1
|
LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Allan TJ, Zalusky MPG, Goffena J, Gibson SB, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel MN, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Gupta S, Jones EA, Weisz-Hubshman M, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT, Neale G, Carvill GL, Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, Mefford HC. Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement. Nat Commun 2024; 15:6524. [PMID: 39107278 PMCID: PMC11303402 DOI: 10.1038/s41467-024-50159-6] [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: 10/20/2023] [Accepted: 06/28/2024] [Indexed: 08/09/2024] Open
Abstract
Sequence-based genetic testing identifies causative variants in ~ 50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. We interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 582 individuals with genetically unsolved DEEs. We identify rare differentially methylated regions (DMRs) and explanatory episignatures to uncover causative and candidate genetic etiologies in 12 individuals. Using long-read sequencing, we identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and four copy number variants. We also identify pathogenic variants associated with episignatures. Finally, we refine the CHD2 episignature using an 850 K methylation array and bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate variants as 2% (12/582) for unsolved DEE cases.
Collapse
Affiliation(s)
- Christy W LaFlamme
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cassandra Rastin
- Department of Pathology & Laboratory Medicine, Western University, London, ON, N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Soham Sengupta
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Helen E Pennington
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Mathematics & Statistics, Rhodes College, Memphis, TN, 38112, USA
| | - Sophie J Russ-Hall
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Amy L Schneider
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Emily S Bonkowski
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Edith P Almanza Fuerte
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Talia J Allan
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Miranda Perez-Galey Zalusky
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Joy Goffena
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Sophia B Gibson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Denis M Nyaga
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Nico Lieffering
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Malavika Hebbar
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Emily V Walker
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Daniel Darnell
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Scott R Olsen
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mohamed Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Dorit Lev
- Institute of Medical Genetics, Wolfson Medical Center, Holon, 58100, Israel
| | - Tally Lerman-Sagie
- Fetal Neurology Clinic, Pediatric Neurology Unit, Wolfson Medical Center, Holon, 58100, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Kristen L Park
- Departments of Pediatrics and Neurology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Marielle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Gerarda Cappuccio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Nicolas Chatron
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | - Leigh Demain
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - David Genevieve
- Montpellier University, Inserm Unit 1183, Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndrome, Clinical Genetic Department, CHU Montpellier, Montpellier, France
| | - Gaetan Lesca
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, NSW, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Damien Sanlaville
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | | | - Sachin Gupta
- TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Elizabeth A Jones
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Monika Weisz-Hubshman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Genetic Department, Houston, TX, 77030, USA
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, 77030, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC, Australia
- Florey Institute and Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Bekim Sadikovic
- Department of Pathology & Laboratory Medicine, Western University, London, ON, N5A 3K7, Canada.
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada.
| | - Heather C Mefford
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| |
Collapse
|
2
|
Zhang Y, Bi C, Nadeef S, Maddirevula S, Alqahtani M, Alkuraya FS, Li M. NanoRanger enables rapid single-base-pair resolution of genomic disorders. MED 2024:S2666-6340(24)00262-9. [PMID: 39047733 DOI: 10.1016/j.medj.2024.07.003] [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: 11/12/2023] [Revised: 04/13/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Delineating base-resolution breakpoints of complex rearrangements is crucial for an accurate clinical understanding of pathogenic variants and for carrier screening within family networks or the broader population. However, despite advances in genetic testing using short-read sequencing (SRS), this task remains costly and challenging. METHODS This study addresses the challenges of resolving missing disease-causing breakpoints in complex genomic disorders with suspected homozygous rearrangements by employing multiple long-read sequencing (LRS) strategies, including a novel and efficient strategy named nanopore-based rapid acquisition of neighboring genomic regions (NanoRanger). NanoRanger does not require large amounts of ultrahigh-molecular-weight DNA and stands out for its ease of use and rapid acquisition of large genomic regions of interest with deep coverage. FINDINGS We describe a cohort of 16 familial cases, each harboring homozygous rearrangements that defied breakpoint determination by SRS and optical genome mapping (OGM). NanoRanger identified the breakpoints with single-base-pair resolution, enabling accurate determination of the carrier status of unaffected family members as well as the founder nature of these genomic lesions and their frequency in the local population. The resolved breakpoints revealed that repetitive DNA, gene regulatory elements, and transcription activity contribute to genome instability in these novel recessive rearrangements. CONCLUSIONS Our data suggest that NanoRanger greatly improves the success rate of resolving base-resolution breakpoints of complex genomic disorders and expands access to LRS for the benefit of patients with Mendelian disorders. FUNDING M.L. is supported by KAUST Baseline Award no. BAS/1/1080-01-01 and KAUST Research Translation Fund Award no. REI/1/4742-01.
Collapse
Affiliation(s)
- Yingzi Zhang
- Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Chongwei Bi
- Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Seba Nadeef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
| | - Mo Li
- Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Bioengineering Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| |
Collapse
|
3
|
Ohori S, Numabe H, Mitsuhashi S, Tsuchida N, Uchiyama Y, Koshimizu E, Hamanaka K, Misawa K, Miyatake S, Mizuguchi T, Fujita A, Matsumoto N. Complex chromosomal 6q rearrangements revealed by combined long-molecule genomics technologies. Genomics 2024; 116:110894. [PMID: 39019410 DOI: 10.1016/j.ygeno.2024.110894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 06/19/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024]
Abstract
Technologies for detecting structural variation (SV) have advanced with the advent of long-read sequencing, which enables the validation of SV at a nucleotide level. Optical genome mapping (OGM), a technology based on physical mapping, can also provide comprehensive SVs analysis. We applied long-read whole genome sequencing (LRWGS) to accurately reconstruct breakpoint (BP) segments in a patient with complex chromosome 6q rearrangements that remained elusive by conventional karyotyping. Although all BPs were precisely identified by LRWGS, there were two possible ways to construct the BP segments in terms of their orders and orientations. Thus, we also used OGM analysis. Notably, OGM recognized entire inversions exceeding 500 kb in size, which LRWGS could not characterize. Consequently, here we successfully unveil the full genomic structure of this complex chromosomal 6q rearrangement and cryptic SVs through combined long-molecule genomic analyses, showcasing how LRWGS and OGM can complement each other in SV analysis.
Collapse
Affiliation(s)
- Sachiko Ohori
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Department of Genetics, Kitasato University Hospital, Sagamihara 252-0375, Japan
| | - Hironao Numabe
- Department of Pediatrics, Tokyo Metropolitan Kita Medical Rehabilitation Center for the Handicapped, Kita-ku, Tokyo, 114-0033, Japan
| | - Satomi Mitsuhashi
- Department of Neurology, St.Marianna University School of Medicine Hospital, Kawasaki 216-8511, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama 236-0004, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; RIKEN Center for Advanced Intelligence Project, Chuo-ku, Tokyo 103-0027, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Department of Clinical Genetics, Yokohama City University Hospital, Yokohama 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama 236-0004, Japan; Department of Clinical Genetics, Yokohama City University Hospital, Yokohama 236-0004, Japan.
| |
Collapse
|
4
|
Kramer M, Goodwin S, Wappel R, Borio M, Offit K, Feldman DR, Stadler ZK, McCombie WR. Exploring the genetic and epigenetic underpinnings of early-onset cancers: Variant prioritization for long read whole genome sequencing from family cancer pedigrees. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601096. [PMID: 39005350 PMCID: PMC11244929 DOI: 10.1101/2024.06.27.601096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Despite significant advances in our understanding of genetic cancer susceptibility, known inherited cancer predisposition syndromes explain at most 20% of early-onset cancers. As early-onset cancer prevalence continues to increase, the need to assess previously inaccessible areas of the human genome, harnessing a trio or quad family-based architecture for variant filtration, may reveal further insights into cancer susceptibility. To assess a broader spectrum of variation than can be ascertained by multi-gene panel sequencing, or even whole genome sequencing with short reads, we employed long read whole genome sequencing using an Oxford Nanopore Technology (ONT) PromethION of 3 families containing an early-onset cancer proband using a trio or quad family architecture. Analysis included 2 early-onset colorectal cancer family trios and one quad consisting of two siblings with testicular cancer, all with unaffected parents. Structural variants (SVs), epigenetic profiles and single nucleotide variants (SNVs) were determined for each individual, and a filtering strategy was employed to refine and prioritize candidate variants based on the family architecture. The family architecture enabled us to focus on inapposite variants while filtering variants shared with the unaffected parents, significantly decreasing background variation that can hamper identification of potentially disease causing differences. Candidate d e novo and compound heterozygous variants were identified in this way. Gene expression, in matched neoplastic and pre-neoplastic lesions, was assessed for one trio. Our study demonstrates the feasibility of a streamlined analysis of genomic variants from long read ONT whole genome sequencing and a way to prioritize key variants for further evaluation of pathogenicity, while revealing what may be missing from panel based analyses.
Collapse
|
5
|
Ou J, Wang J, Sun J, Ni M, Meng Q, Ding J, Fan H, Feng S, Huang Y, Li H, Fei J. Analysis of Preimplantation and Clinical Outcomes of Two Cases by Oxford Nanopore Sequencing. Reprod Sci 2024; 31:2123-2134. [PMID: 38347380 DOI: 10.1007/s43032-024-01470-6] [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: 09/26/2023] [Accepted: 01/19/2024] [Indexed: 07/03/2024]
Abstract
It is challenging to distinguish embryos with a balanced translocation karyotype from a normal karyotype by existing conventional genetic testing methods. However, in germ-cell gamete generation, chromosome exchange and separation through cell meiosis form a different proportion of unbalanced gametes. Adverse birth events may occur, such as repeated miscarriages and fetal birth defects. In this study, the exact breakpoints of structural variation (SV) from two balanced translocation carrier families by using Nanopore long reads sequencing technology were obtained, and haplotype analysis and Sanger verified the accuracy of the detection results, confirming the application value of the Nanopore sequencing technology in the detection of balanced translocation before embryo implantation. Nanopore long-read sequencing was performed to find the precise breakpoint of chromosome-balanced translocation carriers. The breakpoints were subsequently verified by designing primers across the breakpoints and Sanger sequencing. Haplotype linkage analysis of SNPs which can be linked by a read block of families around the breakpoint regions was followed. After frozen (-thawed) embryo transfer (FET), prenatal cytogenetic analysis of amniotic fluid cells confirmed the predicted karyotypes from the transferred embryos. The presence of breakpoints was detected in three embryos of patient 1. No breakpoints were detected in either embryo of patient 2. One balanced translocated embryo from patient 1 and one normal euploid embryo from patient 2 were transplanted back into the patients, and amniotic fluid cells were analyzed for the karyotype of fetuses. The results were entirely consistent with the fetal karyotype. And through late follow-up, both patients successfully had a live birth fetus. The breakpoint location of the balanced chromosome translocation can be accurately found by Nanopore sequencing. The haplotype of carriers can be successfully constructed by Nanopore and sanger sequencing confirmed that the results were accurate. This is very advantageous for preimplantation genetic testing for chromosomal structural rearrangements (PGT-SR) detection in the families without proband.
Collapse
Affiliation(s)
- Jian Ou
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | | | - Jian Sun
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Mengxia Ni
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - QingXia Meng
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Jie Ding
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Haiyang Fan
- Peking Jabrehoo Med-Tech Co., Ltd, Beijing, China
| | - Shaohua Feng
- Peking Jabrehoo Med-Tech Co., Ltd, Beijing, China
| | - Yining Huang
- Peking Jabrehoo Med-Tech Co., Ltd, Beijing, China
| | - Hong Li
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China.
| | - Jia Fei
- Peking Jabrehoo Med-Tech Co., Ltd, Beijing, China.
| |
Collapse
|
6
|
Haffener PE, Al-Riyami AZ, Al-Zadjali S, Al-Rawahi M, Al Hosni S, Al Marhoobi A, Al Sheriyani A, Leffler EM. Characterization of Blood Group Variants in an Omani Population by Comparison of Whole Genome Sequencing and Serology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599396. [PMID: 38948735 PMCID: PMC11212902 DOI: 10.1101/2024.06.17.599396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Although blood group variation was first described over a century ago, our understanding of the genetic variation affecting antigenic expression on the red blood cell surface in many populations is lacking. This deficit limits the ability to accurately type patients, especially as serological testing is not available for all described blood groups, and targeted genotyping panels may lack rare or population-specific variants. Here, we perform serological assays across 24 antigens and whole genome sequencing on 100 Omanis, a population underrepresented in genomic databases. We inferred blood group phenotypes using the most commonly typed genetic variants. The comparison of serological to inferred phenotypes resulted in an average concordance of 96.9%. Among the 22 discordances, we identify seven known variants in four blood groups that, to our knowledge, have not been previously reported in Omanis. Incorporating these variants for phenotype inference, concordance increases to 98.8%. Additionally, we describe five candidate variants in the Lewis, Lutheran, MNS, and P1 blood groups that may affect antigenic expression, although further functional confirmation is required. Notably, we identify several blood group alleles most common in African populations, likely introduced to Oman by gene flow over the last thousand years. These findings highlight the need to evaluate individual populations and their population history when considering variants to include in genotype panels for blood group typing. This research will inform future work in blood banks and transfusion services.
