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Pacheco MA, Cepeda AS, Miller EA, Beckerman S, Oswald M, London E, Mateus-Pinilla NE, Escalante AA. A new long-read mitochondrial-genome protocol (PacBio HiFi) for haemosporidian parasites: a tool for population and biodiversity studies. Malar J 2024; 23:134. [PMID: 38704592 PMCID: PMC11069185 DOI: 10.1186/s12936-024-04961-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/24/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Studies on haemosporidian diversity, including origin of human malaria parasites, malaria's zoonotic dynamic, and regional biodiversity patterns, have used target gene approaches. However, current methods have a trade-off between scalability and data quality. Here, a long-read Next-Generation Sequencing protocol using PacBio HiFi is presented. The data processing is supported by a pipeline that uses machine-learning for analysing the reads. METHODS A set of primers was designed to target approximately 6 kb, almost the entire length of the haemosporidian mitochondrial genome. Amplicons from different samples were multiplexed in an SMRTbell® library preparation. A pipeline (HmtG-PacBio Pipeline) to process the reads is also provided; it integrates multiple sequence alignments, a machine-learning algorithm that uses modified variational autoencoders, and a clustering method to identify the mitochondrial haplotypes/species in a sample. Although 192 specimens could be studied simultaneously, a pilot experiment with 15 specimens is presented, including in silico experiments where multiple data combinations were tested. RESULTS The primers amplified various haemosporidian parasite genomes and yielded high-quality mt genome sequences. This new protocol allowed the detection and characterization of mixed infections and co-infections in the samples. The machine-learning approach converged into reproducible haplotypes with a low error rate, averaging 0.2% per read (minimum of 0.03% and maximum of 0.46%). The minimum recommended coverage per haplotype is 30X based on the detected error rates. The pipeline facilitates inspecting the data, including a local blast against a file of provided mitochondrial sequences that the researcher can customize. CONCLUSIONS This is not a diagnostic approach but a high-throughput method to study haemosporidian sequence assemblages and perform genotyping by targeting the mitochondrial genome. Accordingly, the methodology allowed for examining specimens with multiple infections and co-infections of different haemosporidian parasites. The pipeline enables data quality assessment and comparison of the haplotypes obtained to those from previous studies. Although a single locus approach, whole mitochondrial data provide high-quality information to characterize species pools of haemosporidian parasites.
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Affiliation(s)
- M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA.
| | - Axl S Cepeda
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA
| | - Erica A Miller
- University of Pennsylvania, Wildlife Futures Program, Kennett Square, Philadelphia, PA, 19348, USA
| | | | | | - Evan London
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Nohra E Mateus-Pinilla
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
- Illinois Natural History Survey-Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, 61802, USA
| | - Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA.
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Wu HX, Chu TY, Iqbal J, Jiang HL, Li L, Wu YX, Zhou HD. Response to Letter to the Editor From Hooper: "Cardio-cerebrovascular Outcomes in MODY, Type 1 Diabetes, and Type 2 Diabetes: A Prospective Cohort Study". J Clin Endocrinol Metab 2024; 109:e1416-e1417. [PMID: 38069916 DOI: 10.1210/clinem/dgad720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Indexed: 04/21/2024]
Affiliation(s)
- Hui-Xuan Wu
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, Key Laboratory of Diabetes Immunology Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Tian-Yao Chu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 41000, Hunan, China
| | - Junaid Iqbal
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, Key Laboratory of Diabetes Immunology Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Hong-Li Jiang
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, Key Laboratory of Diabetes Immunology Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Long Li
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, Key Laboratory of Diabetes Immunology Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Yan-Xuan Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 15000, Heilongjiang, China
| | - Hou-De Zhou
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, Key Laboratory of Diabetes Immunology Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
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Cebeci YE, Erturk RA, Ergun MA, Baysan M. Improving somatic exome sequencing performance by biological replicates. BMC Bioinformatics 2024; 25:124. [PMID: 38519906 PMCID: PMC10958848 DOI: 10.1186/s12859-024-05742-5] [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: 09/26/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) technologies offer fast and inexpensive identification of DNA sequences. Somatic sequencing is among the primary applications of NGS, where acquired (non-inherited) variants are based on comparing diseased and healthy tissues from the same individual. Somatic mutations in genetic diseases such as cancer are tightly associated with genomic instability. Genomic instability increases heterogenity, complicating sequencing efforts further, a task already challenged by the presence of short reads and repetitions in human DNA. This leads to low concordance among studies and limits reproducibility. This limitation is a significant problem since identified mutations in somatic sequencing are major biomarkers for diagnosis and the primary input of targeted therapies. Benchmarking studies were conducted to assess the error rates and increase reproducibility. Unfortunately, the number of somatic benchmarking sets is very limited due to difficulties in validating true somatic variants. Moreover, most NGS benchmarking studies are based on relatively simpler germline (inherited) sequencing. Recently, a comprehensive somatic sequencing benchmarking set was published by Sequencing Quality Control Phase 2 (SEQC2). We chose this dataset for our experiments because it is a well-validated, cancer-focused dataset that includes many tumor/normal biological replicates. Our study has two primary goals. First goal is to determine how replicate-based consensus approaches can improve the accuracy of somatic variant detection systems. Second goal is to develop highly predictive machine learning (ML) models by employing replicate-based consensus variants as labels during the training phase. RESULTS Ensemble approaches that combine alternative algorithms are relatively common; here, as an alternative, we study the performance enhancement potential of biological replicates. We first developed replicate-based consensus approaches that utilize the biological replicates available in this study to improve variant calling performance. Subsequently, we trained ML models using these biological replicates and achieved performance comparable to optimal ML models, those trained using high-confidence variants identified in advance. CONCLUSIONS Our replicate-based consensus approach can be used to improve variant calling performance and develop efficient ML models. Given the relative ease of obtaining biological replicates, this strategy allows for the development of efficient ML models tailored to specific datasets or scenarios.
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Affiliation(s)
- Yunus Emre Cebeci
- Department of Computer Engineering, Istanbul Technical University, 34469, Istanbul, Turkey
| | - Rumeysa Aslihan Erturk
- Department of Computer Engineering, Istanbul Technical University, 34469, Istanbul, Turkey
| | - Mehmet Arif Ergun
- Department of Computer Engineering, Istanbul Technical University, 34469, Istanbul, Turkey
| | - Mehmet Baysan
- Department of Computer Engineering, Istanbul Technical University, 34469, Istanbul, Turkey.
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Wu HX, Chu TY, Iqbal J, Jiang HL, Li L, Wu YX, Zhou HD. Cardio-cerebrovascular Outcomes in MODY, Type 1 Diabetes, and Type 2 Diabetes: A Prospective Cohort Study. J Clin Endocrinol Metab 2023; 108:2970-2980. [PMID: 37093977 DOI: 10.1210/clinem/dgad233] [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: 03/14/2023] [Revised: 04/09/2023] [Accepted: 04/20/2023] [Indexed: 04/26/2023]
Abstract
CONTEXT Cardio-cerebrovascular events are severe complications of diabetes. OBJECTIVE We aim to compare the incident risk of cardio-cerebrovascular events in maturity onset diabetes of the young (MODY), type 1 diabetes, and type 2 diabetes. METHODS Type 1 diabetes, type 2 diabetes, and MODY were diagnosed by whole exome sequencing. The primary endpoint was the occurrence of the first major adverse cardiovascular event (MACE), including acute myocardial infarction, heart failure, stroke, unstable angina pectoris, and cardio-cerebrovascular-related mortality. Cox proportional hazards models were applied and adjusted to calculate hazard ratios (HRs) and 95% CIs for the incident risk of MACE in type 1 diabetes, type 2 diabetes, MODY, and MODY subgroups compared with people without diabetes (control group). RESULTS Type 1 diabetes, type 2 diabetes, and MODY accounted for 2.7%, 68.1%, and 11.4% of 26 198 participants with diabetes from UK Biobank. During a median follow-up of 13 years, 1028 MACEs occurred in the control group, contrasting with 70 events in patients with type 1 diabetes (HR 2.15, 95% CI 1.69-2.74, P < .05), 5020 events in patients with type 2 diabetes (HR 7.02, 95% CI 6.56-7.51, P < .05), and 717 events in MODY (HR 5.79, 95% CI 5.26-6.37, P < .05). The hazard of MACE in HNF1B-MODY was highest among MODY subgroups (HR 11.00, 95% CI 5.47-22.00, P = 1.5 × 10-11). CONCLUSION MODY diagnosed by genetic analysis represents higher prevalence than the clinical diagnosis in UK Biobank. The risk of incident cardio-cerebrovascular events in MODY ranks between type 1 diabetes and type 2 diabetes.
