari
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Nuška Pečarič Meglič
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
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15
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A Fetus with Congenital Microcephaly, Microphthalmia and Cataract Was Detected with Biallelic Variants in the OCLN Gene: A Case Report. Diagnostics (Basel) 2021; 11:diagnostics11091576. [PMID: 34573918 PMCID: PMC8472215 DOI: 10.3390/diagnostics11091576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
Microcephaly and microphthalmia are both rare congenital abnormalities, while concurrently, these two are even rarer. The underlying etiology would be complex interplaying between heterogeneous genetic background and the environmental pathogens, particularly during critical periods of early tissue development. Here, we reported a prenatal case with microcephaly, microphthalmia, and bilateral cataracts detected by ultrasonography and confirmed by autopsy. Various routine infection-related tests and invasive genetic testing were negative. Whole genome sequencing of fetus and parents revealed OCLN gene defects may be associated with these multiple congenital abnormalities.
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16
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Babić Božović I, Maver A, Leonardis L, Meznaric M, Osredkar D, Peterlin B. Diagnostic yield of exome sequencing in myopathies: Experience of a Slovenian tertiary centre. PLoS One 2021; 16:e0252953. [PMID: 34106991 PMCID: PMC8189452 DOI: 10.1371/journal.pone.0252953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/25/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Our aim was to present the experience of systematic, routine use of next generation sequencing (NGS) in clinical diagnostics of myopathies. METHODS Exome sequencing was performed on patients with high risk for inherited myopathy, which were selected based on the history of the disease, family history, clinical presentation, and diagnostic workup. Exome target capture was performed, followed by sequencing on HiSeq 2500 or MiSeq platforms. Data analysis was performed using internally developed bioinformatic pipeline. RESULTS The study comprised 86 patients, including 22 paediatric cases (26%). The largest group were patients referred with an unspecified myopathy (47%), due to non-specific or incomplete clinical and laboratory findings, followed by congenital myopathies (22%) and muscular dystrophies (22%), congenital myotonias (6%), and mitochondrial myopathies (3%). Altogether, a diagnostic yield was 52%; a high diagnostic rate was present in paediatric patients (64%), while in patients with unspecified myopathies the rate was 35%. We found 51 pathogenic/likely pathogenic variants in 23 genes and two pathogenic copy number variations. CONCLUSION Our results provide evidence that phenotype driven exome analysis diagnostic approach facilitates the diagnostic rate of complex, heterogeneous disorders, such as myopathies, particularly in paediatric patients and patients with unspecified myopathies.
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Affiliation(s)
- Ivana Babić Božović
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Lea Leonardis
- Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Department of Neurology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Marija Meznaric
- Institute of Anatomy, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Damjan Osredkar
- Department of Paediatric Neurology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
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17
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Molina-Ramírez LP, Kyle C, Ellingford JM, Wright R, Taylor A, Bhaskar SS, Campbell C, Jackson H, Fairclough A, Rousseau A, Burghel GJ, Dutton L, Banka S, Briggs TA, Clayton-Smith J, Douzgou S, Jones EA, Kingston HM, Kerr B, Ealing J, Somarathi S, Chandler KE, Stuart HM, Burkitt-Wright EM, Newman WG, Bruce IA, Black GC, Gokhale D. Personalised virtual gene panels reduce interpretation workload and maintain diagnostic rates of proband-only clinical exome sequencing for rare disorders. J Med Genet 2021; 59:393-398. [PMID: 33879512 PMCID: PMC8961756 DOI: 10.1136/jmedgenet-2020-107303] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 01/17/2021] [Accepted: 02/14/2021] [Indexed: 01/20/2023]
Abstract
Purpose The increased adoption of genomic strategies in the clinic makes it imperative for diagnostic laboratories to improve the efficiency of variant interpretation. Clinical exome sequencing (CES) is becoming a valuable diagnostic tool, capable of meeting the diagnostic demand imposed by the vast array of different rare monogenic disorders. We have assessed a clinician-led and phenotype-based approach for virtual gene panel generation for analysis of targeted CES in patients with rare disease in a single institution. Methods Retrospective survey of 400 consecutive cases presumed by clinicians to have rare monogenic disorders, referred on singleton basis for targeted CES. We evaluated diagnostic yield and variant workload to characterise the usefulness of a clinician-led approach for generation of virtual gene panels that can incorporate up to three different phenotype-driven gene selection methods. Results Abnormalities of the nervous system (54.5%), including intellectual disability, head and neck (19%), skeletal system (16%), ear (15%) and eye (15%) were the most common clinical features reported in referrals. Combined phenotype-driven strategies for virtual gene panel generation were used in 57% of cases. On average, 7.3 variants (median=5) per case were retained for clinical interpretation. The overall diagnostic rate of proband-only CES using personalised phenotype-driven virtual gene panels was 24%. Conclusions Our results show that personalised virtual gene panels are a cost-effective approach for variant analysis of CES, maintaining diagnostic yield and optimising the use of resources for clinical genomic sequencing in the clinic.
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Affiliation(s)
- Leslie Patricia Molina-Ramírez
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Claire Kyle
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Jamie M Ellingford
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Ronnie Wright
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Algy Taylor
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Sanjeev S Bhaskar
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Christopher Campbell
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Harriet Jackson
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Adele Fairclough
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Abigail Rousseau
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - George J Burghel
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Laura Dutton
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Tracy A Briggs
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Jill Clayton-Smith
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Elizabeth A Jones
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Helen M Kingston
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Bronwyn Kerr
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - John Ealing
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK.,Department of Neurology, Salford Royal NHS Foundation Trust, Salford, Salford, UK
| | - Suresh Somarathi
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Kate E Chandler
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Helen M Stuart
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Emma Mm Burkitt-Wright
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Iain A Bruce
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Paediatric ENT Department, Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Graeme C Black
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK .,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - David Gokhale
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
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18
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Vinkšel M, Writzl K, Maver A, Peterlin B. Improving diagnostics of rare genetic diseases with NGS approaches. J Community Genet 2021; 12:247-256. [PMID: 33452619 PMCID: PMC8141085 DOI: 10.1007/s12687-020-00500-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/08/2020] [Indexed: 01/08/2023] Open
Abstract
According to a rough estimate, one in fifteen people worldwide is affected by a rare disease. Rare diseases are therefore common in clinical practice; however, timely diagnosis of rare diseases is still challenging. Introduction of novel methods based on next-generation sequencing (NGS) technology offers a successful diagnosis of genetically heterogeneous disorders, even in case of unclear clinical diagnostic hypothesis. However, the application of novel technology differs among the centres and health systems significantly. Our goal is to discuss the impact of the implementation of NGS in the diagnosis of rare diseases and present advantages along with challenges of diagnostic approach. Systematic implementation of NGS in health systems can significantly improve the access of patients with rare diseases to diagnosis and reduce the dependence of national health systems for cross-border collaboration.
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Affiliation(s)
- Mateja Vinkšel
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia.