Collapse
Affiliation(s)
- Paige E. Haffener
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Arwa Z. Al-Riyami
- Department of Hematology, Sultan Qaboos University Hospital, University Medical City, Muscat, Oman
| | - Shoaib Al-Zadjali
- Sultan Qaboos Comprehensive Cancer Center, University Medical City, Muscat, Oman
| | - Mohammed Al-Rawahi
- Department of Hematology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Saif Al Hosni
- Department of Hematology, Sultan Qaboos University Hospital, University Medical City, Muscat, Oman
| | - Ali Al Marhoobi
- Department of Hematology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | | | - Ellen M. Leffler
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT, USA
| |
Collapse
|
7
|
Jiao K, Cheng N, Huan X, Zhang J, Ding Y, Luan X, Liu L, Wang X, Zhu B, Du K, Fan J, Gao M, Xia X, Wang N, Wang T, Xi J, Luo S, Lu J, Zhao C, Yue D, Zhu W. Pseudoexon activation by deep intronic variation in GNE myopathy with thrombocytopenia. Muscle Nerve 2024; 69:708-718. [PMID: 38558464 DOI: 10.1002/mus.28092] [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: 07/25/2023] [Revised: 03/07/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024]
Abstract
INTRODUCTION/AIMS GNE myopathy is a rare autosomal recessive disorder caused by pathogenic variants in the GNE gene, which is essential for the sialic acid biosynthesis pathway. Although over 300 GNE variants have been reported, some patients remain undiagnosed with monoallelic pathogenic variants. This study aims to analyze the entire GNE genomic region to identify novel pathogenic variants. METHODS Patients with clinically compatible GNE myopathy and monoallelic pathogenic variants in the GNE gene were enrolled. The other GNE pathogenic variant was verified using comprehensive methods including exon 2 quantitative polymerase chain reaction and nanopore long-read single-molecule sequencing (LRS). RESULTS A deep intronic GNE variant, c.862+870C>T, was identified in nine patients from eight unrelated families. This variant generates a cryptic splice site, resulting in the activation of a novel pseudoexon between exons 5 and 6. It results in the insertion of an extra 146 nucleotides into the messengerRNA (mRNA), which is predicted to result in a truncated humanGNE1(hGNE1) protein. Peanut agglutinin(PNA) lectin staining of muscle tissues showed reduced sialylation of mucin O-glycans on sarcolemmal glycoproteins. Notably, a third of patients with the c.862+870C>T variant exhibited thrombocytopenia. A common core haplotype harboring the deep intronic GNE variant was found in all these patients. DISCUSSION The transcript with pseudoexon activation potentially affects sialic acid biosynthesis via nonsense-mediated mRNA decay, or resulting in a truncated hGNE1 protein, which interferes with normal enzyme function. LRS is expected to be more frequently incorporated in genetic analysis given its efficacy in detecting hard-to-find pathogenic variants.
Collapse
Affiliation(s)
- Kexin Jiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Nachuan Cheng
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Xiao Huan
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Jialong Zhang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Yu Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xinghua Luan
- Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - LingChun Liu
- The First People's Hospital of Yunnan Province, Kunming, China
| | - Xilu Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Bochen Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Kunzhao Du
- Jinshan Hospital Center for Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Jiale Fan
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, The Institutes of Brain Science, Shanghai, China
| | - Mingshi Gao
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xingyu Xia
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Ningning Wang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Tao Wang
- Department of Anesthesiology, Zhongshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Sushan Luo
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Jiahong Lu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Dongyue Yue
- Department of Neurology, Jing'an District Center Hospital of Shanghai, Shanghai, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| |
Collapse
|
8
|
Parmar JM, Laing NG, Kennerson ML, Ravenscroft G. Genetics of inherited peripheral neuropathies and the next frontier: looking backwards to progress forwards. J Neurol Neurosurg Psychiatry 2024:jnnp-2024-333436. [PMID: 38744462 DOI: 10.1136/jnnp-2024-333436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Inherited peripheral neuropathies (IPNs) encompass a clinically and genetically heterogeneous group of disorders causing length-dependent degeneration of peripheral autonomic, motor and/or sensory nerves. Despite gold-standard diagnostic testing for pathogenic variants in over 100 known associated genes, many patients with IPN remain genetically unsolved. Providing patients with a diagnosis is critical for reducing their 'diagnostic odyssey', improving clinical care, and for informed genetic counselling. The last decade of massively parallel sequencing technologies has seen a rapid increase in the number of newly described IPN-associated gene variants contributing to IPN pathogenesis. However, the scarcity of additional families and functional data supporting variants in potential novel genes is prolonging patient diagnostic uncertainty and contributing to the missing heritability of IPNs. We review the last decade of IPN disease gene discovery to highlight novel genes, structural variation and short tandem repeat expansions contributing to IPN pathogenesis. From the lessons learnt, we provide our vision for IPN research as we anticipate the future, providing examples of emerging technologies, resources and tools that we propose that will expedite the genetic diagnosis of unsolved IPN families.
Collapse
Affiliation(s)
- Jevin M Parmar
- Rare Disease Genetics and Functional Genomics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Nigel G Laing
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Preventive Genetics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, New South Wales, Australia
| | - Gianina Ravenscroft
- Rare Disease Genetics and Functional Genomics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| |
Collapse
|
9
|
Kumar KR, Cowley MJ, Davis RL. The Next, Next-Generation of Sequencing, Promising to Boost Research and Clinical Practice. Semin Thromb Hemost 2024. [PMID: 38733978 DOI: 10.1055/s-0044-1786756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Affiliation(s)
- Kishore R Kumar
- Molecular Medicine Laboratory and Department of Neurology, Concord Repatriation General Hospital, Concord Clinical School, University of Sydney, Concord, NSW, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Randwick, NSW, Australia
| | - Mark J Cowley
- School of Clinical Medicine, UNSW Sydney, Randwick, NSW, Australia
- Children's Cancer Institute, UNSW Sydney, Randwick, NSW, Australia
| | - Ryan L Davis
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Neurogenetics Research Group, Kolling Institute, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney and Northern Sydney Local Health District, St Leonards, NSW, Australia
| |
Collapse
|
10
|
Dias KR, Shrestha R, Schofield D, Evans CA, O'Heir E, Zhu Y, Zhang F, Standen K, Weisburd B, Stenton SL, Sanchis-Juan A, Brand H, Talkowski ME, Ma A, Ghedia S, Wilson M, Sandaradura SA, Smith J, Kamien B, Turner A, Bakshi M, Adès LC, Mowat D, Regan M, McGillivray G, Savarirayan R, White SM, Tan TY, Stark Z, Brown NJ, Pérez-Jurado LA, Krzesinski E, Hunter MF, Akesson L, Fennell AP, Yeung A, Boughtwood T, Ewans LJ, Kerkhof J, Lucas C, Carey L, French H, Rapadas M, Stevanovski I, Deveson IW, Cliffe C, Elakis G, Kirk EP, Dudding-Byth T, Fletcher J, Walsh R, Corbett MA, Kroes T, Gecz J, Meldrum C, Cliffe S, Wall M, Lunke S, North K, Amor DJ, Field M, Sadikovic B, Buckley MF, O'Donnell-Luria A, Roscioli T. Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort. Genet Med 2024; 26:101076. [PMID: 38258669 DOI: 10.1016/j.gim.2024.101076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
PURPOSE Genome sequencing (GS)-specific diagnostic rates in prospective tightly ascertained exome sequencing (ES)-negative intellectual disability (ID) cohorts have not been reported extensively. METHODS ES, GS, epigenetic signatures, and long-read sequencing diagnoses were assessed in 74 trios with at least moderate ID. RESULTS The ES diagnostic yield was 42 of 74 (57%). GS diagnoses were made in 9 of 32 (28%) ES-unresolved families. Repeated ES with a contemporary pipeline on the GS-diagnosed families identified 8 of 9 single-nucleotide variations/copy-number variations undetected in older ES, confirming a GS-unique diagnostic rate of 1 in 32 (3%). Episignatures contributed diagnostic information in 9% with GS corroboration in 1 of 32 (3%) and diagnostic clues in 2 of 32 (6%). A genetic etiology for ID was detected in 51 of 74 (69%) families. Twelve candidate disease genes were identified. Contemporary ES followed by GS cost US$4976 (95% CI: $3704; $6969) per diagnosis and first-line GS at a cost of $7062 (95% CI: $6210; $8475) per diagnosis. CONCLUSION Performing GS only in ID trios would be cost equivalent to ES if GS were available at $2435, about a 60% reduction from current prices. This study demonstrates that first-line GS achieves higher diagnostic rate than contemporary ES but at a higher cost.
Collapse
Affiliation(s)
- Kerith-Rae Dias
- Neuroscience Research Australia, Sydney, NSW, Australia; Prince of Wales Clinical School, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Rupendra Shrestha
- Centre for Economic Impacts of Genomic Medicine, Macquarie Business School, Macquarie University, Sydney, NSW, Australia
| | - Deborah Schofield
- Centre for Economic Impacts of Genomic Medicine, Macquarie Business School, Macquarie University, Sydney, NSW, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Emily O'Heir
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ying Zhu
- Neuroscience Research Australia, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia; The Genetics of Learning Disability Service, Waratah, NSW, Australia
| | - Futao Zhang
- Neuroscience Research Australia, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Krystle Standen
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sarah L Stenton
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Alan Ma
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia; Specialty of Genomic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Sondy Ghedia
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, NSW, Australia; Northern Clinical School, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia
| | - Sarah A Sandaradura
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia; Disciplines of Child and Adolescent Health and Genetic Medicine, University of Sydney, Sydney, NSW 2050, Australia
| | - Janine Smith
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia; Specialty of Genomic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Benjamin Kamien
- Genetic Services of Western Australia, Perth, WA, Australia; School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
| | - Anne Turner
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Madhura Bakshi
- Department of Clinical Genetics, Liverpool Hospital, Sydney, NSW, Australia
| | - Lesley C Adès
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia; Disciplines of Child and Adolescent Health and Genetic Medicine, University of Sydney, Sydney, NSW 2050, Australia
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Discipline of Paediatrics & Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Regan
- Monash Genetics, Monash Health, Melbourne, VIC, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Luis A Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Institut Hospital del Mar d'Investigacions Mediques (IMIM), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain; Women's and Children's Hospital, South Australian Health and Medical Research Institute & University of Adelaide, Adelaide, SA, Australia
| | - Emma Krzesinski
- Monash Genetics, Monash Health, Melbourne, VIC, Australia; Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Melbourne, VIC, Australia; Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - Lauren Akesson
- Melbourne Pathology, Melbourne, VIC, Australia; Department of Pathology, The Royal Melbourne Hospital, Melbourne, VIC, Australia; Melbourne Medical School, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew Paul Fennell
- Monash Genetics, Monash Health, Melbourne, VIC, Australia; Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Tiffany Boughtwood
- Murdoch Children's Research Institute, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Lisa J Ewans
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Discipline of Paediatrics & Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia; Genomics and Inherited Disease Program, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre London Health Sciences Centre, London, ON, Canada
| | - Christopher Lucas
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Louise Carey
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Hugh French
- Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Melissa Rapadas
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
| | - Igor Stevanovski
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Corrina Cliffe
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - George Elakis
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Edwin P Kirk
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Discipline of Paediatrics & Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
| | | | - Janice Fletcher
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Rebecca Walsh
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Mark A Corbett
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Thessa Kroes
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Cliff Meldrum
- State Wide Service, New South Wales Health Pathology, Sydney, NSW, Australia
| | - Simon Cliffe
- State Wide Service, New South Wales Health Pathology, Sydney, NSW, Australia
| | - Meg Wall
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Kathryn North
- Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia; Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - David J Amor
- Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Michael Field
- The Genetics of Learning Disability Service, Waratah, NSW, Australia
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre London Health Sciences Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Michael F Buckley
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Tony Roscioli
- Neuroscience Research Australia, Sydney, NSW, Australia; Prince of Wales Clinical School, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia.
| |
Collapse
|
11
|
Marchant RG, Bryen SJ, Bahlo M, Cairns A, Chao KR, Corbett A, Davis MR, Ganesh VS, Ghaoui R, Jones KJ, Kornberg AJ, Lek M, Liang C, MacArthur DG, Oates EC, O'Donnell-Luria A, O'Grady GL, Osei-Owusu IA, Rafehi H, Reddel SW, Roxburgh RH, Ryan MM, Sandaradura SA, Scott LW, Valkanas E, Weisburd B, Young H, Evesson FJ, Waddell LB, Cooper ST. Genome and RNA sequencing boost neuromuscular diagnoses to 62% from 34% with exome sequencing alone. Ann Clin Transl Neurol 2024; 11:1250-1266. [PMID: 38544359 DOI: 10.1002/acn3.52041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/24/2024] [Indexed: 05/15/2024] Open
Abstract
OBJECTIVE Most families with heritable neuromuscular disorders do not receive a molecular diagnosis. Here we evaluate diagnostic utility of exome, genome, RNA sequencing, and protein studies and provide evidence-based recommendations for their integration into practice. METHODS In total, 247 families with suspected monogenic neuromuscular disorders who remained without a genetic diagnosis after standard diagnostic investigations underwent research-led massively parallel sequencing: neuromuscular disorder gene panel, exome, genome, and/or RNA sequencing to identify causal variants. Protein and RNA studies were also deployed when required. RESULTS Integration of exome sequencing and auxiliary genome, RNA and/or protein studies identified causal or likely causal variants in 62% (152 out of 247) of families. Exome sequencing alone informed 55% (83 out of 152) of diagnoses, with remaining diagnoses (45%; 69 out of 152) requiring genome sequencing, RNA and/or protein studies to identify variants and/or support pathogenicity. Arrestingly, novel disease genes accounted for <4% (6 out of 152) of diagnoses while 36.2% of solved families (55 out of 152) harbored at least one splice-altering or structural variant in a known neuromuscular disorder gene. We posit that contemporary neuromuscular disorder gene-panel sequencing could likely provide 66% (100 out of 152) of our diagnoses today. INTERPRETATION Our results emphasize thorough clinical phenotyping to enable deep scrutiny of all rare genetic variation in phenotypically consistent genes. Post-exome auxiliary investigations extended our diagnostic yield by 81% overall (34-62%). We present a diagnostic algorithm that details deployment of genomic and auxiliary investigations to obtain these diagnoses today most effectively. We hope this provides a practical guide for clinicians as they gain greater access to clinical genome and transcriptome sequencing.
