1
|
Ge L, Yang Y, Yang Y, Chen Y, Tao N, Zhang L, Zhao C, Zhang X. DMD mutations in pediatric patients with phenotypes of Duchenne/Becker muscular dystrophy. Open Med (Wars) 2024; 19:20240916. [PMID: 39588385 PMCID: PMC11587917 DOI: 10.1515/med-2024-0916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/26/2023] [Accepted: 02/05/2024] [Indexed: 11/27/2024] Open
Abstract
Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are common X-inherited neuromuscular diseases. The genetic diagnosis has been used as the diagnostic choice for DMD/BMD. The study subjects consisted of 37 patients from Southwest China. Peripheral blood was collected for the extraction of genomic DNA. DMD mutation was sequenced using the next-generation sequencing approach. The detected mutation was validated using the multiplex ligation-dependent probe amplification or Sanger sequencing methods. Variation annotation and pathogenicity prediction were performed using the online databases. Pathogenic mutations were identified 3 splicing site, 7 single nucleotide, 1 indel, 23 deletion, and 3 duplication mutations. Novel DMD variants were discovered, including two novel splicing variations (c.1890 + 1G>T; c.1923 + 1G>A), one missense mutation (c.1946G>T), one nonsense mutation (c.7441G>T), one indel mutation (INDEL EX20), and one duplication mutation (DUP EX75-78). The current study provides mutation information of DMD for the genetic diagnosis of DMD/BMD.
Collapse
Affiliation(s)
- Liping Ge
- Department of Endosecretory Genetic and Metabolic Diseases, Kunming Children’s Hospital, Kunming650000, China
| | - Yang Yang
- Department of Endosecretory Genetic and Metabolic Diseases, Kunming Children’s Hospital, Kunming650000, China
| | - Yanfei Yang
- The Special Wards, Kunming Children’s Hospital, Kunming650000, Yunnan Province, China
| | - Yanfei Chen
- Department of Cardiovascular Internal Medicine, Kunming Children’s Hospital, Yunnan Province, Kunming650000, China
| | - Na Tao
- Department of Endosecretory Genetic and Metabolic Diseases, Kunming Children’s Hospital, Kunming650000, China
| | - Liping Zhang
- Medical Department, Kunming Children’s Hospital, Kunming650000, China
| | - Canmiao Zhao
- Department of Endosecretory Genetic and Metabolic Diseases, Kunming Children’s Hospital, Kunming650000, China
| | - Xing Zhang
- Department of Cardiovascular Internal Medicine, Kunming Children’s Hospital, Yunnan Province, Kunming650000, China
| |
Collapse
|
2
|
Xie Z, Liu C, Yu H, Xie Z, Sun C, Zhu Y, Hu X, Bai L, Wei L, Sun P, Lu Y, Lu Y, Zhao Y, Zhang W, Wang Z, Meng L, Yuan Y. Clinical and genetic interpretation of uncertain DMD missense variants: evidence from mRNA and protein studies. Orphanet J Rare Dis 2024; 19:123. [PMID: 38486238 PMCID: PMC10941385 DOI: 10.1186/s13023-024-03128-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 03/03/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Pathogenic missense variants in the dystrophin (DMD) gene are rarely reported in dystrophinopathies. Most DMD missense variants are of uncertain significance and their pathogenicity interpretation remains complicated. We aimed to investigate whether DMD missense variants would cause aberrant splicing and re-interpret their pathogenicity based on mRNA and protein studies. METHODS Nine unrelated patients who had an elevated serum creatine kinase level with or without muscle weakness were enrolled. They underwent a detailed clinical, imaging, and pathological assessment. Routine genetic testing and muscle-derived mRNA and protein studies of dystrophin and sarcoglycan genes were performed in them. RESULTS Three of the 9 patients presented with a Duchenne muscular dystrophy (DMD) phenotype and the remaining 6 patients had a suspected diagnosis of Becker muscular dystrophy (BMD) or sarcoglycanopathy based on their clinical and pathological characteristics. Routine genetic testing detected only 9 predicted DMD missense variants in them, of which 6 were novel and interpreted as uncertain significance. Muscle-derived mRNA studies of sarcoglycan genes didn't reveal any aberrant transcripts in them. Dystrophin mRNA studies confirmed that 3 predicted DMD missense variants (c.2380G > C, c.4977C > G, and c.5444A > G) were in fact splicing and frameshift variants due to aberrant splicing. The 9 DMD variants were re-interpreted as pathogenic or likely pathogenic based on mRNA and protein studies. Therefore, 3 patients with DMD splicing variants and 6 patients with confirmed DMD missense variants were diagnosed with DMD and BMD, respectively. CONCLUSION Our study highlights the importance of muscle biopsy and aberrant splicing for clinical and genetic interpretation of uncertain DMD missense variants.
