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Points to consider in the detection of germline structural variants using next-generation sequencing: A statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100316. [PMID: 36507974 DOI: 10.1016/j.gim.2022.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
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Qu N, Li W, Han DM, Gao JY, Yang ZT, Jiang L, Liu TB, Chen YX, Jiang XS, Zhou L, Wu JH, Huang X. Mutation spectrum in a cohort with familial exudative vitreoretinopathy. Mol Genet Genomic Med 2022; 10:e2021. [PMID: 35876299 PMCID: PMC9482396 DOI: 10.1002/mgg3.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/06/2021] [Accepted: 07/08/2022] [Indexed: 11/11/2022] Open
Abstract
Purpose To expand the mutation spectrum of patients with familial exudative vitreoretinopathy (FEVR) disease. Participants 74 probands (53 families and 21 sporadic probands) with familial exudative vitreoretinopathy (FEVR) disease and their available family members (n = 188) were recruited for sequencing. Methods Panel‐based targeted screening was performed on all subjects. Before sanger sequencing, variants of LRP5, NDP, FZD4, TSPAN12, ZNF408, KIF11, RCBTB1, JAG1, and CTNNA1 genes were verified by a series of bioinformatics tools and genotype–phenotype co‐segregation analysis. Results 40.54% (30/74) of the probands were sighted to possess at least one etiological mutation of the nine FEVR‐causative genes. The etiological mutation detection rate was 37.74% (20/53) in family‐attainable probands while 47.62% (10/21) in sporadic cases. The diagnosis rate of patients in the early‐onset subgroup (≤5 years old, 45.4%) is higher than that of the children or adolescence‐onset subgroup (6–16 years old, 42.1%) and the late‐onset subgroup (≥17 years old, 39.4%). A total of 36 etiological mutations were identified in this study, comprising 26 novel mutations and 10 reported mutations. LRP5 was the most prevalent mutant gene among the 36 mutation types with a percentage of 41.67% (15/36). Followed by FZD4 (10/36, 27.78%), TSPAN12 (5/36, 13.89%), NDP (4/36, 11.11%), KIF11 (1/36, 2.78%), and RCBTB1 (1/36, 2.78%). Among these mutations, 63.89% (23/36) were missense mutations, 25.00% (9/36) were frameshift mutations, 5.56% (2/36) were splicing mutations, 5.56% (2/36) were nonsense mutations. Moreover, the clinical pathogenicity of these variants was defined according to American College of Medical Genetics (ACMG) and genomics guidelines: 41.67% (15/36) were likely pathogenic variants, 27.78% (10/36) pathogenic variants, 30.55% (11/36) variants of uncertain significance. No etiological mutations discovered in the ZNF408, JAG1, and CTNNA1 genes in this FEVR cohort. Conclusions We systematically screened nine FEVR disease‐associated genes in a cohort of 74 Chinese probands with FEVR disease. With a detection rate of 40.54%, 36 etiological mutations of six genes were authenticated in 30 probands, including 26 novel mutations and 10 reported mutations. The most prevalent mutated gene is LRP5, followed by FZD4, TSPAN12, NDP, KIF11, and RCBTB1. In total, a de novo mutation was confirmed. Our study significantly clarified the mutation spectrum of variants bounded up to FEVR disease.
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Affiliation(s)
- Ning Qu
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, The Center of Reproductive Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Wei Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Dong-Ming Han
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jia-Yu Gao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Tao Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Li Jiang
- Department of Ophthalmology, Laizhou City People's Hospital, Yantai, China
| | - Tian-Bin Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan-Xian Chen
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, The Center of Reproductive Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xiao-Sen Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang Zhou
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, The Center of Reproductive Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Ji-Hong Wu
- Department of Ophthalmology, Eye & ENT Hospital of Fudan University, Shanghai, China
| | - Xin Huang
- Department of Ophthalmology, Eye & ENT Hospital of Fudan University, Shanghai, China
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Ding Y, Chen J, Tang Y, Chen LN, Yao RE, Yu T, Yin Y, Wang X, Wang J, Li N. Identification and functional analysis of novel SOX11 variants in Chinese patients with Coffin-Siris syndrome 9. Front Genet 2022; 13:940776. [PMID: 35938035 PMCID: PMC9354949 DOI: 10.3389/fgene.2022.940776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
SOX11 is a transcription factor belonging to the sex determining region Y-related high-mobility group box family that plays a vital role in early embryogenesis and neurogenesis. De novo variants in SOX11 have been initially reported to cause a rare neurodevelopmental disorder, mainly referred to Coffin-siris syndrome 9 (CSS9, OMIM# 615866) which is characterized with growth deficiency, intellectual disability (ID), microcephaly, coarse facies, and hypoplastic nails of the fifth fingers and/or toes. A recent large-scale cohort study suggests that SOX11 variation would result in a clinically and molecularly distinct disease from CSS. Here, we describe three unrelated Chinese cases with variable phenotype, mainly involving developmental delay, ID, short statute, microcephaly, facial deformities (i.e., prominent forehead, arched eye brow, flat nasal bridge, broad nose and short philtrum), and cryptorchidism. Whole-exome sequencing (WES) revealed three novel heterozygous variants in the SOX11 gene, including two missense variants of c.337T>C (p.Y113H) and c.425C>G (p.A142G), and one nonsense variant of c.820A>T (p. K142*). Luciferase reporting assay shows that the two missense variants impair the transcriptional activity of the SOX11 target gene GDF5. Additionally, WES uncovered a 4,300 kb deletion involving the region of 1q24.2-q25.1 (hg19,chr1:169,433,149-173,827,682) in patient 1, which also contributes to the condition of the patient. In summary, this is the first report of Chinese cases with de novo variants of SOX11. Our study partially supports the previous observation that the phenotype caused by SOX11 variants somewhat differs from classical CSS.
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Affiliation(s)
- Yu Ding
- Department of Endocrinology and Metabolism, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiande Chen
- Department of Respiratory Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yijun Tang
- Department of Endocrinology and Metabolism, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-Na Chen
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ru-En Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China
- Shanghai Clinical Research Center for Rare Pediatric Diseases, Shanghai, China
| | - Tingting Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China
- Shanghai Clinical Research Center for Rare Pediatric Diseases, Shanghai, China
| | - Yong Yin
- Department of Respiratory Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiumin Wang
- Department of Endocrinology and Metabolism, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China
- Shanghai Clinical Research Center for Rare Pediatric Diseases, Shanghai, China
- *Correspondence: Niu Li, ; Jian Wang,
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China
- Shanghai Clinical Research Center for Rare Pediatric Diseases, Shanghai, China
- *Correspondence: Niu Li, ; Jian Wang,
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Park J, Yhim HY, Kang KP, Bae TW, Cho YG. Copy number variation analysis using next-generation sequencing identifies the CFHR3/ CFHR1 deletion in atypical hemolytic uremic syndrome: a case report. Hematology 2022; 27:603-608. [PMID: 35617302 DOI: 10.1080/16078454.2022.2075121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES Atypical hemolytic uremic syndrome (aHUS) is characterized by a triad of thrombocytopenia, microangiopathic hemolytic anemia, and acute renal failure resulting from platelet thrombi in the microcirculation of the kidney and other organs, in the absence of a preceding diarrheal illness. This report describes a case in which copy number variation (CNV) analysis using next-generation sequencing (NGS) identified the CFHR3/CFHR1 deletion in a patient with aHUS. METHODS A 49-year-old Korean female was diagnosed with aHUS based on clinical findings, including schistocytes in peripheral blood and marked thrombocytopenia, suggesting the presence of thrombotic microangiopathy, elevated serum lactate dehydrogenase, and acute kidney injury. Sequence variants and CNV generated from NGS data were estimated to determine if there was a potential genetic cause. Multiplex ligation-dependent probe amplification (MLPA) was conducted to confirm the CFHR3/CFHR1 deletion identified by NGS with CNV analysis. RESULTS No known or novel pathogenic single nucleotide variant or small insertion/deletion that would be predicted to have damaging effects that could lead to aHUS were identified. However, CNV analysis of NGS data identified the heterozygous CFHR3/CFHR1 deletion. MLPA confirmed this loss of one copy number between the CFHR3 and the CFHR1 genes on chromosome 1q31.3. CONCLUSION We genetically diagnosed a Korean woman harboring a heterozygous CFHR3/CFHR1 deletion of a known causative gene for aHUS. Our report emphasizes the need for CNV analysis of NGS data and gene dosage assays, such as MLPA, to evaluate large-scale deletions or duplications and generate hybrid CFH genes in patients with suspected aHUS.