Collapse
Affiliation(s)
- Rhett G Marchant
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Samantha J Bryen
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Melanie Bahlo
- Functional Neuromics, Children's Medical Research Institute, Westmead, New South Wales, Australia
- Population Health and Immunity, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Anita Cairns
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Neurosciences Department, Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Katherine R Chao
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alastair Corbett
- Neurology Department, Repatriation General Hospital Concord, Concord, New South Wales, Australia
| | - Mark R Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, Perth, WA, Australia
| | - Vijay S Ganesh
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Neuromuscular Division, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Roula Ghaoui
- Department of Neurology, Central Adelaide Local Health Network/Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Department of Genetics & Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Kristi J Jones
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Clinical Genetics, Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Andrew J Kornberg
- Department of Neurology, Royal Children's Hospital Melbourne, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Neurosciences Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Monkol Lek
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Christina Liang
- Department of Neurology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Neurogenetics, Northern Clinical School, Kolling Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Daniel G MacArthur
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Centre for Population Genomics, Garvan Institute of Medical Research/University of New South Wales, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Emily C Oates
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Randwick, New South Wales, Australia
| | - Anne O'Donnell-Luria
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Gina L O'Grady
- Starship Children's Health, Auckland District Health Board, Auckland, New Zealand
| | - Ikeoluwa A Osei-Owusu
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Haloom Rafehi
- Functional Neuromics, Children's Medical Research Institute, Westmead, New South Wales, Australia
- Population Health and Immunity, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Stephen W Reddel
- Neurology Department, Repatriation General Hospital Concord, Concord, New South Wales, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard H Roxburgh
- Department of Neurology, Auckland District Health Board, Auckland, New Zealand
- Centre of Brain Research Neurogenetics Research Clinic, University of Auckland, Auckland, New Zealand
| | - Monique M Ryan
- Department of Neurology, Royal Children's Hospital Melbourne, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Neurosciences Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Sarah A Sandaradura
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Clinical Genetics, Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Liam W Scott
- Functional Neuromics, Children's Medical Research Institute, Westmead, New South Wales, Australia
- Population Health and Immunity, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Elise Valkanas
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Ben Weisburd
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Helen Young
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Department of Neurology, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Paediatrics, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Frances J Evesson
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Leigh B Waddell
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Sandra T Cooper
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
12
|
Mori T, Fujimaru T, Liu C, Patterson K, Yamamoto K, Suzuki T, Chiga M, Sekine A, Ubara Y, Miller DE, Zalusky MPG, Mandai S, Ando F, Mori Y, Kikuchi H, Susa K, Chong JX, Bamshad MJ, Tan YQ, Zhang F, Uchida S, Sohara E. CFAP47 is a novel causative gene implicated in X-linked polycystic kidney disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24304760. [PMID: 38633811 PMCID: PMC11023651 DOI: 10.1101/2024.04.05.24304760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a well-described condition in which ~80% of cases have a genetic explanation, while the genetic basis of sporadic cystic kidney disease in adults remains unclear in ~30% of cases. This study aimed to identify novel genes associated with polycystic kidney disease (PKD) in patients with sporadic cystic kidney disease in which a clear genetic change was not identified in established genes. A next-generation sequencing panel analyzed known genes related to renal cysts in 118 sporadic cases, followed by whole-genome sequencing on 47 unrelated individuals without identified candidate variants. Three male patients were found to have rare missense variants in the X-linked gene Cilia And Flagella Associated Protein 47 (CFAP47). CFAP47 was expressed in primary cilia of human renal tubules, and knockout mice exhibited vacuolation of tubular cells and tubular dilation, providing evidence that CFAP47 is a causative gene involved in cyst formation. This discovery of CFAP47 as a newly identified gene associated with PKD, displaying X-linked inheritance, emphasizes the need for further cases to understand the role of CFAP47 in PKD.
Collapse
Affiliation(s)
- Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takuya Fujimaru
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chunyu Liu
- Soong Ching Ling Institute of Maternal and Child Health, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Genetic Engineering, Institute of Medical Genetics and Genomics, Fudan University, Shanghai, China
| | - Karynne Patterson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Kohei Yamamoto
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takefumi Suzuki
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Motoko Chiga
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akinari Sekine
- Department of Nephrology and Rheumatology, Toranomon Hospital, Japan
- Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - Yoshifumi Ubara
- Department of Nephrology and Rheumatology, Toranomon Hospital, Japan
- Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Miranda PG Zalusky
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
| | - Shintaro Mandai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Fumiaki Ando
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yutaro Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Kikuchi
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Koichiro Susa
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Jessica X. Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Michael J. Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Feng Zhang
- Soong Ching Ling Institute of Maternal and Child Health, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Genetic Engineering, Institute of Medical Genetics and Genomics, Fudan University, Shanghai, China
| | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| |
Collapse
|
13
|
Sheth J, Sheth H, Sheth F, Thelma BK, Joshi M, Kaur I, Joshi C. 48th annual meeting and international conference of the Indian Society of Human Genetics 2024: fostering collaborations within rare disease research community. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2024; 23:100373. [PMID: 38434479 PMCID: PMC10905951 DOI: 10.1016/j.lansea.2024.100373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024]
Affiliation(s)
- Jayesh Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, Gujarat, India
| | - Harsh Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, Gujarat, India
| | - Frenny Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, Gujarat, India
| | | | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | | | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| |
Collapse
|
14
|
Jin B, Yoon JG, Kim A, Moon J, Kim HJ. Late-Onset Ataxia-Telangiectasia Presenting With Dystonia and Tremor: The Use of Nanopore Long-Read Sequencing Solving the Variant Phase. Neurol Genet 2024; 10:e200141. [PMID: 38854973 PMCID: PMC11157422 DOI: 10.1212/nxg.0000000000200141] [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: 12/21/2023] [Accepted: 01/24/2024] [Indexed: 06/11/2024]
Abstract
Objectives This study investigates atypical late-onset ataxia-telangiectasia (AT) cases in a Korean family, diagnosed via Nanopore long-read sequencing, diverging from the typical early childhood onset caused by biallelic pathogenic ATM variants. Methods A 52-year-old Korean woman exhibiting dystonia and tremor, with a family history of similar symptoms in her older sister, underwent comprehensive tests including routine laboratory tests, neuropsychological assessments, and neuroimaging. Genetic analysis was conducted through targeted sequencing of 29 dystonia-associated genes and Nanopore long-read sequencing to assess the configuration of 2 ATM gene variants. Results Routine blood tests and brain imaging studies returned normal results, except for elevated α-fetoprotein levels. Neurologic examination revealed dystonia in the face, hand, and trunk, along with cervical dystonia in the proband. Her sister exhibited similar symptoms without evident telangiectasia. Genetic testing revealed 2 heterozygous pathogenic ATM gene variants (p.Glu2014Ter and p.Glu2052Lys). Nanopore long-read sequencing confirmed these variants were in trans configuration, establishing a definite molecular diagnosis in the proband. Discussion This report expands the known clinical spectrum of AT, highlighting a familial case of atypical AT. Moreover, it underscores the clinical utility of Nanopore long-read sequencing in phasing variant haplotypes, essential for diagnosing autosomal recessive disorders, especially beneficial for cases without parental samples.
Collapse
Affiliation(s)
- Bora Jin
- From the Department of Neurology (B.J., J.M., H.-J.K.), Seoul National University Hospital and Seoul National University College of Medicine; Department of Genomic Medicine (J.G.Y., J.M.), Seoul National University Hospital; Department of Laboratory Medicine (J.G.Y), Gangnam Severance Hospital and Yonsei University College of Medicine; and Department of Neurology (A.K.), Chungbuk National University Hospital and Chungbuk National University College of Medicine, Cheongju-si, Republic of Korea
| | - Jihoon G Yoon
- From the Department of Neurology (B.J., J.M., H.-J.K.), Seoul National University Hospital and Seoul National University College of Medicine; Department of Genomic Medicine (J.G.Y., J.M.), Seoul National University Hospital; Department of Laboratory Medicine (J.G.Y), Gangnam Severance Hospital and Yonsei University College of Medicine; and Department of Neurology (A.K.), Chungbuk National University Hospital and Chungbuk National University College of Medicine, Cheongju-si, Republic of Korea
| | - Aryun Kim
- From the Department of Neurology (B.J., J.M., H.-J.K.), Seoul National University Hospital and Seoul National University College of Medicine; Department of Genomic Medicine (J.G.Y., J.M.), Seoul National University Hospital; Department of Laboratory Medicine (J.G.Y), Gangnam Severance Hospital and Yonsei University College of Medicine; and Department of Neurology (A.K.), Chungbuk National University Hospital and Chungbuk National University College of Medicine, Cheongju-si, Republic of Korea
| | - Jangsup Moon
- From the Department of Neurology (B.J., J.M., H.-J.K.), Seoul National University Hospital and Seoul National University College of Medicine; Department of Genomic Medicine (J.G.Y., J.M.), Seoul National University Hospital; Department of Laboratory Medicine (J.G.Y), Gangnam Severance Hospital and Yonsei University College of Medicine; and Department of Neurology (A.K.), Chungbuk National University Hospital and Chungbuk National University College of Medicine, Cheongju-si, Republic of Korea
| | - Han-Joon Kim
- From the Department of Neurology (B.J., J.M., H.-J.K.), Seoul National University Hospital and Seoul National University College of Medicine; Department of Genomic Medicine (J.G.Y., J.M.), Seoul National University Hospital; Department of Laboratory Medicine (J.G.Y), Gangnam Severance Hospital and Yonsei University College of Medicine; and Department of Neurology (A.K.), Chungbuk National University Hospital and Chungbuk National University College of Medicine, Cheongju-si, Republic of Korea
| |
Collapse
|
15
|
Rodrigues Alves Barbosa V, Maroilley T, Diao C, Colvin-James L, Perrier R, Tarailo-Graovac M. Single variant, yet "double trouble": TSC and KBG syndrome because of a large de novo inversion. Life Sci Alliance 2024; 7:e202302115. [PMID: 38253421 PMCID: PMC10803213 DOI: 10.26508/lsa.202302115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Despite the advances in high-throughput sequencing, many rare disease patients remain undiagnosed. In particular, the patients with well-defined clinical phenotypes and established clinical diagnosis, yet missing or partial genetic diagnosis, may hold a clue to more complex genetic mechanisms of a disease that could be missed by available clinical tests. Here, we report a patient with a clinical diagnosis of Tuberous sclerosis, combined with unusual secondary features, but negative clinical tests including TSC1 and TSC2 Short-read whole-genome sequencing combined with advanced bioinformatics analyses were successful in uncovering a de novo pericentric 87-Mb inversion with breakpoints in TSC2 and ANKRD11, which explains the TSC clinical diagnosis, and confirms a second underlying monogenic disorder, KBG syndrome. Our findings illustrate how complex variants, such as large inversions, may be missed by clinical tests and further highlight the importance of well-defined clinical diagnoses in uncovering complex molecular mechanisms of a disease, such as complex variants and "double trouble" effects.