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Affiliation(s)
- Hui-Xuan Wu
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, Key Laboratory of Diabetes Immunology Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Tian-Yao Chu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 41000, Hunan, China
| | - Junaid Iqbal
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, Key Laboratory of Diabetes Immunology Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Hong-Li Jiang
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, Key Laboratory of Diabetes Immunology Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Long Li
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, Key Laboratory of Diabetes Immunology Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Yan-Xuan Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 15000, China
| | - Hou-De Zhou
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, Key Laboratory of Diabetes Immunology Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
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Zhao R, Lukacsovich T, Gaut R, Emerson JJ. FREQ-Seq2: a method for precise high-throughput combinatorial quantification of allele frequencies. G3 (BETHESDA, MD.) 2023; 13:jkad162. [PMID: 37494033 PMCID: PMC10542570 DOI: 10.1093/g3journal/jkad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 01/26/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023]
Abstract
The accurate determination of allele frequencies is crucially important across a wide range of problems in genetics, such as developing population genetic models, making inferences from genome-wide association studies, determining genetic risk for diseases, as well as other scientific and medical applications. Furthermore, understanding how allele frequencies change over time in populations is central to ascertaining their evolutionary dynamics. We present a precise, efficient, and economical method (FREQ-Seq2) for quantifying the relative frequencies of different alleles at loci of interest in mixed population samples. Through the creative use of paired barcode sequences, we exponentially increased the throughput of the original FREQ-Seq method from 48 to 2,304 samples. FREQ-Seq2 can be targeted to specific genomic regions of interest, which are amplified using universal barcoded adapters to generate Illumina sequencing libraries. Our enhanced method, available as a kit along with open-source software for analyzing sequenced libraries, enables the detection and removal of errors that are undetectable in the original FREQ-Seq method as well as other conventional methods for allele frequency quantification. Finally, we validated the performance of our sequencing-based approach with a highly multiplexed set of control samples as well as a competitive evolution experiment in Escherichia coli and compare the latter to estimates derived from manual colony counting. Our analyses demonstrate that FREQ-Seq2 is flexible, inexpensive, and produces large amounts of data with low error, low noise, and desirable statistical properties. In summary, FREQ-Seq2 is a powerful method for quantifying allele frequency that provides a versatile approach for profiling mixed populations.
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Affiliation(s)
- Roy Zhao
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
| | - Tamas Lukacsovich
- Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland
| | - Rebecca Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - J J Emerson
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
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6
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Türk E, Ayaz A, Yüksek A, Süzek BE. DEVOUR: Deleterious Variants on Uncovered Regions in Whole-Exome Sequencing. PeerJ 2023; 11:e16026. [PMID: 37727687 PMCID: PMC10506587 DOI: 10.7717/peerj.16026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/13/2023] [Indexed: 09/21/2023] Open
Abstract
The discovery of low-coverage (i.e. uncovered) regions containing clinically significant variants, especially when they are related to the patient's clinical phenotype, is critical for whole-exome sequencing (WES) based clinical diagnosis. Therefore, it is essential to develop tools to identify the existence of clinically important variants in low-coverage regions. Here, we introduce a desktop application, namely DEVOUR (DEleterious Variants On Uncovered Regions), that analyzes read alignments for WES experiments, identifies genomic regions with no or low-coverage (read depth < 5) and then annotates known variants in the low-coverage regions using clinical variant annotation databases. As a proof of concept, DEVOUR was used to analyze a total of 28 samples from a publicly available Hirschsprung disease-related WES project (NCBI Bioproject: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB19327), revealing the potential existence of 98 disease-associated variants in low-coverage regions. DEVOUR is available from https://github.com/projectDevour/DEVOUR under the MIT license.
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Affiliation(s)
- Erdem Türk
- Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey
- Bioinformatics Graduate Program, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Akif Ayaz
- Department of Medical Genetics, School of Medicine, İstanbul Medipol University, İstanbul, Turkey
| | - Ayhan Yüksek
- Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Barış E. Süzek
- Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey
- Bioinformatics Graduate Program, Muğla Sıtkı Koçman University, Muğla, Turkey
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Das S, Biswas NK, Basu A. Mapinsights: deep exploration of quality issues and error profiles in high-throughput sequence data. Nucleic Acids Res 2023; 51:e75. [PMID: 37378434 PMCID: PMC10415152 DOI: 10.1093/nar/gkad539] [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: 12/09/2022] [Revised: 05/16/2023] [Accepted: 06/27/2023] [Indexed: 06/29/2023] Open
Abstract
High-throughput sequencing (HTS) has revolutionized science by enabling super-fast detection of genomic variants at base-pair resolution. Consequently, it poses the challenging problem of identification of technical artifacts, i.e. hidden non-random error patterns. Understanding the properties of sequencing artifacts holds the key in separating true variants from false positives. Here, we develop Mapinsights, a toolkit that performs quality control (QC) analysis of sequence alignment files, capable of detecting outliers based on sequencing artifacts of HTS data at a deeper resolution compared with existing methods. Mapinsights performs a cluster analysis based on novel and existing QC features derived from the sequence alignment for outlier detection. We applied Mapinsights on community standard open-source datasets and identified various quality issues including technical errors related to sequencing cycles, sequencing chemistry, sequencing libraries and across various orthogonal sequencing platforms. Mapinsights also enables identification of anomalies related to sequencing depth. A logistic regression-based model built on the features of Mapinsights shows high accuracy in detecting 'low-confidence' variant sites. Quantitative estimates and probabilistic arguments provided by Mapinsights can be utilized in identifying errors, bias and outlier samples, and also aid in improving the authenticity of variant calls.
