1
|
Kazan HH, Karaca M, Akan G, Özgen Ö, Tuncel G, Özketen AÇ, Balcı MC, Körbeyli HK, Atalar F, Gökçay GF. Oxford nanopore sequencing-based assay for BTD gene screening: Design, clinical validation, and variant frequency assessment in the Turkish population. Gene 2024; 928:148782. [PMID: 39033936 DOI: 10.1016/j.gene.2024.148782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/28/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
Biotinidase deficiency (BTD) is an autosomal recessive disorder characterized by impaired recycling of the water-soluble vitamin biotin which leads to a spectrum of clinical manifestations ranging from mild to severe, including mainly neurological and cutaneous symptoms. Biotin supplementation is a cornerstone of treatment, but diagnosis often relies on measuring serum enzyme activity, which needs to be confirmed by genetic analysis. Thus, molecular methods become necessary in the differential diagnosis of BTD. Accordingly, countries with a high-incidence have implemented next-generation sequencing (NGS) techniques to newborn screening programs for BT. Nevertheless, NGS platforms, while well-established, present challenges in cost, labor, accessibility, and duration for newborn screening programs targeting BTD, therefore these limitations necessitate the exploration of alternative systems to ensure efficient and widespread screening. Here, third-generation sequencing platforms, notably Oxford Nanopore Technology (ONT), present promising solutions to the associated challenges. Hence, in the present study, we aimed to develop an ONT-based assay for the screening of BTD gene. After designing and optimizing primers for long-PCR using reference DNA, we assessed the performance of the ONT assay in BTD patients previously diagnosed by enzyme assay and confirmed using Illumina-based sequencing. The results demonstrate a strong correlation between the two methods, indicating the reliability of the ONT-based assay. Moreover, this first in-house single gene testing specifically tailored for BTD successfully detected previously known genetic variants with high sequencing depths, affirming the effectiveness of ONT-based sequencing in human genetics.
Collapse
Affiliation(s)
- Hasan Hüseyin Kazan
- Department of Medical Biology, Gulhane Faculty of Medicine, University of Health Sciences, Ankara, Turkey
| | - Meryem Karaca
- Division of Pediatric Nutrition and Metabolism, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Gökçe Akan
- DESAM Institute, Near East University, Mersin 10, Turkey
| | - Özge Özgen
- Rare Diseases Research Laboratory, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Gülten Tuncel
- DESAM Institute, Near East University, Mersin 10, Turkey
| | | | - Mehmet Cihan Balcı
- Division of Pediatric Nutrition and Metabolism, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Hüseyin Kutay Körbeyli
- Division of Pediatric Nutrition and Metabolism, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Fatmahan Atalar
- Rare Diseases Research Laboratory, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey; Department of Rare Diseases, Child Health Institute, Istanbul University, Istanbul, Turkey.
| | - Gülden Fatma Gökçay
- Division of Pediatric Nutrition and Metabolism, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| |
Collapse
|
2
|
Scarano C, Veneruso I, De Simone RR, Di Bonito G, Secondino A, D’Argenio V. The Third-Generation Sequencing Challenge: Novel Insights for the Omic Sciences. Biomolecules 2024; 14:568. [PMID: 38785975 PMCID: PMC11117673 DOI: 10.3390/biom14050568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The understanding of the human genome has been greatly improved by the advent of next-generation sequencing technologies (NGS). Despite the undeniable advantages responsible for their widespread diffusion, these methods have some constraints, mainly related to short read length and the need for PCR amplification. As a consequence, long-read sequencers, called third-generation sequencing (TGS), have been developed, promising to overcome NGS. Starting from the first prototype, TGS has progressively ameliorated its chemistries by improving both read length and base-calling accuracy, as well as simultaneously reducing the costs/base. Based on these premises, TGS is showing its potential in many fields, including the analysis of difficult-to-sequence genomic regions, structural variations detection, RNA expression profiling, DNA methylation study, and metagenomic analyses. Protocol standardization and the development of easy-to-use pipelines for data analysis will enhance TGS use, also opening the way for their routine applications in diagnostic contexts.
Collapse
Affiliation(s)
- Carmela Scarano
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Iolanda Veneruso
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Rosa Redenta De Simone
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Gennaro Di Bonito
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Angela Secondino
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Valeria D’Argenio
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Via di Val Cannuta 247, 00166 Roma, Italy
| |
Collapse
|
3
|
Smolka M, Paulin LF, Grochowski CM, Horner DW, Mahmoud M, Behera S, Kalef-Ezra E, Gandhi M, Hong K, Pehlivan D, Scholz SW, Carvalho CMB, Proukakis C, Sedlazeck FJ. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol 2024:10.1038/s41587-023-02024-y. [PMID: 38168980 PMCID: PMC11217151 DOI: 10.1038/s41587-023-02024-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/11/2023] [Indexed: 01/05/2024]
Abstract
Calling structural variations (SVs) is technically challenging, but using long reads remains the most accurate way to identify complex genomic alterations. Here we present Sniffles2, which improves over current methods by implementing a repeat aware clustering coupled with a fast consensus sequence and coverage-adaptive filtering. Sniffles2 is 11.8 times faster and 29% more accurate than state-of-the-art SV callers across different coverages (5-50×), sequencing technologies (ONT and HiFi) and SV types. Furthermore, Sniffles2 solves the problem of family-level to population-level SV calling to produce fully genotyped VCF files. Across 11 probands, we accurately identified causative SVs around MECP2, including highly complex alleles with three overlapping SVs. Sniffles2 also enables the detection of mosaic SVs in bulk long-read data. As a result, we identified multiple mosaic SVs in brain tissue from a patient with multiple system atrophy. The identified SV showed a remarkable diversity within the cingulate cortex, impacting both genes involved in neuron function and repetitive elements.
Collapse
Affiliation(s)
- Moritz Smolka
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | - Luis F Paulin
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | | | - Dominic W Horner
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sairam Behera
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | - Ester Kalef-Ezra
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Mira Gandhi
- Pacific Northwest Research Institute (PNRI), Seattle, WA, USA
| | - Karl Hong
- Bionano Genomics, San Diego, CA, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Pacific Northwest Research Institute (PNRI), Seattle, WA, USA
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
| |
Collapse
|
4
|
Chetruengchai W, Phowthongkum P, Shotelersuk V. Carrier frequency estimation of pathogenic variants of autosomal recessive and X-linked recessive mendelian disorders using exome sequencing data in 1,642 Thais. BMC Med Genomics 2024; 17:9. [PMID: 38167091 PMCID: PMC10762924 DOI: 10.1186/s12920-023-01771-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND People with autosomal recessive disorders often were born without awareness of the carrier status of their parents. The American College of Medical Genetics and Genomics (ACMG) recommends screening 113 genes known to cause autosomal recessive and X-linked conditions in couples seeking to learn about their risk of having children with these disorders to have an appropriate reproductive plan. METHODS We analyzed the exome sequencing data of 1,642 unrelated Thai individuals to identify the pathogenic variant (PV) frequencies in genes recommended by ACMG. RESULTS In the 113 ACMG-recommended genes, 165 PV and likely PVs in 60 genes of 559 exomes (34%, 559/1642) were identified. The carrier rate was increased to 39% when glucose-6-phosphate dehydrogenase (G6PD) was added. The carrier rate was still as high as 14.7% when thalassemia and hemoglobinopathies were excluded. In addition to thalassemia, hemoglobinopathies, and G6PD deficiency, carrier frequencies of > 1% were found for Gaucher disease, primary hyperoxaluria, Pendred syndrome, and Wilson disease. Nearly 2% of the couples were at risk of having offsprings with the tested autosomal recessive conditions. CONCLUSIONS Based on the study samples, the expanded carrier screening, which specifically targeted common autosomal recessive conditions in Thai individuals, will benefit clinical outcomes, regarding preconception/prenatal genetic carrier screening.
Collapse
Affiliation(s)
- Wanna Chetruengchai
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Prasit Phowthongkum
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand.
- Division of Medical Genetics and Genomics, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | - Vorasuk Shotelersuk
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| |
Collapse
|
5
|
Pachchek S, Landoulsi Z, Pavelka L, Schulte C, Buena-Atienza E, Gross C, Hauser AK, Reddy Bobbili D, Casadei N, May P, Krüger R. Accurate long-read sequencing identified GBA1 as major risk factor in the Luxembourgish Parkinson's study. NPJ Parkinsons Dis 2023; 9:156. [PMID: 37996455 PMCID: PMC10667262 DOI: 10.1038/s41531-023-00595-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/24/2023] [Indexed: 11/25/2023] Open
Abstract
Heterozygous variants in the glucocerebrosidase GBA1 gene are an increasingly recognized risk factor for Parkinson's disease (PD). Due to the GBAP1 pseudogene, which shares 96% sequence homology with the GBA1 coding region, accurate variant calling by array-based or short-read sequencing methods remains a major challenge in understanding the genetic landscape of GBA1-associated PD. We analyzed 660 patients with PD, 100 patients with Parkinsonism and 808 healthy controls from the Luxembourg Parkinson's study, sequenced using amplicon-based long-read DNA sequencing technology. We found that 12.1% (77/637) of PD patients carried GBA1 variants, with 10.5% (67/637) of them carrying known pathogenic variants (including severe, mild, risk variants). In comparison, 5% (34/675) of the healthy controls carried GBA1 variants, and among them, 4.3% (29/675) were identified as pathogenic variant carriers. We found four GBA1 variants in patients with atypical parkinsonism. Pathogenic GBA1 variants were 2.6-fold more frequently observed in PD patients compared to controls (OR = 2.6; CI = [1.6,4.1]). Three novel variants of unknown significance (VUS) were identified. Using a structure-based approach, we defined a potential risk prediction method for VUS. This study describes the full landscape of GBA1-related parkinsonism in Luxembourg, showing a high prevalence of GBA1 variants as the major genetic risk for PD. Although the long-read DNA sequencing technique used in our study may be limited in its effectiveness to detect potential structural variants, our approach provides an important advancement for highly accurate GBA1 variant calling, which is essential for providing access to emerging causative therapies for GBA1 carriers.
Collapse
Grants
- FNR/NCER13/BM/11264123 Fonds National de la Recherche Luxembourg (National Research Fund)
- funded by the Luxembourg National Research (FNR/NCER13/BM/11264123), the PEARL program (FNR/P13/6682797 to RK), MotaSYN (12719684 to RK), MAMaSyn (to RK), MiRisk‐PD (C17/BM/11676395 to RK, PM), the FNR/DFG Core INTER (ProtectMove, FNR11250962 to PM), and the PARK-QC DTU (PRIDE17/12244779/PARK-QC to RK, SP)
- Luxembourg National Research Fund (FNR/NCER13/BM/11264123), the PEARL program (FNR/P13/6682797), MotaSYN (12719684), MAMaSyn, MiRisk‐PD (C17/BM/11676395), and the PARK-QC DTU (PRIDE17/12244779/PARK-QC)
Collapse
Affiliation(s)
- Sinthuja Pachchek
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg.
| | - Zied Landoulsi
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg
| | - Lukas Pavelka
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Claudia Schulte
- Department of Neurodegeneration, Center of Neurology, Hertie Institute for Clinical Brain Research, German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Elena Buena-Atienza
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Caspar Gross
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Ann-Kathrin Hauser
- Department of Neurodegeneration, Center of Neurology, Hertie Institute for Clinical Brain Research, German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Dheeraj Reddy Bobbili
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Patrick May
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg.
| | - Rejko Krüger
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg.
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg.
