1
|
Jiang F, Mao AP, Liu YY, Liu FZ, Li YL, Li J, Zhou JY, Tang XW, Ju AP, Li FT, Wan JH, Zuo LD, Li DZ. Detection of rare thalassemia mutations using long-read single-molecule real-time sequencing. Gene 2022; 825:146438. [PMID: 35306112 DOI: 10.1016/j.gene.2022.146438] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Abstract
Gap- polymerase chain reaction (PCR), reverse dot-blot assay (RDB), real-time PCR based multicolor melting curve analysis (MMCA assay), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing are conventional methods to diagnose thalassemia but all of them have limitations. In this study, we applied single-molecule real-time (SMRT) sequencing following multiplex long-range PCR to uncover rare mutations in nine patients and their family members. The patients with different results between Gap-PCR and MMCA assay or with phenotype not matching genotype were included. Using SMRT sequencing, we first identified the carriers with αααanti3.7/HKαα, -α762bpα/αα (chr16:172,648-173,409), ααfusion/αQSα (in a trans configuration), two cases with novel gene rearrangements and another case with a novel 341 bp insertion in α-globin gene cluster, respectively. One carrier with --SEA/αααanti4.2, and two carriers with the coexistence of globin variant and an α-globin gene duplication were also found. Most importantly, we could determine two defects in α-globin gene cluster being a cis or trans configuration in a single test. Our results showed that SMRT has great advantages in detection of α-globin gene triplications, rare deletions and determination of a cis or trans configuration. SMRT is a comprehensive and one-step method for thalassemia screening and diagnosis, especially for detection of rare thalassemia mutations.
Collapse
Affiliation(s)
- Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Ai-Ping Mao
- Berry Genomics Corporation, Beijing, 102200, China
| | - Yin-Yin Liu
- Berry Genomics Corporation, Beijing, 102200, China
| | - Feng-Zhi Liu
- Medical Genetics Laboratory, Foshan Maternal and Child Health Hospital, Foshan, Guangdong, China
| | - Yan-Lin Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Jian Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Jian-Ying Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Xue-Wei Tang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Ai-Ping Ju
- Clinical Laboratory, Huadu District Maternal and Neonatal Healthcare Hospital of Guangzhou, Hu Zhong Hospital, Guangzhou, Guangdong, China
| | - Fa-Tao Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Jun-Hui Wan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Lian-Dong Zuo
- Scientific Research Department, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China.
| |
Collapse
|
2
|
Chen Z, He X. Application of third-generation sequencing in cancer research. MEDICAL REVIEW (BERLIN, GERMANY) 2021; 1:150-171. [PMID: 37724303 PMCID: PMC10388785 DOI: 10.1515/mr-2021-0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/09/2021] [Indexed: 09/20/2023]
Abstract
In the past several years, nanopore sequencing technology from Oxford Nanopore Technologies (ONT) and single-molecule real-time (SMRT) sequencing technology from Pacific BioSciences (PacBio) have become available to researchers and are currently being tested for cancer research. These methods offer many advantages over most widely used high-throughput short-read sequencing approaches and allow the comprehensive analysis of transcriptomes by identifying full-length splice isoforms and several other posttranscriptional events. In addition, these platforms enable structural variation characterization at a previously unparalleled resolution and direct detection of epigenetic marks in native DNA and RNA. Here, we present a comprehensive summary of important applications of these technologies in cancer research, including the identification of complex structure variants, alternatively spliced isoforms, fusion transcript events, and exogenous RNA. Furthermore, we discuss the impact of the newly developed nanopore direct RNA sequencing (RNA-Seq) approach in advancing epitranscriptome research in cancer. Although the unique challenges still present for these new single-molecule long-read methods, they will unravel many aspects of cancer genome complexity in unprecedented ways and present an encouraging outlook for continued application in an increasing number of different cancer research settings.
