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Tayebi Arasteh S, Han T, Lotfinia M, Kuhl C, Kather JN, Truhn D, Nebelung S. Large language models streamline automated machine learning for clinical studies. Nat Commun 2024; 15:1603. [PMID: 38383555 PMCID: PMC10881983 DOI: 10.1038/s41467-024-45879-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/06/2024] [Indexed: 02/23/2024] Open
Abstract
A knowledge gap persists between machine learning (ML) developers (e.g., data scientists) and practitioners (e.g., clinicians), hampering the full utilization of ML for clinical data analysis. We investigated the potential of the ChatGPT Advanced Data Analysis (ADA), an extension of GPT-4, to bridge this gap and perform ML analyses efficiently. Real-world clinical datasets and study details from large trials across various medical specialties were presented to ChatGPT ADA without specific guidance. ChatGPT ADA autonomously developed state-of-the-art ML models based on the original study's training data to predict clinical outcomes such as cancer development, cancer progression, disease complications, or biomarkers such as pathogenic gene sequences. Following the re-implementation and optimization of the published models, the head-to-head comparison of the ChatGPT ADA-crafted ML models and their respective manually crafted counterparts revealed no significant differences in traditional performance metrics (p ≥ 0.072). Strikingly, the ChatGPT ADA-crafted ML models often outperformed their counterparts. In conclusion, ChatGPT ADA offers a promising avenue to democratize ML in medicine by simplifying complex data analyses, yet should enhance, not replace, specialized training and resources, to promote broader applications in medical research and practice.
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Affiliation(s)
- Soroosh Tayebi Arasteh
- Department of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany.
| | - Tianyu Han
- Department of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany.
| | - Mahshad Lotfinia
- Department of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany
- Institute of Heat and Mass Transfer, RWTH Aachen University, Aachen, Germany
| | - Christiane Kuhl
- Department of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
- Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel Truhn
- Department of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Sven Nebelung
- Department of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany
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Liu X, Dai H, Li G, Jia R, Meng X, Yu S, Yang L, Hong J. Screening copy number variations in 35 unsolved inherited retinal disease families. Hum Genet 2024; 143:197-210. [PMID: 38282009 PMCID: PMC10881639 DOI: 10.1007/s00439-023-02631-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/15/2023] [Indexed: 01/30/2024]
Abstract
The purpose of this study was to screen Copy Number Variations (CNVs) in 35 unsolved Inherited Retinal Dystrophy (IRD) families. Initially, next generation sequencing, including a specific Hereditary Eye Disease Enrichment Panel or Whole exome sequencing, was employed to screen (likely) pathogenic Single-nucleotide Variants (SNVs) and small Insertions and Deletions (indels) for these cases. All available SNVs and indels were further validated and co-segregation analyses were performed in available family members by Sanger sequencing. If not, after excluding deep intronic variants, Multiplex ligation-dependent probe amplification (MLPA), quantitative fluorescence PCR (QF-PCR) and Sanger sequencing were employed to screen CNVs. We determined that 18 probands who had heterozygous SNVs/indels or whose parents were not consanguineous but had homozygous SNVs/indels in autosomal recessive IRDs genes had CNVs in another allele of these genes, 11 families had disease-causing hemizygous CNVs in X-linked IRD genes, 6 families had (likely) pathogenic heterozygous CNVs in PRPF31 gene. Of 35 families, 33 different CNVs in 16 IRD-associated genes were detected, with PRPF31, EYS and USH2A the most common disease-causing gene in CNVs. Twenty-six and 7 of them were deletion and duplication CNVs, respectively. Among them, 14 CNVs were first reported in this study. Our research indicates that CNVs contribute a lot to IRDs, and screening of CNVs substantially increases the diagnostic rate of IRD. Our results emphasize that MLPA and QF-PCR are ideal methods to validate CNVs, and the novel CNVs reported herein expand the mutational spectrums of IRDs.
