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Guo W, Lu T, Song Y, Li A, Feng X, Han D, Cao Y, Sun D, Gong X, Li C, Jin R, Du H, Chen K, Xiang J, Hang J, Chen G, Li H. Lymph node metastasis in early invasive lung adenocarcinoma: Prediction model establishment and validation based on genomic profiling and clinicopathologic characteristics. Cancer Med 2024; 13:e70039. [PMID: 39046176 PMCID: PMC11267562 DOI: 10.1002/cam4.70039] [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: 01/06/2024] [Revised: 06/22/2024] [Accepted: 07/12/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND The presence of lymph node (LN) metastasis directly affects the treatment strategy for lung adenocarcinoma (LUAD). Next-generation sequencing (NGS) has been widely used in patients with advanced LUAD to identify targeted genes, while early detection of pathologic LN metastasis using NGS has not been assessed. METHODS Clinicopathologic features and molecular characteristics of 224 patients from Ruijin Hospital were analyzed to detect factors associated with LN metastases. Another 140 patients from Huashan Hospital were set as a test cohort. RESULTS Twenty-four out of 224 patients were found to have lymph node metastases (10.7%). Pathologic LN-positive tumors showed higher mutant allele tumor heterogeneity (p < 0.05), higher tumor mutation burden (p < 0.001), as well as more frequent KEAP1 (p = 0.001), STK11 (p = 0.004), KRAS (p = 0.007), CTNNB1 (p = 0.017), TP53, and ARID2 mutations (both p = 0.02); whereas low frequency of EGFR mutation (p = 0.005). A predictive nomogram involving male sex, solid tumor morphology, higher T stage, EGFR wild-type, and TP53, STK11, CDKN2A, KEAP1, ARID2, KRAS, SDHA, SPEN, CTNNB1, DICER1 mutations showed outstanding efficiency in both the training cohort (AUC = 0.819) and the test cohort (AUC = 0.780). CONCLUSION This study suggests that the integration of genomic profiling and clinical features identifies early-invasive LUAD patients at higher risk of LN metastasis. Improved identification of LN metastasis is beneficial for the optimization of the patient's therapy decisions.
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Affiliation(s)
- Wei Guo
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Tong Lu
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yang Song
- Department of Thoracic SurgeryHuashan Hospital, Fudan UniversityShanghaiChina
| | - Anqi Li
- Department of PathologyRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xijia Feng
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Dingpei Han
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yuqin Cao
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Debin Sun
- Genecast Biotechnology Co., LtdWuxiChina
| | | | - Chengqiang Li
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Runsen Jin
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Hailei Du
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Kai Chen
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Jie Xiang
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Junbiao Hang
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Gang Chen
- Department of Thoracic SurgeryHuashan Hospital, Fudan UniversityShanghaiChina
| | - Hecheng Li
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
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Ji H, Shu Y, Li H. Unveiling a novel GJB2 dominant K22T mutation in a Chinese family with hearing loss. Acta Biochim Biophys Sin (Shanghai) 2024; 56:945-951. [PMID: 38733163 PMCID: PMC11292126 DOI: 10.3724/abbs.2024064] [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: 11/17/2023] [Accepted: 01/16/2024] [Indexed: 05/13/2024] Open
Abstract
Hearing loss constitutes one of the most prevalent conditions within the field of otolaryngology. Recent investigations have revealed that mutations in deafness-associated genes, including point mutations and variations in DNA sequences, can cause hearing impairments. With the ethology of deafness remaining unclear for a substantial portion of the affected population, further screenings for pathogenic mutations are imperative to unveil the underlying mechanisms. On this study, by using next-generation sequencing, we examine 129 commonly implicated deafness-related genes in a Chinese family with hearing loss, revealing a novel heterozygous dominant mutation in the GJB2 gene (GJB2: c.65T>G: p. Lys22Thr). This mutation consistently occurs in affected family members but is not detected in unaffected individuals, strongly suggesting its causative role in hearing loss. Structural analysis indicates potential disruption to the Cx26 gap junction channel's hydrogen bond and electrostatic interactions, aligning with predictions from the PolyPhen and SIFT algorithms. In conclusion, our study provides conclusive evidence that the identified heterozygous GJB2 mutation (GJB2: c.65T>G: p. Lys22Thr), specifically the K22T alteration, is the primary determinant of the family's deafness. This contribution enhances our understanding of the interplay between common deafness-associated genes and hearing loss, offering valuable insights for diagnostic guidance and the formulation of therapeutic strategies for this condition.
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Affiliation(s)
- Haiting Ji
- Department of the Affiliated Eye and ENT HospitalState Key Laboratory of Medical NeurobiologyENT Institute and OtorhinolaryngologyFudan UniversityShanghai200031China
- NHC Key Laboratory of Hearing MedicineFudan UniversityShanghai200031China
- Shanghai Engineering Research Centre of Cochlear ImplantShanghai200031China
- ENT Institute and Otorhinolaryngology Department of Eye & ENT HospitalState Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghai200031China
| | - Yilai Shu
- Department of the Affiliated Eye and ENT HospitalState Key Laboratory of Medical NeurobiologyENT Institute and OtorhinolaryngologyFudan UniversityShanghai200031China
- NHC Key Laboratory of Hearing MedicineFudan UniversityShanghai200031China
- Shanghai Engineering Research Centre of Cochlear ImplantShanghai200031China
- ENT Institute and Otorhinolaryngology Department of Eye & ENT HospitalState Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghai200031China
- Institutes of Biomedical SciencesFudan UniversityShanghai200032China
| | - Huawei Li
- Department of the Affiliated Eye and ENT HospitalState Key Laboratory of Medical NeurobiologyENT Institute and OtorhinolaryngologyFudan UniversityShanghai200031China
- NHC Key Laboratory of Hearing MedicineFudan UniversityShanghai200031China
- Shanghai Engineering Research Centre of Cochlear ImplantShanghai200031China
- ENT Institute and Otorhinolaryngology Department of Eye & ENT HospitalState Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghai200031China
- Institutes of Biomedical SciencesFudan UniversityShanghai200032China
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3
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Wu LS, Luo X, Tan M, Zhang LJ, Luo HF, Huang G, Huang P, Chen J, Chen Y. Prevalence of thalassemia-carrier couples and fertility risk assessment. Int J Hematol 2024; 119:374-382. [PMID: 38411864 DOI: 10.1007/s12185-024-03722-2] [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: 08/02/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/28/2024]
Abstract
Thalassemia is a highly prevalent hematologic disease in Guizhou, China. This study aimed to determine the epidemiological characteristics of thalassemia in couples at childbearing age and assess the neonatal risk of thalassemia in this subpopulation. A cohort of 4481 couples at childbearing age were recruited for thalassemia carrier screening by both traditional hematological tests and next-generation sequencing. Of them, 1314 (14.66%) thalassemia carriers were identified, including 857 (9.76%) α-thalassemia, 391 (4.36%) β-thalassemia, and 48 (0.54%) composite α and β-thalassemia. A total of 12 α-globin gene alterations and 16 β-globin mutations were detected, including four novel thalassemia mutations. SEA was the most common α-thalassemia genotype (26.86%), CD41-42 the most common β-thalassemia genotype (36.57%), and αα/- α3.7 + CD41-42 the most common composite α- and β-thalassemia genotype (18.75%). Ethnically, the Zhuang had the highest rate of thalassemia gene carriers among the ethnic groups. Geographically, Qiannan had the highest rate of thalassemia gene carriers. In addition, 38 of the 48 couples with composite α- and β-thalassemia were high-risk thalassemia carriers, and 4 carrying the -SEA/αα gene needed fertility guidance.
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Affiliation(s)
- Liu-Song Wu
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Xi Luo
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Mei Tan
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Li-Jun Zhang
- Department of Pediatrics, The Qian-Nan-Zhou People's Hospital of Guizhou, Guizhou, China
| | - Hong-Fang Luo
- Department of Pediatrics, The 2nd Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Ge Huang
- Clinical Laboratory, The Qian-Dong-Nan People's Hospital of Guizhou, Guizhou, China
| | - Pei Huang
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Jindong Chen
- Exploring Health, LLC., 3 Lanyue Rd., Huangpu District, Guangzhou, 510663, China.
- Department of Urology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
| | - Yan Chen
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China.
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China.
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China.
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4
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Gupta P, Arvinden VR, Thakur P, Bhoyar RC, Saravanakumar V, Gottumukkala NV, Goswami SG, Nafiz M, Iyer AR, Vignesh H, Soni R, Bhargava N, Gunda P, Jain S, Gupta V, Sivasubbu S, Scaria V, Ramalingam S. Scalable noninvasive amplicon-based precision sequencing (SNAPseq) for genetic diagnosis and screening of β-thalassemia and sickle cell disease using a next-generation sequencing platform. Front Mol Biosci 2023; 10:1244244. [PMID: 38152111 PMCID: PMC10751313 DOI: 10.3389/fmolb.2023.1244244] [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: 06/22/2023] [Accepted: 11/16/2023] [Indexed: 12/29/2023] Open
Abstract
β-hemoglobinopathies such as β-thalassemia (BT) and Sickle cell disease (SCD) are inherited monogenic blood disorders with significant global burden. Hence, early and affordable diagnosis can alleviate morbidity and reduce mortality given the lack of effective cure. Currently, Sanger sequencing is considered to be the gold standard genetic test for BT and SCD, but it has a very low throughput requiring multiple amplicons and more sequencing reactions to cover the entire HBB gene. To address this, we have demonstrated an extraction-free single amplicon-based approach for screening the entire β-globin gene with clinical samples using Scalable noninvasive amplicon-based precision sequencing (SNAPseq) assay catalyzing with next-generation sequencing (NGS). We optimized the assay using noninvasive buccal swab samples and simple finger prick blood for direct amplification with crude lysates. SNAPseq demonstrates high sensitivity and specificity, having a 100% agreement with Sanger sequencing. Furthermore, to facilitate seamless reporting, we have created a much simpler automated pipeline with comprehensive resources for pathogenic mutations in BT and SCD through data integration after systematic classification of variants according to ACMG and AMP guidelines. To the best of our knowledge, this is the first report of the NGS-based high throughput SNAPseq approach for the detection of both BT and SCD in a single assay with high sensitivity in an automated pipeline.
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Affiliation(s)
- Pragya Gupta
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - V. R. Arvinden
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priya Thakur
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rahul C. Bhoyar
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
| | | | | | - Sangam Giri Goswami
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mehwish Nafiz
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Ramdas Iyer
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Harie Vignesh
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
| | - Rajat Soni
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
| | - Nupur Bhargava
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
| | - Padma Gunda
- Thalassemia and Sickle Cell Society, Hyderabad, India
| | - Suman Jain
- Thalassemia and Sickle Cell Society, Hyderabad, India
| | - Vivek Gupta
- Government Institute of Medical Sciences (GIMS), Greater Noida, India
| | - Sridhar Sivasubbu
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vinod Scaria
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sivaprakash Ramalingam
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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5
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Salido-Guadarrama I, Romero-Cordoba SL, Rueda-Zarazua B. Multi-Omics Mining of lncRNAs with Biological and Clinical Relevance in Cancer. Int J Mol Sci 2023; 24:16600. [PMID: 38068923 PMCID: PMC10706612 DOI: 10.3390/ijms242316600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
In this review, we provide a general overview of the current panorama of mining strategies for multi-omics data to investigate lncRNAs with an actual or potential role as biological markers in cancer. Several multi-omics studies focusing on lncRNAs have been performed in the past with varying scopes. Nevertheless, many questions remain regarding the pragmatic application of different molecular technologies and bioinformatics algorithms for mining multi-omics data. Here, we attempt to address some of the less discussed aspects of the practical applications using different study designs for incorporating bioinformatics and statistical analyses of multi-omics data. Finally, we discuss the potential improvements and new paradigms aimed at unraveling the role and utility of lncRNAs in cancer and their potential use as molecular markers for cancer diagnosis and outcome prediction.
