1
|
Linhuan H, Danlei C, Zhiming H, Shu K, Jiayi C, Jiayi P, Chuqi S, Yinghong Y, Ding W, Yingjun X, Yanmin L. The use of high-resolution SNP arrays to detect congenital cardiac defects. J Matern Fetal Neonatal Med 2024; 37:2301831. [PMID: 38311547 DOI: 10.1080/14767058.2024.2301831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024]
Abstract
OBJECTIVE Copy number variations (CNVs) detected by high-resolution single nucleotide polymorphism microarrays (SNP arrays) have been associated with congenital heart defects (CHDs). The genetic mechanism underlying the development of CHDs remains unclear. METHODS High-resolution SNP arrays were used to detect CNVs and traditional chromosomal analyses, respectively, were carried out on 60 and 249 fetuses from gestational 12-37 weeks old, having isolated or complex CHDs that were diagnosed using prenatal ultrasound. RESULTS Twenty of the 60 fetuses (33.5%) had abnormalities, of which 23 CNVs (12 pathogenic, five probable pathogenic and six of undetermined significance) were detected by SNP arrays, and two distinct CNVs were present in three of these fetuses. In addition, in 39 patients with isolated congenital heart disease who had normal karyotypes, abnormal CNVs were present in 28.2% (11/39), and in patients with complex coronary artery disease, 19.0% (4/21) had abnormal karyotypes and 42.9% (9/21) had abnormal CNVs. In patients with complex coronary artery disease, 19.0% (4/21) had abnormal karyotypes and 42.9% (9/21) had abnormal CNVs. CONCLUSIONS In conclusion, genome-wide high-resolution SNP array can improve the diagnostic rate and uncover additional pathogenic CNVs. The submicroscopic deletions and duplications of Online Mendelian Inheritance in Man (OMIM) genes found in this study have haploinsufficient (deletion) or triplosensitive (duplication) traits, which further clarify the etiology and inheritance of CHDs.
Collapse
Affiliation(s)
- Huang Linhuan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Cai Danlei
- Department of Ultrasound, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - He Zhiming
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Kong Shu
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chen Jiayi
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Peng Jiayi
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Su Chuqi
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yang Yinghong
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wang Ding
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xie Yingjun
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Luo Yanmin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| |
Collapse
|
2
|
MacCarrick G, Aradhya S, Bailey M, Chu D, Hunt A, Izzo E, Krakow D, Mackenzie W, Poll S, Raggio C, Shediac R, White KK, McLaughlin HM, Seratti G. Clinical utility of comprehensive gene panel testing for common and rare causes of skeletal dysplasia and other skeletal disorders: Results from the largest cohort to date. Am J Med Genet A 2024:e63646. [PMID: 38702915 DOI: 10.1002/ajmg.a.63646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 04/03/2024] [Accepted: 04/18/2024] [Indexed: 05/06/2024]
Abstract
Molecular genetics enables more precise diagnoses of skeletal dysplasia and other skeletal disorders (SDs). We investigated the clinical utility of multigene panel testing for 5011 unrelated individuals with SD in the United States (December 2019-April 2022). Median (range) age was 8 (0-90) years, 70.5% had short stature and/or disproportionate growth, 27.4% had a positive molecular diagnosis (MDx), and 30 individuals received two MDx. Genes most commonly contributing to MDx were FGFR3 (16.9%), ALPL (13.0%), and COL1A1 (10.3%). Most of the 112 genes associated with ≥1 MDx were primarily involved in signal transduction (n = 35), metabolism (n = 23), or extracellular matrix organization (n = 17). There were implications associated with specific care/treatment options for 84.4% (1158/1372) of MDx-positive individuals; >50% were linked to conditions with targeted therapy approved or in clinical development, including osteogenesis imperfecta, achondroplasia, hypophosphatasia, and mucopolysaccharidosis. Forty individuals with initially inconclusive results became MDx-positive following family testing. Follow-up mucopolysaccharidosis enzyme activity testing was positive in 14 individuals (10 of these were not MDx-positive). Our findings showed that inclusion of metabolic genes associated with SD increased the clinical utility of a gene panel and confirmed that integrated use of comprehensive gene panel testing with orthogonal testing reduced the burden of inconclusive results.
Collapse
Affiliation(s)
- Gretchen MacCarrick
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mitch Bailey
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Dorna Chu
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Abigail Hunt
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Emanuela Izzo
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Deborah Krakow
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - William Mackenzie
- Department of Orthopaedic Surgery, Nemours Children's Hospital, Wilmington, Delaware, USA
| | - Sarah Poll
- Invitae Corporation, San Francisco, California, USA
| | - Cathleen Raggio
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, New York, USA
| | - Renée Shediac
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Klane K White
- Department of Pediatric Orthopedic Surgery, Children's Hospital Colorado, Aurora, Colorado, USA
| | | | | |
Collapse
|
3
|
Lee JK, Kwon H, Park JH, Jang MA, Kim YG, Kim JW, Choi BO, Jang JH. Enhancing the Reliability of PMP22 Copy Number Variation Detection with an Inherited Peripheral Neuropathy Panel. J Mol Diagn 2024; 26:304-309. [PMID: 38301867 DOI: 10.1016/j.jmoldx.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/13/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
The utility of the next-generation sequencing (NGS) panel could be increased in hereditary peripheral neuropathies, given that the duplication of PMP22 is a major abnormality. In the present study, the analytical performance of an algorithm for detecting PMP22 copy number variation (CNV) from the NGS panel data was evaluated. The NGS panel covers 141 genes, including PMP22 and five genes within 1.5-megabase duplicated region at 17p11.2. CNV calling was performed using a laboratory-developed algorithm. Among the 92 cases subjected to targeted NGS panel from March 2018 to January 2021, 26 were suggestive of PMP22 CNV. Multiplex ligation-dependent probe amplification analysis was performed in 58 cases, and the results were 100% concordant with the NGS data (23 duplications, 2 deletions, and 33 negatives). Analytical performance of the pipeline was further validated by another blind data set, including 14 positive and 20 negative samples. Reliable detection of PMP22 CNV was possible by analyzing not only PMP22 but also the adjacent genes within the 1.5-megabase region of 17p11.2. On the basis of the high accuracy of CNV calling for PMP22, the testing strategy for diagnosis of peripheral polyneuropathies could be simplified by reducing the need for multiplex ligation-dependent probe amplification.
Collapse
Affiliation(s)
- Jong Kwon Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyemi Kwon
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong-Ho Park
- Clinical Genomics Center, Samsung Medical Center, Seoul, Republic of Korea
| | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Young-Gon Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Byung-Ok Choi
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Cell and Gene Therapy Institute, Samsung Medical Center, Seoul, Republic of Korea; Samsung Advanced Institute for Health Sciences and Technology, Seoul, Republic of Korea.
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
4
|
Kaur N, Arora K, Radhakrishnan P, Narayanan DL, Shukla A. Intragenic homozygous duplication in HEPACAM is associated with megalencephalic leukoencephalopathy with subcortical cysts type 2A. Neurogenetics 2024; 25:85-91. [PMID: 38280046 DOI: 10.1007/s10048-024-00743-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/05/2024] [Indexed: 01/29/2024]
Abstract
Disease-causing variants in HEPACAM are associated with megalencephalic leukoencephalopathy with subcortical cysts 2A (MLC2A, MIM# 613,925, autosomal recessive), and megalencephalic leukoencephalopathy with subcortical cysts 2B, remitting, with or without impaired intellectual development (MLC2B, MIM# 613,926, autosomal dominant). These disorders are characterised by macrocephaly, seizures, motor delay, cognitive impairment, ataxia, and spasticity. Brain magnetic resonance imaging (MRI) in these individuals shows swollen cerebral hemispheric white matter and subcortical cysts, mainly in the frontal and temporal regions. To date, 45 individuals from 39 families are reported with biallelic and heterozygous variants in HEPACAM, causing MLC2A and MLC2B, respectively. A 9-year-old male presented with developmental delay, gait abnormalities, seizures, macrocephaly, dysarthria, spasticity, and hyperreflexia. MRI revealed subcortical cysts with diffuse cerebral white matter involvement. Whole-exome sequencing (WES) in the proband did not reveal any clinically relevant single nucleotide variants. However, copy number variation analysis from the WES data of the proband revealed a copy number of 4 for exons 3 and 4 of HEPACAM. Validation and segregation were done by quantitative PCR which confirmed the homozygous duplication of these exons in the proband and carrier status in both parents. To the best of our knowledge, this is the first report of an intragenic duplication in HEPACAM causing MLC2A.
Collapse
Affiliation(s)
- Namanpreet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Khyati Arora
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Periyasamy Radhakrishnan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- DBT-Wellcome Trust India Alliance Early Career Clinical and Public Health Research Fellow, Hyderabad, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
| |
Collapse
|
5
|
Neves Rebello Alves L, Valle dos Santos Silveira L, Silva dos Reis Trabach R, Dummer Meira D, de Vargas Wolfgramm dos Santos E, Drumond Louro I. PIGN c.776T>C (p.Phe259Ser) variant present in trans with a pathogenic variant for PIGN-congenital disorder of glycosylation: Bella-Noah syndrome. Heliyon 2024; 10:e27438. [PMID: 38509968 PMCID: PMC10951506 DOI: 10.1016/j.heliyon.2024.e27438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/12/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Glycosylation is the most common protein and lipid post-translational modification in humans. Congenital disorders of glycosylation (CDG) are characterized by both genetic and clinical heterogeneity, presenting multisystemic manifestations, and in most cases are autosomal recessive in inheritance. The PIGN gene is responsible for the addition of phosphoethanolamine to the first mannose in the glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway, a highly conserved process that enables proteins to bind to the cell surface membrane. Here, we report a family with two siblings pediatric cases with the exact same compound heterozygous variants in PIGN. The (c.776T > C) variant of uncertain significance (VUS) together with a known pathogenic variant (c.932T > G), resulting in clinical features compatible with PIGN-related conditions, more specific the CDG. This is the first time that PIGN variant c.776T > C is reported in literature in individuals with PIGN-congenital disorder of glycosylation (PIGN-CDG), and the current submission in ClinVar by Invitae® is specifically of our case. Detailed clinical information and molecular analyses are presented. Here, we show for the first time two affected siblings with one pathogenic variant (c.932T > G) and the c.776T > C VUS in trans. In honor of the family, we propose the name Bella-Noah Syndrome for disorder.
Collapse
Affiliation(s)
- Lyvia Neves Rebello Alves
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória, 29075-910, ES, Brazil
- Programa de Pós-Graduação Em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, 29047-105, ES, Brazil
| | - Lívia Valle dos Santos Silveira
- Centro de Ciências da Saúde, Curso de Medicina, Universidade Federal do Espírito Santo (UFES), Vitória, 29090-040, ES, Brazil
| | - Raquel Silva dos Reis Trabach
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória, 29075-910, ES, Brazil
| | - Débora Dummer Meira
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória, 29075-910, ES, Brazil
- Programa de Pós-Graduação Em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, 29047-105, ES, Brazil
| | - Eldamária de Vargas Wolfgramm dos Santos
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória, 29075-910, ES, Brazil
- Programa de Pós-Graduação Em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, 29047-105, ES, Brazil
| | - Iúri Drumond Louro
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória, 29075-910, ES, Brazil
- Programa de Pós-Graduação Em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, 29047-105, ES, Brazil
| |
Collapse
|
6
|
Gupta V, Vashisht V, Vashisht A, Mondal AK, Alptekin A, Singh H, Kolhe R. Comprehensive Analysis of Clinically Relevant Copy Number Alterations (CNAs) Using a 523-Gene Next-Generation Sequencing Panel and NxClinical Software in Solid Tumors. Genes (Basel) 2024; 15:396. [PMID: 38674331 PMCID: PMC11049607 DOI: 10.3390/genes15040396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Copy number alterations (CNAs) are significant in tumor initiation and progression. Identifying these aberrations is crucial for targeted therapies and personalized cancer diagnostics. Next-generation sequencing (NGS) methods present advantages in scalability and cost-effectiveness, surpassing limitations associated with reference assemblies and probe capacities in traditional laboratory approaches. This retrospective study evaluated CNAs in 50 FFPE tumor samples (breast cancer, ovarian carcinoma, pancreatic cancer, melanoma, and prostate carcinoma) using Illumina's TruSight Oncology 500 (TSO500) and the Affymetrix Oncoscan Molecular Inversion Probe (OS-MIP) (ThermoFisher Scientific, Waltham, MA, USA). NGS analysis with the NxClinical 6.2 software demonstrated a high sensitivity and specificity (100%) for CNA detection, with a complete concordance rate as compared to the OS-MIP. All 54 known CNAs were identified by NGS, with gains being the most prevalent (63%). Notable CNAs were observed in MYC (18%), TP53 (12%), BRAF (8%), PIK3CA, EGFR, and FGFR1 (6%) genes. The diagnostic parameters exhibited high accuracy, including a positive predictive value, negative predictive value, and overall diagnostic accuracy. This study underscores NxClinical as a reliable software for identifying clinically relevant gene alterations using NGS TSO500, offering valuable insights for personalized cancer treatment strategies based on CNA analysis.
Collapse
Affiliation(s)
- Vivek Gupta
- Department of Pathology, Government Institute of Medical Sciences, Greater Noida 201310, India;
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Vishakha Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ashutosh Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ahmet Alptekin
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Harmanpreet Singh
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| |
Collapse
|
7
|
Artaza H, Eriksson D, Lavrichenko K, Aranda-Guillén M, Bratland E, Vaudel M, Knappskog P, Husebye ES, Bensing S, Wolff ASB, Kämpe O, Røyrvik EC, Johansson S. Rare copy number variation in autoimmune Addison's disease. Front Immunol 2024; 15:1374499. [PMID: 38562931 PMCID: PMC10982488 DOI: 10.3389/fimmu.2024.1374499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Autoimmune Addison's disease (AAD) is a rare but life-threatening endocrine disorder caused by an autoimmune destruction of the adrenal cortex. A previous genome-wide association study (GWAS) has shown that common variants near immune-related genes, which mostly encode proteins participating in the immune response, affect the risk of developing this condition. However, little is known about the contribution of copy number variations (CNVs) to AAD susceptibility. We used the genome-wide genotyping data from Norwegian and Swedish individuals (1,182 cases and 3,810 controls) to investigate the putative role of CNVs in the AAD aetiology. Although the frequency of rare CNVs was similar between cases and controls, we observed that larger deletions (>1,000 kb) were more common among patients (OR = 4.23, 95% CI 1.85-9.66, p = 0.0002). Despite this, none of the large case-deletions were conclusively pathogenic, and the clinical presentation and an AAD-polygenic risk score were similar between cases with and without the large CNVs. Among deletions exclusive to individuals with AAD, we highlight two ultra-rare deletions in the genes LRBA and BCL2L11, which we speculate might have contributed to the polygenic risk in these carriers. In conclusion, rare CNVs do not appear to be a major cause of AAD but further studies are needed to ascertain the potential contribution of rare deletions to the polygenic load of AAD susceptibility.
Collapse
Affiliation(s)
- Haydee Artaza
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
| | - Daniel Eriksson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Center for Molecular Medicine, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden
| | - Ksenia Lavrichenko
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Maribel Aranda-Guillén
- Center for Molecular Medicine, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden
| | - Eirik Bratland
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Knappskog
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Eystein S. Husebye
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sophie Bensing
- Department of Endocrinology, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Anette S. B. Wolff
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Olle Kämpe
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ellen C. Røyrvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Bergen, Norway
| | - Stefan Johansson
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| |
Collapse
|
8
|
Takaiso N, Imoto I, Yoshimura A, Ouchi A, Komori K, Iwata H, Shimizu Y. BARD1 deletion in a patient with suspected hereditary colorectal cancer. Hum Genome Var 2024; 11:11. [PMID: 38485918 PMCID: PMC10940602 DOI: 10.1038/s41439-024-00267-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/28/2024] [Accepted: 02/06/2024] [Indexed: 03/18/2024] Open
Abstract
Deleterious germline variants in the BRCA1-associated ring domain (BARD1) gene moderately elevate breast cancer risk; however, their potential association with other neoplasms remains unclear. Here, we present the case of a 43-year-old female patient diagnosed with sigmoid colon adenocarcinoma whose maternal family members met the Amsterdam Criteria II for Lynch syndrome. Comprehensive multigene panel testing revealed a heterozygous BARD1 exon 3 deletion.