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Affiliation(s)
- Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Korea.,Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Ho-Young Yhim
- Department of Internal Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Korea.,Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Kyung Pyo Kang
- Department of Internal Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Korea.,Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Tae Won Bae
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Korea.,Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Yong Gon Cho
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Korea.,Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
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Shi Y, Wang A, Chen B, Wang X, Niu S, Li W, Li S, Zhang Z. Clinical Features and Genetic Spectrum of Patients With Clinically Suspected Hereditary Progressive Spastic Paraplegia. Front Neurol 2022; 13:872927. [PMID: 35572931 PMCID: PMC9097539 DOI: 10.3389/fneur.2022.872927] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/28/2022] [Indexed: 12/27/2022] Open
Abstract
Background and Purpose A variety of hereditary diseases overlap with neurological phenotypes or even share genes with hereditary spastic paraplegia (HSP). The aim of this study was to determine the clinical features and genetic spectrum of patients with clinically suspected HSPs. Methods A total of 52 patients with clinically suspected HSPs were enrolled in this study. All the patients underwent next-generation sequencing (NGS) and triplet repeat primed PCR to screen for the dynamic mutations typical of spinocerebellar ataxia (SCA). Multiplex ligation-dependent probe amplification (MLPA) was further conducted in patients with no causative genetic mutations detected to examine for large deletions and duplications in genes of SPAST, ATL1, REEP1, PGN, and SPG11. Clinical characteristics and findings of brain MRI were analyzed in patients with definite diagnoses. Results The mean age of the patients studied was 36.90 ± 14.57 years. 75% (39/52) of patients manifested a phenotype of complex form of HSPs. A genetic diagnosis was made in 51.9% (27/52) of patients, of whom 40.3% (21/52) of patients had mutations in HSPs genes (SPG4/SPG6/SPG8/SPG11/SPG15/SPG78/SPG5A) and 11.5% (6/52) of patients had mutations in SCAs genes (SCA3/SCA17/SCA28). SPG4 and SPG11 were the most common cause of pure form of HSPs (5/6, 83.3%) and complex form of HSPs (5/15, 33.3%), respectively. Gait disturbance was the most common initial symptom in both the patients with HSPs (15/21) and in patients with SCAs (5/6). Dysarthria and cerebellar ataxia were detected in 28.5% (6/21) and 23.8% (5/21) of patients with HSPs, respectively, and were the most common symptoms in addition to progressive weakness and spasticity of the lower limbs. Cerebellar atrophy was seen on the brain MRI of patients with SPG5A, SCA3, and SCA28. Conclusion Causative genetic mutations were identified in 51.9% of patients with clinically suspected HSPs by NGS and triplet repeat primed PCR. A final diagnosis of HSPs or SCAs was made in 40.3% and 11.5% of patients, respectively. The clinical manifestations and neuroimaging findings overlapped between patients with HSPs and patients with SCAs. Dynamic mutations should be screened in patients with clinically suspected HSPs, especially in those with phenotypes of complex form of HSPs.
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Affiliation(s)
- Yuzhi Shi
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - An Wang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Bin Chen
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xingao Wang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Songtao Niu
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wei Li
- China National Clinical Research Center for Neurological Diseases, Beijing, China.,Monogenic Disease Research Center for Neurological Disorders & Precision Medicine Research Center for Neurological Disorders, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shaowu Li
- Department of Functional Neuroimaging, Beijing Neurosurgical Institute, Beijing, China
| | - Zaiqiang Zhang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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Agaoglu NB, Unal B, Akgun Dogan O, Zolfagharian P, Shairfli P, Karakurt A, Can Senay B, Kizilboga T, Yildiz J, Dinler Doganay G, Doganay L. Determining the Accuracy of Next Generation Sequencing Based Copy Number Variation Analysis in Hereditary Breast and Ovarian Cancer. Expert Rev Mol Diagn 2022; 22:239-246. [PMID: 35240897 DOI: 10.1080/14737159.2022.2048373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Copy number variations (CNVs) are commonly associated with malignancies, including hereditary breast and ovarian cancers. Next generation sequencing (NGS) provides solutions for CNV detection in a single run. This study aimed to compare the accuracy of CNV detection by NGS analysing tool against Multiplex Ligation Dependent Probe Amplification (MLPA). RESEARCH DESIGN AND METHODS In total, 1276 cases were studied by targeted NGS panels and 691 cases (61 calls in 58 NGS-CNV positive and 633 NGS-CNV negative cases) were validated by MLPA. RESULTS Twenty-eight (46%) NGS-CNV positive calls were consistent, whereas 33 (54%) calls showed discordance with MLPA. Two cases were detected as SNV by the NGS and CNV by the MLPA analysis. In total, 2% of the cases showed an MLPA confirmed CNV region in BRCA1/2. The results of this study showed that despite the high false positive call rate of the NGS-CNV algorithm, there were no false negative calls. The cases that were determined to be negative by the NGS and positive by the MLPA were actually carrying SNVs that were located on the MLPA probe binding sites. CONCLUSION The diagnostic performance of NGS-CNV analysis is promising; however, the need for confirmation by different methods remains.
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Affiliation(s)
- Nihat Bugra Agaoglu
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Medical Genetics, Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Busra Unal
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Ozlem Akgun Dogan
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Pediatric Genetics, Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Payam Zolfagharian
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Pari Shairfli
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Aylin Karakurt
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Burak Can Senay
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Tugba Kizilboga
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Jale Yildiz
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Gizem Dinler Doganay
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Levent Doganay
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
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Mei H, Yang L, Xiao T, Wang S, Wu B, Wang H, Lu Y, Dong X, Yang H, Zhou W. Genetic Spectrum Identified by Exome Sequencing in a Chinese Pediatric Cerebral Palsy Cohort. J Pediatr 2022; 242:206-212.e6. [PMID: 34788679 DOI: 10.1016/j.jpeds.2021.11.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To explore the genetic spectrum of cerebral palsy (CP) in a Chinese pediatric cohort. STUDY DESIGN This was a retrospective observational study of patients with CP from the Children's Hospital of Fudan University between June 2015 and December 2019. Their clinical data and exome sequencing data were collected and analyzed. RESULTS A total of 217 patients with CP were enrolled, and genetic variants were identified in 78 subjects (35.9%): 65 patients with single-nucleotide variants (SNVs), 12 patients with copy number variants, and 1 patient with both an SNV and a copy number variant. The genetic diagnosis rates were significantly greater in patients without clinical risk factors than in patients with clinical risk factors (χ2 = 21.705, P = .000) and were significantly greater in patients with a family history than in those without a family history (χ2 = 4.493, P = .034). Variants in genes related to neurologic disorders were the most commonly detected variants, affecting 41 patients (62.1%, 41/66). Among the patients with SNVs detected, the top 12 genes were found to cover 62.1% (41/66) of cases, and 39.4% (26/66) of patients with SNVs had medically actionable genetic findings. CONCLUSIONS The overall genetic diagnostic rate in this study was 35.9%, and patients without any clinical risk factors or with a family history were more likely to have genetic risk factors. The top 12 genes detected in this study as well as genes related to neurologic disorders or other medically actionable disorders should be noted in the analysis of genetic testing results in patients with CP.
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Affiliation(s)
- Hongfang Mei
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Lin Yang
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Tiantian Xiao
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Sujuan Wang
- Department of Rehabilitation, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huijun Wang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yulan Lu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xinran Dong
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Hong Yang
- Department of Rehabilitation, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wenhao Zhou
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
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Abstract
PURPOSE OF REVIEW Liquid biopsies have emerged as a noninvasive alternative to tissue biopsy with potential applications during all stages of pediatric oncology care. The purpose of this review is to provide a survey of pediatric cell-free DNA (cfDNA) studies, illustrate their potential applications in pediatric oncology, and to discuss technological challenges and approaches to overcome these hurdles. RECENT FINDINGS Recent literature has demonstrated liquid biopsies' ability to inform treatment selection at diagnosis, monitor clonal evolution during treatment, sensitively detect minimum residual disease following local control, and provide sensitive posttherapy surveillance. Advantages include reduced procedural anesthesia, molecular profiling unbiased by tissue heterogeneity, and ability to track clonal evolution. Challenges to wider implementation in pediatric oncology, however, include blood volume restrictions and relatively low mutational burden in childhood cancers. Multiomic approaches address challenges presented by low-mutational burden, and novel bioinformatic analyses allow a single assay to yield increasing amounts of information, reducing blood volume requirements. SUMMARY Liquid biopsies hold tremendous promise in pediatric oncology, enabling noninvasive serial surveillance with adaptive care. Already integrated into adult care, recent advances in technologies and bioinformatics have improved applicability to the pediatric cancer landscape.