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19
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Ahmed A, Wang M, Bergant G, Maroofian R, Zhao R, Alfadhel M, Nashabat M, AlRifai MT, Eyaid W, Alswaid A, Beetz C, Qin Y, Zhu T, Tian Q, Xia L, Wu H, Shen L, Dong S, Yang X, Liu C, Ma L, Zhang Q, Khan R, Shah AA, Guo J, Tang B, Leonardis L, Writzl K, Peterlin B, Guo H, Malik S, Xia K, Hu Z. Biallelic loss-of-function variants in NEMF cause central nervous system impairment and axonal polyneuropathy. Hum Genet 2021; 140:579-592. [PMID: 33048237 DOI: 10.1007/s00439-020-02226-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
We aimed to detect the causative gene in five unrelated families with recessive inheritance pattern neurological disorders involving the central nervous system, and the potential function of the NEMF gene in the central nervous system. Exome sequencing (ES) was applied to all families and linkage analysis was performed on family 1. A minigene assay was used to validate the splicing effect of the relevant discovered variants. Immunofluorescence (IF) experiment was performed to investigate the role of the causative gene in neuron development. The large consanguineous family confirms the phenotype-causative relationship with homozygous frameshift variant (NM_004713.6:c.2618del) as revealed by ES. Linkage analysis of the family showed a significant single-point LOD of 4.5 locus. Through collaboration in GeneMatcher, four additional unrelated families' likely pathogenic NEMF variants for a spectrum of central neurological disorders, two homozygous splice-site variants (NM_004713.6:c.574+1G>T and NM_004713.6:c.807-2A>C) and a homozygous frameshift variant (NM_004713.6: c.1234_1235insC) were subsequently identified and segregated with all affected individuals. We further revealed that knockdown (KD) of Nemf leads to impairment of axonal outgrowth and synapse development in cultured mouse primary cortical neurons. Our study demonstrates that disease-causing biallelic NEMF variants result in central nervous system impairment and other variable features. NEMF is an important player in mammalian neuron development.
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Affiliation(s)
- Ashfaque Ahmed
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Meng Wang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Gaber Bergant
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Rongjuan Zhao
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Marwan Nashabat
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Muhammad Talal AlRifai
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Wafaa Eyaid
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research Centre (KAIMRC), King Saud Bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | | | | | - Yan Qin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Tengfei Zhu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qi Tian
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Huidan Wu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Shen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Shanshan Dong
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xinyi Yang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Cenying Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Linya Ma
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qiumeng Zhang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Rizwan Khan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Abid Ali Shah
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, 410008, Hunan, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, 410008, Hunan, China
| | - Lea Leonardis
- Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Department of Neurology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Karin Writzl
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Borut Peterlin
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Hui Guo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Changsha, Hunan, China
| | - Sajid Malik
- Human Genetics Program, Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.
- CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Chinese Academy of Sciences, Shanghai, China.
- Hunan Key Laboratory of Molecular Precisional Medicine, Central South University, Changsha, China.
| | - Zhengmao Hu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Changsha, Hunan, China.
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20
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Bergant G, Maver A, Peterlin B. Whole-Genome Sequencing in Diagnostics of Selected Slovenian Undiagnosed Patients with Rare Disorders. Life (Basel) 2021; 11:life11030205. [PMID: 33807868 PMCID: PMC8001615 DOI: 10.3390/life11030205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 11/16/2022] Open
Abstract
Several patients with rare genetic disorders remain undiagnosed following comprehensive diagnostic testing using whole-exome sequencing (WES). In these patients, pathogenic genetic variants may reside in intronic or regulatory regions or they may emerge through mutational mechanisms not detected by WES. For this reason, we implemented whole-genome sequencing (WGS) in routine clinical diagnostics of patients with undiagnosed genetic disorders and report on the outcome in 30 patients. Criteria for consideration included (1) negative WES, (2) a high likelihood of a genetic cause for the disorders, (3) positive family history, (4) detection of large blocks of homozygosity or (5) detection of a single pathogenic variant in a gene associated with recessive conditions. We successfully discovered a causative genetic variant in 6 cases, a retrotranspositional event in the APC gene, non-coding variants in the intronic region of the OTC gene and the promotor region of the UFM1 gene, repeat expansion in the RFC1 gene and a single exon duplication in the CNGB3 gene. We also discovered one coding variant, an indel, which was missed by variant caller during WES data analysis. Our study demonstrates the impact of WGS in the group of patients with undiagnosed genetic diseases after WES in the clinical setting and the diversity of mutational mechanisms discovered, which would remain undetected using other methods.
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21
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Lassmann T, Francis RW, Weeks A, Tang D, Jamieson SE, Broley S, Dawkins HJS, Dreyer L, Goldblatt J, Groza T, Kamien B, Kiraly-Borri C, McKenzie F, Murphy L, Pachter N, Pathak G, Poulton C, Samanek A, Skoss R, Slee J, Townshend S, Ward M, Baynam GS, Blackwell JM. A flexible computational pipeline for research analyses of unsolved clinical exome cases. NPJ Genom Med 2020; 5:54. [PMID: 33303739 PMCID: PMC7730424 DOI: 10.1038/s41525-020-00161-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/12/2020] [Indexed: 12/25/2022] Open
Abstract
Exome sequencing has enabled molecular diagnoses for rare disease patients but often with initial diagnostic rates of ~25-30%. Here we develop a robust computational pipeline to rank variants for reassessment of unsolved rare disease patients. A comprehensive web-based patient report is generated in which all deleterious variants can be filtered by gene, variant characteristics, OMIM disease and Phenolyzer scores, and all are annotated with an ACMG classification and links to ClinVar. The pipeline ranked 21/34 previously diagnosed variants as top, with 26 in total ranked ≤7th, 3 ranked ≥13th; 5 failed the pipeline filters. Pathogenic/likely pathogenic variants by ACMG criteria were identified for 22/145 unsolved cases, and a previously undefined candidate disease variant for 27/145. This open access pipeline supports the partnership between clinical and research laboratories to improve the diagnosis of unsolved exomes. It provides a flexible framework for iterative developments to further improve diagnosis.
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Affiliation(s)
- Timo Lassmann
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.
| | - Richard W Francis
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Alexia Weeks
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Dave Tang
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Sarra E Jamieson
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Stephanie Broley
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Hugh J S Dawkins
- Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Lauren Dreyer
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Jack Goldblatt
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Tudor Groza
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Benjamin Kamien
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Cathy Kiraly-Borri
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Fiona McKenzie
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
- Faculty of Health and Medical Sciences, Division of Pediatrics, University of Western Australia, Perth, WA, Australia
| | | | - Nicholas Pachter
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Gargi Pathak
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Cathryn Poulton
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Amanda Samanek
- GaRDN Genetics and Rare Diseases Network, Booragoon, WA, Australia
| | - Rachel Skoss
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Jennie Slee
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Sharron Townshend
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Michelle Ward
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Gareth S Baynam
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
- Faculty of Health and Medical Sciences, Division of Pediatrics, University of Western Australia, Perth, WA, Australia
- Western Australian Register of Developmental Anomalies, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Jenefer M Blackwell
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.