Collapse
Affiliation(s)
- Nobue Takaiso
- Risk Assessment Unit, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Issei Imoto
- Risk Assessment Unit, Aichi Cancer Center Hospital, Nagoya, Japan.
- Aichi Cancer Center Research Institute, Nagoya, Japan.
| | - Akiyo Yoshimura
- Risk Assessment Unit, Aichi Cancer Center Hospital, Nagoya, Japan
- Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Akira Ouchi
- Department of Gastroenterological Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Koji Komori
- Department of Gastroenterological Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Hiroji Iwata
- Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yasuhiro Shimizu
- Department of Gastroenterological Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| |
Collapse
|
9
|
Lesack KJ, Wasmuth JD. The impact of FASTQ and alignment read order on structural variant calling from long-read sequencing data. PeerJ 2024; 12:e17101. [PMID: 38500526 PMCID: PMC10946394 DOI: 10.7717/peerj.17101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
Background Structural variant (SV) calling from DNA sequencing data has been challenging due to several factors, including the ambiguity of short-read alignments, multiple complex SVs in the same genomic region, and the lack of "truth" datasets for benchmarking. Additionally, caller choice, parameter settings, and alignment method are known to affect SV calling. However, the impact of FASTQ read order on SV calling has not been explored for long-read data. Results Here, we used PacBio DNA sequencing data from 15 Caenorhabditis elegans strains and four Arabidopsis thaliana ecotypes to evaluate the sensitivity of different SV callers on FASTQ read order. Comparisons of variant call format files generated from the original and permutated FASTQ files demonstrated that the order of input data affected the SVs predicted by each caller. In particular, pbsv was highly sensitive to the order of the input data, especially at the highest depths where over 70% of the SV calls generated from pairs of differently ordered FASTQ files were in disagreement. These demonstrate that read order sensitivity is a complex, multifactorial process, as the differences observed both within and between species varied considerably according to the specific combination of aligner, SV caller, and sequencing depth. In addition to the SV callers being sensitive to the input data order, the SAMtools alignment sorting algorithm was identified as a source of variability following read order randomization. Conclusion The results of this study highlight the sensitivity of SV calling on the order of reads encoded in FASTQ files, which has not been recognized in long-read approaches. These findings have implications for the replication of SV studies and the development of consistent SV calling protocols. Our study suggests that researchers should pay attention to the input order sensitivity of read alignment sorting methods when analyzing long-read sequencing data for SV calling, as mitigating a source of variability could facilitate future replication work. These results also raise important questions surrounding the relationship between SV caller read order sensitivity and tool performance. Therefore, tool developers should also consider input order sensitivity as a potential source of variability during the development and benchmarking of new and improved methods for SV calling.
Collapse
Affiliation(s)
- Kyle J. Lesack
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, Alberta, Canada
| | - James D. Wasmuth
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
10
|
Lo T, Kushima I, Kimura H, Aleksic B, Okada T, Kato H, Inada T, Nawa Y, Torii Y, Yamamoto M, Kimura R, Funabiki Y, Kosaka H, Numata S, Kasai K, Sasaki T, Yokoyama S, Munesue T, Hashimoto R, Yasuda Y, Fujimoto M, Usami M, Itokawa M, Arai M, Ohi K, Someya T, Watanabe Y, Egawa J, Takahashi T, Suzuki M, Yamasue H, Iwata N, Ikeda M, Ozaki N. Association between copy number variations in parkin (PRKN) and schizophrenia and autism spectrum disorder: A case-control study. Neuropsychopharmacol Rep 2024; 44:42-50. [PMID: 37915257 PMCID: PMC10932780 DOI: 10.1002/npr2.12370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/19/2023] [Indexed: 11/03/2023] Open
Abstract
AIM The present study aimed to examine the association between copy number variations (CNVs) in parkin (PRKN) and schizophrenia (SCZ) and autism spectrum disorder (ASD) in a large case-control sample. METHOD Array comparative genomic hybridization was performed on 3111 cases with SCZ, 1236 cases with ASD, and 2713 controls. We systematically prioritized likely pathogenic CNVs (LP-CNVs) in PRKN and examined their association with SCZ and ASD. RESULTS In total, 3014 SCZ cases (96.9%), 1205 ASD cases (97.5%), and 2671 controls (98.5%) passed quality control. We found that monoallelic carriers of LP-CNVs in PRKN were common (70/6890, 1.02%) and were not at higher risk of SCZ (p = 0.29) or ASD (p = 0.72). We observed that the distribution pattern of LP-CNVs in the Japanese population was consistent with those in other populations. We also identified a patient diagnosed with SCZ and early-onset Parkinson's disease carrying biallelic pathogenic CNVs in PRKN. The absence of Parkinson's symptoms in 10 other monoallelic carriers of the same pathogenic CNV further reflects the lack of effect of monoallelic pathogenic variants in PRKN in the absence of a second hit. CONCLUSION The present findings suggest that monoallelic CNVs in PRKN do not confer a significant risk for SCZ or ASD. However, further studies to investigate the association between biallelic CNVs in PRKN and SCZ and ASD are warranted.
Collapse
Grants
- JP15K19720 Japan Society for the Promotion of Science
- JP17H05090 Japan Society for the Promotion of Science
- JP18H04040 Japan Society for the Promotion of Science
- JP18K19511 Japan Society for the Promotion of Science
- JP19K17087 Japan Society for the Promotion of Science
- JP20H03608 Japan Society for the Promotion of Science
- JP20K07942 Japan Society for the Promotion of Science
- JP20K20602 Japan Society for the Promotion of Science
- JP21H00194 Japan Society for the Promotion of Science
- JP21H04815 Japan Society for the Promotion of Science
- JP21H05326 Japan Society for the Promotion of Science
- JP21K07543 Japan Society for the Promotion of Science
- JP22H00986 Japan Society for the Promotion of Science
- JP16dm0107134 Ministry of Education, Culture, Sports, Science and Technology
- JP19ak0101113 Ministry of Education, Culture, Sports, Science and Technology
- JP19dm0207075 Ministry of Education, Culture, Sports, Science and Technology
- JP19ek0109411 Ministry of Education, Culture, Sports, Science and Technology
- JP19km0405216 Ministry of Education, Culture, Sports, Science and Technology
- JP20ek0109488 Ministry of Education, Culture, Sports, Science and Technology
- JP21dk0307103 Ministry of Education, Culture, Sports, Science and Technology
- JP21tm0424220 Ministry of Education, Culture, Sports, Science and Technology
- JP21wm0425007 Ministry of Education, Culture, Sports, Science and Technology
- JP21wm0425008 Ministry of Education, Culture, Sports, Science and Technology
- JP21wm0425012 Ministry of Education, Culture, Sports, Science and Technology
- JP21wm0425019 Ministry of Education, Culture, Sports, Science and Technology
- JP21wm0525024 Ministry of Education, Culture, Sports, Science and Technology
- JP22tm0424222 Ministry of Education, Culture, Sports, Science and Technology
- Otsuka Toshimi Scholarship Foundation
- SENSHIN Medical Research Foundation
- Uehara Memorial Foundation
- Japan Society for the Promotion of Science
- Ministry of Education, Culture, Sports, Science and Technology
- Otsuka Toshimi Scholarship Foundation
- SENSHIN Medical Research Foundation
- Uehara Memorial Foundation
Collapse
Affiliation(s)
- Tzuyao Lo
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Itaru Kushima
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
- Medical Genomics CenterNagoya University HospitalNagoyaJapan
| | - Hiroki Kimura
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Branko Aleksic
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Takashi Okada
- Department of Developmental Disorders, National Institute of Mental HealthNational Center of Neurology and PsychiatryNagoyaJapan
| | - Hidekazu Kato
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Toshiya Inada
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Yoshihiro Nawa
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Youta Torii
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Maeri Yamamoto
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Ryo Kimura
- Department of Anatomy and Developmental BiologyGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Yasuko Funabiki
- Department of Cognitive, Behavioral and Health Sciences, Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
| | - Hirotaka Kosaka
- Department of Neuropsychiatry, Faculty of Medical SciencesUniversity of FukuiFukuiJapan
| | - Shusuke Numata
- Department of Psychiatry, Graduate School of Biomedical ScienceTokushima UniversityTokushimaJapan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of MedicineUniversity of TokyoTokyoJapan
- International Research Center for Neurointelligence at University of Tokyo Institutes for Advanced StudyTokyoJapan
| | - Tsukasa Sasaki
- Laboratory of Health Education, Graduate School of EducationUniversity of TokyoTokyoJapan
| | - Shigeru Yokoyama
- Research Center for Child Mental DevelopmentKanazawa UniversityIshikawaJapan
| | - Toshio Munesue
- Research Center for Child Mental DevelopmentKanazawa UniversityIshikawaJapan
| | - Ryota Hashimoto
- Department of Pathology of Mental DiseasesNational Institute of Mental HealthNational Center of Neurology and PsychiatryTokyoJapan
| | - Yuka Yasuda
- Department of Pathology of Mental DiseasesNational Institute of Mental HealthNational Center of Neurology and PsychiatryTokyoJapan
| | - Michiko Fujimoto
- Department of PsychiatryOsaka University Graduate School of MedicineOsakaJapan
| | - Masahide Usami
- Department of Child and Adolescent PsychiatryKohnodai Hospital, National Center for Global Health and MedicineChibaJapan
| | - Masanari Itokawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral SciencesTokyo Metropolitan Institute of Medical ScienceTokyoJapan
- Department of PsychiatryTokyo Metropolitan Matsuzawa HospitalTokyoJapan
| | - Makoto Arai
- Schizophrenia Research Project, Department of Psychiatry and Behavioral SciencesTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Kazutaka Ohi
- Department of PsychiatryGifu University Graduate School of MedicineGifuJapan
- Department of General Internal MedicineKanazawa Medical UniversityIshikawaJapan
| | - Toshiyuki Someya
- Department of PsychiatryNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Yuichiro Watanabe
- Department of PsychiatryNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Jun Egawa
- Department of PsychiatryNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Tsutomu Takahashi
- Department of NeuropsychiatryUniversity of Toyama Graduate School of Medicine and Pharmaceutical SciencesToyamaJapan
- Research Center for Idling Brain ScienceUniversity of ToyamaToyamaJapan
| | - Michio Suzuki
- Department of NeuropsychiatryUniversity of Toyama Graduate School of Medicine and Pharmaceutical SciencesToyamaJapan
- Research Center for Idling Brain ScienceUniversity of ToyamaToyamaJapan
| | - Hidenori Yamasue
- Department of PsychiatryHamamatsu University School of MedicineHamamatsuJapan
| | - Nakao Iwata
- Department of PsychiatryFujita Health University School of MedicineToyoakeJapan
| | - Masashi Ikeda
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
- Department of PsychiatryFujita Health University School of MedicineToyoakeJapan
| | - Norio Ozaki
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
- Institute for Glyco‐core ResearchNagoya UniversityNagoyaJapan
| |
Collapse
|
11
|
Oluwole OG. The analyses of human MCPH1 DNA repair machinery and genetic variations. Open Med (Wars) 2024; 19:20240917. [PMID: 38463519 PMCID: PMC10921449 DOI: 10.1515/med-2024-0917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 10/29/2023] [Accepted: 02/05/2024] [Indexed: 03/12/2024] Open
Abstract
Causal mutations in the MCPH1 gene have been associated with disorders like microcephaly, and recently congenital hearing impairment. This study examined the MCPH1 DNA repair machinery and identified genetic variations of interest in gnomAD database to discuss the biological roles and effects of rare variants in MCPH1-related diseases. Notably, MCPH1 coordinates two of the seven known mechanisms of DNA repair which confirmed its roles in neurogenesis and chromatin condensation. A pathogenic missense variant in MCPH1 p.Gly753Arg, and two pathogenic frameshifts MCPH1 p.Asn189LysfsTer15 and p.Cys624Ter identified in this study, already had entries in ClinVar and were associated with microcephaly. A pathogenic frameshift in MCPH1 p.Val10SerfsTer5 with a loss-of-function flag and a pathogenic stop gained p.Ser571Ter variants with ultra-rare allele frequency (MAF ≤ 0.001) were identified but have not been linked to any phenotype. The predicted pathogenic ultra-rare variants identified in this study, warranty phenotypic discovery, and also positioned these variants or nearby deleterious variants candidate for screening in MCPH1-associated rare diseases.
Collapse
Affiliation(s)
- Oluwafemi G Oluwole
- Biomedical Research Centre, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Division of Human Genetics, University of Cape Town, Cape Town, South Africa
- Non-communicable Diseases Department, Institute of Primate Research, Nairobi, Kenya
| |
Collapse
|
12
|
Carrillo YD, Rueda-Gaitán P, Gualdrón O, Estrada-Serrato C, Castro-Cuesta TA, Londoño O, Rodríguez-Salazar L, Isaza-Ruget M, Arcos-Burgos M, López Rivera JJ. Diagnostic yield of chromosomal microarray in the largest Latino clinical cohort. Am J Med Genet A 2024; 194:218-225. [PMID: 37795898 DOI: 10.1002/ajmg.a.63427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 08/30/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023]
Abstract
Copy number variants (CNVs) remain a major etiological cause of neurodevelopmental delay and congenital malformations. Chromosomal microarray analysis (CMA) represents the gold standard for CNVs molecular characterization. We applied CMA throughout the patient's clinical diagnostic workup, as the patient's medical provider requested. We collected CMA results of 3380 patients enrolled for 5 years (2016-2021). We found 830 CNVs in 719 patients with potential clinical significance, that is, (i) pathogenic, (ii) likely pathogenic, and (iii) variants of uncertain significance (VUS), from which 10.6% (predominantly involving chromosomes 15 and 22) were most likely the final cause underpinning the patients' clinical phenotype. For those associated with neurodevelopmental phenotypes, the rate of pathogenic or likely pathogenic findings among the patients with CNVs was 60.75%. When considering epileptic phenotypes, it was 59%. Interestingly, our protocol identified two gains harbored in 17q21.31 and 9q34.3, internationally classified initially as VUS. However, because of their high frequency, we propose that these two VUS be reclassified as likely benign in this widely heterogeneous phenotypic population. These results support the diagnostic yield efficiency of CMA in characterizing CNVs to define the final molecular cause of genetic diseases in this cohort of Colombian patients, the most significant sample of patients from a Latino population, and define new benign polymorphic CNVs.
Collapse
Affiliation(s)
- Yina D Carrillo
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
| | - Paula Rueda-Gaitán
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
| | - Orlando Gualdrón
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
- Grupo de investigación INPAC, Grupo Keralty, Bogotá, Colombia
| | - Carlos Estrada-Serrato
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
| | - Taryn A Castro-Cuesta
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
| | - Olga Londoño
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
| | - Luna Rodríguez-Salazar
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
| | - Mario Isaza-Ruget
- Grupo de investigación INPAC, Grupo Keralty, Bogotá, Colombia
- Fundación Universitaria Sanitas, Grupo de investigación INPAC, Bogotá, Colombia
- Laboratorio Clínico y de Patología, Clínica Colsanitas, Grupo Keralty, Bogotá, Colombia
| | - Mauricio Arcos-Burgos
- Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan Javier López Rivera
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
- Grupo de investigación INPAC, Grupo Keralty, Bogotá, Colombia
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
- Clínica Pediátrica, Clínica Colsanitas, Bogotá, Colombia
| |
Collapse
|
13
|
Badura-Stronka M, Wołyńska K, Winczewska-Wiktor A, Marcinkowska J, Karolewska D, Tomkowiak-Kędzia D, Piechota M, Przyborska M, Kochalska N, Steinborn B. Validation of targeted next-generation sequencing panels in a cohort of Polish patients with epilepsy: assessing variable performance across clinical endophenotypes and uncovering novel genetic variants. Front Neurol 2024; 14:1316933. [PMID: 38328757 PMCID: PMC10849089 DOI: 10.3389/fneur.2023.1316933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/26/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction Targeted Next-Generation Sequencing Panels (TNGSP) have become a standard in global clinical practice. Instead of questioning the necessity of next-generation sequencing in epilepsy patients, contemporary large-scale research focuses on factors such as the size of TNGSP, the comparative advantages of exome or genome-wide sequencing over TNGSP, and the impact of clinical, electrophysiological, and demographic variables on genetic test performance. This study aims to elucidate the demographic and clinical factors influencing the performance of TNGSP in 138 Polish patients with epilepsy, recognizing the pivotal role of genetic testing in guiding patient management and therapy. Methods A retrospective analysis was conducted on patients from a genetic clinic in Poznań, Poland, who underwent commercial gene panel studies at Invitae Corporation (USA) between 2020 and 2022. Patient groups were defined based on the age of onset of the first epileptic seizures, seizure type, gender, fever dependence of seizures, presence of intellectual disability or developmental delay, abnormalities in MRI, and the presence of dysmorphic features or congenital malformations. Seizure classification followed the 2017 ILAE criteria. Results Among the 138 patients, 30 (21.7%) exhibited a pathogenic or likely pathogenic variant, with a distribution of 20.7% in males and 22.5% in females. Diagnostic performance correlated with the patient's age at the onset of the first seizure and the type of seizure. Predominant variants were identified in the SCN1A, PRRT2, CDKL5, DEPDC5, TSC2, and SLC2A1 genes. Additionally, 12 genes (CACNA1A, SCN2A, GRIN2A, KCNQ2, CHD2, DYNC1H1, NEXMIF, SCN1B, DDX3X, EEF1A2, NPRL3, UBE3A) exhibited single instances of damage. Notably, novel variants were discovered in DEPDC5, SCN1A, TSC2, CDKL5, NPRL3, DYNC1H1, CHD2, and DDX3X. Discussion Identified variants were present in genes previously recognized in both European and non-European populations. A thorough examination of Variants of Uncertain Significance (VUSs), specifically focusing on gene copy number changes, may unveil more extensive chromosomal aberrations. The relatively frequent occurrence of pathological variants in X chromosome-linked genes in girls warrants further investigation, challenging the prevailing notion of male predominance in X-linked epilepsy.