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg.
| |
Collapse
|
6
|
Gabbert C, Schaake S, Lüth T, Much C, Klein C, Aasly JO, Farrer MJ, Trinh J. GBA1 in Parkinson's disease: variant detection and pathogenicity scoring matters. BMC Genomics 2023; 24:322. [PMID: 37312046 DOI: 10.1186/s12864-023-09417-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/30/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND GBA1 variants are the strongest genetic risk factor for Parkinson's disease (PD). However, the pathogenicity of GBA1 variants concerning PD is still not fully understood. Additionally, the frequency of GBA1 variants varies widely across populations. OBJECTIVES To evaluate Oxford Nanopore sequencing as a strategy, to determine the frequency of GBA1 variants in Norwegian PD patients and controls, and to review the current literature on newly identified variants that add to pathogenicity determination. METHODS We included 462 Norwegian PD patients and 367 healthy controls. We sequenced the full-length GBA1 gene on the Oxford Nanopore GridION as an 8.9 kb amplicon. Six analysis pipelines were compared using two aligners (NGMLR, Minimap2) and three variant callers (BCFtools, Clair3, Pepper-Margin-Deepvariant). Confirmation of GBA1 variants was performed by Sanger sequencing and the pathogenicity of variants was evaluated. RESULTS We found 95.8% (115/120) true-positive GBA1 variant calls, while 4.2% (5/120) variant calls were false-positive, with the NGMLR/Minimap2-BCFtools pipeline performing best. In total, 13 rare GBA1 variants were detected: two were predicted to be (likely) pathogenic and eleven were of uncertain significance. The odds of carrying one of the two common GBA1 variants, p.L483P or p.N409S, in PD patients were estimated to be 4.11 times the odds of carrying one of these variants in controls (OR = 4.11 [1.39, 12.12]). CONCLUSIONS In conclusion, we have demonstrated that Oxford long-read Nanopore sequencing, along with the NGMLR/Minimap2-BCFtools pipeline is an effective tool to investigate GBA1 variants. Further studies on the pathogenicity of GBA1 variants are needed to assess their effect on PD.
Collapse
Affiliation(s)
- Carolin Gabbert
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, Lübeck, 23538, Germany
| | - Susen Schaake
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, Lübeck, 23538, Germany
| | - Theresa Lüth
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, Lübeck, 23538, Germany
| | - Christoph Much
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, Lübeck, 23538, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, Lübeck, 23538, Germany
| | - Jan O Aasly
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Matthew J Farrer
- Department of Neurology, University of Florida, Gainesville, FL, USA
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, Lübeck, 23538, Germany.
| |
Collapse
|
7
|
Jun G, English AC, Metcalf GA, Yang J, Chaisson MJP, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YDI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJ, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. RESEARCH SQUARE 2023:rs.3.rs-2515453. [PMID: 36778386 PMCID: PMC9915771 DOI: 10.21203/rs.3.rs-2515453/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hematologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.
Collapse
Affiliation(s)
- Goo Jun
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
| | - Adam C English
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Ginger A Metcalf
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Jianzhi Yang
- University of Southern California, Los Angeles, CA, USA
| | | | | | - Vipin K Menon
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | | | | | - Albert V Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - John A Lane
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Tom Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Hyun Min Kang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Sejal Salvi
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Qingchang Meng
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Hua Shen
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Divya Pasham
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Sravya Bhamidipati
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Kavya Kottapalli
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Donna K. Arnett
- Department of Epidemiology, University of Kentucky College of Public Health
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | - Paul L. Auer
- Division of Biostatistics and Cancer Center, Medical College of Wisconsin, Milwaukee WI
| | | | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas, Rio Grande Valley School of Medicine, Brownsville, TX
| | - Donald W. Bowden
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA
| | - Yii-Der Ida Chen
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Joanne E. Curran
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tasha Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai
| | | | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - John P Kane
- Cardiovascular Research Institute, University of California, San Francisco
| | - Robert Kaplan
- Department of epidemiology and population health, Albert Einstein College of Medicine, Bronx NY USA
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco CA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stephen T. McGarvey
- Department of Epidemiology, International Health Institute and Department of Anthropology, Brown University
| | - Courtney Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - S. Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA
| | | | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stephen S. Rich
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School
- Cardiovascular Division, Brigham & Women’s Hospital, Harvard University
- Howard Hughes Medical Institute, Harvard University
| | | | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Jennifer A. Smith
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, NC
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Baojun Wu
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Lisa R. Yanek
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Susan K. Dutcher
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | | | | | - Ryan Kim
- Psomagen, Inc.,Rockville, Maryland, USA
| | | | | | | | - James Luo
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
| | - Richard A Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Goncalo Abecasis
- Regeneron Genetics Center
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Fritz J Sedlazeck
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| |
Collapse
|
8
|
Jun G, English AC, Metcalf GA, Yang J, Chaisson MJP, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YDI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJ, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525428. [PMID: 36747810 PMCID: PMC9900832 DOI: 10.1101/2023.01.25.525428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.
Collapse
Affiliation(s)
- Goo Jun
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
| | - Adam C English
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Ginger A Metcalf
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Jianzhi Yang
- University of Southern California, Los Angeles, CA, USA
| | | | | | - Vipin K Menon
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | | | | | - Albert V Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - John A Lane
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Tom Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Hyun Min Kang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Sejal Salvi
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Qingchang Meng
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Hua Shen
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Divya Pasham
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Sravya Bhamidipati
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Kavya Kottapalli
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Donna K. Arnett
- Department of Epidemiology, University of Kentucky College of Public Health
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | - Paul L. Auer
- Division of Biostatistics and Cancer Center, Medical College of Wisconsin, Milwaukee WI
| | | | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas, Rio Grande Valley School of Medicine, Brownsville, TX
| | - Donald W. Bowden
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA
| | - Yii-Der Ida Chen
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Joanne E. Curran
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tasha Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai
| | | | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - John P Kane
- Cardiovascular Research Institute, University of California, San Francisco
| | - Robert Kaplan
- Department of epidemiology and population health, Albert Einstein College of Medicine, Bronx NY USA
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco CA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stephen T. McGarvey
- Department of Epidemiology, International Health Institute and Department of Anthropology, Brown University
| | - Courtney Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - S. Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA
| | | | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stephen S. Rich
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School
- Cardiovascular Division, Brigham & Women’s Hospital, Harvard University
- Howard Hughes Medical Institute, Harvard University
| | | | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA
| | - Jennifer A. Smith
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, NC
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Baojun Wu
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Lisa R. Yanek
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Susan K. Dutcher
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | | | | | - Ryan Kim
- Psomagen, Inc.,Rockville, Maryland, USA
| | | | | | | | - James Luo
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
| | - Richard A Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Goncalo Abecasis
- Regeneron Genetics Center
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Fritz J Sedlazeck
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| |
Collapse
|
9
|
Andini KD, Nielsen M, Suerink M, Helderman NC, Koornstra JJ, Ahadova A, Kloor M, Mourits MJE, Kok K, Sijmons RH, Bajwa-Ten Broeke SW. PMS2-associated Lynch syndrome: Past, present and future. Front Oncol 2023; 13:1127329. [PMID: 36895471 PMCID: PMC9989154 DOI: 10.3389/fonc.2023.1127329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/01/2023] [Indexed: 02/25/2023] Open
Abstract
Carriers of any pathogenic variant in one of the MMR genes (path_MMR carriers) were traditionally thought to be at comparable risk of developing a range of different malignancies, foremost colorectal cancer (CRC) and endometrial cancer. However, it is now widely accepted that their cancer risk and cancer spectrum range notably depending on which MMR gene is affected. Moreover, there is increasing evidence that the MMR gene affected also influences the molecular pathogenesis of Lynch syndrome CRC. Although substantial progress has been made over the past decade in understanding these differences, many questions remain unanswered, especially pertaining to path_PMS2 carriers. Recent findings show that, while the cancer risk is relatively low, PMS2-deficient CRCs tend to show more aggressive behaviour and have a worse prognosis than other MMR-deficient CRCs. This, together with lower intratumoral immune infiltration, suggests that PMS2-deficient CRCs might have more in common biologically with sporadic MMR-proficient CRCs than with other MMR-deficient CRCs. These findings could have important consequences for surveillance, chemoprevention and therapeutic strategies (e.g. vaccines). In this review we discuss the current knowledge, current (clinical) challenges and knowledge gaps that should be targeted by future studies.
Collapse
Affiliation(s)
- Katarina D Andini
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Noah C Helderman
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Jan Jacob Koornstra
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Aysel Ahadova
- Department of Applied Tumour Biology, Institute of Pathology, Heidelberg University Hospital, and Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumour Biology, Institute of Pathology, Heidelberg University Hospital, and Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany
| | - Marian J E Mourits
- Department of Gynaecology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Klaas Kok
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Sanne W Bajwa-Ten Broeke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| |
Collapse
|
10
|
Application of Long-Read Nanopore Sequencing to the Search for Mutations in Hypertrophic Cardiomyopathy. Int J Mol Sci 2022; 23:ijms232415845. [PMID: 36555486 PMCID: PMC9779642 DOI: 10.3390/ijms232415845] [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: 11/24/2022] [Revised: 12/10/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
Increasing evidence suggests that both coding and non-coding regions of sarcomeric protein genes can contribute to hypertrophic cardiomyopathy (HCM). Here, we introduce an experimental workflow (tested on four patients) for complete sequencing of the most common HCM genes (MYBPC3, MYH7, TPM1, TNNT2, and TNNI3) via long-range PCR, Oxford Nanopore Technology (ONT) sequencing, and bioinformatic analysis. We applied Illumina and Sanger sequencing to validate the results, FastQC, Qualimap, and MultiQC for quality evaluations, MiniMap2 to align data, Clair3 to call and phase variants, and Annovar's tools and CADD to assess pathogenicity of variants. We could not amplify the region encompassing exons 6-12 of MYBPC3. A higher sequencing error rate was observed with ONT (6.86-6.92%) than with Illumina technology (1.14-1.35%), mostly for small indels. Pathogenic variant p.Gln1233Ter and benign polymorphism p.Arg326Gln in MYBPC3 in a heterozygous state were found in one patient. We demonstrated the ability of ONT to phase single-nucleotide variants, enabling direct haplotype determination for genes TNNT2 and TPM1. These findings highlight the importance of long-range PCR efficiency, as well as lower accuracy of variant calling by ONT than by Illumina technology; these differences should be clarified prior to clinical application of the ONT method.
Collapse
|
11
|
Enhancing Molecular Testing for Effective Delivery of Actionable Gene Diagnostics. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9120745. [PMID: 36550951 PMCID: PMC9774983 DOI: 10.3390/bioengineering9120745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022]
Abstract
There is a deep need to navigate within our genomic data to find, understand and pave the way for disease-specific treatments, as the clinical diagnostic journey provides only limited guidance. The human genome is enclosed in every nucleated cell, and yet at the single-cell resolution many unanswered questions remain, as most of the sequencing techniques use a bulk approach. Therefore, heterogeneity, mosaicism and many complex structural variants remain partially uncovered. As a conceptual approach, nanopore-based sequencing holds the promise of being a single-molecule-based, long-read and high-resolution technique, with the ability of uncovering the nucleic acid sequence and methylation almost in real time. A key limiting factor of current clinical genetics is the deciphering of key disease-causing genomic sequences. As the technological revolution is expanding regarding genetic data, the interpretation of genotype-phenotype correlations should be made with fine caution, as more and more evidence points toward the presence of more than one pathogenic variant acting together as a result of intergenic interplay in the background of a certain phenotype observed in a patient. This is in conjunction with the observation that many inheritable disorders manifest in a phenotypic spectrum, even in an intra-familial way. In the present review, we summarized the relevant data on nanopore sequencing regarding clinical genomics as well as highlighted the importance and content of pre-test and post-test genetic counselling, yielding a complex approach to phenotype-driven molecular diagnosis. This should significantly lower the time-to-right diagnosis as well lower the time required to complete a currently incomplete genotype-phenotype axis, which will boost the chance of establishing a new actionable diagnosis followed by therapeutical approach.