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Affiliation(s)
- Ivan Salido-Guadarrama
- Departamento de Bioinformatìca y Análisis Estadísticos, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City 11000, Mexico
| | - Sandra L. Romero-Cordoba
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
- Biochemistry Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico
| | - Bertha Rueda-Zarazua
- Posgrado en Ciencias Biológicas, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
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Tu T, Chen D, Jiang H, Ma J, Wang H, Chen C. The Prognosis of Advanced Non-Small Cell Lung Cancer Patients with Precision-Targeted Therapy Guided by NGS Testing or Routine Testing. Cancer Manag Res 2023; 15:1307-1318. [PMID: 38027245 PMCID: PMC10658950 DOI: 10.2147/cmar.s436808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/09/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose We aim to observe the potential survival benefits of driver gene-guided targeted therapy in advanced non-small cell lung cancer (NSCLC) patients compared to non-targeted therapy. Additionally, the study aims to assess whether Next-generation sequencing technology (NGS)-guided targeted therapy can provide survival advantages for advanced NSCLC patients compared to conventional Epidermal growth factor receptor (EGFR)/anaplastic lymphoma kinase (ALK) gene detection. Methods Clinical data, genetic testing results, and treatment information of 1663 advanced lung cancer patients diagnosed by pathology from January 2013 to June 2019 in Jiangsu University Affiliated Lianyungang Hospital were collected. Propensity score matching survival analysis was used to evaluate the differences in overall survival(OS) between groups. Results In the unadjusted survival curve, targeted therapy patients had significantly longer median OS than non-targeted therapy patients (28.3 months vs 15.4 months, Hazard ratio (HR) = 0.5426, 95% confidence interval (CI) 0.4768-0.6176, P < 0.0001); the conclusion was the same after propensity score matching analysis, with targeted therapy group patients having significantly prolonged OS median (27.5 months vs 14.8 months, HR = 0.5572, 95% CI 0.4796-0.6474, P < 0.0001). In the unadjusted survival curve, the NGS group had a significantly prolonged median OS compared to the conventional gene detection group (23.4 months vs 21.2 months, HR = 1.243, 95% CI = 1.017-1.519, P = 0.0495). However, after propensity score matching analysis, no statistically significant difference existed in the median OS between the two patient groups (23.1 months vs 21.5 months, HR = 1.288, 95% CI = 0.9557-1.735, P = 0.0926). Further analysis demonstrated no advantage in the five-, three-, and two-year survival rates of the NGS group compared to conventional gene detection group patients. However, the one-year survival rate of the NGS group was significantly increased (83.2% vs 68.1%, HR = 0.4890, 95% CI = 0.3170-0.7544, P = 0.0015). Conclusion Driver gene-guided targeted precision therapy significantly prolonged the median OS of advanced NSCLC patients compared to non-targeted therapy. NGS detection did not improve the median OS of advanced NSCLC patients compared to conventional EGFR/ALK gene detection but increased the one-year survival rate of patients.
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Affiliation(s)
- Tingting Tu
- Department of Radiotherapy, Lianyungang Clinical Institute, Jiangsu University (The Second People’s Hospital of Lianyungang), Lianyungang, Jiangsu Province, People’s Republic of China
- Department of Radiotherapy, Lianyungang Cancer Hospital, Lianyungang, Jiangsu Province, People’s Republic of China
| | - Dandan Chen
- Department of Radiotherapy, Lianyungang Clinical Institute, Jiangsu University (The Second People’s Hospital of Lianyungang), Lianyungang, Jiangsu Province, People’s Republic of China
- Department of Radiotherapy, Lianyungang Cancer Hospital, Lianyungang, Jiangsu Province, People’s Republic of China
| | - Houjun Jiang
- Department of Radiotherapy, Lianyungang Clinical Institute, Jiangsu University (The Second People’s Hospital of Lianyungang), Lianyungang, Jiangsu Province, People’s Republic of China
- Department of Radiotherapy, Lianyungang Cancer Hospital, Lianyungang, Jiangsu Province, People’s Republic of China
| | - Jianhua Ma
- Department of Radiotherapy, Lianyungang Clinical Institute, Jiangsu University (The Second People’s Hospital of Lianyungang), Lianyungang, Jiangsu Province, People’s Republic of China
- Department of Radiotherapy, Lianyungang Cancer Hospital, Lianyungang, Jiangsu Province, People’s Republic of China
| | - Hongwei Wang
- Department of Radiotherapy, Lianyungang Clinical Institute, Jiangsu University (The Second People’s Hospital of Lianyungang), Lianyungang, Jiangsu Province, People’s Republic of China
- Department of Radiotherapy, Lianyungang Cancer Hospital, Lianyungang, Jiangsu Province, People’s Republic of China
| | - Cheng Chen
- Department of Radiotherapy, Lianyungang Clinical Institute, Jiangsu University (The Second People’s Hospital of Lianyungang), Lianyungang, Jiangsu Province, People’s Republic of China
- Department of Radiotherapy, Lianyungang Cancer Hospital, Lianyungang, Jiangsu Province, People’s Republic of China
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Yang T, Luo X, Liu Y, Lin M, Zhao Q, Zhang W, Chen Z, Dong M, Wang J, Wang Q, Zhang X, Zhong T. Next-generation sequencing analysis of the molecular spectrum of thalassemia in Southern Jiangxi, China. Hum Genomics 2023; 17:77. [PMID: 37592328 PMCID: PMC10436446 DOI: 10.1186/s40246-023-00520-5] [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: 06/05/2023] [Accepted: 07/26/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Thalassemia is an extremely prevalent monogenic inherited blood disorder in southern China. It is important to comprehensively understand the molecular spectrum of thalassemia in an area with such a high prevalence of thalassemia before taking appropriate actions for the prevention and treatment of this disorder. Herein, we explored the clinical feasibility of using next-generation sequencing (NGS) for large-scale population screening to illustrate the prevalence and spectrum of thalassemia in Southern Jiangxi. METHODS Blood samples collected from 136,312 residents of reproductive age in Southern Jiangxi were characterized for thalassemia by NGS. A retrospective analysis was then conducted on blood samples determined to be positive for thalassemia. RESULTS In total, 19,827 (14.545%) subjects were diagnosed as thalassemia carriers, and the thalassemia prevalence rate significantly varied by geographical region (p < 0.001). A total of 40 α-thalassemia genotypes including 21 rare genotypes were identified, with -@-SEA/αα being the most prevalent genotype. 42 β-thalassemia genotypes including 27 rare genotypes were identified, with the most common mutation IVS II-654 C > T accounting for 35.257% of these β-thalassemia genotypes. Furthermore, 74 genotypes were identified among 608 individuals with combined α- and β-thalassemia. Notably, most individuals with rare thalassemia mutations had mildly abnormal hematologic parameters including microcytic hypochromia. CONCLUSIONS Our findings demonstrate the great heterogeneity and diverse spectrum of thalassemia in Southern Jiangxi, emphasizing the importance and necessity of persistent prevention and control of thalassemia in this region. Additionally, our findings further suggest that NGS can effectively identify rare mutations and reduce the misdiagnosis rate of thalassemia.
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Affiliation(s)
- Tong Yang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Xuemei Luo
- Ganzhou Municipal Health Commission, Ganzhou, China
| | - Yanqiu Liu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Min Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Qinfei Zhao
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Wenqian Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Zhigang Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Minghua Dong
- School of Public Health and Health Management, Gannan Medical University, Ganzhou, China
| | - Junli Wang
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Qi Wang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Xiaokang Zhang
- School of Public Health and Health Management, Gannan Medical University, Ganzhou, China.
| | - Tianyu Zhong
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China.
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, China.
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8
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Crooks KR, Farwell Hagman KD, Mandelker D, Santani A, Schmidt RJ, Temple-Smolkin RL, Lincoln SE. Recommendations for Next-Generation Sequencing Germline Variant Confirmation: A Joint Report of the Association for Molecular Pathology and National Society of Genetic Counselors. J Mol Diagn 2023; 25:411-427. [PMID: 37207865 DOI: 10.1016/j.jmoldx.2023.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/27/2023] [Accepted: 03/30/2023] [Indexed: 05/21/2023] Open
Abstract
Clinical laboratory implementation of next-generation sequencing (NGS)-based constitutional genetic testing has been rapid and widespread. In the absence of widely adopted comprehensive guidance, there remains substantial variability among laboratories in the practice of NGS. One issue of sustained discussion in the field is whether and to what extent orthogonal confirmation of genetic variants identified by NGS is necessary or helpful. The Association for Molecular Pathology Clinical Practice Committee convened the NGS Germline Variant Confirmation Working Group to assess current evidence regarding orthogonal confirmation and to establish recommendations for standardizing orthogonal confirmation practices to support quality patient care. On the basis of the results of a survey of the literature, a survey of laboratory practices, and subject expert matter consensus, eight recommendations are presented, providing a common framework for clinical laboratory professionals to develop or refine individualized laboratory policies and procedures regarding orthogonal confirmation of germline variants detected by NGS.
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Affiliation(s)
- Kristy R Crooks
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
| | - Kelly D Farwell Hagman
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California
| | - Diana Mandelker
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Avni Santani
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; LetsGetChecked, PrivaPath Diagnostics, Dublin, Ireland; Veritas Genetics, Danvers, Massachusetts
| | - Ryan J Schmidt
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | | | - Stephen E Lincoln
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; InVitae, Bethesda, Maryland
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Lee H, Lee S, Park C, Yeom M, Lim JW, Vu TTH, Kim E, Song D, Haam S. Rapid Visible Detection of African Swine Fever Virus Using Hybridization Chain Reaction-Sensitized Magnetic Nanoclusters and Affinity Chromatography. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2207117. [PMID: 36960666 DOI: 10.1002/smll.202207117] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/09/2023] [Indexed: 06/18/2023]
Abstract
African swine fever virus (ASFV) is a severe and persistent threat to the global swine industry. As there are no vaccines against ASFV, there is an immense need to develop easy-to-use, cost-effective, and rapid point-of-care (POC) diagnostic platforms to detect and prevent ASFV outbreaks. Here, a novel POC diagnostic system based on affinity column chromatography for the optical detection of ASFV is presented. This system employs an on-particle hairpin chain reaction to sensitize magnetic nanoclusters with long DNA strands in a target-selective manner, which is subsequently fed into a column chromatography device to produce quantitatively readable and colorimetric signals. The detection approach does not require expensive analytical apparatus or immobile instrumentation. The system can detect five genes constituting the ASFV whole genome with a detection limit of ≈19.8 pm in swine serum within 30 min at laboratory room temperature. With an additional pre-amplification step using polymerase chain reaction (PCR), the assay is successfully applied to detect the presence of ASFV in 30 suspected swine samples with 100% sensitivity and specificity, similar to quantitative PCR. Thus, this simple, inexpensive, portable, robust, and customizable platform for the early detection of ASFV can facilitate the timely surveillance and implementation of control measures.
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Affiliation(s)
- Hyo Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sojeong Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Chaewon Park
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Minjoo Yeom
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jong-Woo Lim
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Thi Thu Hang Vu
- Department of Preclinical Science, College of Pharmacy, Korea University Sejong Campus, Sejong City, 30019, Republic of Korea
| | - Eunjung Kim
- Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
- Department of Bioengineering & Nano-Bioengineering, Research Center for Bio Materials and Process Development, Incheon National University, Incheon, 22012, Republic of Korea
| | - Daesub Song
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seungjoo Haam
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul, 03722, Republic of Korea
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Rehm HL. 2022 Curt Stern Award: Advancing genomic medicine through collaboration and data sharing. Am J Hum Genet 2023; 110:410-413. [PMID: 36868203 PMCID: PMC10036750 DOI: 10.1016/j.ajhg.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
This article is based on the address given by the author at the 2022 meeting of The American Society of Human Genetics (ASHG) in Los Angeles, CA. The video of the original address can be found at the ASHG website.
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Affiliation(s)
- Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA.
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11
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Li X, Chen X, Mao M, Peng C, Wang Z. Accelerated CRISPR/Cas12a-based small molecule detection using bivalent aptamer. Biosens Bioelectron 2022; 217:114725. [PMID: 36179433 DOI: 10.1016/j.bios.2022.114725] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022]
Abstract
CRISPR/Cas holds great promise for biosensing applications, however, restricted to nucleic acid targets. Here, we broaden the sensing target of CRISPR/Cas to small molecules via integrating a bivalent aptamer as a recognition component. Using adenosine 5'-triphosphate (ATP) as a model molecule, we found that a bivalent aptamer we selected could shorten the binding time between the aptamer and ATP from 30 min to 3 min, thus dramatically accelerating the detection of ATP. The accelerated bivalent aptamer binding to ATP was mainly ascribed to the extended conformation of the aptamer, which was stabilized through linking with a 5 T bases connector on specific loops of the monovalent aptamer. To facilitate on-site detection, we integrated lateral flow assay (LFA) with the CRISPR/Cas sensing strategy (termed BA-CASLFA) to serve as a visual readout of the presence of ATP. In addition, in the CASLFA platform, due to the unique characteristics of LFA, the thermal step of Cas12a inactivation can be omitted. The BA-CASLFA could output a colorimetric "TURN ON" signal for ATP within 26 min, which could be easily discriminated by the naked eye and sensitively quantified by the portable reader. Furthermore, we showed the versatility of BA-CASLFA for detecting kanamycin using a kanamycin bivalent aptamer obtained through the same design as the ATP bivalent aptamer. Therefore, this strategy is amenable to serve as a general sensing strategy for small molecular targets. The above work opened a new way in developing CRISPR-based on-site sensors for clinic diagnosis, food safety, and environmental analysis.
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Affiliation(s)
- Xiuping Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China
| | - Xiujin Chen
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471000, PR China
| | - Minxin Mao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China
| | - Chifang Peng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China.