Collapse
Affiliation(s)
- Zhiao Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| |
Collapse
|
3
|
Scatena C, Murtas D, Tomei S. Cutaneous Melanoma Classification: The Importance of High-Throughput Genomic Technologies. Front Oncol 2021; 11:635488. [PMID: 34123788 PMCID: PMC8193952 DOI: 10.3389/fonc.2021.635488] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Cutaneous melanoma is an aggressive tumor responsible for 90% of mortality related to skin cancer. In the recent years, the discovery of driving mutations in melanoma has led to better treatment approaches. The last decade has seen a genomic revolution in the field of cancer. Such genomic revolution has led to the production of an unprecedented mole of data. High-throughput genomic technologies have facilitated the genomic, transcriptomic and epigenomic profiling of several cancers, including melanoma. Nevertheless, there are a number of newer genomic technologies that have not yet been employed in large studies. In this article we describe the current classification of cutaneous melanoma, we review the current knowledge of the main genetic alterations of cutaneous melanoma and their related impact on targeted therapies, and we describe the most recent high-throughput genomic technologies, highlighting their advantages and disadvantages. We hope that the current review will also help scientists to identify the most suitable technology to address melanoma-related relevant questions. The translation of this knowledge and all actual advancements into the clinical practice will be helpful in better defining the different molecular subsets of melanoma patients and provide new tools to address relevant questions on disease management. Genomic technologies might indeed allow to better predict the biological - and, subsequently, clinical - behavior for each subset of melanoma patients as well as to even identify all molecular changes in tumor cell populations during disease evolution toward a real achievement of a personalized medicine.
Collapse
Affiliation(s)
- Cristian Scatena
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Daniela Murtas
- Department of Biomedical Sciences, Section of Cytomorphology, University of Cagliari, Cagliari, Italy
| | - Sara Tomei
- Omics Core, Integrated Genomics Services, Research Department, Sidra Medicine, Doha, Qatar
| |
Collapse
|
4
|
Madsen EB, Höijer I, Kvist T, Ameur A, Mikkelsen MJ. Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting. Hum Mutat 2020; 41:1671-1679. [PMID: 32516842 PMCID: PMC7496172 DOI: 10.1002/humu.24063] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 04/29/2020] [Accepted: 06/05/2020] [Indexed: 11/07/2022]
Abstract
Long-read sequencing can resolve regions of the genome that are inaccessible to short reads, and therefore are ideal for genome-gap closure, solving structural rearrangements and sequencing through repetitive elements. Here we introduce the Xdrop technology: a novel microfluidic-based system that allows for targeted enrichment of long DNA molecules starting from only a few nanograms of DNA. Xdrop is based on the isolation of long DNA fragments in millions of droplets, where the droplets containing a target sequence of interest are fluorescently labeled and sorted using flow cytometry. The final product from the Xdrop procedure is an enriched population of long DNA molecules that can be investigated by sequencing. To demonstrate the capability of Xdrop, we performed enrichment of the human papilloma virus 18 integrated into the genome of human HeLa cells. Analysis of the sequencing reads resolved three HPV18-chr8 integrations at base-pair resolution, and the captured fragments extended up to 30 kb into the human genome at the integration sites. Further, we enriched the complete TP53 locus in a leukemia cell line and could successfully phase coexisting mutations using PacBio sequencing. In summary, our results show that Xdrop is an efficient enrichment technology for studying complex genomic regions.
Collapse
Affiliation(s)
| | - Ida Höijer
- Science for Life Laboratory, Department of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | | | - Adam Ameur
- Science for Life Laboratory, Department of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
- Department of Epidemiology and Preventive MedicineMonash UniversityMelbourneAustralia
| | | |
Collapse
|
5
|
Cumbo C, Tota G, Anelli L, Zagaria A, Specchia G, Albano F. TP53 in Myelodysplastic Syndromes: Recent Biological and Clinical Findings. Int J Mol Sci 2020; 21:E3432. [PMID: 32414002 PMCID: PMC7279310 DOI: 10.3390/ijms21103432] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
TP53 dysregulation plays a pivotal role in the molecular pathogenesis of myelodysplastic syndromes (MDS), identifying a subgroup of patients with peculiar features. In this review we report the recent biological and clinical findings of TP53-mutated MDS, focusing on the molecular pathways activation and on its impact on the cellular physiology. In MDS, TP53 mutational status is deeply associated with del(5q) syndrome and its dysregulation impacts on cell cycle, DNA repair and apoptosis inducing chromosomal instability and the clonal evolution of disease. TP53 defects influence adversely the MDS clinical outcome and the treatment response rate, thus new therapeutic approaches are being developed for these patients. TP53 allelic state characterization and the mutational burden evaluation can therefore predict prognosis and identify the subgroup of patients eligible for targeted therapy. For these reasons, in the era of precision medicine, the MDS diagnostic workup cannot do without the complete assessment of TP53 mutational profile.
