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Agha Gholizadeh M, Behjati F, Ghasemi Firouzabadi S, Heidari E, Razmara E, Almadani N, Sharifi Zarchi A, Garshasbi M. Novel splicing variant and gonadal mosaicism in DYRK1A gene identified by whole-genome sequencing in multiplex autism spectrum disorder families. Neurogenetics 2024:10.1007/s10048-024-00768-6. [PMID: 38976082 DOI: 10.1007/s10048-024-00768-6] [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: 05/15/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with considerable genetic heterogeneity. The disorder is clinically diagnosed based on DSM-5 criteria, featuring deficits in social communication and interaction, along with restricted and repetitive behaviours. Here, we performed whole-genome sequencing (WGS) on four individuals with ASD from two multiplex families (MPX), where more than one individual is affected, to identify potential single nucleotide variants (SNVs) and structural variants (SVs) in coding and non-coding regions. A rigorous bioinformatics pipeline was employed for variant detection, followed by segregation analysis. Our investigation revealed an unreported splicing variant in the DYRK1A gene (c.-77 + 2T > C; IVS1 + 2T > C; NM_001396.5), in heterozygote form in two affected children in one of the families (family B), which was absent in the healthy parents and siblings. This finding suggests the presence of gonadal mosaicism in one of the parents, representing the first documented instance of such inheritance for a variant in the DYRK1A gene associated with ASD. Furthermore, we identified a 50 bp deletion in intron 9 of the DLG2 gene in two affected patients from the same family, confirmed by PCR and Sanger sequencing. In Family A, we identified potential candidate variants associated with ASD shared by the two patients. These findings enhance our understanding of the genetic landscape of ASD, particularly in MPX families, and highlight the utility of WGS in uncovering novel genetic contributions to neurodevelopmental disorders.
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Affiliation(s)
- Mehdi Agha Gholizadeh
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Jalah-Al Ahmad Hwy, Tehran, 14117-1316, Iran
| | - Farkhondeh Behjati
- Genetics Research Centre, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Erfan Heidari
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Jalah-Al Ahmad Hwy, Tehran, 14117-1316, Iran
| | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Jalah-Al Ahmad Hwy, Tehran, 14117-1316, Iran
| | - Navid Almadani
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Ali Sharifi Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Jalah-Al Ahmad Hwy, Tehran, 14117-1316, Iran.
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2
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Fehlings DL, Zarrei M, Engchuan W, Sondheimer N, Thiruvahindrapuram B, MacDonald JR, Higginbotham EJ, Thapa R, Behlim T, Aimola S, Switzer L, Ng P, Wei J, Danthi PS, Pellecchia G, Lamoureux S, Ho K, Pereira SL, de Rijke J, Sung WWL, Mowjoodi A, Howe JL, Nalpathamkalam T, Manshaei R, Ghaffari S, Whitney J, Patel RV, Hamdan O, Shaath R, Trost B, Knights S, Samdup D, McCormick A, Hunt C, Kirton A, Kawamura A, Mesterman R, Gorter JW, Dlamini N, Merico D, Hilali M, Hirschfeld K, Grover K, Bautista NX, Han K, Marshall CR, Yuen RKC, Subbarao P, Azad MB, Turvey SE, Mandhane P, Moraes TJ, Simons E, Maxwell G, Shevell M, Costain G, Michaud JL, Hamdan FF, Gauthier J, Uguen K, Stavropoulos DJ, Wintle RF, Oskoui M, Scherer SW. Comprehensive whole-genome sequence analyses provide insights into the genomic architecture of cerebral palsy. Nat Genet 2024; 56:585-594. [PMID: 38553553 DOI: 10.1038/s41588-024-01686-x] [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: 12/23/2022] [Accepted: 02/13/2024] [Indexed: 04/17/2024]
Abstract
We performed whole-genome sequencing (WGS) in 327 children with cerebral palsy (CP) and their biological parents. We classified 37 of 327 (11.3%) children as having pathogenic/likely pathogenic (P/LP) variants and 58 of 327 (17.7%) as having variants of uncertain significance. Multiple classes of P/LP variants included single-nucleotide variants (SNVs)/indels (6.7%), copy number variations (3.4%) and mitochondrial mutations (1.5%). The COL4A1 gene had the most P/LP SNVs. We also analyzed two pediatric control cohorts (n = 203 trios and n = 89 sib-pair families) to provide a baseline for de novo mutation rates and genetic burden analyses, the latter of which demonstrated associations between de novo deleterious variants and genes related to the nervous system. An enrichment analysis revealed previously undescribed plausible candidate CP genes (SMOC1, KDM5B, BCL11A and CYP51A1). A multifactorial CP risk profile and substantial presence of P/LP variants combine to support WGS in the diagnostic work-up across all CP and related phenotypes.
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Affiliation(s)
- Darcy L Fehlings
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Neal Sondheimer
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ritesh Thapa
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Tarannum Behlim
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Sabrina Aimola
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Lauren Switzer
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Pamela Ng
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Prakroothi S Danthi
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Karen Ho
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jill de Rijke
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wilson W L Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alireza Mowjoodi
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jennifer L Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Roozbeh Manshaei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Siavash Ghaffari
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joseph Whitney
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rohan V Patel
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Omar Hamdan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rulan Shaath
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shannon Knights
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Grandview Children's Centre, Oshawa, Ontario, Canada
| | - Dawa Samdup
- Department of Pediatrics, Queen's University, Kingston, Ontario, Canada
| | - Anna McCormick
- Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, Ontario, Canada
| | - Carolyn Hunt
- Grandview Children's Centre, Oshawa, Ontario, Canada
| | - Adam Kirton
- Department of Pediatrics, Department of Clinical Neuroscience, University of Calgary, Calgary, Alberta, Canada
| | - Anne Kawamura
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ronit Mesterman
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Jan Willem Gorter
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Nomazulu Dlamini
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Neurosciences and Mental Health Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Deep Genomics Inc., Toronto, Ontario, Canada
- Vevo Therapeutics Inc., San Francisco, CA, USA
| | - Murto Hilali
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kyle Hirschfeld
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kritika Grover
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nelson X Bautista
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kara Han
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christian R Marshall
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ryan K C Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Padmaja Subbarao
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Meghan B Azad
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Piush Mandhane
- Faculty of Medicine & Dentistry, Pediatrics Department, University of Alberta, Edmonton, Alberta, Canada
| | - Theo J Moraes
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Program in Translation Medicine & Division of Respiratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elinor Simons
- Department of Pediatrics and Child Health, Section of Allergy and Clinical Immunology, University of Manitoba, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - George Maxwell
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Michael Shevell
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Departments of Pediatrics and Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Gregory Costain
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jacques L Michaud
- Departments of Pediatrics and Neurosciences, Université de Montréal, Montréal, Québec, Canada
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
| | - Fadi F Hamdan
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada
| | - Julie Gauthier
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada
| | - Kevin Uguen
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maryam Oskoui
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Departments of Pediatrics and Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada.
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3
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Kvapilova K, Misenko P, Radvanszky J, Brzon O, Budis J, Gazdarica J, Pos O, Korabecna M, Kasny M, Szemes T, Kvapil P, Paces J, Kozmik Z. Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses. BMC Genomics 2024; 25:187. [PMID: 38365587 PMCID: PMC10873937 DOI: 10.1186/s12864-024-10080-0] [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: 09/05/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Whole exome sequencing (WES) and whole genome sequencing (WGS) have become standard methods in human clinical diagnostics as well as in population genomics (POPGEN). Blood-derived genomic DNA (gDNA) is routinely used in the clinical environment. Conversely, many POPGEN studies and commercial tests benefit from easy saliva sampling. Here, we evaluated the quality of variant call sets and the level of genotype concordance of single nucleotide variants (SNVs) and small insertions and deletions (indels) for WES and WGS using paired blood- and saliva-derived gDNA isolates employing genomic reference-based validated protocols. METHODS The genomic reference standard Coriell NA12878 was repeatedly analyzed using optimized WES and WGS protocols, and data calls were compared with the truth dataset published by the Genome in a Bottle Consortium. gDNA was extracted from the paired blood and saliva samples of 10 participants and processed using the same protocols. A comparison of paired blood-saliva call sets was performed in the context of WGS and WES genomic reference-based technical validation results. RESULTS The quality pattern of called variants obtained from genomic-reference-based technical replicates correlates with data calls of paired blood-saliva-derived samples in all levels of tested examinations despite a higher rate of non-human contamination found in the saliva samples. The F1 score of 10 blood-to-saliva-derived comparisons ranged between 0.8030-0.9998 for SNVs and between 0.8883-0.9991 for small-indels in the case of the WGS protocol, and between 0.8643-0.999 for SNVs and between 0.7781-1.000 for small-indels in the case of the WES protocol. CONCLUSION Saliva may be considered an equivalent material to blood for genetic analysis for both WGS and WES under strict protocol conditions. The accuracy of sequencing metrics and variant-detection accuracy is not affected by choosing saliva as the gDNA source instead of blood but much more significantly by the genomic context, variant types, and the sequencing technology used.