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Affiliation(s)
- Subrata Das
- National Institute of Biomedical Genomics, Kalyani, 741251, West Bengal, India
| | - Nidhan K Biswas
- National Institute of Biomedical Genomics, Kalyani, 741251, West Bengal, India
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, 741251, West Bengal, India
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Marzano F, Chiara M, Consiglio A, D’Amato G, Gentile M, Mirabelli V, Piane M, Savio C, Fabiani M, D’Elia D, Sbisà E, Scarano G, Lonardo F, Tullo A, Pesole G, Faienza MF. Whole-Exome and Transcriptome Sequencing Expands the Genotype of Majewski Osteodysplastic Primordial Dwarfism Type II. Int J Mol Sci 2023; 24:12291. [PMID: 37569667 PMCID: PMC10418986 DOI: 10.3390/ijms241512291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Microcephalic Osteodysplastic Primordial Dwarfism type II (MOPDII) represents the most common form of primordial dwarfism. MOPD clinical features include severe prenatal and postnatal growth retardation, postnatal severe microcephaly, hypotonia, and an increased risk for cerebrovascular disease and insulin resistance. Autosomal recessive biallelic loss-of-function genomic variants in the centrosomal pericentrin (PCNT) gene on chromosome 21q22 cause MOPDII. Over the past decade, exome sequencing (ES) and massive RNA sequencing have been effectively employed for both the discovery of novel disease genes and to expand the genotypes of well-known diseases. In this paper we report the results both the RNA sequencing and ES of three patients affected by MOPDII with the aim of exploring whether differentially expressed genes and previously uncharacterized gene variants, in addition to PCNT pathogenic variants, could be associated with the complex phenotype of this disease. We discovered a downregulation of key factors involved in growth, such as IGF1R, IGF2R, and RAF1, in all three investigated patients. Moreover, ES identified a shortlist of genes associated with deleterious, rare variants in MOPDII patients. Our results suggest that Next Generation Sequencing (NGS) technologies can be successfully applied for the molecular characterization of the complex genotypic background of MOPDII.
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Affiliation(s)
- Flaviana Marzano
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM–CNR, 70126 Bari, Italy; (F.M.); (A.T.)
| | - Matteo Chiara
- Department of Biosciences, University of Milan, 20133 Milan, Italy;
| | - Arianna Consiglio
- Institute for Biomedical Technologies, ITB-CNR, 70126 Bari, Italy; (A.C.); (V.M.); (D.D.); (E.S.)
| | - Gabriele D’Amato
- Neonatal Intensive Care Unit, Di Venere Hospital, 70012 Bari, Italy
| | | | - Valentina Mirabelli
- Institute for Biomedical Technologies, ITB-CNR, 70126 Bari, Italy; (A.C.); (V.M.); (D.D.); (E.S.)
| | - Maria Piane
- Department of Clinical and Molecular Medicine, Sapienza University, 00185 Rome, Italy;
| | | | - Marco Fabiani
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy;
| | - Domenica D’Elia
- Institute for Biomedical Technologies, ITB-CNR, 70126 Bari, Italy; (A.C.); (V.M.); (D.D.); (E.S.)
| | - Elisabetta Sbisà
- Institute for Biomedical Technologies, ITB-CNR, 70126 Bari, Italy; (A.C.); (V.M.); (D.D.); (E.S.)
| | - Gioacchino Scarano
- Medical Genetics Unit, AORN “San Pio”, Hosp. “G. Rummo”, 82100 Benevento, Italy; (G.S.); (F.L.)
| | - Fortunato Lonardo
- Medical Genetics Unit, AORN “San Pio”, Hosp. “G. Rummo”, 82100 Benevento, Italy; (G.S.); (F.L.)
| | - Apollonia Tullo
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM–CNR, 70126 Bari, Italy; (F.M.); (A.T.)
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM–CNR, 70126 Bari, Italy; (F.M.); (A.T.)
- Department of Biosciences, Biotechnology and Biofarmaceutics, University of Bari “Aldo Moro”, 70126 Bari, Italy
| | - Maria Felicia Faienza
- Pediatric Section, Department of Precision and Regenerative Medicine and Ionian Area, University “A. Moro” of Bari, 70124 Bari, Italy
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Sakuma I, Nagano H, Hashimoto N, Fujimoto M, Nakayama A, Fuchigami T, Taki Y, Matsuda T, Akamine H, Kono S, Kono T, Yokoyama M, Nishimura M, Yokote K, Ogasawara T, Fujii Y, Ogawa S, Lee E, Miki T, Tanaka T. Identification of genotype-biochemical phenotype correlations associated with fructose 1,6-bisphosphatase deficiency. Commun Biol 2023; 6:787. [PMID: 37507476 PMCID: PMC10382519 DOI: 10.1038/s42003-023-05160-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Fructose-1,6-bisphosphatase (FBPase) deficiency, caused by an FBP1 mutation, is an autosomal recessive disorder characterized by hypoglycemic lactic acidosis. Due to the rarity of FBPase deficiency, the mechanism by which the mutations cause enzyme activity loss still remains unclear. Here we identify compound heterozygous missense mutations of FBP1, c.491G>A (p.G164D) and c.581T>C (p.F194S), in an adult patient with hypoglycemic lactic acidosis. The G164D and F194S FBP1 mutants exhibit decreased FBP1 protein expression and a loss of FBPase enzyme activity. The biochemical phenotypes of all previously reported FBP1 missense mutations in addition to G164D and F194S are classified into three functional categories. Type 1 mutations are located at pivotal residues in enzyme activity motifs and have no effects on protein expression. Type 2 mutations structurally cluster around the substrate binding pocket and are associated with decreased protein expression due to protein misfolding. Type 3 mutations are likely nonpathogenic. These findings demonstrate a key role of protein misfolding in mediating the pathogenesis of FBPase deficiency, particularly for Type 2 mutations. This study provides important insights that certain patients with Type 2 mutations may respond to chaperone molecules.
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Affiliation(s)
- Ikki Sakuma
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
| | - Hidekazu Nagano
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
| | - Naoko Hashimoto
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
- Research Institute of Disaster Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Masanori Fujimoto
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
| | - Akitoshi Nakayama
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
| | - Takahiro Fuchigami
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
| | - Yuki Taki
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
| | - Tatsuma Matsuda
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
| | - Hiroyuki Akamine
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
| | - Satomi Kono
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
| | - Takashi Kono
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
| | - Masataka Yokoyama
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
| | - Motoi Nishimura
- Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, 260-8670, Japan
| | - Koutaro Yokote
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan
| | - Tatsuki Ogasawara
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yoichi Fujii
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Eunyoung Lee
- Research Institute of Disaster Medicine, Chiba University, Chiba, 260-8670, Japan
- Department of Medical Physiology, Chiba University, Graduate School of Medicine, Chiba, 260-8670, Japan
| | - Takashi Miki
- Research Institute of Disaster Medicine, Chiba University, Chiba, 260-8670, Japan
- Department of Medical Physiology, Chiba University, Graduate School of Medicine, Chiba, 260-8670, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba, 260-8670, Japan.
- Research Institute of Disaster Medicine, Chiba University, Chiba, 260-8670, Japan.
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Yaldiz B, Kucuk E, Hampstead J, Hofste T, Pfundt R, Corominas Galbany J, Rinne T, Yntema HG, Hoischen A, Nelen M, Gilissen C. Twist exome capture allows for lower average sequence coverage in clinical exome sequencing. Hum Genomics 2023; 17:39. [PMID: 37138343 PMCID: PMC10155375 DOI: 10.1186/s40246-023-00485-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/20/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. RESULTS We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. CONCLUSION We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques.