Collapse
Affiliation(s)
- Victoria Rodrigues Alves Barbosa
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Tatiana Maroilley
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Catherine Diao
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Leslie Colvin-James
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Renee Perrier
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Maja Tarailo-Graovac
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| |
Collapse
|
16
|
Koshimizu E, Kato M, Misawa K, Uchiyama Y, Tsuchida N, Hamanaka K, Fujita A, Mizuguchi T, Miyatake S, Matsumoto N. Detection of hidden intronic DDC variant in aromatic L-amino acid decarboxylase deficiency by adaptive sampling. J Hum Genet 2024; 69:153-157. [PMID: 38216729 DOI: 10.1038/s10038-023-01217-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 01/14/2024]
Abstract
Aromatic l-amino acid decarboxylase (AADC) deficiency is an autosomal recessive neurotransmitter disorder caused by pathogenic DOPA decarboxylase (DDC) variants. We previously reported Japanese siblings with AADC deficiency, which was confirmed by the lack of enzyme activity; however, only a heterozygous missense variant was detected. We therefore performed targeted long-read sequencing by adaptive sampling to identify any missing variants. Haplotype phasing and variant calling identified a novel deep intronic variant (c.714+255 C > A), which was predicted to potentially activate the noncanonical splicing acceptor site. Minigene assay revealed that wild-type and c.714+255 C > A alleles had different impacts on splicing. Three transcripts, including the canonical transcript, were detected from the wild-type allele, but only the noncanonical cryptic exon was produced from the variant allele, indicating that c.714+255 C > A was pathogenic. Target long-read sequencing may be used to detect hidden pathogenic variants in unresolved autosomal recessive cases with only one disclosed hit variant.
Collapse
Affiliation(s)
- Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Kohei Hamanaka
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan.
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
| |
Collapse
|
17
|
Hiatt SM, Lawlor JM, Handley LH, Latner DR, Bonnstetter ZT, Finnila CR, Thompson ML, Boston LB, Williams M, Nunez IR, Jenkins J, Kelley WV, Bebin EM, Lopez MA, Hurst ACE, Korf BR, Schmutz J, Grimwood J, Cooper GM. Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.22.24304633. [PMID: 38585854 PMCID: PMC10996728 DOI: 10.1101/2024.03.22.24304633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Variant detection from long-read genome sequencing (lrGS) has proven to be considerably more accurate and comprehensive than variant detection from short-read genome sequencing (srGS). However, the rate at which lrGS can increase molecular diagnostic yield for rare disease is not yet precisely characterized. We performed lrGS using Pacific Biosciences "HiFi" technology on 96 short-read-negative probands with rare disease that were suspected to be genetic. We generated hg38-aligned variants and de novo phased genome assemblies, and subsequently annotated, filtered, and curated variants using clinical standards. New disease-relevant or potentially relevant genetic findings were identified in 16/96 (16.7%) probands, eight of which (8/96, 8.33%) harbored pathogenic or likely pathogenic variants. Newly identified variants were visible in both srGS and lrGS in nine probands (~9.4%) and resulted from changes to interpretation mostly from recent gene-disease association discoveries. Seven cases included variants that were only interpretable in lrGS, including copy-number variants, an inversion, a mobile element insertion, two low-complexity repeat expansions, and a 1 bp deletion. While evidence for each of these variants is, in retrospect, visible in srGS, they were either: not called within srGS data, were represented by calls with incorrect sizes or structures, or failed quality-control and filtration. Thus, while reanalysis of older data clearly increases diagnostic yield, we find that lrGS allows for substantial additional yield (7/96, 7.3%) beyond srGS. We anticipate that as lrGS analysis improves, and as lrGS datasets grow allowing for better variant frequency annotation, the additional lrGS-only rare disease yield will grow over time.
Collapse
Affiliation(s)
- Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Lori H. Handley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Donald R. Latner
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | | | | | - Lori Beth Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Melissa Williams
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - E. Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Michael A. Lopez
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Anna C. E. Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Bruce R. Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | |
Collapse
|
18
|
Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson Z, Storz SHR, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.05.24303792. [PMID: 38496498 PMCID: PMC10942501 DOI: 10.1101/2024.03.05.24303792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Less than half of individuals with a suspected Mendelian condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control datasets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project ONT Sequencing Consortium aims to generate LRS data from at least 800 of the 1000 Genomes Project samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37x and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs.
Collapse
Affiliation(s)
- Jonas A. Gustafson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Sophia B. Gibson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nikhita Damaraju
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Miranda PG Zalusky
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lei Yang
- Pacific Northwest Research Institute, Seattle, WA, USA
| | | | | | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Nathan D. Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Human Technopole, Milan, Italy
| | - Qiuhui Li
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Angela L. Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Joy Goffena
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Zachery Anderson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sophie HR Storz
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sydney A. Ward
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Maisha Sinha
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Claudia Gonzaga-Jauregui
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México
| | - Wayne E. Clarke
- New York Genome Center, New York, NY, USA
- Outlier Informatics Inc., Saskatoon, SK, Canada
| | | | | | | | | | | | - Mahler Revsine
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Cate R. Paschal
- Department of Laboratories, Seattle Children’s Hospital, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Christina Zakarian
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Esther Robb
- Department of Computer Science, Stanford University, Stanford, CA, 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
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Justin M. Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mikhail Kolmogorov
- Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Richard N. McLaughlin
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Matt Loose
- Deep Seq, School of Life Sciences, University of Nottingham, Nottingham, England
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Khoury College of Computer Sciences, Northeastern University, Boston, MA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Danny E. Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| |
Collapse
|
19
|
Olivucci G, Iovino E, Innella G, Turchetti D, Pippucci T, Magini P. Long read sequencing on its way to the routine diagnostics of genetic diseases. Front Genet 2024; 15:1374860. [PMID: 38510277 PMCID: PMC10951082 DOI: 10.3389/fgene.2024.1374860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
The clinical application of technological progress in the identification of DNA alterations has always led to improvements of diagnostic yields in genetic medicine. At chromosome side, from cytogenetic techniques evaluating number and gross structural defects to genomic microarrays detecting cryptic copy number variants, and at molecular level, from Sanger method studying the nucleotide sequence of single genes to the high-throughput next-generation sequencing (NGS) technologies, resolution and sensitivity progressively increased expanding considerably the range of detectable DNA anomalies and alongside of Mendelian disorders with known genetic causes. However, particular genomic regions (i.e., repetitive and GC-rich sequences) are inefficiently analyzed by standard genetic tests, still relying on laborious, time-consuming and low-sensitive approaches (i.e., southern-blot for repeat expansion or long-PCR for genes with highly homologous pseudogenes), accounting for at least part of the patients with undiagnosed genetic disorders. Third generation sequencing, generating long reads with improved mappability, is more suitable for the detection of structural alterations and defects in hardly accessible genomic regions. Although recently implemented and not yet clinically available, long read sequencing (LRS) technologies have already shown their potential in genetic medicine research that might greatly impact on diagnostic yield and reporting times, through their translation to clinical settings. The main investigated LRS application concerns the identification of structural variants and repeat expansions, probably because techniques for their detection have not evolved as rapidly as those dedicated to single nucleotide variants (SNV) identification: gold standard analyses are karyotyping and microarrays for balanced and unbalanced chromosome rearrangements, respectively, and southern blot and repeat-primed PCR for the amplification and sizing of expanded alleles, impaired by limited resolution and sensitivity that have not been significantly improved by the advent of NGS. Nevertheless, more recently, with the increased accuracy provided by the latest product releases, LRS has been tested also for SNV detection, especially in genes with highly homologous pseudogenes and for haplotype reconstruction to assess the parental origin of alleles with de novo pathogenic variants. We provide a review of relevant recent scientific papers exploring LRS potential in the diagnosis of genetic diseases and its potential future applications in routine genetic testing.
Collapse
Affiliation(s)
- Giulia Olivucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Surgical and Oncological Sciences, University of Palermo, Palermo, Italy
| | - Emanuela Iovino
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanni Innella
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Daniela Turchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Pamela Magini
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| |
Collapse
|
20
|
Chen Z, Gustavsson EK, Macpherson H, Anderson C, Clarkson C, Rocca C, Self E, Alvarez Jerez P, Scardamaglia A, Pellerin D, Montgomery K, Lee J, Gagliardi D, Luo H, Hardy J, Polke J, Singleton AB, Blauwendraat C, Mathews KD, Tucci A, Fu YH, Houlden H, Ryten M, Ptáček LJ. Adaptive Long-Read Sequencing Reveals GGC Repeat Expansion in ZFHX3 Associated with Spinocerebellar Ataxia Type 4. Mov Disord 2024; 39:486-497. [PMID: 38197134 DOI: 10.1002/mds.29704] [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: 11/03/2023] [Revised: 11/29/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Spinocerebellar ataxia type 4 (SCA4) is an autosomal dominant ataxia with invariable sensory neuropathy originally described in a family with Swedish ancestry residing in Utah more than 25 years ago. Despite tight linkage to the 16q22 region, the molecular diagnosis has since remained elusive. OBJECTIVES Inspired by pathogenic structural variation implicated in other 16q-ataxias with linkage to the same locus, we revisited the index SCA4 cases from the Utah family using novel technologies to investigate structural variation within the candidate region. METHODS We adopted a targeted long-read sequencing approach with adaptive sampling on the Oxford Nanopore Technologies (ONT) platform that enables the detection of segregating structural variants within a genomic region without a priori assumptions about any variant features. RESULTS Using this approach, we found a heterozygous (GGC)n repeat expansion in the last coding exon of the zinc finger homeobox 3 (ZFHX3) gene that segregates with disease, ranging between 48 and 57 GGC repeats in affected probands. This finding was replicated in a separate family with SCA4. Furthermore, the estimation of this GGC repeat size in short-read whole genome sequencing (WGS) data of 21,836 individuals recruited to the 100,000 Genomes Project in the UK and our in-house dataset of 11,258 exomes did not reveal any pathogenic repeats, indicating that the variant is ultrarare. CONCLUSIONS These findings support the utility of adaptive long-read sequencing as a powerful tool to decipher causative structural variation in unsolved cases of inherited neurological disease. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
Collapse
Affiliation(s)
- Zhongbo Chen
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, United Kingdom
| | - Emil K Gustavsson
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, United Kingdom
| | - Hannah Macpherson
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Claire Anderson
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, United Kingdom
| | - Chris Clarkson
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Clarissa Rocca
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Eleanor Self
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Pilar Alvarez Jerez
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Annarita Scardamaglia
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - David Pellerin
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Kylie Montgomery
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, United Kingdom
| | - Jasmaine Lee
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Delia Gagliardi
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Huihui Luo
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - John Hardy
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
- Reta Lila Weston Institute, Queen Square Institute of Neurology, University College London, London, United Kingdom
- UK Dementia Research Institute, University College London, London, United Kingdom
- NIHR University College London Hospitals Biomedical Research Centre, London, United Kingdom
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong, China
| | - James Polke
- The Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Andrew B Singleton
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Katherine D Mathews
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
- Department of Neurology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Arianna Tucci
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Ying-Hui Fu
- Department of Neurology, University of California San Francisco, San Francisco, California, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
- Weill Institute for Neuroscience, University of California San Francisco, San Francisco, California, USA
- Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, California, USA
| | - Henry Houlden
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
- The Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, United Kingdom
| | - Louis J Ptáček
- Department of Neurology, University of California San Francisco, San Francisco, California, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
- Weill Institute for Neuroscience, University of California San Francisco, San Francisco, California, USA
- Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, California, USA
| |
Collapse
|
21
|
Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
Collapse
Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| |
Collapse
|
22
|
Nakamura W, Hirata M, Oda S, Chiba K, Okada A, Mateos RN, Sugawa M, Iida N, Ushiama M, Tanabe N, Sakamoto H, Sekine S, Hirasawa A, Kawai Y, Tokunaga K, Tsujimoto SI, Shiba N, Ito S, Yoshida T, Shiraishi Y. Assessing the efficacy of target adaptive sampling long-read sequencing through hereditary cancer patient genomes. NPJ Genom Med 2024; 9:11. [PMID: 38368425 PMCID: PMC10874402 DOI: 10.1038/s41525-024-00394-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 01/15/2024] [Indexed: 02/19/2024] Open
Abstract
Innovations in sequencing technology have led to the discovery of novel mutations that cause inherited diseases. However, many patients with suspected genetic diseases remain undiagnosed. Long-read sequencing technologies are expected to significantly improve the diagnostic rate by overcoming the limitations of short-read sequencing. In addition, Oxford Nanopore Technologies (ONT) offers adaptive sampling and computationally driven target enrichment technology. This enables more affordable intensive analysis of target gene regions compared to standard non-selective long-read sequencing. In this study, we developed an efficient computational workflow for target adaptive sampling long-read sequencing (TAS-LRS) and evaluated it through application to 33 genomes collected from suspected hereditary cancer patients. Our workflow can identify single nucleotide variants with nearly the same accuracy as the short-read platform and elucidate complex forms of structural variations. We also newly identified several SINE-R/VNTR/Alu (SVA) elements affecting the APC gene in two patients with familial adenomatous polyposis, as well as their sites of origin. In addition, we demonstrated that off-target reads from adaptive sampling, which is typically discarded, can be effectively used to accurately genotype common single-nucleotide polymorphisms (SNPs) across the entire genome, enabling the calculation of a polygenic risk score. Furthermore, we identified allele-specific MLH1 promoter hypermethylation in a Lynch syndrome patient. In summary, our workflow with TAS-LRS can simultaneously capture monogenic risk variants including complex structural variations, polygenic background as well as epigenetic alterations, and will be an efficient platform for genetic disease research and diagnosis.
