1
|
Kim N, Kim TY, Han JY, Park J. Five Years' Experience with Gene Panel Sequencing in Hereditary Hemolytic Anemia Screened by Routine Peripheral Blood Smear Examination. Diagnostics (Basel) 2023; 13:diagnostics13040770. [PMID: 36832257 PMCID: PMC9954878 DOI: 10.3390/diagnostics13040770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Hereditary hemolytic anemia (HHA) is defined as a group of heterogeneous and rare diseases caused by defects of red blood cell (RBC) metabolism and RBC membrane, which leads to lysis or premature clearance. The aim of this study was to investigate individuals with HHA for potential disease-causing variants in 33 genes reported to be associated with HHA. METHODS A total of 14 independent individuals or families diagnosed with suspected HHA, and in particular, RBC membranopathy, RBC enzymopathy, and hemoglobinopathy, were collected after routine peripheral blood smear testing. A custom designed panel, including the 33 genes, was performed using gene panel sequencing on the Ion Torrent PGM™ Dx System. The best candidate disease-causing variants were confirmed by Sanger sequencing. RESULTS Several variants of the HHA-associated genes were detected in 10 out of 14 suspected HHA individuals. After excluding those variants predicted to be benign, 10 pathogenic variants and 1 variant of uncertain significance (VUS) were confirmed in 10 individuals with suspected HHA. Of these variants, the p.Trp704Ter nonsense variant of EPB41 and missense p.Gly151Asp variant of SPTA1 were identified in two out of four hereditary elliptocytoses. The frameshift p.Leu884GlyfsTer27 variant of ANK1, nonsense p.Trp652Ter variant of the SPTB, and missense p.Arg490Trp variant of PKLR were detected in all four hereditary spherocytosis cases. Missense p.Glu27Lys, nonsense p.Lys18Ter variants, and splicing errors such as c.92 + 1G > T and c.315 + 1G > A within HBB were identified in four beta thalassemia cases. CONCLUSIONS This study provides a snapshot of the genetic alterations in a cohort of Korean HHA individuals and demonstrates the clinical utility of using gene panels in HHA. Genetic results can provide precise clinical diagnosis and guidance regarding medical treatment and management for some individuals.
Collapse
Affiliation(s)
- Namsu Kim
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea
| | - Tae Yun Kim
- Department of Thoracic and Cardiovascular Surgery, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea
| | - Ji Yoon Han
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Correspondence: (J.Y.H.); (J.P.); Tel.: +82-42-220-9246 (J.Y.H.); +82-63-250-1218 (J.P.); Fax: +82-42-221-2925 (J.Y.H.); +82-63-250-1200 (J.P.)
| | - Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea
- Research Institute of Clinical Medicine, Jeonbuk National University-Biomedical Research Institute, Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
- Correspondence: (J.Y.H.); (J.P.); Tel.: +82-42-220-9246 (J.Y.H.); +82-63-250-1218 (J.P.); Fax: +82-42-221-2925 (J.Y.H.); +82-63-250-1200 (J.P.)
| |
Collapse
|
2
|
Raju H, Ware JS, Skinner JR, Hedley PL, Arno G, Love DR, van der Werf C, Tfelt-Hansen J, Winkel BG, Cohen MC, Li X, John S, Sharma S, Jeffery S, Wilde AAM, Christiansen M, Sheppard MN, Behr ER. Next-generation sequencing using microfluidic PCR enrichment for molecular autopsy. BMC Cardiovasc Disord 2019; 19:174. [PMID: 31337358 PMCID: PMC6651896 DOI: 10.1186/s12872-019-1154-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/10/2019] [Indexed: 01/11/2023] Open
Abstract
Background We aimed to determine the mutation yield and clinical applicability of “molecular autopsy” following sudden arrhythmic death syndrome (SADS) by validating and utilizing low-cost high-throughput technologies: Fluidigm Access Array PCR-enrichment with Illumina HiSeq 2000 next generation sequencing (NGS). Methods We validated and optimized the NGS platform with a subset of 46 patients by comparison with Sanger sequencing of coding exons of major arrhythmia risk-genes (KCNQ1, KCNH2, SCN5A, KCNE1, KCNE2, RYR2). A combined large multi-ethnic international SADS cohort was sequenced utilizing the NGS platform to determine overall molecular yield; rare variants identified by NGS were subsequently reconfirmed by Sanger sequencing. Results The NGS platform demonstrated 100% sensitivity for pathogenic variants as well as 87.20% sensitivity and 99.99% specificity for all substitutions (optimization subset, n = 46). The positive predictive value (PPV) for NGS for rare substitutions was 16.0% (27 confirmed rare variants of 169 positive NGS calls in 151 additional cases). The overall molecular yield in 197 multi-ethnic SADS cases (mean age 22.6 ± 14.4 years, 68% male) was 5.1% (95% confidence interval 2.0–8.1%), representing 10 cases carrying pathogenic or likely pathogenic risk-mutations. Conclusions Molecular autopsy with Fluidigm Access Array and Illumina HiSeq NGS utilizing a selected panel of LQTS/BrS and CPVT risk-genes offers moderate diagnostic yield, albeit requiring confirmatory Sanger-sequencing of mutational variants. Electronic supplementary material The online version of this article (10.1186/s12872-019-1154-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hariharan Raju
- Cardiovascular Sciences Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, SW17 0RE, UK. .,Health Cardiology, Faculty of Medicine & Health Sciences, Macquarie University, Suite 203, 2 Technology Place, Sydney, NSW, 2109, Australia.
| | - James S Ware
- NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton Hospital, London, UK
| | - Jonathan R Skinner
- Greenlane Paediatric and Congenital Cardiac Services, Starship Childrens Hospital, Auckland, New Zealand
| | - Paula L Hedley
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Gavin Arno
- Cardiovascular Sciences Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, SW17 0RE, UK
| | - Donald R Love
- Diagnostic Genetics, Auckland City Hospital, Auckland, New Zealand
| | - Christian van der Werf
- Amsterdam UMC, Heart Centre, and Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Jacob Tfelt-Hansen
- Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Denmark.,Department of Forensic Medicine, University of Copenhagen, København, Denmark.,ERN-GUARD Heart (European Union), Brussels, Belgium
| | - Bo Gregers Winkel
- Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Denmark.,ERN-GUARD Heart (European Union), Brussels, Belgium
| | - Marta C Cohen
- Histopathology Department, Sheffield Children's Hospital, Sheffield, UK
| | - Xinzhong Li
- NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton Hospital, London, UK.,School of Science, Engineering and Design, Teesside University, Middlesbrough, UK
| | - Shibu John
- NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton Hospital, London, UK
| | - Sanjay Sharma
- Cardiovascular Sciences Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, SW17 0RE, UK
| | - Steve Jeffery
- Cardiovascular Sciences Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, SW17 0RE, UK
| | - Arthur A M Wilde
- Amsterdam UMC, Heart Centre, and Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam, Netherlands.,ERN-GUARD Heart (European Union), Brussels, Belgium
| | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mary N Sheppard
- Cardiovascular Sciences Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, SW17 0RE, UK.,ERN-GUARD Heart (European Union), Brussels, Belgium
| | - Elijah R Behr
- Cardiovascular Sciences Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, SW17 0RE, UK. .,ERN-GUARD Heart (European Union), Brussels, Belgium.
| |
Collapse
|
3
|
Molecular analysis of inherited cardiomyopathy using next generation semiconductor sequencing technologies. J Transl Med 2018; 16:241. [PMID: 30165862 PMCID: PMC6117967 DOI: 10.1186/s12967-018-1605-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/13/2018] [Indexed: 01/16/2023] Open
Abstract
Background Cardiomyopathies are the most common clinical and genetic heterogeneity cardiac diseases, and genetic contribution in particular plays a major role in patients with primary cardiomyopathies. The aim of this study is to investigate cases of inherited cardiomyopathy (IC) for potential disease-causing mutations in 64 genes reported to be associated with IC. Methods A total of 110 independent cases or families diagnosed with various primary cardiomyopathies, including hypertrophic cardiomyopathy, dilated cardiomyopathy, restrictive cardiomyopathy, arrhythmogenic right ventricular cardiomyopathy, left ventricular non-compaction, and undefined cardiomyopathy, were collected after informed consent. A custom designed panel, including 64 genes, was screened using next generation sequencing on the Ion Torrent PGM platform. The best candidate disease-causing variants were verified by Sanger sequencing. Results A total of 78 variants in 73 patients were identified. After excluding the variants predicted to be benign and VUS, 26 pathogenic or likely pathogenic variants were verified in 26 probands (23.6%), including a homozygous variant in the SLC25A4 gene. Of these variants, 15 have been reported in the Human Gene Mutation Database or ClinVar database, while 11 are novel. The majority of variants were observed in the MYH7 (8/26) and MYBPC3 (6/26) gene. Titin (TTN) truncating mutations account for 13% in our dilated cardiomyopathy cases (3/23). Conclusions This study provides an overview of the genetic aberrations in this cohort of Chinese IC patients and demonstrates the power of next generation sequencing in IC. Genetic results can provide precise clinical diagnosis and guidance regarding medical care for some individuals. Electronic supplementary material The online version of this article (10.1186/s12967-018-1605-5) contains supplementary material, which is available to authorized users.
Collapse
|
4
|
Miyata K, Ohno S, Itoh H, Horie M. Bradycardia Is a Specific Phenotype of Catecholaminergic Polymorphic Ventricular Tachycardia Induced by RYR2 Mutations. Intern Med 2018; 57:1813-1817. [PMID: 29434162 PMCID: PMC6064684 DOI: 10.2169/internalmedicine.9843-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Objective Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a lethal inherited disease characterized by ventricular arrhythmias induced by physical exercise or emotional stress. The major cause of CPVT is mutations in RYR2, which encodes the cardiac ryanodine receptor channel. Recent advances in sequencing technology have yielded incidental findings of RYR2 variants in other cardiac diseases. Analyzing the characteristics of RYR2 variants related to CPVT will be useful for differentiation from those related to other cardiac diseases. We examined the phenotypic characteristics of patients with RYR2 variants. Methods Seventy-nine probands carrying RYR2 variants whose diagnoses were either CPVT (n=68) or long QT syndrome (LQTS; n=11) were enrolled. We compared the characteristics of the electrocardiogram (ECG) and the location of the RYR2 mutations-N-terminal (NT), central region (CR) or C-terminal (CT)-between the two patient groups. Results Using the ECGs available from 53 probands before β-blocker therapies, we analyzed the heart rates (HRs). CPVT probands showed bradycardia more frequently (25/44; 57%) than LQTS probands (1/9; 11%; p=0.024). In CPVT patients, 20 mutations were located in NT, 25 in CR and 23 in CT. In LQTS patients, 5 mutations were located in NT, 2 in CR and 4 in CT. There were no significant differences in the locations of the RYR2 mutations between the phenotypes. Conclusion Bradycardia was highly correlated with the phenotype of CPVT. When a clinically-diagnosed LQTS patient with bradycardia carries an RYR2 mutation, we should be careful to avoid making a misdiagnosis, as the patient may actually have CPVT.