Collapse
Affiliation(s)
| | | | | | | | | | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy; (C.C.); (G.T.); (L.A.); (A.Z.); (G.S.)
| |
Collapse
|
6
|
Wu C, Maley AM, Walt DR. Single-molecule measurements in microwells for clinical applications. Crit Rev Clin Lab Sci 2019:1-21. [PMID: 31865834 DOI: 10.1080/10408363.2019.1700903] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ability to detect and analyze proteins, nucleic acids, and other biomolecules is critical for clinical diagnostics and for understanding the underlying mechanisms of disease. Current detection methods in clinical and research laboratories rely upon bulk measurement techniques such as immunoassays, polymerase chain reaction, and mass spectrometry to detect these biomarkers. However, many potentially useful protein or nucleic acid biomarkers in blood, saliva, or other biofluids exist at concentrations well below the detection limits of current methods, necessitating the development of more sensitive technologies. Single-molecule measurements are poised to address this challenge, vastly improving sensitivity for detecting low abundance biomarkers and rare events within a population. Microwell arrays have emerged as a powerful tool for single-molecule measurements, enabling ultrasensitive detection of disease-relevant biomolecules in easily accessible biofluids. This review discusses the development, fundamentals, and clinical applications of microwell-based single-molecule methods, as well as challenges and future directions for translating these methods to the clinic.
Collapse
Affiliation(s)
- Connie Wu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Adam M Maley
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - David R Walt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| |
Collapse
|
7
|
Ardui S, Ameur A, Vermeesch JR, Hestand MS. Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 2019; 46:2159-2168. [PMID: 29401301 PMCID: PMC5861413 DOI: 10.1093/nar/gky066] [Citation(s) in RCA: 400] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/23/2018] [Indexed: 12/30/2022] Open
Abstract
Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule real-time (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems. Here we capsulize how SMRT sequencing is revolutionizing constitutional, reproductive, cancer, microbial and viral genetic testing.
Collapse
Affiliation(s)
- Simon Ardui
- Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala 75108, Sweden.,School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | | | - Matthew S Hestand
- Department of Human Genetics, KU Leuven, Leuven 3000, Belgium.,Department of Clinical Genetics, VU University Medical Center, Amsterdam 1081 BT, The Netherlands
| |
Collapse
|
8
|
Mantere T, Kersten S, Hoischen A. Long-Read Sequencing Emerging in Medical Genetics. Front Genet 2019; 10:426. [PMID: 31134132 PMCID: PMC6514244 DOI: 10.3389/fgene.2019.00426] [Citation(s) in RCA: 227] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/18/2019] [Indexed: 12/12/2022] Open
Abstract
The wide implementation of next-generation sequencing (NGS) technologies has revolutionized the field of medical genetics. However, the short read lengths of currently used sequencing approaches pose a limitation for the identification of structural variants, sequencing repetitive regions, phasing of alleles and distinguishing highly homologous genomic regions. These limitations may significantly contribute to the diagnostic gap in patients with genetic disorders who have undergone standard NGS, like whole exome or even genome sequencing. Now, the emerging long-read sequencing (LRS) technologies may offer improvements in the characterization of genetic variation and regions that are difficult to assess with the prevailing NGS approaches. LRS has so far mainly been used to investigate genetic disorders with previously known or strongly suspected disease loci. While these targeted approaches already show the potential of LRS, it remains to be seen whether LRS technologies can soon enable true whole genome sequencing routinely. Ultimately, this could allow the de novo assembly of individual whole genomes used as a generic test for genetic disorders. In this article, we summarize the current LRS-based research on human genetic disorders and discuss the potential of these technologies to facilitate the next major advancements in medical genetics.
Collapse
Affiliation(s)
- Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Simone Kersten
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Internal Medicine, Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Internal Medicine, Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
9
|
Tuval A, Shlush LI. Evolutionary trajectory of leukemic clones and its clinical implications. Haematologica 2019; 104:872-880. [PMID: 31004016 PMCID: PMC6518877 DOI: 10.3324/haematol.2018.195289] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/04/2019] [Indexed: 12/22/2022] Open
Abstract
The ontogeny of acute myeloid leukemia is a multistep process. It is driven both by features of the malignant clone itself as well as by environmental pressures, making it a unique process in each individual. The technological advancements of recent years has increased our understanding about the different steps that take place at the genomic level. It is now clear that malignant clones evolve, expand and change even during what seem to be clinically healthy or “cured” periods. This opens a wide window for new therapeutic and monitoring opportunities. Moreover, prediction and even early prevention have become possible goals to be pursued. The aim of this review is to shed light upon recent observations in leukemia evolution and their clinical implications. We present a critical view of these concepts in order to assist clinicians when interpreting results of the ever growing myriad of genomic diagnostic tests. We wish to help clinicians incorporate genetic tests into their clinical assessment and enable them to provide genetic counseling to their patients.