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Affiliation(s)
- R Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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De Palma FDE, Nunziato M, D’Argenio V, Savarese M, Esposito G, Salvatore F. Comprehensive Molecular Analysis of DMD Gene Increases the Diagnostic Value of Dystrophinopathies: A Pilot Study in a Southern Italy Cohort of Patients. Diagnostics (Basel) 2021; 11:diagnostics11101910. [PMID: 34679607 PMCID: PMC8534830 DOI: 10.3390/diagnostics11101910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022] Open
Abstract
Duchenne/Becker muscular dystrophy (DMD/BMD) is an X-linked neuromuscular disease due to pathogenic sequence variations in the dystrophin (DMD) gene, one of the largest human genes. More than 70% of DMD gene defects result from genomic rearrangements principally leading to large deletions, while the remaining are small nucleotide variants, including nonsense and missense variants, small insertions/deletions or splicing alterations. Considering the large size of the gene and the wide mutational spectrum, the comprehensive molecular diagnosis of DMD/BMD is complex and may require several laboratory methods, thus increasing the time and costs of the analysis. In an attempt to simplify DMD/BMD molecular diagnosis workflow, we tested an NGS method suitable for the detection of all the different types of genomic variations that may affect the DMD gene. Forty previously analyzed patients were enrolled in this study and re-analyzed using the next generation sequencing (NGS)-based single-step procedure. The NGS results were compared with those from multiplex ligation-dependent probe amplification (MLPA)/multiplex PCR and/or Sanger sequencing. Most of the previously identified deleted/duplicated exons and point mutations were confirmed by NGS and 1 more pathogenic point mutation (a nonsense variant) was identified. Our results show that this NGS-based strategy overcomes limitations of traditionally used methods and is easily transferable to routine diagnostic procedures, thereby increasing the diagnostic power of DMD molecular analysis.
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Affiliation(s)
- Fatima Domenica Elisa De Palma
- CEINGE-Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy; (F.D.E.D.P.); (M.N.); (V.D.); (M.S.)
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Marcella Nunziato
- CEINGE-Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy; (F.D.E.D.P.); (M.N.); (V.D.); (M.S.)
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Valeria D’Argenio
- CEINGE-Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy; (F.D.E.D.P.); (M.N.); (V.D.); (M.S.)
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Via di Val Cannuta 247, 00166 Roma, Italy
| | - Maria Savarese
- CEINGE-Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy; (F.D.E.D.P.); (M.N.); (V.D.); (M.S.)
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Gabriella Esposito
- CEINGE-Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy; (F.D.E.D.P.); (M.N.); (V.D.); (M.S.)
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
- Correspondence: (G.E.); (F.S.); Tel.: +81-746-3146 (G.E.); +81-373-7826 (F.S.)
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy; (F.D.E.D.P.); (M.N.); (V.D.); (M.S.)
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
- Correspondence: (G.E.); (F.S.); Tel.: +81-746-3146 (G.E.); +81-373-7826 (F.S.)
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10
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Lo Faro V, Ten Brink JB, Snieder H, Jansonius NM, Bergen AA. Genome-wide CNV investigation suggests a role for cadherin, Wnt, and p53 pathways in primary open-angle glaucoma. BMC Genomics 2021; 22:590. [PMID: 34348663 PMCID: PMC8336345 DOI: 10.1186/s12864-021-07846-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/18/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND To investigate whether copy number variations (CNVs) are implicated in molecular mechanisms underlying primary open-angle glaucoma (POAG), we used genotype data of POAG individuals and healthy controls from two case-control studies, AGS (n = 278) and GLGS-UGLI (n = 1292). PennCNV, QuantiSNP, and cnvPartition programs were used to detect CNV. Stringent quality controls at both sample and marker levels were applied. The identified CNVs were intersected in CNV region (CNVR). After, we performed burden analysis, CNV-genome-wide association analysis, gene set overrepresentation and pathway analysis. In addition, in human eye tissues we assessed the expression of the genes lying within significant CNVRs. RESULTS We reported a statistically significant greater burden of CNVs in POAG cases compared to controls (p-value = 0,007). In common between the two cohorts, CNV-association analysis identified statistically significant CNVRs associated with POAG that span 11 genes (APC, BRCA2, COL3A1, HLA-DRB1, HLA-DRB5, HLA-DRB6, MFSD8, NIPBL, SCN1A, SDHB, and ZDHHC11). Functional annotation and pathway analysis suggested the involvement of cadherin, Wnt signalling, and p53 pathways. CONCLUSIONS Our data suggest that CNVs may have a role in the susceptibility of POAG and they can reveal more information on the mechanism behind this disease. Additional genetic and functional studies are warranted to ascertain the contribution of CNVs in POAG.
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Affiliation(s)
- Valeria Lo Faro
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands
| | - Jacoline B Ten Brink
- Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nomdo M Jansonius
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arthur A Bergen
- Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands. .,Department of Ophthalmology, Amsterdam UMC, Location AMC, Amsterdam, The Netherlands. .,Netherlands Institute for Neuroscience (NIN-KNAW), Amsterdam, The Netherlands.
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11
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Boev AS, Rakitko AS, Usmanov SR, Kobzeva AN, Popov IV, Ilinsky VV, Kiktenko EO, Fedorov AK. Genome assembly using quantum and quantum-inspired annealing. Sci Rep 2021; 11:13183. [PMID: 34162895 PMCID: PMC8222255 DOI: 10.1038/s41598-021-88321-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 04/09/2021] [Indexed: 02/05/2023] Open
Abstract
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for de novo genome assembly, which is used for the analysis of genomic rearrangements, chromosome phasing, and reconstructing genomes without a reference, require solving tasks of high computational complexity. Here we demonstrate a method for solving genome assembly tasks with the use of quantum and quantum-inspired optimization techniques. Within this method, we present experimental results on genome assembly using quantum annealers both for simulated data and the [Formula: see text]X 174 bacteriophage. Our results pave a way for a significant increase in the efficiency of solving bioinformatics problems with the use of quantum computing technologies and, in particular, quantum annealing might be an effective method. We expect that the new generation of quantum annealing devices would outperform existing techniques for de novo genome assembly. To the best of our knowledge, this is the first experimental study of de novo genome assembly problems both for real and synthetic data on quantum annealing devices and quantum-inspired techniques.
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Affiliation(s)
- A S Boev
- Russian Quantum Center, Skolkovo, Moscow, 143025, Russia
| | | | - S R Usmanov
- Russian Quantum Center, Skolkovo, Moscow, 143025, Russia
| | - A N Kobzeva
- Russian Quantum Center, Skolkovo, Moscow, 143025, Russia
| | - I V Popov
- Genotek ltd., Moscow, 105120, Russia
| | | | - E O Kiktenko
- Russian Quantum Center, Skolkovo, Moscow, 143025, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - A K Fedorov
- Russian Quantum Center, Skolkovo, Moscow, 143025, Russia.
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia.
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12
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Next Generation Cytogenetics in Myeloid Hematological Neoplasms: Detection of CNVs and Translocations. Cancers (Basel) 2021; 13:cancers13123001. [PMID: 34203905 PMCID: PMC8232573 DOI: 10.3390/cancers13123001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/07/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Conventional cytogenetic approaches are the gold standard for the identification of chromosomal alterations in myeloid neoplasms. Next-generation sequencing panels are a new approach for the detection of copy number variations (CNV) or translocations. Here we report on a commercial panel utility including frequent mutations, CNVs and translocations in myeloid neoplasms. A total of 135 patients with myeloid neoplasms and three with acute lymphoblastic leukemia were analyzed by NGS. When comparing with gold standard techniques, 48 frequent alterations were detected by both methodologies, ten of them observed only by conventional methods and another eight only by NGS. Additionally, 38 secondary CNVs were detected in any of the genes included in the panel for mutational analysis. With those results we determine that NGS represents a reliable complementary source of information for the analysis of CNVs and translocations. Abstract Conventional cytogenetics are the gold standard for the identification of chromosomal alterations recurrent in myeloid neoplasms. Some next-generation sequencing (NGS) panels are designed for the detection of copy number variations (CNV) or translocations; however, their use is far from being widespread. Here we report on the results of a commercial panel including frequent mutations, CNVs and translocations in myeloid neoplasms. Frequent chromosomal alterations were analyzed by NGS in 135 patients with myeloid neoplasms and three with acute lymphoblastic leukemia. NGS analysis was performed using the enrichment-capture Myeloid Neoplasm-GeneSGKit (Sistemas Genómicos, Spain) gene panel including 35 genes for mutational analysis and frequent CNVs and translocations. NGS results were validated with cytogenetics and/or MLPA when possible. A total of 66 frequent alterations included in NGS panel were detected, 48 of them detected by NGS and cytogenetics. Ten of them were observed only by cytogenetics (mainly trisomy 8), and another eight only by NGS (mainly deletion of 12p). Aside from this, 38 secondary CNVs were detected in any of the genes included mainly for mutational analysis. NGS represents a reliable complementary source of information for the analysis of CNVs and translocations. Moreover, NGS could be a useful tool for the detection of alterations not observed by conventional cytogenetics.