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Affiliation(s)
- Katerina Kvapilova
- Faculty of Science, Charles University, Albertov 6, Prague, 128 00, Czech Republic.
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic.
| | - Pavol Misenko
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
| | - Jan Radvanszky
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Institute of Clinical and Translational Research, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská Cesta 9, Bratislava, 845 05, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 3278/6, Karlova Ves, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
| | - Ondrej Brzon
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic
| | - Jaroslav Budis
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
- Slovak Centre for Scientific and Technical Information, Staré Mesto, Lamačská Cesta 8A, Bratislava, 811 04, Slovakia
| | - Juraj Gazdarica
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
- Slovak Centre for Scientific and Technical Information, Staré Mesto, Lamačská Cesta 8A, Bratislava, 811 04, Slovakia
| | - Ondrej Pos
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
| | - Marie Korabecna
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, Prague, 128 00, Czech Republic
| | - Martin Kasny
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Tomas Szemes
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 3278/6, Karlova Ves, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
| | - Petr Kvapil
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic
| | - Jan Paces
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 142 20, Czech Republic
| | - Zbynek Kozmik
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 142 20, Czech Republic
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4
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Bhérer C, Eveleigh R, Trajanoska K, St-Cyr J, Paccard A, Nadukkalam Ravindran P, Caron E, Bader Asbah N, McClelland P, Wei C, Baumgartner I, Schindewolf M, Döring Y, Perley D, Lefebvre F, Lepage P, Bourgey M, Bourque G, Ragoussis J, Mooser V, Taliun D. A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome. NPJ Genom Med 2024; 9:8. [PMID: 38326393 PMCID: PMC10850497 DOI: 10.1038/s41525-024-00390-3] [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: 05/12/2023] [Accepted: 12/07/2023] [Indexed: 02/09/2024] Open
Abstract
Whole genome sequencing (WGS) at high-depth (30X) allows the accurate discovery of variants in the coding and non-coding DNA regions and helps elucidate the genetic underpinnings of human health and diseases. Yet, due to the prohibitive cost of high-depth WGS, most large-scale genetic association studies use genotyping arrays or high-depth whole exome sequencing (WES). Here we propose a cost-effective method which we call "Whole Exome Genome Sequencing" (WEGS), that combines low-depth WGS and high-depth WES with up to 8 samples pooled and sequenced simultaneously (multiplexed). We experimentally assess the performance of WEGS with four different depth of coverage and sample multiplexing configurations. We show that the optimal WEGS configurations are 1.7-2.0 times cheaper than standard WES (no-plexing), 1.8-2.1 times cheaper than high-depth WGS, reach similar recall and precision rates in detecting coding variants as WES, and capture more population-specific variants in the rest of the genome that are difficult to recover when using genotype imputation methods. We apply WEGS to 862 patients with peripheral artery disease and show that it directly assesses more known disease-associated variants than a typical genotyping array and thousands of non-imputable variants per disease-associated locus.
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Affiliation(s)
- Claude Bhérer
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Robert Eveleigh
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Katerina Trajanoska
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Janick St-Cyr
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Antoine Paccard
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Praveen Nadukkalam Ravindran
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Elizabeth Caron
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Nimara Bader Asbah
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Peyton McClelland
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Clare Wei
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Iris Baumgartner
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Marc Schindewolf
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Yvonne Döring
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University Munich, Pettenkoferstr 9, 80336, Munich, Germany
| | - Danielle Perley
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - François Lefebvre
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Pierre Lepage
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | | | - Guillaume Bourque
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Vincent Mooser
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Daniel Taliun
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada.
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada.
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada.
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5
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Badura-Stronka M, Wołyńska K, Winczewska-Wiktor A, Marcinkowska J, Karolewska D, Tomkowiak-Kędzia D, Piechota M, Przyborska M, Kochalska N, Steinborn B. Validation of targeted next-generation sequencing panels in a cohort of Polish patients with epilepsy: assessing variable performance across clinical endophenotypes and uncovering novel genetic variants. Front Neurol 2024; 14:1316933. [PMID: 38328757 PMCID: PMC10849089 DOI: 10.3389/fneur.2023.1316933] [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: 10/10/2023] [Accepted: 12/26/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction Targeted Next-Generation Sequencing Panels (TNGSP) have become a standard in global clinical practice. Instead of questioning the necessity of next-generation sequencing in epilepsy patients, contemporary large-scale research focuses on factors such as the size of TNGSP, the comparative advantages of exome or genome-wide sequencing over TNGSP, and the impact of clinical, electrophysiological, and demographic variables on genetic test performance. This study aims to elucidate the demographic and clinical factors influencing the performance of TNGSP in 138 Polish patients with epilepsy, recognizing the pivotal role of genetic testing in guiding patient management and therapy. Methods A retrospective analysis was conducted on patients from a genetic clinic in Poznań, Poland, who underwent commercial gene panel studies at Invitae Corporation (USA) between 2020 and 2022. Patient groups were defined based on the age of onset of the first epileptic seizures, seizure type, gender, fever dependence of seizures, presence of intellectual disability or developmental delay, abnormalities in MRI, and the presence of dysmorphic features or congenital malformations. Seizure classification followed the 2017 ILAE criteria. Results Among the 138 patients, 30 (21.7%) exhibited a pathogenic or likely pathogenic variant, with a distribution of 20.7% in males and 22.5% in females. Diagnostic performance correlated with the patient's age at the onset of the first seizure and the type of seizure. Predominant variants were identified in the SCN1A, PRRT2, CDKL5, DEPDC5, TSC2, and SLC2A1 genes. Additionally, 12 genes (CACNA1A, SCN2A, GRIN2A, KCNQ2, CHD2, DYNC1H1, NEXMIF, SCN1B, DDX3X, EEF1A2, NPRL3, UBE3A) exhibited single instances of damage. Notably, novel variants were discovered in DEPDC5, SCN1A, TSC2, CDKL5, NPRL3, DYNC1H1, CHD2, and DDX3X. Discussion Identified variants were present in genes previously recognized in both European and non-European populations. A thorough examination of Variants of Uncertain Significance (VUSs), specifically focusing on gene copy number changes, may unveil more extensive chromosomal aberrations. The relatively frequent occurrence of pathological variants in X chromosome-linked genes in girls warrants further investigation, challenging the prevailing notion of male predominance in X-linked epilepsy.
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Affiliation(s)
- Magdalena Badura-Stronka
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, Poznań, Poland
- Centers for Medical Genetics GENESIS, Poznań, Poland
| | - Katarzyna Wołyńska
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, Poznań, Poland
| | - Anna Winczewska-Wiktor
- Chair and Department of Developmental Neurology, Poznan University of Medical Sciences, Poznań, Poland
| | - Justyna Marcinkowska
- Chair and Department of Informatics and Statistics, Poznan University of Medical Sciences, Poznań, Poland
| | | | | | | | | | | | - Barbara Steinborn
- Chair and Department of Developmental Neurology, Poznan University of Medical Sciences, Poznań, Poland
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6
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Zarrei M, Burton CL, Engchuan W, Higginbotham EJ, Wei J, Shaikh S, Roslin NM, MacDonald JR, Pellecchia G, Nalpathamkalam T, Lamoureux S, Manshaei R, Howe J, Trost B, Thiruvahindrapuram B, Marshall CR, Yuen RKC, Wintle RF, Strug LJ, Stavropoulos DJ, Vorstman JAS, Arnold P, Merico D, Woodbury-Smith M, Crosbie J, Schachar RJ, Scherer SW. Gene copy number variation and pediatric mental health/neurodevelopment in a general population. Hum Mol Genet 2023; 32:2411-2421. [PMID: 37154571 PMCID: PMC10360394 DOI: 10.1093/hmg/ddad074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/10/2023] Open
Abstract
We assessed the relationship of gene copy number variation (CNV) in mental health/neurodevelopmental traits and diagnoses, physical health and cognition in a community sample of 7100 unrelated children and youth of European or East Asian ancestry (Spit for Science). Clinically significant or susceptibility CNVs were present in 3.9% of participants and were associated with elevated scores on a continuous measure of attention-deficit/hyperactivity disorder (ADHD) traits (P = 5.0 × 10-3), longer response inhibition (a cognitive deficit found in several mental health and neurodevelopmental disorders; P = 1.0 × 10-2) and increased prevalence of mental health diagnoses (P = 1.9 × 10-6, odds ratio: 3.09), specifically ADHD, autism spectrum disorder anxiety and learning problems/learning disorder (P's < 0.01). There was an increased burden of rare deletions in gene-sets related to brain function or expression in brain associated with more ADHD traits. With the current mental health crisis, our data established a baseline for delineating genetic contributors in pediatric-onset conditions.