Collapse
Affiliation(s)
- Amos Tuval
- Department of Immunology, Weizmann Institute of Science, Rehovot .,Hematology Department, Meir Medical Center, Kfar Saba
| | - Liran I Shlush
- Department of Immunology, Weizmann Institute of Science, Rehovot .,Hematology Department, Rambam Healthcare Campus, Haifa, Israel
| |
Collapse
|
10
|
Fam83F induces p53 stabilisation and promotes its activity. Cell Death Differ 2019; 26:2125-2138. [PMID: 30692643 DOI: 10.1038/s41418-019-0281-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 11/08/2022] Open
Abstract
p53 is one of the most important tumour suppressor proteins currently known. It is activated in response to DNA damage and this activation leads to proliferation arrest and cell death. The abundance and activity of p53 are tightly controlled and reductions in p53's activity can contribute to the development of cancer. Here, we show that Fam83F increases p53 protein levels by protein stabilisation. Fam83F interacts with p53 and decreases its ubiquitination and degradation. Fam83F is induced in response to DNA damage and its overexpression also increases p53 activity in cell culture experiments and in zebrafish embryos. Downregulation of Fam83F decreases transcription of p53 target genes in response to DNA damage and increases cell proliferation, identifying Fam83F as an important regulator of the DNA damage response. Overexpression of Fam83F also enhances migration of cells harbouring mutant p53 demonstrating that it can also activate mutant forms of p53.
Collapse
|
11
|
Single-Molecule Sequencing: Towards Clinical Applications. Trends Biotechnol 2019; 37:72-85. [DOI: 10.1016/j.tibtech.2018.07.013] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 12/31/2022]
|
12
|
Höijer I, Tsai Y, Clark TA, Kotturi P, Dahl N, Stattin E, Bondeson M, Feuk L, Gyllensten U, Ameur A. Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing. Hum Mutat 2018; 39:1262-1272. [PMID: 29932473 PMCID: PMC6175010 DOI: 10.1002/humu.23580] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/30/2018] [Accepted: 06/20/2018] [Indexed: 12/24/2022]
Abstract
Amplification of DNA is required as a mandatory step during library preparation in most targeted sequencing protocols. This can be a critical limitation when targeting regions that are highly repetitive or with extreme guanine-cytosine (GC) content, including repeat expansions associated with human disease. Here, we used an amplification-free protocol for targeted enrichment utilizing the CRISPR/Cas9 system (No-Amp Targeted sequencing) in combination with single molecule, real-time (SMRT) sequencing for studying repeat elements in the huntingtin (HTT) gene, where an expanded CAG repeat is causative for Huntington disease. We also developed a robust data analysis pipeline for repeat element analysis that is independent of alignment of reads to a reference genome. The method was applied to 11 diagnostic blood samples, and for all 22 alleles the resulting CAG repeat count agreed with previous results based on fragment analysis. The amplification-free protocol also allowed for studying somatic variability of repeat elements in our samples, without the interference of PCR stutter. In summary, with No-Amp Targeted sequencing in combination with our analysis pipeline, we could accurately study repeat elements that are difficult to investigate using PCR-based methods.
Collapse
Affiliation(s)
- Ida Höijer
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
| | | | | | | | - Niklas Dahl
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
| | - Eva‐Lena Stattin
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
| | - Marie‐Louise Bondeson
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
| | - Lars Feuk
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
| | - Ulf Gyllensten
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
| | - Adam Ameur
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
- School of Public Health and Preventive MedicineMonash UniversityMelbourneVictoriaAustralia
| |
Collapse
|
13
|
Single frequency impedance strategy employed in rapid detection of leukemia cancer cells using an electrospun PES-nanofiber reinforced ternary composite-based cytosensor. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.07.089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
14
|