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China
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12
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Development of a Handheld Nano-centrifugal Device for Visual Virus Detection. JOURNAL OF ANALYSIS AND TESTING 2022; 6:353-364. [PMID: 35966388 PMCID: PMC9361950 DOI: 10.1007/s41664-022-00232-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/12/2022] [Indexed: 11/20/2022]
Abstract
Gold nanoparticles (AuNPs) colorimetric assays based on distance-dependent optical characteristics have been widely employed for bioanalysis. However, this assay is not effective for visually detecting low-concentration targets due to the faint color change. Here, we developed a handheld nano-centrifugal device which could separate the crosslinked and non-crosslinked AuNPs. Results showed that the handheld nano-centrifugal device could easily reach more than 6000 r/min within 10 s simply by stretching and tightening the coiled rope in an appropriate rhythm. Further, combined with the CRISPR/Cas12a nucleic acids recognition system, a field-deployable colorimetric platform termed handheld nano-centrifugal device assisted CRISPR/Cas12a (Hand-CRISPR) has been validated. Moreover, clinical diagnostics applications for Epstein-Barr virus (EBV) and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) detection with high sensitivity and accuracy (100% consistency with reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) test results) have been demonstrated. Overall, the Hand-CRISPR platform showed great promise in point-of-care-test (POCT) application, expected to become a powerful supplement to the standard nucleic acid testing method in remote or poverty-stricken areas.
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Genetic Testing and Hospital Length of Stay in Neonates With Epilepsy. Pediatr Neurol 2022; 133:30-33. [PMID: 35751960 PMCID: PMC9484310 DOI: 10.1016/j.pediatrneurol.2022.05.011] [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: 01/25/2022] [Accepted: 05/25/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND We evaluated changes in genetic testing for neonatal-onset epilepsy and associated short-term outcomes over an 8-year period among a cohort of patients in the neonatal intensive care unit (NICU) at a single institution before and after the introduction of sponsored genetic epilepsy testing in January 2018. METHODS Our primary outcome was a change in length of stay (LOS) after 2018. We also ascertained severity of illness with the Neonatal Sequential Organ Failure Assessment (nSOFA), type and result of genetic testing, turnaround time to molecular diagnosis (TAT), LOS, antiseizure medications (ASMs), and use of technology at discharge. We compared outcomes using nonparametric tests and difference-in-difference analysis. RESULTS Fifty-three infants with genetic testing were included; 20 infants were tested after 2018. A total of 4160 infants in the NICU without genetic testing were used as reference. In the genetic testing group, LOS was 25 days (interquartile range [IQR] 5, 49) pre-2018 and 19 days (IQR 6, 19) post-2018 (P < 0.001 when compared with the reference population in the difference-in-difference analysis). TAT decreased from 51 days to 17 days after 2018 (P = 0.003). ASM number decreased from 4 (IQR 2, 5) to 2 post-2018 (IQR 1, 3) (P = 0.02). Over the same time periods there was no significant change in birth weight, maximum nSOFA score, or technology dependence. CONCLUSIONS In this cohort, changes in genetic testing for neonatal-onset epilepsy were associated with shorter LOS that was not explained by changes in severity of illness, birth weight, or the average LOS in the NICU over time. Validation of these results in a larger, multicenter sample size is warranted.
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Kruse J, Mueller R, Aghdassi AA, Lerch MM, Salloch S. Genetic Testing for Rare Diseases: A Systematic Review of Ethical Aspects. Front Genet 2022; 12:701988. [PMID: 35154238 PMCID: PMC8826556 DOI: 10.3389/fgene.2021.701988] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022] Open
Abstract
Genetic testing is associated with many ethical challenges on the individual, organizational and macro level of health care systems. The provision of genetic testing for rare diseases in particular requires a full understanding of the complexity and multiplicity of related ethical aspects. This systematic review presents a detailed overview of ethical aspects relevant to genetic testing for rare diseases as discussed in the literature. The electronic databases Pubmed, Science Direct and Web of Science were searched, resulting in 55 relevant publications. From the latter, a total of 93 different ethical aspects were identified. These ethical aspects were structured into three main categories (process of testing, consequences of the test outcome and contextual challenges) and 20 subcategories highlighting the diversity and complexity of ethical aspects relevant to genetic testing for rare diseases. This review can serve as a starting point for the further in-depth investigation of particular ethical issues, the education of healthcare professionals regarding this matter and for informing international policy development on genetic testing for rare diseases.
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Affiliation(s)
- Judith Kruse
- Institute of Ethics and History of Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Regina Mueller
- Institute of Ethics and History of Medicine, Medical Faculty, University Tübingen, Tübingen, Germany
| | - Ali A Aghdassi
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | | | - Sabine Salloch
- Institute of Ethics, History and Philosophy of Medicine, Hannover Medical School, Hannover, Germany
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15
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Insights into National Laboratory Newborn Screening and Future Prospects. Medicina (B Aires) 2022; 58:medicina58020272. [PMID: 35208595 PMCID: PMC8879506 DOI: 10.3390/medicina58020272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 01/26/2022] [Accepted: 02/09/2022] [Indexed: 11/17/2022] Open
Abstract
Newborn screening (NBS) is a group of tests that check all newborns for certain rare conditions, covering several genetic or metabolic disorders. The laboratory NBS is performed through blood testing. However, the conditions that newborn babies are screened for vary from one country to another. Since NBS began in the 1960s, technological advances have enabled its expansion to include an increasing number of disorders, and there is a national trend to further expand the NBS program. The use of mass spectrometry (MS) for the diagnosis of inborn errors of metabolism (IEM) obviously helps in the expansion of the screening panels. This technology allows the detection of different metabolic disorders at one run, replacing the use of traditional techniques. Analysis of the targeted pathogenic gene variant is a routine application in the molecular techniques for the NBS program as a confirmatory testing to the positive laboratory screening results. Recently, a lot of molecular investigations, such as next generation sequencing (NGS), have been introduced in the routine NBS program. Nowadays, NGS techniques are widely used in the diagnosis of IMD where its results are rapid, confirmed and reliable, but, due to its uncertainties and the nature of IEM, it necessitates a holistic approach for diagnosis. However, various characteristics found in NGS make it a potentially powerful tool for NBS. A range of disorders can be analyzed with a single assay directly, and samples can reduce costs and can largely be automated. For the implementation of a robust technology such as NGS in a mass NBS program, the main focus should not be just technologically biased; it should also be tested for its long- and short-term impact on the family and the child. The crucial question here is whether large-scale genomic sequencing can provide useful medical information beyond what current NBS is already providing and at what economical and emotional cost? Currently, the topic of newborn genome sequencing as a public health initiative remains argumentative. Thus, this article seeks the answer to the question: NGS for newborn screening- are we there yet?
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Knottnerus JA, Knottnerus BJ. Decision-making given surrogate outcomes. J Clin Epidemiol 2022; 145:174-178. [PMID: 35041971 DOI: 10.1016/j.jclinepi.2022.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Opinions differ about the extent to which intervention research should and can directly assess the main patient-important health outcomes, what role surrogate endpoints can play, and which requirements should then apply to the scientific underpinning of clinical and policy decisions. METHOD In a commentary we elaborate on this and provide guidance for dealing with related dilemmas. CONCLUSIONS Ethical, methodological and practical reasons for decision making based on surrogate endpoints can be that (1) reaching the intended patient-important health outcome would take too long to await direct RCT-based evidence, (2) experimental conditions have limited sustainability over time; and (3) the plausibility of an intervention's clinical efficacy, given the already available evidence regarding surrogate endpoints, goes beyond equipoise. Given an expected increase of interventions with a long term patient-important health outcome perspective, dealing with surrogate endpoints will remain an important challenge. Appropriately dealing with a surrogate endpoint includes (1) the assessment of its predictive value for the intended patient-important outcome, where GRADE guidelines for assessing 'indirectness' and 'causal chain analysis' can be helpful; (2) transparency of (absence of) evidence; (3) adequately updating the 'knowledge mosaic'; (4) weighing different perspectives and values, and (5) monitoring whether adjustments need to be made. The remaining level of uncertainty must be balanced against the urgency of clinical or societal decision making and the disadvantages of postponing this. Criteria for using surrogate endpoints are suggested. Patients, citizens and policy makers can be involved in agreeing upon these criteria.
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Affiliation(s)
- J André Knottnerus
- Professor emeritus of Primary Health Care, Department of Family Practice, Maastricht University Medical Centre, Maastricht, The Netherlands.
| | - Bart J Knottnerus
- Senior researcher primary care physician, Netherlands Institute for Health Services Research (Nivel), Utrecht, The Netherlands
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Preoperative clinical and tumor genomic features associated with pathologic lymph node metastasis in clinical stage I and II lung adenocarcinoma. NPJ Precis Oncol 2021; 5:70. [PMID: 34290393 PMCID: PMC8295366 DOI: 10.1038/s41698-021-00210-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/29/2021] [Indexed: 11/08/2022] Open
Abstract
While next-generation sequencing (NGS) is used to guide therapy in patients with metastatic lung adenocarcinoma (LUAD), use of NGS to determine pathologic LN metastasis prior to surgery has not been assessed. To bridge this knowledge gap, we performed NGS using MSK-IMPACT in 426 treatment-naive patients with clinical N2-negative LUAD. A multivariable logistic regression model that considered preoperative clinical and genomic variables was constructed. Most patients had cN0 disease (85%) with pN0, pN1, and pN2 rates of 80%, 11%, and 9%, respectively. Genes altered at higher rates in pN-positive than in pN-negative tumors were STK11 (p = 0.024), SMARCA4 (p = 0.006), and SMAD4 (p = 0.011). Fraction of genome altered (p = 0.037), copy number amplifications (p = 0.001), and whole-genome doubling (p = 0.028) were higher in pN-positive tumors. Multivariable analysis revealed solid tumor morphology, tumor SUVmax, clinical stage, SMARCA4 and SMAD4 alterations were independently associated with pathologic LN metastasis. Incorporation of clinical and tumor genomic features can identify patients at risk of pathologic LN metastasis; this may guide therapy decisions before surgical resection.
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Huebner T, Scholl C, Steffens M. Cytogenetic and Biochemical Genetic Techniques for Personalized Drug Therapy in Europe. Diagnostics (Basel) 2021; 11:diagnostics11071169. [PMID: 34206978 PMCID: PMC8303692 DOI: 10.3390/diagnostics11071169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
For many authorized drugs, accumulating scientific evidence supports testing for predictive biomarkers to apply personalized therapy and support preventive measures regarding adverse drug reactions and treatment failure. Here, we review cytogenetic and biochemical genetic testing methods that are available to guide therapy with drugs centrally approved in the European Union (EU). We identified several methods and combinations of techniques registered in the Genetic Testing Registry (GTR), which can be used to guide therapy with drugs for which pharmacogenomic-related information is provided in the European public assessment reports. Although this registry provides information on genetic tests offered worldwide, we identified limitations regarding standard techniques applied in clinical practice and the information on test validity rarely provided in the according sections.
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Shen RJ, Wang JG, Li Y, Jin ZB. Consanguinity-based analysis of exome sequencing yields likely genetic causes in patients with inherited retinal dystrophy. Orphanet J Rare Dis 2021; 16:278. [PMID: 34130719 PMCID: PMC8204521 DOI: 10.1186/s13023-021-01902-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/07/2021] [Indexed: 12/11/2022] Open
Abstract
Background Consanguineous families have a relatively high prevalence of genetic disorders caused by bi-allelic mutations in recessive genes. This study aims to evaluate the effectiveness and efficiency of a consanguinity-based exome sequencing approach to capturing genetic mutations in inherited retinal dystrophy families with consanguineous marriages. Methods Ten unrelated consanguineous families with a proband affected by inherited retinal dystrophy were recruited in this study. All participants underwent comprehensive ophthalmic examinations. Whole exome sequencing was performed, followed by a homozygote-prior strategy to rapidly filter disease-causing mutations. Bioinformatic prediction of pathogenicity, Sanger sequencing and co-segregation analysis were carried out for further validation. Results In ten consanguineous families, a total of 10 homozygous mutations in 8 IRD genes were identified, including 2 novel mutations, c.1654_1655delAG (p. R552Afs*5) in gene FAM161A in a patient diagnosed with retinitis pigmentosa, and c.830T > C (p.L277P) in gene CEP78 in a patient diagnosed with cone and rod dystrophy. Conclusion The genetic etiology in consanguineous families with IRD were successfully identified using consanguinity-based analysis of exome sequencing data, suggesting that this approach could provide complementary insights into genetic diagnoses in consanguineous families with variant genetic disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01902-5.
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Affiliation(s)
- Ren-Juan Shen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Jun-Gang Wang
- Department of Ophthalmology, Eye Hospital of Shandong First Medical University, State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yang Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China.