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Affiliation(s)
- Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Christie L Burton
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sabah Shaikh
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nicole M Roslin
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Roozbeh Manshaei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jennifer Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | | | - Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ryan K C Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Lisa J Strug
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Departments of Statistical Sciences, Computer Science and Biostatistics, University of Toronto, Toronto, ON M5G 1Z5, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jacob A S Vorstman
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Paul Arnold
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Mathison Centre for Mental Health Research and Education, University of Calgary, Calgary, AB T2N 1N4, Canada
- Departments of Psychiatry & Medical Genetics, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Deep Genomics Inc., Toronto, ON M5G 1M1, Canada
| | - Marc Woodbury-Smith
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jennifer Crosbie
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Russell J Schachar
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A8, Canada
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Domi T, Robertson A, Lee W, Wintle RF, Stence N, Bernard T, Kirton A, Carlson H, Andrade A, Rafay MF, Bjornson B, Kim D, Dowling M, Bonnett W, Rivkin M, Krishnan P, Shroff M, Ertl-Wagner B, Strother S, Arnott S, Wintermark M, Kassner A, deVeber G, Dlamini N. The development of the pediatric stroke neuroimaging platform (PEDSNIP). Neuroimage Clin 2023; 39:103438. [PMID: 37354865 PMCID: PMC10331307 DOI: 10.1016/j.nicl.2023.103438] [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: 03/18/2023] [Accepted: 05/15/2023] [Indexed: 06/26/2023]
Abstract
Childhood stroke occurs from birth to 18 years of age, ranks among the top ten childhood causes of death, and leaves lifelong neurological impairments. Arterial ischemic stroke in infancy and childhood occurs due to arterial occlusion in the brain, resulting in a focal lesion. Our understanding of mechanisms of injury and repair associated with focal injury in the developing brain remains rudimentary. Neuroimaging can reveal important insights into these mechanisms. In adult stroke population, multi-center neuroimaging studies are common and have accelerated the translation process leading to improvements in treatment and outcome. These studies are centered on the growing evidence that neuroimaging measures and other biomarkers (e.g., from blood and cerebrospinal fluid) can enhance our understanding of mechanisms of risk and injury and be used as complementary outcome markers. These factors have yet to be studied in pediatric stroke because most neuroimaging studies in this population have been conducted in single-centred, small cohorts. By pooling neuroimaging data across multiple sites, larger cohorts of patients can significantly boost study feasibility and power in elucidating mechanisms of brain injury, repair and outcomes. These aims are particularly relevant in pediatric stroke because of the decreased incidence rates and the lack of mechanism-targeted trials. Toward these aims, we developed the Pediatric Stroke Neuroimaging Platform (PEDSNIP) in 2015, funded by The Brain Canada Platform Support Grant, to focus on three identified neuroimaging priorities. These were: developing and harmonizing multisite clinical protocols, creating the infrastructure and methods to import, store and organize the large clinical neuroimaging dataset from multiple sites through the International Pediatric Stroke Study (IPSS), and enabling central searchability. To do this, developed a two-pronged approach that included building 1) A Clinical-MRI Data Repository (standard of care imaging) linked to clinical data and longitudinal outcomes and 2) A Research-MRI neuroimaging data set acquired through our extensive collaborative, multi-center, multidisciplinary network. This dataset was collected prospectively in eight North American centers to test the feasibility and implementation of harmonized advanced Research-MRI, with the addition of clinical information, genetic and proteomic studies, in a cohort of children presenting with acute ischemic stroke. Here we describe the process that enabled the development of PEDSNIP built to provide the infrastructure to support neuroimaging research priorities in pediatric stroke. Having built this Platform, we are now able to utilize the largest neuroimaging and clinical data pool on pediatric stroke data worldwide to conduct hypothesis-driven research. We are actively working on a bioinformatics approach to develop predictive models of risk, injury and repair and accelerate breakthrough discoveries leading to mechanism-targeted treatments that improve outcomes and minimize the burden following childhood stroke. This unique transformational resource for scientists and researchers has the potential to result in a paradigm shift in the management, outcomes and quality of life in children with stroke and their families, with far-reaching benefits for other brain conditions of people across the lifespan.
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Affiliation(s)
- Trish Domi
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amanda Robertson
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wayne Lee
- Research Operations, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nicholas Stence
- Pediatric Neuroradiology, Children's Hospital Colorado, Aurora, CO, United States; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Timothy Bernard
- Child Neurology and Hemophilia and Thrombosis Center, University of Colorado, Aurora, CO, United States; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Adam Kirton
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Helen Carlson
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrea Andrade
- London Health Sciences Centre, London, United Kingdom; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mubeen F Rafay
- Health Sciences Centre Winnipeg, Winnipeg, Manitoba, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Bruce Bjornson
- The University of British Columbia, Vancouver, British Columbia, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Danny Kim
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Dowling
- The University of Texas, Southwestern Austin, TX, United States; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wilmot Bonnett
- The University of Texas, Southwestern Austin, TX, United States; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Rivkin
- Department of Neurology, Boston, MA, United States; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pradeep Krishnan
- Department of Diagnostic Imaging, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Manohar Shroff
- Department of Diagnostic Imaging, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Birgit Ertl-Wagner
- Department of Diagnostic Imaging, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stephen Strother
- Department of Medical Biophysics Rotman Research Institute, Baycrest Hospital, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Steven Arnott
- Department of Medical Biophysics Rotman Research Institute, Baycrest Hospital, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Max Wintermark
- Department of Neuroradiology, MD Anderson, Houston, TX (M.W.), United States; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrea Kassner
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gabrielle deVeber
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nomazulu Dlamini
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada,.
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8
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Brooks PJ, Malkin EZ, De Michino S, Bratman SV. Isolation of salivary cell-free DNA for cancer detection. PLoS One 2023; 18:e0285214. [PMID: 37130100 PMCID: PMC10153704 DOI: 10.1371/journal.pone.0285214] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023] Open
Abstract
Saliva is an emerging source of disease biomarkers, particularly for cancers of the head and neck. Although analysis of cell-free DNA (cfDNA) in saliva holds promise as a liquid biopsy for cancer detection, currently there are no standardized methodologies for the collection and isolation of saliva for the purposes of studying DNA. Here, we evaluated various saliva collection receptacles and DNA purification techniques, comparing DNA quantity, fragment size, source, and stability. Then, using our optimized techniques, we tested the ability to detect human papillomavirus (HPV) DNA- a bona fide cancer biomarker in a subset of head and neck cancers- from patient saliva samples. For saliva collection, we found that the Oragene OG-600 receptacle yielded the highest concentration of total salivary DNA as well as short fragments <300 bp corresponding to mononucleosomal cell-free DNA. Moreover, these short fragments were stabilized beyond 48 hours after collection in contrast to other saliva collection receptacles. For DNA purification from saliva, the QIAamp Circulating Nucleic Acid kit yielded the highest concentration of mononucleosome-sized DNA fragments. Freeze-thaw of saliva samples did not affect DNA yield or fragment size distribution. Salivary DNA isolated from the OG-600 receptacle was found to be composed of both single and double-stranded DNA, including mitochondrial and microbial sources. While levels of nuclear DNA were consistent over time, levels of mitochondrial and microbial DNA were more variable and increased 48 hours after collection. Finally, we found that HPV DNA was stable in OG-600 receptacles, was reliably detected within the saliva of patients with HPV-positive head and neck cancer, and was abundant among mononucleosome-sized cell-free DNA fragments. Our studies have defined optimal techniques for isolating DNA from saliva that will contribute to future applications in liquid biopsy-based cancer detection.