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22
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Cerovic M, Peterlin B, Klemenc-Ketis Z. Genetics-Related Activities in Everyday Practice of Family Physicians in Slovenia. Public Health Genomics 2020; 23:230-236. [PMID: 33227795 DOI: 10.1159/000511561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/14/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Development of genomic technologies has an important impact on patient management in medicine. Nevertheless, translation of new advances of genomic medicine in primary care is challenging and needs to be adapted to the needs of health systems. OBJECTIVE The objective of this study was to analyze the current state of the use and the level of confidence in genetic management activities in everyday clinical practice of family practitioners (FPs) in Slovenia. METHODS We used a cross-sectional observational study design. The dataset was obtained through a questionnaire containing demographics, questions about the use of genetics in everyday practice, and a scale for measuring the responders' confidence in their ability to carry out basic genetic activities during patient treatment. The questionnaire was sent by regular mail to every FP in Slovenia (N = 950). RESULTS The questionnaire was completed by a total of 271 physicians (response rate 28.5%), with an average physicians' age of 45.5 ± 10.6 years. In their everyday clinical practice, the majority of Slovenian FPs report to encounter genetic conditions more than once a month (241, 91.2%). Family medical history is the most commonly used among all activities related to genetic management of patients. Only 5.9% of Slovenian FPs are confident in their ability to carry out basic activities related to genetic patient management. Most of them believe they are only competent enough to obtain family medical history and identify a positive family history. The FPs who reported a lower degree of confidence are those with the lowest level of education in the field of medical genetics and older physicians (age >50 years). CONCLUSIONS Slovenian family physicians commonly encounter patients with genetic conditions but are not confident in their ability to carry out basic medical genetic tasks. Therefore, additional education is necessary.
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Affiliation(s)
- Metka Cerovic
- Department of Family Medicine, Faculty of Medicine, University of Maribor, Taborska, Maribor, Slovenia.,Zdravstveni dom dr. Adolfa Drolca Maribor, Maribor, Slovenia
| | - Borut Peterlin
- Clinical Institute for Genomic Medicine, University Medical Centre Ljubljana, Šlajmerjeva, Ljubljana, Slovenia
| | - Zalika Klemenc-Ketis
- Department of Family Medicine, Faculty of Medicine, University of Maribor, Taborska, Maribor, Slovenia, .,Department of Family Medicine, Faculty of Medicine, University of Ljubljana, Poljanski nasip, Ljubljana, Slovenia, .,Community Health Centre Ljubljana, Metelkova, Ljubljana, Slovenia,
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23
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Hodžić A, Maver A, Plaseska-Karanfilska D, Ristanović M, Noveski P, Zorn B, Terzic M, Kunej T, Peterlin B. De novo mutations in idiopathic male infertility-A pilot study. Andrology 2020; 9:212-220. [PMID: 32860660 DOI: 10.1111/andr.12897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 08/04/2020] [Accepted: 08/22/2020] [Indexed: 01/24/2023]
Abstract
STUDY QUESTION Are de novo mutations in the human genome associated with male infertility? SUMMARY ANSWER We identified de novo mutations in five candidate genes: SEMA5A, NEURL4, BRD2, CD1D, and CD63. WHAT IS KNOWN ALREADY Epidemiological and genetic studies have consistently indicated contribution of genetic factors to the etiology of male infertility, suggesting that more than 1500 genes are involved in spermatogenesis. STUDY DESIGN, SIZE, DURATION First, we searched for de novo mutations in patients with idiopathic azoospermia with whole-exome sequencing (WES). To evaluate the potential functional impact of de novo identified mutations, we analyzed their expression differences on independent testis samples with normal and impaired spermatogenesis. In the next step, we tested additional group of azoospermic patients for mutations in identified genes with de novo mutations. In addition to the analysis of de novo mutations in patients with idiopathic azoospermia, we considered other models of inheritance and searched for candidate genes harboring rare maternally inherited variants and biallelic autosomal and X-chromosome hemizygous variants. PARTICIPANTS/MATERIALS, SETTING, METHODS We performed WES in 13 infertile males with idiopathic azoospermia and their parents. Potential functional impact of de novo identified mutations was evaluated by global gene expression profiling on 20 independent testis samples. To replicate the results, we performed WES in further 16 independent azoospermic males, which were screened for the variants in the same genes. Library preparation was performed with Nextera Coding Exome Capture Kit (Illumina), with subsequent sequencing on Illumina HiSeq 2500 platform. MAIN RESULTS AND THE ROLE OF CHANCE We identified 11 de novo mutations in 10 genes of which 5 were considered potentially associated with azoospermia: SEMA5A, NEURL4, BRD2, CD1D, and CD63. All candidate genes showed significant differential expression in testis samples composed of patients with severely impaired and normal spermatogenesis. Additionally, we identified rare, potentially pathogenic mutations in the genes previously implicated in male infertility-a maternally inherited heterozygous frameshift variant in FKBPL gene and inframe deletion in UPF2 gene, homozygous frameshift variant in CLCA4 gene, and a heterozygous missense variant NR0B1 gene, which represent promising candidates for further clinical implication. LIMITATIONS OF THE STUDY, REASONS FOR CAUTION We provided limited functional support for involvement of de novo identified genes in pathogenesis of male infertility, based on expression analysis. Additionally, the sample size was limited. WIDER IMPLICATIONS OF THE FINDINGS We provide support that de novo mutations might contribute to male infertility and propose five genes as potentially implicated in its pathogenesis.
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Affiliation(s)
- Alenka Hodžić
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov" Macedonian Academy of Sciences and Arts, Skopje, Macedonia
| | - Momčilo Ristanović
- Medical Faculty, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Predrag Noveski
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov" Macedonian Academy of Sciences and Arts, Skopje, Macedonia
| | - Branko Zorn
- Andrology Unit, Reproductive Unit, Department of Obstetrics and Gynecology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Marija Terzic
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov" Macedonian Academy of Sciences and Arts, Skopje, Macedonia
| | - Tanja Kunej
- Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
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24
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Wu D, Wang Y, Huang H. A novel variant of the IFITM5 gene within the 5'-UTR causes neonatal transverse clavicular fracture: Expanding the genetic spectrum. Mol Genet Genomic Med 2020; 8:e1287. [PMID: 32383316 PMCID: PMC7336742 DOI: 10.1002/mgg3.1287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/02/2020] [Accepted: 04/10/2020] [Indexed: 01/04/2023] Open
Abstract
Background Osteogenesis imperfecta (OI) type V is a rare heritable bone disorder caused by pathogenic variants of IFITM5. Only two mutated alleles in IFITM5 have been identified worldwide, the role of which in OI pathology is not fully understood. Methods A neonatal case of suspected OI, clinically manifested as a rare clavicle transection fracture with delayed early fracture healing, was studied. Subtle variants of OI‐associated genes were analyzed by whole exome sequencing and confirmed by Sanger sequencing. Results A de novo heterozygous pathogenic variant of IFITM5 within the 5′‐UTR (c.‐9C > A) was discovered in the proband. Bioinformatics analysis using a combination of various algorithms predicted that the variant would generate a new in‐frame start codon 9 bp upstream of the original and express a mutant IFITM5 protein with three additional amino acids (Met‐Glu‐Pro). After transfection into a eukaryocyte in vitro, the mutant IFITM5 construct produced a longer transcription product than that of wild‐type IFITM5. Conclusion This study identified a novel pathogenic variant of IFITM5, which not only manifested the molecular characteristics of IFITM5, but also provided new evidence for the study of the molecular mechanisms of IFITM5 association with OI.