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13
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Huang H, Cai M, Ma W, Lin N, Xu L. Chromosomal Microarray Analysis for the Prenatal Diagnosis in Fetuses with Nasal Bone Hypoplasia: A Retrospective Cohort Study. Risk Manag Healthc Policy 2021; 14:1533-1540. [PMID: 33889037 PMCID: PMC8054820 DOI: 10.2147/rmhp.s286038] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/27/2021] [Indexed: 01/03/2023] Open
Abstract
Background Previous studies have shown a strong correlation between fetal nasal bone hypoplasia and chromosomal anomaly; however, there is little knowledge on the associations of fetal nasal bone hypoplasia with chromosomal microdeletions and microduplications until now. Chromosomal microarray analysis (CMA) is a high-resolution molecular genetic tool that is effective to detect submicroscopic anomalies including chromosomal microdeletions and microduplications that cannot be detected by karyotyping. This study aimed to examine the performance of CMA for the prenatal diagnosis of nasal bone hypoplasia in the second and third trimesters. Subjects and Methods A total of 84 pregnant women in the second and third trimesters with fetal nasal bone hypoplasia, as revealed by ultrasound examinations, were enrolled, and all women underwent karyotyping and CMA with the Affymetrix CytoScan 750K GeneChip Platform. The subjects included 32 cases with fetal nasal bone hypoplasia alone and 52 cases with fetal nasal bone hypoplasia combined with other ultrasound abnormalities, and the prevalence of genomic abnormality was compared between these two groups. Results Karyotyping detected 21 cases of chromosomal anomaly in the 84 study subjects (21/84, 25%), including trisomy 21 (14 cases), trisomy 18 (3 cases), 46, del (4)(p16) karyotype (2 cases), 47, XYY syndrome (1 case) and 46, XY, del (5) (p15) karyotype (1 case). CMA detected additional four fetuses with pathogenic copy number variations (CNVs) and six fetuses with uncertain clinical significance (VOUS). No significant difference was detected in the prevalence of genomic abnormality in fetuses with nasal bone hypoplasia alone and in combination with other ultrasound abnormalities (13/32 vs 18/52; χ2 = 0.31, P > 0.05). The pregnancy was terminated in 21 fetuses detected with chromosomal abnormality and 4 fetuses detected with pathogenic CNVs. Among the other six fetuses detected with VOUS, the parents chose to continue the pregnancy, and the newborns all had normal clinical phenotypes. Conclusion In addition to chromosomal abnormalities identified in 21 fetuses by karyotyping, CMA detected additional 10 fetuses with abnormal CNVs (10/84, 11.9%) in the study population. CMA is a promising powerful tool for prenatal diagnosis that may provide valuable data for the accurate assessment of fetal prognosis and the decision of pregnancy continuation during the prenatal clinical counseling.
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Affiliation(s)
- Hailong Huang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
| | - Meiying Cai
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
| | - Wei Ma
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China.,School of Clinical Medicine, Fujian Medical University, Fuzhou City, Fujian Province, 350122, People's Republic of China
| | - Na Lin
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
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14
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Hagio K, Amano T, Hayashi H, Takeshita T, Oshino T, Kikuchi J, Ohhara Y, Yabe I, Kinoshita I, Nishihara H, Yamashita H. Impact of clinical targeted sequencing on endocrine responsiveness in estrogen receptor-positive, HER2-negative metastatic breast cancer. Sci Rep 2021; 11:8109. [PMID: 33854152 PMCID: PMC8047009 DOI: 10.1038/s41598-021-87645-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/01/2021] [Indexed: 01/22/2023] Open
Abstract
Clinical targeted sequencing allows for the selection of patients expected to have a better treatment response, and reveals mechanisms of resistance to molecular targeted therapies based on actionable gene mutations. We underwent comprehensive genomic testing with either our original in-house CLHURC system or with OncoPrime. Samples from 24 patients with estrogen receptor-positive, human epidermal growth factor receptor 2-negative metastatic breast cancer underwent targeted sequencing between 2016 and 2018. Germline and somatic gene alterations and patients' prognosis were retrospectively analyzed according to the response to endocrine therapy. All of the patients had one or more germline and/or somatic gene alterations. Four patients with primary or secondary endocrine-resistant breast cancer harbored germline pathogenic variants of BRCA1, BRCA2, or PTEN. Among somatic gene alterations, TP53, PIK3CA, AKT1, ESR1, and MYC were the most frequently mutated genes. TP53 gene mutation was more frequently observed in patients with primary endocrine resistance compared to those with secondary endocrine resistance or endocrine-responsive breast cancer. Recurrent breast cancer patients carrying TP53-mutant tumors had significantly worse overall survival compared to those with TP53-wild type tumors. Our 160-gene cancer panel will be useful to identify clinically actionable gene alterations in breast cancer in clinical practice.
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Affiliation(s)
- Kanako Hagio
- Department of Breast Surgery, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, 060-8648, Japan
| | - Toraji Amano
- Clinical Research and Medical Innovation Center, Hokkaido University Hospital, Sapporo, Japan
| | - Hideyuki Hayashi
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjukuku, Tokyo, 160-8582, Japan
| | - Takashi Takeshita
- Department of Breast Surgery, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, 060-8648, Japan
| | - Tomohiro Oshino
- Department of Breast Surgery, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, 060-8648, Japan
| | - Junko Kikuchi
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
| | - Yoshihito Ohhara
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
| | - Ichiro Yabe
- Division of Clinical Genetics, Hokkaido University Hospital, Sapporo, Japan
| | - Ichiro Kinoshita
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
| | - Hiroshi Nishihara
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjukuku, Tokyo, 160-8582, Japan
| | - Hiroko Yamashita
- Department of Breast Surgery, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, 060-8648, Japan.
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15
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Sanger sequencing is no longer always necessary based on a single-center validation of 1109 NGS variants in 825 clinical exomes. Sci Rep 2021; 11:5697. [PMID: 33707547 PMCID: PMC7952542 DOI: 10.1038/s41598-021-85182-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/22/2021] [Indexed: 01/20/2023] Open
Abstract
Despite the improved accuracy of next-generation sequencing (NGS), it is widely accepted that variants need to be validated using Sanger sequencing before reporting. Validation of all NGS variants considerably increases the turnaround time and costs of clinical diagnosis. We comprehensively assessed this need in 1109 variants from 825 clinical exomes, the largest sample set to date assessed using Illumina chemistry reported. With a concordance of 100%, we conclude that Sanger sequencing can be very useful as an internal quality control, but not so much as a verification method for high-quality single-nucleotide and small insertion/deletions variants. Laboratories might validate and establish their own thresholds before discontinuing Sanger confirmation studies. We also expand and validate 23 copy number variations detected by exome sequencing in 20 samples, observing a concordance of 95.65% (22/23).
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16
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Qi Q, Jiang Y, Zhou X, Meng H, Hao N, Chang J, Bai J, Wang C, Wang M, Guo J, Ouyang Y, Xu Z, Xiao M, Zhang VW, Liu J. Simultaneous Detection of CNVs and SNVs Improves the Diagnostic Yield of Fetuses with Ultrasound Anomalies and Normal Karyotypes. Genes (Basel) 2020; 11:genes11121397. [PMID: 33255631 PMCID: PMC7759943 DOI: 10.3390/genes11121397] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/09/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022] Open
Abstract
The routine assessment to determine the genetic etiology for fetal ultrasound anomalies follows a sequential approach, which usually takes about 6–8 weeks turnaround time (TAT). We evaluated the clinical utility of simultaneous detection of copy number variations (CNVs) and single nucleotide variants (SNVs)/small insertion-deletions (indels) in fetuses with a normal karyotype with ultrasound anomalies. We performed CNV detection by chromosomal microarray analysis (CMA) or low pass CNV-sequencing (CNV-seq), and in parallel SNVs/indels detection by trio-based clinical exome sequencing (CES) or whole exome sequencing (WES). Eight-three singleton pregnancies with a normal fetal karyotype were enrolled in this prospective observational study. Pathogenic or likely pathogenic variations were identified in 30 cases (CNVs in 3 cases, SNVs/indels in 27 cases), indicating an overall molecular diagnostic rate of 36.1% (30/83). Two cases had both a CNV of uncertain significance (VOUS) and likely pathogenic SNV, and one case carried both a VOUS CNV and an SNV. We demonstrated that simultaneous analysis of CNVs and SNVs/indels can improve the diagnostic yield of prenatal diagnosis with shortened reporting time, namely, 2–3 weeks. Due to the relatively long TAT for sequential procedure for prenatal genetic diagnosis, as well as recent sequencing technology advancements, it is clinically necessary to consider the simultaneous evaluation of CNVs and SNVs/indels to enhance the diagnostic yield and timely TAT, especially for cases in the late second trimester or third trimester.