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Affiliation(s)
- Patricia J Brooks
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ethan Z Malkin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Steven De Michino
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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9
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Schulze Johann K, Bauer H, Wiegand P, Pfeiffer H, Vennemann M. Whole-genome sequencing of artificial single-nucleotide variants induced by DNA degradation in biological crime scene traces. Int J Legal Med 2023; 137:33-45. [PMID: 36352329 PMCID: PMC9816238 DOI: 10.1007/s00414-022-02911-0] [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: 08/24/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022]
Abstract
The aim of this study was to identify artificial single-nucleotide variants (SNVs) in degraded trace DNA samples. In a preliminary study, blood samples were stored for up to 120 days and whole-genome sequencing was performed using the Snakemake workflow dna-seq-gatk-variant-calling to identify positions that vary between the time point 0 sample and the aged samples. In a follow-up study on blood and saliva samples stored under humid and dry conditions, potential marker candidates for the estimation of the age of a blood stain (= time since deposition) were identified. Both studies show that a general decrease in the mean fragment size of the libraries over time was observed, presumably due to the formation of abasic sites during DNA degradation which are more susceptible to strand breaks by mechanical shearing of DNA. Unsurprisingly, an increase in the number of failed genotype calls (no coverage) was detected over time. Both studies indicated the presence of artificial SNVs with the majority of changes happening at guanine and cytosine positions. This confirms previous studies and can be explained by depurination through hydrolytic attacks which more likely deplete guanine while deamination leads to cytosine to thymine variants. Even complete genotype switches from homozygote 0/0 genotypes to the opposite 1/1 genotypes were observed. While positions with such drastic changes might provide suitable candidate markers for estimating short-term time since deposition (TsD), 11 markers were identified which show a slower gradual change of the relative abundance of the artificial variant in both blood and saliva samples, irrespective of storage conditions.
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Affiliation(s)
| | - Hannah Bauer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149 Münster, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Heidi Pfeiffer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149 Münster, Germany
| | - Marielle Vennemann
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149 Münster, Germany
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10
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De Paolis E, Perrucci A, Marchetti C, Pietragalla A, Scambia G, Urbani A, Fagotti A, Minucci A. BRCA testing on buccal swab to improve access to healthcare and cancer prevention: a performance evaluation. Int J Gynecol Cancer 2022; 32:ijgc-2022-003718. [PMID: 36028233 DOI: 10.1136/ijgc-2022-003718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVE BRCA1/2 (BRCA) genetic testing allows patients with high-grade serous ovarian cancer to receive appropriate medical management with molecular target therapy and prevention strategies. Most of the BRCA sequencing methods use blood as the primary source of germline DNA. Buccal swab emerged as an alternative collection device due to its convenient and non-invasive characteristics. This study assessed the suitability of buccal swabs as the DNA source in next-generation sequencing-based BRCA genotyping. METHODS Matched buccal swabs and blood samples were collected from 51 patients with high-grade serous ovarian cancer, including 29 BRCA-mutated patients, from June to December 2021. Buccal swabs were self-collected using COPAN FLOQSwabs hDNA Free. BRCA genes were amplified using Devyser's BRCA next-generation sequencing kit and sequenced on the Illumina MiSeq platform. We evaluated collection and extraction procedures, amplification and sequencing performances, coverage data, blood/swab variant calling concordance, and interpretation. RESULTS Comparable sequencing parameters were observed between the two sample types in term of mean total number of reads passing filter for indexed sample (p>0.05) and sequencing coverage distribution, with a widespread overlap of mean depth of coverage/target region between blood and swab samples. An overall concordance of 100% in both polymorphisms and pathogenic variants calling between the two DNA sources were observed, including the copy number variation prediction. CONCLUSIONS Data from this study support the use of buccal swabs as an alternative source of DNA for BRCA evaluation. The use of this alternative delivery mode of BRCA testing may facilitate access to care without compromising patient outcomes.
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Affiliation(s)
- Elisa De Paolis
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Alessia Perrucci
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Claudia Marchetti
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Giovanni Scambia
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Andrea Urbani
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Anna Fagotti
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Angelo Minucci
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
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11
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Nauwelaerts SJD, De Cremer K, Bustos Sierra N, Gand M, Van Geel D, Delvoye M, Vandermassen E, Vercauteren J, Stroobants C, Bernard A, Saenen ND, Nawrot TS, Roosens NHC, De Keersmaecker SCJ. Assessment of the Feasibility of a Future Integrated Larger-Scale Epidemiological Study to Evaluate Health Risks of Air Pollution Episodes in Children. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19148531. [PMID: 35886381 PMCID: PMC9323067 DOI: 10.3390/ijerph19148531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/08/2022] [Accepted: 07/10/2022] [Indexed: 02/07/2023]
Abstract
Air pollution exposure can lead to exacerbation of respiratory disorders in children. Using sensitive biomarkers helps to assess the impact of air pollution on children’s respiratory health and combining protein, genetic and epigenetic biomarkers gives insights on their interrelatedness. Most studies do not contain such an integrated approach and investigate these biomarkers individually in blood, although its collection in children is challenging. Our study aimed at assessing the feasibility of conducting future integrated larger-scale studies evaluating respiratory health risks of air pollution episodes in children, based on a qualitative analysis of the technical and logistic aspects of a small-scale field study involving 42 children. This included the preparation, collection and storage of non-invasive samples (urine, saliva), the measurement of general and respiratory health parameters and the measurement of specific biomarkers (genetic, protein, epigenetic) of respiratory health and air pollution exposure. Bottlenecks were identified and modifications were proposed to expand this integrated study to a higher number of children, time points and locations. This would allow for non-invasive assessment of the impact of air pollution exposure on the respiratory health of children in future larger-scale studies, which is critical for the development of policies or measures at the population level.
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Affiliation(s)
- Sarah J. D. Nauwelaerts
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.J.D.N.); (M.G.); (D.V.G.); (M.D.); (E.V.); (N.H.C.R.)
- Centre for Toxicology and Applied Pharmacology, University Catholique de Louvain, 1200 Brussels, Belgium;
| | - Koen De Cremer
- Platform Chromatography and Mass Spectrometry, Sciensano, 1050 Brussels, Belgium;
| | | | - Mathieu Gand
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.J.D.N.); (M.G.); (D.V.G.); (M.D.); (E.V.); (N.H.C.R.)
| | - Dirk Van Geel
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.J.D.N.); (M.G.); (D.V.G.); (M.D.); (E.V.); (N.H.C.R.)
| | - Maud Delvoye
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.J.D.N.); (M.G.); (D.V.G.); (M.D.); (E.V.); (N.H.C.R.)
| | - Els Vandermassen
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.J.D.N.); (M.G.); (D.V.G.); (M.D.); (E.V.); (N.H.C.R.)
| | - Jordy Vercauteren
- Unit Air, Vlaamse Milieumaatschappij, 2000 Antwerpen, Belgium; (J.V.); (C.S.)
| | | | - Alfred Bernard
- Centre for Toxicology and Applied Pharmacology, University Catholique de Louvain, 1200 Brussels, Belgium;
| | - Nelly D. Saenen
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium; (N.D.S.); (T.S.N.)
| | - Tim S. Nawrot
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium; (N.D.S.); (T.S.N.)
- Department of Public Health and Primary Care, KU Leuven, 3000 Leuven, Belgium
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.J.D.N.); (M.G.); (D.V.G.); (M.D.); (E.V.); (N.H.C.R.)
| | - Sigrid C. J. De Keersmaecker
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.J.D.N.); (M.G.); (D.V.G.); (M.D.); (E.V.); (N.H.C.R.)
- Correspondence:
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12
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Wasilewska K, Gambin T, Rydzanicz M, Szczałuba K, Płoski R. Postzygotic mutations and where to find them - Recent advances and future implications in the field of non-neoplastic somatic mosaicism. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108426. [PMID: 35690331 DOI: 10.1016/j.mrrev.2022.108426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/05/2022] [Accepted: 06/03/2022] [Indexed: 01/01/2023]
Abstract
The technological progress of massively parallel sequencing (MPS) has triggered a remarkable development in the research on postzygotic mutations. Although the overwhelming majority of studies in the field focus on oncogenesis, non-neoplastic diseases are attracting more and more attention. The aim of this review was to summarize some of the most recent findings in the field of somatic mosaicism in diseases other than neoplastic events. We discuss the abundance and role of postzygotic mutations, with a special emphasis on disorders which occur only in a mosaic form (obligatory mosaic diseases; OMDs). Based on the list of OMDs compiled from the published literature and three databases (OMIM, Orphanet and MosaicBase), we demonstrate the prevalence of cancer-related genes across OMDs and suggest other sources to further explore OMDs and OMD-related genes. Additionally, we comment on some practical aspects related to mosaic diseases, such as approaches to tissue sampling, the MPS coverage required to detect variants at a very low frequency, as well as on bioinformatic and molecular tools dedicated to detect somatic mutations in MPS data.