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Affiliation(s)
- Burcu Yaldiz
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Erdi Kucuk
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Juliet Hampstead
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Jordi Corominas Galbany
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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Biegała Ł, Gajek A, Marczak A, Rogalska A. Olaparib-Resistant BRCA2MUT Ovarian Cancer Cells with Restored BRCA2 Abrogate Olaparib-Induced DNA Damage and G2/M Arrest Controlled by the ATR/CHK1 Pathway for Survival. Cells 2023; 12:cells12071038. [PMID: 37048111 PMCID: PMC10093185 DOI: 10.3390/cells12071038] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/07/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The PARP inhibitor (PARPi) olaparib is currently the drug of choice for serous ovarian cancer (OC), especially in patients with homologous recombination (HR) repair deficiency associated with deleterious BRCA1/2 mutations. Unfortunately, OC patients who fail to respond to PARPi or relapse after treatment have limited therapeutic options. To elucidate olaparib resistance and enhance the efficacy of olaparib, intracellular factors exploited by OC cells to achieve decreased sensitivity to PARPi were examined. An olaparib-resistant OC cell line, PEO1-OR, was established from BRCA2MUT PEO1 cells. The anticancer activity and action of olaparib combined with inhibitors of the ATR/CHK1 pathway (ceralasertib as ATRi, MK-8776 as CHK1i) in olaparib-sensitive and -resistant OC cell lines were evaluated. Whole-exome sequencing revealed that PEO1-OR cells acquire resistance through subclonal enrichment of BRCA2 secondary mutations that restore functional full-length protein. Moreover, PEO1-OR cells upregulate HR repair-promoting factors (BRCA1, BRCA2, RAD51) and PARP1. Olaparib-inducible activation of the ATR/CHK1 pathway and G2/M arrest is abrogated in olaparib-resistant cells. Drug sensitivity assays revealed that PEO1-OR cells are less sensitive to ATRi and CHK1i agents. Combined treatment is less effective in olaparib-resistant cells considering inhibition of metabolic activity, colony formation, survival, accumulation of DNA double-strand breaks, and chromosomal aberrations. However, synergistic antitumor activity between compounds is achievable in PEO1-OR cells. Collectively, olaparib-resistant cells display co-existing HR repair-related mechanisms that confer resistance to olaparib, which may be effectively utilized to resensitize them to PARPi via combination therapy. Importantly, the addition of ATR/CHK1 pathway inhibitors to olaparib has the potential to overcome acquired resistance to PARPi.
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12
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Carter MT, Srour M, Au PYB, Buhas D, Dyack S, Eaton A, Inbar-Feigenberg M, Howley H, Kawamura A, Lewis SME, McCready E, Nelson TN, Vallance H. Genetic and metabolic investigations for neurodevelopmental disorders: position statement of the Canadian College of Medical Geneticists (CCMG). J Med Genet 2023; 60:523-532. [PMID: 36822643 DOI: 10.1136/jmg-2022-108962] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/27/2023] [Indexed: 02/25/2023]
Abstract
PURPOSE AND SCOPE The aim of this position statement is to provide recommendations for clinicians regarding the use of genetic and metabolic investigations for patients with neurodevelopmental disorders (NDDs), specifically, patients with global developmental delay (GDD), intellectual disability (ID) and/or autism spectrum disorder (ASD). This document also provides guidance for primary care and non-genetics specialists caring for these patients while awaiting consultation with a clinical geneticist or metabolic specialist. METHODS OF STATEMENT DEVELOPMENT A multidisciplinary group reviewed existing literature and guidelines on the use of genetic and metabolic investigations for the diagnosis of NDDs and synthesised the evidence to make recommendations relevant to the Canadian context. The statement was circulated for comment to the Canadian College of Medical Geneticists (CCMG) membership-at-large and to the Canadian Pediatric Society (Mental Health and Developmental Disabilities Committee); following incorporation of feedback, it was approved by the CCMG Board of Directors on 1 September 2022. RESULTS AND CONCLUSIONS Chromosomal microarray is recommended as a first-tier test for patients with GDD, ID or ASD. Fragile X testing should also be done as a first-tier test when there are suggestive clinical features or family history. Metabolic investigations should be done if there are clinical features suggestive of an inherited metabolic disease, while the patient awaits consultation with a metabolic physician. Exome sequencing or a comprehensive gene panel is recommended as a second-tier test for patients with GDD or ID. Genetic testing is not recommended for patients with NDDs in the absence of GDD, ID or ASD, unless accompanied by clinical features suggestive of a syndromic aetiology or inherited metabolic disease.
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Affiliation(s)
| | - Myriam Srour
- Division of Neurology, McGill University Health Centre, Montreal, Québec, Canada
- Department of Pediatrics, McGill University, Montréal, QC, Canada
| | - Ping-Yee Billie Au
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Daniela Buhas
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sarah Dyack
- Division of Medical Genetics, IWK Health Centre, Halifax, Nova Scotia, Canada
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Alison Eaton
- Department of Medical Genetics, Stollery Children's Hospital, Edmonton, Alberta, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Michal Inbar-Feigenberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Heather Howley
- Office of Research Services, CHEO Research Institute, Ottawa, Ontario, Canada
| | - Anne Kawamura
- Division of Developmental Pediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Mental Health and Developmental Disability Committee, Canadian Pediatric Society, Ottawa, ON, Canada
- Canadian Paediatric Society, Toronto, Ontario, Canada
| | - Suzanne M E Lewis
- Department of Medical Genetics, BC Children's and Women's Hospital, Vancouver, British Columbia, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, McMaster University, Hamilton, ON, Canada, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Tanya N Nelson
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hilary Vallance
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
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13
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Thuesen NH, Klausen MS, Gopalakrishnan S, Trolle T, Renaud G. Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions. Front Immunol 2022; 13:987655. [PMID: 36426357 PMCID: PMC9679531 DOI: 10.3389/fimmu.2022.987655] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2023] Open
Abstract
Identifying the specific human leukocyte antigen (HLA) allele combination of an individual is crucial in organ donation, risk assessment of autoimmune and infectious diseases and cancer immunotherapy. However, due to the high genetic polymorphism in this region, HLA typing requires specialized methods. We investigated the performance of five next-generation sequencing (NGS) based HLA typing tools with a non-restricted license namely HLA*LA, Optitype, HISAT-genotype, Kourami and STC-Seq. This evaluation was done for the five HLA loci, HLA-A, -B, -C, -DRB1 and -DQB1 using whole-exome sequencing (WES) samples from 829 individuals. The robustness of the tools to lower depth of coverage (DOC) was evaluated by subsampling and HLA typing 230 WES samples at DOC ranging from 1X to 100X. The HLA typing accuracy was measured across four typing resolutions. Among these, we present two clinically-relevant typing resolutions (P group and pseudo-sequence), which specifically focus on the peptide binding region. On average, across the five HLA loci examined, HLA*LA was found to have the highest typing accuracy. For the individual loci, HLA-A, -B and -C, Optitype's typing accuracy was the highest and HLA*LA had the highest typing accuracy for HLA-DRB1 and -DQB1. The tools' robustness to lower DOC data varied widely and further depended on the specific HLA locus. For all Class I loci, Optitype had a typing accuracy above 95% (according to the modification of the amino acids in the functionally relevant portion of the HLA molecule) at 50X, but increasing the DOC beyond even 100X could still improve the typing accuracy of HISAT-genotype, Kourami, and STC-seq across all five HLA loci as well as HLA*LA's typing accuracy for HLA-DQB1. HLA typing is also used in studies of ancient DNA (aDNA), which is often based on sequencing data with lower quality and DOC. Interestingly, we found that Optitype's typing accuracy is not notably impaired by short read length or by DNA damage, which is typical of aDNA, as long as the DOC is sufficiently high.