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Affiliation(s)
- Qingwei Qi
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
- Correspondence: ; Tel.: +86-1851-066-6066
| | - Yulin Jiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
| | - Xiya Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
| | - Hua Meng
- Department of Ultrasound, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (H.M.); (Y.O.); (Z.X.); (M.X.)
| | - Na Hao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
| | - Jiazhen Chang
- Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China;
| | - Junjie Bai
- Be Creative Lab Co., Ltd. Beijing 101111, China; (J.B.); (M.W.); (J.G.)
| | - Chunli Wang
- AmCare Genomics Lab, Guangzhou 510335, China; (C.W.); (V.W.Z.)
| | - Mingming Wang
- Be Creative Lab Co., Ltd. Beijing 101111, China; (J.B.); (M.W.); (J.G.)
| | - Jiangshan Guo
- Be Creative Lab Co., Ltd. Beijing 101111, China; (J.B.); (M.W.); (J.G.)
| | - Yunshu Ouyang
- Department of Ultrasound, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (H.M.); (Y.O.); (Z.X.); (M.X.)
| | - Zhonghui Xu
- Department of Ultrasound, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (H.M.); (Y.O.); (Z.X.); (M.X.)
| | - Mengsu Xiao
- Department of Ultrasound, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (H.M.); (Y.O.); (Z.X.); (M.X.)
| | | | - Juntao Liu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
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17
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Moreno-Cabrera JM, Del Valle J, Feliubadaló L, Pineda M, González S, Campos O, Cuesta R, Brunet J, Serra E, Capellà G, Gel B, Lázaro C. Screening of CNVs using NGS data improves mutation detection yield and decreases costs in genetic testing for hereditary cancer. J Med Genet 2020; 59:75-78. [PMID: 33219106 DOI: 10.1136/jmedgenet-2020-107366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Germline CNVs are important contributors to hereditary cancer. In genetic diagnostics, multiplex ligation-dependent probe amplification (MLPA) is commonly used to identify them. However, MLPA is time-consuming and expensive if applied to many genes, hence many routine laboratories test only a subset of genes of interest. METHODS AND RESULTS We evaluated a next-generation sequencing (NGS)-based CNV detection tool (DECoN) as first-tier screening to decrease costs and turnaround time and expand CNV analysis to all genes of clinical interest in our diagnostics routine. We used DECoN in a retrospective cohort of 1860 patients where a limited number of genes were previously analysed by MLPA, and in a prospective cohort of 2041 patients, without MLPA analysis. In the retrospective cohort, 6 new CNVs were identified and confirmed by MLPA. In the prospective cohort, 19 CNVs were identified and confirmed by MLPA, 8 of these would have been lost in our previous MLPA-restricted detection strategy. Also, the number of genes tested by MLPA across all samples decreased by 93.0% in the prospective cohort. CONCLUSION Including an in silico germline NGS CNV detection tool improved our genetic diagnostics strategy in hereditary cancer, both increasing the number of CNVs detected and reducing turnaround time and costs.
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Affiliation(s)
- José Marcos Moreno-Cabrera
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL-ONCOBELL, L'Hospitalet de Llobregat, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.,Hereditary Cancer Group, Program for Predictive and Personalized Medicine of Cancer - Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, Badalona, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL-ONCOBELL, L'Hospitalet de Llobregat, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL-ONCOBELL, L'Hospitalet de Llobregat, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL-ONCOBELL, L'Hospitalet de Llobregat, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Sara González
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL-ONCOBELL, L'Hospitalet de Llobregat, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Olga Campos
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL-ONCOBELL, L'Hospitalet de Llobregat, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Raquel Cuesta
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL-ONCOBELL, L'Hospitalet de Llobregat, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL-ONCOBELL, L'Hospitalet de Llobregat, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, IDIBGi, Girona, Spain
| | - Eduard Serra
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.,Hereditary Cancer Group, Program for Predictive and Personalized Medicine of Cancer - Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, Badalona, Spain
| | - Gabriel Capellà
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL-ONCOBELL, L'Hospitalet de Llobregat, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Bernat Gel
- Hereditary Cancer Group, Program for Predictive and Personalized Medicine of Cancer - Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, Badalona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL-ONCOBELL, L'Hospitalet de Llobregat, Spain .,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
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18
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Sun S, Chen L, Wang Y, Wang J, Li N, Wang X. Further delineation of autosomal recessive intellectual disability syndrome caused by homozygous variant of the NSUN2 gene in a chinese pedigree. Mol Genet Genomic Med 2020; 8:e1518. [PMID: 33002343 PMCID: PMC7767538 DOI: 10.1002/mgg3.1518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/03/2020] [Accepted: 09/17/2020] [Indexed: 11/06/2022] Open
Abstract
Background The enzyme NOP2/Sun RNA methyltransferase 2 (NSUN2) catalyzes the methylation of cytosine to 5‐methylcytosine (m5C) at position 34 of tRNA(Leu; CAA) precursors containing introns that play a vital role in spindle assembly during mitosis and chromosome segregation. Biallelic variants in the NSUN2 gene cause a rare intellectual disability that has been identified only in a few Middle Eastern patients. Affected individuals usually have other deformities, including developmental delay, short stature, microcephaly, and facial dysmorphism. The aim of this study was to identify the genetic cause of three female patients from a Chinese pedigree, who presented with similar phenotype consisting of the above clinical features. Methods Whole‐exome sequencing (WES) was used to screen for causal variants in the genome, and the candidate variants were subsequently verified using Sanger sequencing. Results WES revealed a previously unreported homozygous nonsense variant (NM_017755.5: c.1004T>A, p.Leu335*) in exon 9 of NSUN2, which was consistent with the clinical phenotype of the patients and co‐segregated with the disease in their family. A comparison of this phenotype with that of patients in published reports uncovered several novel clinical features related to NSUN2 variations, including feeding difficulties, slender hands and fingers, severely restricted finger mobility, hallux valgus, varus foot, and elevated α‐hydroxybutyrate dehydrogenase (HBDH). Conclusions These are the first findings of a non‐consanguineous Chinese pedigree with a homozygous NSUN2 variant. We expanded the phenotypic spectrum associated with NSUN2 variations.
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Affiliation(s)
| | - Lin Chen
- Department of Pediatric, Guizhou Provincial People's Hospital, Guizhou University, Guiyang, China
| | - Yuchuan Wang
- Department of Pediatric, Guizhou Provincial People's Hospital, Guizhou University, Guiyang, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xike Wang
- Department of Pediatric, Guizhou Provincial People's Hospital, Guizhou University, Guiyang, China
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Mai K, Chen X, Wang C, Wu S, Yang L, Huang Z, Zhang G, Zhang VW, Wang J, Chen D. B-lymphocyte deficiency and recurrent respiratory infections in a 6-month-old female infant with mosaic monosomy 7. Immunobiology 2020; 225:152005. [PMID: 32962823 DOI: 10.1016/j.imbio.2020.152005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/24/2020] [Accepted: 08/11/2020] [Indexed: 10/23/2022]
Abstract
Monosomy 7 is generally considered as an acquired cytogenetic abnormality within hematopoietic cells, and indicates an especially high risk of progression to bone marrow failure, myelodysplastic syndrome (MDS) or juvenile myelomonocytic leukemia (JMML). We report a case of a 6-month-old female infant with mosaic monosomy 7 who presented with clinical and laboratory evidences of immunodeficiency. The patient had suffered from recurrent respiratory infections since she was born. Peripheral blood lymphocyte subsets revealed an extremely low level of CD19+ B lymphocytes (0.3∼0.8%, normal range: 6.4∼22.6%) and a decreased CD4/CD8 ratio (0.67∼1.12, normal range: 1.4∼2.0). Decreased serum levels of IgG (1.53 g/L, normal range: 4.09∼7.03 g/L), IgA (0.10 g/L, normal range: 0.21∼0.47 g/L) and IgM (0.26 g/L, normal range: 0.33∼0.73 g/L) were detected, while complements were normal. Excepting transient neutropenia, routine blood tests were within normal limits. Clinical exome sequencing identified a de novo mosaic monosomy 7, while no pathogenic mutation associated with immunodeficiency was detected. However, peripheral blood cytogenetic analysis was failure to detect monosomy 7 due to the very few cell mitosis. Subsequent fluorescence in situ hybridization (FISH) identified a mosaic monosomy 7 in 58 cells within a total number of 100 cells, which was consistent with clinical exome sequencing. Therefore, the patient was diagnosed with primary immunodeficiency disease (PID) due to mosaic monosomy 7. Intravenous treatment with multiple antibiotic agents and infusion of gamma globulin could control the patient's respiratory infections effectively. A better understanding of PIDs will enable effective treatments and prevention of infections in these patients.