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Affiliation(s)
- Krystyna Wasilewska
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland.
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13
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Mordenti M, Capicchioni V, Corsini S, Locatelli M, Abelli E, Banchelli F, Boarini M, Sangiorgi L. Preanalytical DNA assessment for downstream applications: How to optimize the management of human biospecimens to support molecular diagnosis-An experimental study. J Clin Lab Anal 2022; 36:e24531. [PMID: 35666551 PMCID: PMC9279999 DOI: 10.1002/jcla.24531] [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] [Received: 02/11/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/09/2022] Open
Abstract
Background The development of next‐generation sequencing approaches has accelerated the diagnostic process, although at present, there is a lack of a clear consensus on efficient management of human samples for downstream applications. This study aims to investigate timeframe (in terms of short preservation), temperature, and additional preservation procedures (i.e., freeze and thaw cycles) for human biospecimens to implement the reliability and reproducibility of molecular investigations. Methods Overall, 45 whole peripheral bloods, 22 peripheral blood mononuclear cells samples, 15 saliva, and 15 buccal swab biospecimens (through the extracted DNA) were investigated, assessing yield, integrity, amplifiability, and sizing accuracy via the most common molecular techniques. Results Based on the overall evaluation criteria, the results indicate that DNA extracted from all samples, shortly preserved, have suitable quality and reliable reproducibility to be used in diagnostic activities and biomedical research, even if DNA from peripheral blood mononuclear cells is more affected by the experimental conditions. Conclusion Our findings confirm the reliability of peripheral blood samples in almost all the experimental conditions. Saliva and buccal swabs are efficient almost as well, while peripheral blood mononuclear cells, albeit remain a primary source of DNA for molecular screenings, represent a less efficient source.
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Affiliation(s)
- Marina Mordenti
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Valentina Capicchioni
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.,Ministry of Education, San Marino, Repubic of San Marino
| | - Serena Corsini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manuela Locatelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Elisabetta Abelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Federico Banchelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manila Boarini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Luca Sangiorgi
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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14
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Zemet R, Van den Veyver IB, Stankiewicz P. Parental mosaicism for apparent de novo genetic variants: Scope, detection, and counseling challenges. Prenat Diagn 2022; 42:811-821. [PMID: 35394072 PMCID: PMC9995893 DOI: 10.1002/pd.6144] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 11/07/2022]
Abstract
The disease burden of de novo mutations (DNMs) has been evidenced only recently when the common application of next-generation sequencing technologies enabled their reliable and affordable detection through family-based clinical exome or genome sequencing. Implementation of exome sequencing into prenatal diagnostics revealed that up to 63% of pathogenic or likely pathogenic variants associated with fetal structural anomalies are apparently de novo, primarily for autosomal dominant disorders. Apparent DNMs have been considered to primarily occur as germline or zygotic events, with consequently negligible recurrence risks. However, there is now evidence that a considerable proportion of them are in fact inherited from a parent mosaic for the variant. Here, we review the burden of DNMs in prenatal diagnostics and the influence of parental mosaicism on the interpretation of apparent DNMs and discuss the challenges with detecting and quantifying parental mosaicism and its effect on recurrence risk. We also describe new bioinformatic and technological tools developed to assess mosaicism and discuss how they improve the accuracy of reproductive risk counseling when parental mosaicism is detected.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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15
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Borden ES, Buetow KH, Wilson MA, Hastings KT. Cancer Neoantigens: Challenges and Future Directions for Prediction, Prioritization, and Validation. Front Oncol 2022; 12:836821. [PMID: 35311072 PMCID: PMC8929516 DOI: 10.3389/fonc.2022.836821] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/07/2022] [Indexed: 12/16/2022] Open
Abstract
Prioritization of immunogenic neoantigens is key to enhancing cancer immunotherapy through the development of personalized vaccines, adoptive T cell therapy, and the prediction of response to immune checkpoint inhibition. Neoantigens are tumor-specific proteins that allow the immune system to recognize and destroy a tumor. Cancer immunotherapies, such as personalized cancer vaccines, adoptive T cell therapy, and immune checkpoint inhibition, rely on an understanding of the patient-specific neoantigen profile in order to guide personalized therapeutic strategies. Genomic approaches to predicting and prioritizing immunogenic neoantigens are rapidly expanding, raising new opportunities to advance these tools and enhance their clinical relevance. Predicting neoantigens requires acquisition of high-quality samples and sequencing data, followed by variant calling and variant annotation. Subsequently, prioritizing which of these neoantigens may elicit a tumor-specific immune response requires application and integration of tools to predict the expression, processing, binding, and recognition potentials of the neoantigen. Finally, improvement of the computational tools is held in constant tension with the availability of datasets with validated immunogenic neoantigens. The goal of this review article is to summarize the current knowledge and limitations in neoantigen prediction, prioritization, and validation and propose future directions that will improve personalized cancer treatment.
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Affiliation(s)
- Elizabeth S Borden
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, United States.,Department of Research and Internal Medicine (Dermatology), Phoenix Veterans Affairs Health Care System, Phoenix, AZ, United States
| | - Kenneth H Buetow
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
| | - Karen Taraszka Hastings
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, United States.,Department of Research and Internal Medicine (Dermatology), Phoenix Veterans Affairs Health Care System, Phoenix, AZ, United States
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16
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Shukralla A, Carton R, Benson KA, El Naggar H, Lacey A, Cavalleri G, Delanty N. Whole exome sequencing studies in epilepsy: A deep analysis of the published literature. Am J Med Genet A 2022; 188:1407-1419. [PMID: 35088532 DOI: 10.1002/ajmg.a.62655] [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: 06/27/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 11/07/2022]
Abstract
To evaluate the quality of whole-exome sequencing (WES) reporting in the epilepsy literature. We aimed to assess the quality of reporting of WES in epilepsy. We compared studies based on journal type and if outcome reporting biases exist. We used a self-constructed benchmark to quantitatively analyze studies. We included 451 publications. Reporting was heterogeneous with poor reporting of (1) ACMG guideline application 13% and (2) Human Phenotype Ontology (HPO) numbers in 3% of studies, 3) VUS in 19%. Predictors of reporting included journal type and journal impact factor. Date of publication and publication type were not predictors of poor reporting. Pairwise comparisons of genetics versus neurology journals using relative risks yielded significant differences in reporting of ACMG guideline application (RR 1.88, 95% CI 1.04-3.38); HPO numbers (RR 8.62, 95% CI 1.08-63.37) and deposition of findings to ClinVar (RR 2.50, 95% CI 1.03-6.1). Reporting of WES literature is heterogeneous in quality, and poor reporting hinders collaboration and accession of data into large databases like OMIM and OrphaNet. This study highlights reporting bias in this area and, formal structural guidelines like the CONSORT guidelines used in the reporting of clinical trials are needed to address the issue.
