1
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Dong ZR, Zhang MY, Qu LX, Zou J, Yang YH, Ma YL, Yang CC, Cao XL, Wang LY, Zhang XL, Li T. Spatial resolved transcriptomics reveals distinct cross-talk between cancer cells and tumor-associated macrophages in intrahepatic cholangiocarcinoma. Biomark Res 2024; 12:100. [PMID: 39256888 PMCID: PMC11389341 DOI: 10.1186/s40364-024-00648-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 08/31/2024] [Indexed: 09/12/2024] Open
Abstract
BACKGROUND Multiple studies have shown that tumor-associated macrophages (TAMs) promote cancer initiation and progression. However, the reprogramming of macrophages in the tumor microenvironment (TME) and the cross-talk between TAMs and malignant subclones in intrahepatic cholangiocarcinoma (iCCA) has not been fully characterized, especially in a spatially resolved manner. Deciphering the spatial architecture of variable tissue cellular components in iCCA could contribute to the positional context of gene expression containing information pathological changes and cellular variability. METHODS Here, we applied spatial transcriptomics (ST) and digital spatial profiler (DSP) technologies with tumor sections from patients with iCCA. RESULTS The results reveal that spatial inter- and intra-tumor heterogeneities feature iCCA malignancy, and tumor subclones are mainly driven by physical proximity. Tumor cells with TME components shaped the intra-sectional heterogenetic spatial architecture. Macrophages are the most infiltrated TME component in iCCA. The protein trefoil factor 3 (TFF3) secreted by the malignant subclone can induce macrophages to reprogram to a tumor-promoting state, which in turn contributes to an immune-suppressive environment and boosts tumor progression. CONCLUSIONS In conclusion, our description of the iCCA ecosystem in a spatially resolved manner provides novel insights into the spatial features and the immune suppressive landscapes of TME for iCCA.
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Affiliation(s)
- Zhao-Ru Dong
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250010, Shandong, China
| | - Meng-Ya Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Ling-Xin Qu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Jie Zou
- Department of Geriatrics, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China
| | - Yong-Heng Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Yun-Long Ma
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250010, Shandong, China
| | - Chun-Cheng Yang
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250010, Shandong, China
| | - Xue-Lei Cao
- Department of Clinical Laboratory, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250010, Shandong, China
| | - Li-Yuan Wang
- Department of Hepatology, Cheeloo Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Xiao-Lu Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
| | - Tao Li
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250010, Shandong, China.
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2
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Chi CS, Tsai CR, Lee HF. Resolving unsolved whole-genome sequencing data in paediatric neurological disorders: a cohort study. Arch Dis Child 2024; 109:730-735. [PMID: 38789118 PMCID: PMC11347223 DOI: 10.1136/archdischild-2024-326985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
OBJECTIVE To resolve unsolved whole-genome sequencing (WGS) data in individuals with paediatric neurological disorders. DESIGN A cohort study method using updated bioinformatic tools, new analysis targets, clinical information and literature databases was employed to reanalyse existing unsolved genome data. PARTICIPANTS From January 2016 to September 2023, a total of 615 individuals who aged under 18 years old, exhibited neurological disorders and received singleton WGS were recruited. 364 cases were unsolved during initial WGS analysis, in which 102 consented to reanalyse existing singleton WGS data. RESULTS Median duration for reanalysis after initial negative WGS results was 2 years and 4 months. The diagnostic yield was 29 of 102 individuals (28.4%) through reanalysis. New disease gene discovery and new target acquisitions contributed to 13 of 29 solved cases (44.8%). The reasons of non-detected causative variants during initial WGS analysis were variant reclassification in 9 individuals (31%), analytical issue in 9 (31%), new emerging disease-gene association in 8 (27.6%) and clinical update in 3 (10.3%). The 29 new diagnoses increased the cumulative diagnostic yield of clinical WGS in the entire study cohort to 45.5% after reanalysis. CONCLUSIONS Unsolved paediatric WGS individuals with neurological disorders could obtain molecular diagnoses through reanalysis within a timeframe of 2-2.5 years. New disease gene, structural variations and deep intronic splice variants make a significant contribution to diagnostic yield. This approach can provide precise genetic counselling to positive reanalysis results and end a diagnostic odyssey.
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Affiliation(s)
- Ching-Shiang Chi
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chi-Ren Tsai
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Hsiu-Fen Lee
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
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3
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da Silva TF, de Azevedo JC, Teixeira EB, Casseb SMM, Moreira FC, de Assumpção PP, dos Santos SEB, Calcagno DQ. From haystack to high precision: advanced sequencing methods to unraveling circulating tumor DNA mutations. Front Mol Biosci 2024; 11:1423470. [PMID: 39165643 PMCID: PMC11333322 DOI: 10.3389/fmolb.2024.1423470] [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: 04/25/2024] [Accepted: 07/11/2024] [Indexed: 08/22/2024] Open
Abstract
Identifying mutations in cancer-associated genes to guide patient treatments is essential for precision medicine. Circulating tumor DNA (ctDNA) offers valuable insights for early cancer detection, treatment assessment, and surveillance. However, a key issue in ctDNA analysis from the bloodstream is the choice of a technique with adequate sensitivity to identify low frequent molecular changes. Next-generation sequencing (NGS) technology, evolving from parallel to long-read capabilities, enhances ctDNA mutation analysis. In the present review, we describe different NGS approaches for identifying ctDNA mutation, discussing challenges to standardized methodologies, cost, specificity, clinical context, and bioinformatics expertise for optimal NGS application.