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One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation. Genet Med 2021; 23:1673-1680. [PMID: 34007000 PMCID: PMC8460443 DOI: 10.1038/s41436-021-01187-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 04/08/2021] [Accepted: 04/11/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE To evaluate the impact of technically challenging variants on the implementation, validation, and diagnostic yield of commonly used clinical genetic tests. Such variants include large indels, small copy-number variants (CNVs), complex alterations, and variants in low-complexity or segmentally duplicated regions. METHODS An interlaboratory pilot study used synthetic specimens to assess detection of challenging variant types by various next-generation sequencing (NGS)-based workflows. One well-performing workflow was further validated and used in clinician-ordered testing of more than 450,000 patients. RESULTS In the interlaboratory study, only 2 of 13 challenging variants were detected by all 10 workflows, and just 3 workflows detected all 13. Limitations were also observed among 11 less-challenging indels. In clinical testing, 21.6% of patients carried one or more pathogenic variants, of which 13.8% (17,561) were classified as technically challenging. These variants were of diverse types, affecting 556 of 1,217 genes across hereditary cancer, cardiovascular, neurological, pediatric, reproductive carrier screening, and other indicated tests. CONCLUSION The analytic and clinical sensitivity of NGS workflows can vary considerably, particularly for prevalent, technically challenging variants. This can have important implications for the design and validation of tests (by laboratories) and the selection of tests (by clinicians) for a wide range of clinical indications.
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21
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Qiao SP, Liu ZN, Li HC, He X, Pan H, Gao YZ. Construction of a CRISPR-Biolayer Interferometry Platform for Real-Time, Sensitive, and Specific DNA Detection. Chembiochem 2021; 22:1974-1984. [PMID: 33682991 DOI: 10.1002/cbic.202100054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/26/2021] [Indexed: 12/26/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) technology has been widely applied for nucleic acid detection because of its high specificity. By using the highly specific and irreversible bond between HaloTag and its alkane chlorine ligand, we modified dCas9 (deactivated CRISPR/Cas9) with biotin as a biosensor to detect nucleic acids. The CRISPR biosensor was facilely prepared to adequately maintain its DNA-recognition capability. Furthermore, by coupling biolayer interferometry (BLI) with the CRISPR biosensor, a real-time, sensitive, and rapid digital system called CRISPR-BLI was established for the detection of double-stranded DNA. The CRISPR biosensor immobilised on the biolayer could recruit the target DNA onto the biosensor surface and change its optical thickness, resulting in a shift in the interference pattern and responding signal of the BLI. The CRISPR-BLI system was further applied to detect the ALP gene of Escherichia coli DH5α combined with a polymerase chain reaction, which demonstrated a linear range from 20 to 20 000 pg and a low detection limit (1.34 pg). The CRISPR-BLI system is a promising approach for rapid and sensitive detection of target DNA analytes.
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Affiliation(s)
- Shan-Peng Qiao
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China
| | - Zhen-Ni Liu
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China
| | - Hai-Chao Li
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China
| | - Xin He
- Department of Jilin City Institute of Biological Products, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 1228 Songjiangnan Road, Jilin, 132013, Jilin, P. R. China
| | - Hong Pan
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China
| | - Yu-Zhou Gao
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China.,Department of Jinan Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3 Gangxing Road, Jinan, 250000, Shandong, P. R. China
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Caso R, Sanchez-Vega F, Tan KS, Mastrogiacomo B, Zhou J, Jones GD, Nguyen B, Schultz N, Connolly JG, Brandt WS, Bott MJ, Rocco G, Molena D, Isbell JM, Liu Y, Mayo MW, Adusumilli PS, Travis WD, Jones DR. The Underlying Tumor Genomics of Predominant Histologic Subtypes in Lung Adenocarcinoma. J Thorac Oncol 2020; 15:1844-1856. [PMID: 32791233 DOI: 10.1016/j.jtho.2020.08.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/24/2020] [Accepted: 08/01/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The purpose of the study is to genomically characterize the biology and related therapeutic opportunities of prognostically important predominant histologic subtypes in lung adenocarcinoma (LUAD). METHODS We identified 604 patients with stage I to III LUAD who underwent complete resection and targeted next-generation sequencing using the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets platform. Tumors were classified according to predominant histologic subtype and grouped by architectural grade (lepidic [LEP], acinar or papillary [ACI/PAP], and micropapillary or solid [MIP/SOL]). Associations among clinicopathologic factors, genomic features, mutational signatures, and recurrence were evaluated within subtypes and, when appropriate, quantified using competing-risks regression, with adjustment for pathologic stage and extent of resection. RESULTS MIP/SOL tumors had higher tumor mutational burden (p < 0.001), fraction of genome altered (p = 0.001), copy number amplifications (p = 0.021), rate of whole-genome doubling (p = 0.008), and number of oncogenic pathways altered ( p < 0.001) as compared with LEP and ACI/PAP tumors. Across all tumors, mutational signatures attributed to APOBEC activity were associated with the highest risk of postresection recurrence: SBS2 (p = 0.021) and SBS13 (p = 0.005). Three oncogenic pathways (p53, Wnt, Myc) were altered with statistical significance in MIP/SOL tumors. Compared with LEP and ACI/PAP tumors, MIP/SOL tumors had a higher frequency of targetable BRAF-V600E mutations (p = 0.046). Among ACI/PAP tumors, alterations in the cell cycle (p < 0.001) and PI3K (p = 0.002) pathways were associated with recurrence; among MIP/SOL tumors, only PI3K alterations were associated with recurrence (p = 0.049). CONCLUSIONS These results provide the first in-depth assessment of tumor genomic profiling of predominant LUAD histologic subtypes, their associations with recurrence, and their correlation with targetable driver alterations in patients with surgically resected LUAD.
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Affiliation(s)
- Raul Caso
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Francisco Sanchez-Vega
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kay See Tan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brooke Mastrogiacomo
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jian Zhou
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gregory D Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bastien Nguyen
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James G Connolly
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Whitney S Brandt
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Matthew J Bott
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Fiona and Stanley Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gaetano Rocco
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Fiona and Stanley Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniela Molena
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Fiona and Stanley Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James M Isbell
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Fiona and Stanley Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yuan Liu
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Fiona and Stanley Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marty W Mayo
- Department of Biochemistry & Molecular Genetics, University of Virginia, Virginia
| | - Prasad S Adusumilli
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Fiona and Stanley Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Travis
- Fiona and Stanley Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David R Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Fiona and Stanley Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York.
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23
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Risoluti R, Caprari P, Gullifa G, Massimi S, Maffei L, Sorrentino F, Carcassi E, Materazzi S. An Innovative Multilevel Test for Hemoglobinopathies: TGA/Chemometrics Simultaneously Identifies and Classifies Sickle Cell Disease From Thalassemia. Front Mol Biosci 2020; 7:141. [PMID: 32850950 PMCID: PMC7396684 DOI: 10.3389/fmolb.2020.00141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/10/2020] [Indexed: 11/13/2022] Open
Abstract
Introduction: Hemoglobinopathies are the most common genetic disorder wordlwide and because of migrations are become an emerging global health problem. Screening programmes for Sickle cell disease and Thalassemia have been implemented in some countries, but are not a common practice, due to a lack in the accuracy of the methods and to the costs of the analyses. Objectives: The objective of this study was the application of the thermogravimetry coupled to chemometrics as new screening method to perform an early diagnosis of thalassemia and sickle cell disease. Methods: Whole blood samples (30 μL) from sickle cell anemia and thalassemia patients were analyzed using the thermobalance TG7 and the resulting curves were compared with those of healthy individuals. A chemometric approach based on Principal Components Analysis (PCA) was exploited to enhance correlation between thermogravimetric profiles and a model of prediction by Partial Least Square Discriminant Analysis (PLS-DA) was developed and validated. Results: The characteristic profile of the blood sample thermal decomposition and the first derivative of the TG curve showed that patients were clearly distinguished from healthy individuals as a result of different amounts of water and corpuscular fraction of blood. The chemometric approach based on PCA allowed a quick identification of differences between healthy subjects and patients and also between thalassemic and sickle cell anemia subjects. Chemometric tools (PLS-DA) were used to validate a model of prediction to process the thermogravimetric curves and to obtain in 1 h an accurate diagnosis. The TGA/Chemometric test permitted to perform first level test for hemoglobinopathies with the same accuracy of confirmatory analyses obtained by the molecular investigation. Conclusions: A screening test based on the coupling of thermogravimetry and chemometrics was optimized for the differential diagnosis of hemoglobinopathies. The novel test is able to simultaneously perform a simple and fast diagnosis of sickle cell anemia or thalassemia, in a single analysis of few microliters of non-pretreated whole blood at low cost, and with high accuracy. Moreover this method results particularly suitable in pediatric patients as it requires small sample volumes and is able to characterize also transfused patients.
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Affiliation(s)
- Roberta Risoluti
- Department of Chemistry, Sapienza - University of Rome, Rome, Italy
| | - Patrizia Caprari
- National Centre for the Control and Evaluation of Medicines, Istituto Superiore di Sanità, Rome, Italy
| | | | - Sara Massimi
- National Centre for the Control and Evaluation of Medicines, Istituto Superiore di Sanità, Rome, Italy
| | - Laura Maffei
- Thalassemia Unit, S. Eugenio Hospital, Rome, Italy
| | | | - Elena Carcassi
- Department of Chemistry, Sapienza - University of Rome, Rome, Italy
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24
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Munkongdee T, Chen P, Winichagoon P, Fucharoen S, Paiboonsukwong K. Update in Laboratory Diagnosis of Thalassemia. Front Mol Biosci 2020; 7:74. [PMID: 32671092 PMCID: PMC7326097 DOI: 10.3389/fmolb.2020.00074] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 03/31/2020] [Indexed: 01/07/2023] Open
Abstract
Alpha- and β-thalassemias and abnormal hemoglobin (Hb) are common in tropical countries. These abnormal globin genes in different combinations lead to many thalassemic diseases including three severe thalassemia diseases, i.e., homozygous β-thalassemia, β-thalassemia/Hb E, and Hb Bart’s hydrops fetalis. Laboratory diagnosis of thalassemia requires a number of tests including red blood cell indices and Hb and DNA analyses. Thalassemic red blood cell analysis with an automated hematology analyzer is a primary screening for thalassemia since microcytosis and decreased Hb content of red blood cells are hallmarks of all thalassemic red blood cells. However, these two red blood cell indices cannot discriminate between thalassemia trait and iron deficiency or between α- and β-thalassemic conditions. Today, Hb analysis may be carried out by either automatic high-performance liquid chromatography (HPLC) or capillary zone electrophoresis (CE) system. These two systems give both qualitative and quantitative analysis of Hb components and help to do thalassemia prenatal and postnatal diagnoses within a short period. Both systems have a good correlation, but the interpretation under the CE system should be done with caution because Hb A2 is clearly separated from Hb E. In case of α-thalassemia gene interaction, it can affect the amount of Hb A2/E. Thalassemia genotypes can be characterized by the intensities between alpha-/beta-globin chains or alpha-/beta-mRNA ratios. However, those are presumptive diagnoses. Only DNA analysis can be made for specific thalassemia mutation diagnosis. Various molecular techniques have been used for point mutation detection in β-thalassemia and large-deletion detection in α-thalassemia. All of these techniques have some advantages and disadvantages. Recently, screening for both α- and β-thalassemia genes by next-generation sequencing (NGS) has been introduced. This technique gives an accurate diagnosis of thalassemia that may be misdiagnosed by other conventional techniques. The major limitation for using NGS in the screening of thalassemia is its cost which is still expensive. All service labs highly recommend to select the technique(s) they are most familiar and most economic one for their routine use.
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Affiliation(s)
- Thongperm Munkongdee
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Ping Chen
- Guangxi Key Laboratory of Thalassemia Research, Guangxi Medical University, Nanning, China
| | - Pranee Winichagoon
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Kittiphong Paiboonsukwong
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
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25
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Wang X, Xiong E, Tian T, Cheng M, Lin W, Wang H, Zhang G, Sun J, Zhou X. Clustered Regularly Interspaced Short Palindromic Repeats/Cas9-Mediated Lateral Flow Nucleic Acid Assay. ACS NANO 2020; 14:2497-2508. [PMID: 32045522 DOI: 10.1021/acsnano.0c00022] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The lateral flow assay is one of the most convenient analytical techniques for analyzing the immune response, but its applicability to precise genetic analyses is limited by the false-positive signal and tedious and inefficient hybridization steps. Here, we introduce the CRISPR (clustered regularly interspaced short palindromic repeats) /Cas system into the lateral flow assay, termed CRISPR/Cas9-mediated lateral flow nucleic acid assay (CASLFA), to address such issues. In this study, CASLFA is utilized to identify Listeria monocytogenes, genetically modified organisms (GMOs), and African swine fever virus (ASFV) at a detection limit of hundreds of copies of genome samples with high specificity within 1 h. We further evaluated the performance of CASLFA in a nonlaboratory environment and successfully confirmed 27 ASFV-infected samples from 110 suspected swine serum samples, with an accuracy of 100% when compared to real-time PCR (RT-PCR) assay. CASLFA satisfies some of the characteristics of a next-generation molecular diagnostics tool due to its rapidity and accuracy, allowing for point-of-care use without the need for technical expertise and complex ancillary equipment. This method has great potential for gene analysis in resource-poor or nonlaboratory environments.