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Affiliation(s)
- Nikolas Hallberg Thuesen
- Evaxion Biotech, Copenhagen, Denmark
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | | | - Shyam Gopalakrishnan
- Section for Hologenomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Gabriel Renaud
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
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14
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Ramarao-Milne P, Kondrashova O, Patch AM, Nones K, Koufariotis LT, Newell F, Addala V, Lakis V, Holmes O, Leonard C, Wood S, Xu Q, Mukhopadhyay P, Naeini MM, Steinfort D, Williamson JP, Bint M, Pahoff C, Nguyen PT, Twaddell S, Arnold D, Grainge C, Basirzadeh F, Fielding D, Dalley AJ, Chittoory H, Simpson PT, Aoude LG, Bonazzi VF, Patel K, Barbour AP, Fennell DA, Robinson BW, Creaney J, Hollway G, Pearson JV, Waddell N. Comparison of actionable events detected in cancer genomes by whole-genome sequencing, in silico whole-exome and mutation panels. ESMO Open 2022; 7:100540. [PMID: 35849877 PMCID: PMC9463385 DOI: 10.1016/j.esmoop.2022.100540] [Citation(s) in RCA: 6] [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: 10/21/2021] [Revised: 06/07/2022] [Accepted: 06/19/2022] [Indexed: 12/14/2022] Open
Abstract
Background Next-generation sequencing is used in cancer research to identify somatic and germline mutations, which can predict sensitivity or resistance to therapies, and may be a useful tool to reveal drug repurposing opportunities between tumour types. Multigene panels are used in clinical practice for detecting targetable mutations. However, the value of clinical whole-exome sequencing (WES) and whole-genome sequencing (WGS) for cancer care is less defined, specifically as the majority of variants found using these technologies are of uncertain significance. Patients and methods We used the Cancer Genome Interpreter and WGS in 726 tumours spanning 10 cancer types to identify drug repurposing opportunities. We compare the ability of WGS to detect actionable variants, tumour mutation burden (TMB) and microsatellite instability (MSI) by using in silico down-sampled data to mimic WES, a comprehensive sequencing panel and a hotspot mutation panel. Results We reveal drug repurposing opportunities as numerous biomarkers are shared across many solid tumour types. Comprehensive panels identify the majority of approved actionable mutations, with WGS detecting more candidate actionable mutations for biomarkers currently in clinical trials. Moreover, estimated values for TMB and MSI vary when calculated from WGS, WES and panel data, and are dependent on whether all mutations or only non-synonymous mutations were used. Our results suggest that TMB and MSI thresholds should not only be tumour-dependent, but also be sequencing platform-dependent. Conclusions There is a large opportunity to repurpose cancer drugs, and these data suggest that comprehensive sequencing is an invaluable source of information to guide clinical decisions by facilitating precision medicine and may provide a wealth of information for future studies. Furthermore, the sequencing and analysis approach used to estimate TMB may have clinical implications if a hard threshold is used to indicate which patients may respond to immunotherapy. Genome analysis revealed that treatment biomarkers are shared across solid tumours, highlighting repurposing opportunities. Comprehensive panels detect most known biomarkers; however, WGS detects more biomarkers for treatments in clinical trials. TMB is well correlated between sequencing methods, but absolute values vary and are dependent on mutation types considered.
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Affiliation(s)
- P Ramarao-Milne
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia; Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia
| | - O Kondrashova
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - A-M Patch
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - K Nones
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - L T Koufariotis
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - F Newell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - V Addala
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - V Lakis
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - O Holmes
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - C Leonard
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - S Wood
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Q Xu
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - P Mukhopadhyay
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - M M Naeini
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - D Steinfort
- Department of Thoracic Medicine, Royal Melbourne Hospital, Melbourne, Australia
| | - J P Williamson
- Department of Thoracic Medicine, Liverpool Hospital Sydney, Sydney, Australia
| | - M Bint
- Department of Thoracic Medicine, Sunshine Coast University Hospital, Birtinya, Australia
| | - C Pahoff
- Department of Respiratory Medicine, Gold Coast University Hospital, Southport, Australia
| | - P T Nguyen
- Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, Australia
| | - S Twaddell
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - D Arnold
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - C Grainge
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - F Basirzadeh
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - D Fielding
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - A J Dalley
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - H Chittoory
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - P T Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - L G Aoude
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - V F Bonazzi
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - K Patel
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - A P Barbour
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia; Upper Gastro-intestinal Surgical Unit, Department of Surgery, Princess Alexandra Hospital, Brisbane, Australia
| | - D A Fennell
- Cancer Research UK Centre Leicester, University of Leicester & University Hospitals of Leicester NHS Trust, Leicester, UK
| | - B W Robinson
- National Centre for Asbestos Related Disease, Institute of Respiratory Health, University of Western Australia, Nedlands, Australia; Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - J Creaney
- National Centre for Asbestos Related Disease, Institute of Respiratory Health, University of Western Australia, Nedlands, Australia; Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - G Hollway
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - J V Pearson
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - N Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
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15
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Long Q, Yuan Y, Li M. RNA-SSNV: A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data. Front Genet 2022; 13:865313. [PMID: 35846154 PMCID: PMC9279659 DOI: 10.3389/fgene.2022.865313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
The usage of expressed somatic mutations may have a unique advantage in identifying active cancer driver mutations. However, accurately calling mutations from RNA-seq data is difficult due to confounding factors such as RNA-editing, reverse transcription, and gap alignment. In the present study, we proposed a framework (named RNA-SSNV, https://github.com/pmglab/RNA-SSNV) to call somatic single nucleotide variants (SSNV) from tumor bulk RNA-seq data. Based on a comprehensive multi-filtering strategy and a machine-learning classification model trained with comprehensively curated features, RNA-SSNV achieved the best precision–recall rate (0.880–0.884) in a testing dataset and robustly retained 0.94 AUC for the precision–recall curve in three validation adult-based TCGA (The Cancer Genome Atlas) datasets. We further showed that the somatic mutations called by RNA-SSNV tended to have a higher functional impact and therapeutic power in known driver genes. Furthermore, VAF (variant allele fraction) analysis revealed that subclonal harboring expressed mutations had evolutional selection advantage and RNA had higher detection power to rescue DNA-omitted mutations. In sum, RNA-SSNV will be a useful approach to accurately call expressed somatic mutations for a more insightful analysis of cancer drive genes and carcinogenic mechanisms.
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Affiliation(s)
- Qihan Long
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Disease Genome Research, Sun Yat-Sen University, Guangzhou, China
| | - Yangyang Yuan
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Disease Genome Research, Sun Yat-Sen University, Guangzhou, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Disease Genome Research, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou, China
- *Correspondence: Miaoxin Li,
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Yuan H, Chen J, Li N, Miao H, Chen Y, Lyu S, Qiao Y, Yang G, Luo H, Chen L, Mao F, Huang L, He Y, Hu S, Miao C, Qian Y, Feng R. Target-Sequencing of Female Infertility Pathogenic Gene Panel and a Novel TUBB8 Loss-of-Function Mutation. Front Genet 2022; 13:865103. [PMID: 35620457 PMCID: PMC9127544 DOI: 10.3389/fgene.2022.865103] [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: 01/29/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic screening is an important approach for etiology determination and helps to optimize administration protocols in reproductive centers. After the first pathogenic gene of female infertility was reported in 2016, more and more new pathogenic genes were discovered, and we sought to develop an efficient and cost-effective method for genetic screening in patients. In this study, we designed a target-sequencing panel with 22 female infertility-related genes, namely, TUBB8, PATL2, WEE2, and PANX1 and sequenced 68 primary infertility (PI) and recurrent pregnancy loss (RPL) patients. We sequenced 68 samples reaching an average depth of 1559× and detected 3,134 variants. Among them, 62.2% were synonymous single-nucleotide variants (SNVs) and 36.3% were non-synonymous SNVs. The remaining 1.5% are indels (insertions and deletions) and stop-gains. DNAH11 and TUBB8 are the two genes that mutated most frequently. We also found a novel TUBB8 variant (c.898_900del; p.300_300del), proved its loss-of-function mechanism, and profiled the interactome of the wild-type (WT) and mutant TUBB8 proteins. Overall, this target-sequencing method provides an efficient and cost-effective approach for screening in IVF clinics and will support researchers for the discovery of new pathogenic variants.