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Affiliation(s)
- Dong Wu
- Department of Obstetrics and Gynecology, 900 Hospital of the Joint Logistics Team or Dongfang Hospital, Fuzhou, Fujian, People's Republic of China
| | - Yuxin Wang
- Department of Ultrasound, 900 Hospital of the Joint Logistics Team or Dongfang Hospital, Fuzhou, Fujian, People's Republic of China
| | - Huijuan Huang
- Department of Obstetrics and Gynecology, 900 Hospital of the Joint Logistics Team or Dongfang Hospital, Fuzhou, Fujian, People's Republic of China
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25
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Abstract
Dysmorphology is the practice of defining the morphologic phenotype of syndromic disorders. Genomic sequencing has advanced our understanding of human variation and molecular dysmorphology has evolved in response to the science of relating embryologic developmental implications of abnormal gene signaling pathways to the resultant phenotypic presentation. Machine learning has enabled the application of deep convoluted neural networks to recognize the comparative likeness of these phenotypes relative to the causal genotype or disrupted gene pathway.
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Affiliation(s)
- Donald Basel
- Department of Pediatrics, Division of Genetics, Medical College of Wisconsin, 9000 West Wisconsin Avenue, MS #716, Milwaukee, WI 53226, USA.
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26
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Stojanovic JR, Miletic A, Peterlin B, Maver A, Mijovic M, Borlja N, Dimitrijevic B, Soldatovic I, Cuturilo G. Diagnostic and Clinical Utility of Clinical Exome Sequencing in Children With Moderate and Severe Global Developmental Delay / Intellectual Disability. J Child Neurol 2020; 35:116-131. [PMID: 31623504 DOI: 10.1177/0883073819879835] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Clinical exome sequencing is currently being used in diagnostics of various genetic disorders, but studies supporting its application in clinical setting are scarce. The aim of this study was to establish diagnostic and clinical utility of clinical exome sequencing in patients with moderate and severe global developmental delay/intellectual disability. Clinical diagnosis was made in 49 of 88 investigated patients, with overall diagnostic yield of 55.7%. Molecular findings are characterized in detail, including the impact of newly made diagnosis on clinical management. Several previously unreported genotype-phenotype correlations and 33 novel variants are described. Genetic and clinical data were shared through publicly available database. In conclusion, clinical exome sequencing allows identification of causative variants in a significant proportion of patients in investigated clinical subgroup. Compared to whole exome sequencing, it shows similar diagnostic and clinical utility with reduced costs, which could be of particular importance for institutions with limited resources.
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Affiliation(s)
| | - Aleksandra Miletic
- University Children's Hospital, Department of Clinical Genetics, Belgrade, Serbia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Marija Mijovic
- University Children's Hospital, Department of Clinical Genetics, Belgrade, Serbia
| | | | | | - Ivan Soldatovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Goran Cuturilo
- University Children's Hospital, Department of Clinical Genetics, Belgrade, Serbia.,Faculty of Medicine, University of Belgrade, Belgrade, Serbia
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27
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Peterlin A, Petrovič D, Peterlin B. Screening for Rare Genetic Variants Associated with Atherosclerosis: Opportunity for Personalized Medicine. Curr Vasc Pharmacol 2020; 17:25-28. [PMID: 29412113 DOI: 10.2174/1570161116666180206111725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 10/01/2017] [Accepted: 11/07/2017] [Indexed: 01/27/2023]
Abstract
Atherosclerosis and its clinical manifestations is a leading cause of disease burden worldwide. Currently, most of the individuals carrying a strong predisposition to complications of atherosclerosis because of monogenic dyslipidaemias remain undiagnosed and consequently are not given an opportunity for prevention. Therefore, one of the main public health challenges remains the identification of individuals with significantly increased risk for atherosclerosis due to monogenic predisposition. Next-Generation Sequencing (NGS) has revolutionized genetic testing in symptomatic patients. Although new genomic technologies are still developing, and evidence on the use of this methodology for screening purposes is still lacking, genome testing might provide a powerful tool for the identification of individuals at risk. This may pave the way for the implementation of personalized medicine in the field of atherosclerosis prevention. In this review, we discuss the potential of genetic screening for atherosclerosis prevention and present the potential target of 17 genes responsible for monogenic dyslipidaemias associated with atherosclerosis.
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Affiliation(s)
- Ana Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Daniel Petrovič
- Institute of Histology and Embryology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
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28
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Liu J, Wu N, Yang N, Takeda K, Chen W, Li W, Du R, Liu S, Zhou Y, Zhang L, Liu Z, Zuo Y, Zhao S, Blank R, Pehlivan D, Dong S, Zhang J, Shen J, Si N, Wang Y, Liu G, Li S, Zhao Y, Zhao H, Chen Y, Zhao Y, Song X, Hu J, Lin M, Tian Y, Yuan B, Yu K, Niu Y, Yu B, Li X, Chen J, Yan Z, Zhu Q, Meng X, Chen X, Su J, Zhao X, Wang X, Ming Y, Li X, Raggio CL, Zhang B, Weng X, Zhang S, Zhang X, Watanabe K, Matsumoto M, Jin L, Shen Y, Sobreira NL, Posey JE, Giampietro PF, Valle D, Liu P, Wu Z, Ikegawa S, Lupski JR, Zhang F, Qiu G. TBX6-associated congenital scoliosis (TACS) as a clinically distinguishable subtype of congenital scoliosis: further evidence supporting the compound inheritance and TBX6 gene dosage model. Genet Med 2019; 21:1548-1558. [PMID: 30636772 DOI: 10.1038/s41436-018-0377-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/09/2018] [Indexed: 02/07/2023] Open
Abstract
PURPOSE To characterize clinically measurable endophenotypes, implicating the TBX6 compound inheritance model. METHODS Patients with congenital scoliosis (CS) from China(N = 345, cohort 1), Japan (N = 142, cohort 2), and the United States (N = 10, cohort 3) were studied. Clinically measurable endophenotypes were compared according to the TBX6 genotypes. A mouse model for Tbx6 compound inheritance (N = 52) was investigated by micro computed tomography (micro-CT). A clinical diagnostic algorithm (TACScore) was developed to assist in clinical recognition of TBX6-associated CS (TACS). RESULTS In cohort 1, TACS patients (N = 33) were significantly younger at onset than the remaining CS patients (P = 0.02), presented with one or more hemivertebrae/butterfly vertebrae (P = 4.9 × 10‒8), and exhibited vertebral malformations involving the lower part of the spine (T8-S5, P = 4.4 × 10‒3); observations were confirmed in two replication cohorts. Simple rib anomalies were prevalent in TACS patients (P = 3.1 × 10‒7), while intraspinal anomalies were uncommon (P = 7.0 × 10‒7). A clinically usable TACScore was developed with an area under the curve (AUC) of 0.9 (P = 1.6 × 10‒15). A Tbx6-/mh (mild-hypomorphic) mouse model supported that a gene dosage effect underlies the TACS phenotype. CONCLUSION TACS is a clinically distinguishable entity with consistent clinically measurable endophenotypes. The type and distribution of vertebral column abnormalities in TBX6/Tbx6 compound inheritance implicate subtle perturbations in gene dosage as a cause of spine developmental birth defects responsible for about 10% of CS.