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Affiliation(s)
- Kailin Mai
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaowen Chen
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chunli Wang
- AmCare Genomics Lab (V.W.Z.), Guangzhou, China
| | - Shangzhi Wu
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Liying Yang
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhanhang Huang
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | - Victor Wei Zhang
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, USA
| | - Jing Wang
- AmCare Genomics Lab (V.W.Z.), Guangzhou, China
| | - Dehui Chen
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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20
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Yang L. A Practical Guide for Structural Variation Detection in the Human Genome. CURRENT PROTOCOLS IN HUMAN GENETICS 2020; 107:e103. [PMID: 32813322 PMCID: PMC7738216 DOI: 10.1002/cphg.103] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Profiling genetic variants-including single nucleotide variants, small insertions and deletions, copy number variations, and structural variations (SVs)-from both healthy individuals and individuals with disease is a key component of genetic and biomedical research. SVs are large-scale changes in the genome and involve breakage and rejoining of DNA fragments. They may affect thousands to millions of nucleotides and can lead to loss, gain, and reshuffling of genes and regulatory elements. SVs are known to impact gene expression and potentially result in altered phenotypes and diseases. Therefore, identifying SVs from the human genomes is particularly important. In this review, I describe advantages and disadvantages of the available high-throughput assays for the discovery of SVs, which are the most challenging genetic alterations to detect. A practical guide is offered to suggest the most suitable strategies for discovering different types of SVs including common germline, rare, somatic, and complex variants. I also discuss factors to be considered, such as cost and performance, for different strategies when designing experiments. Last, I present several approaches to identify potential SV artifacts caused by samples, experimental procedures, and computational analysis. © 2020 Wiley Periodicals LLC.
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Affiliation(s)
- Lixing Yang
- Ben May Department for Cancer Research, Department of Human Genetics, University of Chicago, Chicago, Illinois
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21
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EMQN best practice guidelines for genetic testing in dystrophinopathies. Eur J Hum Genet 2020; 28:1141-1159. [PMID: 32424326 PMCID: PMC7608854 DOI: 10.1038/s41431-020-0643-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/03/2020] [Accepted: 04/28/2020] [Indexed: 02/04/2023] Open
Abstract
Dystrophinopathies are X-linked diseases, including Duchenne muscular dystrophy and Becker muscular dystrophy, due to DMD gene variants. In recent years, the application of new genetic technologies and the availability of new personalised drugs have influenced diagnostic genetic testing for dystrophinopathies. Therefore, these European best practice guidelines for genetic testing in dystrophinopathies have been produced to update previous guidelines published in 2010.These guidelines summarise current recommended technologies and methodologies for analysis of the DMD gene, including testing for deletions and duplications of one or more exons, small variant detection and RNA analysis. Genetic testing strategies for diagnosis, carrier testing and prenatal diagnosis (including non-invasive prenatal diagnosis) are then outlined. Guidelines for sequence variant annotation and interpretation are provided, followed by recommendations for reporting results of all categories of testing. Finally, atypical findings (such as non-contiguous deletions and dual DMD variants), implications for personalised medicine and clinical trials and incidental findings (identification of DMD gene variants in patients where a clinical diagnosis of dystrophinopathy has not been considered or suspected) are discussed.
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22
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Ceylan AC, Erdem HB, Şahin İ, Agarwal M. SMN1 gene copy number analysis for spinal muscular atrophy (SMA) in a Turkish cohort by CODE-SEQ technology, an integrated solution for detection of SMN1 and SMN2 copy numbers and the "2+0" genotype. Neurol Sci 2020; 41:2575-2584. [PMID: 32249332 DOI: 10.1007/s10072-020-04365-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/20/2020] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Spinal muscular atrophy (SMA) is one of the common autosomal recessive disorders with global heterozygous carrier frequency of 1:50. Due to high carrier frequency, significant morbidity associated with the infantile onset disease and prohibitive cost of recently approved therapy, American College of Medical Genetics and Genomics (ACMG) recommends population based screening for SMA carrier status in eligible individuals in the reproductive age group. CODE-SEQ is a novel proprietary next generation sequencing (NGS) based assay, which is capable of detecting homozygous as well as heterozygous SMN1 exon 7 deletions. Along with the copy number estimation, this assay is capable of detecting single nucleotide polymorphisms (SNPs) associated with silent SMA carrier status or "2+0" genotype. METHODS We have validated a proprietary CODE-SEQ technology in a blinded cohort of 80 clinically well characterized samples from Turkish population for the detection of SMA carriers as well as affected cases. The results were correlated with gold standard MLPA assay. RESULTS The copy numbers in exon 7 of SMN1 gene matched with MLPA results in all 80 samples giving 100% correlation. The assay accurately detected the presence/ absence of SNPs associated with "2+0" genotype in the reference samples. None of the tested clinical samples had these SNPs. CONCLUSION The results of this study support the notion that CODE-SEQ will be extremely useful in detecting SMA genotypes in large-scale population-based screening studies.
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Affiliation(s)
| | - Haktan Bağış Erdem
- Department of Medical Genetics, Ankara Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - İbrahim Şahin
- Department of Medical Genetics, Ankara Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - Meenal Agarwal
- Department of Medical Genetics, GenePath Diagnostics India Private Ltd, Medical Genetics, 1260/B, JM road, Pune, 411004, India.
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23
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Xu L, Zhang M, Huang H, Wang Y, Chen L, Chen M, Wang J, Chen C, Li B, Li Z. The Comprehensive Comparison of Bacterial Artificial Chromosomes (BACs)-on-Beads Assay and Copy Number Variation Sequencing in Prenatal Diagnosis of Southern Chinese Women. J Mol Diagn 2020; 22:1324-1332. [PMID: 32858251 DOI: 10.1016/j.jmoldx.2020.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 07/15/2020] [Accepted: 07/28/2020] [Indexed: 11/30/2022] Open
Abstract
Bacterial artificial chromosomes (BACs)-on-Beads (BoBs) assay and copy number variation sequencing (CNV-seq) are two frequently used methods in today's prenatal diagnosis. Several studies were conducted to investigate the performance of each approach, but they were never compared side by side. In this article, a comprehensive comparison of BoBs and CNV-seq was conducted using 1876 amniotic fluid and umbilical cord blood samples collected from Fujian Maternity and Child Health Hospital between 2015 and 2019. Karyotyping was used as the gold standard for chromosome structure variation, and chromosomal microarray analysis was performed to validate inconsistent results. Overall, 174 cases of confirmed chromosome anomalies were detected, including 73 chromosomal aneuploidies, 10 mosaics, 30 pathogenic CNVs, and 61 other structural anomalies. BoBs and CNV-seq achieved a 100% concordance in all 55 pathogenic euchromosome aneuploidies, but CNV-seq had a higher detection rate in sex chromosome aneuploidy and mosaic identification. For CNV detection, all of the 20 pathogenic CNVs discovered by the BoBs assay also were identified by CNV-seq and 10 additional pathogenic CNVs were observed by CNV-seq. The results of this study showed that CNV-seq was a reliable and more favorable method in terms of detection rate, costs, and disease range. In combination with karyotyping, CNV-seq could improve the efficiency and accuracy of a prenatal diagnosis to alleviate maternal emotional anxiety and deduce birth defects.
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Affiliation(s)
- LiangPu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China.
| | - Min Zhang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China
| | - HaiLong Huang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China
| | - Yan Wang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China
| | - LingJi Chen
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China
| | - MeiHuan Chen
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China
| | - Juan Wang
- Annoroad Gene Technology (Beijing) Co., Ltd., Beijing, China
| | - Chen Chen
- Zhejiang Annoroad Biotechnology Co., Ltd., Zhejiang, China
| | - Bo Li
- Annoroad Life Sciences Research Institute, Zhejiang, China
| | - ZhiMin Li
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China; Annoroad Gene Technology (Beijing) Co., Ltd., Beijing, China.
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24
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AlShibli A, Mathkour H. Fuzzy methods for the detection of copy number variations in comparative genomic hybridization arrays. Saudi J Biol Sci 2020; 27:3647-3654. [PMID: 33304176 PMCID: PMC7714972 DOI: 10.1016/j.sjbs.2020.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 11/19/2022] Open
Abstract
Genomic copy number variations (CNVs) are considered as a significant source of genetic diversity and widely involved in gene expression and regulatory mechanism, genetic disorders and disease risk, susceptibility to certain diseases and conditions, and resistance to medical drugs. Many studies have targeted the identification, profiling, analysis, and associations of genetic CNVs. We propose herein two new fuzzy methods, taht is, one based on the fuzzy inference from the pre-processed input, and another based on fuzzy C-means clustering. Our solutions present a higher true positive rate and a lower false negative with no false positive, efficient performance and consumption of least resources.