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Affiliation(s)
- Hongxia Yuan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Jianhua Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Na Li
- The Reproduction Engineer Key Laboratory of Shanxi Health Committee, Department of Reproductive Genetics, Institute of Reproduction and Genetics of Changzhi Medical College, Heping Hospital of Changzhi Medical College, Changzhi, China
| | - Hui Miao
- The Reproduction Engineer Key Laboratory of Shanxi Health Committee, Department of Reproductive Genetics, Institute of Reproduction and Genetics of Changzhi Medical College, Heping Hospital of Changzhi Medical College, Changzhi, China
| | - Yao Chen
- Reproductive Medical Center of the Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shuyan Lyu
- The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Yu Qiao
- The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Guangping Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Hui Luo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Liangliang Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Fei Mao
- Reproductive Medical Center of the Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lingli Huang
- Reproductive Medical Center of the Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanni He
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Saifei Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Congxiu Miao
- The Reproduction Engineer Key Laboratory of Shanxi Health Committee, Department of Reproductive Genetics, Institute of Reproduction and Genetics of Changzhi Medical College, Heping Hospital of Changzhi Medical College, Changzhi, China
| | - Yun Qian
- Reproductive Medical Center of the Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ruizhi Feng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Reproductive Medical Center of the Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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17
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Milbury CA, Creeden J, Yip WK, Smith DL, Pattani V, Maxwell K, Sawchyn B, Gjoerup O, Meng W, Skoletsky J, Concepcion AD, Tang Y, Bai X, Dewal N, Ma P, Bailey ST, Thornton J, Pavlick DC, Frampton GM, Lieber D, White J, Burns C, Vietz C. Clinical and analytical validation of FoundationOne®CDx, a comprehensive genomic profiling assay for solid tumors. PLoS One 2022; 17:e0264138. [PMID: 35294956 PMCID: PMC8926248 DOI: 10.1371/journal.pone.0264138] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/03/2022] [Indexed: 12/14/2022] Open
Abstract
FoundationOne®CDx (F1CDx) is a United States (US) Food and Drug Administration (FDA)-approved companion diagnostic test to identify patients who may benefit from treatment in accordance with the approved therapeutic product labeling for 28 drug therapies. F1CDx utilizes next-generation sequencing (NGS)-based comprehensive genomic profiling (CGP) technology to examine 324 cancer genes in solid tumors. F1CDx reports known and likely pathogenic short variants (SVs), copy number alterations (CNAs), and select rearrangements, as well as complex biomarkers including tumor mutational burden (TMB) and microsatellite instability (MSI), in addition to genomic loss of heterozygosity (gLOH) in ovarian cancer. CGP services can reduce the complexity of biomarker testing, enabling precision medicine to improve treatment decision-making and outcomes for cancer patients, but only if test results are reliable, accurate, and validated clinically and analytically to the highest standard available. The analyses presented herein demonstrate the extensive analytical and clinical validation supporting the F1CDx initial and subsequent FDA approvals to ensure high sensitivity, specificity, and reliability of the data reported. The analytical validation included several in-depth evaluations of F1CDx assay performance including limit of detection (LoD), limit of blank (LoB), precision, and orthogonal concordance for SVs (including base substitutions [SUBs] and insertions/deletions [INDELs]), CNAs (including amplifications and homozygous deletions), genomic rearrangements, and select complex biomarkers. The assay validation of >30,000 test results comprises a considerable and increasing body of evidence that supports the clinical utility of F1CDx to match patients with solid tumors to targeted therapies or immunotherapies based on their tumor’s genomic alterations and biomarkers. F1CDx meets the clinical needs of providers and patients to receive guideline-based biomarker testing, helping them keep pace with a rapidly evolving field of medicine.
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Affiliation(s)
- Coren A. Milbury
- Department Product Development, Cambridge, MA, United States of America
| | - James Creeden
- Global Medical Affairs, Basel, MA, United States of America
- * E-mail:
| | - Wai-Ki Yip
- Department Product Development, Cambridge, MA, United States of America
| | - David L. Smith
- Department of Franchise Development, Cambridge, MA, United States of America
| | - Varun Pattani
- Department Product Development, Cambridge, MA, United States of America
| | - Kristi Maxwell
- Department of Health Economic and Outcomes Research & Payer Policy, Reimbursement, Cambridge, MA, United States of America
| | - Bethany Sawchyn
- Department of Scientific and Medical Publications, Clinical Operations, Cambridge, MA, United States of America
| | - Ole Gjoerup
- Department of Scientific and Medical Publications, Clinical Operations, Cambridge, MA, United States of America
| | - Wei Meng
- Department Product Development, Cambridge, MA, United States of America
| | - Joel Skoletsky
- Department Product Development, Cambridge, MA, United States of America
| | | | - Yanhua Tang
- Department Product Development, Cambridge, MA, United States of America
| | - Xiaobo Bai
- Department Product Development, Cambridge, MA, United States of America
| | - Ninad Dewal
- Department Product Development, Cambridge, MA, United States of America
| | - Pei Ma
- Department Product Development, Cambridge, MA, United States of America
| | - Shannon T. Bailey
- Department Product Development, Cambridge, MA, United States of America
| | - James Thornton
- Department Product Development, Cambridge, MA, United States of America
| | - Dean C. Pavlick
- Department of Cancer Genomics, Cambridge, MA, United States of America
| | | | - Daniel Lieber
- Department of Computational Biology, Cambridge, MA, United States of America
| | - Jared White
- Department of Computational Biology, Cambridge, MA, United States of America
| | - Christine Burns
- Department Product Development, Cambridge, MA, United States of America
| | - Christine Vietz
- Department Product Development, Cambridge, MA, United States of America
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18
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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: 0] [Impact Index Per Article: 0] [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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19
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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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20
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Tran Mau-Them F, Duffourd Y, Vitobello A, Bruel AL, Denommé-Pichon AS, Nambot S, Delanne J, Moutton S, Sorlin A, Couturier V, Bourgeois V, Chevarin M, Poe C, Mosca-Boidron AL, Callier P, Safraou H, Faivre L, Philippe C, Thauvin-Robinet C. Interest of exome sequencing trio-like strategy based on pooled parental DNA for diagnosis and translational research in rare diseases. Mol Genet Genomic Med 2021; 9:e1836. [PMID: 34716697 PMCID: PMC8683640 DOI: 10.1002/mgg3.1836] [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: 05/31/2021] [Revised: 09/22/2021] [Accepted: 10/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background Exome sequencing (ES) has become the most powerful and cost‐effective molecular tool for deciphering rare diseases with a diagnostic yield approaching 30%–40% in solo‐ES and 50% in trio‐ES. We applied an innovative parental DNA pooling method to reduce the parental sequencing cost while maintaining the diagnostic yield of trio‐ES. Methods We pooled six (Agilent‐CRE‐v2–100X) or five parental DNA (TWIST‐HCE–70X) aiming to detect allelic balance around 8–10% for heterozygous status. The strategies were applied as second‐tier (74 individuals after negative solo‐ES) and first‐tier approaches (324 individuals without previous ES). Results The allelic balance of parental‐pool variants was around 8.97%. Sanger sequencing uncovered false positives in 1.5% of sporadic variants. In the second‐tier approach, we evaluated than two thirds of the Sanger validations performed after solo‐ES (41/59–69%) would have been saved if the parental‐pool segregations had been available from the start. The parental‐pool strategy identified a causative diagnosis in 18/74 individuals (24%) in the second‐tier and in 116/324 individuals (36%) in the first‐tier approaches, including 19 genes newly associated with human disorders. Conclusions Parental‐pooling is an efficient alternative to trio‐ES. It provides rapid segregation and extension to translational research while reducing the cost of parental and Sanger sequencing.