Collapse
|
12
|
Overcoming the Pitfalls of Next-Generation Sequencing-Based Molecular Diagnosis of Shwachman-Diamond Syndrome. J Mol Diagn 2022; 24:1240-1253. [PMID: 36162759 DOI: 10.1016/j.jmoldx.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 07/30/2022] [Accepted: 09/09/2022] [Indexed: 01/13/2023] Open
Abstract
Shwachman-Diamond syndrome (SDS) is the second most common cause of exocrine pancreatic insufficiency, and 90% of patients carry mutations in the SBDS gene, the most common being the c.183_184delinsCT and c.258+2T>C variants. However, precise detection of these most contributory variants by conventional short-read next-generation sequencing data analysis is limited because of the SBDS/SBDSP1 highly homologous sequences. In this study, an efficient approach was established to infer the haplotype of SBDS based on the expectation-maximization algorithm. The workflow was retrospectively applied to detect the two most common SBDS variants in a Chinese SDS high-risk cohort, and a systematic comparison of variant detection results was performed between the workflow and conventional next-generation sequencing analysis based on Sanger sequencing validation. Among the Chinese SDS high-risk cohort (n = 47) and their available parents (n = 64), the established workflow improved the diagnostic rate for these two variants by 27.7% (95% CI, 15.6%-42.6%) compared with conventional analysis. For overall variant detection, the established workflow achieved 100% (95% CI, 92.5%-100%) concordance with Sanger sequencing, whereas conventional analysis showed only 65.8% accuracy; these results included 25.2% with missed variant calls, 7.2% with diagnosed but inaccurate variant calls, and 1.8% with false-positive calls. With its favorable result in both SDS patient diagnosis and carrier detection performance, the provided workflow showed its potential in clinical application for SDS molecular diagnosis.
Collapse
|
13
|
Sedaghat-Hamedani F, Rebs S, Kayvanpour E, Zhu C, Amr A, Müller M, Haas J, Wu J, Steinmetz LM, Ehlermann P, Streckfuss-Bömeke K, Frey N, Meder B. Genotype Complements the Phenotype: Identification of the Pathogenicity of an LMNA Splice Variant by Nanopore Long-Read Sequencing in a Large DCM Family. Int J Mol Sci 2022; 23:ijms232012230. [PMID: 36293084 PMCID: PMC9602549 DOI: 10.3390/ijms232012230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Dilated cardiomyopathy (DCM) is a common cause of heart failure (HF) and is of familial origin in 20−40% of cases. Genetic testing by next-generation sequencing (NGS) has yielded a definite diagnosis in many cases; however, some remain elusive. In this study, we used a combination of NGS, human-induced pluripotent-stem-cell-derived cardiomyocytes (iPSC-CMs) and nanopore long-read sequencing to identify the causal variant in a multi-generational pedigree of DCM. A four-generation family with familial DCM was investigated. Next-generation sequencing (NGS) was performed on 22 family members. Skin biopsies from two affected family members were used to generate iPSCs, which were then differentiated into iPSC-CMs. Short-read RNA sequencing was used for the evaluation of the target gene expression, and long-read RNA nanopore sequencing was used to evaluate the relevance of the splice variants. The pedigree suggested a highly penetrant, autosomal dominant mode of inheritance. The phenotype of the family was suggestive of laminopathy, but previous genetic testing using both Sanger and panel sequencing only yielded conflicting evidence for LMNA p.R644C (rs142000963), which was not fully segregated. By re-sequencing four additional affected family members, further non-coding LMNA variants could be detected: rs149339264, rs199686967, rs201379016, and rs794728589. To explore the roles of these variants, iPSC-CMs were generated. RNA sequencing showed the LMNA expression levels to be significantly lower in the iPSC-CMs of the LMNA variant carriers. We demonstrated a dysregulated sarcomeric structure and altered calcium homeostasis in the iPSC-CMs of the LMNA variant carriers. Using targeted nanopore long-read sequencing, we revealed the biological significance of the variant c.356+1G>A, which generates a novel 5′ splice site in exon 1 of the cardiac isomer of LMNA, causing a nonsense mRNA product with almost complete RNA decay and haploinsufficiency. Using novel molecular analysis and nanopore technology, we demonstrated the pathogenesis of the rs794728589 (c.356+1G>A) splice variant in LMNA. This study highlights the importance of precise diagnostics in the clinical management and workup of cardiomyopathies.
Collapse
Affiliation(s)
- Farbod Sedaghat-Hamedani
- Institute for Cardiomyopathies Heidelberg (ICH), University Hospital Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg and Mannheim, 69120 Heidelberg, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Sabine Rebs
- Department of Cardiology and Pneumology, Georg-August-University Göttingen, 37073 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
- Department of Pharmacology and Toxicology, University of Würzburg, 97070 Würzburg, Germany
| | - Elham Kayvanpour
- Institute for Cardiomyopathies Heidelberg (ICH), University Hospital Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg and Mannheim, 69120 Heidelberg, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Chenchen Zhu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ali Amr
- Institute for Cardiomyopathies Heidelberg (ICH), University Hospital Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg and Mannheim, 69120 Heidelberg, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Marion Müller
- Institute for Cardiomyopathies Heidelberg (ICH), University Hospital Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg and Mannheim, 69120 Heidelberg, Germany
- Clinic for General and Interventional Cardiology/Angiology, Herz- und Diabeteszentrum NRW, University Hospital of the Ruhr-Universität Bochum, 32545 Bad Oeynhausen, Germany
| | - Jan Haas
- Institute for Cardiomyopathies Heidelberg (ICH), University Hospital Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg and Mannheim, 69120 Heidelberg, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Jingyan Wu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lars M. Steinmetz
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg and Mannheim, 69120 Heidelberg, Germany
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Philipp Ehlermann
- Institute for Cardiomyopathies Heidelberg (ICH), University Hospital Heidelberg, 69120 Heidelberg, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Katrin Streckfuss-Bömeke
- Department of Cardiology and Pneumology, Georg-August-University Göttingen, 37073 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
- Department of Pharmacology and Toxicology, University of Würzburg, 97070 Würzburg, Germany
| | - Norbert Frey
- Institute for Cardiomyopathies Heidelberg (ICH), University Hospital Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg and Mannheim, 69120 Heidelberg, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Benjamin Meder
- Institute for Cardiomyopathies Heidelberg (ICH), University Hospital Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg and Mannheim, 69120 Heidelberg, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Correspondence:
| |
Collapse
|
14
|
Santos-Lobato BL, Schumacher-Schuh AF, Mata IF. Lack of full sequencing GBA1 studies for patients with Parkinson’s disease in Latin America. NPJ Parkinsons Dis 2022; 8:101. [PMID: 35941142 PMCID: PMC9360049 DOI: 10.1038/s41531-022-00358-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
Full sequencing of the GBA1 gene in patients with Parkinson’s disease provides a wide screening of pathogenic variants, but less developed regions of the world, like Latin America, may have difficulties in performing full sequencing. We performed a systematic review with meta-analysis to explore the prevalence and the odds ratio of specific GBA1 variants in Parkinson’s disease in Latin America. We noted a lack of full sequencing GBA1 studies in Latin America.
Collapse
|
15
|
Toffoli M, Chen X, Sedlazeck FJ, Lee CY, Mullin S, Higgins A, Koletsi S, Garcia-Segura ME, Sammler E, Scholz SW, Schapira AHV, Eberle MA, Proukakis C. Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson's disease-associated GBA gene. Commun Biol 2022; 5:670. [PMID: 35794204 PMCID: PMC9259685 DOI: 10.1038/s42003-022-03610-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/21/2022] [Indexed: 11/30/2022] Open
Abstract
GBA variants carriers are at increased risk of Parkinson’s disease (PD) and Lewy body dementia (LBD). The presence of pseudogene GBAP1 predisposes to structural variants, complicating genetic analysis. We present two methods to resolve recombinant alleles and other variants in GBA: Gauchian, a tool for short-read, whole-genome sequencing data analysis, and Oxford Nanopore sequencing after PCR enrichment. Both methods were concordant for 42 samples carrying a range of recombinants and GBAP1-related mutations, and Gauchian outperformed the GATK Best Practices pipeline. Applying Gauchian to sequencing of over 10,000 individuals shows that copy number variants (CNVs) spanning GBAP1 are relatively common in Africans. CNV frequencies in PD and LBD are similar to controls. Gains may coexist with other mutations in patients, and a modifying effect cannot be excluded. Gauchian detects more GBA variants in LBD than PD, especially severe ones. These findings highlight the importance of accurate GBA analysis in these patients. Two methods fully resolve the GBA gene: Gauchian, a tool for short-read, whole-genome sequencing data analysis, and Oxford Nanopore sequencing after PCR enrichment. The approach improves our understanding of the relationship between GBA, Gaucher disease and Parkinson disease.
Collapse
Affiliation(s)
- Marco Toffoli
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, NW3 2PF, United Kingdom
| | - Xiao Chen
- Illumina Inc., San Diego, CA, USA.,Pacific Biosciences, 1305 O'Brien Dr., Menlo Park, CA, 94025, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Chiao-Yin Lee
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, NW3 2PF, United Kingdom
| | - Stephen Mullin
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, NW3 2PF, United Kingdom.,Institute of Translational and Stratified Medicine, University of Plymouth School of Medicine, Plymouth, United Kingdom
| | - Abigail Higgins
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, NW3 2PF, United Kingdom
| | - Sofia Koletsi
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, NW3 2PF, United Kingdom
| | - Monica Emili Garcia-Segura
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, NW3 2PF, United Kingdom
| | - Esther Sammler
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, 20892, USA.,Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, 21287, USA
| | - Anthony H V Schapira
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, NW3 2PF, United Kingdom
| | - Michael A Eberle
- Illumina Inc., San Diego, CA, USA. .,Pacific Biosciences, 1305 O'Brien Dr., Menlo Park, CA, 94025, USA.
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, NW3 2PF, United Kingdom.
| |
Collapse
|
16
|
Magrinelli F, Lohmann K. PRKRAP1 and Other Pseudogenes in Movement Disorders: The Troublemakers in Genetic Analyses Are More Than Genomic Fossils. Mov Disord Clin Pract 2022; 9:698-702. [PMID: 35844281 PMCID: PMC9274356 DOI: 10.1002/mdc3.13499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/11/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of NeurologyUniversity College LondonLondon
| | - Katja Lohmann
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| |
Collapse
|
17
|
Whitford W, Hawkins V, Moodley KS, Grant MJ, Lehnert K, Snell RG, Jacobsen JC. Proof of concept for multiplex amplicon sequencing for mutation identification using the MinION nanopore sequencer. Sci Rep 2022; 12:8572. [PMID: 35595858 PMCID: PMC9122479 DOI: 10.1038/s41598-022-12613-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/04/2022] [Indexed: 12/22/2022] Open
Abstract
Rapid, cost-effective identification of genetic variants in small candidate genomic regions remains a challenge, particularly for less well equipped or lower throughput laboratories. The application of Oxford Nanopore Technologies’ MinION sequencer has the potential to fulfil this requirement. We demonstrate a proof of concept for a multiplexing assay that pools PCR amplicons for MinION sequencing to enable sequencing of multiple templates from multiple individuals, which could be applied to gene-targeted diagnostics. A combined strategy of barcoding and sample pooling was developed for simultaneous multiplex MinION sequencing of 100 PCR amplicons. The amplicons are family-specific, spanning a total of 30 loci in DNA isolated from 82 human neurodevelopmental cases and family members. The target regions were chosen for further interrogation because a potentially disease-causative variant had been identified in affected individuals following Illumina exome sequencing. The pooled MinION sequences were deconvoluted by aligning to custom references using the minimap2 aligner software. Our multiplexing approach produced an interpretable and expected sequence from 29 of the 30 targeted genetic loci. The sequence variant which was not correctly resolved in the MinION sequence was adjacent to a five nucleotide homopolymer. It is already known that homopolymers present a resolution problem with the MinION approach. Interestingly despite equimolar quantities of PCR amplicon pooled for sequencing, significant variation in the depth of coverage (127×–19,626×; mean = 8321×, std err = 452.99) was observed. We observed independent relationships between depth of coverage and target length, and depth of coverage and GC content. These relationships demonstrate biases of the MinION sequencer for longer templates and those with lower GC content. We demonstrate an efficient approach for variant discovery or confirmation from short DNA templates using the MinION sequencing device. With less than 130 × depth of coverage required for accurate genotyping, the methodology described here allows for rapid highly multiplexed targeted sequencing of large numbers of samples in a minimally equipped laboratory with a potential cost as much 200 × less than that from Sanger sequencing.