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Affiliation(s)
- Tamires Ferreira da Silva
- Programa de Residência Multiprofissional em Saúde (Oncologia), Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Brazil
| | - Juscelino Carvalho de Azevedo
- Programa de Residência Multiprofissional em Saúde (Oncologia), Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Brazil
| | | | | | | | | | | | - Danielle Queiroz Calcagno
- Programa de Residência Multiprofissional em Saúde (Oncologia), Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Brazil
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4
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Jansson L, Aili Fagerholm S, Börkén E, Hedén Gynnå A, Sidstedt M, Forsberg C, Ansell R, Hedman J, Tillmar A. Assessment of DNA quality for whole genome library preparation. Anal Biochem 2024; 695:115636. [PMID: 39111682 DOI: 10.1016/j.ab.2024.115636] [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: 03/11/2024] [Revised: 07/26/2024] [Accepted: 08/03/2024] [Indexed: 08/22/2024]
Abstract
In recent years, more sophisticated DNA technologies for genotyping have enabled considerable progress in various fields such as clinical genetics, archaeogenetics and forensic genetics. DNA samples previously rejected as too challenging to analyze due to low amounts of degraded DNA can now provide useful information. To increase the chances of success with the new methodologies, it is crucial to know the fragment size of the template DNA molecules, and whether the DNA in a sample is mostly single or double stranded. With this knowledge, an appropriate library preparation method can be chosen, and the DNA shearing parameters of the protocol can be adjusted to the DNA fragment size in the sample. In this study, we first developed and evaluated a user-friendly fluorometry-based protocol for estimation of DNA strandedness. We also evaluated different capillary electrophoresis methods for estimation of DNA fragmentation levels. Next, we applied the developed methodologies to a broad variety of DNA samples processed with different DNA extraction protocols. Our findings show that both the applied DNA extraction method and the sample type affect the DNA strandedness and fragmentation. The established protocols and the gained knowledge will be applicable for future sequencing-based high-density SNP genotyping in various fields.
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Affiliation(s)
- Linda Jansson
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | | | - Emelie Börkén
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Arvid Hedén Gynnå
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden
| | - Maja Sidstedt
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden
| | | | - Ricky Ansell
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden; Department of Physics, Chemistry and Biology, IFM, Linköping University, Linköping, Sweden
| | - Johannes Hedman
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.
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5
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Nomakuchi TT, Teferedegn EY, Li D, Muirhead KJ, Dubbs H, Leonard J, Muraresku C, Sergio E, Arnold K, Pizzino A, Skraban CM, Zackai EH, Wang K, Ganetzky RD, Vanderver AL, Ahrens-Nicklas RC, Bhoj EJK. Utility of genome sequencing in exome-negative pediatric patients with neurodevelopmental phenotypes. Am J Med Genet A 2024:e63817. [PMID: 39031459 DOI: 10.1002/ajmg.a.63817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/03/2024] [Accepted: 07/07/2024] [Indexed: 07/22/2024]
Abstract
Exome sequencing (ES) has emerged as an essential tool in the evaluation of neurodevelopmental disorders (NDD) of unknown etiology. Genome sequencing (GS) offers advantages over ES due to improved detection of structural, copy number, repeat number and non-coding variants. However, GS is less commonly utilized due to higher cost and more intense analysis. Here, we present nine cases of pediatric NDD that were molecularly diagnosed with GS between 2017 and 2022, following non-diagnostic ES. All individuals presented with global developmental delay or regression. Other features present in our cohort included epilepsy, white matter abnormalities, brain malformation and dysmorphic features. Two cases were diagnosed on GS due to newly described gene-disease relationship or variant reclassification (MAPK8IP3, CHD3). Additional features missed on ES that were later detected on GS were: intermediate-size deletions in three cases who underwent ES that were not validated for CNV detection, pathogenic variants within the non-protein coding genes SNORD118 and RNU7-1, pathogenic variant within the promoter region of GJB1, and a coding pathogenic variant within BCAP31 which was not sufficiently covered on ES. GS following non-diagnostic ES led to the identification of pathogenic variants in this cohort of nine cases, four of which would not have been identified by reanalysis alone.