Collapse
Affiliation(s)
- Magdalena Badura-Stronka
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, Poznań, Poland
- Centers for Medical Genetics GENESIS, Poznań, Poland
| | - Katarzyna Wołyńska
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, Poznań, Poland
| | - Anna Winczewska-Wiktor
- Chair and Department of Developmental Neurology, Poznan University of Medical Sciences, Poznań, Poland
| | - Justyna Marcinkowska
- Chair and Department of Informatics and Statistics, Poznan University of Medical Sciences, Poznań, Poland
| | | | | | | | | | | | - Barbara Steinborn
- Chair and Department of Developmental Neurology, Poznan University of Medical Sciences, Poznań, Poland
| |
Collapse
|
14
|
Nagaraj CB, Brightman DS, Rea H, Wakefield E, Harkavy NVG, Dyer L, Zhang W. Detection of a novel gross deletion in the UNC13D gene ends the diagnostic odyssey for a family with familial hemophagocytic lymphohistiocytosis 3. BMC Pediatr 2024; 24:34. [PMID: 38212754 PMCID: PMC10782673 DOI: 10.1186/s12887-023-04510-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Familial hemophagocytic lymphohistiocytosis (FHL) is an immunological disorder characterized by overactivation of macrophages and T lymphocytes. This autosomal recessive condition has been characterized into multiple types depending on the genetic etiology. FHL type 3 is associated with bi-allelic pathogenic variants in the UNC13D gene. CASE PRESENTATION We present a 12-year diagnostic odyssey for a family with FHL that signifies the advances of FHL genetic testing in a clinical genetic diagnostic laboratory setting. We describe the first case of a large UNC13D gross deletion in trans to a nonsense variant in a family with FHL3, which may have been mediated by Alu elements within introns 12 and 25 of the UNC13D gene. CONCLUSIONS This case highlights the importance of re-evaluating past genetic testing for a patient and family as test technology evolves in order to end a diagnostic odyssey.
Collapse
Affiliation(s)
- Chinmayee B Nagaraj
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Diana S Brightman
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH, 45229, USA
| | - Hannah Rea
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH, 45229, USA
| | - Emily Wakefield
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH, 45229, USA
| | - Nina V G Harkavy
- Department of OB/GYN, Columbia University Vagelos College of Physicians and Surgeons, New York City, NY, USA
| | - Lisa Dyer
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Wenying Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| |
Collapse
|
15
|
James KN, Chowdhury S, Ding Y, Batalov S, Watkins K, Kwon YH, Van Der Kraan L, Ellsworth K, Kingsmore SF, Guidugli L. Genome sequencing detects a wide range of clinically relevant copy-number variants and other genomic alterations. Genet Med 2024; 26:101006. [PMID: 37869996 DOI: 10.1016/j.gim.2023.101006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
PURPOSE Copy-number variants (CNVs) and other non-single nucleotide variant/indel variant types contribute an important proportion of diagnoses in individuals with suspected genetic disease. This study describes the range of such variants detected by genome sequencing (GS). METHODS For a pediatric cohort of 1032 participants undergoing clinical GS, we characterize the CNVs and other non-single nucleotide variant/indel variant types that were reported, including aneuploidies, mobile element insertions, and uniparental disomies, and we describe the bioinformatic pipeline used to detect these variants. RESULTS Together, these genetic alterations accounted for 15.8% of reported variants. Notably, 67.9% of these were deletions, 32.9% of which overlapped a single gene, and many deletions were reported together with a second variant in the same gene in cases of recessive disease. A retrospective medical record review in a subset of this cohort revealed that up to 6 additional genetic tests were ordered in 68% (26/38) of cases, some of which failed to report the CNVs/rare variants reported on GS. CONCLUSION GS detected a broad range of reported variant types, including CNVs ranging in size from 1 Kb to 46 Mb.
Collapse
Affiliation(s)
- Kiely N James
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Kelly Watkins
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Yong Hyun Kwon
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | | | | | - Lucia Guidugli
- Rady Children's Institute for Genomic Medicine, San Diego, CA.
| |
Collapse
|
16
|
Louw N, Carstens N, Lombard Z. Incorporating CNV analysis improves the yield of exome sequencing for rare monogenic disorders-an important consideration for resource-constrained settings. Front Genet 2023; 14:1277784. [PMID: 38155715 PMCID: PMC10753787 DOI: 10.3389/fgene.2023.1277784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
Exome sequencing (ES) is a recommended first-tier diagnostic test for many rare monogenic diseases. It allows for the detection of both single-nucleotide variants (SNVs) and copy number variants (CNVs) in coding exonic regions of the genome in a single test, and this dual analysis is a valuable approach, especially in limited resource settings. Single-nucleotide variants are well studied; however, the incorporation of copy number variant analysis tools into variant calling pipelines has not been implemented yet as a routine diagnostic test, and chromosomal microarray is still more widely used to detect copy number variants. Research shows that combined single and copy number variant analysis can lead to a diagnostic yield of up to 58%, increasing the yield with as much as 18% from the single-nucleotide variant only pipeline. Importantly, this is achieved with the consideration of computational costs only, without incurring any additional sequencing costs. This mini review provides an overview of copy number variant analysis from exome data and what the current recommendations are for this type of analysis. We also present an overview on rare monogenic disease research standard practices in resource-limited settings. We present evidence that integrating copy number variant detection tools into a standard exome sequencing analysis pipeline improves diagnostic yield and should be considered a significantly beneficial addition, with relatively low-cost implications. Routine implementation in underrepresented populations and limited resource settings will promote generation and sharing of CNV datasets and provide momentum to build core centers for this niche within genomic medicine.
Collapse
Affiliation(s)
- Nadja Louw
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | |
Collapse
|
17
|
Li Y, Zhang Y, Sun D, Zhang X, Long S, Feng J, Wang Z. Integration of genomics and transcriptomics highlights the crucial role of chromosome 5 open reading frame 34 in various human malignancies. Aging (Albany NY) 2023; 15:14384-14410. [PMID: 38078888 PMCID: PMC10756085 DOI: 10.18632/aging.205310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/06/2023] [Indexed: 12/21/2023]
Abstract
Although some data suggest that chromosome 5 open reading frame 34 (C5orf34) plays a pivotal part in the onset and disease progression of various cancers, there is no pan-cancer investigation of C5orf34 at present. This study sought to establish the predictive importance of C5orf34 in a variety of human malignancies and to understand its fundamental immunological function. In our research, we applied a combination of several bioinformatics techniques and basic experiments to investigate the differential expression of C5orf34, and its relationship with prognosis, methylation, single nucleotide variant, clinical characteristics, microsatellite instability, tumor mutational burden, copy number variation, and immune cell infiltration of several cancers from the database that is publicly available with the aim of identifying the potential prognostic markers. In this study we found that C5orf34 expression differed significantly among cancers types, according to the findings. The expression level of C5orf34 is markedly increased in the majority of malignancies when compared to normal tissues, which is significantly correlated with an unfavorable prognosis of patients. Immunohistochemical staining confirmed the findings that C5orf34 expression was remarkably up-regulated in a variety of gynecologic cancers. Moreover, C5orf34 expression was shown to be correlated with the clinical features of patients. C5orf34 was also found to be expressed with genes that code for the major immune suppressors, chemokines, immune activators, chemokine receptors, and histocompatibility complex. Finally, our study shows that C5orf34 has the potential to be employed as a prognostic biomarker. Moreover, it might regulate the immune microenvironment in a variety of malignancies.
Collapse
Affiliation(s)
- Yilin Li
- Department of Gynecology, Dalian Women and Children’s Medical Center (Group), Dalian, China
| | - Yong Zhang
- School of Clinical Medicine, Fujian Medical University, Department of General Surgery, Ningde Municipal Hospital, Ningde, China
| | - Dan Sun
- Department of Gynecology, Dalian Women and Children’s Medical Center (Group), Dalian, China
| | - Xiaofeng Zhang
- School of Clinical Medicine, Fujian Medical University, Department of Obstetrics and Gynecology, Ningde Municipal Hospital, Ningde, China
| | - Shangqin Long
- Department of Obstetrics and Gynecology, Dalian No.3 People’s Hospital, Dalian, China
| | - Jiuxiang Feng
- Department of Gynecology, Dalian Women and Children’s Medical Center (Group), Dalian, China
| | - Zhongmin Wang
- Department of Gynecology, Dalian Women and Children’s Medical Center (Group), Dalian, China
| |
Collapse
|
18
|
Al Eissa MM, Alotibi RS, Alhaddad B, Aloraini T, Samman MS, AlAsiri A, Abouelhoda M, AlQahtani AS. Reclassifying variations of unknown significance in diseases affecting Saudi Arabia's population reveal new associations. Front Genet 2023; 14:1250317. [PMID: 38028588 PMCID: PMC10646566 DOI: 10.3389/fgene.2023.1250317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Physicians face diagnostic dilemmas upon reports indicating disease variants of unknown significance (VUS). The most puzzling cases are patients with rare diseases, where finding another matched genotype and phenotype to associate their results is challenging. This study aims to prove the value of updating patient files with new classifications, potentially leading to better assessment and prevention. Methodology: We recruited retrospective phenotypic and genotypic data from King Saud Medical City, Riyadh, Kingdom of Saudi Arabia. Between September 2020 and December 2021, 1,080 patients' genetic profiles were tested in a College of American Pathologists accredited laboratory. We excluded all confirmed pathogenic variants, likely pathogenic variants and copy number variations. Finally, we further reclassified 194 VUS using different local and global databases, employing in silico prediction to justify the phenotype-genotype association. Results: Of the 194 VUS, 90 remained VUS, and the other 104 were reclassified as follows: 16 pathogenic, 49 likely pathogenic, nine benign, and 30 likely benign. Moreover, most of these variants had never been observed in other local or international databases. Conclusion: Reclassifying the VUS adds value to understanding the causality of the phenotype if it has been reported in another family or population. The healthcare system should establish guidelines for re-evaluating VUS, and upgrading VUS should reflect on individual/family risks and management strategies.
Collapse
Affiliation(s)
- Mariam M. Al Eissa
- Public Health Authority, Public Health Lab, Molecular Genetics Laboratory, Riyadh, Saudi Arabia
- Medical School, AlFaisal University, Riyadh, Saudi Arabia
| | - Raniah S. Alotibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Bader Alhaddad
- Laboratory Medicine Department, King Fahd University Hospital, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Molecular Genetics Department, King Saud Medical City, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
- Department of Genetics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Manar S. Samman
- Department of Pathology and Clinical Laboratory Medicine Administration, King Fahad Medical City (KFMC), Riyadh, Saudi Arabia
| | - Abdulrahman AlAsiri
- Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Mohamed Abouelhoda
- Chairman Computational Science Department at King Faisal Specialised Hospital and Research Center, KFSHRC, Riyadh, Saudi Arabia
| | - Amerh S. AlQahtani
- Medical Genetics Department, King Saud Medical City, Riyadh, Saudi Arabia
| |
Collapse
|
19
|
García-Vielma C, Lazalde-Córdova LG, Arzola-Hernández JC, González-Aceves EN, López-Zertuche H, Guzmán-Delgado NE, González-Salazar F. Identification of variants in genes associated with hypertrophic cardiomyopathy in Mexican patients. Mol Genet Genomics 2023; 298:1289-1299. [PMID: 37498360 PMCID: PMC10657276 DOI: 10.1007/s00438-023-02048-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/22/2023] [Indexed: 07/28/2023]
Abstract
The objective of this work was to identify genetic variants in Mexican patients diagnosed with hypertrophic cardiomyopathy (HCM). According to world literature, the genes mainly involved are MHY7 and MYBPC3, although variants have been found in more than 50 genes related to heart disease and sudden death, and to our knowledge there are no studies in the Mexican population. These variants are reported and classified in the ClinVar (PubMed) database and only some of them are recognized in the Online Mendelian Information in Men (OMIM). The present study included 37 patients, with 14 sporadic cases and 6 familial cases, with a total of 21 index cases. Next-generation sequencing was performed on a predesigned panel of 168 genes associated with heart disease and sudden death. The sequencing analysis revealed twelve (57%) pathogenic or probably pathogenic variants, 9 of them were familial cases, managing to identify pathogenic variants in relatives without symptoms of the disease. At the molecular level, nine of the 12 variants (75%) were single nucleotide changes, 2 (17%) deletions, and 1 (8%) splice site alteration. The genes involved were MYH7 (25%), MYBPC3 (25%) and ACADVL, KCNE1, TNNI3, TPM1, SLC22A5, TNNT2 (8%). In conclusion; we found five variants that were not previously reported in public databases. It is important to follow up on the reclassification of variants, especially those of uncertain significance in patients with symptoms of the condition. All patients included in the study and their relatives received family genetic counseling.