Collapse
Affiliation(s)
- Zhiying Xie
- Department of Neurology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Chang Liu
- Department of Neurology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Haiyan Yu
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, 100034, China
| | - Zhihao Xie
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Chengyue Sun
- Department of Neurology, Peking University People's Hospital, Beijing, 100044, China
| | - Ying Zhu
- Department of Radiology, Peking University First Hospital, Beijing, 100034, China
| | - Xiaoyu Hu
- Department of Radiology, Peking University First Hospital, Beijing, 100034, China
| | - Li Bai
- Department of Neurology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Luhua Wei
- Department of Neurology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Peng Sun
- Department of Neurology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Yanyu Lu
- Department of Neurology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Yunlong Lu
- Department of Neurology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Yawen Zhao
- Department of Neurology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Lingchao Meng
- Department of Neurology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, China.
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, China.
| |
Collapse
|
3
|
Ling C, Dai Y, Geng C, Pan S, Quan W, Ding Q, Yang X, Shen D, Tao Q, Li J, Li J, Wang Y, Jiang S, Wang Y, Chen L, Cui L, Wang D. Uncovering the true features of dystrophin gene rearrangement and improving the molecular diagnosis of Duchenne and Becker muscular dystrophies. iScience 2023; 26:108365. [PMID: 38047063 PMCID: PMC10690541 DOI: 10.1016/j.isci.2023.108365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/19/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023] Open
Abstract
Duchenne and Becker muscular dystrophies (DMD/BMD) are caused by complex mutations in the dystrophin gene (DMD). Currently, there is no integrative method for the precise detection of all potential DMD variants, a gap which we aimed to address using long-read sequencing. The captured long-read sequencing panel developed in this study was applied to 129 subjects, including 11 who had previously unsolved cases. The results showed that this method accurately detected DMD mutations, ranging from single-nucleotide variations to structural variations. Furthermore, our findings revealed that continuous exon duplication/deletion in the DMD/BMD cohort may be attributed to complex segmental rearrangements and that noncontiguous duplication/deletion is generally attributed to intragenic inversion or interchromosome translocation. Mutations in the deep introns were confirmed to produce a pseudoexon. Moreover, variations in female carriers were precisely identified. The integrated and precise DMD gene screening method proposed in this study could improve the molecular diagnosis of DMD/BMD.
Collapse
Affiliation(s)
- Chao Ling
- The Laboratory of Clinical Genetics, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Chang Geng
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Shirang Pan
- Grandomics Biosciences, Beijing 102200, China
| | | | - Qingyun Ding
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Xunzhe Yang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Dongchao Shen
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Qing Tao
- Grandomics Biosciences, Beijing 102200, China
| | - Jingjing Li
- Grandomics Biosciences, Beijing 102200, China
| | - Jia Li
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yinbing Wang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Shan Jiang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yang Wang
- Grandomics Biosciences, Beijing 102200, China
| | - Lin Chen
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Depeng Wang
- Grandomics Biosciences, Beijing 102200, China
| |
Collapse
|
4
|
Szűcs Z, Pinti É, Haltrich I, Szén OP, Nagy T, Barta E, Méhes G, Bidiga L, Török O, Ujfalusi A, Koczok K, Balogh I. An Ultra-Rare Manifestation of an X-Linked Recessive Disorder: Duchenne Muscular Dystrophy in a Female Patient. Int J Mol Sci 2022; 23:ijms232113076. [PMID: 36361862 PMCID: PMC9655586 DOI: 10.3390/ijms232113076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/30/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is the most common inherited muscle dystrophy. Patients are characterized by muscle weakness, gross motor delay, and elevated serum creatinine kinase (CK) levels. The disease is caused by mutations in the DMD gene located on the X chromosome. Due to the X-linked recessive inheritance pattern, DMD most commonly affects males, who are generally diagnosed between the age of 3–5 years. Here we present an ultra-rare manifestation of DMD in a female patient. Cytogenetic examination showed that she has a t(X;10)(p21.1;p12.1) translocation, which turned out to affect the DMD gene with one of the breakpoints located in exon 54 (detected by genome sequencing). The X-inactivation test revealed skewed X-inactivation (ratio 99:1). Muscle histology and dystrophin immunohistochemistry showed severe dystrophic changes and highly reduced dystrophin expression, respectively. These results, in accordance with the clinical picture and a highly elevated serum CK, led to the diagnosis of DMD. In conclusion, although in very rare cases, DMD can manifest in female patients as well. In this case, a balanced X-autosome reciprocal translocation disrupts the DMD gene and skewed X-inactivation leads to the manifestation of the DMD phenotype.
