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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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2
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Hook C, Chatterjee U, Sheng H, Zhu Q, Robinson T, Roh JM, Laurent CA, Lee C, Delmerico J, Lo JC, Ambrosone CB, Kushi LH, Kwan ML, Yao S. A polygenic score associated with fracture risk in breast cancer patients treated with aromatase inhibitors. NPJ Breast Cancer 2024; 10:9. [PMID: 38245540 PMCID: PMC10799916 DOI: 10.1038/s41523-024-00615-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
Identifying women at high risk of osteoporotic fracture from aromatase inhibitor (AI) therapy for breast cancer is largely based on known risk factors for healthy postmenopausal women, which might not accurately reflect the risk in breast cancer patients post-AI therapy. To determine whether a polygenic score associated with fracture in healthy women is also significant in women treated with AIs for breast cancer, we used data from a prospective observational cohort of 2152 women diagnosed with hormonal receptor positive breast cancer treated with AIs as the initial endocrine therapy and examined a polygenic score of heel quantitative ultrasound speed of sound (gSOS) in relation to incident osteoporotic fracture after AI therapy during a median 6.1 years of follow up after AI initiation. In multivariable models, patients with the second and third highest tertiles (T) versus the lowest tertile of gSOS had significantly lower risk of fracture (T2: adjusted HR = 0.61, 95% CI: 0.46-0.80; T3: adjusted HR = 0.53, 95% CI: 0.40-0.70). The lower risk of fracture in patients with the highest tertile of gSOS remained significant after further adjustment for BMD at the hip (T3: adjusted HR = 0.62, 95% CI: 0.42-0.91). In conclusion, our analysis showed gSOS as a novel genetic predictor for fracture risk independent of BMD among breast cancer patients treated with AIs. Future studies are warranted to evaluate the performance of incorporating gSOS in prediction models for the risk of AI-related fracture in breast cancer patients.
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Affiliation(s)
- Christine Hook
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Udit Chatterjee
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Haiyang Sheng
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Department of Biostatistics, University at Buffalo, Buffalo, NY, USA
| | - Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Timothy Robinson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Janise M Roh
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Cecile A Laurent
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Catherine Lee
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Jennifer Delmerico
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Joan C Lo
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Marilyn L Kwan
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Song Yao
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
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3
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Yang HJ, Seo SI, Lee J, Huh CW, Kim JS, Park JC, Kim H, Shin H, Shin CM, Park CH, Lee SK. Sample Collection Methods in Upper Gastrointestinal Research. J Korean Med Sci 2023; 38:e255. [PMID: 37582502 PMCID: PMC10427214 DOI: 10.3346/jkms.2023.38.e255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/16/2023] [Indexed: 08/17/2023] Open
Abstract
In recent years, significant translational research advances have been made in the upper gastrointestinal (GI) research field. Endoscopic evaluation is a reasonable option for acquiring upper GI tissue for research purposes because it has minimal risk and can be applied to unresectable gastric cancer. The optimal number of biopsy samples and sample storage is crucial and might influence results. Furthermore, the methods for sample acquisition can be applied differently according to the research purpose; however, there have been few reports on methods for sample collection from endoscopic biopsies. In this review, we suggested a protocol for collecting study samples for upper GI research, including microbiome, DNA, RNA, protein, single-cell RNA sequencing, and organoid culture, through a comprehensive literature review. For microbiome analysis, one or two pieces of biopsied material obtained using standard endoscopic forceps may be sufficient. Additionally, 5 mL of gastric fluid and 3-4 mL of saliva is recommended for microbiome analyses. At least one gastric biopsy tissue is necessary for most DNA or RNA analyses, while proteomics analysis may require at least 2-3 biopsy tissues. Single cell-RNA sequencing requires at least 3-5 tissues and additional 1-2 tissues, if possible. For successful organoid culture, multiple sampling is necessary to improve the quality of specimens.