Collapse
Affiliation(s)
- Wataru Nakamura
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa, Japan
| | - Makoto Hirata
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoyo Oda
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Division of Laboratory Medicine, National Cancer Center Hospital, Tokyo, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Ai Okada
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Raúl Nicolás Mateos
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahiro Sugawa
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Iida
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Mineko Ushiama
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Noriko Tanabe
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Hiromi Sakamoto
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Shigeki Sekine
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Akira Hirasawa
- Department of Clinical Genetics and Genomic Medicine, Okayama University Hospital, Okayama, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Central Biobank, National Center Biobank Network, Tokyo, Japan
| | - Shin-Ichi Tsujimoto
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa, Japan
| | - Norio Shiba
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa, Japan
| | - Shuichi Ito
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa, Japan
| | - Teruhiko Yoshida
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.
| |
Collapse
|
23
|
Kawakami R, Hiraide T, Watanabe K, Miyamoto S, Hira K, Komatsu K, Ishigaki H, Sakaguchi K, Maekawa M, Yamashita K, Fukuda T, Miyairi I, Ogata T, Saitsu H. RNA sequencing and target long-read sequencing reveal an intronic transposon insertion causing aberrant splicing. J Hum Genet 2024; 69:91-99. [PMID: 38102195 DOI: 10.1038/s10038-023-01211-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]
Abstract
More than half of cases with suspected genetic disorders remain unsolved by genetic analysis using short-read sequencing such as exome sequencing (ES) and genome sequencing (GS). RNA sequencing (RNA-seq) and long-read sequencing (LRS) are useful for interpretation of candidate variants and detection of structural variants containing repeat sequences, respectively. Recently, adaptive sampling on nanopore sequencers enables target LRS more easily. Here, we present a Japanese girl with premature chromatid separation (PCS)/mosaic variegated aneuploidy (MVA) syndrome. ES detected a known pathogenic maternal heterozygous variant (c.1402-5A>G) in intron 10 of BUB1B (NM_001211.6), a known responsive gene for PCS/MVA syndrome with autosomal recessive inheritance. Minigene splicing assay revealed that almost all transcripts from the c.1402-5G allele have mis-splicing with 4-bp insertion. GS could not detect another pathogenic variant, while RNA-seq revealed abnormal reads in intron 2. To extensively explore variants in intron 2, we performed adaptive sampling and identified a paternal 3.0 kb insertion. Consensus sequence of 16 reads spanning the insertion showed that the insertion consists of Alu and SVA elements. Realignment of RNA-seq reads to the new reference sequence containing the insertion revealed that 16 reads have 5' splice site within the insertion and 3' splice site at exon 3, demonstrating causal relationship between the insertion and aberrant splicing. In addition, immunoblotting showed severely diminished BUB1B protein level in patient derived cells. These data suggest that detection of transcriptomic abnormalities by RNA-seq can be a clue for identifying pathogenic variants, and determination of insert sequences is one of merits of LRS.
Collapse
Affiliation(s)
- Ryota Kawakami
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takuya Hiraide
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kazuki Watanabe
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Sachiko Miyamoto
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kota Hira
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kazuyuki Komatsu
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hidetoshi Ishigaki
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kimiyoshi Sakaguchi
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masato Maekawa
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Keita Yamashita
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tokiko Fukuda
- Department of Hamamatsu Child Health and Developmental Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Isao Miyairi
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tsutomu Ogata
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
- Department of Pediatrics, Hamamatsu Medical Center, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.
| |
Collapse
|
24
|
Friedman JM, Bombard Y, Carleton B, Issa AM, Knoppers B, Plon SE, Rahimzadeh V, Relling MV, Williams MS, van Karnebeek C, Vears D, Cornel MC. Should secondary pharmacogenomic variants be actively screened and reported when diagnostic genome-wide sequencing is performed in a child? Genet Med 2024; 26:101033. [PMID: 38007624 DOI: 10.1016/j.gim.2023.101033] [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: 04/24/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/27/2023] Open
Abstract
This white paper was prepared by the Global Alliance for Genomics and Health Regulatory and Ethics Work Stream's Pediatric Task Team to review and provide perspective with respect to ethical, legal, and social issues regarding the return of secondary pharmacogenomic variants in children who have a serious disease or developmental disorder and are undergoing exome or genome sequencing to identify a genetic cause of their condition. We discuss actively searching for and reporting pharmacogenetic/genomic variants in pediatric patients, different methods of returning secondary pharmacogenomic findings to the patient/parents and/or treating clinicians, maintaining these data in the patient's health record over time, decision supports to assist using pharmacogenetic results in future treatment decisions, and sharing information in public databases to improve the clinical interpretation of pharmacogenetic variants identified in other children. We conclude by presenting a series of points to consider for clinicians and policymakers regarding whether, and under what circumstances, routine screening and return of pharmacogenomic variants unrelated to the indications for testing is appropriate in children who are undergoing genome-wide sequencing to assist in the diagnosis of a suspected genetic disease.
Collapse
Affiliation(s)
- Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Yvonne Bombard
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Bruce Carleton
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada; Division of Translational Therapeutics, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pharmaceutical Outcomes Programme, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Amalia M Issa
- Personalized Precision Medicine & Targeted Therapeutics, Springfield, MA; Health Policy, University of the Sciences, Philadelphia, PA; Pharmaceutical Sciences, University of the Sciences, Philadelphia, PA; Family Medicine, McGill University, Montreal, Quebec, Canada
| | - Bartha Knoppers
- Centre of Genomics and Policy, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Sharon E Plon
- Department of Pediatrics, Texas Children's Cancer and Hematology Center, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Vasiliki Rahimzadeh
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Mary V Relling
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Clara van Karnebeek
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands; Departments of Pediatrics and Human Genetics, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, The Netherlands; United for Metabolic Diseases, The Netherlands; Radboud Center for Mitochondrial and Metabolic Medicine, Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Danya Vears
- University of Melbourne, Carlton, Melbourne, Australia; Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Martina C Cornel
- Department of Human Genetics and Amsterdam Public Health Research Institute, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| |
Collapse
|
25
|
Mandal AK. Recent insights into crosstalk between genetic parasites and their host genome. Brief Funct Genomics 2024; 23:15-23. [PMID: 36307128 PMCID: PMC10799329 DOI: 10.1093/bfgp/elac032] [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: 08/04/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 01/21/2024] Open
Abstract
The bulk of higher order organismal genomes is comprised of transposable element (TE) copies, i.e. genetic parasites. The host-parasite relation is multi-faceted, varying across genomic region (genic versus intergenic), life-cycle stages, tissue-type and of course in health versus pathological state. The reach of functional genomics though, in investigating genotype-to-phenotype relations, has been limited when TEs are involved. The aim of this review is to highlight recent progress made in understanding how TE origin biochemical activity interacts with the central dogma stages of the host genome. Such interaction can also bring about modulation of the immune context and this could have important repercussions in disease state where immunity has a role to play. Thus, the review is to instigate ideas and action points around identifying evolutionary adaptations that the host genome and the genetic parasite have evolved and why they could be relevant.
Collapse
Affiliation(s)
- Amit K Mandal
- Corresponding author: A.K. Mandal, Nuffield Department of Surgical Sciences (NDS), University of Oxford, Old Road Campus Research building (ORCRB), Oxford OX3 7DQ, UK. Tel: +44 (0)1865 617123; Fax: +44 (0)1865 768876; E-mail:
| |
Collapse
|
26
|
Wang J, Yang L, Cheng A, Tham CY, Tan W, Darmawan J, de Sessions PF, Wan Y. Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome. Nat Commun 2024; 15:481. [PMID: 38212309 PMCID: PMC10784512 DOI: 10.1038/s41467-023-44656-3] [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: 02/09/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024] Open
Abstract
Abundant cellular transcripts occupy most of the sequencing reads in the transcriptome, making it challenging to assay for low-abundant transcripts. Here, we utilize the adaptive sampling function of Oxford Nanopore sequencing to selectively deplete and enrich RNAs of interest without biochemical manipulation before sequencing. Adaptive sampling performed on a pool of in vitro transcribed RNAs resulted in a net increase of 22-30% in the proportion of transcripts of interest in the population. Enriching and depleting different proportions of the Candida albicans transcriptome also resulted in a 11-13.5% increase in the number of reads on target transcripts, with longer and more abundant transcripts being more efficiently depleted. Depleting all currently annotated Candida albicans transcripts did not result in an absolute enrichment of remaining transcripts, although we identified 26 previously unknown transcripts and isoforms, 17 of which are antisense to existing transcripts. Further improvements in the adaptive sampling of RNAs will allow the technology to be widely applied to study RNAs of interest in diverse transcriptomes.
Collapse
Affiliation(s)
- Jiaxu Wang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, 138672, Singapore
| | - Lin Yang
- Oxford Nanopore Technologies, Singapore, 138667, Singapore
| | - Anthony Cheng
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, 138672, Singapore
| | | | - Wenting Tan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, 138672, Singapore
| | - Jefferson Darmawan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, 138672, Singapore
| | | | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, 138672, Singapore.
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore.
| |
Collapse
|
27
|
Damaraju N, Miller AL, Miller DE. Long-Read DNA and RNA Sequencing to Streamline Clinical Genetic Testing and Reduce Barriers to Comprehensive Genetic Testing. J Appl Lab Med 2024; 9:138-150. [PMID: 38167773 DOI: 10.1093/jalm/jfad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/24/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Obtaining a precise molecular diagnosis through clinical genetic testing provides information about disease prognosis or progression, allows accurate counseling about recurrence risk, and empowers individuals to benefit from precision therapies or take part in N-of-1 trials. Unfortunately, more than half of individuals with a suspected Mendelian condition remain undiagnosed after a comprehensive clinical evaluation, and the results of any individual clinical genetic test ordered during a typical evaluation may take weeks or months to return. Furthermore, commonly used technologies, such as short-read sequencing, are limited in the types of disease-causing variation they can identify. New technologies, such as long-read sequencing (LRS), are poised to solve these problems. CONTENT Recent technical advances have improved accuracy, increased throughput, and decreased the costs of commercially available LRS technologies. This has resolved many historical concerns about the use of LRS in the clinical environment and opened the door to widespread clinical adoption of LRS. Here, we review LRS technology, how it has been used in the research setting to clarify complex variants or identify disease-causing variation missed by prior clinical testing, and how it may be used clinically in the near future. SUMMARY LRS is unique in that, as a single data source, it has the potential to replace nearly every other clinical genetic test offered today. When analyzed in a stepwise fashion, LRS will simplify laboratory processes, reduce barriers to comprehensive genetic testing, increase the rate of genetic diagnoses, and shorten the amount of time required to make a molecular diagnosis.
Collapse
Affiliation(s)
- Nikhita Damaraju
- Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, United States
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, United States
| | - Angela L Miller
- Department of Pediatrics, University of Washington, Seattle, WA 98195, United States
| | - Danny E Miller
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, United States
- Department of Pediatrics, University of Washington, Seattle, WA 98195, United States
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, United States
| |
Collapse
|
28
|
Harvey WT, Ebert P, Ebler J, Audano PA, Munson KM, Hoekzema K, Porubsky D, Beck CR, Marschall T, Garimella K, Eichler EE. Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall. Genome Res 2023; 33:2029-2040. [PMID: 38190646 PMCID: PMC10760522 DOI: 10.1101/gr.278070.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/03/2023] [Indexed: 01/10/2024]
Abstract
Advances in long-read sequencing (LRS) technologies continue to make whole-genome sequencing more complete, affordable, and accurate. LRS provides significant advantages over short-read sequencing approaches, including phased de novo genome assembly, access to previously excluded genomic regions, and discovery of more complex structural variants (SVs) associated with disease. Limitations remain with respect to cost, scalability, and platform-dependent read accuracy and the tradeoffs between sequence coverage and sensitivity of variant discovery are important experimental considerations for the application of LRS. We compare the genetic variant-calling precision and recall of Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) HiFi platforms over a range of sequence coverages. For read-based applications, LRS sensitivity begins to plateau around 12-fold coverage with a majority of variants called with reasonable accuracy (F1 score above 0.5), and both platforms perform well for SV detection. Genome assembly increases variant-calling precision and recall of SVs and indels in HiFi data sets with HiFi outperforming ONT in quality as measured by the F1 score of assembly-based variant call sets. While both technologies continue to evolve, our work offers guidance to design cost-effective experimental strategies that do not compromise on discovering novel biology.