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Affiliation(s)
- Xiaozhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Hehua Dai
- Department of Ophthalmology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China
| | - Genlin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, 100730, China
| | - Ruixuan Jia
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Xiang Meng
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Shicheng Yu
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China.
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China.
| | - Jing Hong
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China.
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China.
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Yuan L, Yu X, Xiao H, Deng S, Xia H, Xu H, Yang Y, Deng H. Identification of novel compound heterozygous variants in the DNAH1 gene of a Chinese family with left-right asymmetry disorder. Front Mol Biosci 2023; 10:1190162. [PMID: 37457836 PMCID: PMC10345202 DOI: 10.3389/fmolb.2023.1190162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Most internal organs in humans and other vertebrates exhibit striking left-right asymmetry in position and structure. Variation of normal organ positioning results in left-right asymmetry disorders and presents as internal organ reversal or randomization. Up to date, at least 82 genes have been identified as the causative genetic factors of left-right asymmetry disorders. This study sought to discover potential pathogenic variants responsible for left-right asymmetry disorder present in a Han-Chinese family using whole exome sequencing combined with Sanger sequencing. Novel compound heterozygous variants, c.5690A>G (p.Asn1897Ser) and c.7759G>A (p.Val2587Met), in the dynein axonemal heavy chain 1 gene (DNAH1), were found in the proband and absent in unaffected family members. Conservation analysis has shown that the variants affect evolutionarily conserved residues, which may impact the tertiary structure of the DNAH1 protein. The novel compound heterozygous variants may potentially bear responsibility for left-right asymmetry disorder, which results from a perturbation of left-right axis coordination at the earliest embryonic development stages. This study broadens the variant spectrum of left-right asymmetry disorders and may be helpful for genetic counseling and healthcare management for the diagnosed individual, and promotes a greater understanding of the pathophysiology.
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Affiliation(s)
- Lamei Yuan
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
- Disease Genome Research Center, Central South University, Changsha, China
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xuehui Yu
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Heng Xiao
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Sheng Deng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Hong Xia
- Department of Emergency, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hongbo Xu
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yan Yang
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
- Disease Genome Research Center, Central South University, Changsha, China
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
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Savenko IV, Garbaruk ES, Boboshko MY. [The issue of auditory neuropathy: from origins to the present]. Vestn Otorinolaringol 2022; 87:60-69. [PMID: 35274894 DOI: 10.17116/otorino20228701160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The issue of auditory neuropathy spectrum disorders (ANSD) has been in a focus of specialists attention for a relatively short time, but during this time a huge amount of scientific and practical knowledge about this hearing disorder has been accumulated. ANSD is a specific auditory deficit caused by dysfunction of periphery part of the auditory system, which may affect the inner hair cells, the spiral ganglion neurons and the auditory nerve, as well as the area of synaptic contact between them, while the outer hair cells, as a rule, remain intact. As a result, a specific condition is formed, in which a patient's otoacoustic emissions and/or cochlear microphonics are present, auditory brainstem responses are abnormal or absent, electrophysiological data may not correlate with hearing level, the discrepancy between pure tone audiometry and speech discrimination is observed. ANSD prevalence, epidemiology, contemporary views on its etiology, including detailed information on hereditary forms of the disorder and its risk factors are considered in the review. The data on the basic rungs of the ANSD pathogenesis, which underlie the development of various forms of the disorder and mainly determine the rehabilitation approach, are presented. The detailed clinical and audiological characteristics of ANSD are presented; contemporary approach to ANSD diagnosis and rehabilitation, including indications for surgical treatment, are considered.