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Affiliation(s)
- Tomoki T Nomakuchi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Eden Y Teferedegn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Dong Li
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kayla J Muirhead
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Holly Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jacqueline Leonard
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Colleen Muraresku
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Emily Sergio
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kaley Arnold
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Amy Pizzino
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Cara M Skraban
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kai Wang
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rebecca D Ganetzky
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Adeline L Vanderver
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rebecca C Ahrens-Nicklas
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth J K Bhoj
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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6
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Chen J, Jia Y, Zhong J, Zhang K, Dai H, He G, Li F, Zeng L, Fan C, Xu H. Novel mutation leading to splice donor loss in a conserved site of DMD gene causes Duchenne muscular dystrophy with cryptorchidism. J Med Genet 2024; 61:741-749. [PMID: 38621993 PMCID: PMC11287555 DOI: 10.1136/jmg-2024-109896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/04/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND As one of the most common congenital abnormalities in male births, cryptorchidism has been found to have a polygenic aetiology according to previous studies of common variants. However, little is known about genetic predisposition of rare variants for cryptorchidism, since rare variants have larger effective size on diseases than common variants. METHODS In this study, a cohort of 115 Chinese probands with cryptorchidism was analysed using whole-genome sequencing, alongside 19 parental controls and 2136 unaffected men. Additionally, CRISPR-Cas9 editing of a conserved variant was performed in a mouse model, with MRI screening used to observe the phenotype. RESULTS In 30 of 115 patients (26.1%), we identified four novel genes (ARSH, DMD, MAGEA4 and SHROOM2) affecting at least five unrelated patients and four known genes (USP9Y, UBA1, BCORL1 and KDM6A) with the candidate rare pathogenic variants affecting at least two cases. Burden tests of rare variants revealed the genome-wide significances for newly identified genes (p<2.5×10-6) under the Bonferroni correction. Surprisingly, novel and known genes were mainly found on X chromosome (seven on X and one on Y) and all rare X-chromosomal segregating variants exhibited a maternal inheritance rather than de novo origin. CRISPR-Cas9 mouse modelling of a splice donor loss variant in DMD (NC_000023.11:g.32454661C>G), which resides in a conserved site across vertebrates, replicated bilateral cryptorchidism phenotypes, confirmed by MRI at 4 and 10 weeks. The movement tests further revealed symptoms of Duchenne muscular dystrophy (DMD) in transgenic mice. CONCLUSION Our results revealed the role of the DMD gene mutation in causing cryptorchidism. The results also suggest that maternal-X inheritance of pathogenic defects could have a predominant role in the development of cryptorchidism.
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Affiliation(s)
- Jianhai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Yangying Jia
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA
| | - Jie Zhong
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Kun Zhang
- Department of Radiology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hongzheng Dai
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Fuping Li
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Clinical Research Center for Birth Defects of Sichuan Province, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Li Zeng
- Department of Pediatric Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Huayan Xu
- Department of Radiology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
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7
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Ji S, Zhu T, Sethia A, Wang W. Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples. Genome Res 2024; 34:633-641. [PMID: 38589250 PMCID: PMC11146589 DOI: 10.1101/gr.278456.123] [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: 08/29/2023] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
Accurate detection of somatic mutations in DNA sequencing data is a fundamental prerequisite for cancer research. Previous analytical challenges were overcome by consensus mutation calling from four to five popular callers. This, however, increases the already nontrivial computing time from individual callers. Here, we launch MuSE 2, powered by multistep parallelization and efficient memory allocation, to resolve the computing time bottleneck. MuSE 2 speeds up 50 times more than MuSE 1 and eight to 80 times more than other popular callers. Our benchmark study suggests combining MuSE 2 and the recently accelerated Strelka2 achieves high efficiency and accuracy in analyzing large cancer genomic data sets.
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Affiliation(s)
- Shuangxi Ji
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Tong Zhu
- NVIDIA Corporation, Santa Clara, California 95051, USA
| | - Ankit Sethia
- NVIDIA Corporation, Santa Clara, California 95051, USA
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
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8
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Pankotai-Bodó G, Oláh-Németh O, Sükösd F, Pankotai T. Routine molecular applications and recent advances in breast cancer diagnostics. J Biotechnol 2024; 380:20-28. [PMID: 38122830 DOI: 10.1016/j.jbiotec.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Cancer stands as one of the most common and lethal diseases, imposing a substantial burden on global mortality rates. Breast cancer is distinct from other forms of cancer in which it is the primary cause of death for women. Early detection of breast cancer can significantly lower the risk of mortality, improving the prognosis for those who are affected. The death rate of breast cancer has been steadily rising, according to epidemiological data, especially since the COVID-19 pandemic. This emphasizes the necessity of sensitive and precise technologies that can be utilized in early breast cancer diagnosis. In this process, biomarkers play a pivotal role by facilitating the early detection and diagnosis of breast cancer. Currently, a wide variety of cancer biomarkers have been identified, improving the accuracy of cancer diagnosis. These biomarkers can be applied in liquid biopsies as well as on solid tissues. In the context of breast cancer, biomarkers are particularly valuable for determining who is predisposed to the disease, predicting prognosis at the time of diagnosis, and selecting the best course of therapy. This review comprehensively explores the recently developed gene-based biomarkers from biofluids that are used in the context of breast cancer, as well as the conventional and cutting-edge techniques that have been employed for breast cancer diagnosis.
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Affiliation(s)
- Gabriella Pankotai-Bodó
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, Szeged H-6725, Hungary
| | - Orsolya Oláh-Németh
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, Szeged H-6725, Hungary; Hungarian Centre of Excellence for Molecular Medicine (HCEMM), Genome Integrity and DNA Repair Core Group, Budapesti út 9, Szeged H-6728, Hungary
| | - Farkas Sükösd
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, Szeged H-6725, Hungary
| | - Tibor Pankotai
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, Szeged H-6725, Hungary; Hungarian Centre of Excellence for Molecular Medicine (HCEMM), Genome Integrity and DNA Repair Core Group, Budapesti út 9, Szeged H-6728, Hungary; Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, Dugonics tér 13, Szeged H-6720, Hungary.