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Affiliation(s)
- Hyo-Joon Yang
- Division of Gastroenterology, Department of Internal Medicine and Gastrointestinal Cancer Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung In Seo
- Division of Gastroenterology, Department of Internal Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
| | - Jin Lee
- Department of Internal Medicine, Inje University College of Medicine, Haeundae Paik Hospital, Busan, Korea
| | - Cheal Wung Huh
- Division of Gastroenterology, Department of Internal Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin, Korea
| | - Joon Sung Kim
- Division of Gastroenterology, Department of Internal Medicine, College of Medicine, Incheon St. Mary's Hospital, The Catholic University of Korea, Incheon, Korea
| | - Jun Chul Park
- Division of Gastroenterology, Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Hyunki Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Hakdong Shin
- Department of Food Science and Biotechnology, Sejong University, Seoul, Korea
| | - Cheol Min Shin
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Chan Hyuk Park
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea.
| | - Sang Kil Lee
- Division of Gastroenterology, Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea.
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4
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Zhou G, Zhou M, Zeng F, Zhang N, Sun Y, Qiao Z, Guo X, Zhou S, Yun G, Xie J, Wang X, Liu F, Fan C, Wang Y, Fang Z, Tian Z, Dai W, Sun J, Peng Z, Song L. Performance characterization of PCR-free whole genome sequencing for clinical diagnosis. Medicine (Baltimore) 2022; 101:e28972. [PMID: 35451387 PMCID: PMC8913097 DOI: 10.1097/md.0000000000028972] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/10/2022] [Indexed: 01/04/2023] Open
Abstract
To evaluate the performance of polymerase chain reaction (PCR)-free whole genome sequencing (WGS) for clinical diagnosis, and thereby revealing how experimental parameters affect variant detection.Five NA12878 samples were sequenced using MGISEQ-2000. NA12878 samples underwent WGS with differing deoxyribonucleic acid (DNA) input and library preparation protocol (PCR-based vs PCR-free protocols for library preparation). The depth of coverage and genotype quality of each sample were compared. The performance of each sample was measured for sensitivity, coverage of depth and breadth of coverage of disease-related genes, and copy number variants. We also developed a systematic WGS pipeline (PCR-free) for the analysis of 11 clinical cases.In general, NA12878-2 (PCR-free WGS) showed better depth of coverage and genotype quality distribution than NA12878-1 (PCR-based WGS). With a mean depth of ∼40×, the sensitivity of homozygous and heterozygous single nucleotide polymorphisms (SNPs) of NA12878-2 showed higher sensitivity (>99.77% and >99.82%) than NA12878-1, and positive predictive value exceeded 99.98% and 99.07%. The sensitivity and positive predictive value of homozygous and heterozygous indels for NA12878-2 (PCR-free WGS) showed great improvement than NA128878-1. The breadths of coverage for disease-related genes and copy number variants are slightly better for samples with PCR-free library preparation protocol than the sample with PCR-based library preparation protocol. DNA input also influences the performance of variant detection in samples with PCR-free WGS. All the 19 previously confirmed variants in 11 clinical cases were successfully detected by our WGS pipeline (PCR free).Different experimental parameters may affect variant detection for clinical WGS. Clinical scientists should know the range of sensitivity of variants for different methods of WGS, which would be useful when interpreting and delivering clinical reports.
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Affiliation(s)
- Guiju Zhou
- Department Obstetrics and Gynecology, The Second Affiliated Hospital, Anhui Medical University, Hefei, China
| | | | - Fanwei Zeng
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Ningzhi Zhang
- Fuyang People's Hospital, 63 Luci Street, Fuyang, Anhui Province, China
| | - Yan Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zhihong Qiao
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Xueqin Guo
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Shihao Zhou
- Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, Hunan Province, China
| | - Guojun Yun
- Rehabilitation Ward, Shenzhen Children's Hospital, 7019 Yitian Road, Futian District, Shenzhen, Guangdong Province, China
| | - Jiansheng Xie
- Department of Prenatal Diagnosis, The University of Hongkong Shenzhen Hospital, 1 Haiyuan one Road, Shenzhen, Guangdong Province, China
| | - Xiaodan Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Fengxia Liu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Chunna Fan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhonghai Fang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhongming Tian
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Wentao Dai
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lijie Song
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
- Bacterial Interactions and Evolution Group, Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
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5
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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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6
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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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7
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Liu T, Chen Z, Chen W, Chen X, Hosseini M, Yang Z, Li J, Ho D, Turay D, Gheorghe CP, Jones W, Wang C. A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples. iScience 2021; 24:102892. [PMID: 34308277 PMCID: PMC8294598 DOI: 10.1016/j.isci.2021.102892] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/07/2021] [Accepted: 07/16/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging new type of coronavirus that is responsible for the COVID-19 pandemic and the unprecedented global health emergency. Whole-genome sequencing (WGS) of SARS-CoV-2 plays a critical role in understanding the disease. Performance variation exists across SARS-CoV-2 viral WGS technologies, but there is currently no benchmarking study comparing different WGS sequencing protocols. We compared seven different SARS-CoV-2 WGS library protocols using RNA from patient nasopharyngeal swab samples under two storage conditions with low and high viral inputs. We found large differences in mappability and genome coverage, and variations in sensitivity, reproducibility, and precision of single-nucleotide variant calling across different protocols. For certain amplicon-based protocols, an appropriate primer trimming step is critical for accurate single-nucleotide variant calling. We ranked the performance of protocols based on six different metrics. Our findings offer guidance in choosing appropriate WGS protocols to characterize SARS-CoV-2 and its evolution.