Collapse
Affiliation(s)
- Kazuaki Miyata
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Japan
- Department of Cardiovascular Medicine, Iga City General Hospital, Japan
| | - Seiko Ohno
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Japan
| | - Hideki Itoh
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Japan
| | - Minoru Horie
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Japan
| |
Collapse
|
5
|
Bennett CW, Berchem G, Kim YJ, El-Khoury V. Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer. Oncotarget 2018; 7:71013-71035. [PMID: 27589834 PMCID: PMC5342606 DOI: 10.18632/oncotarget.11717] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/11/2016] [Indexed: 12/13/2022] Open
Abstract
Personalized medicine has emerged as the future of cancer care to ensure that patients receive individualized treatment specific to their needs. In order to provide such care, molecular techniques that enable oncologists to diagnose, treat, and monitor tumors are necessary. In the field of lung cancer, cell free DNA (cfDNA) shows great potential as a less invasive liquid biopsy technique, and next-generation sequencing (NGS) is a promising tool for analysis of tumor mutations. In this review, we outline the evolution of cfDNA and NGS and discuss the progress of using them in a clinical setting for patients with lung cancer. We also present an analysis of the role of cfDNA as a liquid biopsy technique and NGS as an analytical tool in studying EGFR and MET, two frequently mutated genes in lung cancer. Ultimately, we hope that using cfDNA and NGS for cancer diagnosis and treatment will become standard for patients with lung cancer and across the field of oncology.
Collapse
Affiliation(s)
- Catherine W Bennett
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Guy Berchem
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg.,Centre Hospitalier de Luxembourg, L-1210 Luxembourg, Luxembourg
| | - Yeoun Jin Kim
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Victoria El-Khoury
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| |
Collapse
|
6
|
Allali I, Arnold JW, Roach J, Cadenas MB, Butz N, Hassan HM, Koci M, Ballou A, Mendoza M, Ali R, Azcarate-Peril MA. A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome. BMC Microbiol 2017; 17:194. [PMID: 28903732 PMCID: PMC5598039 DOI: 10.1186/s12866-017-1101-8] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 08/29/2017] [Indexed: 12/16/2022] Open
Abstract
Background Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Results Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU picking), UPARSE1 and UPARSE2 (each pair differs only in the use of chimera depletion methods), and DADA2 (for Illumina data only). GS FLX+ yielded the longest reads and highest quality scores, while MiSeq generated the largest number of reads after quality filtering. Declines in quality scores were observed starting at bases 150–199 for GS FLX+ and bases 90–99 for MiSeq. Scores were stable for PGM-generated data. Overall microbiome compositional profiles were comparable between platforms; however, average relative abundance of specific taxa varied depending on sequencing platform, library preparation method, and bioinformatics analysis. Specifically, QIIME with de novo OTU picking yielded the highest number of unique species and alpha diversity was reduced with UPARSE and DADA2 compared to QIIME. Conclusions The three platforms compared in this study were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological conclusions. Our results demonstrate that while there were differences in depth of coverage and phylogenetic diversity, all workflows revealed comparable treatment effects on microbial diversity. To increase reproducibility and reliability and to retain consistency between similar studies, it is important to consider the impact on data quality and relative abundance of taxa when selecting NGS platforms and analysis tools for microbiome studies. Electronic supplementary material The online version of this article (10.1186/s12866-017-1101-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Imane Allali
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA.,Laboratory of Biochemistry & Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Jason W Arnold
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Jeffrey Roach
- Research Computing, University of North Carolina, Chapel Hill, NC, USA
| | - Maria Belen Cadenas
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Natasha Butz
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Hosni M Hassan
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Matthew Koci
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Anne Ballou
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Mary Mendoza
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Rizwana Ali
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA.
| |
Collapse
|
7
|
Care M, Chauhan V, Spears D. Genetic Testing in Inherited Heart Diseases: Practical Considerations for Clinicians. Curr Cardiol Rep 2017; 19:88. [PMID: 28812208 DOI: 10.1007/s11886-017-0885-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW Genetic testing has become an important element in the care of patients with inherited cardiac conditions (ICCs). The purpose of this review is to provide clinicians with insights into the utility of genetic testing as well as challenges associated with interpreting results. RECENT FINDINGS Genetic testing may be indicated for individuals who are affected with or who have family histories of various ICCs. Various testing options are available and determining the most appropriate test for any given clinical scenario is key when interpreting results. Newly published guidelines as well as various publicly accessible tools are available to clinicians to help with interpretation of genetic findings; however the subjectivity with respect to variant classification can make accurate assessment challenging. Genetic information can provide highly useful and relevant information for patients, their family members, and their healthcare providers. Given the potential ramifications of variant misclassification, expertise in both clinical phenotyping and molecular genetics is imperative in order to provide accurate diagnosis, management recommendations, and family risk assessment for this patient population.
Collapse
Affiliation(s)
- Melanie Care
- Division of Cardiology, Department of Medicine, Peter Munk Cardiac Centre, Toronto General Hospital, University Health Network, 200 Elizabeth St., Toronto, ON, M5G 2C4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Vijay Chauhan
- Division of Cardiology, Department of Medicine, Peter Munk Cardiac Centre, Toronto General Hospital, University Health Network, 200 Elizabeth St., Toronto, ON, M5G 2C4, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Danna Spears
- Division of Cardiology, Department of Medicine, Peter Munk Cardiac Centre, Toronto General Hospital, University Health Network, 200 Elizabeth St., Toronto, ON, M5G 2C4, Canada. .,Department of Medicine, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
8
|
Harmer SC, Tinker A. The impact of recent advances in genetics in understanding disease mechanisms underlying the long QT syndromes. Biol Chem 2017; 397:679-93. [PMID: 26910742 DOI: 10.1515/hsz-2015-0306] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/18/2016] [Indexed: 11/15/2022]
Abstract
Long QT syndrome refers to a characteristic abnormality of the electrocardiogram and it is associated with a form of ventricular tachycardia known as torsade-de-pointes and sudden arrhythmic death. It can occur as part of a hereditary syndrome or can be acquired usually because of drug administration. Here we review recent genetic, molecular and cellular discoveries and outline how they have furthered our understanding of this disease. Specifically we focus on compound mutations, genome wide association studies of QT interval, modifier genes and the therapeutic implications of this recent work.
Collapse
|
9
|
Riman S, Kiesler KM, Borsuk LA, Vallone PM. Characterization of NIST human mitochondrial DNA SRM-2392 and SRM-2392-I standard reference materials by next generation sequencing. Forensic Sci Int Genet 2017; 29:181-192. [DOI: 10.1016/j.fsigen.2017.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/17/2017] [Accepted: 04/04/2017] [Indexed: 12/12/2022]
|
10
|
Hori I, Otomo T, Nakashima M, Miya F, Negishi Y, Shiraishi H, Nonoda Y, Magara S, Tohyama J, Okamoto N, Kumagai T, Shimoda K, Yukitake Y, Kajikawa D, Morio T, Hattori A, Nakagawa M, Ando N, Nishino I, Kato M, Tsunoda T, Saitsu H, Kanemura Y, Yamasaki M, Kosaki K, Matsumoto N, Yoshimori T, Saitoh S. Defects in autophagosome-lysosome fusion underlie Vici syndrome, a neurodevelopmental disorder with multisystem involvement. Sci Rep 2017; 7:3552. [PMID: 28615637 PMCID: PMC5471274 DOI: 10.1038/s41598-017-02840-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/18/2017] [Indexed: 02/08/2023] Open
Abstract
Vici syndrome (VICIS) is a rare, autosomal recessive neurodevelopmental disorder with multisystem involvement characterized by agenesis of the corpus callosum, cataracts, cardiomyopathy, combined immunodeficiency, developmental delay, and hypopigmentation. Mutations in EPG5, a gene that encodes a key autophagy regulator, have been shown to cause VICIS, however, the precise pathomechanism underlying VICIS is yet to be clarified. Here, we describe detailed clinical (including brain MRI and muscle biopsy) and genetic features of nine Japanese patients with VICIS. Genetic dissection of these nine patients from seven families identified 14 causative mutations in EPG5. These included five nonsense, two frameshift, three splicing, one missense, and one multi-exon deletion mutations, and two initiation codon variants. Furthermore, cultured skin fibroblasts (SFs) from two affected patients demonstrated partial autophagic dysfunction. To investigate the function of EPG5, siRNA based EPG5 knock-down, and CRISPR/Cas9 mediated EPG5 knock-out HeLa cells were generated. EPG5-depleted cells exhibited a complete block of autophagic flux caused by defective autophagosome-lysosome fusion. Unexpectedly, endocytic degradation was normal in both VICIS SFs and EPG5 depleted cells, suggesting that EPG5 function is limited to the regulation of autophagosome-lysosome fusion.
Collapse
Affiliation(s)
- Ikumi Hori
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
| | - Takanobu Otomo
- Department of Genetics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
- Research Center for Autophagy, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Mitsuko Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Fuyuki Miya
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Yutaka Negishi
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
| | - Hideaki Shiraishi
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan
| | - Yutaka Nonoda
- Department of Pediatrics, Kitasato University School of Medicine, Sagamihara, 252-0373, Japan
| | - Shinichi Magara
- Department of Pediatrics, Epilepsy Center, Nishi-Niigata Chuo National Hospital, Niigata, 950-2085, Japan
| | - Jun Tohyama
- Department of Pediatrics, Epilepsy Center, Nishi-Niigata Chuo National Hospital, Niigata, 950-2085, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, 594-1101, Japan
| | - Takeshi Kumagai
- Department of Pediatrics, Wakayama Medical University, Wakayama, 641-8509, Japan
| | - Konomi Shimoda
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Yoshiya Yukitake
- Department of Neonatology, Ibaraki Children's Hospital, Mito, 311-4145, Japan
| | - Daigo Kajikawa
- Department of Child Health, Faculty of Medicine, Tsukuba University, Tsukuba, 305-8576, Japan
| | - Tomohiro Morio
- Department of Pediatrics, Faculty of Medicine, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Ayako Hattori
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
| | - Motoo Nakagawa
- Department of Radiology, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
| | - Naoki Ando
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8551, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, 142-8666, Japan
| | - Tatsuhiko Tsunoda
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Yonehiro Kanemura
- Division of Regenerative Medicine, Institute for Clinical Research, Osaka National Hospital, National Hospital Organization, Osaka, 540-0006, Japan
- Department of Neurosurgery, Osaka National Hospital, National Hospital Organization, Osaka, 540-0006, Japan
| | - Mami Yamasaki
- Department of Neurosurgery, Takatsuki General Hospital, Osaka, 569-1192, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Tamotsu Yoshimori
- Department of Genetics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
- Research Center for Autophagy, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan.
| |
Collapse
|
11
|
Reiman A, Pandey S, Lloyd KL, Dyer N, Khan M, Crockard M, Latten MJ, Watson TL, Cree IA, Grammatopoulos DK. Molecular testing for familial hypercholesterolaemia-associated mutations in a UK-based cohort: development of an NGS-based method and comparison with multiplex polymerase chain reaction and oligonucleotide arrays. Ann Clin Biochem 2016; 53:654-662. [PMID: 26748104 DOI: 10.1177/0004563216629170] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background Detection of disease-associated mutations in patients with familial hypercholesterolaemia is crucial for early interventions to reduce risk of cardiovascular disease. Screening for these mutations represents a methodological challenge since more than 1200 different causal mutations in the low-density lipoprotein receptor has been identified. A number of methodological approaches have been developed for screening by clinical diagnostic laboratories. Methods Using primers targeting, the low-density lipoprotein receptor, apolipoprotein B, and proprotein convertase subtilisin/kexin type 9, we developed a novel Ion Torrent-based targeted re-sequencing method. We validated this in a West Midlands-UK small cohort of 58 patients screened in parallel with other mutation-targeting methods, such as multiplex polymerase chain reaction (Elucigene FH20), oligonucleotide arrays (Randox familial hypercholesterolaemia array) or the Illumina next-generation sequencing platform. Results In this small cohort, the next-generation sequencing method achieved excellent analytical performance characteristics and showed 100% and 89% concordance with the Randox array and the Elucigene FH20 assay. Investigation of the discrepant results identified two cases of mutation misclassification of the Elucigene FH20 multiplex polymerase chain reaction assay. A number of novel mutations not previously reported were also identified by the next-generation sequencing method. Conclusions Ion Torrent-based next-generation sequencing can deliver a suitable alternative for the molecular investigation of familial hypercholesterolaemia patients, especially when comprehensive mutation screening for rare or unknown mutations is required.