Collapse
Affiliation(s)
- Zsuzsanna Szűcs
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Éva Pinti
- 2nd Department of Pediatrics, Semmelweis University, 1094 Budapest, Hungary
| | - Irén Haltrich
- 2nd Department of Pediatrics, Semmelweis University, 1094 Budapest, Hungary
| | - Orsolya Pálné Szén
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Tibor Nagy
- Bioinformatics and Functional Genome Analysis Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Endre Barta
- Bioinformatics and Functional Genome Analysis Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Department of Genetics and Genomics, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - László Bidiga
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Olga Török
- Medical and Health Science Centre, Department of Obstetrics and Gynaecology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Anikó Ujfalusi
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Katalin Koczok
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (K.K.); (I.B.)
| | - István Balogh
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (K.K.); (I.B.)
| |
Collapse
|
5
|
Predominance of Dystrophinopathy Genotypes in Mexican Male Patients Presenting as Muscular Dystrophy with A Normal Multiplex Polymerase Chain Reaction DMD Gene Result: A Study Including Targeted Next-Generation Sequencing. Genes (Basel) 2019; 10:genes10110856. [PMID: 31671740 PMCID: PMC6895915 DOI: 10.3390/genes10110856] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 01/02/2023] Open
Abstract
The complete mutational spectrum of dystrophinopathies and limb-girdle muscular dystrophy (LGMD) remains unknown in Mexican population. Seventy-two unrelated Mexican male patients (73% of pediatric age) with clinical suspicion of muscular dystrophy and no evidence of DMD gene deletion on multiplex polymerase chain reaction (mPCR) analysis were analyzed by multiplex ligation-dependent probe amplification (MLPA). Those with a normal result were subjected to Sanger sequencing or to next-generation sequencing for DMD plus 10 selected LGMD-related genes. We achieved a diagnostic genotype in 80.5% (n = 58/72) of patients with predominance of dystrophinopathy-linked genotypes (68%, n = 49/72), followed by autosomal recessive LGMD-related genotypes (types 2A-R1, 2C-R5, 2E-R4, 2D-R3 and 2I-R9; 12.5%, n = 9/72). MLPA showed 4.2% of false-negatives for DMD deletions assessed by mPCR. Among the small DMD variants, 96.5% (n = 28/29) corresponded to null-alleles, most of which (72%) were inherited through a carrier mother. The FKRP p.[Leu276Ile]; [Asn463Asp] genotype is reported for the first time in Mexican patients as being associated with dilated cardiomyopathy. Absence of dysferlinopathies could be related to the small sample size and/or the predominantly pediatric age of patients. The employed strategy seems to be an affordable diagnosis approach for Mexican muscular dystrophy male patients and their families.
Collapse
|
6
|
Zhang Y, Yang W, Wen G, Wu Y, Jing Z, Li D, Tang M, Liu G, Wei X, Zhong Y, Li Y, Deng Y. Application whole exome sequencing for the clinical molecular diagnosis of patients with Duchenne muscular dystrophy; identification of four novel nonsense mutations in four unrelated Chinese DMD patients. Mol Genet Genomic Med 2019; 7:e622. [PMID: 30938079 PMCID: PMC6503051 DOI: 10.1002/mgg3.622] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/19/2019] [Accepted: 02/11/2019] [Indexed: 12/17/2022] Open
Abstract
Background Duchenne muscular dystrophy (DMD) is the most common form of inherited muscular dystrophy. Germline mutations in dystrophin (DMD) gene cause DMD, with a X‐linked recessive mode of inheritance. Patients with DMD are usually characterized by weakness of muscle, usually started since childhood and gradually the patient will unable to stand and walk. Methods In our present study, we identified four unrelated Chinese patients with DMD from four Chinese families. Whole exome sequencing was performed for genetic molecular analysis for these probands. Results Whole exome sequencing and confirmatory Sanger sequencing identified four novel nonsense mutations in these four unrelated Chinese patients, respectively. All these four mutations lead to the formation of a truncated DMD protein by formation of a premature stop codon. According to the variant interpretation guidelines of American College of Medical Genetics and Genomics (ACMG), these four novel nonsense mutations are categorized as “likely pathogenic” variants. Conclusion Our present finding not only identified four novel loss‐of‐function mutations in dystrophin (DMD) gene but also strongly emphasized the significance of whole exome sequencing as the most efficient way of identifying the candidate genes and mutations which enables us for easy and rapid clinical diagnosis, follow‐up, and management of DMD patients.