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Affiliation(s)
- Xusheng Wang
- College of Biophotonics & School of Life Sciences , South China Normal University , Guangzhou 510631 , China
| | - Erhu Xiong
- College of Biophotonics & School of Life Sciences , South China Normal University , Guangzhou 510631 , China
| | - Tian Tian
- College of Biophotonics & School of Life Sciences , South China Normal University , Guangzhou 510631 , China
| | - Meng Cheng
- College of Biophotonics & School of Life Sciences , South China Normal University , Guangzhou 510631 , China
| | - Wei Lin
- College of Biophotonics & School of Life Sciences , South China Normal University , Guangzhou 510631 , China
| | - Heng Wang
- Guangdong Laboratory for Lingnan Modern Agriculture , Guangzhou 510642 , China
- Research Center for African Swine Fever Prevention and Control , South China Agricultural University , Guangzhou 510642 , China
| | - Guihong Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture , Guangzhou 510642 , China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria , South China Agricultural University , Guangzhou 510642 , China
- Research Center for African Swine Fever Prevention and Control , South China Agricultural University , Guangzhou 510642 , China
| | - Jian Sun
- Guangdong Laboratory for Lingnan Modern Agriculture , Guangzhou 510642 , China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria , South China Agricultural University , Guangzhou 510642 , China
- Research Center for African Swine Fever Prevention and Control , South China Agricultural University , Guangzhou 510642 , China
| | - Xiaoming Zhou
- College of Biophotonics & School of Life Sciences , South China Normal University , Guangzhou 510631 , China
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26
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Zhao J, Li J, Lai Q, Yu Y. Combined use of gap-PCR and next-generation sequencing improves thalassaemia carrier screening among premarital adults in China. J Clin Pathol 2020; 73:488-492. [PMID: 31980563 PMCID: PMC7398480 DOI: 10.1136/jclinpath-2019-206339] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022]
Abstract
Aims Thalassaemia is one of the most common genetics disorders in the world, especially in southern China. The aim of the present study was to investigate the feasibility of combining the gap-PCR and next-generation sequencing (NGS) for thalassaemia carrier screening in the Chinese population. Methods Blood samples were obtained from 944 prepregnancy couples; thalassaemia carrier screening was performed by using a routine haematological method and a combination of gap-PCR and NGS method. Results We found that the α thalassaemia carrier rate was 11% (207/1888); the β thalassaemia carrier rate was 3.7% (70/1888); the composite α thalassaemia and β thalassaemia carrier rate was 0.4% (8/1888). We also identified seven novel mutations, including HBA1: c.412A>G, −50 (G>A), HBB: c.*+129T>A, HBB: c.-64G>C, HBB: c.-180G>C, HBB: c.*+5G>A and HBB: c.-113A>G. By comparing the combined gap-PCR and NGS method, the MCV+MCH and HbA2 detection strategy showed a lower sensitivity of 61.05% (105/172) and a higher missed diagnosis ratio of 38.95% (67/172) for α thalassaemia mutations. The sensitivity was improved with the MCV+MCH and HbA2 detection screen when compared with MCV+MCH detection for β thalassaemia (98.51% vs 85.90%). Conclusions Our study suggests the combined gap-PCR and NGS method is a cost-effective method for the thalassaemia carrier screening, particularly for the α thalassaemia mutation carriers.
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Affiliation(s)
- Jianghong Zhao
- Department of Obstetrics and Gynecology, Xiaolan Hospital Affiliated to Southern Medical University, Zhongshan, Guangdong province, China
| | - Jia Li
- Department of Thyroid and Breast, Shanghai Tenth People's Hospital, Shanghai, China
| | - Qiaohong Lai
- Department of Obstetrics and Gynecology, Xiaolan Hospital Affiliated to Southern Medical University, Zhongshan, Guangdong province, China
| | - Yanping Yu
- Department of Obstetrics and Gynecology, Xiaolan Hospital Affiliated to Southern Medical University, Zhongshan, Guangdong province, China
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27
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Metatranscriptomics and Metaproteomics for Microbial Communities Profiling. UNRAVELLING THE SOIL MICROBIOME 2020. [DOI: 10.1007/978-3-030-15516-2_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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28
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Zhou J, Sanchez-Vega F, Caso R, Tan KS, Brandt WS, Jones GD, Yan S, Adusumilli PS, Bott M, Huang J, Isbell JM, Sihag S, Molena D, Rusch VW, Chatila WK, Rekhtman N, Yang F, Ladanyi M, Solit DB, Berger MF, Schultz N, Jones DR. Analysis of Tumor Genomic Pathway Alterations Using Broad-Panel Next-Generation Sequencing in Surgically Resected Lung Adenocarcinoma. Clin Cancer Res 2019; 25:7475-7484. [PMID: 31455678 DOI: 10.1158/1078-0432.ccr-19-1651] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/22/2019] [Accepted: 08/23/2019] [Indexed: 12/16/2022]
Abstract
PURPOSE The majority of broad-panel tumor genomic profiling has used a gene-centric approach, although much of that data is unused in clinical decision making. We hypothesized that a pathway-centric approach using next-generation sequencing (NGS), combined with conventional clinicopathologic features, may better predict disease-free survival (DFS) in early stage lung adenocarcinoma. EXPERIMENTAL DESIGN Utilizing our prospectively maintained database, we analyzed 492 patients with primary, untreated, completely surgically resected lung adenocarcinoma. Ten canonical pathways were analyzed using broad-panel NGS. The correlations of DFS and number (and type) of pathway (NPA) were analyzed using the Kaplan-Meier method and log-rank test. Associations between altered pathways and clinicopathologic variables, as well as identification of actionable therapeutic strategies were explored. RESULTS Median NPA for the cohort was two (range, 0-5). Smoking status, solid morphologic appearance on preoperative CT, maximal standardized uptake value, pathologic tumor size, aggressive histologic subtype, lymphovascular invasion, visceral pleural invasion, and positive lymph nodes were significantly associated with NPA (P < 0.05). Of 543 actionable genetic alterations identified, 455 (84%) were within the RTK/RAS pathway. A total of 86 tumors had actionable therapeutic genomic alterations in >1 pathway. On multivariable analysis, higher NPA was significantly associated with worse DFS (HR, 1.31; P = 0.014). CONCLUSIONS NPA and specific pathway alterations are associated with clinicopathologic features in patients with surgically resected lung adenocarcinoma. Cell cycle, Hippo, TGFβ, and p53 pathway alterations are associated with poor DFS. Finally, NPA is an independent risk factor for poor DFS in our cohort.See related commentary by Blakely, p. 7269.
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Affiliation(s)
- Jian Zhou
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Thoracic Department, Peking University People's Hospital, Beijing, China
| | - Francisco Sanchez-Vega
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Raul Caso
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kay See Tan
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Whitney S Brandt
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gregory D Jones
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shi Yan
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Prasad S Adusumilli
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Matthew Bott
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James Huang
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James M Isbell
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Smita Sihag
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniela Molena
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Valerie W Rusch
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K Chatila
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fan Yang
- Thoracic Department, Peking University People's Hospital, Beijing, China
| | - Marc Ladanyi
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David R Jones
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York. .,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
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29
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Lincoln SE, Truty R, Lin CF, Zook JM, Paul J, Ramey VH, Salit M, Rehm HL, Nussbaum RL, Lebo MS. A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing-Detected Variants with an Orthogonal Method in Clinical Genetic Testing. J Mol Diagn 2019; 21:318-329. [PMID: 30610921 PMCID: PMC6629256 DOI: 10.1016/j.jmoldx.2018.10.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/28/2018] [Accepted: 10/24/2018] [Indexed: 12/17/2022] Open
Abstract
Orthogonal confirmation of next-generation sequencing (NGS)-detected germline variants is standard practice, although published studies have suggested that confirmation of the highest-quality calls may not always be necessary. The key question is how laboratories can establish criteria that consistently identify those NGS calls that require confirmation. Most prior studies addressing this question have had limitations: they have been generally of small scale, omitted statistical justification, and explored limited aspects of underlying data. The rigorous definition of criteria that separate high-accuracy NGS calls from those that may or may not be true remains a crucial issue. We analyzed five reference samples and over 80,000 patient specimens from two laboratories. Quality metrics were examined for approximately 200,000 NGS calls with orthogonal data, including 1662 false positives. A classification algorithm used these data to identify a battery of criteria that flag 100% of false positives as requiring confirmation (CI lower bound, 98.5% to 99.8%, depending on variant type) while minimizing the number of flagged true positives. These criteria identify false positives that the previously published criteria miss. Sampling analysis showed that smaller data sets resulted in less effective criteria. Our methodology for determining test- and laboratory-specific criteria can be generalized into a practical approach that can be used by laboratories to reduce the cost and time burdens of confirmation without affecting clinical accuracy.
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Affiliation(s)
| | | | - Chiao-Feng Lin
- Laboratory for Molecular Medicine, Partners HealthCare, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Justin M Zook
- National Institute of Standards and Technology, Gaithersburg, Maryland
| | | | | | - Marc Salit
- National Institute of Standards and Technology, Gaithersburg, Maryland; Joint Initiative for Metrology in Biology, Stanford, California
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners HealthCare, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Robert L Nussbaum
- Invitae, San Francisco, California; Department of Medicine, University of California San Francisco, San Francisco, California
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Partners HealthCare, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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30
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Daoud H, Ghani M, Nfonsam L, Potter R, Ordorica S, Haslett V, Santos N, Derksen H, Lahey D, McGill M, Trudel V, Antoniuk B, Vasli N, Chisholm C, Mettler G, Sinclair-Bourque E, McGowan-Jordan J, Smith A, Roberts R, Jarinova O. Genetic Diagnostic Testing for Inherited Cardiomyopathies: Considerations for Offering Multi-Gene Tests in a Health Care Setting. J Mol Diagn 2019; 21:437-448. [PMID: 30731207 DOI: 10.1016/j.jmoldx.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 11/16/2018] [Accepted: 01/03/2019] [Indexed: 02/07/2023] Open
Abstract
Inherited cardiomyopathies (ICs) are a major cause of heart disease. Given their marked clinical and genetic heterogeneity, the content and clinical utility of IC multi-gene panels has been the topic of continuous debate. Our genetics diagnostic laboratory has been providing clinical diagnostic testing for ICs since 2012. We began by testing nine genes and expanded our panel by fivefold in 2015. Here, we describe the implementation of a cost-effective next-generation sequencing (NGS)-based assay for testing of IC genes, including a protocol that minimizes the amount of Sanger sequencing required to confirm variants identified by NGS, which reduces the cost and time of testing. The NGS assay was developed for the simultaneous analysis of 45 IC genes and was assessed for the impact of panel expansion on variant detection, turnaround time, and cost of testing in a cohort of 993 patients. The assay led to a considerable reduction in test cost and turnaround time. However, only a marginal increase was observed in the diagnostic yield, whereas the rate of inconclusive findings increased considerably. These findings suggest that the ongoing evaluation of gene content and monitoring of clinical utility for multi-gene tests are essential to achieve maximum clinical utility of multi-gene tests in a publicly funded health care setting.
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Affiliation(s)
- Hussein Daoud
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.
| | - Mahdi Ghani
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Landry Nfonsam
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Ryan Potter
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Shelley Ordorica
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Virginia Haslett
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Nathaniel Santos
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Heather Derksen
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Donelda Lahey
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Martha McGill
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Vanessa Trudel
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Brittany Antoniuk
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Nasim Vasli
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Caitlin Chisholm
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Gabrielle Mettler
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Jean McGowan-Jordan
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Amanda Smith
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Robert Roberts
- University of Arizona College of Medicine, Tucson, Arizona
| | - Olga Jarinova
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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Carvalho RA, Urtremari B, Jorge AAL, Santana LS, Quedas EPS, Sekiya T, Longuini VC, Montenegro FLM, Lerario AM, Toledo SPA, Marx SJ, Toledo RA, Lourenço DM. Germline mutation landscape of multiple endocrine neoplasia type 1 using full gene next-generation sequencing. Eur J Endocrinol 2018; 179:391-407. [PMID: 30324798 DOI: 10.1530/eje-18-0430] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 09/24/2018] [Indexed: 12/17/2022]
Abstract
Background Loss-of-function germline MEN1 gene mutations account for 75-95% of patients with multiple endocrine neoplasia type 1 (MEN1). It has been postulated that mutations in non-coding regions of MEN1 might occur in some of the remaining patients; however, this hypothesis has not yet been fully investigated. Objective To sequence for the entire MEN1 including promoter, exons and introns in a large MEN1 cohort and determine the mutation profile. Methods and patients A target next-generation sequencing (tNGS) assay comprising 7.2 kb of the full MEN1 was developed to investigate germline mutations in 76 unrelated MEN1 probands (49 familial, 27 sporadic). tNGS results were validated by Sanger sequencing (SS), and multiplex ligation-dependent probe amplification (MLPA) assay was applied when no mutations were identifiable by both tNGS and SS. Results Germline MEN1 variants were verified in coding region and splicing sites of 57/76 patients (74%) by both tNGS and SS (100% reproducibility). Thirty-eight different pathogenic or likely pathogenic variants were identified, including 13 new and six recurrent variants. Three large deletions were detected by MLPA only. No mutation was detected in 16 patients. In untranslated, regulatory or in deep intronic MEN1 regions of the 76 MEN1 cases, no point or short indel pathogenic variants were found in untranslated, although 33 benign/likely benign and three new VUS variants were detected. Conclusions Our study documents that point or short indel mutations in non-coding regions of MEN1 are very rare events. Also, tNGS proved to be a highly effective technology for routine genetic MEN1 testing.