Collapse
Affiliation(s)
- Anne Reiman
- 1 Division of Translational and Systems Medicine, Warwick Medical School, UK
| | - Sarojini Pandey
- 2 Pathology Service, University Hospital Coventry and Warwickshire, UK
| | | | - Nigel Dyer
- 3 Systems Biology, University of Warwick, UK
| | - Mike Khan
- 4 Department of Endocrinology and Diabetes, University Hospital Coventry and Warwickshire, UK
| | - Martin Crockard
- 5 Molecular Diagnostics Group, Randox Laboratories Limited, UK
| | - Mark J Latten
- 5 Molecular Diagnostics Group, Randox Laboratories Limited, UK
| | - Tracey L Watson
- 5 Molecular Diagnostics Group, Randox Laboratories Limited, UK
| | - Ian A Cree
- 2 Pathology Service, University Hospital Coventry and Warwickshire, UK
| | - Dimitris K Grammatopoulos
- 1 Division of Translational and Systems Medicine, Warwick Medical School, UK.,2 Pathology Service, University Hospital Coventry and Warwickshire, UK
| |
Collapse
|
12
|
Lee HK, Lee CK, Tang JWT, Loh TP, Koay ESC. Contamination-controlled high-throughput whole genome sequencing for influenza A viruses using the MiSeq sequencer. Sci Rep 2016; 6:33318. [PMID: 27624998 PMCID: PMC5022032 DOI: 10.1038/srep33318] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/24/2016] [Indexed: 12/04/2022] Open
Abstract
Accurate full-length genomic sequences are important for viral phylogenetic studies. We developed a targeted high-throughput whole genome sequencing (HT-WGS) method for influenza A viruses, which utilized an enzymatic cleavage-based approach, the Nextera XT DNA library preparation kit, for library preparation. The entire library preparation workflow was adapted for the Sentosa SX101, a liquid handling platform, to automate this labor-intensive step. As the enzymatic cleavage-based approach generates low coverage reads at both ends of the cleaved products, we corrected this loss of sequencing coverage at the termini by introducing modified primers during the targeted amplification step to generate full-length influenza A sequences with even coverage across the whole genome. Another challenge of targeted HTS is the risk of specimen-to-specimen cross-contamination during the library preparation step that results in the calling of false-positive minority variants. We included an in-run, negative system control to capture contamination reads that may be generated during the liquid handling procedures. The upper limits of 99.99% prediction intervals of the contamination rate were adopted as cut-off values of contamination reads. Here, 148 influenza A/H3N2 samples were sequenced using the HTS protocol and were compared against a Sanger-based sequencing method. Our data showed that the rate of specimen-to-specimen cross-contamination was highly significant in HTS.
Collapse
Affiliation(s)
- Hong Kai Lee
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Chun Kiat Lee
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Julian Wei-Tze Tang
- Department of Infection, Immunity, Inflammation, University of Leicester, Leicester, UK.,Clinical Microbiology, Leicester Royal Infirmary, Leicester, UK
| | - Tze Ping Loh
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Evelyn Siew-Chuan Koay
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore.,Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| |
Collapse
|
13
|
Pilato B, Pinto R, De Summa S, Petriella D, Lacalamita R, Danza K, Paradiso A, Tommasi S. BRCA1-2 diagnostic workflow from next-generation sequencing technologies to variant identification and final report. Genes Chromosomes Cancer 2016; 55:803-13. [PMID: 27225819 DOI: 10.1002/gcc.22383] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/23/2016] [Accepted: 05/23/2016] [Indexed: 12/14/2022] Open
Abstract
The BRCA1-BRCA2 genes predispose to hereditary breast and ovarian cancer, and the germline and mutational status of these genes defines a target population that can benefit from PARP inhibitor treatments. To respond to the increasing number of BRCA1-BRCA2 tests, it is necessary to shift to high-throughput technologies that are reliable and less time consuming. Different methodological platforms are dedicated to this purpose with different approaches and algorithms for analysis. Our aim was to set up a cost-effective and low time-consuming BRCA1-BRCA2 mutation detection workflow using the Ion Torrent PGM technology. A retrospective cohort of 40 patients with familial breast/ovarian cancer previously tested by Sanger sequencing and a prospective cohort of 72 patients (validation set) were analyzed. The validation set included 64 patients affected by familial breast/ovarian cancer and eight sporadic ovarian cancer cases, who are potential candidates for PARPi treatments. A complete and standardized workflow easily usable and suitable in a certified laboratory has been proved and validated. This includes all steps from library preparation to the final report. The use of next-generation sequencing will be of benefit for patients enrolled in the genetic counseling process and, moreover, will enhance the process of selecting patients eligible for personalized treatments. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Brunella Pilato
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Rosamaria Pinto
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Simona De Summa
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Daniela Petriella
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Rosanna Lacalamita
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Katia Danza
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Angelo Paradiso
- Experimental Medical Oncology Unit, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Stefania Tommasi
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| |
Collapse
|
14
|
Maggi E, Patterson NE, Montagna C. Technological advances in precision medicine and drug development. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016; 1:331-343. [PMID: 27622214 DOI: 10.1080/23808993.2016.1176527] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
New technologies are rapidly becoming available to expand the arsenal of tools accessible for precision medicine and to support the development of new therapeutics. Advances in liquid biopsies, which analyze cells, DNA, RNA, proteins, or vesicles isolated from the blood, have gained particular interest for their uses in acquiring information reflecting the biology of tumors and metastatic tissues. Through advancements in DNA sequencing that have merged unprecedented accuracy with affordable cost, personalized treatments based on genetic variations are becoming a real possibility. Extraordinary progress has been achieved in the development of biological therapies aimed to even further advance personalized treatments. We provide a summary of current and future applications of blood based liquid biopsies and how new technologies are utilized for the development of biological therapeutic treatments. We discuss current and future sequencing methods with an emphasis on how technological advances will support the progress in the field of precision medicine.
Collapse
Affiliation(s)
- Elaine Maggi
- Department of Genetics Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nicole E Patterson
- Department of Genetics Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Cristina Montagna
- Department of Genetics Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Pathology Albert Einstein College of Medicine, Bronx, NY 10461, USA
| |
Collapse
|
15
|
Zhao Y, Cao H, Song Y, Feng Y, Ding X, Pang M, Zhang Y, Zhang H, Ding J, Xia X. Identification of novel mutations including a double mutation in patients with inherited cardiomyopathy by a targeted sequencing approach using the Ion Torrent PGM system. Int J Mol Med 2016; 37:1511-20. [PMID: 27082122 PMCID: PMC4867886 DOI: 10.3892/ijmm.2016.2565] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 04/08/2016] [Indexed: 12/19/2022] Open
Abstract
Inherited cardiomyopathy is the major cause of sudden cardiac death (SCD) and heart failure (HF). The disease is associated with extensive genetic heterogeneity; pathogenic mutations in cardiac sarcomere protein genes, cytoskeletal protein genes and nuclear envelope protein genes have been linked to its etiology. Early diagnosis is conducive to clinical monitoring and allows for presymptomatic interventions as needed. In the present study, the entire coding sequences and flanking regions of 12 major disease (cardiomyopathy)-related genes [namely myosin, heavy chain 7, cardiac muscle, β (MYH7); myosin binding protein C, cardiac (MYBPC3); lamin A/C (LMNA); troponin I type 3 (cardiac) (TNNI3); troponin T type 2 (cardiac) (TNNT2); actin, α, cardiac muscle 1 (ACTC1); tropomyosin 1 (α) (TPM1); sodium channel, voltage gated, type V alpha subunit (SCN5A); myosin, light chain 2, regulatory, cardiac, slow (MYL2); myosin, heavy chain 6, cardiac muscle, α (MYH6); myosin, light chain 3, alkali, ventricular, skeletal, slow (MYL3); and protein kinase, AMP-activated, gamma 2 non-catalytic subunit (PRKAG2)] in 8 patients with dilated cardiomyopathy (DCM) and in 8 patients with hypertrophic cardiomyopathy (HCM) were amplified and then sequenced using the Ion Torrent Personal Genome Machine (PGM) system. As a result, a novel heterozygous mutation (MYH7, p.Asn885Thr) and a variant of uncertain significance (TNNT2, p.Arg296His) were identified in 2 patients with HCM. These 2 missense mutations, which were absent in the samples obtained from the 200 healthy control subjects, altered the amino acid that was evolutionarily conserved among a number of vertebrate species; this illustrates that these 2 non-synonymous mutations play a role in the pathogenesis of HCM. Moreover, a double heterozygous mutation (PRKAG2, p.Gly100Ser plus MYH7, p.Arg719Trp) was identified in a patient with severe familial HCM, for the first time to the best of our knowledge. This patient provided us with more information regarding the genotype-phenotype correlation between mutations of MYH7 and PRKAG2. Taken together, these findings provide insight into the molecular mechanisms underlying inherited cardiomyopathy. The mutations identified in this study may be further investigated in the future in order to improve the diagnosis and treatment of patients with inherited cardiomyopathy. Furthermore, our findings indicated that sequencing using the Ion Torrent PGM system is a useful approach for the identification of pathogenic mutations associated with inherited cardiomyopathy, and it may be used for the risk evaluation of individuals with a possible susceptibility to inherited cardiomyopathy.