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Affiliation(s)
- Jiaqi Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China. .,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | | | - Nan Yang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Kazuki Takeda
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan.,Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Weiyu Li
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, China
| | - Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sen Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Yangzhong Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Internal Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ling Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, China
| | - Zhenlei Liu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yuzhi Zuo
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Robert Blank
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shuangshuang Dong
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, China
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Jianxiong Shen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Nuo Si
- The McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yipeng Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Gang Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Shugang Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yanxue Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Hong Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yixin Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Yu Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jianhua Hu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Mao Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Ye Tian
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Keyi Yu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bin Yu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jia Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zihui Yan
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Qiankun Zhu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Xiaolu Meng
- The McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoli Chen
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, China
| | - Jianzhong Su
- College of Biomedical Engineering, The Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiuli Zhao
- The McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyue Wang
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yue Ming
- PET-CT Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao Li
- Department of Radiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Cathleen L Raggio
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Baozhong Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xisheng Weng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuyang Zhang
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xue Zhang
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,The McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Kota Watanabe
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Morio Matsumoto
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | | | - Li Jin
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Yiping Shen
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Nara L Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Philip F Giampietro
- Department of Pediatrics, Drexel University College of Medicine, Philadelphia, PA, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Departments of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China. .,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China.
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29
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Abstract
We report the case of a 41-year-old man on conservative treatment for more than 20 years for chronic renal insufficiency, chronic hepatitis and recurrent cholangitis. Following lengthy and extensive diagnostics, the differential diagnosis included primary sclerosing cholangitis and Caroli’s disease (CD). To solve the diagnostic challenge, next generation sequencing (NGS) was performed to distinguish between the disorders possibly present in the patient. The diagnosis of CD became evident after two rare known pathogenic mutations were detected in the poly-ductin 1 (PKHD1) gene, c.370C>T (p.Arg124Ter) and c.4870C>T (p.Arg1624Trp). In this case, NGS was instrumental in solving the diagnostic challenge, allowing differentiation among the proposed genetic and non-genetic ethiologies.
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Čaplovičová M, Moslerová V, Dupej J, Macek M, Zemková D, Hoffmannová E, Havlovicová M, Velemínská J. Modeling age-specific facial development in Williams-Beuren-, Noonan-, and 22q11.2 deletion syndromes in cohorts of Czech patients aged 3-18 years: A cross-sectional three-dimensional geometric morphometry analysis of their facial gestalt. Am J Med Genet A 2018; 176:2604-2613. [PMID: 30380201 DOI: 10.1002/ajmg.a.40659] [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: 05/30/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 11/08/2022]
Abstract
Three-dimensional (3D) virtual facial models facilitate genotype-phenotype correlations and diagnostics in clinical dysmorphology. Within cross-sectional analysis of both genders we evaluated facial features in representative cohorts of Czech patients with Williams-Beuren-(WBS; 12 cases), Noonan-(NS; 14), and 22q11.2 deletion syndromes (22q11.2DS; 20) and compared their age-related developmental trajectories to 21 age, sex and ethnically matched controls in 3-18 years of age. Using geometric morphometry statistically significant differences in facial morphology were found in all cases compared to controls. The dysmorphic features observed in WBS were specific and manifested in majority of cases. During ontogenesis, dysmorphic features associated with increased facial convexity become more pronounced whereas other typical features remained relatively stable. Dysmorphic features observed in NS cases were mostly apparent during childhood and gradually diminished with age. Facial development had a similar progress as in controls, while there has been increased growth of patients' nose and chin in adulthood. Facial characteristics observed in 22q11.2DS, except for hypoplastic alae nasi, did not correspond with the standard description of its facial phenotype because of marked facial heterogeneity of this clinical entity. Because of the sensitivity of 3D facial morphometry we were able to reach statistical significance even in smaller retrospective patient cohorts, which proves its clinical utility within the routine setting.
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Affiliation(s)
- Martina Čaplovičová
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Veronika Moslerová
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague 2, Czech Republic.,Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague 5, Czech Republic
| | - Ján Dupej
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague 2, Czech Republic.,Department of Software and Computer Science, Faculty of Mathematics and Physics, Charles University, Prague 2, Czech Republic
| | - Milan Macek
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague 5, Czech Republic
| | - Dana Zemková
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague 5, Czech Republic
| | - Eva Hoffmannová
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Markéta Havlovicová
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague 5, Czech Republic
| | - Jana Velemínská
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague 2, Czech Republic
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Tumienė B, Maver A, Writzl K, Hodžić A, Čuturilo G, Kuzmanić-Šamija R, Čulić V, Peterlin B. Diagnostic exome sequencing of syndromic epilepsy patients in clinical practice. Clin Genet 2018; 93:1057-1062. [PMID: 29286531 DOI: 10.1111/cge.13203] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 02/04/2023]
Abstract
Although genetic revolution of recent years has vastly expanded a list of genes implicated in epilepsies, complex architecture of epilepsy genetics is still largely unknown, consequently, universally accepted workflows for epilepsy genetic testing in a clinical practice are missing. We present a comprehensive NGS-based diagnostic approach addressing both the clinical and genetic heterogeneity of disorders involving epilepsy or seizures. A bioinformatic panel of 862 epilepsy- or seizure-associated genes was applied to Mendeliome (4813 genes) or whole-exome sequencing data as a first stage, while the second stage included untargeted variant interpretation. Eighty-six consecutive patients with epilepsy or seizures associated with neurodevelopmental disorders and/or congenital malformations were investigated. Of the 86 probands, 42 harbored pathogenic and likely pathogenic variants, giving a diagnostic yield of 49%. Two patients were diagnosed with pathogenic copy number variations and 2 had causative mitochondrial DNA variants. Eleven patients (13%) were diagnosed with diseases with specific treatments. Besides, genomic approach in diagnostics had multiple additional benefits due to mostly non-specific, overlapping, not full-blown phenotypes and abilities to diagnose novel and ultra rare epilepsy-associated diseases. Likely pathogenic variants were identified in SOX5 gene, not previously associated with epilepsy, and UBA5, a recently associated with epilepsy gene.