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Affiliation(s)
- Tiantian Liu
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Zhong Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Wanqiu Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Xin Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
- Division of Microbiology & Molecular Genetics, Department of Basic Science, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Maryam Hosseini
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Zhaowei Yang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Jing Li
- Division of Microbiology & Molecular Genetics, Department of Basic Science, School of Medicine, Loma Linda University, Loma Linda, CA, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Diana Ho
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - David Turay
- Department of Surgery, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Ciprian P. Gheorghe
- Department of Gynecology & Obstetrics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Wendell Jones
- EA Genomics, Division of Q Solutions, Morrisville, NC, USA
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
- Division of Microbiology & Molecular Genetics, Department of Basic Science, School of Medicine, Loma Linda University, Loma Linda, CA, USA
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8
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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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9
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Sun Y, Liu F, Fan C, Wang Y, Song L, Fang Z, Han R, Wang Z, Wang X, Yang Z, Xu Z, Peng J, Shi C, Zhang H, Dong W, Huang H, Li Y, Le Y, Sun J, Peng Z. Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders. BMC Med Genomics 2021; 14:102. [PMID: 33849535 PMCID: PMC8045368 DOI: 10.1186/s12920-021-00948-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 03/31/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Due to its reduced cost and incomparable advantages, WGS is likely to lead to changes in clinical diagnosis of rare and undiagnosed diseases. However, the sensitivity and breadth of coverage of clinical WGS as a diagnostic test for genetic disorders has not been fully evaluated. METHODS Here, the performance of WGS in NA12878, the YH cell line, and the Chinese trios were measured by assessing their sensitivity, PPV, depth and breadth of coverage using MGISEQ-2000. We also compared the performance of WES and WGS using NA12878. The sensitivity and PPV were tested using the family-based trio design for the Chinese trios. We further developed a systematic WGS pipeline for the analysis of 8 clinical cases. RESULTS In general, the sensitivity and PPV for SNV/indel detection increased with mean depth and reached a plateau at an ~ 40X mean depth using down-sampling samples of NA12878. With a mean depth of 40X, the sensitivity of homozygous and heterozygous SNPs of NA12878 was > 99.25% and > 99.50%, respectively, and the PPV was 99.97% and 98.96%. Homozygous and heterozygous indels showed lower sensitivity and PPV. The sensitivity and PPV were still not 100% even with a mean depth of ~ 150X. We also observed a substantial variation in the sensitivity of CNV detection across different tools, especially in CNVs with a size less than 1 kb. In general, the breadth of coverage for disease-associated genes and CNVs increased with mean depth. The sensitivity and coverage of WGS (~ 40X) was better than WES (~ 120X). Among the Chinese trios with an ~ 40X mean depth, the sensitivity among offspring was > 99.48% and > 96.36% for SNP and indel detection, and the PPVs were 99.86% and 97.93%. All 12 previously validated variants in the 8 clinical cases were successfully detected using our WGS pipeline. CONCLUSIONS The current standard of a mean depth of 40X may be sufficient for SNV/indel detection and identification of most CNVs. It would be advisable for clinical scientists to determine the range of sensitivity and PPV for different classes of variants for a particular WGS pipeline, which would be useful when interpreting and delivering clinical reports.