Collapse
Affiliation(s)
- Yue Zhao
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Hong Cao
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Yindi Song
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Yue Feng
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Xiaoxue Ding
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Mingjie Pang
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Yunmei Zhang
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Hong Zhang
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Jiahuan Ding
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| |
Collapse
|
16
|
Togawa T, Sugiura T, Ito K, Endo T, Aoyama K, Ohashi K, Negishi Y, Kudo T, Ito R, Kikuchi A, Arai-Ichinoi N, Kure S, Saitoh S. Molecular Genetic Dissection and Neonatal/Infantile Intrahepatic Cholestasis Using Targeted Next-Generation Sequencing. J Pediatr 2016; 171:171-7.e1-4. [PMID: 26858187 DOI: 10.1016/j.jpeds.2016.01.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 12/21/2015] [Accepted: 01/05/2016] [Indexed: 12/18/2022]
Abstract
OBJECTIVES To ascertain a molecular genetic diagnosis for subjects with neonatal/infantile intrahepatic cholestasis (NIIC) by the use of next-generation sequencing (NGS) and to perform a genotype-phenotype correlation. STUDY DESIGN We recruited Japanese subjects with NIIC who had no definitive molecular genetic diagnosis. We developed a diagnostic custom panel of 18 genes, and the amplicon library was sequenced via NGS. We then compared clinical data between the molecular genetically confirmed subjects with NIIC. RESULTS We analyzed 109 patients with NIIC ("genetic cholestasis," 31 subjects; "unknown with complications" such as prematurity, 46 subjects; "unknown without complications," 32 subjects), and a molecular genetic diagnosis was made for 28 subjects (26%). The rate of positive molecular genetic diagnosis in each category was 22 of 31 (71%) for the "genetic cholestasis" group, 2 of 46 (4.3%) for the "unknown with complications" group, and 4 of 32 (12.5%) for the "unknown without complications" group. The grouping of the molecular diagnoses in the group with genetic cholestasis was as follows: 12 with Alagille syndrome, 5 with neonatal Dubin-Johnson syndrome, 5 with neonatal intrahepatic cholestasis caused by citrin deficiency, and 6 with progressive familial intrahepatic cholestasis or benign recurrent intrahepatic cholestasis with low gamma-glutamyl transpeptidase levels. Several clinical datasets, including age of onset, direct bilirubin, and aminotransferases, were significantly different between the disorders confirmed using molecular genetic diagnosis. CONCLUSION Targeted NGS can be used for molecular genetic diagnosis in subjects with NIIC. Clinical diagnosis should be accordingly redefined in the view of molecular genetic findings.
Collapse
Affiliation(s)
- Takao Togawa
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Tokio Sugiura
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan.
| | - Koichi Ito
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Takeshi Endo
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Kohei Aoyama
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Kei Ohashi
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yutaka Negishi
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Toyoichiro Kudo
- Department of Hepatology, National Medical Center for Children and Mothers, National Center for Child Health and Development, Tokyo, Japan
| | - Reiko Ito
- Department of Hepatology, National Medical Center for Children and Mothers, National Center for Child Health and Development, Tokyo, Japan
| | - Atsuo Kikuchi
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | | | - Shigeo Kure
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| |
Collapse
|
17
|
A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India. J Clin Microbiol 2016; 54:1500-1511. [PMID: 27008882 PMCID: PMC4879288 DOI: 10.1128/jcm.00235-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/20/2016] [Indexed: 11/20/2022] Open
Abstract
A major challenge to global malaria control and elimination is early detection and containment of emerging drug resistance. Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-throughput surveillance of molecular markers of drug resistance. We have developed an amplicon sequencing method on the Ion Torrent PGM platform for targeted resequencing of a panel of six Plasmodium falciparum genes implicated in resistance to first-line antimalarial therapy, including artemisinin combination therapy, chloroquine, and sulfadoxine-pyrimethamine. The protocol was optimized using 12 geographically diverse P. falciparum reference strains and successfully applied to multiplexed sequencing of 16 clinical isolates from India. The sequencing results from the reference strains showed 100% concordance with previously reported drug resistance-associated mutations. Single-nucleotide polymorphisms (SNPs) in clinical isolates revealed a number of known resistance-associated mutations and other nonsynonymous mutations that have not been implicated in drug resistance. SNP positions containing multiple allelic variants were used to identify three clinical samples containing mixed genotypes indicative of multiclonal infections. The amplicon sequencing protocol has been designed for the benchtop Ion Torrent PGM platform and can be operated with minimal bioinformatics infrastructure, making it ideal for use in countries that are endemic for the disease to facilitate routine large-scale surveillance of the emergence of drug resistance and to ensure continued success of the malaria treatment policy.
Collapse
|
18
|
Development of a Comprehensive Sequencing Assay for Inherited Cardiac Condition Genes. J Cardiovasc Transl Res 2016; 9:3-11. [PMID: 26888179 PMCID: PMC4767849 DOI: 10.1007/s12265-016-9673-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/07/2016] [Indexed: 12/15/2022]
Abstract
Inherited cardiac conditions (ICCs) are characterised by marked genetic and allelic heterogeneity and require extensive sequencing for genetic characterisation. We iteratively optimised a targeted gene capture panel for ICCs that includes disease-causing, putatively pathogenic, research and phenocopy genes (n = 174 genes). We achieved high coverage of the target region on both MiSeq (>99.8 % at ≥20× read depth, n = 12) and NextSeq (>99.9 % at ≥20×, n = 48) platforms with 100 % sensitivity and precision for single nucleotide variants and indels across the protein-coding target on the MiSeq. In the final assay, 40 out of 43 established ICC genes informative in clinical practice achieved complete coverage (100 % at ≥20×). By comparison, whole exome sequencing (WES; ∼80×), deep WES (∼500×) and whole genome sequencing (WGS; ∼70×) had poorer performance (88.1, 99.2 and 99.3 % respectively at ≥20×) across the ICC target. The assay described here delivers highly accurate and affordable sequencing of ICC genes, complemented by accessible cloud-based computation and informatics. See Editorial in this issue (DOI: 10.1007/s12265-015-9667-8).
Collapse
|
19
|
Ballester LY, Luthra R, Kanagal-Shamanna R, Singh RR. Advances in clinical next-generation sequencing: target enrichment and sequencing technologies. Expert Rev Mol Diagn 2016; 16:357-72. [PMID: 26680590 DOI: 10.1586/14737159.2016.1133298] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The huge parallel sequencing capabilities of next generation sequencing technologies have made them the tools of choice to characterize genomic aberrations for research and diagnostic purposes. For clinical applications, screening the whole genome or exome is challenging owing to the large genomic area to be sequenced, associated costs, complexity of data, and lack of known clinical significance of all genes. Consequently, routine screening involves limited markers with established clinical relevance. This process, referred to as targeted genome sequencing, requires selective enrichment of the genomic areas comprising these markers via one of several primer or probe-based enrichment strategies, followed by sequencing of the enriched genomic areas. Here, the authors review current target enrichment approaches and next generation sequencing platforms, focusing on the underlying principles, capabilities, and limitations of each technology along with validation and implementation for clinical testing.
Collapse
Affiliation(s)
- Leomar Y Ballester
- a Department of Pathology and Immunology , Baylor College of Medicine , Houston , TX , USA
| | - Rajyalakshmi Luthra
- b Department of Hematopathology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Rashmi Kanagal-Shamanna
- b Department of Hematopathology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Rajesh R Singh
- b Department of Hematopathology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| |
Collapse
|
20
|
Singh RR, Luthra R, Routbort MJ, Patel KP, Medeiros LJ. Implementation of next generation sequencing in clinical molecular diagnostic laboratories: advantages, challenges and potential. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016. [DOI: 10.1080/23808993.2015.1120401] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
21
|
Saam J, Arnell C, Theisen A, Moyes K, Marino I, Roundy KM, Wenstrup RJ. Patients Tested at a Laboratory for Hereditary Cancer Syndromes Show an Overlap for Multiple Syndromes in Their Personal and Familial Cancer Histories. Oncology 2015; 89:288-93. [DOI: 10.1159/000437307] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/27/2015] [Indexed: 11/19/2022]
|
22
|
Lay-Son RG, León PL. [Current perspectives on genome-based diagnostic tests in Pediatrics]. REVISTA CHILENA DE PEDIATRIA 2015. [PMID: 26223391 DOI: 10.1016/j.rchipe.2015.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Etiological diagnosis is essential in the clinical management of individual patients. Some children with complex medical conditions are subjected to numerous testing, known as "diagnostic odyssey", which often gives no conclusive results. In recent years, a revolution in genomic medicine is underway with the use of technologies that promise to increase the ability to make a diagnosis and reduce the time involved. The main advantages and limitations of genomic diagnosis, as opposed to usual methodologies are reviewed with an emphasis on Pediatrics.
Collapse
Affiliation(s)
- R Guillermo Lay-Son
- Centro de Genética y Genómica, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile; Hospital Padre Hurtado, San Ramón, Santiago, Chile.
| | - P Luis León
- Centro de Genética y Genómica, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| |
Collapse
|
23
|
Crona J, Ljungström V, Welin S, Walz MK, Hellman P, Björklund P. Bioinformatic Challenges in Clinical Diagnostic Application of Targeted Next Generation Sequencing: Experience from Pheochromocytoma. PLoS One 2015; 10:e0133210. [PMID: 26230854 PMCID: PMC4521794 DOI: 10.1371/journal.pone.0133210] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 06/24/2015] [Indexed: 11/28/2022] Open
Abstract
Background Recent studies have demonstrated equal quality of targeted next generation sequencing (NGS) compared to Sanger Sequencing. Whereas these novel sequencing processes have a validated robust performance, choice of enrichment method and different available bioinformatic software as reliable analysis tool needs to be further investigated in a diagnostic setting. Methods DNA from 21 patients with genetic variants in SDHB, VHL, EPAS1, RET, (n=17) or clinical criteria of NF1 syndrome (n=4) were included. Targeted NGS was performed using Truseq custom amplicon enrichment sequenced on an Illumina MiSEQ instrument. Results were analysed in parallel using three different bioinformatics pipelines; (1) Commercially available MiSEQ Reporter, fully automatized and integrated software, (2) CLC Genomics Workbench, graphical interface based software, also commercially available, and ICP (3) an in-house scripted custom bioinformatic tool. Results A tenfold read coverage was achieved in between 95-98% of targeted bases. All workflows had alignment of reads to SDHA and NF1 pseudogenes. Compared to Sanger sequencing, variant calling revealed a sensitivity ranging from 83 to 100% and a specificity of 99.9-100%. Only MiSEQ reporter identified all pathogenic variants in both sequencing runs. Conclusions We conclude that targeted next generation sequencing have equal quality compared to Sanger sequencing. Enrichment specificity and the bioinformatic performance need to be carefully assessed in a diagnostic setting. As acceptable accuracy was noted for a fully automated bioinformatic workflow, we suggest that processing of NGS data could be performed without expert bioinformatics skills utilizing already existing commercially available bioinformatics tools.