Collapse
Affiliation(s)
- Whitney Whitford
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand. .,Centre for Brain Research, The University of Auckland, Auckland, New Zealand.
| | - Victoria Hawkins
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Kriebashne S Moodley
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Matthew J Grant
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Klaus Lehnert
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Russell G Snell
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Jessie C Jacobsen
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| |
Collapse
|
18
|
Schmidt J, Berghaus S, Blessing F, Herbeck H, Blessing J, Schierack P, Rödiger S, Roggenbuck D, Wenzel F. Genotyping of familial Mediterranean fever gene (MEFV)-Single nucleotide polymorphism-Comparison of Nanopore with conventional Sanger sequencing. PLoS One 2022; 17:e0265622. [PMID: 35298548 PMCID: PMC8929590 DOI: 10.1371/journal.pone.0265622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/04/2022] [Indexed: 11/18/2022] Open
Abstract
Background Through continuous innovation and improvement, Nanopore sequencing has become a powerful technology. Because of its fast processing time, low cost, and ability to generate long reads, this sequencing technique would be particularly suitable for clinical diagnostics. However, its raw data accuracy is inferior in contrast to other sequencing technologies. This constraint still results in limited use of Nanopore sequencing in the field of clinical diagnostics and requires further validation and IVD certification. Methods We evaluated the performance of latest Nanopore sequencing in combination with a dedicated data-analysis pipeline for single nucleotide polymorphism (SNP) genotyping of the familial Mediterranean fever gene (MEFV) by amplicon sequencing of 47 clinical samples. Mutations in MEFV are associated with Mediterranean fever, a hereditary periodic fever syndrome. Conventional Sanger sequencing, which is commonly applied in clinical genetic diagnostics, was used as a reference method. Results Nanopore sequencing enabled the sequencing of 10 target regions within MEFV with high read depth (median read depth 7565x) in all samples and identified a total of 435 SNPs in the whole sample collective, of which 29 were unique. Comparison of both sequencing workflows showed a near perfect agreement with no false negative calls. Precision, Recall, and F1-Score of the Nanopore sequencing workflow were > 0.99, respectively. Conclusions These results demonstrated the great potential of current Nanopore sequencing for application in clinical diagnostics, at least for SNP genotyping by amplicon sequencing. Other more complex applications, especially structural variant identification, require further in-depth clinical validation.
Collapse
Affiliation(s)
- Jonas Schmidt
- Institute for Laboratory Medicine, Singen, Germany
- Faculty of Medical and Life Sciences, Furtwangen University, Villingen-Schwenningen, Germany
- Faculty Environment and Natural Sciences, Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | | | - Frithjof Blessing
- Institute for Laboratory Medicine, Singen, Germany
- Faculty of Medical and Life Sciences, Furtwangen University, Villingen-Schwenningen, Germany
| | | | | | - Peter Schierack
- Faculty Environment and Natural Sciences, Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences Brandenburg, Brandenburg University of Technology Cottbus–Senftenberg, Senftenberg, Germany
| | - Stefan Rödiger
- Faculty Environment and Natural Sciences, Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences Brandenburg, Brandenburg University of Technology Cottbus–Senftenberg, Senftenberg, Germany
| | - Dirk Roggenbuck
- Faculty Environment and Natural Sciences, Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences Brandenburg, Brandenburg University of Technology Cottbus–Senftenberg, Senftenberg, Germany
- * E-mail:
| | - Folker Wenzel
- Faculty of Medical and Life Sciences, Furtwangen University, Villingen-Schwenningen, Germany
| |
Collapse
|
19
|
Marsili L, Duque KR, Bode RL, Kauffman MA, Espay AJ. Uncovering Essential Tremor Genetics: The Promise of Long-Read Sequencing. Front Neurol 2022; 13:821189. [PMID: 35401394 PMCID: PMC8983820 DOI: 10.3389/fneur.2022.821189] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/25/2022] [Indexed: 12/23/2022] Open
Abstract
Long-read sequencing (LRS) technologies have been recently introduced to overcome intrinsic limitations of widely-used next-generation sequencing (NGS) technologies, namely the sequencing limited to short-read fragments (150–300 base pairs). Since its introduction, LRS has permitted many successes in unraveling hidden mutational mechanisms. One area in clinical neurology in need of rethinking as it applies to genetic mechanisms is essential tremor (ET). This disorder, among the most common in neurology, is a syndrome often exhibiting an autosomal dominant pattern of inheritance whose large phenotypic spectrum suggest a multitude of genetic etiologies. Exome sequencing has revealed the genetic etiology only in rare ET families (FUS, SORT1, SCN4A, NOS3, KCNS2, HAPLN4/BRAL2, and USP46). We hypothesize that a reason for this shortcoming may be non-classical genetic mechanism(s) underpinning ET, among them trinucleotide, tetranucleotide, or pentanucleotide repeat disorders. In support of this hypothesis, trinucleotide (e.g., GGC repeats in NOTCH2NLC) and pentanucleotide repeat disorders (e.g., ATTTC repeats in STARD7) have been revealed as pathogenic in patients with a past history of what has come to be referred to as “ET plus,” bilateral hand tremor associated with epilepsy and/or leukoencephalopathy. A systematic review of LRS in neurodegenerative disorders showed that 10 of the 22 (45%) genetic etiologies ascertained by LRS include tremor in their phenotypic spectrum, suggesting that future clinical applications of LRS for tremor disorders may uncover genetic subtypes of familial ET that have eluded NGS, particularly those with associated leukoencephalopathy or family history of epilepsy. LRS provides a pathway for potentially uncovering novel genes and genetic mechanisms, helping narrow the large proportion of “idiopathic” ET.
Collapse
Affiliation(s)
- Luca Marsili
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
| | - Kevin R. Duque
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
| | - Rachel L. Bode
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
| | - Marcelo A. Kauffman
- Consultorio y Laboratorio de Neurogenética, Centro Universitario de Neurología José María Ramos Mejía, Buenos Aires, Argentina
| | - Alberto J. Espay
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
- *Correspondence: Alberto J. Espay
| |
Collapse
|
20
|
Hewat TI, Johnson MB, Flanagan SE. Congenital Hyperinsulinism: Current Laboratory-Based Approaches to the Genetic Diagnosis of a Heterogeneous Disease. Front Endocrinol (Lausanne) 2022; 13:873254. [PMID: 35872984 PMCID: PMC9302115 DOI: 10.3389/fendo.2022.873254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
Congenital hyperinsulinism is characterised by the inappropriate release of insulin during hypoglycaemia. This potentially life-threatening disorder can occur in isolation, or present as a feature of syndromic disease. Establishing the underlying aetiology of the hyperinsulinism is critical for guiding medical management of this condition especially in children with diazoxide-unresponsive hyperinsulinism where the underlying genetics determines whether focal or diffuse pancreatic disease is present. Disease-causing single nucleotide variants affecting over 30 genes are known to cause persistent hyperinsulinism with mutations in the KATP channel genes (ABCC8 and KCNJ11) most commonly identified in children with severe persistent disease. Defects in methylation, changes in chromosome number, and large deletions and duplications disrupting multiple genes are also well described in congenital hyperinsulinism, further highlighting the genetic heterogeneity of this condition. Next-generation sequencing has revolutionised the approach to genetic testing for congenital hyperinsulinism with targeted gene panels, exome, and genome sequencing being highly sensitive methods for the analysis of multiple disease genes in a single reaction. It should though be recognised that limitations remain with next-generation sequencing with no single application able to detect all reported forms of genetic variation. This is an important consideration for hyperinsulinism genetic testing as comprehensive screening may require multiple investigations.
Collapse
|
21
|
Khayat MM, Sahraeian SME, Zarate S, Carroll A, Hong H, Pan B, Shi L, Gibbs RA, Mohiyuddin M, Zheng Y, Sedlazeck FJ. Hidden biases in germline structural variant detection. Genome Biol 2021; 22:347. [PMID: 34930391 PMCID: PMC8686633 DOI: 10.1186/s13059-021-02558-x] [Citation(s) in RCA: 12] [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: 08/14/2020] [Accepted: 11/24/2021] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Genomic structural variations (SV) are important determinants of genotypic and phenotypic changes in many organisms. However, the detection of SV from next-generation sequencing data remains challenging. RESULTS In this study, DNA from a Chinese family quartet is sequenced at three different sequencing centers in triplicate. A total of 288 derivative data sets are generated utilizing different analysis pipelines and compared to identify sources of analytical variability. Mapping methods provide the major contribution to variability, followed by sequencing centers and replicates. Interestingly, SV supported by only one center or replicate often represent true positives with 47.02% and 45.44% overlapping the long-read SV call set, respectively. This is consistent with an overall higher false negative rate for SV calling in centers and replicates compared to mappers (15.72%). Finally, we observe that the SV calling variability also persists in a genotyping approach, indicating the impact of the underlying sequencing and preparation approaches. CONCLUSIONS This study provides the first detailed insights into the sources of variability in SV identification from next-generation sequencing and highlights remaining challenges in SV calling for large cohorts. We further give recommendations on how to reduce SV calling variability and the choice of alignment methodology.
Collapse
Affiliation(s)
- Michael M Khayat
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | - Huixiao Hong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Bohu Pan
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China.
- Institute of Thoracic Oncology, Fudan University, Shanghai, China.
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
22
|
Christopher H, Burns A, Josephat E, Makani J, Schuh A, Nkya S. Using DNA testing for the precise, definite, and low-cost diagnosis of sickle cell disease and other Haemoglobinopathies: findings from Tanzania. BMC Genomics 2021; 22:902. [PMID: 34915846 PMCID: PMC8679995 DOI: 10.1186/s12864-021-08220-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/22/2021] [Indexed: 11/30/2022] Open
Abstract
Background Sickle cell disease (SCD) is an important cause of under-five mortality. Tanzania is the 5th country in the world with the highest births prevalence of SCD individuals. Significant advances in the neonatal diagnosis of SCD using rapid point-of-care testing have been made. However genetic confirmation is still required for positive cases, in uncertain cases, in multiply transfused patients, to resolve compound heterozygosity (Hb S/ β0 Thal or Hb S/ β+ thal) not uncommon in the coastal regions of East Africa and increasingly also for pre-marital counselling and potentially for future curative approaches such as gene therapy. The currently available DNA tests are prohibitively expensive. Here, we describe an easy-to-use, affordable and accurate β-globin sequencing approach that can be easily integrated within existing NBS for SCD and other haemoglobinopathies especially in Low- and Middle-income Countries. Aim To evaluate an affordable DNA technology for the diagnosis of Sickle cell disease and other haemoglobinopathies in a resource-limited setting. Methods Laboratory-based validation study was conducted by Muhimbili University of Health and Allied Sciences and the University of Oxford involving sequencing of the entire β -haemoglobin locus using the Oxford Nanopore MinION platform. A total number of 36 Dried blood spots and whole blood samples were subjected to conventional protein-based methods (isoelectric focusing, HPLC), and/or sequenced by the Sanger method as comparators. Results Sequencing results for SCD using the MinION were 100% concordant with those from the Sanger method. In addition, the long-read DNA sequencing method enabled the resolution of cases with unusual phenotypes which make up 1% of all children in Tanzania. The cost is £11/ sample for consumables, which is cheaper compared to other sequencing platforms. Conclusions This is the first report of a comprehensive single DNA assay as a definitive diagnostic test for SCD and other haemoglobinopathies. The test is fast, precise, accurate and affordable.