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Affiliation(s)
- B Tumienė
- Clinical Institute for Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Department of Human and Medical Genetics, Centre for Medical Genetics, Vilnius University, Vilnius, Lithuania
| | - A Maver
- Clinical Institute for Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - K Writzl
- Clinical Institute for Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - A Hodžić
- Clinical Institute for Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - G Čuturilo
- Department of Medical Genetics, University Children's Hospital, Belgrade, Serbia
| | | | - V Čulić
- Department of Pediatrics, University Hospital Split, Split, Croatia
| | - B Peterlin
- Clinical Institute for Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Likar T, Hasanhodžić M, Teran N, Maver A, Peterlin B, Writzl K. Diagnostic outcomes of exome sequencing in patients with syndromic or non-syndromic hearing loss. PLoS One 2018; 13:e0188578. [PMID: 29293505 PMCID: PMC5749682 DOI: 10.1371/journal.pone.0188578] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/09/2017] [Indexed: 12/30/2022] Open
Abstract
Hereditary hearing loss (HL) is a common sensory disorder, with an incidence of 1–2 per 1000 newborns, and has a genetic etiology in over 50% of cases. It occurs either as part of a syndrome or in isolation and is genetically very heterogeneous which poses a challenge for clinical and molecular diagnosis. We used exome sequencing to seek a genetic cause in a group of 56 subjects (49 probands) with HL: 32 with non-syndromic non-GJB2 HL and 17 with syndromic HL. Following clinical examination and clinical exome sequencing, an etiological diagnosis was established in 15 probands (15/49; 30%); eight (8/17;47%) from the syndromic group and seven (7/32; 21%) from the non-syndromic non-GJB2 subgroup. Fourteen different (half of them novel) non-GJB2 variants causing HL were found in 10 genes (CHD7, HDAC8, MITF, NEFL, OTOF, SF3B4, SLC26A4, TECTA, TMPRSS3, USH2A) among 13 probands, confirming the genetic heterogeneity of hereditary HL. Different genetic causes for HL were found in a single family while three probands with apparent syndromic HL were found to have HL as a separate clinical feature, distinct from the complex phenotype. Clinical exome sequencing proved to be an effective tool used to comprehensively address the genetic heterogeneity of HL, to detect clinically unrecognized HL syndromes, and to decipher complex phenotypes in which HL is a separate feature and not part of a syndrome.
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Affiliation(s)
- Tina Likar
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Mensuda Hasanhodžić
- Policlinic of Medical Genetics with Genetic Counseling for Out-Patient Care, Department of Paediatrics, University Clinical Centre Tuzla, Tuzla, Bosnia and Herzegovina
| | - Nataša Teran
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Karin Writzl
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
- * E-mail:
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Kernohan KD, Hartley T, Alirezaie N, Robinson PN, Dyment DA, Boycott KM. Evaluation of exome filtering techniques for the analysis of clinically relevant genes. Hum Mutat 2017; 39:197-201. [DOI: 10.1002/humu.23374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 11/20/2017] [Accepted: 11/26/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Kristin D. Kernohan
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Ontario Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Ontario Canada
| | - Najmeh Alirezaie
- McGill University and Genome Quebec Innovation Centre; Montreal Quebec Canada
| | - Peter N. Robinson
- The Jackson Laboratory for Genomic Medicine; Farmington Connecticut
- Institute for Systems Genomics; University of Connecticut; Farmington Connecticut
| | - David A. Dyment
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Ontario Canada
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
| | - Kym M. Boycott
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Ontario Canada
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
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Bergant G, Maver A, Lovrecic L, Čuturilo G, Hodzic A, Peterlin B. Comprehensive use of extended exome analysis improves diagnostic yield in rare disease: a retrospective survey in 1,059 cases. Genet Med 2017; 20:303-312. [PMID: 28914264 DOI: 10.1038/gim.2017.142] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/27/2017] [Indexed: 01/02/2023] Open
Abstract
PurposeWe sought to determine the analytical sensitivity of several extended exome variation analysis approaches in terms of their contribution to diagnostic yield and their clinical feasibility.MethodsWe retrospectively analyzed the results of genetic testing in 1,059 distinct cases referred for exome sequencing to our institution. In these, we routinely employed extended exome analysis approaches in addition to basic variant analysis, including (i) copy-number variation (CNV) detection, (ii) nonconsensus splice defect detection, (ii) genomic breakpoint detection, (iv) homozygosity mapping, and (v) mitochondrial variant analysis.ResultsExtended exome analysis approaches assisted in identification of causative genetic variant in 44 cases, which represented a 4.2% increase in diagnostic yield. The greatest contribution was associated with CNV analysis (1.8%) and splice variant prediction (1.2%), and the remaining approaches contributed an additional 1.2%. Analysis of workload has shown that on average nine additional variants per case had to be interpreted in the extended analysis.ConclusionWe show that extended exome analysis approaches improve the diagnostic yield of heterogeneous genetic disorders and result in considerable increase of diagnostic yield of exome sequencing with a minor increase of interpretative workload.
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Affiliation(s)
- Gaber Bergant
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Luca Lovrecic
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Goran Čuturilo
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,University Children's Hospital, Belgrade, Serbia
| | - Alenka Hodzic
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Allegrini D, Penco S, Pece A, Autelitano A, Montesano G, Paci S, Montanari C, Maver A, Peterlin B, Damante G, Rossetti L. Cataract and optic disk drusen in a patient with glycogenosis and di George syndrome: clinical and molecular report. BMC Ophthalmol 2017; 17:107. [PMID: 28659124 PMCID: PMC5490087 DOI: 10.1186/s12886-017-0499-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 06/20/2017] [Indexed: 11/29/2022] Open
Abstract
Background We report the ophthalmic findings of a patient with type Ia glycogen storage disease (GSD Ia), DiGeorge syndrome (DGS), cataract and optic nerve head drusen (ONHD). Case presentation A 26-year-old white woman, born at term by natural delivery presented with a post-natal diagnosis of GSD Ia. Genetic testing by array-comparative genomic hybridization (CGH) for DGS was required because of her low levels of serum calcium. The patient has been followed from birth, attending the day-hospital every six months at the San Paolo Hospital, Milan, outpatient clinic for metabolic diseases and previously at another eye center. During the last day-hospital visit, a complete eye examination showed ONHD and cataract in both eyes. Next Generation Sequencing (NGS) was subsequently done to check for any association between the eye problems and metabolic aspects. Conclusions This is the first description of ocular changes in a patient with GSD Ia and DGS. Mutations explaining GSD Ia and DGS were found but no specific causative mutation for cataract and ONHD. The metabolic etiology of her lens changes is known, whereas the pathogenesis of ONHD is not clear. Although the presence of cataract and ONHD could be a coincidence; the case reported could suggest that hypocalcemia due to DGS could be the common biochemical pathway.