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Affiliation(s)
- Arif Shukralla
- The National Epilepsy Programme, Beaumont Hospital, Dublin, Ireland
| | - Robert Carton
- FutureNeuro, The SFI Research Centre for Chronic and Rare Neurological Disease, Dublin, Ireland.,The Royal College of Surgeons in Ireland, Dublin, Ireland.,School of Pharmacy and Biomolecular Science, RCSI, Dublin, Ireland
| | - Katherine A Benson
- FutureNeuro, The SFI Research Centre for Chronic and Rare Neurological Disease, Dublin, Ireland.,The Royal College of Surgeons in Ireland, Dublin, Ireland.,School of Pharmacy and Biomolecular Science, RCSI, Dublin, Ireland
| | - Hany El Naggar
- The National Epilepsy Programme, Beaumont Hospital, Dublin, Ireland.,FutureNeuro, The SFI Research Centre for Chronic and Rare Neurological Disease, Dublin, Ireland.,The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Austin Lacey
- FutureNeuro, The SFI Research Centre for Chronic and Rare Neurological Disease, Dublin, Ireland.,The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Gianpiero Cavalleri
- FutureNeuro, The SFI Research Centre for Chronic and Rare Neurological Disease, Dublin, Ireland.,The Royal College of Surgeons in Ireland, Dublin, Ireland.,School of Pharmacy and Biomolecular Science, RCSI, Dublin, Ireland
| | - Norman Delanty
- The National Epilepsy Programme, Beaumont Hospital, Dublin, Ireland.,FutureNeuro, The SFI Research Centre for Chronic and Rare Neurological Disease, Dublin, Ireland.,The Royal College of Surgeons in Ireland, Dublin, Ireland
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17
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Vacca D, Fiannaca A, Tramuto F, Cancila V, La Paglia L, Mazzucco W, Gulino A, La Rosa M, Maida CM, Morello G, Belmonte B, Casuccio A, Maugeri R, Iacopino G, Balistreri CR, Vitale F, Tripodo C, Urso A. Direct RNA Nanopore Sequencing of SARS-CoV-2 Extracted from Critical Material from Swabs. Life (Basel) 2022; 12:69. [PMID: 35054462 PMCID: PMC8778588 DOI: 10.3390/life12010069] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/24/2021] [Accepted: 12/28/2021] [Indexed: 12/30/2022] Open
Abstract
In consideration of the increasing prevalence of COVID-19 cases in several countries and the resulting demand for unbiased sequencing approaches, we performed a direct RNA sequencing (direct RNA seq.) experiment using critical oropharyngeal swab samples collected from Italian patients infected with SARS-CoV-2 from the Palermo region in Sicily. Here, we identified the sequences SARS-CoV-2 directly in RNA extracted from critical samples using the Oxford Nanopore MinION technology without prior cDNA retrotranscription. Using an appropriate bioinformatics pipeline, we could identify mutations in the nucleocapsid (N) gene, which have been reported previously in studies conducted in other countries. In conclusion, to the best of our knowledge, the technique used in this study has not been used for SARS-CoV-2 detection previously owing to the difficulties in the extraction of RNA of sufficient quantity and quality from routine oropharyngeal swabs. Despite these limitations, this approach provides the advantages of true native RNA sequencing and does not include amplification steps that could introduce systematic errors. This study can provide novel information relevant to the current strategies adopted in SARS-CoV-2 next-generation sequencing.
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Affiliation(s)
- Davide Vacca
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Antonino Fiannaca
- CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, a5c, 90146 Palermo, Italy; (A.F.); (L.L.P.); (M.L.R.); (A.U.)
| | - Fabio Tramuto
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, Hygiene Section, University of Palermo, 90127 Palermo, Italy; (F.T.); (W.M.); (C.M.M.); (A.C.); (F.V.)
| | - Valeria Cancila
- Tumor Immunology Unit, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy; (V.C.); (G.M.); (B.B.); (C.T.)
| | - Laura La Paglia
- CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, a5c, 90146 Palermo, Italy; (A.F.); (L.L.P.); (M.L.R.); (A.U.)
| | - Walter Mazzucco
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, Hygiene Section, University of Palermo, 90127 Palermo, Italy; (F.T.); (W.M.); (C.M.M.); (A.C.); (F.V.)
| | - Alessandro Gulino
- Cogentech srl Società Benefit, FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy;
| | - Massimo La Rosa
- CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, a5c, 90146 Palermo, Italy; (A.F.); (L.L.P.); (M.L.R.); (A.U.)
| | - Carmelo Massimo Maida
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, Hygiene Section, University of Palermo, 90127 Palermo, Italy; (F.T.); (W.M.); (C.M.M.); (A.C.); (F.V.)
| | - Gaia Morello
- Tumor Immunology Unit, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy; (V.C.); (G.M.); (B.B.); (C.T.)
| | - Beatrice Belmonte
- Tumor Immunology Unit, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy; (V.C.); (G.M.); (B.B.); (C.T.)
| | - Alessandra Casuccio
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, Hygiene Section, University of Palermo, 90127 Palermo, Italy; (F.T.); (W.M.); (C.M.M.); (A.C.); (F.V.)
| | - Rosario Maugeri
- Department of Experimental Biomedicine and Clinical Neurosciences, School of Medicine, Neurosurgical Clinic, University of Palermo, 90127 Palermo, Italy; (R.M.); (G.I.)
| | - Gerardo Iacopino
- Department of Experimental Biomedicine and Clinical Neurosciences, School of Medicine, Neurosurgical Clinic, University of Palermo, 90127 Palermo, Italy; (R.M.); (G.I.)
| | - Carmela Rita Balistreri
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), University of Palermo, 90134 Palermo, Italy;
| | - Francesco Vitale
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, Hygiene Section, University of Palermo, 90127 Palermo, Italy; (F.T.); (W.M.); (C.M.M.); (A.C.); (F.V.)
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy; (V.C.); (G.M.); (B.B.); (C.T.)
| | - Alfonso Urso
- CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, a5c, 90146 Palermo, Italy; (A.F.); (L.L.P.); (M.L.R.); (A.U.)
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18
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Van Asselt AJ, Ehli EA. Whole-Genome Genotyping Using DNA Microarrays for Population Genetics. Methods Mol Biol 2022; 2418:269-287. [PMID: 35119671 DOI: 10.1007/978-1-0716-1920-9_16] [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] [Indexed: 06/14/2023]
Abstract
The field of population genetics has exploded in the last two decades following the sequencing of the human genome in 2001 (Green et al. Nature 526:29-31, 2015). Tools to measure genetic variation have matured significantly throughout this advancement in knowledge (Lenoir and Giannella. J Biomed Discov Collab 1:11, 2006; Marzancola et al. Methods Mol Biol 1368:161-178, 2016). In this chapter, the focus is on the laboratory methods developed to perform genome-wide genotyping utilizing DNA microarrays, which is one of the most commonly used molecular techniques to assess global genetic variation (Heller MJ, Annu Rev Biomed Eng 4:129-153, 2002). DNA microarrays allow for the interrogation of hundreds of thousands of SNPs (single nucleotide polymorphisms) at once utilizing array-based technology in conjunction with fluorescent molecular labels in a process referred to as genotyping (Marzancola et al. Methods Mol Biol 1368:161-178, 2016). Genotype data can be utilized to associate certain phenotypes in relation with specific genetic variants within a population in a process known as genome-wide association studies or GWAS (Charlesworth and Charlesworth. Heredity (Edinb) 118(1):2-9, 2017; Casillas and Barbadilla. Genetics 205(3):1003-1035, 2017). This experimental technique is a multiple-day process involving the combination of DNA extraction, amplification, fragmentation, binding, and staining (Illumina Infinium HTS Assay Protocol Guide, 2013). Many vendors supply platforms and products to assess global genetic variation using DNA microarrays (Illumina Infinium HTS Assay Protocol Guide, 2013). In this chapter, the focus is on the methods utilized to generate high-quality genotype data with the Illumina® Infinium Global Screening Array. Although data analysis and quality control are not the focus for this chapter, they are also briefly addressed.
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Affiliation(s)
- Austin J Van Asselt
- Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD, USA
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - Erik A Ehli
- Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD, USA.
- Department of Psychiatry, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA.
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19
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Contribution of Multiple Inherited Variants to Autism Spectrum Disorder (ASD) in a Family with 3 Affected Siblings. Genes (Basel) 2021; 12:genes12071053. [PMID: 34356069 PMCID: PMC8303619 DOI: 10.3390/genes12071053] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/21/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is the most common neurodevelopmental disorder in children and shows high heritability. However, how inherited variants contribute to ASD in multiplex families remains unclear. Using whole-genome sequencing (WGS) in a family with three affected children, we identified multiple inherited DNA variants in ASD-associated genes and pathways (RELN, SHANK2, DLG1, SCN10A, KMT2C and ASH1L). All are shared among the three children, except ASH1L, which is only present in the most severely affected child. The compound heterozygous variants in RELN, and the maternally inherited variant in SHANK2, are considered to be major risk factors for ASD in this family. Both genes are involved in neuron activities, including synaptic functions and the GABAergic neurotransmission system, which are highly associated with ASD pathogenesis. DLG1 is also involved in synapse functions, and KMT2C and ASH1L are involved in chromatin organization. Our data suggest that multiple inherited rare variants, each with a subthreshold and/or variable effect, may converge to certain pathways and contribute quantitatively and additively, or alternatively act via a 2nd-hit or multiple-hits to render pathogenicity of ASD in this family. Additionally, this multiple-hits model further supports the quantitative trait hypothesis of a complex genetic, multifactorial etiology for the development of ASDs.