Collapse
Affiliation(s)
- Heavenlight Christopher
- Sickle cell programme, Department of haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.
| | - Adam Burns
- Oxford Molecular Diagnostics Centre, University of Oxford, Oxford, UK
| | - Emmanuel Josephat
- Sickle cell programme, Department of haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Julie Makani
- Sickle cell programme, Department of haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Anna Schuh
- Sickle cell programme, Department of haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,Oxford Molecular Diagnostics Centre, University of Oxford, Oxford, UK
| | - Siana Nkya
- Sickle cell programme, Department of haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,Department of Biological Sciences, Dar es Salaam University College of Education (DUCE), Dar es Salaam, Tanzania
| |
Collapse
|
23
|
Drelichman GI, Fernández Escobar N, Soberon BC, Basack NF, Frabasil J, Schenone AB, Aguilar G, Larroudé MS, Knight JR, Zhao D, Ruan J, Mistry PK. Long-read single molecule real-time (SMRT) sequencing of GBA1 locus in Gaucher disease national cohort from Argentina reveals high frequency of complex allele underlying severe skeletal phenotypes: Collaborative study from the Argentine Group for Diagnosis and Treatment of Gaucher Disease. Mol Genet Metab Rep 2021; 29:100820. [PMID: 34820281 PMCID: PMC8600149 DOI: 10.1016/j.ymgmr.2021.100820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 10/27/2022] Open
Abstract
Gaucher disease is reckoned for extreme phenotypic diversity that does not show consistent genotype/phenotype correlations. In Argentina, a national collaborative group, Grupo Argentino de Diagnóstico y Tratamiento de la Enfermedad de Gaucher, GADTEG, have delineated uniformly severe type 1 Gaucher disease manifestations presenting in childhood with large burden of irreversible skeletal disease. Here using Long-Read Single Molecule Real-Time (SMRT) Sequencing of GBA1 locus, we show that RecNciI allele is highly prevalent and associates with severe skeletal manifestations in childhood.
Collapse
Affiliation(s)
- Guillermo I Drelichman
- Unidad de Hematología, Hospital de Niños "Ricardo Gutiérrez", Ciudad Autónoma de Buenos Aires, Argentina
| | - Nicolas Fernández Escobar
- Unidad de Hematología, Hospital de Niños "Ricardo Gutiérrez", Ciudad Autónoma de Buenos Aires, Argentina
| | - Barbara C Soberon
- Unidad de Hematología, Hospital de Niños "Ricardo Gutiérrez", Ciudad Autónoma de Buenos Aires, Argentina
| | - Nora F Basack
- Unidad de Hematología, Hospital de Niños "Ricardo Gutiérrez", Ciudad Autónoma de Buenos Aires, Argentina
| | - Joaquin Frabasil
- Laboratorio de Neuroquímica "Dr. N. A. Chamoles", Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrea B Schenone
- Laboratorio de Neuroquímica "Dr. N. A. Chamoles", Ciudad Autónoma de Buenos Aires, Argentina
| | - Gabriel Aguilar
- Centro de Diagnóstico Dr. Rossi, Ciudad Autónoma de Buenos Aires, Argentina
| | - Maria S Larroudé
- Centro de Diagnóstico Dr. Rossi, Ciudad Autónoma de Buenos Aires, Argentina
| | - James R Knight
- Yale University Center for Genome Analysis, Yale School of Medicine, New Haven, CT, United States
| | - Dejian Zhao
- Yale University Center for Genome Analysis, Yale School of Medicine, New Haven, CT, United States
| | - Jiapeng Ruan
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT. United States
| | - Pramod K Mistry
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT. United States
| | | |
Collapse
|
24
|
Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing. Sci Rep 2021; 11:22372. [PMID: 34785703 PMCID: PMC8595663 DOI: 10.1038/s41598-021-01749-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/26/2021] [Indexed: 01/31/2023] Open
Abstract
More than 900 variants have been described in the GLA gene. Some intronic variants and copy number variants in GLA can cause Fabry disease but will not be detected by classical Sanger sequence. We aimed to design and validate a method for sequencing the GLA gene using long-read Oxford Nanopore sequencing technology. Twelve Fabry patients were blindly analyzed, both by conventional Sanger sequence and by long-read sequencing of a 13 kb PCR amplicon. We used minimap2 to align the long-read data and Nanopolish and Sniffles to call variants. All the variants detected by Sanger (including a deep intronic variant) were also detected by long-read sequencing. One patient had a deletion that was not detected by Sanger sequencing but was detected by the new technology. Our long-read sequencing-based method was able to detect missense variants and an exonic deletion, with the added advantage of intronic analysis. It can be used as an efficient and cost-effective tool for screening and diagnosing Fabry disease.
Collapse
|
25
|
Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 2021; 39:1348-1365. [PMID: 34750572 PMCID: PMC8988251 DOI: 10.1038/s41587-021-01108-x] [Citation(s) in RCA: 486] [Impact Index Per Article: 162.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/22/2021] [Indexed: 12/13/2022]
Abstract
Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.
Collapse
Affiliation(s)
- Yunhao Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yue Zhao
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA
| | - Audrey Bollas
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yuru Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
26
|
Vieira SRL, Schapira AHV. Glucocerebrosidase mutations: A paradigm for neurodegeneration pathways. Free Radic Biol Med 2021; 175:42-55. [PMID: 34450264 DOI: 10.1016/j.freeradbiomed.2021.08.230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023]
Abstract
Biallelic (homozygous or compound heterozygous) glucocerebrosidase gene (GBA) mutations cause Gaucher disease, whereas heterozygous mutations are numerically the most important genetic risk factor for Parkinson disease (PD) and are associated with the development of other synucleinopathies, notably Dementia with Lewy Bodies. This phenomenon is not limited to GBA, with converging evidence highlighting further examples of autosomal recessive disease genes increasing neurodegeneration risk in heterozygous mutation carriers. Nevertheless, despite extensive research, the cellular mechanisms by which mutations in GBA, encoding lysosomal enzyme β-glucocerebrosidase (GCase), predispose to neurodegeneration remain incompletely understood. Alpha-synuclein (A-SYN) accumulation, autophagic lysosomal dysfunction, mitochondrial abnormalities, ER stress and neuroinflammation have been proposed as candidate pathogenic pathways in GBA-linked PD. The observation of GCase and A-SYN interactions in PD initiated the development and evaluation of GCase-targeted therapeutics in PD clinical trials.
Collapse
Affiliation(s)
- Sophia R L Vieira
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, United Kingdom
| | - Anthony H V Schapira
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, United Kingdom.
| |
Collapse
|
27
|
Do Not Miss the (Genetic) Diagnosis of Gaucher Syndrome: A Narrative Review on Diagnostic Clues and Management in Severe Prenatal and Perinatal-Lethal Sporadic Cases. J Clin Med 2021; 10:jcm10214890. [PMID: 34768410 PMCID: PMC8585001 DOI: 10.3390/jcm10214890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/11/2021] [Accepted: 10/21/2021] [Indexed: 01/01/2023] Open
Abstract
With a growing number of proved therapies and clinical trials for many lysosomal storage disorders (LSDs), a lot of hope for many patients and families exists. However, there are sometimes cases with poor prognosis, fatal outcomes when our efforts must be directed towards a prompt and correct genetic diagnosis, which offers the only possibility of providing the family with appropriate prevention and treatment. To address this issue, in this article, we present the clinical and genetic hallmarks of the lethal form of Gaucher disease (PLGD) and discuss the potential management. We hope that this will draw attention to its specific manifestations (such as collodion-baby phenotype, ichthyosis, arthrogryposis), which differ from best-known GD complications and ensure appropriate diagnostic assessment to provide families at risk with reliable counselling and treatment to avoid the medical complication of GD.
Collapse
|
28
|
Higgins AL, Toffoli M, Mullin S, Lee CY, Koletsi S, Avenali M, Blandini F, Schapira AH. The remote assessment of parkinsonism supporting ongoing development of interventions in Gaucher disease. Neurodegener Dis Manag 2021; 11:451-458. [PMID: 34666501 DOI: 10.2217/nmt-2021-0032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Mutations in GBA which are causative of Gaucher disease in their biallelic form, are the most common genetic risk factor for Parkinson's disease (PD). The diagnosis of PD relies upon clinically defined motor features which appear after irreversible neurodegeneration. Prodromal symptoms of PD may provide a means to predict latent pathology, years before the onset of motor features. Previous work has reported prodromal features of PD in GBA mutation carriers, however this has been insufficiently sensitive to identify those that will develop PD. The Remote Assessment of Parkinsonism Supporting Ongoing Development of Interventions in Gaucher Disease (RAPSODI GD) study assesses a large cohort of GBA mutation carriers, to aid development of procedures for earlier diagnosis of PD.
Collapse
Affiliation(s)
- Abigail Louise Higgins
- Department of Clinical & Movement Neurosciences, University College London, Queen Square Institute of Neurology, London, UK
| | - Marco Toffoli
- Department of Clinical & Movement Neurosciences, University College London, Queen Square Institute of Neurology, London, UK
| | - Stephen Mullin
- Institute of Translational and Stratified Medicine, University of Plymouth Peninsula School of Medicine, Plymouth, UK
| | - Chiao-Yin Lee
- Department of Clinical & Movement Neurosciences, University College London, Queen Square Institute of Neurology, London, UK.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sofia Koletsi
- Department of Clinical & Movement Neurosciences, University College London, Queen Square Institute of Neurology, London, UK.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Micol Avenali
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy.,Neurorehabilitation Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Fabio Blandini
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy.,Cellular and Molecular Neurobiology Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Anthony Hv Schapira
- Department of Clinical & Movement Neurosciences, University College London, Queen Square Institute of Neurology, London, UK.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| |
Collapse
|
29
|
Abstract
Long-read sequencing technologies have now reached a level of accuracy and yield that allows their application to variant detection at a scale of tens to thousands of samples. Concomitant with the development of new computational tools, the first population-scale studies involving long-read sequencing have emerged over the past 2 years and, given the continuous advancement of the field, many more are likely to follow. In this Review, we survey recent developments in population-scale long-read sequencing, highlight potential challenges of a scaled-up approach and provide guidance regarding experimental design. We provide an overview of current long-read sequencing platforms, variant calling methodologies and approaches for de novo assemblies and reference-based mapping approaches. Furthermore, we summarize strategies for variant validation, genotyping and predicting functional impact and emphasize challenges remaining in achieving long-read sequencing at a population scale.
Collapse
Affiliation(s)
- Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
30
|
Day JO, Mullin S. The Genetics of Parkinson's Disease and Implications for Clinical Practice. Genes (Basel) 2021; 12:genes12071006. [PMID: 34208795 PMCID: PMC8304082 DOI: 10.3390/genes12071006] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 12/17/2022] Open
Abstract
The genetic landscape of Parkinson’s disease (PD) is characterised by rare high penetrance pathogenic variants causing familial disease, genetic risk factor variants driving PD risk in a significant minority in PD cases and high frequency, low penetrance variants, which contribute a small increase of the risk of developing sporadic PD. This knowledge has the potential to have a major impact in the clinical care of people with PD. We summarise these genetic influences and discuss the implications for therapeutics and clinical trial design.