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Affiliation(s)
- Frederic Tran Mau-Them
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Yannis Duffourd
- Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France.,FHU-TRANSLAD, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Ange-Line Bruel
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Julian Delanne
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Sebastien Moutton
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Arthur Sorlin
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | -
- FHU-TRANSLAD, Dijon, France
| | - Victor Couturier
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Valentin Bourgeois
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Martin Chevarin
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Charlotte Poe
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | | | - Patrick Callier
- Laboratoire de Génétique Chromosomique et Moléculaire, CHU de Dijon, France
| | - Hana Safraou
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Laurence Faivre
- Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France.,FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares «Déficiences Intellectuelles de Causes Rares», Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
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21
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Lee IH, Lin Y, Alvarez WJ, Hernandez-Ferrer C, Mandl KD, Kong SW. WEScover: selection between clinical whole exome sequencing and gene panel testing. BMC Bioinformatics 2021; 22:259. [PMID: 34016036 PMCID: PMC8139020 DOI: 10.1186/s12859-021-04178-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/09/2021] [Indexed: 11/18/2022] Open
Abstract
Background Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for several exons in clinically implicated genes. In some cases, a targeted gene panel testing may be a dependable option to ascertain true negatives for genomic variants in known disease-associated genes. We developed a web-based tool to quickly gauge whether all genes of interest would be reliably covered by WES or whether targeted gene panel testing should be considered instead to minimize false negatives in candidate genes. Results WEScover is a novel web application that provides an intuitive user interface for discovering breadth and depth of coverage across population-scale WES datasets, searching either by phenotype, by targeted gene panel(s) or by gene(s). Moreover, the application shows metrics from the Genome Aggregation Database to provide gene-centric view on breadth of coverage. Conclusions WEScover allows users to efficiently query genes and phenotypes for the coverage of associated exons by WES and recommends use of panel tests for the genes with potential incomplete coverage by WES. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04178-5.
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Affiliation(s)
- In-Hee Lee
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA
| | - Yufei Lin
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA
| | - William Jefferson Alvarez
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA.,Agios Pharmaceuticals, Boston, MA, USA
| | - Carles Hernandez-Ferrer
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA.,Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Barcelona, Spain
| | - Kenneth D Mandl
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
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22
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Adolfsson E, Qvick A, Gréen H, Kling D, Gunnarsson C, Jonasson J, Gréen A. Technical in-depth comparison of two massive parallel DNA-sequencing methods for formalin-fixed paraffin-embedded tissue from victims of sudden cardiac death. Forensic Sci Int Genet 2021; 53:102522. [PMID: 33945952 DOI: 10.1016/j.fsigen.2021.102522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/24/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022]
Abstract
Sudden cardiac death (SCD) is a tragic and traumatic event. SCD is often associated with hereditary genetic disease and in such cases, sequencing of stored formalin fixed paraffin embedded (FFPE) tissue is often crucial in trying to find a causal genetic variant. This study was designed to compare two massive parallel sequencing assays for differences in sensitivity and precision regarding variants related to SCD in FFPE material. From eight cases of SCD where DNA from blood had been sequenced using HaloPlex, corresponding FFPE samples were collected six years later. DNA from FFPE samples were amplified using HaloPlex HS, sequenced on MiSeq, representing the first method, as well as amplified using modified Twist and sequenced on NextSeq, representing the second method. Molecular barcodes were included to distinguish artefacts from true variants. In both approaches, read coverage, uniformity and variant detection were compared using genomic DNA isolated from blood and corresponding FFPE tissue, respectively. In terms of coverage uniformity, Twist performed better than HaloPlex HS for FFPE samples. Despite higher overall coverage, amplicon-based HaloPlex technologies, both for blood and FFPE tissue, suffered from design and/or performance issues resulting in genes lacking complete coverage. Although Twist had considerably lower overall mean coverage, high uniformity resulted in equal or higher fraction of genes covered at ≥ 20X. By comparing variants found in the matched samples in a pre-defined cardiodiagnostic gene panel, HaloPlex HS for FFPE material resulted in high sensitivity, 98.0% (range 96.6-100%), and high precision, 99.9% (range 99.5-100%) for moderately fragmented samples, but suffered from reduced sensitivity (range 74.2-91.1%) in more severely fragmented samples due to lack of coverage. Twist had high sensitivity, 97.8% (range 96.8-98.7%) and high precision, 99.9% (range 99.3-100%) in all analyzed samples, including the severely fragmented samples.
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Affiliation(s)
- Emma Adolfsson
- Department of Laboratory Medicine, Örebro University Hospital, Sweden; Faculty of Medicine and Health, Örebro University, Örebro Sweden.
| | - Alvida Qvick
- Department of Laboratory Medicine, Örebro University Hospital, Sweden; Faculty of Medicine and Health, Örebro University, Örebro Sweden
| | - Henrik Gréen
- Division of Drug Research, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Daniel Kling
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Cecilia Gunnarsson
- Department of Clinical Genetics and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Centre for Rare Diseases in South East Region of Sweden, Linköping University, Linköping, Sweden
| | - Jon Jonasson
- Department of Laboratory Medicine, Örebro University Hospital, Sweden; Department of Clinical Genetics and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Anna Gréen
- Department of Laboratory Medicine, Örebro University Hospital, Sweden; Faculty of Medicine and Health, Örebro University, Örebro Sweden
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23
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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] [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. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-00948-5.
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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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24
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The Utility of Whole Exome Sequencing in Diagnosing Pediatric Neurological Disorders. Balkan J Med Genet 2021; 23:17-24. [PMID: 33816068 PMCID: PMC8009565 DOI: 10.2478/bjmg-2020-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Pediatric neurological disorders have a wide spectrum of clinical presentations and can be challenging to diagnose. Whole exome sequencing (WES) is increasingly becoming an integral diagnostic tool in medicine. It is cost-effective and has high diagnostic yield, especially in consanguineous populations. This study aims to review WES results and its value in diagnosing neurological disorders. A retrospective chart review was performed for WES results between the period of January 2018 to November 2019. Whole exome sequencing was requested for children with unexplained neurological signs and symptoms such as epilepsy, developmental delay, visual impairment, spasticity, hypotonia and magnetic resonance imaging (MRI) brain changes. It was conducted for children in a pediatric neurology clinic of a tertiary center at Jeddah, Saudi Arabia. Twenty-six children with undiagnosed neurological conditions were identified and underwent WES diagnosis. Nineteen patients (73.0%) of the cohort were diagnosed with pathogenic variants, likely pathogenic variants or variants of unknown significance (VUS). Consanguinity was positive in 18 families of the cohort (69.0%). Seven patients showed homozygous mutations. Five patients had heterozygous mutations. There were six patients with VUS and six patients had negative WES results. Whole exome sequencing showed a high diagnostic rate in this group of children with variable neurological disorders.
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25
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Wonkam-Tingang E, Schrauwen I, Esoh KK, Bharadwaj T, Nouel-Saied LM, Acharya A, Nasir A, Leal SM, Wonkam A. A novel variant in DMXL2 gene is associated with autosomal dominant non-syndromic hearing impairment (DFNA71) in a Cameroonian family. Exp Biol Med (Maywood) 2021; 246:1524-1532. [PMID: 33715530 DOI: 10.1177/1535370221999746] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Approximately half of congenital hearing impairment cases are inherited, with non-syndromic hearing impairment (NSHI) being the most frequent clinical entity of genetic hearing impairment cases. A family from Cameroon with NSHI was investigated by performing exome sequencing using DNA samples obtained from three family members, followed by direct Sanger sequencing in additional family members and controls participants. We identified an autosomal dominantly inherited novel missense variant [NM_001174116.2:c.918G>T; p.(Q306H)] in DMXL2 gene (MIM:612186) that co-segregates with mild to profound non-syndromic sensorineural hearing impairment . The p.(Q306H) variant which substitutes a highly conserved glutamine residue is predicted deleterious by various bioinformatics tools and is absent from several genome databases. This variant was also neither found in 121 apparently healthy controls without a family history of hearing impairment , nor 112 sporadic NSHI cases from Cameroon. There is one previous report of a large Han Chinese NSHI family that segregates a missense variant in DMXL2. The present study provides additional evidence that DMXL2 is involved in hearing impairment etiology, and we suggest DMXL2 should be considered in diagnostic hearing impairment panels.