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Affiliation(s)
- Yan Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Fengxia Liu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Chunna Fan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lijie Song
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhonghai Fang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Rui Han
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhonghua Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Xiaodan Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Ziying Yang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhenpeng Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jiguang Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Chaonan Shi
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | | | - Wei Dong
- BGI-Beijing Clinical Laboratories, BGI-Shenzhen, Beijing, 101300, China
| | - Hui Huang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yun Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yanqun Le
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
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10
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Kairov U, Molkenov A, Rakhimova S, Kozhamkulov U, Sharip A, Karabayev D, Daniyarov A, H Lee J, D Terwilliger J, Akilzhanova A, Zhumadilov Z. Whole-genome sequencing data of Kazakh individuals. BMC Res Notes 2021; 14:45. [PMID: 33541395 PMCID: PMC7863413 DOI: 10.1186/s13104-021-05464-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/28/2021] [Indexed: 11/22/2022] Open
Abstract
Objectives Kazakhstan is a Central Asian crossroad of European and Asian populations situated along the way of the Great Silk Way. The territory of Kazakhstan has historically been inhabited by nomadic tribes and today is the multi-ethnic country with the dominant Kazakh ethnic group. We sequenced and analyzed the whole-genomes of five ethnic healthy Kazakh individuals with high coverage using next-generation sequencing platform. This whole-genome sequence data of healthy Kazakh individuals can be a valuable reference for biomedical studies investigating disease associations and population-wide genomic studies of ethnically diverse Central Asian region. Data description Blood samples have been collected from five ethnic healthy Kazakh individuals living in Kazakhstan. The genomic DNA was extracted from blood and sequenced. Sequencing was performed on Illumina HiSeq2000 next-generation sequencing platform. We sequenced and analyzed the whole-genomes of ethnic Kazakh individuals with the coverage ranging from 26 to 32X. Ranging from 98.85 to 99.58% base pairs were totally mapped and aligned on the human reference genome GRCh37 hg19. Het/Hom and Ts/Tv ratios for each whole genome ranged from 1.35 to 1.49 and from 2.07 to 2.08, respectively. Sequencing data are available in the National Center for Biotechnology Information SRA database under the accession number PRJNA374772.
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Affiliation(s)
- Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.
| | - Askhat Molkenov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Aigul Sharip
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Daniyar Karabayev
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Asset Daniyarov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | | | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
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11
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Schizophrenic Psychosis Symptoms in a Background of Mild-To-Moderate Carnitine Palmitoyltransferase II Deficiency: A Case Report. REPORTS 2020. [DOI: 10.3390/reports3040031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Schizophrenia is a multifaceted mental illness characterized by cognitive and neurobehavioral abnormalities. Carnitine palmitoyltransferase II (CPT II) deficiency is a metabolic disorder resulting in impaired transport of long-chain fatty acids from the cytosol to the mitochondrial inner membrane, where fatty acid β-oxidation takes place. Here, we present an interesting clinical case of an adolescent male that presented with psychosis and a history of mild-to-moderate CPT II deficiency. To identify germline genetic variation that may contribute to the phenotypes observed, we performed whole-exome sequencing on DNA from the proband, unaffected fraternal twin, and biological parents. The proband was identified to be homozygous for the p.Val368Ile and heterozygous for the p.Met647Val variant in CPT2. Each of these variants are benign on their own; however, their combined effect is unclear. Further, variation was identified in the dopamine β-hydroxylase (DBH) gene (c.339+2T>C), which may contribute to decreased activity of DBH; however, based on the patient’s presentation, severe DBH deficiency is unlikely. In conclusion, the variants identified in this study do not clearly explain the observed patient phenotypes, indicating that the complex phenotypes are likely caused by an interplay of genetic and environmental factors that warrant further investigation.