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9
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Weisschuh N, Mazzola P, Zuleger T, Schaeferhoff K, Kühlewein L, Kortüm F, Witt D, Liebmann A, Falb R, Pohl L, Reith M, Stühn LG, Bertrand M, Müller A, Casadei N, Kelemen O, Kelbsch C, Kernstock C, Richter P, Sadler F, Demidov G, Schütz L, Admard J, Sturm M, Grasshoff U, Tonagel F, Heinrich T, Nasser F, Wissinger B, Ossowski S, Kohl S, Riess O, Stingl K, Haack TB. Diagnostic genome sequencing improves diagnostic yield: a prospective single-centre study in 1000 patients with inherited eye diseases. J Med Genet 2024; 61:186-195. [PMID: 37734845 PMCID: PMC10850689 DOI: 10.1136/jmg-2023-109470] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/10/2023] [Indexed: 09/23/2023]
Abstract
PURPOSE Genome sequencing (GS) is expected to reduce the diagnostic gap in rare disease genetics. We aimed to evaluate a scalable framework for genome-based analyses 'beyond the exome' in regular care of patients with inherited retinal degeneration (IRD) or inherited optic neuropathy (ION). METHODS PCR-free short-read GS was performed on 1000 consecutive probands with IRD/ION in routine diagnostics. Complementary whole-blood RNA-sequencing (RNA-seq) was done in a subset of 74 patients. An open-source bioinformatics analysis pipeline was optimised for structural variant (SV) calling and combined RNA/DNA variation interpretation. RESULTS A definite genetic diagnosis was established in 57.4% of cases. For another 16.7%, variants of uncertain significance were identified in known IRD/ION genes, while the underlying genetic cause remained unresolved in 25.9%. SVs or alterations in non-coding genomic regions made up for 12.7% of the observed variants. The RNA-seq studies supported the classification of two unclear variants. CONCLUSION GS is feasible in clinical practice and reliably identifies causal variants in a substantial proportion of individuals. GS extends the diagnostic yield to rare non-coding variants and enables precise determination of SVs. The added diagnostic value of RNA-seq is limited by low expression levels of the major IRD disease genes in blood.
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Affiliation(s)
- Nicole Weisschuh
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Pascale Mazzola
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Theresia Zuleger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Karin Schaeferhoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Laura Kühlewein
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Friederike Kortüm
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Dennis Witt
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Alexandra Liebmann
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Ruth Falb
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Lisa Pohl
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Milda Reith
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Lara G Stühn
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Amelie Müller
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Olga Kelemen
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Carina Kelbsch
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Christoph Kernstock
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Paul Richter
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Francoise Sadler
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Leon Schütz
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Felix Tonagel
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Tilman Heinrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- MVZ für Humangenetik und Molekularpathologie, Rostock, Germany
| | - Fadi Nasser
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Disease, University of Tübingen, Tübingen, Germany
| | - Katarina Stingl
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Disease, University of Tübingen, Tübingen, Germany
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10
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Yang C, Zhou Y, Song Y, Wu D, Zeng Y, Nie L, Liu P, Zhang S, Chen G, Xu J, Zhou H, Zhou L, Qian X, Liu C, Tan S, Zhou C, Dai W, Xu M, Qi Y, Wang X, Guo L, Fan G, Wang A, Deng Y, Zhang Y, Jin J, He Y, Guo C, Guo G, Zhou Q, Xu X, Yang H, Wang J, Xu S, Mao Y, Jin X, Ruan J, Zhang G. The complete and fully-phased diploid genome of a male Han Chinese. Cell Res 2023; 33:745-761. [PMID: 37452091 PMCID: PMC10542383 DOI: 10.1038/s41422-023-00849-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Since the release of the complete human genome, the priority of human genomic study has now been shifting towards closing gaps in ethnic diversity. Here, we present a fully phased and well-annotated diploid human genome from a Han Chinese male individual (CN1), in which the assemblies of both haploids achieve the telomere-to-telomere (T2T) level. Comparison of this diploid genome with the CHM13 haploid T2T genome revealed significant variations in the centromere. Outside the centromere, we discovered 11,413 structural variations, including numerous novel ones. We also detected thousands of CN1 alleles that have accumulated high substitution rates and a few that have been under positive selection in the East Asian population. Further, we found that CN1 outperforms CHM13 as a reference genome in mapping and variant calling for the East Asian population owing to the distinct structural variants of the two references. Comparison of SNP calling for a large cohort of 8869 Chinese genomes using CN1 and CHM13 as reference respectively showed that the reference bias profoundly impacts rare SNP calling, with nearly 2 million rare SNPs miss-called with different reference genomes. Finally, applying the CN1 as a reference, we discovered 5.80 Mb and 4.21 Mb putative introgression sequences from Neanderthal and Denisovan, respectively, including many East Asian specific ones undetected using CHM13 as the reference. Our analyses reveal the advances of using CN1 as a reference for population genomic studies and paleo-genomic studies. This complete genome will serve as an alternative reference for future genomic studies on the East Asian population.