Collapse
Affiliation(s)
- Joakim Crona
- Department of Surgical Sciences, Uppsala University, SE-75185, Uppsala, Sweden
- * E-mail:
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-75185, Uppsala, Sweden
| | - Staffan Welin
- Departments of Medical Sciences, Uppsala University, SE-75185, Uppsala, Sweden
| | - Martin K. Walz
- Department for Surgery and Centre of Minimal Invasive Surgery, Kliniken Essen-Mitte, Academic Teaching Hospital of the University of Duisburg-Essen, DE-45136 Essen, Germany
| | - Per Hellman
- Department of Surgical Sciences, Uppsala University, SE-75185, Uppsala, Sweden
| | - Peyman Björklund
- Department of Surgical Sciences, Uppsala University, SE-75185, Uppsala, Sweden
| |
Collapse
|
24
|
Oliveira TG, Mitne-Neto M, Cerdeira LT, Marsiglia JD, Arteaga-Fernandez E, Krieger JE, Pereira AC. A Variant Detection Pipeline for Inherited Cardiomyopathy–Associated Genes Using Next-Generation Sequencing. J Mol Diagn 2015; 17:420-30. [DOI: 10.1016/j.jmoldx.2015.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 02/11/2015] [Accepted: 02/26/2015] [Indexed: 01/26/2023] Open
|
25
|
Kotoula V, Lyberopoulou A, Papadopoulou K, Charalambous E, Alexopoulou Z, Gakou C, Lakis S, Tsolaki E, Lilakos K, Fountzilas G. Evaluation of two highly-multiplexed custom panels for massively parallel semiconductor sequencing on paraffin DNA. PLoS One 2015; 10:e0128818. [PMID: 26039550 PMCID: PMC4454570 DOI: 10.1371/journal.pone.0128818] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 04/30/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND AIM Massively parallel sequencing (MPS) holds promise for expanding cancer translational research and diagnostics. As yet, it has been applied on paraffin DNA (FFPE) with commercially available highly multiplexed gene panels (100s of DNA targets), while custom panels of low multiplexing are used for re-sequencing. Here, we evaluated the performance of two highly multiplexed custom panels on FFPE DNA. METHODS Two custom multiplex amplification panels (B, 373 amplicons; T, 286 amplicons) were coupled with semiconductor sequencing on DNA samples from FFPE breast tumors and matched peripheral blood samples (n samples: 316; n libraries: 332). The two panels shared 37% DNA targets (common or shifted amplicons). Panel performance was evaluated in paired sample groups and quartets of libraries, where possible. RESULTS Amplicon read ratios yielded similar patterns per gene with the same panel in FFPE and blood samples; however, performance of common amplicons differed between panels (p<0.001). FFPE genotypes were compared for 1267 coding and non-coding variant replicates, 999 out of which (78.8%) were concordant in different paired sample combinations. Variant frequency was highly reproducible (Spearman's rho 0.959). Repeatedly discordant variants were of high coverage / low frequency (p<0.001). Genotype concordance was (a) high, for intra-run duplicates with the same panel (mean±SD: 97.2±4.7, 95%CI: 94.8-99.7, p<0.001); (b) modest, when the same DNA was analyzed with different panels (mean±SD: 81.1±20.3, 95%CI: 66.1-95.1, p = 0.004); and (c) low, when different DNA samples from the same tumor were compared with the same panel (mean±SD: 59.9±24.0; 95%CI: 43.3-76.5; p = 0.282). Low coverage / low frequency variants were validated with Sanger sequencing even in samples with unfavourable DNA quality. CONCLUSIONS Custom MPS may yield novel information on genomic alterations, provided that data evaluation is adjusted to tumor tissue FFPE DNA. To this scope, eligibility of all amplicons along with variant coverage and frequency need to be assessed.
Collapse
Affiliation(s)
- Vassiliki Kotoula
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
- Department of Pathology, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
- * E-mail:
| | - Aggeliki Lyberopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Elpida Charalambous
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | | | - Chryssa Gakou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Sotiris Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Eleftheria Tsolaki
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Konstantinos Lilakos
- Department of Haematology, “Laikon” General Hospital, University of Athens Medical School, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| |
Collapse
|
26
|
Glotov AS, Kazakov SV, Zhukova EA, Alexandrov AV, Glotov OS, Pakin VS, Danilova MM, Poliakova IV, Niyazova SS, Chakova NN, Komissarova SM, Kurnikova EA, Sarana AM, Sherbak SG, Sergushichev AA, Shalyto AA, Baranov VS. Targeted next-generation sequencing (NGS) of nine candidate genes with custom AmpliSeq in patients and a cardiomyopathy risk group. Clin Chim Acta 2015; 446:132-40. [PMID: 25892673 DOI: 10.1016/j.cca.2015.04.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 03/23/2015] [Accepted: 04/08/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hypertrophic cardiomyopathy is a common genetic cardiac disease. Prevention and early diagnosis of this disease are very important. Because of the large number of causative genes and the high rate of mutations involved in the pathogenesis of this disease, traditional methods of early diagnosis are ineffective. METHODS We developed a custom AmpliSeq panel for NGS sequencing of the coding sequences of ACTC1, MYBPC3, MYH7, MYL2, MYL3, TNNI3, TNNT2, TPM1, and CASQ2. A genetic analysis of student cohorts (with and without cardiomyopathy risk in their medical histories) and patients with cardiomyopathies was performed. For the statistical and bioinformatics analysis, Polyphen2, SIFT, SnpSift and PLINK software were used. To select genetic markers in the patients with cardiomyopathy and in the students of the high risk group, four additive models were applied. RESULTS Our AmpliSeq custom panel allowed us to efficiently explore targeted sequences. Based on the score analysis, we detected three substitutions in the MYBPC3 and CASQ2 genes and six combinations between loci in the MYBPC3, MYH7 and CASQ2 genes that were responsible for cardiomyopathy risk in our cohorts. We also detected substitutions in the TNNT2 gene that can be considered as protective against cardiomyopathy. CONCLUSION We used NGS with AmpliSeq libraries and Ion PGM sequencing to develop improved predictive information for patients at risk of cardiomyopathy.
Collapse
Affiliation(s)
- Andrey S Glotov
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya nab., 7-9, St. Petersburg 199034, Russia; Laboratory of Prenatal Diagnostics of Hereditary Diseases, Federal State Budget Scientific Institution "The Research Institute of Obstetrics, Gynecology and Reproductology named after D.O.Ott", Mendeleyevskaya lin., 3, St. Petersburg 199034, Russia.
| | - Sergey V Kazakov
- Computer Technologies Laboratory, ITMO University, Kronverksky pr., 49, St. Petersburg 197101, Russia
| | - Elena A Zhukova
- Laboratory of Prenatal Diagnostics of Hereditary Diseases, Federal State Budget Scientific Institution "The Research Institute of Obstetrics, Gynecology and Reproductology named after D.O.Ott", Mendeleyevskaya lin., 3, St. Petersburg 199034, Russia
| | - Anton V Alexandrov
- Computer Technologies Laboratory, ITMO University, Kronverksky pr., 49, St. Petersburg 197101, Russia
| | - Oleg S Glotov
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya nab., 7-9, St. Petersburg 199034, Russia; Laboratory of Prenatal Diagnostics of Hereditary Diseases, Federal State Budget Scientific Institution "The Research Institute of Obstetrics, Gynecology and Reproductology named after D.O.Ott", Mendeleyevskaya lin., 3, St. Petersburg 199034, Russia
| | - Vladimir S Pakin
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya nab., 7-9, St. Petersburg 199034, Russia; Laboratory of Prenatal Diagnostics of Hereditary Diseases, Federal State Budget Scientific Institution "The Research Institute of Obstetrics, Gynecology and Reproductology named after D.O.Ott", Mendeleyevskaya lin., 3, St. Petersburg 199034, Russia
| | - Maria M Danilova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya nab., 7-9, St. Petersburg 199034, Russia; Laboratory of Prenatal Diagnostics of Hereditary Diseases, Federal State Budget Scientific Institution "The Research Institute of Obstetrics, Gynecology and Reproductology named after D.O.Ott", Mendeleyevskaya lin., 3, St. Petersburg 199034, Russia
| | - Irina V Poliakova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya nab., 7-9, St. Petersburg 199034, Russia; Laboratory of Prenatal Diagnostics of Hereditary Diseases, Federal State Budget Scientific Institution "The Research Institute of Obstetrics, Gynecology and Reproductology named after D.O.Ott", Mendeleyevskaya lin., 3, St. Petersburg 199034, Russia
| | - Svetlana S Niyazova
- Laboratory of Modelling of Genetic Processes, Institute of Genetics and Cytology, National Academy of Sciences, Akademicheskaya str., 27, Minsk 220072, Belarus
| | - Natalia N Chakova
- Laboratory of Modelling of Genetic Processes, Institute of Genetics and Cytology, National Academy of Sciences, Akademicheskaya str., 27, Minsk 220072, Belarus
| | - Svetlana M Komissarova
- Scientific and Practical center of Cardiology, Rozy Luxemburg str., 110, Minsk 220036, Belarus
| | - Elena A Kurnikova
- Department of Faculty Therapy on Behalf of Prof. VA Waldman, Saint Petersburg State Pediatric Medical University, Lithuanian str., 2, St. Petersburg 194100, Russia
| | - Andrey M Sarana
- City Hospital No. 40, Borisov str., 9, Sestroretsk, St. Petersburg 197706, Russia
| | - Sergey G Sherbak
- City Hospital No. 40, Borisov str., 9, Sestroretsk, St. Petersburg 197706, Russia
| | - Alexey A Sergushichev
- Computer Technologies Laboratory, ITMO University, Kronverksky pr., 49, St. Petersburg 197101, Russia
| | - Anatoly A Shalyto
- Computer Technologies Laboratory, ITMO University, Kronverksky pr., 49, St. Petersburg 197101, Russia
| | - Vladislav S Baranov
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya nab., 7-9, St. Petersburg 199034, Russia; Laboratory of Prenatal Diagnostics of Hereditary Diseases, Federal State Budget Scientific Institution "The Research Institute of Obstetrics, Gynecology and Reproductology named after D.O.Ott", Mendeleyevskaya lin., 3, St. Petersburg 199034, Russia
| |
Collapse
|
27
|
Chapla A, Mruthyunjaya MD, Asha HS, Varghese D, Varshney M, Vasan SK, Venkatesan P, Nair V, Mathai S, Paul TV, Thomas N. Maturity onset diabetes of the young in India - a distinctive mutation pattern identified through targeted next-generation sequencing. Clin Endocrinol (Oxf) 2015; 82:533-42. [PMID: 25041077 DOI: 10.1111/cen.12541] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/01/2014] [Accepted: 06/30/2014] [Indexed: 01/04/2023]
Abstract
OBJECTIVE To establish and utilize a Next-Generation Sequencing (NGS)-based strategy to screen for maturity onset diabetes of the young (MODY) gene mutations in subjects with early-onset diabetes. PATIENTS AND METHODS Maturity onset diabetes of the young (MODY) genetic testing was carried out in 80 subjects of Asian Indian origin with young onset diabetes to identify mutations in a comprehensive panel of ten MODY genes. A novel multiplex polymerase chain reaction (PCR)-based target enrichment was established, followed by NGS on the Ion Torrent Personal Genome Machine (PGM). All the mutations and rare variants were confirmed by Sanger sequencing. RESULTS We identified mutations in 11 (19%) of the 56 clinically diagnosed MODY subjects and seven of these mutations were novel. The identified mutations include p.H241Q, p.E59Q, c.-162G>A 5' UTR in NEUROD1, p.V169I cosegregating with c.493-4G>A and c.493-20C>T, p.E271K in HNF4A, p.A501S in HNF1A, p.E440X in GCK, p.V177M in PDX1, p.L92F in HNF1B and p.R31L in PAX4 genes. Interestingly, two patients with NEUROD1 mutation were also positive for the p.E224K mutation in PDX1 gene. These patients with coexisting NEUROD1-PDX1 mutations showed a marked reduction in glucose-induced insulin secretion. All 24 subjects who had not met the clinical criteria of MODY were negative for the mutations. To the best of our knowledge, this is the first report of PDX1, HNF1B, NEUROD1 and PAX4 mutations from India. CONCLUSIONS Multiplex PCR coupled with NGS provides a rapid, cost-effective and accurate method for comprehensive parallelized genetic testing of MODY. When compared to earlier reports, we have identified a higher frequency and a novel digenic mutation pattern involving NEUROD1 and PDX1 genes.