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Affiliation(s)
- D Allegrini
- Eye Unit, Humanitas Gavazzeni Hospital, Humanitas University, Bergamo, Italy.
| | - S Penco
- Medical Genetics Unit, Niguarda Ca' Granda Hospital, Milan, Italy
| | - A Pece
- Eye Unit, Melegnano Hospital, Vizzolo Predabissi, Milan, Italy
| | - A Autelitano
- Eye Unit, San Paolo Hospital, University of Milan, Milan, Italy
| | - G Montesano
- Eye Unit, San Paolo Hospital, University of Milan, Milan, Italy
| | - S Paci
- Pediatric Department, San Paolo Hospital, University of Milan, Milan, Italy
| | - C Montanari
- Pediatric Department, San Paolo Hospital, University of Milan, Milan, Italy
| | - A Maver
- Clinical Institute for Medical Genetics, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - B Peterlin
- Clinical Institute for Medical Genetics, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - G Damante
- Medical Genetics Unit, University of Udine, Udine, Italy
| | - L Rossetti
- Eye Unit, San Paolo Hospital, University of Milan, Milan, Italy
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36
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Mackley MP, Capps B. Expect the unexpected: screening for secondary findings in clinical genomics research. Br Med Bull 2017; 122:109-122. [PMID: 28398474 DOI: 10.1093/bmb/ldx009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/10/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Due to decreasing cost, and increasing speed and precision, genomic sequencing in research is resulting in the generation of vast amounts of genetic data. The question of how to manage that information has been an area of significant debate. In particular, there has been much discussion around the issue of 'secondary findings' (SF)-findings unrelated to the research that have diagnostic significance. SOURCES OF DATA The following includes ethical commentaries, guidelines and policies in respect to large-scale clinical genomics studies. AREAS OF AGREEMENT Research participant autonomy and their informed consent are paramount-policies around SF must be made clear and participants must have the choice as to which results they wish to receive, if any. AREAS OF CONTROVERSY While many agree that clinically 'actionable' findings should be returned, some question whether they should be actively sought within a research protocol. GROWING POINTS SF present challenges to a growing field; diverse policies around their management have the potential to hinder collaboration and future research. AREAS TIMELY FOR DEVELOPING RESEARCH The impact of returning SF and accurate estimates of their clinical utility are needed to inform future protocol design.
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Affiliation(s)
- Michael P Mackley
- Radcliffe Department of Medicine, University of Oxford, Level 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Benjamin Capps
- Department of Bioethics, Faculty of Medicine, Dalhousie University, 5849 University Avenue, Room C-312, CRC Bldg, PO Box 15000, Halifax NS, Canada B3H 4R2
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Baynam G, Broley S, Bauskis A, Pachter N, McKenzie F, Townshend S, Slee J, Kiraly-Borri C, Vasudevan A, Hawkins A, Schofield L, Helmholz P, Palmer R, Kung S, Walker CE, Molster C, Lewis B, Mina K, Beilby J, Pathak G, Poulton C, Groza T, Zankl A, Roscioli T, Dinger ME, Mattick JS, Gahl W, Groft S, Tifft C, Taruscio D, Lasko P, Kosaki K, Wilhelm H, Melegh B, Carapetis J, Jana S, Chaney G, Johns A, Owen PW, Daly F, Weeramanthri T, Dawkins H, Goldblatt J. Initiating an undiagnosed diseases program in the Western Australian public health system. Orphanet J Rare Dis 2017; 12:83. [PMID: 28468665 PMCID: PMC5415708 DOI: 10.1186/s13023-017-0619-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 03/26/2017] [Indexed: 02/02/2023] Open
Abstract
Background New approaches are required to address the needs of complex undiagnosed diseases patients. These approaches include clinical genomic diagnostic pipelines, utilizing intra- and multi-disciplinary platforms, as well as specialty-specific genomic clinics. Both are advancing diagnostic rates. However, complementary cross-disciplinary approaches are also critical to address those patients with multisystem disorders who traverse the bounds of multiple specialties and remain undiagnosed despite existing intra-specialty and genomic-focused approaches. The diagnostic possibilities of undiagnosed diseases include genetic and non-genetic conditions. The focus on genetic diseases addresses some of these disorders, however a cross-disciplinary approach is needed that also simultaneously addresses other disorder types. Herein, we describe the initiation and summary outcomes of a public health system approach for complex undiagnosed patients - the Undiagnosed Diseases Program-Western Australia (UDP-WA). Results Briefly the UDP-WA is: i) one of a complementary suite of approaches that is being delivered within health service, and with community engagement, to address the needs of those with severe undiagnosed diseases; ii) delivered within a public health system to support equitable access to health care, including for those from remote and regional areas; iii) providing diagnoses and improved patient care; iv) delivering a platform for in-service and real time genomic and phenomic education for clinicians that traverses a diverse range of specialties; v) retaining and recapturing clinical expertise; vi) supporting the education of junior and more senior medical staff; vii) designed to integrate with clinical translational research; and viii) is supporting greater connectedness for patients, families and medical staff. Conclusion The UDP-WA has been initiated in the public health system to complement existing clinical genomic approaches; it has been targeted to those with a specific diagnostic need, and initiated by redirecting existing clinical and financial resources. The UDP-WA supports the provision of equitable and sustainable diagnostics and simultaneously supports capacity building in clinical care and translational research, for those with undiagnosed, typically rare, conditions. Electronic supplementary material The online version of this article (doi:10.1186/s13023-017-0619-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gareth Baynam
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia. .,School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia. .,Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia. .,Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia. .,Telethon Kids Institute, University of Western Australia, Perth, WA, Australia. .,Western Australian Register of Developmental Anomalies, Perth, WA, Australia. .,School of Spatial Sciences, Curtin University, Perth, WA, Australia.