Ebbert MTW, Farrugia SL, Sens JP, Jansen-West K, Gendron TF, Prudencio M, McLaughlin IJ, Bowman B, Seetin M, DeJesus-Hernandez M, Jackson J, Brown PH, Dickson DW, van Blitterswijk M, Rademakers R, Petrucelli L, Fryer JD. Long-read sequencing across the C9orf72 'GGGGCC' repeat expansion: implications for clinical use and genetic discovery efforts in human disease. Mol Neurodegener 2018; 13:46. [PMID: 30126445 PMCID: PMC6102925 DOI: 10.1186/s13024-018-0274-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like the C9orf72 'GGGGCC' (G4C2) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, are too long to sequence using short-read sequencing technologies. It is unclear whether long-read sequencing technologies can traverse these long, challenging repeat expansions. Here, we demonstrate that two long-read sequencing technologies, Pacific Biosciences' (PacBio) and Oxford Nanopore Technologies' (ONT), can sequence through disease-causing repeats cloned into plasmids, including the FTD/ALS-causing G4C2 repeat expansion. We also report the first long-read sequencing data characterizing the C9orf72 G4C2 repeat expansion at the nucleotide level in two symptomatic expansion carriers using PacBio whole-genome sequencing and a no-amplification (No-Amp) targeted approach based on CRISPR/Cas9. RESULTS Both the PacBio and ONT platforms successfully sequenced through the repeat expansions in plasmids. Throughput on the MinION was a challenge for whole-genome sequencing; we were unable to attain reads covering the human C9orf72 repeat expansion using 15 flow cells. We obtained 8× coverage across the C9orf72 locus using the PacBio Sequel, accurately reporting the unexpanded allele at eight repeats, and reading through the entire expansion with 1324 repeats (7941 nucleotides). Using the No-Amp targeted approach, we attained > 800× coverage and were able to identify the unexpanded allele, closely estimate expansion size, and assess nucleotide content in a single experiment. We estimate the individual's repeat region was > 99% G4C2 content, though we cannot rule out small interruptions. CONCLUSIONS Our findings indicate that long-read sequencing is well suited to characterizing known repeat expansions, and for discovering new disease-causing, disease-modifying, or risk-modifying repeat expansions that have gone undetected with conventional short-read sequencing. The PacBio No-Amp targeted approach may have future potential in clinical and genetic counseling environments. Larger and deeper long-read sequencing studies in C9orf72 expansion carriers will be important to determine heterogeneity and whether the repeats are interrupted by non-G4C2 content, potentially mitigating or modifying disease course or age of onset, as interruptions are known to do in other repeat-expansion disorders. These results have broad implications across all diseases where the genetic etiology remains unclear.
Collapse
Affiliation(s)
- Mark T. W. Ebbert
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Mayo Graduate School, Mayo Clinic, Rochester, MN 55905 USA
| | | | - Jonathon P. Sens
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Mayo Graduate School, Mayo Clinic, Rochester, MN 55905 USA
| | | | - Tania F. Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | | | | | | | | | - Jazmyne Jackson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | | | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Mayo Graduate School, Mayo Clinic, Rochester, MN 55905 USA
| | - John D. Fryer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Mayo Graduate School, Mayo Clinic, Rochester, MN 55905 USA
| |
Collapse
|
15
|
Pollard MO, Gurdasani D, Mentzer AJ, Porter T, Sandhu MS. Long reads: their purpose and place. Hum Mol Genet 2018; 27:R234-R241. [PMID: 29767702 PMCID: PMC6061690 DOI: 10.1093/hmg/ddy177] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/08/2018] [Indexed: 12/20/2022] Open
Abstract
In recent years long-read technologies have moved from being a niche and specialist field to a point of relative maturity likely to feature frequently in the genomic landscape. Analogous to next generation sequencing, the cost of sequencing using long-read technologies has materially dropped whilst the instrument throughput continues to increase. Together these changes present the prospect of sequencing large numbers of individuals with the aim of fully characterizing genomes at high resolution. In this article, we will endeavour to present an introduction to long-read technologies showing: what long reads are; how they are distinct from short reads; why long reads are useful and how they are being used. We will highlight the recent developments in this field, and the applications and potential of these technologies in medical research, and clinical diagnostics and therapeutics.
Collapse
Affiliation(s)
- Martin O Pollard
- Human Genetics - Wellcome Sanger Institute, Hinxton, Cambridge, UK
- University of Cambridge - Department of Medicine, Addenbrookes Hospital, Box 157, Hills Road, Cambridge, UK
| | - Deepti Gurdasani
- Human Genetics - Wellcome Sanger Institute, Hinxton, Cambridge, UK
- University of Cambridge - Department of Medicine, Addenbrookes Hospital, Box 157, Hills Road, Cambridge, UK
| | - Alexander J Mentzer
- Human Genetics - Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - Tarryn Porter
- Human Genetics - Wellcome Sanger Institute, Hinxton, Cambridge, UK
- University of Cambridge - Department of Medicine, Addenbrookes Hospital, Box 157, Hills Road, Cambridge, UK
| | - Manjinder S Sandhu
- Human Genetics - Wellcome Sanger Institute, Hinxton, Cambridge, UK
- University of Cambridge - Department of Medicine, Addenbrookes Hospital, Box 157, Hills Road, Cambridge, UK
| |
Collapse
|