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Affiliation(s)
- Rafael A Carvalho
- Unidade de Endocrinologia Genetica UEG, Laboratorio de Endocrinologia Celular e Molecular LIM-25, Disciplina de Endocrinologia
| | - Betsaida Urtremari
- Unidade de Endocrinologia Genetica UEG, Laboratorio de Endocrinologia Celular e Molecular LIM-25, Disciplina de Endocrinologia
| | - Alexander A L Jorge
- Unidade de Endocrinologia Genetica UEG, Laboratorio de Endocrinologia Celular e Molecular LIM-25, Disciplina de Endocrinologia
| | - Lucas S Santana
- Unidade de Endocrinologia Genetica UEG, Laboratorio de Endocrinologia Celular e Molecular LIM-25, Disciplina de Endocrinologia
| | - Elisangela P S Quedas
- Unidade de Endocrinologia Genetica UEG, Laboratorio de Endocrinologia Celular e Molecular LIM-25, Disciplina de Endocrinologia
| | - Tomoko Sekiya
- Unidade de Endocrinologia Genetica UEG, Laboratorio de Endocrinologia Celular e Molecular LIM-25, Disciplina de Endocrinologia
| | - Viviane C Longuini
- Unidade de Endocrinologia Genetica UEG, Laboratorio de Endocrinologia Celular e Molecular LIM-25, Disciplina de Endocrinologia
| | - Fabio L M Montenegro
- Unidade de Paratireoide, Laboratorio de Cirurgia Vascular e da Cabeça e Pescoço LIM-28, Disciplina de Cirurgia de Cabeça e Pescoço, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Antonio M Lerario
- Division of Metabolism, Department of Internal Medicine, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
| | - Sergio P A Toledo
- Unidade de Endocrinologia Genetica UEG, Laboratorio de Endocrinologia Celular e Molecular LIM-25, Disciplina de Endocrinologia
- Endocrinology Division, Federal University of Sao Paulo (UNIFESP), São Paulo, Brazil
| | - Stephen J Marx
- Unidade de Endocrinologia Genetica UEG, Laboratorio de Endocrinologia Celular e Molecular LIM-25, Disciplina de Endocrinologia
- Endocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, Maryland, USA
| | | | - Delmar M Lourenço
- Unidade de Endocrinologia Genetica UEG, Laboratorio de Endocrinologia Celular e Molecular LIM-25, Disciplina de Endocrinologia
- Disciplina de Endocrinologia, Instituto do Cancer do Estado de Sao Paulo ICESP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
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Presley CJ, Tang D, Soulos PR, Chiang AC, Longtine JA, Adelson KB, Herbst RS, Zhu W, Nussbaum NC, Sorg RA, Agarwala V, Abernethy AP, Gross CP. Association of Broad-Based Genomic Sequencing With Survival Among Patients With Advanced Non-Small Cell Lung Cancer in the Community Oncology Setting. JAMA 2018; 320:469-477. [PMID: 30088010 PMCID: PMC6142984 DOI: 10.1001/jama.2018.9824] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
IMPORTANCE Broad-based genomic sequencing is being used more frequently for patients with advanced non-small cell lung cancer (NSCLC). However, little is known about the association between broad-based genomic sequencing and treatment selection or survival among patients with advanced NSCLC in a community oncology setting. OBJECTIVE To compare clinical outcomes between patients with advanced NSCLC who received broad-based genomic sequencing vs a control group of patients who received routine testing for EGFR mutations and/or ALK rearrangements alone. DESIGN, SETTING, AND PARTICIPANTS Retrospective cohort study of patients with chart-confirmed advanced NSCLC between January 1, 2011, and July 31, 2016, and who received care at 1 of 191 oncology practices across the United States using the Flatiron Health Database. Patients were diagnosed with stage IIIB/IV or unresectable nonsquamous NSCLC who received at least 1 line of antineoplastic treatment. EXPOSURES Receipt of either broad-based genomic sequencing or routine testing (EGFR and/or ALK only). Broad-based genomic sequencing included any multigene panel sequencing assay examining more than 30 genes prior to third-line treatment. MAIN OUTCOMES AND MEASURES Primary outcomes were 12-month mortality and overall survival from the start of first-line treatment. Secondary outcomes included frequency of genetic alterations and treatments received. RESULTS Among 5688 individuals with advanced NSCLC (median age, 67 years [interquartile range, 41-85], 63.6% white, 80% with a history of smoking); 875 (15.4%) received broad-based genomic sequencing and 4813 (84.6%) received routine testing. Among patients who received broad-based genomic sequencing, 4.5% received targeted treatment based on testing results, 9.8% received routine EGFR/ALK targeted treatment, and 85.1% received no targeted treatment. Unadjusted mortality rates at 12 months were 49.2% for patients undergoing broad-based genomic sequencing and 35.9% for patients undergoing routine testing. Using an instrumental variable analysis, there was no significant association between broad-based genomic sequencing and 12-month mortality (predicted probability of death at 12 months, 41.1% for broad-based genomic sequencing vs 44.4% for routine testing; difference -3.6% [95% CI, -18.4% to 11.1%]; P = .63). The results were consistent in the propensity score-matched survival analysis (42.0% vs 45.1%; hazard ratio, 0.92 [95% CI, 0.73 to 1.11]; P = .40) vs unmatched cohort (hazard ratio, 0.69 [95% CI, 0.62 to 0.77]; log-rank P < .001). CONCLUSIONS AND RELEVANCE Among patients with advanced non-small cell lung cancer receiving care in the community oncology setting, broad-based genomic sequencing directly informed treatment in a minority of patients and was not independently associated with better survival.
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Affiliation(s)
| | - Daiwei Tang
- Yale School of Public Health, New Haven, Connecticut
| | | | | | | | | | | | - Weiwei Zhu
- Yale School of Medicine, New Haven, Connecticut
| | - Nathan C. Nussbaum
- Flatiron Health, New York, New York
- New York University School of Medicine, New York
| | | | - Vineeta Agarwala
- Flatiron Health, New York, New York
- Stanford University School of Medicine, Stanford, California
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Sanna-Cherchi S, Westland R, Ghiggeri GM, Gharavi AG. Genetic basis of human congenital anomalies of the kidney and urinary tract. J Clin Invest 2018; 128:4-15. [PMID: 29293093 DOI: 10.1172/jci95300] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The clinical spectrum of congenital anomalies of the kidney and urinary tract (CAKUT) encompasses a common birth defect in humans that has significant impact on long-term patient survival. Overall, data indicate that approximately 20% of patients may have a genetic disorder that is usually not detected based on standard clinical evaluation, implicating many different mutational mechanisms and pathogenic pathways. In particular, 10% to 15% of CAKUT patients harbor an unsuspected genomic disorder that increases risk of neurocognitive impairment and whose early recognition can impact clinical care. The emergence of high-throughput genomic technologies is expected to provide insight into the common and rare genetic determinants of diseases and offer opportunities for early diagnosis with genetic testing.
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Affiliation(s)
- Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA.,Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, Netherlands
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis and Transplantation, Istituto Giannina Gaslini, Genoa, Italy
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
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Abstract
Viral suppression of human immunodeficiency virus (HIV) with combination antiviral therapy (cART) has led to increasing longevity but has not enabled a complete return to health among aging HIV-infected individuals (HIV+). Viral coinfections are prevalent in the HIV+ host and are implicated in cancer, liver disease, and accelerated aging. We must move beyond a simplistic notion of HIV becoming a "chronic controllable illness" and develop an understanding of how viral suppression alters the natural history of HIV infection, especially at the intersection of HIV with other common viral coinfections in the context of an altered, aging immune system.
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Smith RA, Sillars A, Chesnut RP, Zhu X. Investigating Married Adults' Communal Coping with Genetic Health Risk and Perceived Discrimination. COMMUNICATION MONOGRAPHS 2017; 85:181-202. [PMID: 29731540 PMCID: PMC5930874 DOI: 10.1080/03637751.2017.1404618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 02/28/2017] [Indexed: 06/08/2023]
Abstract
Increased genetic testing in personalized medicine presents unique challenges for couples, including managing disease risk and potential discrimination as a couple. This study investigated couples' conflicts and support gaps as they coped with perceived genetic discrimination. We also explored the degree to which communal coping was beneficial in reducing support gaps, and ultimately stress. Dyadic analysis of married adults (N = 266, 133 couples), in which one person had the genetic risk for serious illness, showed that perceived discrimination predicted more frequent conflicts about AATD-related treatment, privacy boundaries, and finances, which, in turn, predicted wider gaps in emotion and esteem support, and greater stress for both spouses. Communal coping predicted lower support gaps for both partners and marginally lower stress.
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Affiliation(s)
| | | | | | - Xun Zhu
- The Pennsylvania State University
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36
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Worthey EA. Analysis and Annotation of Whole-Genome or Whole-Exome Sequencing Derived Variants for Clinical Diagnosis. ACTA ACUST UNITED AC 2017; 95:9.24.1-9.24.28. [PMID: 29044471 DOI: 10.1002/cphg.49] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Over the last 10 years, next-generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing, and also in the systems required for analysis of these large volumes of data. This technology is now being used as a standard molecular diagnostic test in some clinical settings. The advances in sequencing have come so rapidly that the major bottleneck in identification of causal variants is no longer the sequencing or analysis (given access to appropriate tools), but rather clinical interpretation. Interpretation of genetic findings in a complex and ever changing clinical setting is scarcely a new challenge, but the task is increasingly complex in clinical genome-wide sequencing given the dramatic increase in dataset size and complexity. This increase requires application of appropriate interpretation tools, as well as development and application of appropriate methodologies and standard procedures. This unit provides an overview of these items. Specific challenges related to implementation of genome-wide sequencing in a clinical setting are discussed. © 2017 by John Wiley & Sons, Inc.
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Chacón-Camacho OF, García-Montaño LA, Zenteno JC. The clinical implications of molecular monitoring and analyses of inherited retinal diseases. Expert Rev Mol Diagn 2017; 17:1009-1021. [DOI: 10.1080/14737159.2017.1384314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Oscar F. Chacón-Camacho
- Genetics Department-research Unit, Institute of Ophthalmology ‘Conde de Valenciana’, Mexico City, Mexico
| | - Leopoldo A. García-Montaño
- Genetics Department-research Unit, Institute of Ophthalmology ‘Conde de Valenciana’, Mexico City, Mexico
| | - Juan C Zenteno
- Genetics Department-research Unit, Institute of Ophthalmology ‘Conde de Valenciana’, Mexico City, Mexico
- Biochemistry Department, Faculty of Medicine, UNAM, Mexico City, Mexico
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Shang X, Peng Z, Ye Y, Asan, Zhang X, Chen Y, Zhu B, Cai W, Chen S, Cai R, Guo X, Zhang C, Zhou Y, Huang S, Liu Y, Chen B, Yan S, Chen Y, Ding H, Yin X, Wu L, He J, Huang D, He S, Yan T, Fan X, Zhou Y, Wei X, Zhao S, Cai D, Guo F, Zhang Q, Li Y, Zhang X, Lu H, Huang H, Guo J, Zhu F, Yuan Y, Zhang L, Liu N, Li Z, Jiang H, Zhang Q, Zhang Y, Juhari WKW, Hanafi S, Zhou W, Xiong F, Yang H, Wang J, Zilfalil BA, Qi M, Yang Y, Yin Y, Mao M, Xu X. Rapid Targeted Next-Generation Sequencing Platform for Molecular Screening and Clinical Genotyping in Subjects with Hemoglobinopathies. EBioMedicine 2017; 23:150-159. [PMID: 28865746 PMCID: PMC5605365 DOI: 10.1016/j.ebiom.2017.08.015] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/15/2017] [Accepted: 08/15/2017] [Indexed: 12/17/2022] Open
Abstract
Hemoglobinopathies are among the most common autosomal-recessive disorders worldwide. A comprehensive next-generation sequencing (NGS) test would greatly facilitate screening and diagnosis of these disorders. An NGS panel targeting the coding regions of hemoglobin genes and four modifier genes was designed. We validated the assay by using 2522 subjects affected with hemoglobinopathies and applied it to carrier testing in a cohort of 10,111 couples who were also screened through traditional methods. In the clinical genotyping analysis of 1182 β-thalassemia subjects, we identified a group of additional variants that can be used for accurate diagnosis. In the molecular screening analysis of the 10,111 couples, we detected 4180 individuals in total who carried 4840 mutant alleles, and identified 186 couples at risk of having affected offspring. 12.1% of the pathogenic or likely pathogenic variants identified by our NGS assay, which were undetectable by traditional methods. Compared with the traditional methods, our assay identified an additional at-risk 35 couples. We describe a comprehensive NGS-based test that offers advantages over the traditional screening/molecular testing methods. To our knowledge, this is among the first large-scale population study to systematically evaluate the application of an NGS technique in carrier screening and molecular diagnosis of hemoglobinopathies.