Collapse
Affiliation(s)
- Aaron Chapla
- Department of Endocrinology, Diabetes and Metabolism, Christian Medical College, Vellore, India
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Galindo-González L, Pinzón-Latorre D, Bergen EA, Jensen DC, Deyholos MK. Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome. PLANT METHODS 2015; 11:19. [PMID: 25788971 PMCID: PMC4363359 DOI: 10.1186/s13007-015-0062-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/02/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Detection of induced mutations is valuable for inferring gene function and for developing novel germplasm for crop improvement. Many reverse genetics approaches have been developed to identify mutations in genes of interest within a mutagenized population, including some approaches that rely on next-generation sequencing (e.g. exome capture, whole genome resequencing). As an alternative to these genome or exome-scale methods, we sought to develop a scalable and efficient method for detection of induced mutations that could be applied to a small number of target genes, using Ion Torrent technology. We developed this method in flax (Linum usitatissimum), to demonstrate its utility in a crop species. RESULTS We used an amplicon-based approach in which DNA samples from an ethyl methanesulfonate (EMS)-mutagenized population were pooled and used as template in PCR reactions to amplify a region of each gene of interest. Barcodes were incorporated during PCR, and the pooled amplicons were sequenced using an Ion Torrent PGM. A pilot experiment with known SNPs showed that they could be detected at a frequency > 0.3% within the pools. We then selected eight genes for which we wanted to discover novel mutations, and applied our approach to screen 768 individuals from the EMS population, using either the Ion 314 or Ion 316 chips. Out of 29 potential mutations identified after processing the NGS reads, 16 mutations were confirmed using Sanger sequencing. CONCLUSIONS The methodology presented here demonstrates the utility of Ion Torrent technology in detecting mutation variants in specific genome regions for large populations of a species such as flax. The methodology could be scaled-up to test >100 genes using the higher capacity chips now available from Ion Torrent.
Collapse
Affiliation(s)
| | - David Pinzón-Latorre
- />Department of Biological Sciences, University of Alberta, Edmonton, AB Canada T6G 2E9
| | - Erik A Bergen
- />Department of Biological Sciences, University of Alberta, Edmonton, AB Canada T6G 2E9
| | - Dustin C Jensen
- />Department of Computing Sciences, Kings University College, Edmonton, AB Canada T6B 2H3
| | - Michael K Deyholos
- />IK Barber School of Arts & Sciences, University of British Columbia, Okanagan campus, Kelowna, BC Canada V1V 1 V7
| |
Collapse
|
29
|
Morini E, Sangiuolo F, Caporossi D, Novelli G, Amati F. Application of Next Generation Sequencing for personalized medicine for sudden cardiac death. Front Genet 2015; 6:55. [PMID: 25784923 PMCID: PMC4345839 DOI: 10.3389/fgene.2015.00055] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/05/2015] [Indexed: 11/25/2022] Open
Abstract
Sudden cardiac death (SCD) is a serious public health problem. In the United States, more than 300,000 people are affected by SCD every year. Significantly, sudden deaths represent 20% of the total mortality and 50% of cardiovascular mortality in Western countries. In addition, SCD constitutes one of the most important unsolved challenges in the practice of forensic pathology because of the failure to determine the exact cause of sudden death. In young individuals, SCD is frequently caused by cardiomyopathies and channelopathies, that have generally an autosomal dominant pattern of inheritance. The impact of genetics and genetic testing on the clinical management of these diseases is unquestioned. In particular, genetic tests are an important tool for identifying pre-symptomatic individuals carrying genetic variant that predisposes them to SCD. High-throughput sequencing technologies offer novel opportunities to deeper investigate the genetic background underlying these fatal diseases and to early identify individuals at risk for SCD. In this review, we provide an overview of the development of Next-Generation Sequencing (NGS) technologies and of guidelines useful to design an efficient sequencing protocol and to perform an accurate data analysis. We suggest a flow chart to follow for the set up of a genetic screening protocol for the prevention of cardiac pathologies, in particular SCD events, in young athletes.
Collapse
Affiliation(s)
- Elena Morini
- Department of Movement, Human and Health Sciences, University of Rome Foro Italico Rome, Italy ; Department of Biomedicine and Prevention, University of RomeTor Vergata Rome, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of RomeTor Vergata Rome, Italy
| | - Daniela Caporossi
- Department of Movement, Human and Health Sciences, University of Rome Foro Italico Rome, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of RomeTor Vergata Rome, Italy
| | - Francesca Amati
- Department of Biomedicine and Prevention, University of RomeTor Vergata Rome, Italy
| |
Collapse
|
30
|
Gan C, Love C, Beshay V, Macrae F, Fox S, Waring P, Taylor G. Applicability of next generation sequencing technology in microsatellite instability testing. Genes (Basel) 2015; 6:46-59. [PMID: 25685876 PMCID: PMC4377833 DOI: 10.3390/genes6010046] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 01/27/2015] [Indexed: 11/16/2022] Open
Abstract
Microsatellite instability (MSI) is a useful marker for risk assessment, prediction of chemotherapy responsiveness and prognosis in patients with colorectal cancer. Here, we describe a next generation sequencing approach for MSI testing using the MiSeq platform. Different from other MSI capturing strategies that are based on targeted gene capture, we utilize “deep resequencing”, where we focus the sequencing on only the microsatellite regions of interest. We sequenced a series of 44 colorectal tumours with normal controls for five MSI loci (BAT25, BAT26, BAT34c4, D18S55, D5S346) and a second series of six colorectal tumours (no control) with two mononucleotide loci (BAT25, BAT26). In the first series, we were able to determine 17 MSI-High, 1 MSI-Low and 26 microsatellite stable (MSS) tumours. In the second series, there were three MSI-High and three MSS tumours. Although there was some variation within individual markers, this NGS method produced the same overall MSI status for each tumour, as obtained with the traditional multiplex PCR-based method.
Collapse
Affiliation(s)
- Chun Gan
- Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.
- Department of Colorectal Medicine and Genetics, Familial Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia.
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria 3050, Australia.
| | - Clare Love
- Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.
| | - Victoria Beshay
- Department of Pathology and Sir Peter MacCallum Department of Oncology, University of Melbourne, East Melbourne, Victoria 3002, Australia.
| | - Finlay Macrae
- Department of Colorectal Medicine and Genetics, Familial Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia.
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria 3050, Australia.
| | - Stephen Fox
- Department of Pathology and Sir Peter MacCallum Department of Oncology, University of Melbourne, East Melbourne, Victoria 3002, Australia.
| | - Paul Waring
- Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.
| | - Graham Taylor
- Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.
| |
Collapse
|
31
|
Cao YY, Qu YJ, Song F, Zhang T, Bai JL, Jin YW, Wang H. Fast clinical molecular diagnosis of hyperphenylalaninemia using next-generation sequencing-based on a custom AmpliSeq™ panel and Ion Torrent PGM sequencing. Mol Genet Metab 2014; 113:261-6. [PMID: 25456745 DOI: 10.1016/j.ymgme.2014.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/05/2014] [Accepted: 10/05/2014] [Indexed: 12/15/2022]
Abstract
Hyperphenylalaninemia (HPA) can be classified into phenylketonuria (PKU) and tetrahydrobiopterin deficiency (BH4D), according to the defect of enzyme activity, both of which vary substantially in severity, treatment, and prognosis of the disease. To set up a fast and comprehensive assay in order to achieve early etiological diagnosis and differential diagnosis for children with HPA, we designed a custom AmpliSeq™ panel for the sequencing of coding DNA sequence (CDS), flanking introns, 5' untranslated region (UTR) and 3' UTR from five HPA-causing genes (PAH, PTS, QDPR, GCH1, and PCBD1) using the Ion Torrent Personal Genome Machine (PGM) Sequencer. A standard group of 15 samples with previously known DNA sequences and a test group of 37 HPA patients with unknown mutations were used for assay validation and application, respectively. All variations were confirmed by Sanger sequencing. In the standard group, all the known mutations were detected and were consistent with the results of previous Sanger sequencing. In the test group, we identified mutations in 71 of 74 alleles, with a mutation detection rate of 95.9%. We also found a frame shift deletion p.Ile25Metfs*13 in PAH that was previously unreported. In addition, 1 of 37 in the test group was inconsistent with either the molecular diagnosis or clinical diagnosis by traditional differential methods. In conclusion, our comprehensive assay based on a custom AmpliSeq™ panel and Ion Torrent PGM sequencing has wider coverage, higher throughput, is much faster, and more efficient when compared with the traditional molecular detection method for HPA patients, which could meet the medical need for individualized diagnosis and treatment.
Collapse
Affiliation(s)
- Yan-yan Cao
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Yu-jin Qu
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Fang Song
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Ting Zhang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Jin-li Bai
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Yu-wei Jin
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Hong Wang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| |
Collapse
|
32
|
de Koning TJ, Jongbloed JDH, Sikkema-Raddatz B, Sinke RJ. Targeted next-generation sequencing panels for monogenetic disorders in clinical diagnostics: the opportunities and challenges. Expert Rev Mol Diagn 2014; 15:61-70. [PMID: 25367078 DOI: 10.1586/14737159.2015.976555] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Next-generation sequencing (NGS) will soon be used for clinically heterogeneous, inherited disorders and the increasing number of disease-causing genes reported. Diagnostic laboratories therefore need to decide which NGS methods they are going to invest in and how to implement them. We discuss here the challenges and opportunities of using targeted resequencing (TRS) panels for diagnosing monogenetic disorders. Of the different NGS approaches available, TRS panels offer the opportunity to sequence and analyze a limited set of predetermined target genes. At present, TRS panels offer better base-pair coverage, running times, costs and dataset handling than other NGS applications such as whole genome sequencing and whole exome sequencing. However, working with TRS panels also poses new challenges in variant interpretation, data handling and bioinformatic analyses. To optimize the analyses, TRS panel testing should be performed by bioinformaticians, clinicians and laboratory staff in close collaboration.
Collapse
Affiliation(s)
- Tom J de Koning
- University of Groningen, University Medical Center Groningen, Department of Genetics, CB 50, PO Box 30.001, 9700 RB Groningen, The Netherlands
| | | | | | | |
Collapse
|
33
|
Gómez J, Reguero JR, Morís C, Martín M, Alvarez V, Alonso B, Iglesias S, Coto E. Mutation analysis of the main hypertrophic cardiomyopathy genes using multiplex amplification and semiconductor next-generation sequencing. Circ J 2014; 78:2963-71. [PMID: 25342278 DOI: 10.1253/circj.cj-14-0628] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Mutations in at least 30 genes have been linked to hypertrophic cardiomyopathy (HCM). Due to the large size of the main HCM genes, Sanger sequencing is labor intensive and expensive. The purpose was to develop a next-generation sequencing (NGS) procedure for the main HCM genes. METHODS AND RESULTS: Multiplex amplification of the coding exons of MYH7,MYBPC3,TNNT2,TNNI3,ACTC1,TNNC1,MYL2,MYL3, and TPM1 was designated, followed by NGS with the Ion Torrent PGM (Life Technologies). A total of 8 pools containing DNA from HCM patients were sequenced in a 2-step approach. First, a total of 60 patients (validation cohort) underwent both PGM and Sanger sequencing for the 9 genes. No false-negative variants were found on NGS (100% sensitivity), and a specificity of 97% and 80% was achieved for single-nucleotide and insertion/deletion variants, respectively. Second, the PGM was used to search for mutations in a total of 76 cases not previously studied (discovery cohort). A total of 19 putative mutations were identified in the discovery pools, which were confirmed and assigned to specific patients on Sanger sequencing. CONCLUSIONS An NGS procedure has been developed for the main sarcomeric genes that would facilitate the screening of large cohorts of patients. In addition, this procedure would facilitate the uncovering of rare gene variants on a population scale.