Collapse
Affiliation(s)
- Catalina García-Vielma
- Centro de Investigación Biomédica del Noreste, Departamento de Citogenética, Instituto Mexicano del Seguro Social, Monterrey, NL, México.
| | - Luis Gerardo Lazalde-Córdova
- Centro de Investigación Biomédica del Noreste, Departamento de Citogenética, Instituto Mexicano del Seguro Social, Monterrey, NL, México
| | - José Cruz Arzola-Hernández
- Departamento de Electrofisiología, Instituto Mexicano del Seguro Social, Unidad Médica de Alta Especialidad. Hospital de cardiología No. 34 "Dr. Alfonso J. Treviño Treviño" del Centro Médico Nacional del Noreste, Monterrey, NL, México
| | - Erick Noel González-Aceves
- Departamento de Electrofisiología, Instituto Mexicano del Seguro Social, Unidad Médica de Alta Especialidad. Hospital de cardiología No. 34 "Dr. Alfonso J. Treviño Treviño" del Centro Médico Nacional del Noreste, Monterrey, NL, México
| | | | - Nancy Elena Guzmán-Delgado
- Departamento de Electrofisiología, Instituto Mexicano del Seguro Social, Unidad Médica de Alta Especialidad. Hospital de cardiología No. 34 "Dr. Alfonso J. Treviño Treviño" del Centro Médico Nacional del Noreste, Monterrey, NL, México.
| | - Francisco González-Salazar
- Centro de Investigación Biomédica del Noreste, Departamento de Citogenética, Instituto Mexicano del Seguro Social, Monterrey, NL, México
| |
Collapse
|
20
|
Chen E, Facio FM, Aradhya KW, Rojahn S, Hatchell KE, Aguilar S, Ouyang K, Saitta S, Hanson-Kwan AK, Capurro NN, Takamine E, Jamuar SS, McKnight D, Johnson B, Aradhya S. Rates and Classification of Variants of Uncertain Significance in Hereditary Disease Genetic Testing. JAMA Netw Open 2023; 6:e2339571. [PMID: 37878314 PMCID: PMC10600581 DOI: 10.1001/jamanetworkopen.2023.39571] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/12/2023] [Indexed: 10/26/2023] Open
Abstract
Importance Variants of uncertain significance (VUSs) are rampant in clinical genetic testing, frustrating clinicians, patients, and laboratories because the uncertainty hinders diagnoses and clinical management. A comprehensive assessment of VUSs across many disease genes is needed to guide efforts to reduce uncertainty. Objective To describe the sources, gene distribution, and population-level attributes of VUSs and to evaluate the impact of the different types of evidence used to reclassify them. Design, Setting, and Participants This cohort study used germline DNA variant data from individuals referred by clinicians for diagnostic genetic testing for hereditary disorders. Participants included individuals for whom gene panel testing was conducted between September 9, 2014, and September 7, 2022. Data were analyzed from September 1, 2022, to April 1, 2023. Main Outcomes and Measures The outcomes of interest were VUS rates (stratified by age; clinician-reported race, ethnicity, and ancestry groups; types of gene panels; and variant attributes), percentage of VUSs reclassified as benign or likely benign vs pathogenic or likely pathogenic, and enrichment of evidence types used for reclassifying VUSs. Results The study cohort included 1 689 845 individuals ranging in age from 0 to 89 years at time of testing (median age, 50 years), with 1 203 210 (71.2%) female individuals. There were 39 150 Ashkenazi Jewish individuals (2.3%), 64 730 Asian individuals (3.8%), 126 739 Black individuals (7.5%), 5539 French Canadian individuals (0.3%), 169 714 Hispanic individuals (10.0%), 5058 Native American individuals (0.3%), 2696 Pacific Islander individuals (0.2%), 4842 Sephardic Jewish individuals (0.3%), and 974 383 White individuals (57.7%). Among all individuals tested, 692 227 (41.0%) had at least 1 VUS and 535 385 (31.7%) had only VUS results. The number of VUSs per individual increased as more genes were tested, and most VUSs were missense changes (86.6%). More VUSs were observed per sequenced gene in individuals who were not from a European White population, in middle-aged and older adults, and in individuals who underwent testing for disorders with incomplete penetrance. Of 37 699 unique VUSs that were reclassified, 30 239 (80.2%) were ultimately categorized as benign or likely benign. A mean (SD) of 30.7 (20.0) months elapsed for VUSs to be reclassified to benign or likely benign, and a mean (SD) of 22.4 (18.9) months elapsed for VUSs to be reclassified to pathogenic or likely pathogenic. Clinical evidence contributed most to reclassification. Conclusions and Relevance This cohort study of approximately 1.6 million individuals highlighted the need for better methods for interpreting missense variants, increased availability of clinical and experimental evidence for variant classification, and more diverse representation of race, ethnicity, and ancestry groups in genomic databases. Data from this study could provide a sound basis for understanding the sources and resolution of VUSs and navigating appropriate next steps in patient care.
Collapse
Affiliation(s)
- Elaine Chen
- Invitae Corporation, San Francisco, California
| | | | | | | | | | | | | | - Sulagna Saitta
- Division of Clinical Genetics, Departments of Pediatrics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | | | - Nicole Nakousi Capurro
- School of Medicine, University of Valparaíso, Valparaíso, Chile
- Facultad de Medicina, Universidad Andrés Bello, Viña del Mar, Chile
| | - Eriko Takamine
- Department of Medical Genetics, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Saumya Shekhar Jamuar
- Genetics Service, KK Women’s and Children’s Hospital, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | | | | | - Swaroop Aradhya
- Invitae Corporation, San Francisco, California
- Department of Pathology, Stanford University, Stanford, California
| |
Collapse
|
21
|
Poplawska K, Griffiths A, Temme R, Adamko DJ, Nykamp K, Shapiro AJ. Deletions in DNAL1 Cause Primary Ciliary Dyskinesia Across North American Indigenous Populations. J Pediatr 2023; 261:113362. [PMID: 36841509 DOI: 10.1016/j.jpeds.2023.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/18/2022] [Accepted: 01/29/2023] [Indexed: 02/27/2023]
Abstract
We report 4 cases of primary ciliary dyskinesia in unrelated indigenous North American children caused by identical, homozygous, likely pathogenic deletions in the DNAL1 gene. These shared DNAL1 deletions among dispersed indigenous populations suggest that primary ciliary dyskinesia accounts for more lung disease with bronchiectasis than previously recognized in indigenous North Americans.
Collapse
Affiliation(s)
- Karolina Poplawska
- Department of Pediatrics, McGill University Health Center Research Institute, Montreal, Quebec, Canada
| | - Anne Griffiths
- Department of Pediatrics, Children's Minnesota, Minneapolis, MN
| | - Renee Temme
- Department of Genetics, Children's Minnesota, Minneapolis, MN
| | - Darryl J Adamko
- Department of Pediatrics, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Adam J Shapiro
- Department of Pediatrics, McGill University Health Center Research Institute, Montreal, Quebec, Canada.
| |
Collapse
|
22
|
Sorscher S, LoPiccolo J, Heald B, Chen E, Bristow SL, Michalski ST, Nielsen SM, Lacoste A, Keyder E, Lee H, Nussbaum RL, Martins R, Esplin ED. Rate of Pathogenic Germline Variants in Patients With Lung Cancer. JCO Precis Oncol 2023; 7:e2300190. [PMID: 37992258 PMCID: PMC10681406 DOI: 10.1200/po.23.00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 11/24/2023] Open
Abstract
PURPOSE Germline genetic testing (GGT) is now recommended for all patients diagnosed with ovarian or pancreatic cancer and for a large proportion of patients based solely on a diagnosis of colorectal or breast cancer. However, GGT is not yet recommended for all patients diagnosed with lung cancer (LC), primarily because of a lack of evidence that supports a significant frequency of identifying pathogenic germline variants (PGVs) in these patients. This study characterizes GGT results in a cohort of patients with LC. METHODS We reviewed deidentified data for 7,788 patients with GGT (2015-2022). PGV frequencies were compared to a control cohort of unaffected individuals. GGT results were stratified by genomic ancestry, history of cancer, and PGV clinical actionability per current guidelines. RESULTS Of all patients with LC, 14.9% (1,161/7,788) had PGVs. The rate was similar when restricted to patients with no cancer family history (FH) or personal history (PH) of other cancers (14.3%). PGVs were significantly enriched in BRCA2, ATM, CHEK2, BRCA1, and mismatch repair genes compared with controls. Patients of European (EUR) genomic ancestry had the highest PGV rate (18%) and variants of uncertain significance were significantly higher in patients of non-EUR genomic ancestry. Of the PGVs identified, 61.3% were in DNA damage repair (DDR) genes and 95% were clinically actionable. CONCLUSION This retrospective study shows a LC diagnosis identifies patients with a significant likelihood of having a cancer-predisposing PGV across genomic ancestries. Enrichment of PGVs in DDR genes suggests that these PGVs may contribute to LC cancer predisposition. The frequency of PGVs among patients with LC did not differ significantly according to FH or PH of other cancers.
Collapse
Affiliation(s)
| | - Jaclyn LoPiccolo
- Hematology/Oncology Division, Dana-Farber Cancer Center, Boston, MA
| | | | | | | | | | | | | | | | - Hayan Lee
- Nuclear Dynamics and Cancer Program, Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA
| | | | - Renato Martins
- Hematology, Oncology and Palliative Care Division, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA
| | | |
Collapse
|
23
|
Aradhya S, Facio FM, Metz H, Manders T, Colavin A, Kobayashi Y, Nykamp K, Johnson B, Nussbaum RL. Applications of artificial intelligence in clinical laboratory genomics. Am J Med Genet C Semin Med Genet 2023; 193:e32057. [PMID: 37507620 DOI: 10.1002/ajmg.c.32057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
The transition from analog to digital technologies in clinical laboratory genomics is ushering in an era of "big data" in ways that will exceed human capacity to rapidly and reproducibly analyze those data using conventional approaches. Accurately evaluating complex molecular data to facilitate timely diagnosis and management of genomic disorders will require supportive artificial intelligence methods. These are already being introduced into clinical laboratory genomics to identify variants in DNA sequencing data, predict the effects of DNA variants on protein structure and function to inform clinical interpretation of pathogenicity, link phenotype ontologies to genetic variants identified through exome or genome sequencing to help clinicians reach diagnostic answers faster, correlate genomic data with tumor staging and treatment approaches, utilize natural language processing to identify critical published medical literature during analysis of genomic data, and use interactive chatbots to identify individuals who qualify for genetic testing or to provide pre-test and post-test education. With careful and ethical development and validation of artificial intelligence for clinical laboratory genomics, these advances are expected to significantly enhance the abilities of geneticists to translate complex data into clearly synthesized information for clinicians to use in managing the care of their patients at scale.
Collapse
Affiliation(s)
- Swaroop Aradhya
- Invitae Corporation, San Francisco, California, USA
- Adjunct Clinical Faculty, Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | | | - Hillery Metz
- Invitae Corporation, San Francisco, California, USA
| | - Toby Manders
- Invitae Corporation, San Francisco, California, USA
| | | | | | - Keith Nykamp
- Invitae Corporation, San Francisco, California, USA
| | | | - Robert L Nussbaum
- Invitae Corporation, San Francisco, California, USA
- Volunteer Faculty, School of Medicine, University of California San Francisco, San Francisco, California, USA
| |
Collapse
|
24
|
Bonini KE, Thomas-Wilson A, Marathe PN, Sebastin M, Odgis JA, Biase MD, Kelly NR, Ramos MA, Insel BJ, Scarimbolo L, Rehman AU, Guha S, Okur V, Abhyankar A, Phadke S, Nava C, Gallagher KM, Elkhoury L, Edelmann L, Zinberg RE, Abul-Husn NS, Diaz GA, Greally JM, Suckiel SA, Horowitz CR, Kenny EE, Wasserstein M, Gelb BD, Jobanputra V. Identification of copy number variants with genome sequencing: Clinical experiences from the NYCKidSeq program. Clin Genet 2023; 104:210-225. [PMID: 37334874 PMCID: PMC10505482 DOI: 10.1111/cge.14365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/28/2023] [Accepted: 05/15/2023] [Indexed: 06/21/2023]
Abstract
Copy number variations (CNVs) play a significant role in human disease. While chromosomal microarray has traditionally been the first-tier test for CNV detection, use of genome sequencing (GS) is increasing. We report the frequency of CNVs detected with GS in a diverse pediatric cohort from the NYCKidSeq program and highlight specific examples of its clinical impact. A total of 1052 children (0-21 years) with neurodevelopmental, cardiac, and/or immunodeficiency phenotypes received GS. Phenotype-driven analysis was used, resulting in 183 (17.4%) participants with a diagnostic result. CNVs accounted for 20.2% of participants with a diagnostic result (37/183) and ranged from 0.5 kb to 16 Mb. Of participants with a diagnostic result (n = 183) and phenotypes in more than one category, 5/17 (29.4%) were solved by a CNV finding, suggesting a high prevalence of diagnostic CNVs in participants with complex phenotypes. Thirteen participants with a diagnostic CNV (35.1%) had previously uninformative genetic testing, of which nine included a chromosomal microarray. This study demonstrates the benefits of GS for reliable detection of CNVs in a pediatric cohort with variable phenotypes.
Collapse
Affiliation(s)
- Katherine E. Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Priya N. Marathe
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Jacqueline A. Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Nicole R. Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Michelle A. Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Beverly J. Insel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Laura Scarimbolo
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Saurav Guha
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Volkan Okur
- Molecular Diagnostics, New York Genome Center, New York, NY
| | | | - Shruti Phadke
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Caroline Nava
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Katie M. Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | | | | | - Randi E. Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Noura S. Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - George A. Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - John M. Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Sabrina A. Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Carol R. Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Bruce D. Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
| |
Collapse
|
25
|
Truty R, Rojahn S, Ouyang K, Kautzer C, Kennemer M, Pineda-Alvarez D, Johnson B, Stafford A, Basel-Salmon L, Saitta S, Slavotinek A, Chandrasekharappa SC, Suarez CJ, Burnett L, Nussbaum RL, Aradhya S. Patterns of mosaicism for sequence and copy-number variants discovered through clinical deep sequencing of disease-related genes in one million individuals. Am J Hum Genet 2023; 110:551-564. [PMID: 36933558 PMCID: PMC10119133 DOI: 10.1016/j.ajhg.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
DNA variants that arise after conception can show mosaicism, varying in presence and extent among tissues. Mosaic variants have been reported in Mendelian diseases, but further investigation is necessary to broadly understand their incidence, transmission, and clinical impact. A mosaic pathogenic variant in a disease-related gene may cause an atypical phenotype in terms of severity, clinical features, or timing of disease onset. Using high-depth sequencing, we studied results from one million unrelated individuals referred for genetic testing for almost 1,900 disease-related genes. We observed 5,939 mosaic sequence or intragenic copy number variants distributed across 509 genes in nearly 5,700 individuals, constituting approximately 2% of molecular diagnoses in the cohort. Cancer-related genes had the most mosaic variants and showed age-specific enrichment, in part reflecting clonal hematopoiesis in older individuals. We also observed many mosaic variants in genes related to early-onset conditions. Additional mosaic variants were observed in genes analyzed for reproductive carrier screening or associated with dominant disorders with low penetrance, posing challenges for interpreting their clinical significance. When we controlled for the potential involvement of clonal hematopoiesis, most mosaic variants were enriched in younger individuals and were present at higher levels than in older individuals. Furthermore, individuals with mosaicism showed later disease onset or milder phenotypes than individuals with non-mosaic variants in the same genes. Collectively, the large compendium of variants, disease correlations, and age-specific results identified in this study expand our understanding of the implications of mosaic DNA variation for diagnosis and genetic counseling.
Collapse
Affiliation(s)
- Rebecca Truty
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Susan Rojahn
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Karen Ouyang
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | | | | | - Britt Johnson
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | - Lina Basel-Salmon
- Rabin Medical Center-Beilinson Hospital and Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Sulagna Saitta
- Division of Clinical Genetics, Departments of Pediatrics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Anne Slavotinek
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carlos Jose Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA
| | | | - Robert L Nussbaum
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; School of Medicine, University of California - San Francisco, San Francisco, CA, USA
| | - Swaroop Aradhya
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA.
| |
Collapse
|
26
|
Papadopoulou E, Pepe G, Konitsiotis S, Chondrogiorgi M, Grigoriadis N, Kimiskidis VK, Tsivgoulis G, Mitsikostas DD, Chroni E, Domouzoglou E, Tsaousis G, Nasioulas G. The evolution of comprehensive genetic analysis in neurology: Implications for precision medicine. J Neurol Sci 2023; 447:120609. [PMID: 36905813 DOI: 10.1016/j.jns.2023.120609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
Technological advancements have facilitated the availability of reliable and thorough genetic analysis in many medical fields, including neurology. In this review, we focus on the importance of selecting the appropriate genetic test to aid in the accurate identification of disease utilizing currently employed technologies for analyzing monogenic neurological disorders. Moreover, the applicability of comprehensive analysis via NGS for various genetically heterogeneous neurological disorders is reviewed, revealing its efficiency in clarifying a frequently cloudy diagnostic picture and delivering a conclusive and solid diagnosis that is essential for the proper management of the patient. The feasibility and effectiveness of medical genetics in neurology require interdisciplinary cooperation among several medical specialties and geneticists, to select and perform the most relevant test according to each patient's medical history, using the most appropriate technological tools. The prerequisites for a comprehensive genetic analysis are discussed, highlighting the utility of appropriate gene selection, variant annotation, and classification. Moreover, genetic counseling and interdisciplinary collaboration could improve diagnostic yield further. Additionally, a sub-analysis is conducted on the 1,502,769 variation records with submitted interpretations in the Clinical Variation (ClinVar) database, with a focus on neurology-related genes, to clarify the value of suitable variant categorization. Finally, we review the current applications of genetic analysis in the diagnosis and personalized management of neurological patients and the advances in the research and scientific knowledge of hereditary neurological disorders that are evolving the utility of genetic analysis towards the individualization of the treatment strategy.