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12
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Quality of whole genome sequencing from blood versus saliva derived DNA in cardiac patients. BMC Med Genomics 2020; 13:11. [PMID: 31996208 PMCID: PMC6988365 DOI: 10.1186/s12920-020-0664-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/20/2020] [Indexed: 01/03/2023] Open
Abstract
Background Whole-genome sequencing (WGS) is becoming an increasingly important tool for detecting genomic variation. Blood derived DNA is the current standard for WGS for research or clinical purposes but may not always be feasible to acquire. The usability of DNA from saliva for WGS is not known. We compared the quality of WGS between blood versus saliva derived DNA. Methods WGS was performed in DNA from 531 blood and 502 saliva samples (including 5 paired samples) from participants enrolled in a heart disease biorepository. We compared the proportion of sequencing reads that mapped to non-human sources (microbiome), the sequencing coverage, and the yield and concordance of single nucleotide variant (SNV) and copy number variant (CNV) calls between blood and saliva genomes. Results Of 531 blood and 502 saliva samples, 46% saliva DNA failed quality control (QC) requirements for WGS compared to 6% QC failure for blood DNA. An average of 10.7% WGS reads in the saliva samples mapped to the human oral microbiome compared to 0.09% WGS reads in blood samples. However, these reads were readily excluded by excluding reads that did not map to the human reference genome. Sequencing coverage met or exceeded the target sequencing depth of 30x in all the blood samples and 4 of the 5 saliva samples; the fifth saliva sample had an average sequencing depth of 22.6x. Over 95% of SNVs identified in saliva were concordant with those identified in blood across the genome, within all gene coding regions, and within cardiovascular disease-related gene coding regions. Rare SNVs, defined as those with a minor allele frequency of less than 1% in the Genome Aggregation Database, had a lower concordance of 90% between blood and saliva genomes. CNVs had only 76% concordance between blood and saliva samples. Conclusions High quality saliva samples that meet stringent QC criteria can be used for WGS when blood-derived DNA is not available or is not suitable. Saliva DNA provides an acceptable yield of SNV calls but has a lower yield for CNV calls compared to blood DNA.
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13
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Abstract
Objectives: Research on the genetic basis of tinnitus is still in its first steps. A group of scientists dedicated to tinnitus genetics within European Tinnitus Network (TINNET) network recognize that further progress requires multicenter collaborative efforts for defining contributing genes. The purpose of the present work is to provide instructions regarding collection, processing, storage, and shipment of samples intended for genetic studies in auditory research. Design: One part of the recommendations has a general character; another part is of particular importance for auditory healthcare practitioners such as otolaryngology physicians, audiologists, and general practitioners. Results: We provide a set of instructions and various options for obtaining samples. We give advice regarding sample processing, storage, and shipment and define the minimal and essential clinical information that should accompany the samples collected for genetic processing. Conclusions: These recommendations offer a basis to standardize and optimize collaborations between geneticists and healthcare practitioners specialized in tinnitus and hearing disorders.
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14
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Huss WJ, Hu Q, Glenn ST, Gangavarapu KJ, Wang J, Luce JD, Quinn PK, Brese EA, Zhan F, Conroy JM, Paragh G, Foster BA, Morrison CD, Liu S, Wei L. Comparison of SureSelect and Nextera Exome Capture Performance in Single-Cell Sequencing. Hum Hered 2019; 83:153-162. [PMID: 30669152 DOI: 10.1159/000490506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Advances in single-cell sequencing provide unprecedented opportunities for clinical examination of circulating tumor cells, cancer stem cells, and other rare cells responsible for disease progression and drug resistance. On the genomic level, single-cell whole exome sequencing (scWES) started to gain popularity with its unique potentials in characterizing mutational landscapes at a single-cell level. Currently, there is little known about the performance of different exome capture kits in scWES. Nextera rapid capture (NXT; Illumina, Inc.) has been the only exome capture kit recommended for scWES by Fluidigm C1, a widely accessed system in single-cell preparation. RESULTS In this study, we compared the performance of NXT following Fluidigm's protocol with Agilent SureSelectXT Target Enrichment System (AGL), another exome capture kit widely used for bulk sequencing. We created DNA libraries of 192 single cells isolated from spheres grown from a melanoma specimen using Fluidigm C1. Twelve high-yield cells were selected to perform dual-exome capture and sequencing using AGL and NXT in parallel. After mapping and coverage analysis, AGL outperformed NXT in coverage uniformity, mapping rates of reads, exome capture rates, and low PCR duplicate rates. For germline variant calling, AGL achieved better performance in overlap with known variants in dbSNP and transition-transversion ratios. Using calls from high coverage bulk sequencing from blood DNA as the golden standard, AGL-based scWES demonstrated high positive predictive values, and medium to high sensitivity. Lastly, we evaluated somatic mutation calling by comparing single-cell data with the matched blood sequence as control. On average, 300 mutations were identified in each cell. In 10 of 12 cells, higher numbers of mutations were identified using AGL than NXT, probably caused by coverage depth. When mutations are adequately covered in both AGL and NXT data, the two methods showed very high concordance (93-100% per cell). CONCLUSIONS Our results suggest that AGL can also be used for scWES when there is sufficient DNA, and it yields better data quality than the current Fluidigm's protocol using NXT.