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20
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Herzig AF, Velo-Suárez L, Le Folgoc G, Boland A, Blanché H, Olaso R, Le Roux L, Delmas C, Goldberg M, Zins M, Lethimonnier F, Deleuze JF, Génin E. Evaluation of saliva as a source of accurate whole-genome and microbiome sequencing data. Genet Epidemiol 2021; 45:537-548. [PMID: 33998042 DOI: 10.1002/gepi.22386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 11/08/2022]
Abstract
This study sets out to establish the suitability of saliva-based whole-genome sequencing (WGS) through a comparison against blood-based WGS. To fully appraise the observed differences, we developed a novel technique of pseudo-replication. We also investigated the potential of characterizing individual salivary microbiomes from non-human DNA fragments found in saliva. We observed that the majority of discordant genotype calls between blood and saliva fell into known regions of the human genome that are typically sequenced with low confidence; and could be identified by quality control measures. Pseudo-replication demonstrated that the levels of discordance between blood- and saliva-derived WGS data were entirely similar to what one would expect between technical replicates if an individual's blood or saliva had been sequenced twice. Finally, we successfully sequenced salivary microbiomes in parallel to human genomes as demonstrated by a comparison against the Human Microbiome Project.
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Affiliation(s)
| | - Lourdes Velo-Suárez
- Univ Brest, EFS, UMR 1078, GGB, Inserm, Brest, France.,Brest Center for Microbiota Analysis (CBAM), CHU Brest, Brest, France
| | | | - Anne Boland
- National Center for Research in Human Genomics (CNRGH), François Jacob Institute of Biology, CEA, Paris-Saclay University, Evry, France.,Laboratory of Excellence GENMED (Medical Genomics), Paris, France
| | - Hélène Blanché
- Laboratory of Excellence GENMED (Medical Genomics), Paris, France.,Fondation Jean Dausset-CEPH, Paris, France
| | - Robert Olaso
- National Center for Research in Human Genomics (CNRGH), François Jacob Institute of Biology, CEA, Paris-Saclay University, Evry, France.,Laboratory of Excellence GENMED (Medical Genomics), Paris, France
| | - Liana Le Roux
- Clinical Investigation Center 1412, Inserm, CHU Brest, Brest, France
| | | | - Marcel Goldberg
- Inserm-Paris Saclay University, University of Paris, Villejuif, France
| | - Marie Zins
- Inserm-Paris Saclay University, University of Paris, Villejuif, France
| | - Franck Lethimonnier
- National Alliance for Life and Health Sciences (Aviesan), Multiorganism thematic institute, Health technologies, INSERM, Paris, France
| | - Jean-François Deleuze
- National Center for Research in Human Genomics (CNRGH), François Jacob Institute of Biology, CEA, Paris-Saclay University, Evry, France.,Laboratory of Excellence GENMED (Medical Genomics), Paris, France.,Fondation Jean Dausset-CEPH, Paris, France.,Center of Reference, Innovation and Expertize (CREFIX), US39, French Atomic Energy and Alternative Energies Commission, Evry, France
| | - Emmanuelle Génin
- Univ Brest, EFS, UMR 1078, GGB, Inserm, Brest, France.,CHU Brest, Brest, France
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21
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Corbett RD, Eveleigh R, Whitney J, Barai N, Bourgey M, Chuah E, Johnson J, Moore RA, Moradin N, Mungall KL, Pereira S, Reuter MS, Thiruvahindrapuram B, Wintle RF, Ragoussis J, Strug LJ, Herbrick JA, Aziz N, Jones SJM, Lathrop M, Scherer SW, Staffa A, Mungall AJ. A Distributed Whole Genome Sequencing Benchmark Study. Front Genet 2020; 11:612515. [PMID: 33335541 PMCID: PMC7736078 DOI: 10.3389/fgene.2020.612515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/10/2020] [Indexed: 12/30/2022] Open
Abstract
Population sequencing often requires collaboration across a distributed network of sequencing centers for the timely processing of thousands of samples. In such massive efforts, it is important that participating scientists can be confident that the accuracy of the sequence data produced is not affected by which center generates the data. A study was conducted across three established sequencing centers, located in Montreal, Toronto, and Vancouver, constituting Canada's Genomics Enterprise (www.cgen.ca). Whole genome sequencing was performed at each center, on three genomic DNA replicates from three well-characterized cell lines. Secondary analysis pipelines employed by each site were applied to sequence data from each of the sites, resulting in three datasets for each of four variables (cell line, replicate, sequencing center, and analysis pipeline), for a total of 81 datasets. These datasets were each assessed according to multiple quality metrics including concordance with benchmark variant truth sets to assess consistent quality across all three conditions for each variable. Three-way concordance analysis of variants across conditions for each variable was performed. Our results showed that the variant concordance between datasets differing only by sequencing center was similar to the concordance for datasets differing only by replicate, using the same analysis pipeline. We also showed that the statistically significant differences between datasets result from the analysis pipeline used, which can be unified and updated as new approaches become available. We conclude that genome sequencing projects can rely on the quality and reproducibility of aggregate data generated across a network of distributed sites.
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Affiliation(s)
- Richard D. Corbett
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Robert Eveleigh
- McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Joe Whitney
- The Centre for Applied Genomics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Namrata Barai
- The Centre for Applied Genomics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Mathieu Bourgey
- McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Eric Chuah
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Joanne Johnson
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Richard A. Moore
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Neda Moradin
- The Centre for Applied Genomics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Karen L. Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Sergio Pereira
- The Centre for Applied Genomics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Miriam S. Reuter
- Canada’s Genomics Enterprise (CGEn), The Hospital for Sick Children, Toronto, ON, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Richard F. Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | | | - Lisa J. Strug
- The Centre for Applied Genomics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Jo-Anne Herbrick
- The Centre for Applied Genomics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Naveed Aziz
- Canada’s Genomics Enterprise (CGEn), The Hospital for Sick Children, Toronto, ON, Canada
| | - Steven J. M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Mark Lathrop
- McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Alfredo Staffa
- McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Andrew J. Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, Canada
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22
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Samson CA, Whitford W, Snell RG, Jacobsen JC, Lehnert K. Contaminating DNA in human saliva alters the detection of variants from whole genome sequencing. Sci Rep 2020; 10:19255. [PMID: 33159102 PMCID: PMC7648094 DOI: 10.1038/s41598-020-76022-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/18/2020] [Indexed: 12/11/2022] Open
Abstract
Cells obtained from human saliva are commonly used as an alternative DNA source when blood is difficult or less convenient to collect. Although DNA extracted from saliva is considered to be of comparable quality to that derived from blood, recent studies have shown that non-human contaminating DNA derived from saliva can confound whole genome sequencing results. The most concerning complication is that non-human reads align to the human reference genome using standard methodology, which can critically affect the resulting variant genotypes identified in a genome. We identified clusters of anomalous variants in saliva DNA derived reads which aligned in an atypical manner. These reads had only short regions of identity to the human reference sequence, flanked by soft clipped sequence. Sequence comparisons of atypically aligning reads from eight human saliva-derived samples to RefSeq genomes revealed the majority to be of bacterial origin (63.46%). To partition the non-human reads during the alignment step, a decoy of the most prevalent bacterial genome sequences was designed and utilised. This reduced the number of atypically aligning reads when trialled on the eight saliva-derived samples by 44% and most importantly prevented the associated anomalous genotype calls. Saliva derived DNA is often contaminated by DNA from other species. This can lead to non-human reads aligning to the human reference genome using current alignment best-practices, impacting variant identification. This problem can be diminished by using a bacterial decoy in the alignment process.
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Affiliation(s)
- C A Samson
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - W Whitford
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - R G Snell
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - J C Jacobsen
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand.
| | - K Lehnert
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
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23
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Hargreaves KA, Pratt VM, Medeiros EB, Lynnes TC, Granfield CA, Skaar TC, Iwata-Otsubo A, Tillman EM. Tracheal Aspirate as an Alternative Biologic Sample for Pharmacogenomics Testing in Mechanically Ventilated Pediatric Patients. Clin Transl Sci 2020; 14:497-501. [PMID: 32702149 PMCID: PMC7993287 DOI: 10.1111/cts.12847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 06/29/2020] [Indexed: 11/26/2022] Open
Abstract
Patients in the pediatric intensive care unit are exposed to multiple medications and are at high risk for adverse drug reactions. Pharmacogenomic (PGx) testing could help decrease their risk of adverse reactions. Although whole blood is preferred for PGx testing, blood volume in this population is often limited. However, for patients on mechanical ventilation, tracheal secretions are abundant, frequently suctioned, and discarded. Thus, the aim of this pilot study was to determine if tracheal aspirates could be used as a source of human genomic DNA for PGx testing. We successfully extracted DNA from tracheal secretions of all 23 patients in the study. The samples were successfully genotyped for 10 clinically actionable single nucleotide variants across 3 cytochrome P450 genes (CYP2D6, CYP2C19, and CYP3A5). Using DNA from whole blood samples in 11 of the patients, we confirmed the accuracy of the genotyping with 100% concordance. Therefore, our results support the use of tracheal aspirates from mechanically ventilated children as an adequate biospecimen for clinical genetic testing.