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Affiliation(s)
- Ahmad AlShibli
- Department of computer science, College of computer and information sciences, King Saud University, Riyadh, Saudi Arabia
- Corresponding author at: P.O. Box 230734, Riyadh, Saudi Arabia.
| | - Hassan Mathkour
- Department of computer science, College of computer and information sciences, King Saud University, Riyadh, Saudi Arabia
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25
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Ding Y, Li N, Lou D, Zhang Q, Chang G, Li J, Li X, Li Q, Huang X, Wang J, Jiang F, Wang X. Clinical and genetic analysis in a Chinese cohort of children and adolescents with diabetes/persistent hyperglycemia. J Diabetes Investig 2020; 12:48-62. [PMID: 32531870 PMCID: PMC7779271 DOI: 10.1111/jdi.13322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 12/11/2022] Open
Abstract
Aims/Introduction To investigate the genetic etiology and evaluate the diagnostic application of next‐generation sequencing for diabetes/persistent hyperglycemia in children and adolescents. Materials and Methods Patients with diabetes/persistent hyperglycemia, presenting with at least one other clinical manifestation (other than diabetes) or with a family history of diabetes, were recruited. The clinical and laboratory characteristics of the patients were recorded. Next‐generation sequencing was carried out, and candidate variants were verified by Sanger sequencing. Variant pathogenicity was further evaluated according to the American College of Medical Genetics and Genomics guidelines. Results This study included 101 potential probands, 36 of whom were identified as positive by genetic testing. A further 51.2 and 20.9% of variants were determined to be pathogenic or likely pathogenic, respectively. Variants associated with the disease were primarily identified in 21 genes and three regions of copy number variants. Among the 39 variants in 21 genes, 61.5% (24/39) were novel. The genetic diagnosis of 23 patients was confirmed based on genetic evidence and associated clinical manifestations. We reported GCK variants (21.7%, 5/23) as the most common etiology in our cohort. Different clinical manifestations were observed in one family with WFS1 variants. Conclusions Our findings support the use of next‐generation sequencing as a standard method in patients with diabetes/persistent hyperglycemia and provide insights into the etiologies of these conditions.
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Affiliation(s)
- Yu Ding
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dan Lou
- Department of Pediatrics, the First Affiliated Hospital of Henan University of Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Qianwen Zhang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Guoying Chang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Juan Li
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xin Li
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qun Li
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaodong Huang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Fan Jiang
- Department of Developmental and Behavioral Pediatrics, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiumin Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Xie B, Fan X, Lei Y, Yi S, Yang Q, Wang J, Qin Z, Shen F, Luo J, Shen Y. Novel compound heterozygous variant of BSCL2 identified by whole exome sequencing and multiplex ligation‑dependent probe amplification in an infant with congenital generalized lipodystrophy. Mol Med Rep 2020; 21:2296-2302. [PMID: 32236581 PMCID: PMC7185175 DOI: 10.3892/mmr.2020.11036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/06/2020] [Indexed: 11/29/2022] Open
Abstract
Congenital generalized lipodystrophy (CGL) is a clinically and genetically heterogeneous condition with autosomal recessive inheritance. CGL is classified into four subtypes on the basis of causative genes. This study reported on a 2-month-old male infant diagnosed with CGL with generalized lipoatrophy and skin hyperpigmentation. Whole exome sequencing (WES) identified a heterozygous small insertion (c.545_546insCCG) in Berardinelli-Seip congenital lipodystrophy 2 (BSCL2) that was inherited from the infant's mother. Copy number variation analysis using exome data suggested a heterozygous deletion involving exon 3 that was inherited from the infant's father. This finding was confirmed by multiplex ligation-dependent probe amplification test. Gap-PCR revealed breakpoints and confirmed a 1274 bp heterozygous deletion encompassing exon 3 of BSCL2 (c.213-1081_c.294+111). This deletion is different from the founder 3.3 kb deletion involving exon 3 of BSCL2 in the Peruvian population. An 11-bp microhomology at the breakpoints may mediate the deletion, and its presence indicates the independent origins of the exon 3 deletion between Chinese and Peruvian populations. The present results expanded the mutational spectrum of the BSCL2 gene in the Chinese population and suggested that introns 2 and 3 of BSCL2 are prone to recombination. Thus, exon 3 deletion should be considered for patients with CGL2 when only one BSCL2 variant is detected through WES.
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Affiliation(s)
- Bobo Xie
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, Guangxi 530023, P.R. China
| | - Xin Fan
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, Guangxi 530023, P.R. China
| | - Yaqin Lei
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, Guangxi 530023, P.R. China
| | - Shang Yi
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, Guangxi 530023, P.R. China
| | - Qi Yang
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, Guangxi 530023, P.R. China
| | - Jin Wang
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, Guangxi 530023, P.R. China
| | - Zailong Qin
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, Guangxi 530023, P.R. China
| | - Fei Shen
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, Guangxi 530023, P.R. China
| | - Jingsi Luo
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, Guangxi 530023, P.R. China
| | - Yiping Shen
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, Guangxi 530023, P.R. China
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Thuriot F, Gravel E, Buote C, Doyon M, Lapointe E, Marcoux L, Larue S, Nadeau A, Chénier S, Waters PJ, Jacques PÉ, Gravel S, Lévesque S. Molecular diagnosis of muscular diseases in outpatient clinics: A Canadian perspective. NEUROLOGY-GENETICS 2020; 6:e408. [PMID: 32337335 PMCID: PMC7164974 DOI: 10.1212/nxg.0000000000000408] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/24/2020] [Indexed: 12/18/2022]
Abstract
Objective To evaluate the diagnostic yield of an 89-gene panel in a large cohort of patients with suspected muscle disorders and to compare the diagnostic yield of gene panel and exome sequencing approaches. Methods We tested 1,236 patients from outpatient clinics across Canada using a gene panel and performed exome sequencing for 46 other patients with sequential analysis of 89 genes followed by all mendelian genes. Sequencing and analysis were performed in patients with muscle weakness or symptoms suggestive of a muscle disorder and showing at least 1 supporting clinical laboratory. Results We identified a molecular diagnosis in 187 (15.1%) of the 1,236 patients tested with the 89-gene panel. Diagnoses were distributed across 40 different genes, but 6 (DMD, RYR1, CAPN3, PYGM, DYSF, and FKRP) explained about half of all cases. Cardiac anomalies, positive family history, age <60 years, and creatine kinase >1,000 IU/L were all associated with increased diagnostic yield. Exome sequencing identified a diagnosis in 10 (21.7%) of the 46 patients tested. Among these, 3 were attributed to genes not included in the 89-gene panel. Despite differences in median coverage, only 1 of the 187 diagnoses that were identified on gene panel in the 1,236 patients could have been potentially missed if exome sequencing had been performed instead. Conclusions Our study supports the use of gene panel testing in patients with suspected muscle disorders from outpatient clinics. It also shows that exome sequencing has a low risk of missing diagnoses compared with gene panel, while potentially increasing the diagnostic yield of patients with muscle disorders.
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Affiliation(s)
- Fanny Thuriot
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Elaine Gravel
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Caroline Buote
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Marianne Doyon
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Elvy Lapointe
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Lydia Marcoux
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Sandrine Larue
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Amélie Nadeau
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Sébastien Chénier
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Paula J Waters
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Pierre-Étienne Jacques
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Serge Gravel
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Sébastien Lévesque
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
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Stavber L, Hovnik T, Kotnik P, Lovrečić L, Kovač J, Tesovnik T, Bertok S, Dovč K, Debeljak M, Battelino T, Avbelj Stefanija M. High frequency of pathogenic ACAN variants including an intragenic deletion in selected individuals with short stature. Eur J Endocrinol 2020; 182:243-253. [PMID: 31841439 PMCID: PMC7087498 DOI: 10.1530/eje-19-0771] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/13/2019] [Indexed: 12/30/2022]
Abstract
CONTEXT Defining the underlying etiology of idiopathic short stature (ISS) improves the overall management of an individual. OBJECTIVE To assess the frequency of pathogenic ACAN variants in selected individuals. DESIGN The single-center cohort study was conducted at a tertiary university children's hospital. From 51 unrelated patients with ISS, the 16 probands aged between 3 and 18 years (12 females) with advanced bone age and/or autosomal dominant inheritance pattern of short stature were selected for the study. Fifteen family members of ACAN-positive probands were included. Exome sequencing was performed in all probands, and additional copy number variation (CNV) detection was applied in selected probands with a distinct ACAN-associated phenotype. RESULTS Systematic phenotyping of the study cohort yielded 37.5% (6/16) ACAN-positive probands, with all novel pathogenic variants, including a 6.082 kb large intragenic deletion, detected by array comparative genomic hybridization (array CGH) and exome data analysis. All variants were co-segregated with short stature phenotype, except in one family member with the intragenic deletion who had an unexpected growth pattern within the normal range (-0.5 SDS). One patient presented with otosclerosis, a sign not previously associated with aggrecanopathy. CONCLUSIONS ACAN pathogenic variants presented a common cause of familial ISS. The selection criteria used in our study were suggested for a personalized approach to genetic testing of the ACAN gene in clinical practice. Our results expanded the number of pathogenic ACAN variants, including the first intragenic deletion, and suggested CNV evaluation in patients with typical clinical features of aggrecanopathy as reasonable. Intra-familial phenotypic variability in growth patterns should be considered.