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Affiliation(s)
- Chentao Yang
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yang Zhou
- BGI-Shenzhen, Shenzhen, Guangdong, China
- BGI Research-Wuhan, BGI, Wuhan, Hubei, China
| | - Yanni Song
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Dongya Wu
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Zeng
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Lei Nie
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Guangji Chen
- BGI-Shenzhen, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinjin Xu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Hongling Zhou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaobo Qian
- BGI-Shenzhen, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chenlu Liu
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | | | | | - Wei Dai
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Mengyang Xu
- BGI-Shenzhen, Shenzhen, Guangdong, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Yanwei Qi
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Xiaobo Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lidong Guo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Aijun Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Yuan Deng
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yong Zhang
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Yunqiu He
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chunxue Guo
- BGI-Shenzhen, Shenzhen, Guangdong, China
- BGI-Hangzhou, Hangzhou, Zhejiang, China
| | - Guoji Guo
- School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qing Zhou
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, International Joint Center of Genomics of Jiangsu Province School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yafei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.
| | - Guojie Zhang
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, Zhejiang, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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11
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Davidson AL, Dressel U, Norris S, Canson DM, Glubb DM, Fortuno C, Hollway GE, Parsons MT, Vidgen ME, Holmes O, Koufariotis LT, Lakis V, Leonard C, Wood S, Xu Q, McCart Reed AE, Pickett HA, Al-Shinnag MK, Austin RL, Burke J, Cops EJ, Nichols CB, Goodwin A, Harris MT, Higgins MJ, Ip EL, Kiraly-Borri C, Lau C, Mansour JL, Millward MW, Monnik MJ, Pachter NS, Ragunathan A, Susman RD, Townshend SL, Trainer AH, Troth SL, Tucker KM, Wallis MJ, Walsh M, Williams RA, Winship IM, Newell F, Tudini E, Pearson JV, Poplawski NK, Mar Fan HG, James PA, Spurdle AB, Waddell N, Ward RL. The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants-a multi-site prospective cohort study. Genome Med 2023; 15:74. [PMID: 37723522 PMCID: PMC10507925 DOI: 10.1186/s13073-023-01223-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 08/18/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Many families and individuals do not meet criteria for a known hereditary cancer syndrome but display unusual clusters of cancers. These families may carry pathogenic variants in cancer predisposition genes and be at higher risk for developing cancer. METHODS This multi-centre prospective study recruited 195 cancer-affected participants suspected to have a hereditary cancer syndrome for whom previous clinical targeted genetic testing was either not informative or not available. To identify pathogenic disease-causing variants explaining participant presentation, germline whole-genome sequencing (WGS) and a comprehensive cancer virtual gene panel analysis were undertaken. RESULTS Pathogenic variants consistent with the presenting cancer(s) were identified in 5.1% (10/195) of participants and pathogenic variants considered secondary findings with potential risk management implications were identified in another 9.7% (19/195) of participants. Health economic analysis estimated the marginal cost per case with an actionable variant was significantly lower for upfront WGS with virtual panel ($8744AUD) compared to standard testing followed by WGS ($24,894AUD). Financial analysis suggests that national adoption of diagnostic WGS testing would require a ninefold increase in government annual expenditure compared to conventional testing. CONCLUSIONS These findings make a case for replacing conventional testing with WGS to deliver clinically important benefits for cancer patients and families. The uptake of such an approach will depend on the perspectives of different payers on affordability.
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Affiliation(s)
- Aimee L Davidson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Uwe Dressel
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Sarah Norris
- Faculty of Medicine and Health, University of Sydney, L2.22 The Quadrangle (A14), Sydney, NSW, 2006, Australia
| | - Daffodil M Canson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Dylan M Glubb
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Cristina Fortuno
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Georgina E Hollway
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Michael T Parsons
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Miranda E Vidgen
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Lambros T Koufariotis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Amy E McCart Reed
- Centre for Clinical Research, University of Queensland, Brisbane, QLD, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Mohammad K Al-Shinnag
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Rachel L Austin
- Australian Genomics, Melbourne, VIC, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Jo Burke
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Elisa J Cops
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Cassandra B Nichols
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Annabel Goodwin
- Cancer Genetics Department, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- University of Sydney, Sydney, NSW, Australia
| | - Marion T Harris
- Monash Health Familial Cancer, Monash Health, Melbourne, VIC, Australia
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Megan J Higgins
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Emilia L Ip
- Cancer Genetics, Liverpool Hospital, Sydney, NSW, Australia
| | | | - Chiyan Lau
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genomics, Pathology Queensland, Brisbane, QLD, Australia
| | - Julia L Mansour
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Michael W Millward
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Melissa J Monnik
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Nicholas S Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, Australia
| | - Abiramy Ragunathan
- Familial Cancer Services, The Crown Princess Mary Cancer Centre, Westmead Hospital, Westmead, NSW, Australia
| | - Rachel D Susman
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Sharron L Townshend
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Alison H Trainer
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - Simon L Troth
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Katherine M Tucker
- Prince of Wales Clinical School, UNSW Medicine and Health, The University of New South Wales, Sydney, NSW, Australia
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Mathew J Wallis
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Maie Walsh
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Rachel A Williams
- Prince of Wales Clinical School, UNSW Medicine and Health, The University of New South Wales, Sydney, NSW, Australia
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Ingrid M Winship
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
- Genomic Medicine and Familial Cancer Clinic, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Emma Tudini
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Nicola K Poplawski
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Helen G Mar Fan
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda B Spurdle
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia.