Collapse
Affiliation(s)
- Jacob Oliver Day
- Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK;
| | - Stephen Mullin
- Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK;
- Department of Clinical and Movement Neurosciences, University College London Institute of Neurology, London WC1N 3BG, UK
- Correspondence:
| |
Collapse
|
31
|
Woo EG, Tayebi N, Sidransky E. Next-Generation Sequencing Analysis of GBA1: The Challenge of Detecting Complex Recombinant Alleles. Front Genet 2021; 12:684067. [PMID: 34234814 PMCID: PMC8255797 DOI: 10.3389/fgene.2021.684067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/27/2021] [Indexed: 01/23/2023] Open
Affiliation(s)
- Elizabeth G Woo
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Nahid Tayebi
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Ellen Sidransky
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
32
|
Toffoli M, Higgins A, Lee C, Koletsi S, Chen X, Eberle M, Sedlazeck FJ, Mullin S, Proukakis C, Schapira AH. Intronic Haplotypes in the GBA Gene Do Not Predict Age at Diagnosis of Parkinson's Disease. Mov Disord 2021; 36:1456-1460. [PMID: 34008887 PMCID: PMC8436748 DOI: 10.1002/mds.28616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND GBA mutations are a common risk factor for Parkinson's disease (PD). A recent study has suggested that GBA haplotypes, identified by intronic variants, can affect age at diagnosis of PD. OBJECTIVES In this study, we assess this hypothesis using long reads across a large cohort and the publicly available Accelerating Medicines Partnership-Parkinson's Disease (AMP-PD) cohort. METHODS We recruited a PD cohort through the Remote Assessment of Parkinsonism Supporting Ongoing Development of Interventions in Gaucher Disease study (RAPSODI) and sequenced GBA using Oxford Nanopore technology. Genetic and clinical data on the full AMP-PD cohort were obtained from the online portal of the consortium. RESULTS A total of 1417 participants were analyzed. There was no significant difference in age at PD diagnosis between the two main haplotypes of the GBA gene. CONCLUSIONS GBA haplotypes do not affect age at diagnosis of PD in the two independent cohorts studied. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
Collapse
Affiliation(s)
- Marco Toffoli
- Department of Clinical and Movement NeurosciencesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| | - Abigail Higgins
- Department of Clinical and Movement NeurosciencesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| | - Chiao Lee
- Department of Clinical and Movement NeurosciencesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| | - Sofia Koletsi
- Department of Clinical and Movement NeurosciencesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| | - Xiao Chen
- Research and Technology DevelopmentIllumina Inc.San DiegoCaliforniaUSA
| | - Michael Eberle
- Research and Technology DevelopmentIllumina Inc.San DiegoCaliforniaUSA
| | | | - Stephen Mullin
- Institute of Translational and Stratified MedicineUniversity of Plymouth Peninsula School of MedicinePlymouthUnited Kingdom
| | - Christos Proukakis
- Department of Clinical and Movement NeurosciencesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| | - Anthony H.V. Schapira
- Department of Clinical and Movement NeurosciencesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| |
Collapse
|
33
|
Sun X, Song L, Yang W, Zhang L, Liu M, Li X, Tian G, Wang W. Nanopore Sequencing and Its Clinical Applications. Methods Mol Biol 2021; 2204:13-32. [PMID: 32710311 DOI: 10.1007/978-1-0716-0904-0_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nanopore sequencing is a method for determining the order and modifications of DNA/RNA nucleotides by detecting the electric current variations when DNA/RNA oligonucleotides pass through the nanometer-sized hole (nanopore). Nanopore-based DNA analysis techniques have been commercialized by Oxford Nanopore Technologies, NabSys, and Sequenom, and widely used in scientific researches recently including human genomics, cancer, metagenomics, plant sciences, etc., moreover, it also has potential applications in the field of healthcare due to its fast turn-around time, portable and real-time data analysis. Those features make it a promising technology for the point-of-care testing (POCT) and its potential clinical applications are briefly discussed in this chapter.
Collapse
Affiliation(s)
- Xue Sun
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Lei Song
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Wenjuan Yang
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Lili Zhang
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Meng Liu
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Xiaoshuang Li
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Weiwei Wang
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China.
| |
Collapse
|
34
|
Kumar RD, Burrage LC, Bartos J, Ali S, Schmitt E, Nagamani SCS, LeMons C. A deep intronic variant is a common cause of OTC deficiency in individuals with previously negative genetic testing. Mol Genet Metab Rep 2021; 26:100706. [PMID: 33489762 PMCID: PMC7809430 DOI: 10.1016/j.ymgmr.2020.100706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 12/31/2022] Open
Abstract
Pathogenic variants in non-coding regions of genes encoding enzymes or transporters of the urea cycle can lead to urea cycle disorders (UCDs). However, not all commercially available testing platforms interrogate these regions. Here, we used a gene panel based on massively parallel sequencing (MPS) in 10 individuals with clinical or pedigree-based evidence of a proximal UCD but without a molecular confirmation of the diagnosis. We identified causal variant(s) in 5 of 10 individuals, including in 3 of 7 individuals in whom prior molecular testing was unrevealing. We show that a deep-intronic pathogenic variant in OTC, c.540+265G>A, is an important cause of ornithine transcarbamylase (OTC) deficiency.
Collapse
Affiliation(s)
- Runjun D Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Jan Bartos
- National Urea Cycle Disorders Foundation, Pasadena, CA, USA
| | - Saima Ali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Cynthia LeMons
- National Urea Cycle Disorders Foundation, Pasadena, CA, USA
| |
Collapse
|
35
|
Huang J, Pallotti S, Zhou Q, Kleber M, Xin X, King DA, Napolioni V. PERHAPS: Paired-End short Reads-based HAPlotyping from next-generation Sequencing data. Brief Bioinform 2020; 22:6025504. [PMID: 33285565 DOI: 10.1093/bib/bbaa320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/11/2020] [Accepted: 10/19/2020] [Indexed: 11/13/2022] Open
Abstract
The identification of rare haplotypes may greatly expand our knowledge in the genetic architecture of both complex and monogenic traits. To this aim, we developed PERHAPS (Paired-End short Reads-based HAPlotyping from next-generation Sequencing data), a new and simple approach to directly call haplotypes from short-read, paired-end Next Generation Sequencing (NGS) data. To benchmark this method, we considered the APOE classic polymorphism (*1/*2/*3/*4), since it represents one of the best examples of functional polymorphism arising from the haplotype combination of two Single Nucleotide Polymorphisms (SNPs). We leveraged the big Whole Exome Sequencing (WES) and SNP-array data obtained from the multi-ethnic UK BioBank (UKBB, N=48,855). By applying PERHAPS, based on piecing together the paired-end reads according to their FASTQ-labels, we extracted the haplotype data, along with their frequencies and the individual diplotype. Concordance rates between WES directly called diplotypes and the ones generated through statistical pre-phasing and imputation of SNP-array data are extremely high (>99%), either when stratifying the sample by SNP-array genotyping batch or self-reported ethnic group. Hardy-Weinberg Equilibrium tests and the comparison of obtained haplotype frequencies with the ones available from the 1000 Genome Project further supported the reliability of PERHAPS. Notably, we were able to determine the existence of the rare APOE*1 haplotype in two unrelated African subjects from UKBB, supporting its presence at appreciable frequency (approximatively 0.5%) in the African Yoruba population. Despite acknowledging some technical shortcomings, PERHAPS represents a novel and simple approach that will partly overcome the limitations in direct haplotype calling from short read-based sequencing.
Collapse
Affiliation(s)
- Jie Huang
- Department of Global Health, School of Public Health, Peking University, Beijing, China
| | - Stefano Pallotti
- Genetics and Animal Breeding Group, School of Pharmacy, University of Camerino, Italy
| | - Qianling Zhou
- Department of Maternal and Child Health, School of Public Health, Peking University, Beijing, China
| | - Marcus Kleber
- Department of Medicine, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany and at SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | | | - Daniel A King
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Valerio Napolioni
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| |
Collapse
|
36
|
Maestri S, Maturo MG, Cosentino E, Marcolungo L, Iadarola B, Fortunati E, Rossato M, Delledonne M. A Long-Read Sequencing Approach for Direct Haplotype Phasing in Clinical Settings. Int J Mol Sci 2020; 21:E9177. [PMID: 33271988 PMCID: PMC7731377 DOI: 10.3390/ijms21239177] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/20/2020] [Accepted: 11/27/2020] [Indexed: 11/17/2022] Open
Abstract
The reconstruction of individual haplotypes can facilitate the interpretation of disease risks; however, high costs and technical challenges still hinder their assessment in clinical settings. Second-generation sequencing is the gold standard for variant discovery but, due to the production of short reads covering small genomic regions, allows only indirect haplotyping based on statistical methods. In contrast, third-generation methods such as the nanopore sequencing platform developed by Oxford Nanopore Technologies (ONT) generate long reads that can be used for direct haplotyping, with fewer drawbacks. However, robust standards for variant phasing in ONT-based target resequencing efforts are not yet available. In this study, we presented a streamlined proof-of-concept workflow for variant calling and phasing based on ONT data in a clinically relevant 12-kb region of the APOE locus, a hotspot for variants and haplotypes associated with aging-related diseases and longevity. Starting with sequencing data from simple amplicons of the target locus, we demonstrated that ONT data allow for reliable single-nucleotide variant (SNV) calling and phasing from as little as 60 reads, although the recognition of indels is less efficient. Even so, we identified the best combination of ONT read sets (600) and software (BWA/Minimap2 and HapCUT2) that enables full haplotype reconstruction when both SNVs and indels have been identified previously using a highly-accurate sequencing platform. In conclusion, we established a rapid and inexpensive workflow for variant phasing based on ONT long reads. This allowed for the analysis of multiple samples in parallel and can easily be implemented in routine clinical practice, including diagnostic testing.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Marzia Rossato
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (S.M.); (M.G.M.); (E.C.); (L.M.); (B.I.); (E.F.); (M.D.)
| | | |
Collapse
|
37
|
Bruzek AK, Ravi K, Muruganand A, Wadden J, Babila CM, Cantor E, Tunkle L, Wierzbicki K, Stallard S, Dickson RP, Wolfe I, Mody R, Schwartz J, Franson A, Robertson PL, Muraszko KM, Maher CO, Garton HJL, Qin T, Koschmann C. Electronic DNA Analysis of CSF Cell-free Tumor DNA to Quantify Multi-gene Molecular Response in Pediatric High-grade Glioma. Clin Cancer Res 2020; 26:6266-6276. [PMID: 33087334 DOI: 10.1158/1078-0432.ccr-20-2066] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/07/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Pediatric high-grade glioma (pHGG) diagnosis portends poor prognosis and therapeutic monitoring remains difficult. Tumors release cell-free tumor DNA (cf-tDNA) into cerebrospinal fluid (CSF), allowing for potential detection of tumor-associated mutations by CSF sampling. We hypothesized that direct, electronic analysis of cf-tDNA with a handheld platform (Oxford Nanopore MinION) could quantify patient-specific CSF cf-tDNA variant allele fraction (VAF) with improved speed and limit of detection compared with established methods. EXPERIMENTAL DESIGN We performed ultra-short fragment (100-200 bp) PCR amplification of cf-tDNA for clinically actionable alterations in CSF and tumor samples from patients with pHGG (n = 12) alongside nontumor CSF (n = 6). PCR products underwent rapid amplicon-based sequencing by Oxford Nanopore Technology (Nanopore) with quantification of VAF. Additional comparison to next-generation sequencing (NGS) and droplet digital PCR (ddPCR) was performed. RESULTS Nanopore demonstrated 85% sensitivity and 100% specificity in CSF samples (n = 127 replicates) with 0.1 femtomole DNA limit of detection and 12-hour results, all of which compared favorably with NGS. Multiplexed analysis provided concurrent analysis of H3.3A (H3F3A) and H3C2 (HIST1H3B) mutations in a nonbiopsied patient and results were confirmed by ddPCR. Serial CSF cf-tDNA sequencing by Nanopore demonstrated correlation of radiological response on a clinical trial, with one patient showing dramatic multi-gene molecular response that predicted long-term clinical response. CONCLUSIONS Nanopore sequencing of ultra-short pHGG CSF cf-tDNA fragments is feasible, efficient, and sensitive with low-input samples thus overcoming many of the barriers restricting wider use of CSF cf-tDNA diagnosis and monitoring in this patient population.