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Affiliation(s)
- Xuan Shang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Zhiyu Peng
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China
| | - Yuhua Ye
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Asan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Xinhua Zhang
- Department of Hematology, 303rd Hospital of the People's Liberation Army, Nanning, Guangxi, China
| | - Yan Chen
- The Second Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou, China
| | - Baosheng Zhu
- Genetic Diagnosis Center, First People's Hospital of Yunnan Province, Medical School of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Wangwei Cai
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, Hainan, China
| | - Shaoke Chen
- Department of Genetic and Metabolic Laboratory, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, Guangxi, China
| | - Ren Cai
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Xiaoling Guo
- Maternity and Child Health Care Hospital of Foshan City, Foshan, Guangdong, China
| | - Chonglin Zhang
- Guilin Women and Children health care hospital, Guilin, Guangxi, China
| | - Yuqiu Zhou
- Department of Clinical Laboratory, Zhuhai Municipal Maternal and Child Healthcare Hospital, Zhuhai Institute of Medical Genetics, Zhuhai, Guangdong, China
| | - Shuodan Huang
- Maternal and Child Health Hospital in Meizhou, Meizhou, Guangdong, China
| | - Yanhui Liu
- Department of Prenatal Diagnosis Center, Dong Guan Maternal and Child Health Hospital, Dongguan, Guangdong, China
| | - Biyan Chen
- Baise Women and Children Care Hospital, Baise, Guangxi, China
| | - Shanhuo Yan
- Genetic Laboratory, Qinzhou Maternaland Child Health Hospital, Qingzhou, Guangxi, China
| | - Yajun Chen
- Women and Children's Health Hospital of Shaoguan, Shaoguan, Guangdong, China
| | - Hongmei Ding
- Department of Gynecology and Obstetrics, The People's Hospital of Yunfu City, Yunfu, Guangdong, China
| | - Xiaolin Yin
- Department of Hematology, 303rd Hospital of the People's Liberation Army, Nanning, Guangxi, China
| | - Liusong Wu
- The Second Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou, China
| | - Jing He
- Genetic Diagnosis Center, First People's Hospital of Yunnan Province, Medical School of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Dongai Huang
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, Hainan, China
| | - Sheng He
- Department of Genetic and Metabolic Laboratory, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, Guangxi, China
| | - Tizhen Yan
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Xin Fan
- Department of Genetic and Metabolic Laboratory, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, Guangxi, China
| | - Yuehong Zhou
- Pingguo Women and Children Care Hospital, Baise, Guangxi, China
| | - Xiaofeng Wei
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Sumin Zhao
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Decheng Cai
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Fengyu Guo
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Qianqian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Yun Li
- BGI Clinical Laboratories-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Xuelian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Haorong Lu
- BGI Clinical Laboratories-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Huajie Huang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Junfu Guo
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Fei Zhu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Yuan Yuan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Li Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Na Liu
- BGI Clinical Laboratories-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Zhiming Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Hui Jiang
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China
| | - Qiang Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Yijia Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | | | - Sarifah Hanafi
- Department of Paediatric, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Wanjun Zhou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Fu Xiong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Huanming Yang
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China; James D. Watson Institute of Genome Sciences, Hangzhou, Zhejiang, China
| | - Jian Wang
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China; James D. Watson Institute of Genome Sciences, Hangzhou, Zhejiang, China
| | - Bin Alwi Zilfalil
- Department of Paediatric, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Ming Qi
- School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Center for Genetic & Genomic Medicine, Zhejiang University Medical School 1st Affiliated Hospital, James Watson Institute of Genome Sciences, Hangzhou, Zhejiang, China
| | - Yaping Yang
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
| | - Ye Yin
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China
| | - Mao Mao
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China.
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China.
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Hunting for a needle in a haystack: investigating inherited diseases of sheep. Vet Rec 2017; 181:164-166. [DOI: 10.1136/vr.j3748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Panel-Based Clinical Genetic Testing in 85 Children with Inherited Retinal Disease. Ophthalmology 2017; 124:985-991. [PMID: 28341476 DOI: 10.1016/j.ophtha.2017.02.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 11/20/2022] Open
Abstract
PURPOSE To assess the clinical usefulness of genetic testing in a pediatric population with inherited retinal disease (IRD). DESIGN Single-center retrospective case series. PARTICIPANTS Eighty-five unrelated children with a diagnosis of isolated or syndromic IRD who were referred for clinical genetic testing between January 2014 and July 2016. METHODS Participants underwent a detailed ophthalmic examination, accompanied by electrodiagnostic testing (EDT) and dysmorphologic assessment where appropriate. Ocular and extraocular features were recorded using Human Phenotype Ontology terms. Subsequently, multigene panel testing (105 or 177 IRD-associated genes) was performed in an accredited diagnostic laboratory, followed by clinical variant interpretation. MAIN OUTCOME MEASURES Diagnostic yield and clinical usefulness of genetic testing. RESULTS Overall, 78.8% of patients (n = 67) received a probable molecular diagnosis; 7.5% (n = 5) of these had autosomal dominant disease, 25.4% (n = 17) had X-linked disease, and 67.2% (n = 45) had autosomal recessive disease. In a further 5.9% of patients (n = 5), a single heterozygous ABCA4 variant was identified; all these participants had a spectrum of clinical features consistent with ABCA4 retinopathy. Most participants (84.7%; n = 72) had undergone EDT and 81.9% (n = 59) of these patients received a probable molecular diagnosis. The genes most frequently mutated in the present cohort were CACNA1F and ABCA4, accounting for 14.9% (n = 10) and 11.9% (n = 8) of diagnoses respectively. Notably, in many cases, genetic testing helped to distinguish stationary from progressive IRD subtypes and to establish a precise diagnosis in a timely fashion. CONCLUSIONS Multigene panel testing pointed to a molecular diagnosis in 84.7% of children with IRD. The diagnostic yield in the study population was significantly higher compared with that in previously reported unselected IRD cohorts. Approaches similar to the one described herein are expected to become a standard component of care in pediatric ophthalmology. We propose the introduction of genetic testing early in the diagnostic pathway in children with clinical and/or electrophysiologic findings, suggestive of IRD.
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Romero CJ, Mehta L, Rapaport R. Genetic Techniques in the Evaluation of Short Stature. Endocrinol Metab Clin North Am 2016; 45:345-58. [PMID: 27241969 DOI: 10.1016/j.ecl.2016.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Normal growth is a complex dynamic process dependent on the coordination of multiple factors including genetics, nutrition and hormones that are all working in balance. This chapter will review selected features of commonly utilized genetic techniques such as chromosomal analysis, microarray analysis, targeted gene screening and whole exome sequencing that are being used to identify genes influencing growth. As genetic technologies continue to improve and become more accessible many of these techniques will help to provide a better understanding of mechanisms underlying abnormal growth and will eventually lead to novel management approaches for abnormal growth.
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Affiliation(s)
- Christopher J Romero
- Division of Pediatric Endocrinology and Diabetes, Kravis Children's Hospital at Mount Sinai, One Gustave L. Levy Place, Box 1616, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1616, New York, NY 10029, USA.
| | - Lakshmi Mehta
- Division of Medical Genetics, Department of Genetics and Genomic Sciences & Department of Pediatrics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1616, New York, NY 10029, USA
| | - Robert Rapaport
- Division of Pediatric Endocrinology and Diabetes, Kravis Children's Hospital at Mount Sinai, One Gustave L. Levy Place, Box 1616, New York, NY 10029, USA; Division of Pediatric Endocrinology and Diabetes, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1616, New York, NY 10029, USA
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Strande NT, Berg JS. Defining the Clinical Value of a Genomic Diagnosis in the Era of Next-Generation Sequencing. Annu Rev Genomics Hum Genet 2016; 17:303-32. [PMID: 27362341 DOI: 10.1146/annurev-genom-083115-022348] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As with all fields of medicine, the first step toward medical management of genetic disorders is obtaining an accurate diagnosis, which often requires testing at the molecular level. Unfortunately, given the large number of genetic conditions without a specific intervention, only rarely does a genetic diagnosis alter patient management-which raises the question, what is the added value of obtaining a molecular diagnosis? Given the fast-paced advancement of genomic technologies, this is an important question to address in the context of genome-scale testing. Here, we address the value of establishing a diagnosis using genome-scale testing and highlight the benefits and drawbacks of such testing. We also review and compare recent major studies implementing genome-scale sequencing methods to identify a molecular diagnosis in cohorts manifesting a broad range of Mendelian monogenic disorders. Finally, we discuss potential future applications of genomic sequencing, such as screening for rare conditions.
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Affiliation(s)
- Natasha T Strande
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599; ,
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599; ,
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Curnutte MA, Frumovitz KL, Bollinger JM, Cook-Deegan RM, McGuire AL, Majumder MA. Developing context-specific next-generation sequencing policy. Nat Biotechnol 2016; 34:466-70. [PMID: 27153269 PMCID: PMC5117622 DOI: 10.1038/nbt.3545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Margaret Ann Curnutte
- Baylor College of Medicine, Center for Medical Ethics and Health Policy, Houston, Texas, USA
| | - Karen L Frumovitz
- Baylor College of Medicine, Center for Medical Ethics and Health Policy, Houston, Texas, USA
| | - Juli M Bollinger
- Berman Institute of Bioethics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Robert M Cook-Deegan
- Sanford School of Public Policy, Duke University, Durham, North Carolina, USA
- School for the Future of Innovation in Society, Arizona State University, Tempe, Arizona, USA
| | - Amy L McGuire
- Baylor College of Medicine, Center for Medical Ethics and Health Policy, Houston, Texas, USA
| | - Mary A Majumder
- Baylor College of Medicine, Center for Medical Ethics and Health Policy, Houston, Texas, USA
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Ales M, Luca L, Marija V, Gorazd R, Karin W, Ana B, Alenka H, Peterlin B. Phenotype-driven gene target definition in clinical genome-wide sequencing data interpretation. Genet Med 2016; 18:1102-1110. [DOI: 10.1038/gim.2016.22] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/25/2016] [Indexed: 12/22/2022] Open
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Qin H, Samuels JF, Wang Y, Zhu Y, Grados MA, Riddle MA, Greenberg BD, Knowles JA, Fyer AJ, McCracken JT, Murphy DL, Rasmussen SA, Cullen BA, Piacentini J, Geller D, Stewart SE, Pauls D, Bienvenu OJ, Goes FS, Maher B, Pulver AE, Valle D, Lange C, Mattheisen M, McLaughlin NC, Liang KY, Nurmi EL, Askland KD, Nestadt G, Shugart YY. Whole-genome association analysis of treatment response in obsessive-compulsive disorder. Mol Psychiatry 2016; 21:270-6. [PMID: 25824302 PMCID: PMC5027902 DOI: 10.1038/mp.2015.32] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 01/16/2015] [Accepted: 02/11/2015] [Indexed: 12/16/2022]
Abstract
Up to 30% of patients with obsessive-compulsive disorder (OCD) exhibit an inadequate response to serotonin reuptake inhibitors (SRIs). To date, genetic predictors of OCD treatment response have not been systematically investigated using genome-wide association study (GWAS). To identify specific genetic variations potentially influencing SRI response, we conducted a GWAS study in 804 OCD patients with information on SRI response. SRI response was classified as 'response' (n=514) or 'non-response' (n=290), based on self-report. We used the more powerful Quasi-Likelihood Score Test (the MQLS test) to conduct a genome-wide association test correcting for relatedness, and then used an adjusted logistic model to evaluate the effect size of the variants in probands. The top single-nucleotide polymorphism (SNP) was rs17162912 (P=1.76 × 10(-8)), which is near the DISP1 gene on 1q41-q42, a microdeletion region implicated in neurological development. The other six SNPs showing suggestive evidence of association (P<10(-5)) were rs9303380, rs12437601, rs16988159, rs7676822, rs1911877 and rs723815. Among them, two SNPs in strong linkage disequilibrium, rs7676822 and rs1911877, located near the PCDH10 gene, gave P-values of 2.86 × 10(-6) and 8.41 × 10(-6), respectively. The other 35 variations with signals of potential significance (P<10(-4)) involve multiple genes expressed in the brain, including GRIN2B, PCDH10 and GPC6. Our enrichment analysis indicated suggestive roles of genes in the glutamatergic neurotransmission system (false discovery rate (FDR)=0.0097) and the serotonergic system (FDR=0.0213). Although the results presented may provide new insights into genetic mechanisms underlying treatment response in OCD, studies with larger sample sizes and detailed information on drug dosage and treatment duration are needed.