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Robyn L Ward
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
- Faculty of Medicine and Health, University of Sydney, L2.22 The Quadrangle (A14), Sydney, NSW, 2006, Australia.
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12
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Zhong Y, Zeng K, Adnan A, Li YZ, Hou XK, Pan Y, Li A, Zhu XM, Lv P, Du Z, Yang Y, Yao J. Discrimination of monozygotic twins using mtDNA heteroplasmy through probe capture enrichment and massively parallel sequencing. Int J Legal Med 2023; 137:1337-1345. [PMID: 37270462 DOI: 10.1007/s00414-023-03033-x] [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: 04/05/2023] [Accepted: 05/30/2023] [Indexed: 06/05/2023]
Abstract
Differentiating between monozygotic (MZ) twins remains difficult because they have the same genetic makeup. Applying the traditional STR genotyping approach cannot differentiate one from the other. Heteroplasmy refers to the presence of two or more different mtDNA copies within a single cell and this phenomenon is common in humans. The levels of heteroplasmy cannot change dramatically during transmission in the female germ line but increase or decrease during germ-line transmission and in somatic tissues during life. As massively parallel sequencing (MPS) technology has advanced, it has shown the extraordinary quantity of mtDNA heteroplasmy in humans. In this study, a probe hybridization technique was used to obtain mtDNA and then MPS was performed with an average sequencing depth of above 4000. The results showed us that all ten pairs of MZ twins were clearly differentiated with the minor heteroplasmy threshold at 1.0%, 0.5%, and 0.1%, respectively. Finally, we used a probe that targeted mtDNA to boost sequencing depth without interfering with nuclear DNA and this technique can be used in forensic genetics to differentiate the MZ twins.
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Affiliation(s)
- Yang Zhong
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Kuo Zeng
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Atif Adnan
- Department of Forensic Sciences, College of Criminal Justice, Naif University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Yu-Zhang Li
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Xi-Kai Hou
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Ying Pan
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Ang Li
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Xiu-Mei Zhu
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Peng Lv
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Zhe Du
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Ying Yang
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, China.
| | - Jun Yao
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China.
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China.
- China Medical University Center of Forensic Investigation, Chengdu, China.
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13
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Ji S, Zhu T, Sethia A, Wang W. Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.04.547569. [PMID: 37461467 PMCID: PMC10350007 DOI: 10.1101/2023.07.04.547569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Accurate detection of somatic mutations in DNA sequencing data is a fundamental prerequisite for cancer research. Previous analytical challenge was overcome by consensus mutation calling from four to five popular callers. This, however, increases the already nontrivial computing time from individual callers. Here, we launch MuSE2.0, powered by multi-step parallelization and efficient memory allocation, to resolve the computing time bottleneck. MuSE2.0 speeds up 50 times than MuSE1.0 and 8-80 times than other popular callers. Our benchmark study suggests combining MuSE2.0 and the recently expedited Strelka2 can achieve high efficiency and accuracy in analyzing large cancer genomic datasets.
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Affiliation(s)
- Shuangxi Ji
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tong Zhu
- NVIDIA Corporation, Santa Clara, CA, USA
| | | | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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14
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Shugg T, Ly RC, Osei W, Rowe EJ, Granfield CA, Lynnes TC, Medeiros EB, Hodge JC, Breman AM, Schneider BP, Sahinalp SC, Numanagić I, Salisbury BA, Bray SM, Ratcliff R, Skaar TC. Computational pharmacogenotype extraction from clinical next-generation sequencing. Front Oncol 2023; 13:1199741. [PMID: 37469403 PMCID: PMC10352904 DOI: 10.3389/fonc.2023.1199741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/22/2023] [Indexed: 07/21/2023] Open
Abstract
Background Next-generation sequencing (NGS), including whole genome sequencing (WGS) and whole exome sequencing (WES), is increasingly being used for clinic care. While NGS data have the potential to be repurposed to support clinical pharmacogenomics (PGx), current computational approaches have not been widely validated using clinical data. In this study, we assessed the accuracy of the Aldy computational method to extract PGx genotypes from WGS and WES data for 14 and 13 major pharmacogenes, respectively. Methods Germline DNA was isolated from whole blood samples collected for 264 patients seen at our institutional molecular solid tumor board. DNA was used for panel-based genotyping within our institutional Clinical Laboratory Improvement Amendments- (CLIA-) certified PGx laboratory. DNA was also sent to other CLIA-certified commercial laboratories for clinical WGS or WES. Aldy v3.3 and v4.4 were used to extract PGx genotypes from these NGS data, and results were compared to the panel-based genotyping reference standard that contained 45 star allele-defining variants within CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, CYP4F2, DPYD, G6PD, NUDT15, SLCO1B1, TPMT, and VKORC1. Results Mean WGS read depth was >30x for all variant regions except for G6PD (average read depth was 29 reads), and mean WES read depth was >30x for all variant regions. For 94 patients with WGS, Aldy v3.3 diplotype calls were concordant with those from the genotyping reference standard in 99.5% of cases when excluding diplotypes with additional major star alleles not tested by targeted genotyping, ambiguous phasing, and CYP2D6 hybrid alleles. Aldy v3.3 identified 15 additional clinically actionable star alleles not covered by genotyping within CYP2B6, CYP2C19, DPYD, SLCO1B1, and NUDT15. Within the WGS cohort, Aldy v4.4 diplotype calls were concordant with those from genotyping in 99.7% of cases. When excluding patients with CYP2D6 copy number variation, all Aldy v4.4 diplotype calls except for one CYP3A4 diplotype call were concordant with genotyping for 161 patients in the WES cohort. Conclusion Aldy v3.3 and v4.4 called diplotypes for major pharmacogenes from clinical WES and WGS data with >99% accuracy. These findings support the use of Aldy to repurpose clinical NGS data to inform clinical PGx.