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Affiliation(s)
- I V Savenko
- Pavlov State Medical University, St. Petersburg, Russia
| | - E S Garbaruk
- Pavlov State Medical University, St. Petersburg, Russia.,St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
| | - M Yu Boboshko
- Pavlov State Medical University, St. Petersburg, Russia.,Mechnikov North-Western State Medical University, St. Petersburg, Russia
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Xia H, Huang X, Deng S, Xu H, Yang Y, Liu X, Yuan L, Deng H. DNAH11 compound heterozygous variants cause heterotaxy and congenital heart disease. PLoS One 2021; 16:e0252786. [PMID: 34133440 PMCID: PMC8208527 DOI: 10.1371/journal.pone.0252786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/21/2021] [Indexed: 12/16/2022] Open
Abstract
Heterotaxy (HTX), a condition characterized by internal organs not being arranged as expected relative to each other and to the left-right axis, is often accompanied with congenital heart disease (CHD). The purpose was to detect the pathogenic variants in a Chinese family with HTX and CHD. A non-consanguineous Han Chinese family with HTX and CHD, and 200 unrelated healthy subjects were enlisted. Exome sequencing and Sanger sequencing were applied to identify the genetic basis of the HTX family. Compound heterozygous variants, c.3426-1G>A and c.4306C>T (p.(Arg1436Trp)), in the dynein axonemal heavy chain 11 gene (DNAH11) were identified in the proband via exome sequencing and further confirmed by Sanger sequencing. Neither c.3426-1G>A nor c.4306C>T variant in the DNAH11 gene was detected in 200 healthy controls. The DNAH11 c.3426-1G>A variant was predicted as altering the acceptor splice site and most likely affecting splicing. The DNAH11 c.4306C>T variant was predicted to be damaging, which may reduce the phenotype severity. The compound heterozygous variants, c.3426-1G>A and c.4306C>T, in the DNAH11 gene might be the pathogenic alterations resulting in HTX and CHD in this family. These findings broaden the variant spectrum of the DNAH11 gene and increase knowledge used in genetic counseling for the HTX family.
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Affiliation(s)
- Hong Xia
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Emergency, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiangjun Huang
- Department of General Surgery, The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Sheng Deng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongbo Xu
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yan Yang
- Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin Liu
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lamei Yuan
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- * E-mail: (HD); (LY)
| | - Hao Deng
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- * E-mail: (HD); (LY)
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Huang Y, Yuan L, Cao Y, Tang R, Xu H, Tang Z, Deng H. Novel compound heterozygous mutations in the CHST6 gene cause macular corneal dystrophy in a Han Chinese family. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:622. [PMID: 33987320 PMCID: PMC8106006 DOI: 10.21037/atm-20-7178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Macular corneal dystrophy (MCD), a rare autosomal recessive disorder, is caused by pathogenic mutations in the carbohydrate sulfotransferase 6 gene (CHST6) and is characterized by bilateral progressive stromal clouding and vision loss. Corneal transplantation is often necessary. This study aimed to identify disease-causing mutations in a Han-Chinese MCD patient. METHODS A 37-year-old female diagnosed with MCD was recruited. The clinical materials were observed and described, and peripheral blood sample was extracted. Whole exome sequencing (WES) and Sanger sequencing were used to reveal genetic defects. The pathogenicity of identified mutations was assessed using in silico analysis. RESULTS The patient had typical features of MCD, including decreased vision, multiple irregular gray-white corneal opacities, and corneal thinning. A novel nonsense mutation c.544C>T (p.Gln182Ter) and a validated missense mutation c.631C>G (p.Arg211Gly) were identified in the CHST6 gene coding region, both classified as "pathogenic" following the American College of Medical Genetics and Genomics standards and guidelines. CONCLUSIONS This study reports a Han-Chinese MCD patient with a novel nonsense mutation c.544C>T (p.Gln182Ter) and a recurrent missense mutation c.631C>G (p.Arg211Gly), which expand the spectrum of genetic mutations. The results of this study extend genotype-phenotype correlations between the CHST6 gene mutations and MCD clinical findings, contributing to a more accurate diagnosis and the development of potential gene-targeted MCD therapies. KEYWORDS Carbohydrate sulfotransferase 6 gene (CHST6); compound heterozygous mutations; Han Chinese family; macular corneal dystrophy (MCD).