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Affiliation(s)
- Wendy J Huss
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Qiang Hu
- Departments of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Sean T Glenn
- Center of Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA.,Department of Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Kalyan J Gangavarapu
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Jianmin Wang
- Departments of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Jesse D Luce
- Center of Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Paul K Quinn
- Center of Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Elizabeth A Brese
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Fenglin Zhan
- PET/CT Center, The First Affiliated Hospital of the University of Science and Technology of China, Hefei, China
| | - Jeffrey M Conroy
- Center of Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Gyorgy Paragh
- Department of Dermatology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA.,Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Barbara A Foster
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Carl D Morrison
- Center of Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Song Liu
- Departments of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Lei Wei
- Departments of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA,
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15
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Kong SW, Lee IH, Liu X, Hirschhorn JN, Mandl KD. Measuring coverage and accuracy of whole-exome sequencing in clinical context. Genet Med 2018; 20:1617-1626. [PMID: 29789557 PMCID: PMC6185824 DOI: 10.1038/gim.2018.51] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 02/16/2018] [Indexed: 01/21/2023] Open
Abstract
PURPOSE To evaluate the coverage and accuracy of whole-exome sequencing (WES) across vendors. METHODS Blood samples from three trios underwent WES at three vendors. Relative performance of the three WES services was measured for breadth and depth of coverage. The false-negative rates (FNRs) were estimated using the segregation pattern within each trio. RESULTS Mean depth of coverage for all genes was 189.0, 124.9, and 38.3 for the three vendor services. Fifty-five of the American College of Medical Genetics and Genomics 56 genes, but only 56 of 63 pharmacogenes, were 100% covered at 10 × in at least one of the nine individuals for all vendors; however, there was substantial interindividual variability. For the two vendors with mean depth of coverage >120 ×, analytic positive predictive values (aPPVs) exceeded 99.1% for single-nucleotide variants and homozygous indels, and sensitivities were 98.9-99.9%; however, heterozygous indels showed lower accuracy and sensitivity. Among the trios, FNRs in the offspring were 0.07-0.62% at well-covered variants concordantly called in both parents. CONCLUSION The current standard of 120 × coverage for clinical WES may be insufficient for consistent breadth of coverage across the exome. Ordering clinicians and researchers would benefit from vendors' reports that estimate sensitivity and aPPV, including depth of coverage across the exome.
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Affiliation(s)
- Sek Won Kong
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA,To whom correspondence should be addressed at: Sek Won Kong, MD, 300 Longwood Avenue, Boston Children’s Hospital, Boston, MA 02115, T: 617-919-2689, F: 617-730-0817,
| | - In-Hee Lee
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Xuanshi Liu
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Joel N. Hirschhorn
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA,Broad Institute, Cambridge, MA 02142, USA
| | - Kenneth D. Mandl
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA,Department of Biomedical Informatics, Harvard Medical School, Boson, MA 02115, USA
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16
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Tuzov N. A framework for the estimation of the proportion of true discoveries in single nucleotide variant detection studies for human data. PLoS One 2018; 13:e0196058. [PMID: 29694377 PMCID: PMC5918994 DOI: 10.1371/journal.pone.0196058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 04/05/2018] [Indexed: 12/30/2022] Open
Abstract
Any single nucleotide variant detection study could benefit from a fast and cheap method of measuring the quality of variant call list. It is advantageous to be able to see how the call list quality is affected by different variant filtering thresholds and other adjustments to the study parameters. Here we look into a possibility of estimating the proportion of true positives in a single nucleotide variant call list for human data. Using whole-exome and whole-genome gold standard data sets for training, we focus on building a generic model that only relies on information available from any variant caller. We assess and compare the performance of different candidate models based on their practical accuracy. We find that the generic model delivers decent accuracy most of the time. Further, we conclude that its performance could be improved substantially by leveraging the variant quality metrics that are specific to each variant calling tool.