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Affiliation(s)
- Tyler Shugg
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Reynold C. Ly
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Wilberforce Osei
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Elizabeth J. Rowe
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Caitlin A. Granfield
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Ty C. Lynnes
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Elizabeth B. Medeiros
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jennelle C. Hodge
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Amy M. Breman
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Bryan P. Schneider
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - S. Cenk Sahinalp
- Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, United States
| | - Ibrahim Numanagić
- Department of Computer Science, University of Victoria, Victoria, BC, Canada
| | | | | | | | - Todd C. Skaar
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
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15
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Yang Z, Yang X, Sun Y, Wang Y, Song L, Qiao Z, Fang Z, Wang Z, Liu L, Chen Y, Yan S, Guo X, Zhang J, Fan C, Liu F, Peng Z, Peng H, Sun J, Chen W. Test development, optimization and validation of a WGS pipeline for genetic disorders. BMC Med Genomics 2023; 16:74. [PMID: 37020281 PMCID: PMC10077614 DOI: 10.1186/s12920-023-01495-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND With advances in massive parallel sequencing (MPS) technology, whole-genome sequencing (WGS) has gradually evolved into the first-tier diagnostic test for genetic disorders. However, deployment practice and pipeline testing for clinical WGS are lacking. METHODS In this study, we introduced a whole WGS pipeline for genetic disorders, which included the entire process from obtaining a sample to clinical reporting. All samples that underwent WGS were constructed using polymerase chain reaction (PCR)-free library preparation protocols and sequenced on the MGISEQ-2000 platform. Bioinformatics pipelines were developed for the simultaneous detection of various types of variants, including single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs) and balanced rearrangements, mitochondrial (MT) variants, and other complex variants such as repeat expansion, pseudogenes and absence of heterozygosity (AOH). A semiautomatic pipeline was developed for the interpretation of potential SNVs and CNVs. Forty-five samples (including 14 positive commercially available samples, 23 laboratory-held positive cell lines and 8 clinical cases) with known variants were used to validate the whole pipeline. RESULTS In this study, a whole WGS pipeline for genetic disorders was developed and optimized. Forty-five samples with known variants (6 with SNVs and Indels, 3 with MT variants, 5 with aneuploidies, 1 with triploidy, 23 with CNVs, 5 with balanced rearrangements, 2 with repeat expansions, 1 with AOHs, and 1 with exon 7-8 deletion of SMN1 gene) validated the effectiveness of our pipeline. CONCLUSIONS This study has been piloted in test development, optimization, and validation of the WGS pipeline for genetic disorders. A set of best practices were recommended using our pipeline, along with a dataset of positive samples for benchmarking.
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Affiliation(s)
- Ziying Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Xu Yang
- Department of Paediatrics, Pu'er People's Hospital, Pu'er, 665000, China
| | - Yan Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lijie Song
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- DTU Bioengineering, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Zhihong Qiao
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhonghai Fang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhonghua Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lipei Liu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yunmei Chen
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Saiying Yan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Xueqin Guo
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 430074, China
| | - Junqing Zhang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Chunna Fan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Fengxia Liu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huanhuan Peng
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.
| | - Wei Chen
- Pu'er People's Hospital, Pu'er, 665000, China.
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Jia Y, Chen J, Zhong J, He X, Zeng L, Wang Y, Li J, Xia S, Ye E, Zhao J, Ke B, Li C. Novel rare mutation in a conserved site of PTPRB causes human hypoplastic left heart syndrome. Clin Genet 2023; 103:79-86. [PMID: 36148623 DOI: 10.1111/cge.14234] [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: 08/17/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 12/14/2022]
Abstract
Hypoplastic left heart syndrome (HLHS) is a rare but fatal birth defect in which the left side of the heart is underdeveloped. HLHS accounts for 2% to 4% of congenital heart anomalies. Whole genome sequencing (WGS) was conducted for a family trio consisting of a proband and his parents. A homozygous rare variant was detected in the PTPRB (Protein Tyrosine Phosphatase Receptor Type B) gene of the proband by functional annotation and co-segregation analysis. Sanger sequencing was used to confirm genotypes of the variant. The in silico prediction tools, including Mutation Taster, SpliceAI, and CADD, were used to predict the impact of the mutation. The allele frequencies across populations were compared based on multiple databases, including "1000 genomes" and "gnomAD". We used two vectors (pcMINI and pcDNA3.1) to generate a minigene construct to validate the mutational effect at the transcriptional level. Family-based WGS analyses showed that only a homozygous splice acceptor variant (NC_000012.12: g.70636068T>G, NM_001109754.4: c.56-2A>C, NG_029940.2: g.6373A>C) at the exon-intron border of PTPRB gene associates with HLHS. This variant is also within the region with the enhancer activity based on UCSC genome annotation. Genotyping and Sanger sequencing revealed that the proband's parents are heterozygous for this variant. Evolutionary conservation analysis revealed that the site (NC_000012.12: g.70636068) is extremely conserved across species, supporting the evolutionary functional constraints of the ancestral wild type (T). In silico tools universally predicted a deleterious or disease-causing impact of the mutation from T to G. The mutation was not found in the 1000 genomes and gnomAD databases, which indicates that this mutation is very rare in most human populations. A splicing assay indicated that the mutated minigene caused aberrant splicing of mRNA, in which a 3 bp missing in the second exon resulted in the deletion of one amino acid (NP_001103224.1:p.Glu19del) compared to the normal protein of PRPTB (also the VE-PTP). Structure prediction revealed that the deletion occurred within the C-region of the signal peptide of VE-PTP, suggesting signal peptide-related defects as a potential mechanism for the HLHS cellular pathogeny. We report a rare homozygous variant with splicing error in PTPRB associated with HLHS. Previous model species studies revealed conserved functions of PTPRB in cardiovascular and heart development in mice and zebrafish. Our study is the first report to show the association between PTPRB and HLHS in humans.