Collapse
Affiliation(s)
| | - Georgia Pepe
- GeneKor Medical SA, Spaton 52, Gerakas 15344, Greece
| | - Spiridon Konitsiotis
- Department of Neurology, University of Ioannina, Stavrou Niarchou Avenue, Ioannina 45500, Greece
| | - Maria Chondrogiorgi
- Department of Neurology, University of Ioannina, Stavrou Niarchou Avenue, Ioannina 45500, Greece
| | - Nikolaos Grigoriadis
- Second Department of Neurology, "AHEPA" University Hospital, Aristotle University of Thessaloniki, St. Kiriakidis 1, Thessaloniki 54636, Greece
| | - Vasilios K Kimiskidis
- First Department of Neurology, "AHEPA" University hospital, Aristotle University of Thessaloniki, St. Kiriakidis 1, Thessaloniki 54636, Greece
| | - Georgios Tsivgoulis
- Second Department of Neurology, School of Medicine, "Attikon" University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimos D Mitsikostas
- First Department of Neurology, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Elisabeth Chroni
- Department of Neurology, School of Medicine, University of Patras, Rio-Patras, Greece
| | - Eleni Domouzoglou
- Department of Pediatrics, University Hospital of Ioannina, Stavrou Niarchou Avenue, Ioannina 45500, Greece
| | | | | |
Collapse
|
27
|
Kamps-Hughes N, Carlton VEH, Fresard L, Osazuwa S, Starks E, Vincent JJ, Albritton S, Nussbaum RL, Nykamp K. A Systematic Method for Detecting Abnormal mRNA Splicing and Assessing Its Clinical Impact in Individuals Undergoing Genetic Testing for Hereditary Cancer Syndromes. J Mol Diagn 2023; 25:156-167. [PMID: 36563937 DOI: 10.1016/j.jmoldx.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/22/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Nearly 14% of disease-causing germline variants result from the disruption of mRNA splicing. Most (67%) DNA variants predicted in silico to disrupt splicing are classified as variants of uncertain significance. An analytic workflow-splice effect event resolver (SPEER)-was developed and validated to use mRNA sequencing to reveal significant deviations in splicing, pinpoint the DNA variants potentially involved, and measure the deleterious effects of the altered splicing on mRNA transcripts, providing evidence for assessing the pathogenicity of the variant. SPEER was used to analyze leukocyte RNA encoding 63 hereditary cancer syndrome-related genes in 20,317 patients. Among 3563 patients (17.5%) with at least one DNA variant predicted to affect splicing, 971 (4.8%) had altered splicing with a deleterious effect on the transcript, and 40 had altered splicing due to a DNA variant located outside of the reportable range of the test. Integrating SPEER results into the interpretation of variants allowed variants of uncertain significance to be reclassified as pathogenic or likely pathogenic in 0.4%, and as benign or likely benign in 5.9%, of the 20,317 patients. SPEER-based evidence was associated with a significantly greater effect on classifications of pathogenic or likely pathogenic and benign or likely benign in nonwhite versus non-Hispanic white patients, illustrating that evidence derived from mRNA splicing analysis may help to reduce ethnic/ancestral disparities in genetic testing.
Collapse
|
28
|
Skrahin A, Cheema HA, Hussain M, Rana NN, Rehman KU, Kumar R, Oprea G, Ameziane N, Rolfs A, Skrahina V. Secondary findings in a large Pakistani cohort tested with whole genome sequencing. Life Sci Alliance 2023; 6:e202201673. [PMID: 36635046 PMCID: PMC9838216 DOI: 10.26508/lsa.202201673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023] Open
Abstract
Studies on genomic secondary findings (SFs) are diverse in participants' characteristics, sequencing methods, and versions of the ACMG SF list. Based on whole genome sequencing and the version 3.1 of the ACMG SF list, we studied SFs in 863 individuals from five different regions in Pakistan. We identified 24 ACMG SFs in 23 (2.7%) of 863 individuals: 18 of 24 were related to cardiovascular disease and four to cancer syndromes. In addition to ACMG SFs, we identified 16 (1.9%) participants with pathogenic and likely pathogenic variants in genes that were not related to the participants' clinical conditions but with clear medical actionability (non-ACMG SFs): 4 of 16 were related to eye diseases, two to metabolic disorders, and two to urinary system disorders. By testing a large Pakistani cohort with whole genome sequencing, we concluded that in countries such as Pakistan, the ACMG SF list could be expanded, and our non-ACMG SF list is one example.
Collapse
Affiliation(s)
| | - Huma Arshad Cheema
- University of Child Health Sciences, the Children's Hospital, Lahore, Pakistan
| | | | | | | | - Raman Kumar
- Liaquat National Hospital, Karachi, Pakistan
| | | | | | - Arndt Rolfs
- Arcensus GmbH, Rostock, Germany
- University of Rostock, Medical Faculty, Rostock, Germany
| | | |
Collapse
|
29
|
Divakar MK, Jain A, Bhoyar RC, Senthivel V, Jolly B, Imran M, Sharma D, Bajaj A, Gupta V, Scaria V, Sivasubbu S. Whole-genome sequencing of 1029 Indian individuals reveals unique and rare structural variants. J Hum Genet 2023; 68:409-417. [PMID: 36813834 DOI: 10.1038/s10038-023-01131-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 02/24/2023]
Abstract
Structural variants contribute to genetic variability in human genomes and they can be presented in population-specific patterns. We aimed to understand the landscape of structural variants in the genomes of healthy Indian individuals and explore their potential implications in genetic disease conditions. For the identification of structural variants, a whole genome sequencing dataset of 1029 self-declared healthy Indian individuals from the IndiGen project was analysed. Further, these variants were evaluated for potential pathogenicity and their associations with genetic diseases. We also compared our identified variations with the existing global datasets. We generated a compendium of total 38,560 high-confident structural variants, comprising 28,393 deletions, 5030 duplications, 5038 insertions, and 99 inversions. Particularly, we identified around 55% of all these variants were found to be unique to the studied population. Further analysis revealed 134 deletions with predicted pathogenic/likely pathogenic effects and their affected genes were majorly enriched for neurological disease conditions, such as intellectual disability and neurodegenerative diseases. The IndiGenomes dataset helped us to understand the unique spectrum of structural variants in the Indian population. More than half of identified variants were not present in the publicly available global dataset on structural variants. Clinically important deletions identified in IndiGenomes might aid in improving the diagnosis of unsolved genetic diseases, particularly in neurological conditions. Along with basal allele frequency data and clinically important deletions, IndiGenomes data might serve as a baseline resource for future studies on genomic structural variant analysis in the Indian population.
Collapse
Affiliation(s)
- Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Abhinav Jain
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, 110025, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Disha Sharma
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anjali Bajaj
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vishu Gupta
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
30
|
Jun G, English AC, Metcalf GA, Yang J, Chaisson MJP, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YDI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJ, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. Res Sq 2023:rs.3.rs-2515453. [PMID: 36778386 PMCID: PMC9915771 DOI: 10.21203/rs.3.rs-2515453/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hematologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.
Collapse
Affiliation(s)
- Goo Jun
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
| | - Adam C English
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Ginger A Metcalf
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Jianzhi Yang
- University of Southern California, Los Angeles, CA, USA
| | | | | | - Vipin K Menon
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | | | | | - Albert V Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - John A Lane
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Tom Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Hyun Min Kang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Sejal Salvi
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Qingchang Meng
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Hua Shen
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Divya Pasham
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Sravya Bhamidipati
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Kavya Kottapalli
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Donna K. Arnett
- Department of Epidemiology, University of Kentucky College of Public Health
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | - Paul L. Auer
- Division of Biostatistics and Cancer Center, Medical College of Wisconsin, Milwaukee WI
| | | | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas, Rio Grande Valley School of Medicine, Brownsville, TX
| | - Donald W. Bowden
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA
| | - Yii-Der Ida Chen
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Joanne E. Curran
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tasha Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai
| | | | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - John P Kane
- Cardiovascular Research Institute, University of California, San Francisco
| | - Robert Kaplan
- Department of epidemiology and population health, Albert Einstein College of Medicine, Bronx NY USA
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco CA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stephen T. McGarvey
- Department of Epidemiology, International Health Institute and Department of Anthropology, Brown University
| | - Courtney Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - S. Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA
| | | | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stephen S. Rich
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School
- Cardiovascular Division, Brigham & Women’s Hospital, Harvard University
- Howard Hughes Medical Institute, Harvard University
| | | | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Jennifer A. Smith
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, NC
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Baojun Wu
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Lisa R. Yanek
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Susan K. Dutcher
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | | | | | - Ryan Kim
- Psomagen, Inc.,Rockville, Maryland, USA
| | | | | | | | - James Luo
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
| | - Richard A Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Goncalo Abecasis
- Regeneron Genetics Center
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Fritz J Sedlazeck
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| |
Collapse
|
31
|
Jun G, English AC, Metcalf GA, Yang J, Chaisson MJP, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YDI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJ, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. bioRxiv 2023:2023.01.25.525428. [PMID: 36747810 PMCID: PMC9900832 DOI: 10.1101/2023.01.25.525428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.
Collapse
Affiliation(s)
- Goo Jun
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
| | - Adam C English
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Ginger A Metcalf
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Jianzhi Yang
- University of Southern California, Los Angeles, CA, USA
| | | | | | - Vipin K Menon
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | | | | | - Albert V Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - John A Lane
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Tom Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Hyun Min Kang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Sejal Salvi
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Qingchang Meng
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Hua Shen
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Divya Pasham
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Sravya Bhamidipati
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Kavya Kottapalli
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Donna K. Arnett
- Department of Epidemiology, University of Kentucky College of Public Health
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | - Paul L. Auer
- Division of Biostatistics and Cancer Center, Medical College of Wisconsin, Milwaukee WI
| | | | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas, Rio Grande Valley School of Medicine, Brownsville, TX
| | - Donald W. Bowden
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA
| | - Yii-Der Ida Chen
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Joanne E. Curran
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tasha Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai
| | | | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - John P Kane
- Cardiovascular Research Institute, University of California, San Francisco
| | - Robert Kaplan
- Department of epidemiology and population health, Albert Einstein College of Medicine, Bronx NY USA
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco CA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stephen T. McGarvey
- Department of Epidemiology, International Health Institute and Department of Anthropology, Brown University
| | - Courtney Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - S. Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA
| | | | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stephen S. Rich
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School
- Cardiovascular Division, Brigham & Women’s Hospital, Harvard University
- Howard Hughes Medical Institute, Harvard University
| | | | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA
| | - Jennifer A. Smith
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, NC
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Baojun Wu
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Lisa R. Yanek
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Susan K. Dutcher
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | | | | | - Ryan Kim
- Psomagen, Inc.,Rockville, Maryland, USA
| | | | | | | | - James Luo
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
| | - Richard A Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Goncalo Abecasis
- Regeneron Genetics Center
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Fritz J Sedlazeck
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| |
Collapse
|
32
|
DeVries AA, Dennis J, Tyrer JP, Peng PC, Coetzee SG, Reyes AL, Plummer JT, Davis BD, Chen SS, Dezem FS, Aben KKH, Anton-Culver H, Antonenkova NN, Beckmann MW, Beeghly-Fadiel A, Berchuck A, Bogdanova NV, Bogdanova-Markov N, Brenton JD, Butzow R, Campbell I, Chang-Claude J, Chenevix-Trench G, Cook LS, DeFazio A, Doherty JA, Dörk T, Eccles DM, Eliassen AH, Fasching PA, Fortner RT, Giles GG, Goode EL, Goodman MT, Gronwald J, Håkansson N, Hildebrandt MAT, Huff C, Huntsman DG, Jensen A, Kar S, Karlan BY, Khusnutdinova EK, Kiemeney LA, Kjaer SK, Kupryjanczyk J, Labrie M, Lambrechts D, Le ND, Lubiński J, May T, Menon U, Milne RL, Modugno F, Monteiro AN, Moysich KB, Odunsi K, Olsson H, Pearce CL, Pejovic T, Ramus SJ, Riboli E, Riggan MJ, Romieu I, Sandler DP, Schildkraut JM, Setiawan VW, Sieh W, Song H, Sutphen R, Terry KL, Thompson PJ, Titus L, Tworoger SS, Van Nieuwenhuysen E, Edwards DV, Webb PM, Wentzensen N, Whittemore AS, Wolk A, Wu AH, Ziogas A, Freedman ML, Lawrenson K, Pharoah PDP, Easton DF, Gayther SA, Jones MR. Copy Number Variants Are Ovarian Cancer Risk Alleles at Known and Novel Risk Loci. J Natl Cancer Inst 2022; 114:1533-1544. [PMID: 36210504 PMCID: PMC9949586 DOI: 10.1093/jnci/djac160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/13/2022] [Accepted: 08/18/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Known risk alleles for epithelial ovarian cancer (EOC) account for approximately 40% of the heritability for EOC. Copy number variants (CNVs) have not been investigated as EOC risk alleles in a large population cohort. METHODS Single nucleotide polymorphism array data from 13 071 EOC cases and 17 306 controls of White European ancestry were used to identify CNVs associated with EOC risk using a rare admixture maximum likelihood test for gene burden and a by-probe ratio test. We performed enrichment analysis of CNVs at known EOC risk loci and functional biofeatures in ovarian cancer-related cell types. RESULTS We identified statistically significant risk associations with CNVs at known EOC risk genes; BRCA1 (PEOC = 1.60E-21; OREOC = 8.24), RAD51C (Phigh-grade serous ovarian cancer [HGSOC] = 5.5E-4; odds ratio [OR]HGSOC = 5.74 del), and BRCA2 (PHGSOC = 7.0E-4; ORHGSOC = 3.31 deletion). Four suggestive associations (P < .001) were identified for rare CNVs. Risk-associated CNVs were enriched (P < .05) at known EOC risk loci identified by genome-wide association study. Noncoding CNVs were enriched in active promoters and insulators in EOC-related cell types. CONCLUSIONS CNVs in BRCA1 have been previously reported in smaller studies, but their observed frequency in this large population-based cohort, along with the CNVs observed at BRCA2 and RAD51C gene loci in EOC cases, suggests that these CNVs are potentially pathogenic and may contribute to the spectrum of disease-causing mutations in these genes. CNVs are likely to occur in a wider set of susceptibility regions, with potential implications for clinical genetic testing and disease prevention.