Collapse
Affiliation(s)
- William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195-5065, USA
| | - Peter Ebert
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
- Core Unit Bioinformatics, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jana Ebler
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Peter A Audano
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195-5065, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195-5065, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195-5065, USA
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut 06030-6403, USA
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Kiran Garimella
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195-5065, USA;
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| |
Collapse
|
29
|
Ling C, Dai Y, Geng C, Pan S, Quan W, Ding Q, Yang X, Shen D, Tao Q, Li J, Li J, Wang Y, Jiang S, Wang Y, Chen L, Cui L, Wang D. Uncovering the true features of dystrophin gene rearrangement and improving the molecular diagnosis of Duchenne and Becker muscular dystrophies. iScience 2023; 26:108365. [PMID: 38047063 PMCID: PMC10690541 DOI: 10.1016/j.isci.2023.108365] [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: 08/03/2023] [Revised: 09/19/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023] Open
Abstract
Duchenne and Becker muscular dystrophies (DMD/BMD) are caused by complex mutations in the dystrophin gene (DMD). Currently, there is no integrative method for the precise detection of all potential DMD variants, a gap which we aimed to address using long-read sequencing. The captured long-read sequencing panel developed in this study was applied to 129 subjects, including 11 who had previously unsolved cases. The results showed that this method accurately detected DMD mutations, ranging from single-nucleotide variations to structural variations. Furthermore, our findings revealed that continuous exon duplication/deletion in the DMD/BMD cohort may be attributed to complex segmental rearrangements and that noncontiguous duplication/deletion is generally attributed to intragenic inversion or interchromosome translocation. Mutations in the deep introns were confirmed to produce a pseudoexon. Moreover, variations in female carriers were precisely identified. The integrated and precise DMD gene screening method proposed in this study could improve the molecular diagnosis of DMD/BMD.
Collapse
Affiliation(s)
- Chao Ling
- The Laboratory of Clinical Genetics, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Chang Geng
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Shirang Pan
- Grandomics Biosciences, Beijing 102200, China
| | | | - Qingyun Ding
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Xunzhe Yang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Dongchao Shen
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Qing Tao
- Grandomics Biosciences, Beijing 102200, China
| | - Jingjing Li
- Grandomics Biosciences, Beijing 102200, China
| | - Jia Li
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yinbing Wang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Shan Jiang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yang Wang
- Grandomics Biosciences, Beijing 102200, China
| | - Lin Chen
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Depeng Wang
- Grandomics Biosciences, Beijing 102200, China
| |
Collapse
|
30
|
AlAbdi L, Shamseldin HE, Khouj E, Helaby R, Aljamal B, Alqahtani M, Almulhim A, Hamid H, Hashem MO, Abdulwahab F, Abouyousef O, Jaafar A, Alshidi T, Al-Owain M, Alhashem A, Al Tala S, Khan AO, Mardawi E, Alkuraya H, Faqeih E, Afqi M, Alkhalifi S, Rahbeeni Z, Hagos ST, Al-Ahmadi W, Nadeef S, Maddirevula S, Khabar KSA, Putra A, Angelov A, Park C, Reyes-Ramos AM, Umer H, Ullah I, Driguez P, Fukasawa Y, Cheung MS, Gallouzi IE, Alkuraya FS. Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases. Genome Med 2023; 15:114. [PMID: 38098057 PMCID: PMC10720148 DOI: 10.1186/s13073-023-01270-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelian diseases is largely unknown. METHODS In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform. RESULTS Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level. CONCLUSIONS Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.
Collapse
Affiliation(s)
- Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Bayan Aljamal
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Aisha Almulhim
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Halima Hamid
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abouyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Pediatric Department, Division of Genetic and Metabolic Medicine, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Saeed Al Tala
- Pediatric Department, Neonatal Unit, Armed Forces Hospital, Khamis Mushayt, Saudi Arabia
| | - Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Elham Mardawi
- Maternal Fetal Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Hisham Alkuraya
- Vitreoretinal Surgery and Ocular Genetics, Global Eye Care/Specialized Medical Center Hospital, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, King Fahad Medical City, Children's Specialist Hospital, Riyadh, Saudi Arabia
| | - Manal Afqi
- Metabolic and Genetic Center, King Salman Bin Abdulaziz Medical City, Almadinah Almunwarah, Saudi Arabia
| | - Salwa Alkhalifi
- Newborn Screening, Ministry of Health, Eastern Province, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Samya T Hagos
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Wijdan Al-Ahmadi
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Seba Nadeef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Alexander Putra
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Angel Angelov
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Changsook Park
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ana M Reyes-Ramos
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Husen Umer
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ikram Ullah
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Patrick Driguez
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Yoshinori Fukasawa
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ming Sin Cheung
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Imed Eddine Gallouzi
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| |
Collapse
|
31
|
Wrenn DC, Drown DM. Nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communities. GIGABYTE 2023; 2023:gigabyte103. [PMID: 38111521 PMCID: PMC10726737 DOI: 10.46471/gigabyte.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/07/2023] [Indexed: 12/20/2023] Open
Abstract
Antimicrobial resistance (AMR) is a global public health threat. Environmental microbial communities act as reservoirs for AMR, containing genes associated with resistance, their precursors, and the selective pressures promoting their persistence. Genomic surveillance could provide insights into how these reservoirs change and impact public health. Enriching for AMR genomic signatures in complex microbial communities would strengthen surveillance efforts and reduce time-to-answer. Here, we tested the ability of nanopore sequencing and adaptive sampling to enrich for AMR genes in a mock community of environmental origin. Our setup implemented the MinION mk1B, an NVIDIA Jetson Xavier GPU, and Flongle flow cells. Using adaptive sampling, we observed consistent enrichment by composition. On average, adaptive sampling resulted in a target composition 4× higher than without adaptive sampling. Despite a decrease in total sequencing output, adaptive sampling increased target yield in most replicates. We also demonstrate enrichment in a diverse community using an environmental sample. This method enables rapid and flexible genomic surveillance.
Collapse
Affiliation(s)
- Danielle C. Wrenn
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Devin M. Drown
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| |
Collapse
|
32
|
Steigerwald C, Borsuk J, Pappas J, Galey M, Scott A, Devaney JM, Miller DE, Abreu NJ. CLN2 disease resulting from a novel homozygous deep intronic splice variant in TPP1 discovered using long-read sequencing. Mol Genet Metab 2023; 140:107713. [PMID: 37922835 DOI: 10.1016/j.ymgme.2023.107713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023]
Abstract
Neuronal ceroid lipofuscinosis type 2 (CLN2) is an autosomal recessive neurodegenerative disorder with enzyme replacement therapy available. We present two siblings with a clinical diagnosis of CLN2 disease, but no identifiable TPP1 variants after standard clinical testing. Long-read sequencing identified a homozygous deep intronic variant predicted to affect splicing, confirmed by clinical DNA and RNA sequencing. This case demonstrates how traditional laboratory assays can complement emerging molecular technologies to provide a precise molecular diagnosis.
Collapse
Affiliation(s)
- Connolly Steigerwald
- Division of Neurogenetics, Department of Neurology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jill Borsuk
- Division of Clinical Genetics, Department of Pediatrics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - John Pappas
- Division of Clinical Genetics, Department of Pediatrics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Miranda Galey
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA 98195, USA
| | - Anna Scott
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Department of Laboratories, Seattle Children's Hospital, Seattle, WA 08105, USA
| | | | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
| | - Nicolas J Abreu
- Division of Neurogenetics, Department of Neurology, NYU Grossman School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
33
|
LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Galey M, Goffena J, Gibson SB, Allan TJ, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel N, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Hubshman MW, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT, Neale G, Carvill GL, Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, Mefford HC. Diagnostic Utility of Genome-wide DNA Methylation Analysis in Genetically Unsolved Developmental and Epileptic Encephalopathies and Refinement of a CHD2 Episignature. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.11.23296741. [PMID: 37873138 PMCID: PMC10592992 DOI: 10.1101/2023.10.11.23296741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sequence-based genetic testing currently identifies causative genetic variants in ∼50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. Rare epigenetic variations ("epivariants") can drive disease by modulating gene expression at single loci, whereas genome-wide DNA methylation changes can result in distinct "episignature" biomarkers for monogenic disorders in a growing number of rare diseases. Here, we interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 516 individuals with genetically unsolved DEEs who had previously undergone extensive genetic testing. We identified rare differentially methylated regions (DMRs) and explanatory episignatures to discover causative and candidate genetic etiologies in 10 individuals. We then used long-read sequencing to identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and two copy number variants. We also identify pathogenic sequence variants associated with episignatures; some had been missed by previous exome sequencing. Although most DEE genes lack known episignatures, the increase in diagnostic yield for DNA methylation analysis in DEEs is comparable to the added yield of genome sequencing. Finally, we refine an episignature for CHD2 using an 850K methylation array which was further refined at higher CpG resolution using bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate genetic causes as ∼2% (10/516) for unsolved DEE cases.
Collapse
|
34
|
Lenahan AL, Squire AE, Miller DE. Panels, Exomes, Genomes, and More-Finding the Best Path Through the Diagnostic Odyssey. Pediatr Clin North Am 2023; 70:905-916. [PMID: 37704349 DOI: 10.1016/j.pcl.2023.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Selecting the ideal test to evaluate an individual with a suspected genetic disorder can be challenging. While several clinical testing options are available, no single test yet captures all potentially causative genetic variants. Thus, clinicians may order testing in a stepwise fashion, and what to order after non-diagnostic testing can be challenging to determine. Here, we provide an overview of commonly used clinical genetic tests, guidance on when they are best used, and what they may miss. We conclude with a discussion of how new technologies might be used to identify challenging variants and simplify clinical testing in the future.
Collapse
Affiliation(s)
- Arthur L Lenahan
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA 98105, USA
| | - Audrey E Squire
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA 98105, USA
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA 98105, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
| |
Collapse
|
35
|
Chrisman B, He C, Jung JY, Stockham N, Paskov K, Washington P, Petereit J, Wall DP. Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity. Genome Res 2023; 33:1734-1746. [PMID: 37879860 PMCID: PMC10691534 DOI: 10.1101/gr.277175.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 05/25/2023] [Indexed: 10/27/2023]
Abstract
Although it is ubiquitous in genomics, the current human reference genome (GRCh38) is incomplete: It is missing large sections of heterochromatic sequence, and as a singular, linear reference genome, it does not represent the full spectrum of human genetic diversity. To characterize gaps in GRCh38 and human genetic diversity, we developed an algorithm for sequence location approximation using nuclear families (ASLAN) to identify the region of origin of reads that do not align to GRCh38. Using unmapped reads and variant calls from whole-genome sequences (WGSs), ASLAN uses a maximum likelihood model to identify the most likely region of the genome that a subsequence belongs to given the distribution of the subsequence in the unmapped reads and phasings of families. Validating ASLAN on synthetic data and on reads from the alternative haplotypes in the decoy genome, ASLAN localizes >90% of 100-bp sequences with >92% accuracy and ∼1 Mb of resolution. We then ran ASLAN on 100-mers from unmapped reads from WGS from more than 700 families, and compared ASLAN localizations to alignment of the 100-mers to the recently released T2T-CHM13 assembly. We found that many unmapped reads in GRCh38 originate from telomeres and centromeres that are gaps in GRCh38. ASLAN localizations are in high concordance with T2T-CHM13 alignments, except in the centromeres of the acrocentric chromosomes. Comparing ASLAN localizations and T2T-CHM13 alignments, we identified sequences missing from T2T-CHM13 or sequences with high divergence from their aligned region in T2T-CHM13, highlighting new hotspots for genetic diversity.
Collapse
Affiliation(s)
- Brianna Chrisman
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA;
- Nevada Bioinformatics Center, University of Nevada, Reno, Nevada 89557, USA
| | - Chloe He
- Department of Biomedical Data Science, Stanford University, Stanford, California 94305, USA
| | - Jae-Yoon Jung
- Department of Pediatrics (Systems Medicine), Stanford University, Stanford, California 94305, USA
| | - Nate Stockham
- Department of Neuroscience, Stanford University, Stanford, California 94305, USA
| | - Kelley Paskov
- Department of Biomedical Data Science, Stanford University, Stanford, California 94305, USA
| | - Peter Washington
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Juli Petereit
- Nevada Bioinformatics Center, University of Nevada, Reno, Nevada 89557, USA
| | - Dennis P Wall
- Department of Biomedical Data Science, Stanford University, Stanford, California 94305, USA
- Department of Pediatrics (Systems Medicine), Stanford University, Stanford, California 94305, USA
| |
Collapse
|
36
|
Wang R, Helbig I, Edmondson AC, Lin L, Xing Y. Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis. Brief Bioinform 2023; 24:bbad284. [PMID: 37580177 PMCID: PMC10516351 DOI: 10.1093/bib/bbad284] [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: 03/14/2023] [Revised: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 08/16/2023] Open
Abstract
Genomic variants affecting pre-messenger RNA splicing and its regulation are known to underlie many rare genetic diseases. However, common workflows for genetic diagnosis and clinical variant interpretation frequently overlook splice-altering variants. To better serve patient populations and advance biomedical knowledge, it has become increasingly important to develop and refine approaches for detecting and interpreting pathogenic splicing variants. In this review, we will summarize a few recent developments and challenges in using RNA sequencing technologies for rare disease investigation. Moreover, we will discuss how recent computational splicing prediction tools have emerged as complementary approaches for revealing disease-causing variants underlying splicing defects. We speculate that continuous improvements to sequencing technologies and predictive modeling will not only expand our understanding of splicing regulation but also bring us closer to filling the diagnostic gap for rare disease patients.