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Affiliation(s)
- Yangying Jia
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jianhai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jie Zhong
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xuefei He
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Li Zeng
- The Department of Pediatric Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yanmin Wang
- Chinese Institute for Brain Research, Beijing, China
| | - Jiakun Li
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Erdengqieqieke Ye
- Department of Prenatal Diagnosis, Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Jing Zhao
- Department of Prenatal Diagnosis, Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Bin Ke
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
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17
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Chen J, Ying L, Zeng L, Li C, Jia Y, Yang H, Yang G. The novel compound heterozygous rare variants may impact positively selected regions of TUBGCP6, a microcephaly associated gene. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1059477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
IntroductionThe microcephaly is a rare and severe disease probably under purifying selection due to the reduction of human brain-size. In contrast, the brain-size enlargement is most probably driven by positive selection, in light of this critical phenotypical innovation during primates and human evolution. Thus, microcephaly-related genes were extensively studied for signals of positive selection. However, whether the pathogenic variants of microcephaly-related genes could affect the regions of positive selection is still unclear.MethodsHere, we conducted whole genome sequencing (WGS) and positive selection analysis.ResultsWe identified novel compound heterozygous variants, p.Y613* and p.E1368K in TUBGCP6, related to microcephaly in a Chinese family. The genotyping and the sanger sequencing revealed the maternal and the paternal origin for the first and second variant, respectively. The p.Y613* occurred before the second and third domain of TUBGCP6 protein, while p.E1368K located within the linker region of the second and third domain. Interestingly, using multiple positive selection analyses, we revealed the potential impacts of these variants on the regions of positive selection of TUBGCP6. The truncating variant p.Y613* could lead to the deletions of two positively selected domains DUF5401 and Spc97_Spc98, while p.E1368K could impose a rare mutation burden on the linker region between these two domains.DiscussionOur investigation expands the list of candidate pathogenic variants of TUBGCP6 that may cause microcephaly. Moreover, the study provides insights into the potential pathogenic effects of variants that truncate or distribute within the positively selected regions.
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18
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Tengsujaritkul M, Suratannon N, Ittiwut C, Ittiwut R, Chatchatee P, Suphapeetiporn K, Shotelersuk V. Phenotypic heterogeneity and genotypic spectrum of inborn errors of immunity identified through whole exome sequencing in a Thai patient cohort. Pediatr Allergy Immunol 2022; 33:e13701. [PMID: 34796988 DOI: 10.1111/pai.13701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Inborn errors of immunity (IEI) comprise more than 400 rare diseases with potential life-threatening conditions. Clinical manifestations and genetic defects are heterogeneous and diverse among populations. Here, we aimed to characterize the clinical, immunologic, and genetic features of Thai pediatric patients with IEI. The use of whole-exome sequencing (WES) in diagnosis and clinical decision making was also assessed. METHODS Thirty six unrelated patients with clinical and laboratory findings consistent with IEI were recruited from January 2010 to December 2020. WES was performed to identify the underlying genetic defects. RESULTS The median age of disease onset was 4 months (range: 1 month to 13 years), and 24 were male (66.7%). Recurrent sinopulmonary tract infection was the most common clinical presentation followed by septicemia and severe pneumonia. Using WES, we successfully identified the underlying genetic defects in 18 patients (50%). Of the 20 variants identified, six have not been previously described (30%). According to the International Union of Immunological Societies (IUIS), 38.9% of these detected cases (7/18) were found to harbor variants associated with genes in combined immunodeficiencies with associated or syndromic features (Class II). CONCLUSION The diagnostic yield of WES in this patient cohort was 50%. Six novel genetic variants in IEI genes were identified. The clinical usefulness of WES in IEI was demonstrated, emphasizing it as an effective diagnostic strategy in these genetically heterogeneous disorders.
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Affiliation(s)
- Maliwan Tengsujaritkul
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.,Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, Thailand
| | - Narissara Suratannon
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, the Thai Red Cross Society, Bangkok, Thailand
| | - Chupong Ittiwut
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.,Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, Thailand
| | - Rungnapa Ittiwut
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.,Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, Thailand
| | - Pantipa Chatchatee
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, the Thai Red Cross Society, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.,Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.,Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, Thailand
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