Collapse
Grants
- P01 CA017054 NCI NIH HHS
- UM1 CA176726 NCI NIH HHS
- R01 CA058860 NCI NIH HHS
- P50 CA105009 NCI NIH HHS
- R01-CA122443 NIH HHS
- 076113 Wellcome Trust
- G0401527 Medical Research Council
- U19-CA148112 NCI NIH HHS
- N01 CN025403 NCI NIH HHS
- P50 CA136393 NCI NIH HHS
- C490/A10119 C490/A10124 Cancer Research UK
- 1000143 Medical Research Council
- R01-CA54419 NIH HHS
- C8221/A19170 Cancer Research UK
- R01 CA049449 NCI NIH HHS
- P50 CA159981 NCI NIH HHS
- T32 GM118288 NIGMS NIH HHS
- CA1X01HG007491-01 NIH HHS
- Z01-ES044005 NIEHS NIH HHS
- R01 CA106414 NCI NIH HHS
- R01 CA095023 NCI NIH HHS
- N01 PC067010 NCI NIH HHS
- R01 CA058598 NCI NIH HHS
- U01 CA176726 NCI NIH HHS
- S10 RR025141 NCRR NIH HHS
- M01 RR000056 NCRR NIH HHS
- Department of Health
- 5T32GM118288-03 NIH HHS
- MR/N003284/1 Medical Research Council
- P30 CA014089 NCI NIH HHS
- K07-CA080668 NCI NIH HHS
- 14136 Cancer Research UK
- Worldwide Cancer Research
- MR_UU_12023 Medical Research Council
- R01 CA067262 NCI NIH HHS
- UM1 CA186107 NCI NIH HHS
- P30 CA015083 NCI NIH HHS
- G1000143 Medical Research Council
- R01 CA076016 NCI NIH HHS
- NHGRI NIH HHS
- P01 CA087969 NCI NIH HHS
- R01- CA61107 NCI NIH HHS
- R01-CA58598 NIH HHS
- U19 CA148112 NCI NIH HHS
- ULTR000445 NCATS NIH HHS
- R03 CA115195 NCI NIH HHS
- Wellcome Trust
- Breast Cancer Now
- R01 CA160669 NCI NIH HHS
- R01-CA058860 NIH HHS
- MC_UU_00004/01 Medical Research Council
- C570/A16491 Cancer Research UK
- R01-CA76016 NIH HHS
- R01-CA106414-A2 NIH HHS
- 001 World Health Organization
- Z01 ES049033 Intramural NIH HHS
- R01 CA126841 NCI NIH HHS
- MR/M012190/1 Medical Research Council
- 209057 Wellcome Trust
- R03 CA113148 NCI NIH HHS
- R01 CA149429 NCI NIH HHS
- National Institute of General Medical Sciences
- National Institutes of Health
- CSMC Precision Health Initiative
- Tell Every Amazing Lady About Ovarian Cancer Louisa M. McGregor Ovarian Cancer Foundation
- Ovarian Cancer Research Fund thanks
- National Cancer Institute
- National Human Genome Research Institute
- Canadian Institutes of Health Research
- Ovarian Cancer Research Fund
- European Commission’s Seventh Framework Programme
- Army Medical Research and Materiel Command
- National Health & Medical Research Council of Australia
- Cancer Councils of New South Wales, Victoria, Queensland, South Australia and Tasmania and Cancer Foundation of Western Australia
- Ovarian Cancer Australia
- Peter MacCallum Foundation
- University of Erlangen-Nuremberg
- National Kankerplan
- Breast Cancer Now, Institute of Cancer Research
- National Center for Advancing Translational Sciences
- European Commission
- International Agency for Research on Cancer
- Danish Cancer Society
- Ligue Contre le Cancer, Institut Gustave Roussy, Mutuelle Générale de l’Education Nationale
- Institut National de la Santé et de la Recherche Médicale
- German Cancer Aid; German Cancer Research Center
- Federal Ministry of Education and Research
- Hellenic Health Foundation
- Associazione Italiana per la Ricerca sul Cancro-AIRC-Italy
- National Research Council
- Dutch Ministry of Public Health, Welfare and Sports
- Netherlands Cancer Registry
- LK Research Funds
- Dutch Prevention Funds
- World Cancer Research Fund
- Nordforsk, Nordic Centre of Excellence programme on Food, Nutrition and Health
- Health Research Fund
- Regional Governments of Andalucía, Asturias, Basque Country, Murcia and Navarra
- Swedish Cancer Society, Swedish Research Council and County Councils of Skåne and Västerbotten
- German Federal Ministry of Education and Research, Programme of Clinical Biomedical Research
- German Cancer Research Center
- Rudolf-Bartling Foundation
- Helsinki University Hospital Research Fund
- University of Pittsburgh School of Medicine Dean’s Faculty Advancement Award
- Department of Defense
- NCI
- Swedish Cancer Society, Swedish Research Council, Beta Kamprad Foundation
- Danish Cancer Society, Copenhagen
- Mayo Foundation
- Minnesota Ovarian Cancer Alliance
- Fred C. and Katherine B. Andersen Foundation
- VicHealth and Cancer Council Victoria, Cancer Council Victoria
- National Health and Medical Research Council of Australia
- NHMRC
- DOD Ovarian Cancer Research Program
- Moffitt Cancer Center
- Merck Pharmaceuticals
- Radboud University Medical Centre
- UK National Institute for Health Research Biomedical Research Centres at the University of Cambridge
- National Institute of Environmental Health Sciences
- The Swedish Cancer Foundation
- the Swedish Research Council
- American Cancer Society
- Celma Mastry Ovarian Cancer Foundation
- Lon V Smith Foundation
- The Eve Appeal
- National Institute for Health Research University College London Hospitals Biomedical Research Centre
- California Cancer Research Program
- National Science Centre
- NIH
Collapse
Affiliation(s)
- Amber A DeVries
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Pei-Chen Peng
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Simon G Coetzee
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alberto L Reyes
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jasmine T Plummer
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Brian D Davis
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stephanie S Chen
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Felipe Segato Dezem
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Katja K H Aben
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-European Metropolitan Region of Nuremberg, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Andrew Berchuck
- Department of Gynecologic Oncology, Duke University Hospital, Durham, NC, USA
| | - Natalia V Bogdanova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | | | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ralf Butzow
- Department of Pathology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Ian Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Linda S Cook
- Epidemiology, School of Public Health, University of Colorado, Aurora, CO, USA
- Community Health Sciences, University of Calgary, Calgary, AB, Canada
| | - Anna DeFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- The Daffodil Centre, a joint venture with Cancer Council NSW, The University of Sydney, Sydney, New South Wales, Australia
| | - Jennifer A Doherty
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-European Metropolitan Region of Nuremberg, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Renée T Fortner
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Ellen L Goode
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Marc T Goodman
- Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Niclas Håkansson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Chad Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David G Huntsman
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Allan Jensen
- Department of Lifestyle, Reproduction and Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Siddhartha Kar
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Section of Translational Epidemiology, Division of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Saint Petersburg State University, Saint Petersburg, Russia
| | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susanne K Kjaer
- Department of Lifestyle, Reproduction and Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Marilyne Labrie
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nhu D Le
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Taymaa May
- Division of Gynecologic Oncology, University Health Network, Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Usha Menon
- MRC Clinical Trials Unit, Institute of Clinical Trials & Methodology, University College London, London, UK
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Francesmary Modugno
- Women's Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kunle Odunsi
- Department of Oncology, University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA
- Department of Obstetrics and Gynecology, University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA
| | - Håkan Olsson
- Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Celeste L Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Tanja Pejovic
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, USA
| | - Susan J Ramus
- School of Women's and Children's Health, Faculty of Medicine and Health, University of NSW Sydney, Sydney, New South Wales, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of NSW Sydney, Sydney, New South Wales, Australia
| | | | - Marjorie J Riggan
- Department of Gynecologic Oncology, Duke University Hospital, Durham, NC, USA
| | - Isabelle Romieu
- Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Joellen M Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - V Wendy Setiawan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Weiva Sieh
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Honglin Song
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Rebecca Sutphen
- Epidemiology Center, College of Medicine, University of South Florida, Tampa, FL, USA
| | - Kathryn L Terry
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Pamela J Thompson
- Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Linda Titus
- Muskie School of Public Policy, Public Health, Portland, ME, USA
| | - Shelley S Tworoger
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Els Van Nieuwenhuysen
- Division of Gynecologic Oncology, Department of Gynecology and Obstetrics, Leuven Cancer Institute, Leuven, Belgium
| | - Digna Velez Edwards
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Department of Biomedical Sciences, Women's Health Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Penelope M Webb
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alice S Whittemore
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Argyrios Ziogas
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kate Lawrenson
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Women's Cancer Program at the Samuel Oschin Cancer Institute Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michelle R Jones
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| |
Collapse
|
33
|
Rojahn S, Hambuch T, Adrian J, Gafni E, Gileta A, Hatchell H, Johnson B, Kallman B, Karfilis K, Kautzer C, Kennemer M, Kirk L, Kvitek D, Lettes J, Macrae F, Mendez F, Paul J, Pellegrino M, Preciado R, Risinger J, Schultz M, Spurka L, Swamy S, Truty R, Usem N, Velenich A, Aradhya S. Scalable detection of technically challenging variants through modified next-generation sequencing. Mol Genet Genomic Med 2022; 10:e2072. [PMID: 36251442 PMCID: PMC9747563 DOI: 10.1002/mgg3.2072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Some clinically important genetic variants are not easily evaluated with next-generation sequencing (NGS) methods due to technical challenges arising from high- similarity copies (e.g., PMS2, SMN1/SMN2, GBA1, HBA1/HBA2, CYP21A2), repetitive short sequences (e.g., ARX polyalanine repeats, FMR1 AGG interruptions in CGG repeats, CFTR poly-T/TG repeats), and other complexities (e.g., MSH2 Boland inversions). METHODS We customized our NGS processes to detect the technically challenging variants mentioned above with adaptations including target enrichment and bioinformatic masking of similar sequences. Adaptations were validated with samples of known genotypes. RESULTS Our adaptations provided high-sensitivity and high-specificity detection for most of the variants and provided a high-sensitivity primary assay to be followed with orthogonal disambiguation for the others. The sensitivity of the NGS adaptations was 100% for all of the technically challenging variants. Specificity was 100% for those in PMS2, GBA1, SMN1/SMN2, and HBA1/HBA2, and for the MSH2 Boland inversion; 97.8%-100% for CYP21A2 variants; and 85.7% for ARX polyalanine repeats. CONCLUSIONS NGS assays can detect technically challenging variants when chemistries and bioinformatics are jointly refined. The adaptations described support a scalable, cost-effective path to identifying all clinically relevant variants within a single sample.
Collapse
|
34
|
Ewans LJ, Minoche AE, Schofield D, Shrestha R, Puttick C, Zhu Y, Drew A, Gayevskiy V, Elakis G, Walsh C, Adès LC, Colley A, Ellaway C, Evans CA, Freckmann ML, Goodwin L, Hackett A, Kamien B, Kirk EP, Lipke M, Mowat D, Palmer E, Rajagopalan S, Ronan A, Sachdev R, Stevenson W, Turner A, Wilson M, Worgan L, Morel-Kopp MC, Field M, Buckley MF, Cowley MJ, Dinger ME, Roscioli T. Whole exome and genome sequencing in mendelian disorders: a diagnostic and health economic analysis. Eur J Hum Genet 2022; 30:1121-31. [PMID: 35970915 DOI: 10.1038/s41431-022-01162-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 06/01/2022] [Accepted: 07/20/2022] [Indexed: 12/15/2022] Open
Abstract
Whole genome sequencing (WGS) improves Mendelian disorder diagnosis over whole exome sequencing (WES); however, additional diagnostic yields and costs remain undefined. We investigated differences between diagnostic and cost outcomes of WGS and WES in a cohort with suspected Mendelian disorders. WGS was performed in 38 WES-negative families derived from a 64 family Mendelian cohort that previously underwent WES. For new WGS diagnoses, contemporary WES reanalysis determined whether variants were diagnosable by original WES or unique to WGS. Diagnostic rates were estimated for WES and WGS to simulate outcomes if both had been applied to the 64 families. Diagnostic costs were calculated for various genomic testing scenarios. WGS diagnosed 34% (13/38) of WES-negative families. However, contemporary WES reanalysis on average 2 years later would have diagnosed 18% (7/38 families) resulting in a WGS-specific diagnostic yield of 19% (6/31 remaining families). In WES-negative families, the incremental cost per additional diagnosis using WGS following WES reanalysis was AU$36,710 (£19,407;US$23,727) and WGS alone was AU$41,916 (£22,159;US$27,093) compared to WES-reanalysis. When we simulated the use of WGS alone as an initial genomic test, the incremental cost for each additional diagnosis was AU$29,708 (£15,705;US$19,201) whereas contemporary WES followed by WGS was AU$36,710 (£19,407;US$23,727) compared to contemporary WES. Our findings confirm that WGS is the optimal genomic test choice for maximal diagnosis in Mendelian disorders. However, accepting a small reduction in diagnostic yield, WES with subsequent reanalysis confers the lowest costs. Whether WES or WGS is utilised will depend on clinical scenario and local resourcing and availability.
Collapse
|
35
|
Johnson B, Ouyang K, Frank L, Truty R, Rojahn S, Morales A, Aradhya S, Nykamp K. Systematic use of phenotype evidence in clinical genetic testing reduces the frequency of variants of uncertain significance. Am J Med Genet A 2022; 188:2642-2651. [PMID: 35570716 PMCID: PMC9544038 DOI: 10.1002/ajmg.a.62779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 01/24/2023]
Abstract
Guidelines for variant interpretation include criteria for incorporating phenotype evidence, but this evidence is inconsistently applied. Systematic approaches to using phenotype evidence are needed. We developed a method for curating disease phenotypes as highly or moderately predictive of variant pathogenicity based on the frequency of their association with disease-causing variants. To evaluate this method's accuracy, we retrospectively reviewed variants with clinical classifications that had evolved from uncertain to definitive in genes associated with curated predictive phenotypes. To demonstrate the clinical validity and utility of this approach, we compared variant classifications determined with and without predictive phenotype evidence. The curation method was accurate for 93%-98% of eligible variants. Among variants interpreted using highly predictive phenotype evidence, the percentage classified as pathogenic or likely pathogenic was 80%, compared with 46%-54% had the evidence not been used. Positive results among individuals harboring variants with highly predictive phenotype-guided interpretations would have been missed in 25%-37% of diagnostic tests and 39%-50% of carrier screens had other approaches to phenotype evidence been used. In summary, predictive phenotype evidence associated with specific curated genes can be systematically incorporated into variant interpretation to reduce uncertainty and increase the clinical utility of genetic testing.
Collapse
Affiliation(s)
| | | | | | | | | | - Ana Morales
- Invitae CorporationSan FranciscoCaliforniaUSA
| | | | | |
Collapse
|
36
|
Kushima I, Imaeda M, Tanaka S, Kato H, Oya-Ito T, Nakatochi M, Aleksic B, Ozaki N. Contribution of copy number variations to the risk of severe eating disorders. Psychiatry Clin Neurosci 2022; 76:423-428. [PMID: 35611833 PMCID: PMC9546291 DOI: 10.1111/pcn.13430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/10/2022] [Accepted: 05/18/2022] [Indexed: 11/28/2022]
Abstract
AIM Eating disorders (EDs) are complex, multifactorial psychiatric conditions. Previous studies identified pathogenic copy number variations associated with NDDs (NDD-CNVs) in ED patients. However, no statistical evidence for an association between NDD-CNVs and EDs has been demonstrated. Therefore, we examined whether NDD-CNVs confer risk for EDs. METHODS Using array comparative genomic hybridization (aCGH), we conducted a high-resolution CNV analysis of 71 severe female ED patients and 1045 female controls. According to the American College of Medical Genetics guidelines, we identified NDD-CNVs or pathogenic/likely pathogenic CNVs in NDD-linked loci. Gene set analysis was performed to examine the involvement of synaptic dysfunction in EDs. Clinical data were retrospectively examined for ED patients with NDD-CNVs. RESULTS Of the samples analyzed with aCGH, 70 severe ED patients (98.6%) and 1036 controls (99.1%) passed our quality control filtering. We obtained 189 and 2539 rare CNVs from patients and controls, respectively. NDD-CNVs were identified in 10.0% (7/70) of patients and 2.3% (24/1036) of controls. Statistical analysis revealed a significant association between NDD-CNVs and EDs (odds ratio = 4.69, P = 0.0023). NDD-CNVs in ED patients included 45,X and deletions at KATNAL2, DIP2A, PTPRT, RBFOX1, CNTN4, MACROD2, and FAM92B. Four of these genes were related to synaptic function. In gene set analysis, we observed a nominally significant enrichment of rare exonic CNVs in synaptic signaling in ED patients (odds ratio = 2.55, P = 0.0254). CONCLUSION Our study provides the first preliminary evidence that NDD-CNVs may confer risk for severe EDs. The pathophysiology may involve synaptic dysfunction.
Collapse
Affiliation(s)
- Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Miho Imaeda
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Clinical Oncology and Chemotherapy, Nagoya University Hospital, Nagoya, Japan
| | - Satoshi Tanaka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,National Hospital Organization Higashiowari National Hospital, Nagoya, Japan.,The Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Hidekazu Kato
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoko Oya-Ito
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Nutrition, Shubun University, Nagoya, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| |
Collapse
|
37
|
Dellefave-Castillo LM, Cirino AL, Callis TE, Esplin ED, Garcia J, Hatchell KE, Johnson B, Morales A, Regalado E, Rojahn S, Vatta M, Nussbaum RL, McNally EM. Assessment of the Diagnostic Yield of Combined Cardiomyopathy and Arrhythmia Genetic Testing. JAMA Cardiol 2022; 7:966-974. [PMID: 35947370 PMCID: PMC9366660 DOI: 10.1001/jamacardio.2022.2455] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Importance Genetic testing can guide management of both cardiomyopathies and arrhythmias, but cost, yield, and uncertain results can be barriers to its use. It is unknown whether combined disease testing can improve diagnostic yield and clinical utility for patients with a suspected genetic cardiomyopathy or arrhythmia. Objective To evaluate the diagnostic yield and clinical management implications of combined cardiomyopathy and arrhythmia genetic testing through a no-charge, sponsored program for patients with a suspected genetic cardiomyopathy or arrhythmia. Design, Setting, and Participants This cohort study involved a retrospective review of DNA sequencing results for cardiomyopathy- and arrhythmia-associated genes. The study included 4782 patients with a suspected genetic cardiomyopathy or arrhythmia who were referred for genetic testing by 1203 clinicians; all patients participated in a no-charge, sponsored genetic testing program for cases of suspected genetic cardiomyopathy and arrhythmia at a single testing site from July 12, 2019, through July 9, 2020. Main Outcomes and Measures Positive gene findings from combined cardiomyopathy and arrhythmia testing were compared with findings from smaller subtype-specific gene panels and clinician-provided diagnoses. Results Among 4782 patients (mean [SD] age, 40.5 [21.3] years; 2551 male [53.3%]) who received genetic testing, 39 patients (0.8%) were Ashkenazi Jewish, 113 (2.4%) were Asian, 571 (11.9%) were Black or African American, 375 (7.8%) were Hispanic, 2866 (59.9%) were White, 240 (5.0%) were of multiple races and/or ethnicities, 138 (2.9%) were of other races and/or ethnicities, and 440 (9.2%) were of unknown race and/or ethnicity. A positive result (molecular diagnosis) was confirmed in 954 of 4782 patients (19.9%). Of those, 630 patients with positive results (66.0%) had the potential to inform clinical management associated with adverse clinical outcomes, increased arrhythmia risk, or targeted therapies. Combined cardiomyopathy and arrhythmia gene panel testing identified clinically relevant variants for 1 in 5 patients suspected of having a genetic cardiomyopathy or arrhythmia. If only patients with a high suspicion of genetic cardiomyopathy or arrhythmia had been tested, at least 137 positive results (14.4%) would have been missed. If testing had been restricted to panels associated with the clinician-provided diagnostic indications, 75 of 689 positive results (10.9%) would have been missed; 27 of 75 findings (36.0%) gained through combined testing involved a cardiomyopathy indication with an arrhythmia genetic finding or vice versa. Cascade testing of family members yielded 402 of 958 positive results (42.0%). Overall, 2446 of 4782 patients (51.2%) had only variants of uncertain significance. Patients referred for arrhythmogenic cardiomyopathy had the lowest rate of variants of uncertain significance (81 of 176 patients [46.0%]), and patients referred for catecholaminergic polymorphic ventricular tachycardia had the highest rate (48 of 76 patients [63.2%]). Conclusions and Relevance In this study, comprehensive genetic testing for cardiomyopathies and arrhythmias revealed diagnoses that would have been missed by disease-specific testing. In addition, comprehensive testing provided diagnostic and prognostic information that could have potentially changed management and monitoring strategies for patients and their family members. These results suggest that this improved diagnostic yield may outweigh the burden of uncertain results.