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Affiliation(s)
- Nik Tuzov
- Partek Incorporated, Saint Louis, Missouri, United States of America
- * E-mail:
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17
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Pitfalls of improperly procured adjacent non-neoplastic tissue for somatic mutation analysis using next-generation sequencing. BMC Med Genomics 2016; 9:64. [PMID: 27756300 PMCID: PMC5070097 DOI: 10.1186/s12920-016-0226-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 10/07/2016] [Indexed: 12/21/2022] Open
Abstract
Background The rapid adoption of next-generation sequencing provides an efficient system for detecting somatic alterations in neoplasms. The detection of such alterations requires a matched non-neoplastic sample for adequate filtering of non-somatic events such as germline polymorphisms. Non-neoplastic tissue adjacent to the excised neoplasm is often used for this purpose as it is simultaneously collected and generally contains the same tissue type as the neoplasm. Following NGS analysis, we and others have frequently observed low-level somatic mutations in these non-neoplastic tissues, which may impose additional challenges to somatic mutation detection as it complicates germline variant filtering. Methods We hypothesized that the low-level somatic mutation observed in non-neoplastic tissues may be entirely or partially caused by inadvertent contamination by neoplastic cells during the surgical pathology gross assessment or tissue procurement process. To test this hypothesis, we applied a systematic protocol designed to collect multiple grossly non-neoplastic tissues using different methods surrounding each single neoplasm. The procedure was applied in two breast cancer lumpectomy specimens. In each case, all samples were first sequenced by whole-exome sequencing to identify somatic mutations in the neoplasm and determine their presence in the adjacent non-neoplastic tissues. We then generated ultra-deep coverage using targeted sequencing to assess the levels of contamination in non-neoplastic tissue samples collected under different conditions. Results Contamination levels in non-neoplastic tissues ranged up to 3.5 and 20.9 % respectively in the two cases tested, with consistent pattern correlated with the manner of grossing and procurement. By carefully controlling the conditions of various steps during this process, we were able to eliminate any detectable contamination in both patients. Conclusion The results demonstrated that the process of tissue procurement contributes to the level of contamination in non-neoplastic tissue, and contamination can be reduced to below detectable levels by using a carefully designed collection method. A standard protocol dedicated for acquiring adjacent non-neoplastic tissue that minimizes neoplasm contamination should be implemented for all somatic mutation detection studies. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0226-1) contains supplementary material, which is available to authorized users.
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18
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Chung J, Son DS, Jeon HJ, Kim KM, Park G, Ryu GH, Park WY, Park D. The minimal amount of starting DNA for Agilent's hybrid capture-based targeted massively parallel sequencing. Sci Rep 2016; 6:26732. [PMID: 27220682 PMCID: PMC4879621 DOI: 10.1038/srep26732] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/06/2016] [Indexed: 12/18/2022] Open
Abstract
Targeted capture massively parallel sequencing is increasingly being used in clinical settings, and as costs continue to decline, use of this technology may become routine in health care. However, a limited amount of tissue has often been a challenge in meeting quality requirements. To offer a practical guideline for the minimum amount of input DNA for targeted sequencing, we optimized and evaluated the performance of targeted sequencing depending on the input DNA amount. First, using various amounts of input DNA, we compared commercially available library construction kits and selected Agilent’s SureSelect-XT and KAPA Biosystems’ Hyper Prep kits as the kits most compatible with targeted deep sequencing using Agilent’s SureSelect custom capture. Then, we optimized the adapter ligation conditions of the Hyper Prep kit to improve library construction efficiency and adapted multiplexed hybrid selection to reduce the cost of sequencing. In this study, we systematically evaluated the performance of the optimized protocol depending on the amount of input DNA, ranging from 6.25 to 200 ng, suggesting the minimal input DNA amounts based on coverage depths required for specific applications.
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Affiliation(s)
- Jongsuk Chung
- Samsung Biomedical Research Institute, Samsung Advanced Institute of Technology, Samsung Electronics Co. Ltd., Seoul 06351, Korea.,Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Dae-Soon Son
- Samsung Biomedical Research Institute, Samsung Advanced Institute of Technology, Samsung Electronics Co. Ltd., Seoul 06351, Korea.,Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Hyo-Jeong Jeon
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Gahee Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Gyu Ha Ryu
- Office of Research and Development Strategy &Planning, Samsung Medical Center, Seoul 06351, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Donghyun Park
- Samsung Biomedical Research Institute, Samsung Advanced Institute of Technology, Samsung Electronics Co. Ltd., Seoul 06351, Korea.,Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
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