Collapse
Affiliation(s)
- Yan Zhang
- Department of Pathology, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, P.R. China
| | - Weikang Yang
- Department of Prevention and health care, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Guoming Wen
- Department of Outpatient, Shenzhen Longhua District Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Yanxia Wu
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Zhiliang Jing
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Dazhou Li
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Minshan Tang
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Guanglong Liu
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Xuxuan Wei
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Yan Zhong
- Department of Pathology, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, P.R. China
| | - Yanhua Li
- Department of Pathology, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, P.R. China
| | - Yongjian Deng
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| |
Collapse
|
7
|
Zhang K, Yang X, Lin G, Han Y, Li J. Molecular genetic testing and diagnosis strategies for dystrophinopathies in the era of next generation sequencing. Clin Chim Acta 2019; 491:66-73. [PMID: 30660698 DOI: 10.1016/j.cca.2019.01.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/16/2019] [Accepted: 01/16/2019] [Indexed: 12/14/2022]
Abstract
Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive, inherited neuromuscular disorders, caused by pathogenic variants in the dystrophin gene that encodes the dystrophin protein. A number of mutations have been identified in the past years, producing dystrophin diversity and resulting in mild to severe phenotypes in patients. Mutations in the dystrophin gene can be characterized by laboratory testing to confirm a clinical diagnosis of DMD/BMD. Traditional genetic diagnostic strategy for DMD/BMD involves the initial detection of large mutations, followed by the detection of smaller mutations, where two or more analytical methods are employed. With the development of next generation sequencing (NGS) technology, comprehensive mutational screening for all variant types can be performed on a single platform in patients and carriers, although further optimization and validation are required. Furthermore, the discovery of cell-free fetal DNA (cffDNA) in maternal plasma provides basis for noninvasive prenatal diagnosis of DMD/BMD. Here, we discuss the correlation between genotype and phenotype, the current methods of molecular genetic testing and genetic diagnostic strategy for probands and female carriers of DMD/BMD, the diagnostic ability of a comprehensive targeted NGS strategy and the possibility of it replacing conventional methods.
Collapse
Affiliation(s)
- Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Xin Yang
- The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong 264000, People's Republic of China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.
| |
Collapse
|
8
|
Wierbowski SD, Fragoza R, Liang S, Yu H. Extracting Complementary Insights from Molecular Phenotypes for Prioritization of Disease-Associated Mutations. CURRENT OPINION IN SYSTEMS BIOLOGY 2018; 11:107-116. [PMID: 31086831 PMCID: PMC6510504 DOI: 10.1016/j.coisb.2018.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Rapid advances in next-generation sequencing technology have resulted in an explosion of whole-exome/genome sequencing data, providing an unprecedented opportunity to identify disease- and trait-associated variants in humans on a large scale. To date, the long-standing paradigm has leveraged fitness-based approximations to translate this ever-expanding sequencing data into causal insights in disease. However, while this approach robustly identifies variants under evolutionary constraint, it fails to provide molecular insights. Moreover, complex disease phenomena often violate standard assumptions of a direct organismal phenotype to overall fitness effect relationship. Here we discuss the potential of a molecular phenotype-oriented paradigm to uniquely identify candidate disease-causing mutations from the human genetic background. By providing a direct connection between single nucleotide mutations and observable organismal and cellular phenotypes associated with disease, we suggest that molecular phenotypes can readily incorporate alongside established fitness-based methodologies to provide complementary insights to the functional impact of human mutations. Lastly, we discuss how integrated approaches between molecular phenotypes and fitness-based perspectives facilitate new insights into the molecular mechanisms underlying disease-associated mutations while also providing a platform for improved interpretation of epistasis in human disease.
Collapse
Affiliation(s)
- Shayne D. Wierbowski
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Robert Fragoza
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Siqi Liang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Haiyuan Yu
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|