Collapse
Affiliation(s)
- Juan Gómez
- Molecular Genetics Dept-Laboratory of Medicine-Renal Foundation (IRSIN-FRIAT), Hospital Central Asturias
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Diekstra A, Bosgoed E, Rikken A, van Lier B, Kamsteeg EJ, Tychon M, Derks RC, van Soest RA, Mensenkamp AR, Scheffer H, Neveling K, Nelen MR. Translating sanger-based routine DNA diagnostics into generic massive parallel ion semiconductor sequencing. Clin Chem 2014; 61:154-62. [PMID: 25274553 DOI: 10.1373/clinchem.2014.225250] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Dideoxy-based chain termination sequencing developed by Sanger is the gold standard sequencing approach and allows clinical diagnostics of disorders with relatively low genetic heterogeneity. Recently, new next generation sequencing (NGS) technologies have found their way into diagnostic laboratories, enabling the sequencing of large targeted gene panels or exomes. The development of benchtop NGS instruments now allows the analysis of single genes or small gene panels, making these platforms increasingly competitive with Sanger sequencing. METHODS We developed a generic automated ion semiconductor sequencing work flow that can be used in a clinical setting and can serve as a substitute for Sanger sequencing. Standard amplicon-based enrichment remained identical to PCR for Sanger sequencing. A novel postenrichment pooling strategy was developed, limiting the number of library preparations and reducing sequencing costs up to 70% compared to Sanger sequencing. RESULTS A total of 1224 known pathogenic variants were analyzed, yielding an analytical sensitivity of 99.92% and specificity of 99.99%. In a second experiment, a total of 100 patient-derived DNA samples were analyzed using a blind analysis. The results showed an analytical sensitivity of 99.60% and specificity of 99.98%, comparable to Sanger sequencing. CONCLUSIONS Ion semiconductor sequencing can be a first choice mutation scanning technique, independent of the genes analyzed.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Hans Scheffer
- Department of Human Genetics and Donders Center for Neurosciences, Radboud university medical center, Nijmegen, the Netherlands
| | | | | |
Collapse
|
35
|
Motoike IN, Matsumoto M, Danjoh I, Katsuoka F, Kojima K, Nariai N, Sato Y, Yamaguchi-Kabata Y, Ito S, Kudo H, Nishijima I, Nishikawa S, Pan X, Saito R, Saito S, Saito T, Shirota M, Tsuda K, Yokozawa J, Igarashi K, Minegishi N, Tanabe O, Fuse N, Nagasaki M, Kinoshita K, Yasuda J, Yamamoto M. Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population. BMC Genomics 2014; 15:673. [PMID: 25109789 PMCID: PMC4138778 DOI: 10.1186/1471-2164-15-673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 08/01/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously. RESULTS Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%. CONCLUSIONS Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.
Collapse
Affiliation(s)
- Ikuko N Motoike
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Mitsuyo Matsumoto
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Inaho Danjoh
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Fumiki Katsuoka
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Kaname Kojima
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Naoki Nariai
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Yukuto Sato
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Yumi Yamaguchi-Kabata
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Shin Ito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Hisaaki Kudo
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Ichiko Nishijima
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Satoshi Nishikawa
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Xiaoqing Pan
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Rumiko Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Sakae Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Tomo Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Matsuyuki Shirota
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
- />United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, 1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Kaoru Tsuda
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Junji Yokozawa
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Kazuhiko Igarashi
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Naoko Minegishi
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Osamu Tanabe
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Nobuo Fuse
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masao Nagasaki
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Kengo Kinoshita
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
- />Institute of Development, Aging, and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku Sendai, Sendai, 980-8575 Japan
| | - Jun Yasuda
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masayuki Yamamoto
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| |
Collapse
|
36
|
Ekici H, Rao SD, Sönnerborg A, Ramprasad VL, Gupta R, Neogi U. Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries. J Antimicrob Chemother 2014; 69:3349-55. [PMID: 25085657 DOI: 10.1093/jac/dku278] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES Increased trends of primary drug resistance mutations (DRMs) among treatment-naive HIV-1-infected patients in low- and middle-income countries (LMICs) and the non-availability of pre-antiretroviral therapy (ART) genotypic resistance testing (GRT) may severely affect future therapeutic outcomes. The main objective of this study was therefore to develop a simplified, cost- and labour-efficient but high-throughput GRT protocol to be applied in the large-scale surveillance of DRMs in LMICs. PATIENTS AND METHODS Ninety-six therapy-naive HIV-1-infected patients belonging to three cohorts were included: Indian patients followed at St John's Medical College Hospital, Bangalore, India (n = 49); East Africans (n = 21), who had migrated to Sweden; and Caucasians (n = 26) living in Sweden. GRT by population sequencing (GRT-PS) on individual plasma samples and GRT by next-generation sequencing (GRT-NGS) on equimolar multiplexed samples (n = 24) using Illumina MiSeq were performed. RESULTS The multiplexing procedure was shown to be technically feasible and gave high-quality reads independent of whether HIV-1 subtype C or B was analysed. GRT-NGS detected all the DRMs found by GRT-PS. Additional clinically important low-abundance (<20% of the viral population) major DRMs (e.g. K101E, K103N, Y181C and M184V) were detected by GRT-NGS but not by GRT-PS. The frequency of low-abundance DRMs was higher among East African compared with Indian and Caucasian individuals. CONCLUSIONS Our high-throughput next-generation sequencing with a multiplexed amplicon is a cost-efficient and promising approach for the large-scale surveillance of primary DRMs in LMICs where routine pre-ART GRT is not the standard of care. This strategy may be useful in optimizing future therapeutic regimens in those settings.
Collapse
Affiliation(s)
- Halime Ekici
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Shwetha D Rao
- Hematology Research Unit, Division of Molecular Medicine, St John's Research Institute, Bangalore, India
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | | | - Ravi Gupta
- SciGenom Labs Pvt. Ltd, Cochin, Kerala, India
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden Hematology Research Unit, Division of Molecular Medicine, St John's Research Institute, Bangalore, India
| |
Collapse
|
37
|
Hamoy IG, Ribeiro-Dos-Santos AM, Alvarez L, Barbosa S, Silva A, Santos S, Gusmão L, Ribeiro-Dos-Santos A. A Protocol for mtGenome Analysis on Large Sample Numbers. Bioinform Biol Insights 2014; 8:127-34. [PMID: 25002812 PMCID: PMC4069038 DOI: 10.4137/bbi.s14623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/09/2014] [Accepted: 03/10/2014] [Indexed: 01/04/2023] Open
Abstract
The mitochondrial genome is widely studied in a variety of fields, such as population, forensic, and human and medical genetics. Most studies have been limited to a small portion of the sequence that, although highly diverse, does not describe the total variability. The arrival of modern high-throughput sequencing technologies has made it possible to investigate larger sequences in a shorter amount of time as well as in a more affordable fashion. This work aims to describe a protocol for sequencing and analyzing the complete mitochondrial genome with the Ion PGM™ platform. To evaluate the protocol, the mitochondrial genome was sequenced to approximately 210 Mbp, with high-quality sequences distributed between 12 samples that had an average coverage of 1023× per sample. Several variant callers were compared to improve the protocol outcome. The results suggest that it is possible to run up to 120 samples per run without any loss of any significant quality. Therefore, this protocol is an efficient and accurate tool for full mitochondrial genome analysis.
Collapse
Affiliation(s)
- Igor G Hamoy
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. ; Universidade Federal Rural da Amazônia, Campus de Capanema, PA, Brazil
| | | | - Luiz Alvarez
- Institute of Molecular Pathology and Immunology of the University of Porto, Universidade do Porto. Porto, Portugal
| | - Silvanira Barbosa
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Artur Silva
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Sidney Santos
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. ; Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
| | - Leonor Gusmão
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. ; Institute of Molecular Pathology and Immunology of the University of Porto, Universidade do Porto. Porto, Portugal
| | - Andrea Ribeiro-Dos-Santos
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. ; Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
| |
Collapse
|
38
|
Yeo ZX, Wong JCL, Rozen SG, Lee ASG. Evaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes. BMC Genomics 2014; 15:516. [PMID: 24962530 PMCID: PMC4079958 DOI: 10.1186/1471-2164-15-516] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 06/19/2014] [Indexed: 12/30/2022] Open
Abstract
Background The Ion Torrent PGM is a popular benchtop sequencer that shows promise in replacing conventional Sanger sequencing as the gold standard for mutation detection. Despite the PGM’s reported high accuracy in calling single nucleotide variations, it tends to generate many false positive calls in detecting insertions and deletions (indels), which may hinder its utility for clinical genetic testing. Results Recently, the proprietary analytical workflow for the Ion Torrent sequencer, Torrent Suite (TS), underwent a series of upgrades. We evaluated three major upgrades of TS by calling indels in the BRCA1 and BRCA2 genes. Our analysis revealed that false negative indels could be generated by TS under both default calling parameters and parameters adjusted for maximum sensitivity. However, indel calling with the same data using the open source variant callers, GATK and SAMtools showed that false negatives could be minimised with the use of appropriate bioinformatics analysis. Furthermore, we identified two variant calling measures, Quality-by-Depth (QD) and VARiation of the Width of gaps and inserts (VARW), which substantially reduced false positive indels, including non-homopolymer associated errors without compromising sensitivity. In our best case scenario that involved the TMAP aligner and SAMtools, we achieved 100% sensitivity, 99.99% specificity and 29% False Discovery Rate (FDR) in indel calling from all 23 samples, which is a good performance for mutation screening using PGM. Conclusions New versions of TS, BWA and GATK have shown improvements in indel calling sensitivity and specificity over their older counterpart. However, the variant caller of TS exhibits a lower sensitivity than GATK and SAMtools. Our findings demonstrate that although indel calling from PGM sequences may appear to be noisy at first glance, proper computational indel calling analysis is able to maximize both the sensitivity and specificity at the single base level, paving the way for the usage of this technology for future clinical genetic testing. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-516) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | - Steven G Rozen
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.
| | | |
Collapse
|
39
|
Direct observation of genomic heterogeneity through local haplotyping analysis. BMC Genomics 2014; 15:418. [PMID: 24888354 PMCID: PMC4053652 DOI: 10.1186/1471-2164-15-418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 05/08/2014] [Indexed: 01/06/2023] Open
Abstract
Background It has been an abiding belief among geneticists that multicellular organisms’ genomes can be analyzed under the assumption that a single individual has a uniform genome in all its cells. Despite some evidence to the contrary, this belief has been used as an axiomatic assumption in most genome analysis software packages. In this paper we present observations in human whole genome data, human whole exome data and in mouse whole genome data to challenge this assumption. We show that heterogeneity is in fact ubiquitous and readily observable in ordinary Next Generation Sequencing (NGS) data. Results Starting with the assumption that a single NGS read (or read pair) must come from one haplotype, we built a procedure for directly observing haplotypes at a local level by examining 2 or 3 adjacent single nucleotide polymorphisms (SNPs) which are close enough on the genome to be spanned by individual reads. We applied this procedure to NGS data from three different sources: whole genome of a Central European trio from the 1000 genomes project, whole genome data from laboratory-bred strains of mouse, and whole exome data from a set of patients of head and neck tumors. Thousands of loci were found in each genome where reads spanning 2 or 3 SNPs displayed more than two haplotypes, indicating that the locus is heterogeneous. We show that such loci are ubiquitous in the genome and cannot be explained by segmental duplications. We explain them on the basis of cellular heterogeneity at the genomic level. Such heterogeneous loci were found in all normal and tumor genomes examined. Conclusions Our results highlight the need for new methods to analyze genomic variation because existing ones do not systematically consider local haplotypes. Identification of cancer somatic mutations is complicated because of tumor heterogeneity. It is further complicated if, as we show, normal tissues are also heterogeneous. Methods for biomarker discovery must consider contextual haplotype information rather than just whether a variant “is present”. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-418) contains supplementary material, which is available to authorized users.