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Affiliation(s)
- H Qin
- Unit on Statistical Genomics, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - JF Samuels
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Y Wang
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Y Zhu
- Department of Epidemiology, Tulane University, School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - MA Grados
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - MA Riddle
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - BD Greenberg
- Department of Psychiatry and Human Behavior, Brown Medical School, Butler Hospital, Brown University, Providence, RI 02906, USA
| | - JA Knowles
- Department of Psychiatry, Keck Medical School, University of Southern California, Los Angeles, CA 90089, USA
| | - AJ Fyer
- College of Physicians and Surgeons at Columbia University, 630 West 168th Street, New York, NY 10032
| | - JT McCracken
- Department of Psychiatry and Biobehavioral Sciences, School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - DL Murphy
- Laboratory of Clinical Science, NIMH, NIH, Bethesda, MD 20892, USA
| | - SA Rasmussen
- Department of Psychiatry and Human Behavior, Brown Medical School, Butler Hospital, Brown University, Providence, RI 02906, USA
| | - BA Cullen
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - J Piacentini
- Department of Psychiatry and Biobehavioral Sciences, School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - D Geller
- Departments of Psychiatry and Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - SE Stewart
- Department of Psychiatry, University of British Columbia, A3-118, West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - D Pauls
- Department of Psychiatry and Human Behavior, Brown Medical School, Butler Hospital, Brown University, Providence, RI 02906, USA
| | - OJ Bienvenu
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - FS Goes
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - B Maher
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - AE Pulver
- Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Baltimore, MD 21205, USA
| | - D Valle
- Hopkins University School of Medicine, Institute of Human Genetics, Departments of Pediatrics, Ophthalmology and Molecular Biology & Genetics, Baltimore, MD 21205, USA
| | - C Lange
- Harvard School of Public Health, Department of Biostatistics, Boston, MA 02114, USA,Department of Genomic Mathematics, University of Bonn, Bonn 53113, Germany
| | - M Mattheisen
- Harvard School of Public Health, Department of Biostatistics, Boston, MA 02114, USA,Department of Genomic Mathematics, University of Bonn, Bonn 53113, Germany,Department of Biomedicine and Center for Integrated Sequencing (iSEQ), Aarhus University, Aarhus 8000, Denmark
| | - NC McLaughlin
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - K-Y Liang
- Johns Hopkins University Bloomberg School of Public Health, Department of Mental Health, Baltimore, MD 21205, USA
| | - EL Nurmi
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Jane & Terry Semel Institute of Neuroscience and Human Behavior, 760 Westwood Plaza, Los Angeles, CA 90095, USA
| | - KD Askland
- Department of Psychiatry and Human Behavior, Butler Hospital, The Warren Alpert School of Medicine of Brown University, Providence, Rhode Island 02903, USA
| | - G Nestadt
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - YY Shugart
- Unit on Statistical Genomics, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
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Jolly RD, Dittmer KE, Blair HT. Animal medical genetics: a perspective on the epidemiology and control of inherited disorders. N Z Vet J 2016; 64:135-44. [DOI: 10.1080/00480169.2015.1129296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Van Driest SL, Wells QS, Stallings S, Bush WS, Gordon A, Nickerson DA, Kim JH, Crosslin DR, Jarvik GP, Carrell DS, Ralston JD, Larson EB, Bielinski SJ, Olson JE, Ye Z, Kullo IJ, Abul-Husn NS, Scott SA, Bottinger E, Almoguera B, Connolly J, Chiavacci R, Hakonarson H, Rasmussen-Torvik LJ, Pan V, Persell SD, Smith M, Chisholm RL, Kitchner TE, He MM, Brilliant MH, Wallace JR, Doheny KF, Shoemaker MB, Li R, Manolio TA, Callis TE, Macaya D, Williams MS, Carey D, Kapplinger JD, Ackerman MJ, Ritchie MD, Denny JC, Roden DM. Association of Arrhythmia-Related Genetic Variants With Phenotypes Documented in Electronic Medical Records. JAMA 2016; 315:47-57. [PMID: 26746457 PMCID: PMC4758131 DOI: 10.1001/jama.2015.17701] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
IMPORTANCE Large-scale DNA sequencing identifies incidental rare variants in established Mendelian disease genes, but the frequency of related clinical phenotypes in unselected patient populations is not well established. Phenotype data from electronic medical records (EMRs) may provide a resource to assess the clinical relevance of rare variants. OBJECTIVE To determine the clinical phenotypes from EMRs for individuals with variants designated as pathogenic by expert review in arrhythmia susceptibility genes. DESIGN, SETTING, AND PARTICIPANTS This prospective cohort study included 2022 individuals recruited for nonantiarrhythmic drug exposure phenotypes from October 5, 2012, to September 30, 2013, for the Electronic Medical Records and Genomics Network Pharmacogenomics project from 7 US academic medical centers. Variants in SCN5A and KCNH2, disease genes for long QT and Brugada syndromes, were assessed for potential pathogenicity by 3 laboratories with ion channel expertise and by comparison with the ClinVar database. Relevant phenotypes were determined from EMRs, with data available from 2002 (or earlier for some sites) through September 10, 2014. EXPOSURES One or more variants designated as pathogenic in SCN5A or KCNH2. MAIN OUTCOMES AND MEASURES Arrhythmia or electrocardiographic (ECG) phenotypes defined by International Classification of Diseases, Ninth Revision (ICD-9) codes, ECG data, and manual EMR review. RESULTS Among 2022 study participants (median age, 61 years [interquartile range, 56-65 years]; 1118 [55%] female; 1491 [74%] white), a total of 122 rare (minor allele frequency <0.5%) nonsynonymous and splice-site variants in 2 arrhythmia susceptibility genes were identified in 223 individuals (11% of the study cohort). Forty-two variants in 63 participants were designated potentially pathogenic by at least 1 laboratory or ClinVar, with low concordance across laboratories (Cohen κ = 0.26). An ICD-9 code for arrhythmia was found in 11 of 63 (17%) variant carriers vs 264 of 1959 (13%) of those without variants (difference, +4%; 95% CI, -5% to +13%; P = .35). In the 1270 (63%) with ECGs, corrected QT intervals were not different in variant carriers vs those without (median, 429 vs 439 milliseconds; difference, -10 milliseconds; 95% CI, -16 to +3 milliseconds; P = .17). After manual review, 22 of 63 participants (35%) with designated variants had any ECG or arrhythmia phenotype, and only 2 had corrected QT interval longer than 500 milliseconds. CONCLUSIONS AND RELEVANCE Among laboratories experienced in genetic testing for cardiac arrhythmia disorders, there was low concordance in designating SCN5A and KCNH2 variants as pathogenic. In an unselected population, the putatively pathogenic genetic variants were not associated with an abnormal phenotype. These findings raise questions about the implications of notifying patients of incidental genetic findings.
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Affiliation(s)
| | - Quinn S Wells
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - William S Bush
- Vanderbilt University Medical Center, Nashville, Tennessee2Case Western Reserve University, Cleveland, Ohio
| | | | | | | | | | | | | | | | - Eric B Larson
- Group Health Research Institute, Seattle, Washington
| | | | | | - Zi Ye
- Mayo Clinic, Rochester, Minnesota
| | | | | | - Stuart A Scott
- Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Berta Almoguera
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - John Connolly
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Hakon Hakonarson
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania8Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | | | - Vivian Pan
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Stephen D Persell
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Maureen Smith
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Rex L Chisholm
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | | | - Max M He
- Marshfield Clinic Research Foundation, Marshfield, Wisconsin
| | | | | | | | | | - Rongling Li
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | | | | | | | - David Carey
- Geisinger Health System, Danville, Pennsylvania
| | | | | | - Marylyn D Ritchie
- Pennsylvania State University, University Park16Geisinger Health System, Danville, Pennsylvania
| | - Joshua C Denny
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dan M Roden
- Vanderbilt University Medical Center, Nashville, Tennessee
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Abstract
Inborn errors of metabolism are single gene disorders resulting from the defects in the biochemical pathways of the body. Although these disorders are individually rare, collectively they account for a significant portion of childhood disability and deaths. Most of the disorders are inherited as autosomal recessive whereas autosomal dominant and X-linked disorders are also present. The clinical signs and symptoms arise from the accumulation of the toxic substrate, deficiency of the product, or both. Depending on the residual activity of the deficient enzyme, the initiation of the clinical picture may vary starting from the newborn period up until adulthood. Hundreds of disorders have been described until now and there has been a considerable clinical overlap between certain inborn errors. Resulting from this fact, the definite diagnosis of inborn errors depends on enzyme assays or genetic tests. Especially during the recent years, significant achievements have been gained for the biochemical and genetic diagnosis of inborn errors. Techniques such as tandem mass spectrometry and gas chromatography for biochemical diagnosis and microarrays and next-generation sequencing for the genetic diagnosis have enabled rapid and accurate diagnosis. The achievements for the diagnosis also enabled newborn screening and prenatal diagnosis. Parallel to the development the diagnostic methods; significant progress has also been obtained for the treatment. Treatment approaches such as special diets, enzyme replacement therapy, substrate inhibition, and organ transplantation have been widely used. It is obvious that by the help of the preclinical and clinical research carried out for inborn errors, better diagnostic methods and better treatment approaches will high likely be available.
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El Shanti H, Chouchane L, Badii R, Gallouzi IE, Gasparini P. Genetic testing and genomic analysis: a debate on ethical, social and legal issues in the Arab world with a focus on Qatar. J Transl Med 2015; 13:358. [PMID: 26572608 PMCID: PMC4647661 DOI: 10.1186/s12967-015-0720-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 10/31/2015] [Indexed: 11/10/2022] Open
Abstract
In 2013 both Saudi Arabia and Qatar launched genome projects with the aim of providing information for better diagnosis, treatment and prevention of diseases and, ultimately to realize personalized medicine by sequencing hundred thousands samples. These population based genome activities raise a series of relevant ethical, legal and social issues general, related to the specific population structure as well as to the Islamic perspective on genomic analysis and genetic testing. To contribute to the debate, the Authors after reviewing the existing literature and taking advantage of their professional experience in the field and in the geographic area, discuss and provide their opinions. In particular, the Authors focus on the impact of consanguinity on population structure and disease frequency in the Arab world, on genetic testing and genomic analysis (i.e. technical aspects, impact, etc.) and on their regulations. A comparison between the Islamic perspective and the ethical, social and legal issues raised in other population contexts is also carried. In conclusion, this opinion article with an up-to-date contribution to the discussion on the relevance and impact of genomic analysis and genetic testing in the Arab world, might help in producing specific national guidelines on genetic testing and genomic analysis and help accelerate the implementation and roll out of genome projects in Muslim countries and more specifically in Qatar, and other countries of the Gulf.
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Affiliation(s)
- Hatem El Shanti
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University (HBKU), Doha, Qatar.
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Qatar Foundation, Education City, Doha, Qatar.
| | - Ramin Badii
- Molecular Genetics Laboratory, Hamad Medical Corporation, Doha, Qatar.
| | - Imed Eddine Gallouzi
- Hamad Bin Khalifa University (HBKU), College of Sciences and Engineering, Life Sciences Division, Doha, Qatar.
| | - Paolo Gasparini
- Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar.
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50
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Aronson SJ, Rehm HL. Building the foundation for genomics in precision medicine. Nature 2015; 526:336-42. [PMID: 26469044 PMCID: PMC5669797 DOI: 10.1038/nature15816] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 08/11/2015] [Indexed: 01/04/2023]
Abstract
Precision medicine has the potential to profoundly improve the practice of medicine. However, the advances required will take time to implement. Genetics is already being used to direct clinical decision-making and its contribution is likely to increase. To accelerate these advances, fundamental changes are needed in the infrastructure and mechanisms for data collection, storage and sharing. This will create a continuously learning health-care system with seamless cycling between clinical care and research. Patients must be educated about the benefits of sharing data. The building blocks for such a system are already forming and they will accelerate the adoption of precision medicine.
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Affiliation(s)
- Samuel J Aronson
- Partners HealthCare Personalized Medicine, Boston, Massachusetts 02115, USA
- Partners HealthCare Research Information Services and Computing, Charlestown, Massachusetts 02129, USA
| | - Heidi L Rehm
- Partners HealthCare Personalized Medicine, Boston, Massachusetts 02115, USA
- Department of Pathology, Brigham &Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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