Collapse
Affiliation(s)
- Lisa M Dellefave-Castillo
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Allison L Cirino
- Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts.,Institute of Health Professions, Massachusetts General Hospital, Boston
| | | | | | - John Garcia
- Invitae Corporation, San Francisco, California
| | | | | | - Ana Morales
- Invitae Corporation, San Francisco, California
| | | | | | | | | | - Elizabeth M McNally
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| |
Collapse
|
38
|
El Kadiri Y, Ratbi I, Sefiani A, Lyahyai J. Novel copy number variation of COLQ gene in a Moroccan patient with congenital myasthenic syndrome: a case report and review of the literature. BMC Neurol 2022; 22:292. [PMID: 35932018 PMCID: PMC9354381 DOI: 10.1186/s12883-022-02822-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/29/2022] [Indexed: 11/11/2022] Open
Abstract
Background Congenital myasthenic syndromes (CMSs) are rare genetic diseases due to abnormalities of the neuromuscular junction leading to permanent or transient muscle fatigability and weakness. To date, 32 genes were found to be involved in CMSs with autosomal dominant and/or recessive inheritance patterns. CMS with acetylcholinesterase deficiency, in particular, was determined to be due to biallelic mutations of COLQ gene with early-onset clinical signs. Here, we report clinical features and novel molecular findings of COLQ-related CMS in a Moroccan patient with a review of the literature for this rare form. Case presentation In this study, we report the case of a 28-month-old Moroccan female patient with hypotonia, associated to axial muscle weakness, global motor delay, bilateral ptosis, unilateral partial visual field deficiency with normal ocular motility, and fatigable muscle weakness. Clinical exome sequencing revealed a novel homozygous deletion of exon 13 in COLQ gene, NM_005677.4(COLQ):c.(814+1_815-1)_(954+1_955-1) del p.(Gly272Aspfs*11). This finding was subsequently confirmed by quantitative real-time PCR (qPCR) in the proband and her parents. In silico analysis of protein-protein interaction network by STRING tool revealed that 12 proteins are highly associated to COLQ with an elevated confidence score. Treatment with Salbutamol resulted in clear benefits and recovery. Conclusions This clinical observation illustrates the important place of next-generation sequencing in the precise molecular diagnosis of heterogeneous forms of CMS, the appropriate management and targeted treatment, and genetic counseling of families, with a better characterization of the mutational profile of this rare disease in the Moroccan population.
Collapse
Affiliation(s)
- Youssef El Kadiri
- Research Team in Genomics and Molecular Epidemiology of Genetic Diseases, Genomics Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, 10 100 Rabat, Morocco. .,Department of Medical Genetics, National Institute of Health, BP 769-Agdal, 10 090, Rabat, Morocco.
| | - Ilham Ratbi
- Research Team in Genomics and Molecular Epidemiology of Genetic Diseases, Genomics Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, 10 100 Rabat, Morocco
| | - Abdelaziz Sefiani
- Research Team in Genomics and Molecular Epidemiology of Genetic Diseases, Genomics Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, 10 100 Rabat, Morocco.,Department of Medical Genetics, National Institute of Health, BP 769-Agdal, 10 090, Rabat, Morocco
| | - Jaber Lyahyai
- Research Team in Genomics and Molecular Epidemiology of Genetic Diseases, Genomics Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, 10 100 Rabat, Morocco
| |
Collapse
|
39
|
Commission on Novel Technologies for Neurodevelopmental Copy Number Variants. Neurodevelopmental copy-number variants: A roadmap to improving outcomes by uniting patient advocates, researchers, and clinicians for collective impact. Am J Hum Genet 2022; 109:1353-65. [PMID: 35931048 DOI: 10.1016/j.ajhg.2022.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Copy-number variants and structural variants (CNVs/SVs) drive many neurodevelopmental-related disorders. While many neurodevelopmental-related CNVs/SVs give rise to complex phenotypes, the overlap in phenotypic presentation between independent CNVs can be extensive and provides a motivation for shared approaches. This confluence at the level of clinical phenotype implies convergence in at least some aspects of the underlying genomic mechanisms. With this perspective, our Commission on Novel Technologies for Neurodevelopmental CNVs asserts that the time has arrived to approach neurodevelopmental-related CNVs/SVs as a class of disorders that can be identified, investigated, and treated on the basis of shared mechanisms and/or pathways (e.g., molecular, neurological, or developmental). To identify common etiologic mechanisms among uncommon neurodevelopmental-related disorders and to potentially identify common therapies, it is paramount for teams of scientists, clinicians, and patients to unite their efforts. We bring forward novel, collaborative, and integrative strategies to translational CNV/SV research that engages diverse stakeholders to help expedite therapeutic outcomes. We articulate a clear vision for piloted roadmap strategies to reduce patient/caregiver burden and redundancies, increase efficiency, avoid siloed data, and accelerate translational discovery across CNV/SV-based syndromes.
Collapse
|
40
|
Heald B, Mokhtary S, Nielsen SM, Rojahn S, Yang S, Michalski ST, Esplin ED. Unexpected actionable genetic variants revealed by multigene panel testing of patients with uterine cancer. Gynecol Oncol 2022; 166:344-350. [PMID: 35691755 DOI: 10.1016/j.ygyno.2022.05.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/09/2022] [Accepted: 05/28/2022] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Hereditary uterine cancer (UC) is traditionally associated with pathogenic/likely pathogenic germline variants (PGVs) in Lynch syndrome genes or PTEN; however, growing evidence supports a role for other genes that may reveal new clinical management options. In this study we assessed the prevalence and potential clinical impact of PGVs identified in UC patients referred for comprehensive germline genetic testing that combined testing for Lynch syndrome, PTEN, and other cancer predisposition genes. METHODS Prevalence of PGVs in patients referred to a single clinical lab for germline genetic testing with an indication of uterine or endometrial cancer were retrospectively assessed and compared by syndrome type, patient age at testing, and self-reported ancestry. Potential clinical actionability of PGVs was based on established guidelines for clinical management, targeted therapies, and clinical trial eligibility. RESULTS PGVs were detected in 13.6% of the cohort (880/6490). PGVs were most frequently observed in Lynch syndrome genes (60.4%) and PTEN (1.5%), with 38.1% in another cancer predisposition gene (i.e., CHEK2, BRCA1/BRCA2). PGV prevalence was similar for patients <50 years and those ≥50 years (15.1% vs 13.2%). Nearly all PGVs (97.2%) were associated with guideline-recommended management, including cascade testing; 60.5% were associated with FDA-approved therapies; and 35.2% were associated with clinical trials. CONCLUSIONS Focusing germline testing on Lynch syndrome genes and PTEN and limiting testing to patients <50 years of age at diagnosis may overlook a substantial proportion of UC patients who harbor actionable PGVs. Universal comprehensive genetic testing of UC patients could benefit many patients and at-risk family members.
Collapse
Affiliation(s)
- Brandie Heald
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Sara Mokhtary
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | - Susan Rojahn
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Shan Yang
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | | |
Collapse
|
41
|
Koczwara KE, Lake NJ, DeSimone AM, Lek M. Neuromuscular disorders: finding the missing genetic diagnoses. Trends Genet 2022; 38:956-971. [PMID: 35908999 DOI: 10.1016/j.tig.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022]
Abstract
Neuromuscular disorders (NMDs) are a wide-ranging group of diseases that seriously affect the quality of life of affected individuals. The development of next-generation sequencing revolutionized the diagnosis of NMD, enabling the discovery of hundreds of NMD genes and many more pathogenic variants. However, the diagnostic yield of genetic testing in NMD cohorts remains incomplete, indicating a large number of genetic diagnoses are not identified through current methods. Fortunately, recent advancements in sequencing technologies, analytical tools, and high-throughput functional screening provide an opportunity to circumvent current challenges. Here, we discuss reasons for missing genetic diagnoses in NMD, how emerging technologies and tools can overcome these hurdles, and examine future approaches to improving diagnostic yields in NMD.
Collapse
Affiliation(s)
- Katherine E Koczwara
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Nicole J Lake
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Alec M DeSimone
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Monkol Lek
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
| |
Collapse
|
42
|
Ossa Gomez CA, Achatz MI, Hurtado M, Sanabria-Salas MC, Sullcahuaman Y, Chávarri-Guerra Y, Dutil J, Nielsen SM, Esplin ED, Michalski ST, Bristow SL, Hatchell KE, Nussbaum RL, Pineda-Alvarez DE, Ashton-Prolla P. Germline Pathogenic Variant Prevalence Among Latin American and US Hispanic Individuals Undergoing Testing for Hereditary Breast and Ovarian Cancer: A Cross-Sectional Study. JCO Glob Oncol 2022; 8:e2200104. [PMID: 35867948 PMCID: PMC9812461 DOI: 10.1200/go.22.00104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
PURPOSE To report on pathogenic germline variants detected among individuals undergoing genetic testing for hereditary breast and/or ovarian cancer (HBOC) from Latin America and compare them with self-reported Hispanic individuals from the United States. METHODS In this cross-sectional study, unrelated individuals with a personal/family history suggestive of HBOC who received clinician-ordered germline multigene sequencing were grouped according to the location of the ordering physician: group A, Mexico, Central America, and the Caribbean; group B, South America; and group C, United States with individuals who self-reported Hispanic ethnicity. Relatives who underwent cascade testing were analyzed separately. RESULTS Among 24,075 unrelated probands across all regions, most were female (94.9%) and reported a personal history suggestive of HBOC (range, 65.0%-80.6%); the mean age at testing was 49.1 ± 13.1 years. The average number of genes analyzed per patient was highest in group A (A 63 ± 28, B 56 ± 29, and C 40 ± 28). Between 9.1% and 18.7% of patients had pathogenic germline variants in HBOC genes (highest yield in group A), with the majority associated with high HBOC risk. Compared with US Hispanics individuals the overall yield was significantly higher in both Latin American regions (A v C P = 1.64×10-9, B v C P < 2.2×10-16). Rates of variants of uncertain significance were similar across all three regions (33.7%-42.6%). Cascade testing uptake was low in all regions (A 6.6%, B 4.5%, and C 1.9%). CONCLUSION This study highlights the importance of multigene panel testing in Latin American individuals with newly diagnosed or history of HBOC, who can benefit from medical management changes including targeted therapies, eligibility to clinical trials, risk-reducing surgeries, surveillance and prevention of secondary malignancy, and genetic counseling and subsequent cascade testing of at-risk relatives.
Collapse
Affiliation(s)
| | - Maria Isabel Achatz
- Department of Oncology, Hospital Sírio-Libanês, Brasília, Distrito Federal, Brazil
| | - Mabel Hurtado
- Instituto Oncológico, Fundación Arturo López Pérez, Santiago, Chile
| | | | - Yasser Sullcahuaman
- Universidad Peruana de Ciencias Aplicadas, Lima, Peru,Instituto de Investigación Genomica, Lima, Peru
| | - Yanin Chávarri-Guerra
- Department of Hemato-Oncology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Julie Dutil
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Pone, Puerto Rico
| | | | | | | | | | | | | | - Daniel E. Pineda-Alvarez
- Invitae, San Francisco, CA,Daniel E. Pineda-Alvarez, MD, Medical Affairs, Invitae Corporation, 1400 16th Street, San Francisco, CA, 94103; e-mail:
| | - Patricia Ashton-Prolla
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil,Serviço de Genética Médica e Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| |
Collapse
|
43
|
Stamou MI, Brand H, Wang M, Wong I, Lippincott MF, Plummer L, Crowley WF, Talkowski M, Seminara S, Balasubramanian R. Prevalence and Phenotypic Effects of Copy Number Variants in Isolated Hypogonadotropic Hypogonadism. J Clin Endocrinol Metab 2022; 107:2228-2242. [PMID: 35574646 PMCID: PMC9282252 DOI: 10.1210/clinem/dgac300] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Indexed: 12/24/2022]
Abstract
CONTEXT The genetic architecture of isolated hypogonadotropic hypogonadism (IHH) has not been completely defined. OBJECTIVE To determine the role of copy number variants (CNVs) in IHH pathogenicity and define their phenotypic spectrum. METHODS Exome sequencing (ES) data in IHH probands (n = 1394) (Kallmann syndrome [IHH with anosmia; KS], n = 706; normosmic IHH [nIHH], n = 688) and family members (n = 1092) at the Reproductive Endocrine Unit and the Center for Genomic Medicine of Massachusetts General Hospital were analyzed for CNVs and single nucleotide variants (SNVs)/indels in 62 known IHH genes. IHH subjects without SNVs/indels in known genes were considered "unsolved." Phenotypes associated with CNVs were evaluated through review of patient medical records. A total of 29 CNVs in 13 genes were detected (overall IHH cohort prevalence: ~2%). Almost all (28/29) CNVs occurred in unsolved IHH cases. While some genes (eg, ANOS1 and FGFR1) frequently harbor both CNVs and SNVs/indels, the mutational spectrum of others (eg, CHD7) was restricted to SNVs/indels. Syndromic phenotypes were seen in 83% and 63% of IHH subjects with multigenic and single gene CNVs, respectively. CONCLUSION CNVs in known genes contribute to ~2% of IHH pathogenesis. Predictably, multigenic contiguous CNVs resulted in syndromic phenotypes. Syndromic phenotypes resulting from single gene CNVs validate pleiotropy of some IHH genes. Genome sequencing approaches are now needed to identify novel genes and/or other elusive variants (eg, noncoding/complex structural variants) that may explain the remaining missing etiology of IHH.