Collapse
|
40
|
A labor- and cost-effective non-optical semiconductor (Ion Torrent) next-generation sequencing of the SLC12A3 and CLCNKA/B genes in Gitelman's syndrome patients. J Hum Genet 2014; 59:376-80. [PMID: 24830959 DOI: 10.1038/jhg.2014.37] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 03/29/2014] [Accepted: 04/17/2014] [Indexed: 12/22/2022]
Abstract
Gitelman's syndrome (GS) is a rare recessive disorder caused by mutations in the renal salt-handling genes SLC12A3 and CLCNKB. Our aim was to develop a next-generation sequencing (NGS) procedure for these genes based on two-tubes multiplex amplification of DNA pools and semiconductor sequencing with the Ion Torrent Personal Genome Machine (PGM). We created one pool with DNA from 20 GS patients previously Sanger sequenced for the coding exons of SLC12A3. A total of 13 mutations present in 11 of these patients were used as control variants to validate the NGS procedure. The full coding sequence of SLC12A3, CLCNKB and CLCNKA was amplified in only two Ampliseq tubes and processed and sequenced with the PGM. Large SLC12A3 and CLCNKB deletions were ascertained through multiplex ligation-dependent probe amplification in some patients. With the exception of the SLC12A3 exon 9, all the amplicons were successfully read and 12 of the 13 control variants were detected. The analysis of CLCNKB showed four putative mutations in the GS pool that were further assigned to specific patients. Two patients were heterozygous compounds for a single-nucleotide mutation and a large deletion at SLC12A3 or CLCNKB. We reported a NGS procedure that would facilitate the rapid and cost-effective large-scale screening of the three renal salt-handling genes. In addition to characterize the mutational spectrum of GS patients, the described procedure would facilitate the rapid and cost-effective screening of these genes at a population scale.
Collapse
|
41
|
Glover M, Ware J, Henry A, Wolley M, Walsh R, Wain L, Xu S, Van’t Hoff W, Tobin M, Hall I, Cook S, Gordon R, Stowasser M, O’Shaughnessy K. Detection of mutations in KLHL3 and CUL3 in families with FHHt (familial hyperkalaemic hypertension or Gordon's syndrome). Clin Sci (Lond) 2014; 126:721-6. [PMID: 24266877 PMCID: PMC3963521 DOI: 10.1042/cs20130326] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 11/11/2013] [Accepted: 11/25/2013] [Indexed: 11/29/2022]
Abstract
The study of families with rare inherited forms of hypo- and hyper-tension has been one of the most successful strategies to probe the molecular pathophysiology of blood pressure control and has revealed dysregulation of distal nephron Na+ reabsorption to be a common mechanism. FHHt (familial hyperkalaemic hypertension; also known as Gordon's syndrome) is a salt-dependent form of hypertension caused by mutations in the regulators of the thiazide-sensitive Na+-Cl- co-transporter NCC [also known as SLC12A3 (solute carrier family 12 member 3)] and is effectively treated by thiazide diuretics and/or dietary salt restriction. Variation in at least four genes can cause FHHt, including WNK1 [With No lysine (=K) 1] and WNK4, KLHL3 (kelch-like family member 3), and CUL3 (cullin 3). In the present study we have identified novel disease-causing variants in CUL3 and KLHL3 segregating in 63% of the pedigrees with previously unexplained FHHt, confirming the importance of these recently described FHHt genes. We have demonstrated conclusively, in two unrelated affected individuals, that rare intronic variants in CUL3 cause the skipping of exon 9 as has been proposed previously. KLHL3 variants all occur in kelch-repeat domains and so probably disrupt WNK complex binding. We have found no evidence of any plausible disease-causing variants within SLC4A8 (an alternative thiazide-sensitive sodium transporter) in this population. The results of the present study support the existing evidence that the CUL3 and KLHL3 gene products are physiologically important regulators of thiazide-sensitive distal nephron NaCl reabsorption, and hence potentially interesting novel anti-hypertensive drug targets. As a third of our non-WNK FHHt families do not have plausible CUL3 or KLHL3 variants, there are probably additional, as yet undiscovered, regulators of the thiazide-sensitive pathways.
Collapse
Key Words
- diuretic
- gordon's syndrome
- hypertension
- hyperkalaemia
- pseudohypoaldosteronism
- thiazide
- cul3, cullin 3
- fhht, familial hyperkalaemic hypertension
- gan, gigaxonin
- ibd, identity by descent
- klhl3, kelch-like family member 3
- ncc, na+–cl− co-transporter
- ngs, next-generation sequencing
- slc, solute carrier
- snp, single nucleotide polymorphism
- spak, ste20/sps1-related proline/alanine-rich kinase
- ste20, sterile 20
- wnk, with no lysine (=k)
Collapse
Affiliation(s)
- Mark Glover
- *Division of Therapeutics and Molecular Medicine, University of Nottingham,
Nottingham, U.K
| | - James S. Ware
- †NIHR Biomedical Research Unit in Cardiovascular Disease at Royal Brompton and
Harefield NHS Foundation Trust and Imperial College London, London, U.K
- ‡National Heart and Lung Institute, Imperial College, London, U.K
| | - Amanda Henry
- *Division of Therapeutics and Molecular Medicine, University of Nottingham,
Nottingham, U.K
| | - Martin Wolley
- §Endocrine Hypertension Research Centre, University of Queensland School of
Medicine, Brisbane, Australia
| | - Roddy Walsh
- †NIHR Biomedical Research Unit in Cardiovascular Disease at Royal Brompton and
Harefield NHS Foundation Trust and Imperial College London, London, U.K
| | - Louise V. Wain
- ¶Genetic Epidemiology Group, University of Leicester, Leicester, U.K
| | - Shengxin Xu
- §Endocrine Hypertension Research Centre, University of Queensland School of
Medicine, Brisbane, Australia
| | - William G. Van’t Hoff
- ∥Paediatric Nephrology Department, Great Ormond Street Hospital for Children,
London, U.K
| | - Martin D. Tobin
- ¶Genetic Epidemiology Group, University of Leicester, Leicester, U.K
| | - Ian P. Hall
- *Division of Therapeutics and Molecular Medicine, University of Nottingham,
Nottingham, U.K
| | - Stuart Cook
- ‡National Heart and Lung Institute, Imperial College, London, U.K
- **Cardiovascular and Metabolic Disorders Program, Duke-National
University of Singapore, Singapore
- ††National Heart Centre Singapore, Singapore
| | - Richard D. Gordon
- §Endocrine Hypertension Research Centre, University of Queensland School of
Medicine, Brisbane, Australia
| | - Michael Stowasser
- §Endocrine Hypertension Research Centre, University of Queensland School of
Medicine, Brisbane, Australia
| | | |
Collapse
|
42
|
Pant S, Weiner R, Marton MJ. Navigating the rapids: the development of regulated next-generation sequencing-based clinical trial assays and companion diagnostics. Front Oncol 2014; 4:78. [PMID: 24860780 PMCID: PMC4029014 DOI: 10.3389/fonc.2014.00078] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/28/2014] [Indexed: 12/11/2022] Open
Abstract
Over the past decade, next-generation sequencing (NGS) technology has experienced meteoric growth in the aspects of platform, technology, and supporting bioinformatics development allowing its widespread and rapid uptake in research settings. More recently, NGS-based genomic data have been exploited to better understand disease development and patient characteristics that influence response to a given therapeutic intervention. Cancer, as a disease characterized by and driven by the tumor genetic landscape, is particularly amenable to NGS-based diagnostic (Dx) approaches. NGS-based technologies are particularly well suited to studying cancer disease development, progression and emergence of resistance, all key factors in the development of next-generation cancer Dxs. Yet, to achieve the promise of NGS-based patient treatment, drug developers will need to overcome a number of operational, technical, regulatory, and strategic challenges. Here, we provide a succinct overview of the state of the clinical NGS field in terms of the available clinically targeted platforms and sequencing technologies. We discuss the various operational and practical aspects of clinical NGS testing that will facilitate or limit the uptake of such assays in routine clinical care. We examine the current strategies for analytical validation and Food and Drug Administration (FDA)-approval of NGS-based assays and ongoing efforts to standardize clinical NGS and build quality control standards for the same. The rapidly evolving companion diagnostic (CDx) landscape for NGS-based assays will be reviewed, highlighting the key areas of concern and suggesting strategies to mitigate risk. The review will conclude with a series of strategic questions that face drug developers and a discussion of the likely future course of NGS-based CDx development efforts.
Collapse
Affiliation(s)
- Saumya Pant
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
| | - Russell Weiner
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
| | - Matthew J Marton
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
| |
Collapse
|
43
|
Non optical semi-conductor next generation sequencing of the main cardiac QT-interval duration genes in pooled DNA samples. J Cardiovasc Transl Res 2013; 7:133-7. [PMID: 24190697 DOI: 10.1007/s12265-013-9516-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 10/21/2013] [Indexed: 12/20/2022]
Abstract
DNA variants at the genes encoding cardiac channels have been associated with inherited arrhythmias and the QT interval in the general population. Next generation sequencing technologies would be of special interest to uncover the genetic variation at these genes. The amplification and sequencing of DNA pools (instead of single individuals) would facilitate the rapid and cost-effective screening of large amounts of individuals. However, this pooling strategy could result in a signal of the rare variants below the detection capacity. To validate this approach, a pool of 20 individuals with known rare unique variants in five genes was amplified in only two tubes and sequenced using the non optical semi-conductor (Ion Torrent PGM, Life Technologies) technology. We show that this could be an effective strategy for the screening of large cohorts. Among others, this would facilitate the discovery of new sequence variants linked to cardiac arrhythmia in the general population.
Collapse
|