Collapse
Affiliation(s)
- Amy K Bruzek
- Department of Neurosurgery, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Karthik Ravi
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Ashwath Muruganand
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jack Wadden
- Department of Computer Engineering, University of Michigan, Ann Arbor, Michigan
| | - Clarissa May Babila
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Evan Cantor
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Leo Tunkle
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Kyle Wierzbicki
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Stefanie Stallard
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Robert P Dickson
- Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Ian Wolfe
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Rajen Mody
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | | | - Andrea Franson
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Patricia L Robertson
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Karin M Muraszko
- Department of Neurosurgery, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Cormac O Maher
- Department of Neurosurgery, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Hugh J L Garton
- Department of Neurosurgery, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Tingtin Qin
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Carl Koschmann
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan.
| |
Collapse
|
38
|
Blauwendraat C, Reed X, Krohn L, Heilbron K, Bandres-Ciga S, Tan M, Gibbs JR, Hernandez DG, Kumaran R, Langston R, Bonet-Ponce L, Alcalay RN, Hassin-Baer S, Greenbaum L, Iwaki H, Leonard HL, Grenn FP, Ruskey JA, Sabir M, Ahmed S, Makarious MB, Pihlstrøm L, Toft M, van Hilten JJ, Marinus J, Schulte C, Brockmann K, Sharma M, Siitonen A, Majamaa K, Eerola-Rautio J, Tienari PJ, Pantelyat A, Hillis AE, Dawson TM, Rosenthal LS, Albert MS, Resnick SM, Ferrucci L, Morris CM, Pletnikova O, Troncoso J, Grosset D, Lesage S, Corvol JC, Brice A, Noyce AJ, Masliah E, Wood N, Hardy J, Shulman LM, Jankovic J, Shulman JM, Heutink P, Gasser T, Cannon P, Scholz SW, Morris H, Cookson MR, Nalls MA, Gan-Or Z, Singleton AB. Genetic modifiers of risk and age at onset in GBA associated Parkinson's disease and Lewy body dementia. Brain 2020; 143:234-248. [PMID: 31755958 DOI: 10.1093/brain/awz350] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/07/2019] [Accepted: 09/17/2019] [Indexed: 11/14/2022] Open
Abstract
Parkinson's disease is a genetically complex disorder. Multiple genes have been shown to contribute to the risk of Parkinson's disease, and currently 90 independent risk variants have been identified by genome-wide association studies. Thus far, a number of genes (including SNCA, LRRK2, and GBA) have been shown to contain variability across a spectrum of frequency and effect, from rare, highly penetrant variants to common risk alleles with small effect sizes. Variants in GBA, encoding the enzyme glucocerebrosidase, are associated with Lewy body diseases such as Parkinson's disease and Lewy body dementia. These variants, which reduce or abolish enzymatic activity, confer a spectrum of disease risk, from 1.4- to >10-fold. An outstanding question in the field is what other genetic factors that influence GBA-associated risk for disease, and whether these overlap with known Parkinson's disease risk variants. Using multiple, large case-control datasets, totalling 217 165 individuals (22 757 Parkinson's disease cases, 13 431 Parkinson's disease proxy cases, 622 Lewy body dementia cases and 180 355 controls), we identified 1691 Parkinson's disease cases, 81 Lewy body dementia cases, 711 proxy cases and 7624 controls with a GBA variant (p.E326K, p.T369M or p.N370S). We performed a genome-wide association study and analysed the most recent Parkinson's disease-associated genetic risk score to detect genetic influences on GBA risk and age at onset. We attempted to replicate our findings in two independent datasets, including the personal genetics company 23andMe, Inc. and whole-genome sequencing data. Our analysis showed that the overall Parkinson's disease genetic risk score modifies risk for disease and decreases age at onset in carriers of GBA variants. Notably, this effect was consistent across all tested GBA risk variants. Dissecting this signal demonstrated that variants in close proximity to SNCA and CTSB (encoding cathepsin B) are the most significant contributors. Risk variants in the CTSB locus were identified to decrease mRNA expression of CTSB. Additional analyses suggest a possible genetic interaction between GBA and CTSB and GBA p.N370S induced pluripotent cell-derived neurons were shown to have decreased cathepsin B expression compared to controls. These data provide a genetic basis for modification of GBA-associated Parkinson's disease risk and age at onset, although the total contribution of common genetics variants is not large. We further demonstrate that common variability at genes implicated in lysosomal function exerts the largest effect on GBA associated risk for disease. Further, these results have implications for selection of GBA carriers for therapeutic interventions.
Collapse
Affiliation(s)
- Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Xylena Reed
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Lynne Krohn
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | | - Sara Bandres-Ciga
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Manuela Tan
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Ravindran Kumaran
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Rebekah Langston
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Luis Bonet-Ponce
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Roy N Alcalay
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA.,Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Sharon Hassin-Baer
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel.,Movement Disorders Institute, Sheba Medical Center, Tel Hashomer, Israel.,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Lior Greenbaum
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel.,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Hirotaka Iwaki
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Francis P Grenn
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer A Ruskey
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Marya Sabir
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sarah Ahmed
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mary B Makarious
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Jacobus J van Hilten
- Department of Neurology, Leiden University Medical Center, Leiden, The Netherlands
| | - Johan Marinus
- Department of Neurology, Leiden University Medical Center, Leiden, The Netherlands
| | - Claudia Schulte
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tuebingen, Germany
| | - Kathrin Brockmann
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tuebingen, Germany
| | - Manu Sharma
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tubingen, Germany
| | - Ari Siitonen
- Institute of Clinical Medicine, Department of Neurology, University of Oulu, Oulu, Finland.,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Kari Majamaa
- Institute of Clinical Medicine, Department of Neurology, University of Oulu, Oulu, Finland.,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Johanna Eerola-Rautio
- Department of Neurology, Helsinki University Hospital, and Molecular Neurology, Research Programs Unit, Biomedicum, University of Helsinki, Helsinki, Finland
| | - Pentti J Tienari
- Department of Neurology, Helsinki University Hospital, and Molecular Neurology, Research Programs Unit, Biomedicum, University of Helsinki, Helsinki, Finland
| | | | - Alexander Pantelyat
- Neuroregeneration and Stem Cell Program, Institute for Cell Engineering, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Argye E Hillis
- Neuroregeneration and Stem Cell Program, Institute for Cell Engineering, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Program, Institute for Cell Engineering, Johns Hopkins University Medical Center, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Liana S Rosenthal
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Marilyn S Albert
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD, USA
| | - Christopher M Morris
- Newcastle Brain Tissue Resource, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Olga Pletnikova
- Department of Pathology (Neuropathology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Juan Troncoso
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA.,Department of Pathology (Neuropathology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Donald Grosset
- Department of Neurology, Institute of Neurological Sciences, Queen Elizabeth University Hospital, Glasgow, UK
| | - Suzanne Lesage
- Inserm U1127, Sorbonne Universités, UPMC Univ Paris 06 UMR S1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Jean-Christophe Corvol
- Inserm U1127, Sorbonne Universités, UPMC Univ Paris 06 UMR S1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Alexis Brice
- Inserm U1127, Sorbonne Universités, UPMC Univ Paris 06 UMR S1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Alastair J Noyce
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.,Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, UK
| | - Eliezer Masliah
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Nick Wood
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - John Hardy
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Lisa M Shulman
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joseph Jankovic
- Department of Neurology, Baylor College of Medicine, Houston, USA
| | - Joshua M Shulman
- Department of Neurology, Baylor College of Medicine, Houston, USA.,Departments of Molecular and Human Genetics and Neuroscience, Baylor College of Medicine, Houston, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, USA
| | - Peter Heutink
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tuebingen, Germany
| | - Thomas Gasser
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tuebingen, Germany
| | | | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.,Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Huw Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.,Data Tecnica International, Glen Echo, MD, USA
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
39
|
Majidian S, Sedlazeck FJ. PhaseME: Automatic rapid assessment of phasing quality and phasing improvement. Gigascience 2020; 9:giaa078. [PMID: 32706368 PMCID: PMC7379178 DOI: 10.1093/gigascience/giaa078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/28/2020] [Accepted: 07/01/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The detection of which mutations are occurring on the same DNA molecule is essential to predict their consequences. This can be achieved by phasing the genomic variations. Nevertheless, state-of-the-art haplotype phasing is currently a black box in which the accuracy and quality of the reconstructed haplotypes are hard to assess. FINDINGS Here we present PhaseME, a versatile method to provide insights into and improvement of sample phasing results based on linkage data. We showcase the performance and the importance of PhaseME by comparing phasing information obtained from Pacific Biosciences including both continuous long reads and high-quality consensus reads, Oxford Nanopore Technologies, 10x Genomics, and Illumina sequencing technologies. We found that 10x Genomics and Oxford Nanopore phasing can be significantly improved while retaining a high N50 and completeness of phase blocks. PhaseME generates reports and summary plots to provide insights into phasing performance and correctness. We observed unique phasing issues for each of the sequencing technologies, highlighting the necessity of quality assessments. PhaseME is able to decrease the Hamming error rate significantly by 22.4% on average across all 5 technologies. Additionally, a significant improvement is obtained in the reduction of long switch errors. Especially for high-quality consensus reads, the improvement is 54.6% in return for only a 5% decrease in phase block N50 length. CONCLUSIONS PhaseME is a universal method to assess the phasing quality and accuracy and improves the quality of phasing using linkage information. The package is freely available at https://github.com/smajidian/phaseme.
Collapse
Affiliation(s)
- Sina Majidian
- School of Electrical Engineering, Iran University of Science & Technology, Narmak, Tehran 1684613114, Iran
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| |
Collapse
|
40
|
Liau Y, Maggo S, Miller AL, Pearson JF, Kennedy MA, Cree SL. Nanopore sequencing of the pharmacogene CYP2D6 allows simultaneous haplotyping and detection of duplications. Pharmacogenomics 2020; 20:1033-1047. [PMID: 31559921 DOI: 10.2217/pgs-2019-0080] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: Long read sequencing offers the promise of overcoming some of the challenges in accurate genotyping of complex genes, along with the advantage of straightforward variant phasing. We have established methods for sequencing and haplotyping of the whole CYP2D6 gene using nanopore sequencing. Materials and methods: 32 samples covering various haplotypes including gene duplication were sequenced on the GridION platform. Results: Haplotypes of 52 alleles matched accurately to known star (*) allele subvariants, with the remaining 12 being assigned as new alleles, or new subvariants of known alleles. Duplicated alleles could be detected by analyzing the allelic balance. Conclusion: Nanopore sequencing of CYP2D6 offers a high throughput method for accurate haplotyping, detection of new variants and determination of duplicated alleles.
Collapse
Affiliation(s)
- Yusmiati Liau
- Department of Pathology & Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simran Maggo
- Department of Pathology & Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Allison L Miller
- Department of Pathology & Biomedical Science, University of Otago, Christchurch, New Zealand
| | - John F Pearson
- Department of Pathology & Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology & Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simone L Cree
- Department of Pathology & Biomedical Science, University of Otago, Christchurch, New Zealand
| |
Collapse
|
41
|
Gilpatrick T, Lee I, Graham JE, Raimondeau E, Bowen R, Heron A, Downs B, Sukumar S, Sedlazeck FJ, Timp W. Targeted nanopore sequencing with Cas9-guided adapter ligation. Nat Biotechnol 2020; 38:433-438. [PMID: 32042167 PMCID: PMC7145730 DOI: 10.1038/s41587-020-0407-5] [Citation(s) in RCA: 213] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/06/2020] [Indexed: 12/21/2022]
Abstract
Despite recent improvements in sequencing methods, there remains a need for assays that provide high sequencing depth and comprehensive variant detection. Current methods1-4 are limited by the loss of native modifications, short read length, high input requirements, low yield or long protocols. In the present study, we describe nanopore Cas9-targeted sequencing (nCATS), an enrichment strategy that uses targeted cleavage of chromosomal DNA with Cas9 to ligate adapters for nanopore sequencing. We show that nCATS can simultaneously assess haplotype-resolved single-nucleotide variants, structural variations and CpG methylation. We apply nCATS to four cell lines, to a cell-line-derived xenograft, and to normal and paired tumor/normal primary human breast tissue. Median sequencing coverage was 675× using a MinION flow cell and 34× using the smaller Flongle flow cell. The nCATS sequencing requires only ~3 μg of genomic DNA and can target a large number of loci in a single reaction. The method will facilitate the use of long-read sequencing in research and in the clinic.