Collapse
Affiliation(s)
- Maria I Stamou
- Reproductive Endocrine Unit, Massachusetts General Hospital and the Center for Reproductive Medicine, Boston, MA 02141, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02141, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02141, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02141, USA
| | - Mei Wang
- Reproductive Endocrine Unit, Massachusetts General Hospital and the Center for Reproductive Medicine, Boston, MA 02141, USA
| | - Isaac Wong
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02141, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02141, USA
| | - Margaret F Lippincott
- Reproductive Endocrine Unit, Massachusetts General Hospital and the Center for Reproductive Medicine, Boston, MA 02141, USA
| | - Lacey Plummer
- Reproductive Endocrine Unit, Massachusetts General Hospital and the Center for Reproductive Medicine, Boston, MA 02141, USA
| | - William F Crowley
- Endocrine Division, Massachusetts General Hospital, Boston, MA 02141, USA
| | - Michael Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02141, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02141, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Stephanie Seminara
- Reproductive Endocrine Unit, Massachusetts General Hospital and the Center for Reproductive Medicine, Boston, MA 02141, USA
| | - Ravikumar Balasubramanian
- Reproductive Endocrine Unit, Massachusetts General Hospital and the Center for Reproductive Medicine, Boston, MA 02141, USA
| |
Collapse
|
44
|
Astiazaran-Symonds E, Kim J, Haley JS, Kim SY, Rao HS, Genetics Center R, Carey DJ, Stewart DR, Goldstein AM. A Genome-First Approach to Estimate Prevalence of Germline Pathogenic Variants and Risk of Pancreatic Cancer in Select Cancer Susceptibility Genes. Cancers (Basel) 2022; 14. [PMID: 35805029 DOI: 10.3390/cancers14133257] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 12/20/2022] Open
Abstract
Patients with germline pathogenic variants (GPV) in cancer predisposition genes are at increased risk of pancreatic ductal adenocarcinoma (PDAC), the most common type of pancreatic cancer. The genes most frequently found to harbor GPV in unselected PDAC cases are ATM, BRCA1, BRCA2, CDKN2A, CHEK2, and PALB2. However, GPV prevalence and gene-specific associations have not been extensively studied in the general population. To further explore these associations, we analyzed genomic and phenotypic data obtained from the UK Biobank (UKB) and Geisinger MyCode Community Health Initiative (GHS) cohorts comprising 200,600 and 175,449 participants, respectively. We estimated the frequency and calculated relative risks (RRs) of heterozygotes in both cohorts and a subset of individuals with PDAC. The combined frequency of heterozygous carriers of GPV in the general population ranged from 1.22% for CHEK2 to 0.05% for CDKN2A. The frequency of GPV in PDAC cases varied from 2.38% (ATM) to 0.19% (BRCA1 and CDKN2A). The RRs of PDAC were elevated for all genes except for BRCA1 and varied widely by gene from high (ATM) to low (CHEK2, BRCA2). This work expands our understanding of the frequencies of GPV heterozygous carriers and associations between PDAC and GPV in several important PDAC susceptibility genes.
Collapse
|
45
|
Lin X, Yang Y, Melton PE, Singh V, Simpson-Yap S, Burdon KP, Taylor BV, Zhou Y. Integrating Genetic Structural Variations and Whole-Genome Sequencing Into Clinical Neurology. Neurol Genet 2022. [DOI: 10.1212/nxg.0000000000200005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Advances in genome sequencing technologies have unlocked new possibilities in identifying disease-associated and causative genetic markers, which may in turn enhance disease diagnosis and improve prognostication and management strategies. With the capability of examining genetic variations ranging from single-nucleotide mutations to large structural variants, whole-genome sequencing (WGS) is an increasingly adopted approach to dissect the complex genetic architecture of neurologic diseases. There is emerging evidence for different structural variants and their roles in major neurologic and neurodevelopmental diseases. This review first describes different structural variants and their implicated roles in major neurologic and neurodevelopmental diseases, and then discusses the clinical relevance of WGS applications in neurology. Notably, WGS-based detection of structural variants has shown promising potential in enhancing diagnostic power of genetic tests in clinical settings. Ongoing WGS-based research in structural variations and quantifying mutational constraints can also yield clinical benefits by improving variant interpretation and disease diagnosis, while supporting biomarker discovery and therapeutic development. As a result, wider integration of WGS technologies into health care will likely increase diagnostic yields in difficult-to-diagnose conditions and define potential therapeutic targets or intervention points for genome-editing strategies.
Collapse
|
46
|
Yang Y, Zhao S, Sun G, Chen F, Zhang T, Song J, Yang W, Wang L, Zhan N, Yang X, Zhu X, Rao B, Yin Z, Zhou J, Yan H, Huang Y, Ye J, Huang H, Cheng C, Zhu S, Guo J, Xu X, Chen X. Genomic architecture of fetal central nervous system anomalies using whole-genome sequencing. NPJ Genom Med 2022; 7:31. [PMID: 35562572 PMCID: PMC9106651 DOI: 10.1038/s41525-022-00301-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/06/2022] [Indexed: 11/09/2022] Open
Abstract
Structural anomalies of the central nervous system (CNS) are one of the most common fetal anomalies found during prenatal imaging. However, the genomic architecture of prenatal imaging phenotypes has not yet been systematically studied in a large cohort. Patients diagnosed with fetal CNS anomalies were identified from medical records and images. Fetal samples were subjected to low-pass and deep whole-genome sequencing (WGS) for aneuploid, copy number variation (CNV), single-nucleotide variant (SNV, including insertions/deletions (indels)), and small CNV identification. The clinical significance of variants was interpreted based on a candidate gene list constructed from ultrasound phenotypes. In total, 162 fetuses with 11 common CNS anomalies were enrolled in this study. Primary diagnosis was achieved in 62 cases, with an overall diagnostic rate of 38.3%. Causative variants included 18 aneuploids, 17 CNVs, three small CNVs, and 24 SNVs. Among the 24 SNVs, 15 were novel mutations not reported previously. Furthermore, 29 key genes of diagnostic variants and critical genes of pathogenic CNVs were identified, including five recurrent genes: i.e., TUBA1A, KAT6B, CC2D2A, PDHA1, and NF1. Diagnostic variants were present in 34 (70.8%) out of 48 fetuses with both CNS and non-CNS malformations, and in 28 (24.6%) out of 114 fetuses with CNS anomalies only. Hypoplasia of the cerebellum (including the cerebellar vermis) and holoprosencephaly had the highest primary diagnosis yields (>70%), while only four (11.8%) out of 34 neural tube defects achieved genetic diagnosis. Compared with the control group, rare singleton loss-of-function variants (SLoFVs) were significantly accumulated in the patient cohort.
Collapse
Affiliation(s)
- Ying Yang
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Sheng Zhao
- Maternal and Child Health Hospital of Hubei Province, Hubei, 430070, China
| | - Guoqiang Sun
- Maternal and Child Health Hospital of Hubei Province, Hubei, 430070, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Jieping Song
- Maternal and Child Health Hospital of Hubei Province, Hubei, 430070, China
| | - Wenzhong Yang
- Maternal and Child Health Hospital of Hubei Province, Hubei, 430070, China
| | - Lin Wang
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xiaohong Yang
- Maternal and Child Health Hospital of Hubei Province, Hubei, 430070, China
| | - Xia Zhu
- Maternal and Child Health Hospital of Hubei Province, Hubei, 430070, China
| | - Bin Rao
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Jing Zhou
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | | | - Jingyu Ye
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Hui Huang
- Maternal and Child Health Hospital of Hubei Province, Hubei, 430070, China
| | - Chen Cheng
- Maternal and Child Health Hospital of Hubei Province, Hubei, 430070, China
| | - Shida Zhu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jian Guo
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xinlin Chen
- Maternal and Child Health Hospital of Hubei Province, Hubei, 430070, China.
| |
Collapse
|
47
|
Espinel W, Champine M, Hampel H, Jeter J, Sweet K, Pilarski R, Pearlman R, Shane K, Brock P, Westman JA, Kipnis L, Sotelo J, Chittenden A, Culver S, Stopfer JE, Schneider KA, Sacca R, Koeller DR, Gaonkar S, Vaccari E, Kane S, Michalski ST, Yang S, Nielsen SM, Bristow SL, Lincoln SE, Nussbaum RL, Esplin ED. Clinical Impact of Pathogenic Variants in DNA Damage Repair Genes beyond BRCA1 and BRCA2 in Breast and Ovarian Cancer Patients. Cancers (Basel) 2022; 14:cancers14102426. [PMID: 35626031 PMCID: PMC9139211 DOI: 10.3390/cancers14102426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary The clinical utility of positive findings in DNA damage-repair (DDR) genes BRCA1 and BRCA2 for the treatment of patients with breast or ovarian cancer is well established. However, multigene panel genetic testing for patients with breast and ovarian cancer now commonly includes DDR genes in addition to BRCA1 and BRCA2, a number of which are considered moderate or low-risk genes. This study aimed to describe the clinical utility of positive results from genetic testing when the findings were in one of these other DDR genes. In a group of 101 women with positive findings in a cancer gene other than BRCA1 or BRCA2 (often in a DDR gene), nearly three-fifths (58%) had a clinical recommendation made based on their positive genetic test result and two-thirds (65%) had the clinician make recommendations for family members that may be at risk. This real-world data provides evidence that positive findings from genetic testing for moderate and low-risk genes, including DDR genes, can have clinical utility and can impact a patient’s clinical management. Abstract Consensus guidelines for hereditary breast and ovarian cancer include management recommendations for pathogenic/likely pathogenic (P/LP) variants in ATM, CHEK2, PALB2, and other DNA damage repair (DDR) genes beyond BRCA1 or BRCA2. We report on clinical management decisions across three academic medical centers resulting from P/LP findings in DDR genes in breast/ovarian cancer patients. Among 2184 patients, 156 (7.1%) carried a P/LP variant in a DDR gene. Clinical follow-up information was available for 101/156 (64.7%) patients. Genetic test result-based management recommendations were made for 57.8% (n = 59) of patients and for 64.7% (n = 66) of patients’ family members. Most recommendations were made for moderate-to-high risk genes and were consistent with guidelines. Sixty-six percent of patients (n = 39/59) implemented recommendations. This study suggests that P/LP variants in DDR genes beyond BRCA1 and BRCA2 can change clinical management recommendations for patients and their family members, facilitate identification of new at-risk carriers, and impact treatment decisions. Additional efforts are needed to improve the implementation rates of genetic-testing-based management recommendations for patients and their family members.
Collapse
Affiliation(s)
- Whitney Espinel
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA; (W.E.); (M.C.)
| | - Marjan Champine
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA; (W.E.); (M.C.)
| | - Heather Hampel
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Joanne Jeter
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Kevin Sweet
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Robert Pilarski
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Rachel Pearlman
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Kate Shane
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Pamela Brock
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Judith A. Westman
- Ohio State University Medical Center, Columbus, OH 43210, USA; (H.H.); (J.J.); (K.S.); (R.P.); (R.P.); (K.S.); (P.B.); (J.A.W.)
| | - Lindsay Kipnis
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Jilliane Sotelo
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Anu Chittenden
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Samantha Culver
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Jill E. Stopfer
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Katherine A. Schneider
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Rosalba Sacca
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Diane R. Koeller
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Shraddha Gaonkar
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Erica Vaccari
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Sarah Kane
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (L.K.); (J.S.); (A.C.); (S.C.); (J.E.S.); (K.A.S.); (R.S.); (D.R.K.); (S.G.); (E.V.); (S.K.)
| | - Scott T. Michalski
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
| | - Shan Yang
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
| | - Sarah M. Nielsen
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
| | - Sara L. Bristow
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
| | - Stephen E. Lincoln
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
| | - Robert L. Nussbaum
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
| | - Edward D. Esplin
- Invitae, San Francisco, CA 94103, USA; (S.T.M.); (S.Y.); (S.M.N.); (S.L.B.); (S.E.L.); (R.L.N.)
- Correspondence: ; Tel.: +1-800-436-3037
| |
Collapse
|
48
|
Wang J, Wang Y, Jiang Y, Li X, Xiao X, Li S, Jia X, Sun W, Wang P, Zhang Q. Autosomal Dominant Retinitis Pigmentosa-Associated TOPORS Protein Truncating Variants Are Exclusively Located in the Region of Amino Acid Residues 807 to 867. Invest Ophthalmol Vis Sci 2022; 63:19. [PMID: 35579903 PMCID: PMC9123486 DOI: 10.1167/iovs.63.5.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Heterozygous truncating variants of TOPORS have been reported to cause autosomal dominant retinitis pigmentosa (adRP). The purpose of this study was to investigate whether all heterozygous truncating variants, including copy number variants (CNVs), are pathogenic. Methods TOPORS truncating variants were collected and reviewed through an in-house dataset and existing databases. Individuals with truncating variants underwent ophthalmological evaluation. Results Six truncating variants were detected in seven families. Three N-terminus truncating variants were detected in three families without RP, and the other three were identified in four unrelated families with typical RP. Based on the in-house dataset and published literature, 17 truncating variants were identified in 47 families with RP. All RP-associated truncating alleles, except one, were distributed in the last exon of TOPORS and clustered in amino acid residues 807 to 867 (46/47, 97.9%). Conversely, in the gnomAD database, only one truncating allele (1/27, 3.7%) was in this region, and the others were outside (26/27, 96.3%), suggesting that the pathogenic truncating variants were significantly clustered in residues 807 to 867 (χ2 = 65.6, P = 1.1 × 10–17). Additionally, three CNVs involving the N-terminus of TOPORS were recorded in control populations but were absent in affected patients. Conclusions This study suggests that all pathogenic truncating variants of TOPORS were clustered in residues 807 to 867, whereas the truncating variants outside this region and the CNVs involving the N-terminus were not associated with RP. A dominant-negative effect, rather than haploinsufficiency, is speculated to be the underlying pathogenesis. These findings provide valuable information for interpreting variation in TOPORS and other genes in similar situations, especially for CNVs.
Collapse
Affiliation(s)
- Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yingwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xueqing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| |
Collapse
|
49
|
Hannah WB, Seifert BA, Truty R, Zariwala MA, Ameel K, Zhao Y, Nykamp K, Gaston B. The global prevalence and ethnic heterogeneity of primary ciliary dyskinesia gene variants: a genetic database analysis. Lancet Respir Med 2022; 10:459-468. [PMID: 35051411 PMCID: PMC9064931 DOI: 10.1016/s2213-2600(21)00453-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 01/02/2023]
Abstract
BACKGROUND Primary ciliary dyskinesia (PCD) is a motile ciliopathy characterised by otosinopulmonary infections. Inheritance is commonly autosomal recessive, with extensive locus and allelic heterogeneity. The prevalence is uncertain. Most genetic studies have been done in North America or Europe. The aim of the study was to estimate the worldwide prevalence and ethnic heterogeneity of PCD. METHODS We calculated the allele frequency of disease-causing variants in 29 PCD genes associated with autosomal recessive inheritance in 182 681 unique individuals to estimate the global prevalence of PCD in seven ethnicities (African or African American, Latino, Ashkenazi Jewish, Finnish, non-Finnish European, east Asian, and south Asian). We began by aggregating variants that had been interpreted by Invitae, San Francisco, CA, USA, a genetics laboratory with PCD expertise. We then determined the allele frequency of each variant (pathogenic, likely pathogenic, or variant of uncertain significance [VUS]) in the Genome Aggregation Database (gnomAD), a publicly available next-generation sequencing database that aggregates exome and genome sequencing information from a wide variety of large-scale projects and stratifies allele counts by ethnicity. Using the Hardy-Weinberg equilibrium equation, we were able to calculate a lower-end prevalence of PCD for each ethnicity by including only pathogenic and likely pathogenic variants; and upper-end prevalence by also including VUS. This approach was similar to previous work on Li-Fraumeni (TP53 variants) prevalence. We were not diagnosing PCD, but rather estimating prevalence based on known variants. FINDINGS The overall minimum global prevalence of PCD is calculated to be at least one in 7554 individuals, although this is likely to be an underestimate because some variants currently classified as VUS might be disease-causing and some pathogenic variants might not be detected by our methods. In the overall cohort, Invitae data could be included for variants without gnomAD data for a primary ethnicity. When using only gnomAD allele frequencies to calculate prevalence in individual ethnicities, the estimated prevalence of PCD was lower in each ethnicity compared with the overall cohort. This is because the overall cohort includes additional data from the Invitae database such as copy number variants and other variants not present in gnomAD. With gnomAD we found the expected PCD frequency to be higher in individuals of African ancestry than in most other populations (excluding VUS: 1 in 9906 in African or African American vs 1 in 10 388 in non-Finnish European vs 1 in 14 606 in east Asian vs 1 in 16 309 in Latino; including VUS: 1 in 106 in African or African American vs 1 in 178 in non-Finnish European vs 1 in 196 in Latino vs 1 in 188 in east Asian). In addition, we found that the top 5 genes most commonly implicated in PCD differed across ethnic ancestries and contrasted commonly published findings. INTERPRETATION PCD appears to be more common than has been recognised, particularly in individuals of African ancestry. We identified gene distributions that differ from those in previous European and North American studies. These results could have an international impact on case identification. Our analytic approach can be expanded as more PCD loci are identified, and could be adapted to study the prevalence of other inherited diseases. FUNDING None.
Collapse
Affiliation(s)
- William B Hannah
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Bryce A Seifert
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | | | - Maimoona A Zariwala
- Department of Pathology and Laboratory Medicine, Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Kristen Ameel
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Yi Zhao
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Benjamin Gaston
- Herman Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.
| |
Collapse
|
50
|
Affiliation(s)
- Katalin Komlósi
- Institute of Human Genetics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Attila Gyenesei
- Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentagothai Research Center, University of Pécs, Pécs, Hungary
| | - Judit Bene
- Department of Medical Genetics, Clinical Centre, Medical School, University of Pécs, Pécs, Hungary
| |
Collapse
|