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Affiliation(s)
- Katherine A Hargreaves
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Elizabeth B Medeiros
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ty C Lynnes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Caitlin A Granfield
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Todd C Skaar
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Aiko Iwata-Otsubo
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Emma M Tillman
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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24
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Rockowitz S, LeCompte N, Carmack M, Quitadamo A, Wang L, Park M, Knight D, Sexton E, Smith L, Sheidley B, Field M, Holm IA, Brownstein CA, Agrawal PB, Kornetsky S, Poduri A, Snapper SB, Beggs AH, Yu TW, Williams DA, Sliz P. Children's rare disease cohorts: an integrative research and clinical genomics initiative. NPJ Genom Med 2020; 5:29. [PMID: 32655885 PMCID: PMC7338382 DOI: 10.1038/s41525-020-0137-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
While genomic data is frequently collected under distinct research protocols and disparate clinical and research regimes, there is a benefit in streamlining sequencing strategies to create harmonized databases, particularly in the area of pediatric rare disease. Research hospitals seeking to implement unified genomics workflows for research and clinical practice face numerous challenges, as they need to address the unique requirements and goals of the distinct environments and many stakeholders, including clinicians, researchers and sequencing providers. Here, we present outcomes of the first phase of the Children’s Rare Disease Cohorts initiative (CRDC) that was completed at Boston Children’s Hospital (BCH). We have developed a broadly sharable database of 2441 exomes from 15 pediatric rare disease cohorts, with major contributions from early onset epilepsy and early onset inflammatory bowel disease. All sequencing data is integrated and combined with phenotypic and research data in a genomics learning system (GLS). Phenotypes were both manually annotated and pulled automatically from patient medical records. Deployment of a genomically-ordered relational database allowed us to provide a modular and robust platform for centralized storage and analysis of research and clinical data, currently totaling 8516 exomes and 112 genomes. The GLS integrates analytical systems, including machine learning algorithms for automated variant classification and prioritization, as well as phenotype extraction via natural language processing (NLP) of clinical notes. This GLS is extensible to additional analytic systems and growing research and clinical collections of genomic and other types of data.
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Affiliation(s)
- Shira Rockowitz
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Nicholas LeCompte
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Mary Carmack
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Andrew Quitadamo
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Lily Wang
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Meredith Park
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Devon Knight
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Emma Sexton
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Lacey Smith
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Beth Sheidley
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Michael Field
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA 02115 USA
| | - Ingrid A Holm
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA
| | - Catherine A Brownstein
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA
| | - Pankaj B Agrawal
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115 USA
| | - Susan Kornetsky
- Research Administration, Boston Children's Hospital, Boston, MA 02115 USA
| | - Annapurna Poduri
- Harvard Medical School, Boston, MA 02115 USA.,Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Scott B Snapper
- Harvard Medical School, Boston, MA 02115 USA.,Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA 02115 USA
| | - Alan H Beggs
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA
| | - Timothy W Yu
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA
| | - David A Williams
- Harvard Medical School, Boston, MA 02115 USA.,Division of Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115 USA
| | - Piotr Sliz
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
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25
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Lanillos J, Santos M, Carcajona M, Roldan-Romero JM, Martinez AM, Calsina B, Monteagudo M, Leandro-García LJ, Montero-Conde C, Cascón A, Maietta P, Alvarez S, Robledo M, Rodriguez-Antona C. A Novel Approach for the Identification of Pharmacogenetic Variants in MT-RNR1 through Next-Generation Sequencing Off-Target Data. J Clin Med 2020; 9:jcm9072082. [PMID: 32630724 PMCID: PMC7408883 DOI: 10.3390/jcm9072082] [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] [Received: 06/03/2020] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 11/17/2022] Open
Abstract
Specific genetic variants in the mitochondrially encoded 12S ribosomal RNA gene (MT-RNR1) cause aminoglycoside-induced irreversible hearing loss. Mitochondrial DNA is usually not included in targeted sequencing experiments; however, off-target data may deliver this information. Here, we extract MT-RNR1 genetic variation, including the most relevant ototoxicity variant m.1555A>G, using the off-target reads of 473 research samples, sequenced through a capture-based, custom-targeted panel and whole exome sequencing (WES), and of 1245 diagnostic samples with clinical WES. Sanger sequencing and fluorescence-based genotyping were used for genotype validation. There was a correlation between off-target reads and mitochondrial coverage (rcustomPanel = 0.39, p = 2 × 10−13 and rWES = 0.67, p = 7 × 10−21). The median read depth of MT-RNR1 m.1555 was similar to the average mitochondrial genome coverage, with saliva and blood samples giving comparable results. The genotypes from 415 samples, including three m.1555G carriers, were concordant with fluorescence-based genotyping data. In clinical WES, median MT-RNR1 coverage was 56×, with 90% of samples having ≥20 reads at m.1555 position, and one m.1494T and three m.1555G carriers were identified with no evidence for heteroplasmy. Altogether, this study shows that obtaining MT-RNR1 genotypes through off-target reads is an efficient strategy that can impulse preemptive pharmacogenetic screening of this mitochondrial gene.
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Affiliation(s)
- Javier Lanillos
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - María Santos
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | | | - Juan María Roldan-Romero
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - Angel M. Martinez
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - Bruna Calsina
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - María Monteagudo
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - Luis Javier Leandro-García
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - Cristina Montero-Conde
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - Alberto Cascón
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Paolo Maietta
- Nimgenetics, 28049 Madrid, Spain; (M.C.); (P.M.); (S.A.)
| | - Sara Alvarez
- Nimgenetics, 28049 Madrid, Spain; (M.C.); (P.M.); (S.A.)
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Cristina Rodriguez-Antona
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-91-732-8000 (ext. 3321)
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26
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Khalil AIS, Khyriem C, Chattopadhyay A, Sanyal A. Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes. BMC Bioinformatics 2020; 21:147. [PMID: 32299346 PMCID: PMC7160937 DOI: 10.1186/s12859-020-3480-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 04/01/2020] [Indexed: 12/15/2022] Open
Abstract
Background Detection of DNA copy number alterations (CNAs) is critical to understand genetic diversity, genome evolution and pathological conditions such as cancer. Cancer genomes are plagued with widespread multi-level structural aberrations of chromosomes that pose challenges to discover CNAs of different length scales, and distinct biological origins and functions. Although several computational tools are available to identify CNAs using read depth (RD) signal, they fail to distinguish between large-scale and focal alterations due to inaccurate modeling of the RD signal of cancer genomes. Additionally, RD signal is affected by overdispersion-driven biases at low coverage, which significantly inflate false detection of CNA regions. Results We have developed CNAtra framework to hierarchically discover and classify ‘large-scale’ and ‘focal’ copy number gain/loss from a single whole-genome sequencing (WGS) sample. CNAtra first utilizes a multimodal-based distribution to estimate the copy number (CN) reference from the complex RD profile of the cancer genome. We implemented Savitzky-Golay smoothing filter and Modified Varri segmentation to capture the change points of the RD signal. We then developed a CN state-driven merging algorithm to identify the large segments with distinct copy numbers. Next, we identified focal alterations in each large segment using coverage-based thresholding to mitigate the adverse effects of signal variations. Using cancer cell lines and patient datasets, we confirmed CNAtra’s ability to detect and distinguish the segmental aneuploidies and focal alterations. We used realistic simulated data for benchmarking the performance of CNAtra against other single-sample detection tools, where we artificially introduced CNAs in the original cancer profiles. We found that CNAtra is superior in terms of precision, recall and f-measure. CNAtra shows the highest sensitivity of 93 and 97% for detecting large-scale and focal alterations respectively. Visual inspection of CNAs revealed that CNAtra is the most robust detection tool for low-coverage cancer data. Conclusions CNAtra is a single-sample CNA detection tool that provides an analytical and visualization framework for CNA profiling without relying on any reference control. It can detect chromosome-level segmental aneuploidies and high-confidence focal alterations, even from low-coverage data. CNAtra is an open-source software implemented in MATLAB®. It is freely available at https://github.com/AISKhalil/CNAtra.
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Affiliation(s)
- Ahmed Ibrahim Samir Khalil
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Costerwell Khyriem
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Anupam Chattopadhyay
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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