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Affiliation(s)
- L Stavber
- Unit for Special Laboratory Diagnostics, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - T Hovnik
- Unit for Special Laboratory Diagnostics, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - P Kotnik
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - L Lovrečić
- Clinical Institute of Medical Genetics, University Medical Centre, Ljubljana, Slovenia
| | - J Kovač
- Unit for Special Laboratory Diagnostics, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - T Tesovnik
- Unit for Special Laboratory Diagnostics, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - S Bertok
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - K Dovč
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - M Debeljak
- Unit for Special Laboratory Diagnostics, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - T Battelino
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - M Avbelj Stefanija
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
- Correspondence should be addressed to M Avbelj Stefanija;
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Diagnostic gene sequencing panels: from design to report-a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2019; 22:453-461. [PMID: 31732716 DOI: 10.1038/s41436-019-0666-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 12/20/2022] Open
Abstract
Gene sequencing panels are a powerful diagnostic tool for many clinical presentations associated with genetic disorders. Advances in DNA sequencing technology have made gene panels more economical, flexible, and efficient. Because the genes included on gene panels vary widely between laboratories in gene content (e.g., number, reason for inclusion, evidence level for gene-disease association) and technical completeness (e.g., depth of coverage), standards that address technical and clinical aspects of gene panels are needed. This document serves as a technical standard for laboratories designing, offering, and reporting gene panel testing. Although these principles can apply to multiple indications for genetic testing, the primary focus is on diagnostic gene panels (as opposed to carrier screening or predictive testing) with emphasis on technical considerations for the specific genes being tested. This technical standard specifically addresses the impact of gene panel content on clinical sensitivity, specificity, and validity-in the context of gene evidence for contribution to and strength of evidence for gene-disease association-as well as technical considerations such as sequencing limitations, presence of pseudogenes/gene families, mosaicism, transcript choice, detection of copy-number variants, reporting, and disclosure of assay limitations.
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30
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Jourdain A, Petit F, Odou M, Balduyck M, Brunelle P, Dufour W, Boussion S, Brischoux‐Boucher E, Colson C, Dieux A, Gérard M, Ghoumid J, Giuliano F, Goldenberg A, Khau Van Kien P, Lehalle D, Morin G, Moutton S, Smol T, Vanlerberghe C, Manouvrier‐Hanu S, Escande F. Multiplex targeted high‐throughput sequencing in a series of 352 patients with congenital limb malformations. Hum Mutat 2019; 41:222-239. [DOI: 10.1002/humu.23912] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/31/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Anne‐Sophie Jourdain
- Service de Biochimie et Biologie MoléculaireCHU LilleLille France
- EA7364 RADEMEUniv. LilleLille France
| | - Florence Petit
- EA7364 RADEMEUniv. LilleLille France
- Clinique de Génétique Guy FontaineCHU LilleLille France
| | - Marie‐Françoise Odou
- Service de Biochimie et Biologie MoléculaireCHU LilleLille France
- Faculty of Pharmacy, UMR995, LIRIC (Lille Inflammation Research International Center)University of LilleLille France
| | - Malika Balduyck
- Service de Biochimie et Biologie MoléculaireCHU LilleLille France
- EA7364 RADEMEUniv. LilleLille France
| | - Perrine Brunelle
- Service de Biochimie et Biologie MoléculaireCHU LilleLille France
- Clinique de Génétique Guy FontaineCHU LilleLille France
| | | | | | | | | | - Anne Dieux
- Clinique de Génétique Guy FontaineCHU LilleLille France
| | | | - Jamal Ghoumid
- EA7364 RADEMEUniv. LilleLille France
- Clinique de Génétique Guy FontaineCHU LilleLille France
| | | | | | | | - Daphné Lehalle
- Reference Center for Developmental Anomalies, Department of Medical GeneticsDijon University HospitalDijon France
| | - Gilles Morin
- Centre d'activité de Génétique et d'OncogénétiqueCHU Amiens PicardieAmiens France
| | - Sébastien Moutton
- Reference Center for Developmental Anomalies, Department of Medical GeneticsDijon University HospitalDijon France
| | - Thomas Smol
- EA7364 RADEMEUniv. LilleLille France
- Institut de Génétique MédicaleCHU LilleLille France
| | - Clémence Vanlerberghe
- EA7364 RADEMEUniv. LilleLille France
- Clinique de Génétique Guy FontaineCHU LilleLille France
| | - Sylvie Manouvrier‐Hanu
- EA7364 RADEMEUniv. LilleLille France
- Clinique de Génétique Guy FontaineCHU LilleLille France
| | - Fabienne Escande
- Service de Biochimie et Biologie MoléculaireCHU LilleLille France
- EA7364 RADEMEUniv. LilleLille France
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31
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Ansar Z, Nasir A, Moatter T, Khan S, Kirmani S, Ibrahim S, Imam K, Ather A, Samreen A, Hasan Z. MLPA Analyses Reveal a Spectrum of Dystrophin Gene Deletions/Duplications in Pakistani Patients Suspected of Having Duchenne/Becker Muscular Dystrophy: A Retrospective Study. Genet Test Mol Biomarkers 2019; 23:468-472. [DOI: 10.1089/gtmb.2018.0262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Zeeshan Ansar
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Asghar Nasir
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Tariq Moatter
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Sara Khan
- Department of Pediatrics & Child Health, Aga Khan University, Karachi, Pakistan
| | - Salman Kirmani
- Department of Pediatrics & Child Health, Aga Khan University, Karachi, Pakistan
| | - Shahnaz Ibrahim
- Department of Pediatrics & Child Health, Aga Khan University, Karachi, Pakistan
| | - Kahkashan Imam
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Anif Ather
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Azra Samreen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
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32
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Yao R, Yu T, Qing Y, Wang J, Shen Y. Evaluation of copy number variant detection from panel-based next-generation sequencing data. Mol Genet Genomic Med 2018; 7:e00513. [PMID: 30565893 PMCID: PMC6382442 DOI: 10.1002/mgg3.513] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/21/2018] [Accepted: 10/26/2018] [Indexed: 12/23/2022] Open
Abstract
Background Targeted gene capture and next‐generation sequencing (NGS) has been widely utilized as a robust and cost‐effective approach for detecting small variants among a group of disease genes. Copy number variations (CNV) can also be inferred from the read‐depth information but the accuracy of CNVs called from panel‐based NGS data has not been well evaluated. Methods Sequencing data were acquired from patients underwent routine clinical targeted panel sequencing testing. Pathogenic CNVs detected from targeted panel sequencing data were evaluated using CNVs generated by two clinical accepted platforms, namely chromosome microarray analysis (CMA) and multiple ligation‐dependent probe amplification (MLPA) as benchmarks. CNVkit was used in our study to call CNVs from sequencing data using read‐depth information. CMA and MLPA tests were used to confirm and further assess the size and breakpoints of CNVs. Results The size of CNVs detected using panel‐based NGS data are over 300 kb. The sizes of CNVs detected are slightly larger (102.3% on average) using the NGS platform than using the CMA platform, and the size accuracy improved as the size of variants increases. The breakpoints of CNVs detected using NGS data are quite close (within 2.3% of margin) to the breakpoints detected by CMA. CNVs on sex chromosomes, however, are less concordant between NGS and CMA platforms. Conclusion Copy number variations covering adequate exons on autosomes can be accurately detected using targeted panel sequencing data as using CMA. CNVs detected from sex chromosomes need further evaluation and validation. Except for exon‐level deletion/duplication and CNV on sex chromosome, our data support the use of panel‐based NGS data for routine clinical detection of pathogenic CNVs.
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Affiliation(s)
- Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute for Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Tingting Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute for Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yanrong Qing
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute for Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute for Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yiping Shen
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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