Collapse
Affiliation(s)
- Timothy Gilpatrick
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Isac Lee
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | | | | | | | - Bradley Downs
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Molecular Biology and Genetics, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
42
|
Minervini CF, Cumbo C, Orsini P, Anelli L, Zagaria A, Specchia G, Albano F. Nanopore Sequencing in Blood Diseases: A Wide Range of Opportunities. Front Genet 2020; 11:76. [PMID: 32140171 PMCID: PMC7043087 DOI: 10.3389/fgene.2020.00076] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/23/2020] [Indexed: 12/20/2022] Open
Abstract
The molecular pathogenesis of hematological diseases is often driven by genetic and epigenetic alterations. Next-generation sequencing has considerably increased our genomic knowledge of these disorders becoming ever more widespread in clinical practice. In 2012 Oxford Nanopore Technologies (ONT) released the MinION, the first long-read nanopore-based sequencer, overcoming the main limits of short-reads sequences generation. In the last years, several nanopore sequencing approaches have been performed in various "-omic" sciences; this review focuses on the challenge to introduce ONT devices in the hematological field, showing advantages, disadvantages and future perspectives of this technology in the precision medicine era.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari, Italy
| |
Collapse
|
43
|
Malekkou A, Sevastou I, Mavrikiou G, Georgiou T, Vilageliu L, Moraitou M, Michelakakis H, Prokopiou C, Drousiotou A. A novel mutation deep within intron 7 of the GBA gene causes Gaucher disease. Mol Genet Genomic Med 2020; 8:e1090. [PMID: 31943857 PMCID: PMC7057115 DOI: 10.1002/mgg3.1090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Mutations in the GBA gene that encodes the lysosomal enzyme acid β-glucocerebrosidase cause Gaucher disease (GD), the most common lysosomal storage disorder. Most of the mutations are missense/nonsense, however, a few splicing mutations within or close to conserved consensus donor or acceptor splice sites have also been described. The aim of the study was to identify the mutation(s) in a Cypriot patient with type I GD. METHODS The genomic DNA of the proband was screened for nine common mutations using Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. All exons and exon-intron boundaries, and the 5'UTR and 3'UTR regions of the GBA gene, were investigated by Sanger sequencing. RNA analysis was performed using standard procedures, and the abnormal transcript was further cloned into pGEM-T-Easy plasmid vector and sequenced. The relevant intronic region was further sequenced by the Sanger method to identify the genetic variant. RESULTS A novel point mutation, g.12599C > A (c.999 + 242C > A), was detected deep in intron 7 of the GBA gene. This type of mutation has been previously described for other diseases but this is the first time, as far as we know, that it is described for GD. This mutation creates a new donor splice site leading to aberrant splicing and resulting in the insertion of the first 239nt of intron 7 as a pseudoexon in the mRNA, creating a premature stop codon. CONCLUSION This study expands the mutation spectrum of GD and highlights the importance of RNA sequencing for the molecular diagnosis of patients bearing mutations in nonexonic regions.
Collapse
Affiliation(s)
- Anna Malekkou
- Department of Biochemical Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Ioanna Sevastou
- Department of Biochemical Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Gavriella Mavrikiou
- Department of Biochemical Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Theodoros Georgiou
- Department of Biochemical Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Lluisa Vilageliu
- Department of Genetics, Faculty of Biology, Universitat de Barcelona, IBUB, CIBERER, Barcelona, Spain
| | - Marina Moraitou
- Department of Enzymology and Cellular Function, Institute of Child Health, Athens, Greece
| | - Helen Michelakakis
- Department of Enzymology and Cellular Function, Institute of Child Health, Athens, Greece
| | | | - Anthi Drousiotou
- Department of Biochemical Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| |
Collapse
|
44
|
Sakamoto Y, Sereewattanawoot S, Suzuki A. A new era of long-read sequencing for cancer genomics. J Hum Genet 2020; 65:3-10. [PMID: 31474751 PMCID: PMC6892365 DOI: 10.1038/s10038-019-0658-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/19/2019] [Accepted: 07/21/2019] [Indexed: 02/08/2023]
Abstract
Cancer is a disease largely caused by genomic aberrations. Utilizing many rapidly emerging sequencing technologies, researchers have studied cancer genomes to understand the molecular statuses of cancer cells and to reveal their vulnerabilities, such as driver mutations or gene expression. Long-read technologies enable us to identify and characterize novel types of cancerous mutations, including complicated structural variants in haplotype resolution. In this review, we introduce three representative platforms for long-read sequencing and research trends of cancer genomics with long-read data. Further, we describe that aberrant transcriptome and epigenome statuses, namely, fusion transcripts, as well as aberrant transcript isoforms and the phase information of DNA methylation, are able to be elucidated by long-read sequencers. Long-read sequencing may shed light on novel types of aberrations in cancer genomics that are being missed by conventional short-read sequencing analyses.
Collapse
Affiliation(s)
- Yoshitaka Sakamoto
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Sarun Sereewattanawoot
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
| |
Collapse
|
45
|
Graham OEE, Pitcher TL, Liau Y, Miller AL, Dalrymple-Alford JC, Anderson TJ, Kennedy MA. Nanopore sequencing of the glucocerebrosidase (GBA) gene in a New Zealand Parkinson's disease cohort. Parkinsonism Relat Disord 2019; 70:36-41. [PMID: 31809948 DOI: 10.1016/j.parkreldis.2019.11.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Bi-allelic mutations in the gene for glucocerebrosidase (GBA) cause Gaucher disease, an autosomal recessive lysosomal storage disorder. Gaucher disease causing GBA mutations in the heterozygous state are also high risk factors for Parkinson's disease (PD). GBA analysis is challenging due to a related pseudogene and structural variations (SVs) that can occur at this locus. We have applied and refined a recently developed nanopore DNA sequencing method to analyze GBA variants in a clinically assessed New Zealand longitudinal cohort of PD. METHOD We examined amplicons encompassing the coding region of GBA (8.9 kb) from 229 PD cases and 50 healthy controls using the GridION nanopore sequencing platform, and Sanger validation. RESULTS We detected 23 variants in 21 PD cases (9.2% of patients). We detected modest PD risk variant p.N409S (rs76763715) in one case, p.E365K (rs2230288) in 12 cases, and p.T408 M (rs75548401) in seven cases, one of whom also had p.E365K. We additionally detected the possible risk variants p.R78C (rs146774384) in one case, p.D179H (rs147138516) in one case which occurred on the same haplotype as p.E365K, and one novel variant c.335C > T or p.(L335 = ), that potentially impacts splicing of GBA transcripts. Additionally, we found a higher prevalence of dementia among patients with GBA variants. CONCLUSION This work confirmed the utility of nanopore sequencing as a high-throughput method to identify known and novel GBA variants, and to assign precise haplotypes. Our observations may contribute to improved understanding of the effects of variants on disease pathogenesis, and to the development of more targeted treatments.
Collapse
Affiliation(s)
- O E E Graham
- Gene Structure and Function Laboratory, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - T L Pitcher
- Department of Medicine, University of Otago, Christchurch, New Zealand; New Zealand Brain Research Institute, Christchurch, New Zealand
| | - Y Liau
- Gene Structure and Function Laboratory, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - A L Miller
- Gene Structure and Function Laboratory, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - J C Dalrymple-Alford
- New Zealand Brain Research Institute, Christchurch, New Zealand; School of Psychology, Speech and Hearing, University of Canterbury, Christchurch, New Zealand
| | - T J Anderson
- Department of Medicine, University of Otago, Christchurch, New Zealand; New Zealand Brain Research Institute, Christchurch, New Zealand; Neurology Department, Christchurch Hospital, Christchurch, New Zealand
| | - M A Kennedy
- Gene Structure and Function Laboratory, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| |
Collapse
|
46
|
Mahmoud M, Gobet N, Cruz-Dávalos DI, Mounier N, Dessimoz C, Sedlazeck FJ. Structural variant calling: the long and the short of it. Genome Biol 2019; 20:246. [PMID: 31747936 PMCID: PMC6868818 DOI: 10.1186/s13059-019-1828-7] [Citation(s) in RCA: 309] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/19/2019] [Indexed: 02/08/2023] Open
Abstract
Recent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases, regulation of gene expression, ethnic diversity, and large-scale chromosome evolution-giving rise to the differences within populations and among species. Nevertheless, characterizing SVs and determining the optimal approach for a given experimental design remains a computational and scientific challenge. Multiple approaches have emerged to target various SV classes, zygosities, and size ranges. Here, we review these approaches with respect to their ability to infer SVs across the full spectrum of large, complex variations and present computational methods for each approach.
Collapse
Affiliation(s)
- Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, USA
| | - Nastassia Gobet
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Diana Ivette Cruz-Dávalos
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Ninon Mounier
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Christophe Dessimoz
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London, UK.
- Department of Computer Science, University College London, London, UK.
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, USA.
| |
Collapse
|
47
|
Li SJ, Zheng WW, Sun MY, Qi JY, Jiang B. [Clinical features and genetic manifestations of two families with Gaucher's disease]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2019; 40:774-776. [PMID: 31648483 PMCID: PMC7342435 DOI: 10.3760/cma.j.issn.0253-2727.2019.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Indexed: 11/05/2022]
Affiliation(s)
- S J Li
- Department of Hematology, Tianjin Fourth Central Hospital, Tianjin 300140, China
| | - W W Zheng
- GCP Center, Institute of Hematology & Blood Diseases Hospital, CAMS & PUMC, Tianjin 300020, China
| | - M Y Sun
- GCP Center, Institute of Hematology & Blood Diseases Hospital, CAMS & PUMC, Tianjin 300020, China
| | - J Y Qi
- GCP Center, Institute of Hematology & Blood Diseases Hospital, CAMS & PUMC, Tianjin 300020, China
| | - B Jiang
- GCP Center, Institute of Hematology & Blood Diseases Hospital, CAMS & PUMC, Tianjin 300020, China
| |
Collapse
|
48
|
De Coster W, Van Broeckhoven C. Newest Methods for Detecting Structural Variations. Trends Biotechnol 2019; 37:973-982. [DOI: 10.1016/j.tibtech.2019.02.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 01/28/2023]
|
49
|
Abstract
The practice of genomic medicine stands to revolutionize our approach to medical care, and to realize this goal will require discovery of the relationship between rare variation at each of the ~ 20,000 protein-coding genes and their consequent impact on individual health and expression of Mendelian disease. The step-wise evolution of broad-based, genome-wide cytogenetic and molecular genomic testing approaches (karyotyping, chromosomal microarray [CMA], exome sequencing [ES]) has driven much of the rare disease discovery to this point, with genome sequencing representing the newest member of this team. Each step has brought increased sensitivity to interrogate individual genomic variation in an unbiased method that does not require clinical prediction of the locus or loci involved. Notably, each step has also brought unique limitations in variant detection, for example, the low sensitivity of ES for detection of triploidy, and of CMA for detection of copy neutral structural variants. The utility of genome sequencing (GS) as a clinical molecular diagnostic test, and the increased sensitivity afforded by addition of long-read sequencing or other -omics technologies such as RNAseq or metabolomics, are not yet fully explored, though recent work supports improved sensitivity of variant detection, at least in a subset of cases. The utility of GS will also rely upon further elucidation of the complexities of genetic and allelic heterogeneity, multilocus rare variation, and the impact of rare and common variation at a locus, as well as advances in functional annotation of identified variants. Much discovery remains to be done before the potential utility of GS is fully appreciated.
Collapse
Affiliation(s)
- Jennifer E Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, T603, Houston, TX, 77030, USA.
| |
Collapse
|
50
|
Lukas J, Hermann A, Giese AK. Silent but significant - A synonymous SNV alters prognosis in Pompe disease. EBioMedicine 2019; 43:20-21. [PMID: 30982766 PMCID: PMC6562060 DOI: 10.1016/j.ebiom.2019.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 04/05/2019] [Indexed: 11/19/2022] Open
Affiliation(s)
- Jan Lukas
- Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany.
| | - Andreas Hermann
- Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany; German Center for Neurodegenerative Diseases (DZNE) Rostock/Greifswald, 18147 Rostock, Germany
| | - Anne-Katrin Giese
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| |
Collapse
|