Collapse
Affiliation(s)
- Robert Wang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ingo Helbig
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew C Edmondson
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lan Lin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
37
|
Grimes SM, Kim HS, Roy S, Sathe A, Ayala C, Bai X, Almeda-Notestine A, Haebe S, Shree T, Levy R, Lau B, Ji H. Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer. NAR Cancer 2023; 5:zcad034. [PMID: 37435532 PMCID: PMC10331933 DOI: 10.1093/narcan/zcad034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/18/2023] [Accepted: 06/15/2023] [Indexed: 07/13/2023] Open
Abstract
In this proof-of-concept study, we developed a single-cell method that provides genotypes of somatic alterations found in coding regions of messenger RNAs and integrates these transcript-based variants with their matching cell transcriptomes. We used nanopore adaptive sampling on single-cell complementary DNA libraries to validate coding variants in target gene transcripts, and short-read sequencing to characterize cell types harboring the mutations. CRISPR edits for 16 targets were identified using a cancer cell line, and known variants in the cell line were validated using a 352-gene panel. Variants in primary cancer samples were validated using target gene panels ranging from 161 to 529 genes. A gene rearrangement was also identified in one patient, with the rearrangement occurring in two distinct tumor sites.
Collapse
Affiliation(s)
- Susan M Grimes
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Heon Seok Kim
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sharmili Roy
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anuja Sathe
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carlos I Ayala
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xiangqi Bai
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alison F Almeda-Notestine
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah Haebe
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tanaya Shree
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ronald Levy
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Billy T Lau
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Engineering, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
38
|
Yoshida-Tanaka K, Ikemoto K, Kuribayashi R, Unoki M, Takano T, Fujimoto A. Long-read sequencing reveals the complex structure of extra dic(21;21) chromosome and its biological effects. Hum Genet 2023; 142:1375-1384. [PMID: 37432452 PMCID: PMC10449678 DOI: 10.1007/s00439-023-02583-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/27/2023] [Indexed: 07/12/2023]
Abstract
Complex congenital chromosome abnormalities are rare but often cause severe symptoms. However, the structures and biological impacts of such abnormalities have seldomly been analyzed at the molecular level. Previously, we reported a Japanese female patient with severe developmental defects. The patient had an extra dicentric chromosome 21 (chr21) consisting of two partial chr21 copies fused together within their long arms along with two centromeres and many copy number changes. In this study, we performed whole-genome, transcriptional, and DNA methylation analyses, coupled with novel bioinformatic approaches, to reveal the complex structure of the extra chromosome and its transcriptional and epigenetic changes. Long-read sequencing accurately identified the structures of junctions related to the copy number changes in extra chr21 and suggested the mechanism of the structural changes. Our transcriptome analysis showed the overexpression of genes in extra chr21. Additionally, an allele-specific DNA methylation analysis of the long-read sequencing data suggested that the centromeric region of extra chr21 was hypermethylated, a property associated with the inactivation of one centromere in the extra chromosome. Our comprehensive analysis provides insights into the molecular mechanism underlying the generation of the extra chromosome and its pathogenic roles.
Collapse
Affiliation(s)
- Kugui Yoshida-Tanaka
- Department of Human Genetics, School of International Health, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Ko Ikemoto
- Department of Human Genetics, School of International Health, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Ryoji Kuribayashi
- Department of Human Genetics, School of International Health, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Motoko Unoki
- Department of Human Genetics, School of International Health, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Takako Takano
- Department of Child Health, Tokyo Kasei University, 1-18-1 Kaga, Itabashi-Ku, Tokyo, 173-8602, Japan.
- Tokyo Metropolitan Tobu Medical Center for Children with Developmental Disabilities, Tokyo, Japan.
| | - Akihiro Fujimoto
- Department of Human Genetics, School of International Health, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
| |
Collapse
|
39
|
Abstract
DNA sequencing has revolutionized medicine over recent decades. However, analysis of large structural variation and repetitive DNA, a hallmark of human genomes, has been limited by short-read technology, with read lengths of 100-300 bp. Long-read sequencing (LRS) permits routine sequencing of human DNA fragments tens to hundreds of kilobase pairs in size, using both real-time sequencing by synthesis and nanopore-based direct electronic sequencing. LRS permits analysis of large structural variation and haplotypic phasing in human genomes and has enabled the discovery and characterization of rare pathogenic structural variants and repeat expansions. It has also recently enabled the assembly of a complete, gapless human genome that includes previously intractable regions, such as highly repetitive centromeres and homologous acrocentric short arms. With the addition of protocols for targeted enrichment, direct epigenetic DNA modification detection, and long-range chromatin profiling, LRS promises to launch a new era of understanding of genetic diversity and pathogenic mutations in human populations.
Collapse
Affiliation(s)
- Peter E Warburton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
40
|
Romagnoli S, Bartalucci N, Vannucchi AM. Resolving complex structural variants via nanopore sequencing. Front Genet 2023; 14:1213917. [PMID: 37674481 PMCID: PMC10479017 DOI: 10.3389/fgene.2023.1213917] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/26/2023] [Indexed: 09/08/2023] Open
Abstract
The recent development of high-throughput sequencing platforms provided impressive insights into the field of human genetics and contributed to considering structural variants (SVs) as the hallmark of genome instability, leading to the establishment of several pathologic conditions, including neoplasia and neurodegenerative and cognitive disorders. While SV detection is addressed by next-generation sequencing (NGS) technologies, the introduction of more recent long-read sequencing technologies have already been proven to be invaluable in overcoming the inaccuracy and limitations of NGS technologies when applied to resolve wide and structurally complex SVs due to the short length (100-500 bp) of the sequencing read utilized. Among the long-read sequencing technologies, Oxford Nanopore Technologies developed a sequencing platform based on a protein nanopore that allows the sequencing of "native" long DNA molecules of virtually unlimited length (typical range 1-100 Kb). In this review, we focus on the bioinformatics methods that improve the identification and genotyping of known and novel SVs to investigate human pathological conditions, discussing the possibility of introducing nanopore sequencing technology into routine diagnostics.
Collapse
Affiliation(s)
| | | | - Alessandro Maria Vannucchi
- CRIMM, Center of Research and Innovation of Myeloproliferative Neoplasms, DENOTHE Excellence Center, Careggi University Hospital and Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| |
Collapse
|
41
|
Shiraishi Y, Koya J, Chiba K, Okada A, Arai Y, Saito Y, Shibata T, Kataoka K. Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv. Nucleic Acids Res 2023; 51:e74. [PMID: 37336583 PMCID: PMC10415145 DOI: 10.1093/nar/gkad526] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/23/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023] Open
Abstract
We present our novel software, nanomonsv, for detecting somatic structural variations (SVs) using tumor and matched control long-read sequencing data with a single-base resolution. The current version of nanomonsv includes two detection modules, Canonical SV module, and Single breakend SV module. Using tumor/control paired long-read sequencing data from three cancer and their matched lymphoblastoid lines, we demonstrate that Canonical SV module can identify somatic SVs that can be captured by short-read technologies with higher precision and recall than existing methods. In addition, we have developed a workflow to classify mobile element insertions while elucidating their in-depth properties, such as 5' truncations, internal inversions, as well as source sites for 3' transductions. Furthermore, Single breakend SV module enables the detection of complex SVs that can only be identified by long-reads, such as SVs involving highly-repetitive centromeric sequences, and LINE1- and virus-mediated rearrangements. In summary, our approaches applied to cancer long-read sequencing data can reveal various features of somatic SVs and will lead to a better understanding of mutational processes and functional consequences of somatic SVs.
Collapse
Affiliation(s)
- Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Junji Koya
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Ai Okada
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Hematology, Keio University School of Medicine, Tokyo, Japan
| |
Collapse
|
42
|
Gupta P, Nakamichi K, Bonnell AC, Yanagihara R, Radulovich N, Hisama FM, Chao JR, Mustafi D. Familial co-segregation and the emerging role of long-read sequencing to re-classify variants of uncertain significance in inherited retinal diseases. NPJ Genom Med 2023; 8:20. [PMID: 37558662 PMCID: PMC10412581 DOI: 10.1038/s41525-023-00366-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023] Open
Abstract
Phasing genetic variants is essential in determining those that are potentially disease-causing. In autosomal recessive inherited retinal diseases (IRDs), reclassification of variants of uncertain significance (VUS) can provide a genetic diagnosis in indeterminate compound heterozygote cases. We report four cases in which familial co-segregation demonstrated a VUS resided in trans to a known pathogenic variant, which in concert with other supporting criteria, led to the reclassification of the VUS to likely pathogenic, thereby providing a genetic diagnosis in each case. We also demonstrate in a simplex patient without access to family members for co-segregation analysis that targeted long-read sequencing can provide haplotagged variant calling. This can elucidate if variants reside in trans and provide phase of genetic variants from the proband alone without parental testing. This emerging method can alleviate the bottleneck of haplotype analysis in cases where genetic testing of family members is unfeasible to provide a complete genetic diagnosis.
Collapse
Affiliation(s)
- Pankhuri Gupta
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Kenji Nakamichi
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA
| | - Alyssa C Bonnell
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA
| | - Ryan Yanagihara
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA
| | - Nick Radulovich
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA
| | - Fuki M Hisama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Jennifer R Chao
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA
| | - Debarshi Mustafi
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA.
- Division of Ophthalmology, Seattle Children's Hospital, Seattle, WA, 98105, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195, USA.
| |
Collapse
|
43
|
Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O'Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: What's next in diagnostic testing for Mendelian conditions. Am J Hum Genet 2023; 110:1229-1248. [PMID: 37541186 PMCID: PMC10432150 DOI: 10.1016/j.ajhg.2023.06.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 08/06/2023] Open
Abstract
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order, and emerging technologies, such as optical genome mapping and long-read DNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to research consortia focused on elucidating the underlying cause of rare unsolved genetic disorders.
Collapse
Affiliation(s)
- Monica H Wojcik
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M Reuter
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Michael H Duyzend
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hayk Barseghyan
- Center for Genetics Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC 20010, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Philip M Boone
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emily E Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emmanuèle C Délot
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA; Center for Genetics Medicine Research, Children's National Research and Innovation Campus, Washington, DC, USA; Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen B Montgomery
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Bamshad
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jessica X Chong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Matthew T Wheeler
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seth I Berger
- Center for Genetics Medicine Research and Rare Disease Institute, Children's National Hospital, Washington, DC 20010, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Danny E Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
44
|
Ohori S, Miyauchi A, Osaka H, Lourenco CM, Arakaki N, Sengoku T, Ogata K, Honjo RS, Kim CA, Mitsuhashi S, Frith MC, Seyama R, Tsuchida N, Uchiyama Y, Koshimizu E, Hamanaka K, Misawa K, Miyatake S, Mizuguchi T, Saito K, Fujita A, Matsumoto N. Biallelic structural variations within FGF12 detected by long-read sequencing in epilepsy. Life Sci Alliance 2023; 6:e202302025. [PMID: 37286232 PMCID: PMC10248215 DOI: 10.26508/lsa.202302025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023] Open
Abstract
We discovered biallelic intragenic structural variations (SVs) in FGF12 by applying long-read whole genome sequencing to an exome-negative patient with developmental and epileptic encephalopathy (DEE). We also found another DEE patient carrying a biallelic (homozygous) single-nucleotide variant (SNV) in FGF12 that was detected by exome sequencing. FGF12 heterozygous recurrent missense variants with gain-of-function or heterozygous entire duplication of FGF12 are known causes of epilepsy, but biallelic SNVs/SVs have never been described. FGF12 encodes intracellular proteins interacting with the C-terminal domain of the alpha subunit of voltage-gated sodium channels 1.2, 1.5, and 1.6, promoting excitability by delaying fast inactivation of the channels. To validate the molecular pathomechanisms of these biallelic FGF12 SVs/SNV, highly sensitive gene expression analyses using lymphoblastoid cells from the patient with biallelic SVs, structural considerations, and Drosophila in vivo functional analysis of the SNV were performed, confirming loss-of-function. Our study highlights the importance of small SVs in Mendelian disorders, which may be overlooked by exome sequencing but can be detected efficiently by long-read whole genome sequencing, providing new insights into the pathomechanisms of human diseases.