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Affiliation(s)
- Yanxia Huang
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Lamei Yuan
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Yanna Cao
- Department of Ophthalmology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Renhong Tang
- Department of Ophthalmology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Hongbo Xu
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Ziqian Tang
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China;,Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, China;,Disease Genome Research Center, Central South University, Changsha, China
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Hearing Phenotypes of Patients with Hearing Loss Homozygous for the GJB2 c.235delc Mutation. Neural Plast 2020; 2020:8841522. [PMID: 32802038 PMCID: PMC7416285 DOI: 10.1155/2020/8841522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/18/2020] [Accepted: 06/30/2020] [Indexed: 01/17/2023] Open
Abstract
Hereditary hearing loss is characterized by remarkable phenotypic heterogeneity. Patients with the same pathogenic mutations may exhibit various hearing loss phenotypes. In the Chinese population, the c.235delC mutation is the most common pathogenic mutation of GJB2 and is closely related to hereditary recessive hearing loss. Here, we investigated the hearing phenotypes of patients with hearing loss associated with the homozygous c.235delC mutation, paying special attention to asymmetric interaural hearing loss. A total of 244 patients with the GJB2 c.235delC homozygous mutation encountered from 2007 to 2015 were enrolled. The severity of hearing loss was scaled with the American Speech-Language-Hearing Association (ASHA). Auditory phenotypes were analyzed, and three types of interaural asymmetry were defined based on audiograms: Type A (asymmetry of hearing loss severity), Type B (asymmetry of audiogram shape), and Type C (Type A plus Type B). Of the 488 ears (244 cases) examined, 71.93% (351) presented with profound hearing loss, 14.34% (70) with severe hearing loss, and 9.43% (46) with moderate to severe hearing loss. The most common audiogram shapes were descending (31.15%) and flat (24.18%). A total of 156 (63.93%) of the 244 patients exhibited asymmetric interaural hearing loss in terms of severity and/or audiogram shape. Type A was evident in 14 of these cases, Type B in 106, and Type C in 36. In addition, 211 of 312 ears (67.63%) in the interaural hearing asymmetry group showed profound hearing loss, and 59 (18.91%) exhibited severe hearing loss, with the most common audiogram shapes being flat (27.88%) and descending (22.12%). By contrast, in the interaural hearing symmetry group, profound hearing loss was observed in 140 ears (79.55%), and the most common audiograms were descending (46.59%) and residual (21.59%). Hearing loss associated with the GJB2 c.235delC homozygous mutation shows diverse phenotypes, and a considerable proportion of patients show bilateral hearing loss asymmetry.
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Huang CY, Tsai YH, Tsai YC, Lu YC, Chan YH, Hsu CJ, Chiou SH, Wu CC, Cheng YF. Establishment of an induced pluripotent stem cell (iPSC) line from a 7-year-old male patient with profound hearing loss carrying c.235delC in GJB2 gene. Stem Cell Res 2020; 45:101795. [PMID: 32388442 DOI: 10.1016/j.scr.2020.101795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 10/24/2022] Open
Abstract
Gap junction protein beta 2 gene (GJB2) mutations are the most frequent cause of hereditary hearing impairment. The recessive c.235delC mutation in the GJB2 gene is the most common mutation causing severe to profound sensorineural hearing loss in the Asian population. The induced pluripotent stem cell (iPSC) line was generated using the integration-free Sendai virus method from peripheral blood mononuclear cells (PBMCs) of a hearing-impaired patient with homozygous GJB2 c.235delC mutation. This cell line may serve as a cellular model for studying the pathogenic mechanisms of deafness caused by GJB2 mutations.
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Affiliation(s)
- Chun-Ying Huang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yi-Hsiu Tsai
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yi-Ching Tsai
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ying-Chang Lu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yen-Hui Chan
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan; Department of Otolaryngology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan
| | - Chuan-Jen Hsu
- Department of Otolaryngology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan; Institute of Pharmacology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan.
| | - Yen-Fu Cheng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei, Taiwan; School of Medicine, National Yang-Ming University, Taipei, Taiwan.
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