| | - Stephanie Broley
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Alicia Bauskis
- Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Nicholas Pachter
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
| | - Fiona McKenzie
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
| | - Sharron Townshend
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Jennie Slee
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Cathy Kiraly-Borri
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Anand Vasudevan
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Anne Hawkins
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Lyn Schofield
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia.,Centre for Comparative Genomics, Murdoch University, Perth, WA, Australia
| | - Petra Helmholz
- School of Spatial Sciences, Curtin University, Perth, WA, Australia.,Cooperative Research Centre for Spatial Information, Perth, WA, Australia
| | - Richard Palmer
- School of Spatial Sciences, Curtin University, Perth, WA, Australia.,Cooperative Research Centre for Spatial Information, Perth, WA, Australia
| | - Stefanie Kung
- School of Spatial Sciences, Curtin University, Perth, WA, Australia.,Cooperative Research Centre for Spatial Information, Perth, WA, Australia
| | - Caroline E Walker
- Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Caron Molster
- Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Barry Lewis
- Diagnostic Genomics, PathWest, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Kym Mina
- Diagnostic Genomics, PathWest, Department of Health, Government of Western Australia, Perth, WA, Australia.,School of Pathology and Laboratory Medicine, University of Western Australia, Perth, WA, Australia
| | - John Beilby
- Diagnostic Genomics, PathWest, Department of Health, Government of Western Australia, Perth, WA, Australia.,School of Pathology and Laboratory Medicine, University of Western Australia, Perth, WA, Australia
| | | | | | - Tudor Groza
- Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia
| | - Andreas Zankl
- Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, Australia.,The Children's Hospital at Westmead, Clinical Genetics Service, Westmead, NSW, Australia
| | - Tony Roscioli
- Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, Australia
| | - John S Mattick
- Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia
| | - William Gahl
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Rockville, MD, USA.,Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Rockville, MD, USA
| | - Stephen Groft
- National Centre for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Cynthia Tifft
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Rockville, MD, USA.,Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Rockville, MD, USA
| | - Domenica Taruscio
- Instituto Superiore di Sanità, National Center for Rare Diseases, Rome, Italy
| | - Paul Lasko
- Canadian Institutes of Health Research, Institute of Genetics, Montreal, Canada
| | | | | | - Bela Melegh
- Department of Medical Genetics, University of Pécs, Pécs, Hungary
| | - Jonathan Carapetis
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.,Perth Children's Hospital, Perth, WA, Australia
| | - Sayanta Jana
- King Edward Memorial Hospital, Perth, WA, Australia
| | | | | | | | - Frank Daly
- Perth Children's Hospital, Perth, WA, Australia
| | - Tarun Weeramanthri
- Public Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Hugh Dawkins
- Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia.,Centre for Population Health Research, Curtin Health Innovation Research Institute, Curtin University of Technology, Perth, WA, Australia.,School of Pathology and Laboratory Medicine, University of Western Australia, Perth, WA, Australia.,Centre for Comparative Genomics, Murdoch University, Perth, WA, Australia
| | - Jack Goldblatt
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
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Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1031:55-94. [PMID: 29214566 DOI: 10.1007/978-3-319-67144-4_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Public health relies on technologies to produce and analyse data, as well as effectively develop and implement policies and practices. An example is the public health practice of epidemiology, which relies on computational technology to monitor the health status of populations, identify disadvantaged or at risk population groups and thereby inform health policy and priority setting. Critical to achieving health improvements for the underserved population of people living with rare diseases is early diagnosis and best care. In the rare diseases field, the vast majority of diseases are caused by destructive but previously difficult to identify protein-coding gene mutations. The reduction in cost of genetic testing and advances in the clinical use of genome sequencing, data science and imaging are converging to provide more precise understandings of the 'person-time-place' triad. That is: who is affected (people); when the disease is occurring (time); and where the disease is occurring (place). Consequently we are witnessing a paradigm shift in public health policy and practice towards 'precision public health'.Patient and stakeholder engagement has informed the need for a national public health policy framework for rare diseases. The engagement approach in different countries has produced highly comparable outcomes and objectives. Knowledge and experience sharing across the international rare diseases networks and partnerships has informed the development of the Western Australian Rare Diseases Strategic Framework 2015-2018 (RD Framework) and Australian government health briefings on the need for a National plan.The RD Framework is guiding the translation of genomic and other technologies into the Western Australian health system, leading to greater precision in diagnostic pathways and care, and is an example of how a precision public health framework can improve health outcomes for the rare diseases population.Five vignettes are used to illustrate how policy decisions provide the scaffolding for translation of new genomics knowledge, and catalyze transformative change in delivery of clinical services. The vignettes presented here are from an Australian perspective and are not intended to be comprehensive, but rather to provide insights into how a new and emerging 'precision public health' paradigm can improve the experiences of patients living with rare diseases, their caregivers and families.The conclusion is that genomic public health is informed by the individual and family needs, and the population health imperatives of an early and accurate diagnosis; which is the portal to best practice care. Knowledge sharing is critical for public health policy development and improving the lives of people living with rare diseases.
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Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJS, DeMare LE, Devereau AD, de Vries BBA, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MWM, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JOB, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN. The Human Phenotype Ontology in 2017. Nucleic Acids Res 2016; 45:D865-D876. [PMID: 27899602 PMCID: PMC5210535 DOI: 10.1093/nar/gkw1039] [Citation(s) in RCA: 501] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/28/2016] [Indexed: 12/14/2022] Open
Abstract
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.
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Affiliation(s)
- Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nicole A Vasilevsky
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Mark Engelstad
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Erin Foster
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julie McMurry
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ségolène Aymé
- Institut du Cerveau et de la Moelle épinière-ICM, CNRS UMR 7225-Inserm U 1127-UPMC-P6 UMR S 1127, Hôpital Pitié-Salpêtrière, 47, bd de l'Hôpital, 75013 Paris, France
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital Department of Health, Government of Western Australia, Perth, WA 6008, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6008, Australia
| | - Susan M Bello
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Cornelius F Boerkoel
- Imagenetics Research, Sanford Health, PO Box 5039, Route 5001, Sioux Falls, SD 57117-5039, USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Orion J Buske
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.,NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Valentina Cipriani
- UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Hugh J S Dawkins
- Office of Population Health Genomics, Public Health Division, Health Department of Western Australia, 189 Royal Street, Perth, WA, 6004 Australia
| | - Laura E DeMare
- Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA
| | - Andrew D Devereau
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University, University Medical Centre, Nijmegen, The Netherlands
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Daniel Greene
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ingo Helbig
- Division of Neurology, The Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA.,Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Courtney Hum
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1H3, Canada
| | - Johanna A Jähn
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Roger James
- NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Roland Krause
- LuxembourgCentre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | | | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, NY 11797, USA
| | - Soichi Ogishima
- Dept of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Tohoku Medical Megabank Organization Bldg 7F room #741,736, Seiryo 2-1, Aoba-ku, Sendai Miyagi 980-8573 Japan
| | - Annie Olry
- Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France
| | - Willem H Ouwehand
- Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Ana Rath
- Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France
| | - Franz Schaefer
- Division of Pediatric Nephrology and KFH Children's Kidney Center, Center for Pediatrics and Adolescent Medicine, 69120 Heidelberg, Germany
| | - Richard H Scott
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Michael Segal
- SimulConsult Inc., 27 Crafts Road, Chestnut Hill, MA 02467, USA
| | | | - Richard Sever
- Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA
| | - Cynthia L Smith
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Rachel Thompson
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Catherine Turner
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Ernest Turro
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Marijcke W M Veltman
- NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Tom Vulliamy
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Jing Yu
- Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Julie von Ziegenweidt
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK
| | - Andreas Zankl
- Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Australia.,Academic Department of Medical Genetics, Sydney Childrens Hospitals Network (Westmead), Australia
| | - Stephan Züchner
- JD McDonald Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Tomasz Zemojtel
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Julius O B Jacobsen
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Tudor Groza
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Australia
| | - Damian Smedley
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Melissa Haendel
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA .,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
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