Collapse
Affiliation(s)
- Sachiko Ohori
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Genetics, Kitasato University Hospital, Sagamihara, Japan
| | - Akihiko Miyauchi
- Department of Pediatrics, Jichi Medical School, Shimotsuke, Japan
| | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical School, Shimotsuke, Japan
| | - Charles Marques Lourenco
- Neurogenetics Department, Faculdade de Medicina de São José do Rio Preto, São Jose do Rio Preto, Brazil
- Personalized Medicine Department, Special Education Sector at DLE/Grupo Pardini, Belo Horizonte, Brazil
| | - Naohiro Arakaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Shizuoka, Japan
| | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Rachel Sayuri Honjo
- Unidade de Genética Médica do Instituto da Criança, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Chong Ae Kim
- Unidade de Genética Médica do Instituto da Criança, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Satomi Mitsuhashi
- Department of Neurology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Martin C Frith
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
- Computational Bio Big-Data Open Innovation Laboratory, AIST, Tokyo, Japan
| | - Rie Seyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kuniaki Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Shizuoka, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| |
Collapse
|
45
|
Liu Q, Xu F, Liu Q, Liu X. Comparative analysis of five etiological detecting techniques for the positive rates in the diagnosis of tuberculous granuloma. J Clin Tuberc Other Mycobact Dis 2023; 32:100378. [PMID: 37293271 PMCID: PMC10245093 DOI: 10.1016/j.jctube.2023.100378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Abstract
Purpose To examine the relationship between the positive rate and types of necrosis in pathological examinations of tuberculosis granulomas with necrosis, to improve the detection rate of positive cases. Methods Specimens from 381 patients were collected in Wuhan Pulmonary Hospital from Jan 2022 to Feb 2023. The samples were examined using various methods such as AFB smear microscopy, mycobacterial culture, PCR, SAT-TB, and X-pert MTB/RIF rapid molecular detection. Result There were 3 types of necrosis. Including 270 cases of caseous necrosis, 30 cases of coagulation necrosis, and 76 cases of an abscess. Five cases were non-necrotizing granulomas.In the pathological specimen testing for tuberculosis, five detection techniques were used and their positive rates detected in descending order were X-pert, TBDNA, SAT-TB, tuberculosis culture, AFB. Comparison between different examinations in the group: X-pert had the highest positive rate in each group, and it was significantly higher than TBDNA (P < 0.01) in caseous necrosis specimens. Compared with the same examination between the groups, the detection rates of X-pert and TBDNA in abscess and caseous necrosis specimens were significantly higher than in coagulation necrosis specimens (P < 0.01). Conclusion The positive rates of the five etiological detection techniques in tuberculous granuloma with different types of necrosis were quite different. The specimens of caseous necrosis or abscess could be selected for detection, and X-pert had the highest positive rate.
Collapse
Affiliation(s)
- Qibin Liu
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng Road, Qiaokou District, Wuhan City, Hubei Province, China
| | - Feng Xu
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng, Road, Qiaokou District, Wuhan City, Hubei Province, China
| | - Qiliang Liu
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng, Road, Qiaokou District, Wuhan City, Hubei Province, China
| | - Xiaoyu Liu
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng Road, Qiaokou District, Wuhan City, Hubei Province, China
| |
Collapse
|
46
|
Hort Y, Sullivan P, Wedd L, Fowles L, Stevanovski I, Deveson I, Simons C, Mallett A, Patel C, Furlong T, Cowley MJ, Shine J, Mallawaarachchi A. Atypical splicing variants in PKD1 explain most undiagnosed typical familial ADPKD. NPJ Genom Med 2023; 8:16. [PMID: 37419908 DOI: 10.1038/s41525-023-00362-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/26/2023] [Indexed: 07/09/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenic cause of kidney failure and is primarily associated with PKD1 or PKD2. Approximately 10% of patients remain undiagnosed after standard genetic testing. We aimed to utilise short and long-read genome sequencing and RNA studies to investigate undiagnosed families. Patients with typical ADPKD phenotype and undiagnosed after genetic diagnostics were recruited. Probands underwent short-read genome sequencing, PKD1 and PKD2 coding and non-coding analyses and then genome-wide analysis. Targeted RNA studies investigated variants suspected to impact splicing. Those undiagnosed then underwent Oxford Nanopore Technologies long-read genome sequencing. From over 172 probands, 9 met inclusion criteria and consented. A genetic diagnosis was made in 8 of 9 (89%) families undiagnosed on prior genetic testing. Six had variants impacting splicing, five in non-coding regions of PKD1. Short-read genome sequencing identified novel branchpoint, AG-exclusion zone and missense variants generating cryptic splice sites and a deletion causing critical intron shortening. Long-read sequencing confirmed the diagnosis in one family. Most undiagnosed families with typical ADPKD have splice-impacting variants in PKD1. We describe a pragmatic method for diagnostic laboratories to assess PKD1 and PKD2 non-coding regions and validate suspected splicing variants through targeted RNA studies.
Collapse
Affiliation(s)
- Yvonne Hort
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia
| | - Patricia Sullivan
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Laura Wedd
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia
| | - Lindsay Fowles
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Igor Stevanovski
- Genomic Technologies, Garvan Institute of Medical Research, Sydney, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, Australia
| | - Ira Deveson
- Genomic Technologies, Garvan Institute of Medical Research, Sydney, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, Australia
| | - Cas Simons
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Andrew Mallett
- Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Timothy Furlong
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - John Shine
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia
| | - Amali Mallawaarachchi
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia.
- Clinical Genetics Service, Institute of Precision Medicine and Bioinformatics, Royal Prince Alfred Hospital, Sydney, Australia.
| |
Collapse
|
47
|
Laufer VA, Glover TW, Wilson TE. Applications of advanced technologies for detecting genomic structural variation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108475. [PMID: 37931775 PMCID: PMC10792551 DOI: 10.1016/j.mrrev.2023.108475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.
Collapse
Affiliation(s)
- Vincent A Laufer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas W Glover
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas E Wilson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| |
Collapse
|
48
|
Noveski P, Plaseski T, Dimitrovska M, Plaseska-Karanfilska D. Androgen Insensitivity Syndrome DUE to Non-Coding Variation in the Androgen Receptor Gene: Review of the Literature and Case Report of a Patient with Mosaic c.-547C>T Variant. Balkan J Med Genet 2023; 26:51-56. [PMID: 37576790 PMCID: PMC10413879 DOI: 10.2478/bjmg-2023-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
Sexual development (SD) is a complex process with strict spatiotemporal regulation of gene expression. Despite advancements in molecular diagnostics, disorders of sexual development (DSD) have a diagnostic rate of ~50%. Androgen insensitivity syndrome (AIS) represents the most common form of 46,XY DSD, with a spectrum of defects in androgen action. Considering the importance of very strict regulation of the SD, it is reasonable to assume that the genetic cause for proportion of the DSD lies in the non-coding part of the genome that regulates proper gene functioning. Here we present a patient with partial AIS (PAIS) due to a mosaic de novo c.-547C>T pathogenic variant in the 5'UTR of androgen receptor (AR) gene. The same mutation was previously described as inherited, in two unrelated patients with complete AIS (CAIS). Thus, our case further confirms the previous findings that variable gene expressivity could be attributed to mosaicism. Mutations in 5'UTR could create new upstream open reading frames (uORFs) or could disrupt the existing one. A recent systematic genome-wide study identified AR as a member of a subset of genes where modifications of uORFs represents an important disease mechanism. Only a small number of studies are reporting non-coding mutations in the AR gene and our case emphasizes the importance of molecular testing of the entire AR locus in AIS patients. The introduction of new methods for comprehensive molecular testing in routine genetic diagnosis, accompanied with new tools for in sillico analysis could improve the genetic diagnosis of AIS, and DSD in general.
Collapse
Affiliation(s)
- P Noveski
- Research Centre for Genetic Engineering and Biotechnology ‘Georgi D. Efremov’, Macedonian Academy of Sciences and Arts, 1000Skopje, Republic of North Macedonia
| | - T Plaseski
- University Clinic of Endocrinology, Diabetes and Metabolic Disorders, Clinical Centre “Mother Teresa“, 1000Skopje, Republic of North Macedonia
| | - M Dimitrovska
- University Clinic of Endocrinology, Diabetes and Metabolic Disorders, Clinical Centre “Mother Teresa“, 1000Skopje, Republic of North Macedonia
| | - D Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology ‘Georgi D. Efremov’, Macedonian Academy of Sciences and Arts, 1000Skopje, Republic of North Macedonia
| |
Collapse
|
49
|
Yahya S, Watson CM, Carr I, McKibbin M, Crinnion LA, Taylor M, Bonin H, Fletcher T, El-Asrag ME, Ali M, Toomes C, Inglehearn CF. Long-Read Nanopore Sequencing of RPGR ORF15 is Enhanced Following DNase I Treatment of MinION Flow Cells. Mol Diagn Ther 2023; 27:525-535. [PMID: 37284979 PMCID: PMC10299921 DOI: 10.1007/s40291-023-00656-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2023] [Indexed: 06/08/2023]
Abstract
INTRODUCTION RPGR ORF15 is an exon present almost exclusively in the retinal transcript of RPGR. It is purine-rich, repetitive and notoriously hard to sequence, but is a hotspot for mutations causing X-linked retinitis pigmentosa. METHODS Long-read nanopore sequencing on MinION and Flongle flow cells was used to sequence RPGR ORF15 in genomic DNA from patients with inherited retinal dystrophy. A flow cell wash kit was used on a MinION flow cell to increase yield. Findings were confirmed by PacBio SMRT long-read sequencing. RESULTS We showed that long-read nanopore sequencing successfully reads through a 2 kb PCR-amplified fragment containing ORF15. We generated reads of sufficient quality and cumulative read-depth to detect pathogenic RP-causing variants. However, we observed that this G-rich, repetitive DNA segment rapidly blocks the available pores, resulting in sequence yields less than 5% of the expected output. This limited the extent to which samples could be pooled, increasing cost. We tested the utility of a MinION wash kit containing DNase I to digest DNA fragments remaining on the flow cell, regenerating the pores. Use of the DNase I treatment allowed repeated re-loading, increasing the sequence reads obtained. Our customised workflow was used to screen pooled amplification products from previously unsolved inherited retinal disease (IRD) in patients, identifying two new cases with pathogenic ORF15 variants. DISCUSSION We report the novel finding that long-read nanopore sequencing can read through RPGR-ORF15, a DNA sequence not captured by short-read next-generation sequencing (NGS), but with a more reduced yield. Use of a flow cell wash kit containing DNase I unblocks the pores, allowing reloading of further library aliquots over a 72-h period, increasing yield. The workflow we describe provides a novel solution to the need for a rapid, robust, scalable, cost-effective ORF15 screening protocol.
Collapse
Affiliation(s)
- Samar Yahya
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- Department of Medical Genetics, School of Medicine, King Abdulaziz University, Rabigh, Kingdom of Saudi Arabia
| | - Christopher M Watson
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | - Ian Carr
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Martin McKibbin
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- Department of Ophthalmology, St. James's University Hospital, Leeds, UK
| | - Laura A Crinnion
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Morag Taylor
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Hope Bonin
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Tracy Fletcher
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Mohammed E El-Asrag
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- Department of Zoology, Faculty of Science, Benha University, Banha, Egypt
- Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, UK
| | - Manir Ali
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Carmel Toomes
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK.
| |
Collapse
|
50
|
Wrenn DC, Drown DM. Nanopore Adaptive Sampling Enriches for Antimicrobial Resistance Genes in Microbial Communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546783. [PMID: 37425917 PMCID: PMC10327016 DOI: 10.1101/2023.06.27.546783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Antimicrobial resistance (AMR) is a global public health threat. Environmental microbial communities act as reservoirs for AMR, containing genes associated with resistance, their precursors, and the selective pressures to encourage their persistence. Genomic surveillance could provide insight into how these reservoirs are changing and their impact on public health. The ability to enrich for AMR genomic signatures in complex microbial communities would strengthen surveillance efforts and reduce time-to-answer. Here, we test the ability of nanopore sequencing and adaptive sampling to enrich for AMR genes in a mock community of environmental origin. Our setup implemented the MinION mk1B, an NVIDIA Jetson Xavier GPU, and flongle flow cells. We observed consistent enrichment by composition when using adaptive sampling. On average, adaptive sampling resulted in a target composition that was 4x higher than a treatment without adaptive sampling. Despite a decrease in total sequencing output, the use of adaptive sampling increased target yield in most replicates.
Collapse
Affiliation(s)
- Danielle C. Wrenn
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Devin M. Drown
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| |
Collapse
|