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Affiliation(s)
- Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Kevin K Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Liz M Nouel-Saied
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Suzanne M Leal
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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26
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Abstract
Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.
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Affiliation(s)
- Juliann M. Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, United States
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27
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McInerney-Leo AM, Duncan EL. Massively Parallel Sequencing for Rare Genetic Disorders: Potential and Pitfalls. Front Endocrinol (Lausanne) 2021; 11:628946. [PMID: 33679611 PMCID: PMC7933540 DOI: 10.3389/fendo.2020.628946] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/21/2020] [Indexed: 01/04/2023] Open
Abstract
There have been two major eras in the history of gene discovery. The first was the era of linkage analysis, with approximately 1,300 disease-related genes identified by positional cloning by the turn of the millennium. The second era has been powered by two major breakthroughs: the publication of the human genome and the development of massively parallel sequencing (MPS). MPS has greatly accelerated disease gene identification, such that disease genes that would have taken years to map previously can now be determined in a matter of weeks. Additionally, the number of affected families needed to map a causative gene and the size of such families have fallen: de novo mutations, previously intractable by linkage analysis, can be identified through sequencing of the parent-child trio, and genes for recessive disease can be identified through MPS even of a single affected individual. MPS technologies include whole exome sequencing (WES), whole genome sequencing (WGS), and panel sequencing, each with their strengths. While WES has been responsible for most gene discoveries through MPS, WGS is superior in detecting copy number variants, chromosomal rearrangements, and repeat-rich regions. Panels are commonly used for diagnostic purposes as they are extremely cost-effective and generate manageable quantities of data, with no risk of unexpected findings. However, in instances of diagnostic uncertainty, it can be challenging to choose the right panel, and in these circumstances WES has a higher diagnostic yield. MPS has ethical, social, and legal implications, many of which are common to genetic testing generally but amplified due to the magnitude of data (e.g., relationship misattribution, identification of variants of uncertain significance, and genetic discrimination); others are unique to WES and WGS technologies (e.g., incidental or secondary findings). Nonetheless, MPS is rapidly translating into clinical practice as an extremely useful part of the clinical armamentarium.
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Affiliation(s)
- Aideen M. McInerney-Leo
- Dermatology Research Centre, University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Emma L. Duncan
- Department of Twin Research & Genetic Epidemiology, Faculty of Life Sciences and Medicine, School of Life Course Sciences, King’s College London, London, United Kingdom
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28
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Fontsere C, Alvarez-Estape M, Lester J, Arandjelovic M, Kuhlwilm M, Dieguez P, Agbor A, Angedakin S, Ayuk Ayimisin E, Bessone M, Brazzola G, Deschner T, Eno-Nku M, Granjon AC, Head J, Kadam P, Kalan AK, Kambi M, Langergraber K, Lapuente J, Maretti G, Jayne Ormsby L, Piel A, Robbins MM, Stewart F, Vergnes V, Wittig RM, Kühl HS, Marques-Bonet T, Hughes DA, Lizano E. Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments. Mol Ecol Resour 2020; 21:745-761. [PMID: 33217149 DOI: 10.1111/1755-0998.13300] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 10/15/2020] [Accepted: 11/13/2020] [Indexed: 11/30/2022]
Abstract
Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal samples with an endogenous DNA content below 1% is a common problem when prior selection of samples from a large collection is not possible. However, samples classified as unfavourable for target capture sequencing might be the only representatives of unique specific geographical locations, or to answer the question of interest. To explore how library complexity may be increased without repeating DNA extractions and generating new libraries, in this study we captured the exome of 60 chimpanzees (Pan troglodytes) using faecal samples with very low proportions of endogenous content (<1%). Our results indicate that by performing additional hybridizations of the same libraries, the molecular complexity can be maintained to achieve higher coverage. Also, whenever possible, the starting DNA material for capture should be increased. Finally, we specifically calculated the sequencing effort needed to avoid exhausting the library complexity of enriched faecal samples with low endogenous DNA content. This study provides guidelines, schemes and tools for laboratories facing the challenges of working with noninvasive samples containing extremely low amounts of endogenous DNA.
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Affiliation(s)
- Claudia Fontsere
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Marina Alvarez-Estape
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Jack Lester
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martin Kuhlwilm
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anthony Agbor
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Mattia Bessone
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Gregory Brazzola
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tobias Deschner
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | - Josephine Head
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Parag Kadam
- School of Biological and Environmental Sciences, Liverpool John Moores University, James Parsons Building, Liverpool, UK
| | - Ammie K Kalan
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mohamed Kambi
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kevin Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Juan Lapuente
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Comoé Chimpanzee Conservation Project, Kakpin, Comoé National Park, Ivory Coast, Côte d'Ivoire
| | - Giovanna Maretti
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lucy Jayne Ormsby
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alex Piel
- Department of Anthropology, University College London, London, UK
| | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fiona Stewart
- School of Biological and Environmental Sciences, Liverpool John Moores University, James Parsons Building, Liverpool, UK.,Department of Anthropology, University College London, London, UK
| | | | - Roman M Wittig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Hjalmar S Kühl
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Esther Lizano
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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29
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How geneticists think about Differences/Disorders of Sexual Development (DSD): A conversation. J Pediatr Urol 2020; 16:760-767. [PMID: 32893165 DOI: 10.1016/j.jpurol.2020.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/27/2022]
Abstract
A multidisciplinary DSD clinic offers the opportunity for different specialties to learn from each other, as each provides their own perspective and expertise to the management of these complex patients, leading to collaborative care. For the patient, a multi-disciplinary clinic can improve access to care and decrease stress, as patients see all of the specialists on one day. For urologists seeing patients with DSD within a multi-disciplinary DSD clinic as well as independently, understanding what other specialists provide can help facilitate care and referral. Medical genetics is part of a multi-disciplinary DSD clinic. Given the recent advances in genetic diagnostics, many of the offered tests may be less familiar to the pediatric urologist. Therefore, this conversation reviews the clinical presentations and genetic testing options including chromosomal microarray, genetic testing panel, whole exome sequencing, and whole genome sequencing and how these can be helpful in the diagnosis and management of patients with DSD conditions.
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30
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Diñeiro M, Capín R, Cifuentes GÁ, Fernández‐Vega B, Villota E, Otero A, Santiago A, Pruneda PC, Castillo D, Viejo‐Díaz M, Hernando I, Durán NS, Álvarez R, Lago CG, Ordóñez GR, Fernández‐Vega Á, Cabanillas R, Cadiñanos J. Comprehensive genomic diagnosis of inherited retinal and optical nerve disorders reveals hidden syndromes and personalized therapeutic options. Acta Ophthalmol 2020; 98:e1034-e1048. [PMID: 32483926 PMCID: PMC7754416 DOI: 10.1111/aos.14479] [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: 12/20/2019] [Accepted: 04/29/2020] [Indexed: 01/14/2023]
Abstract
PURPOSE In the era of precision medicine, genomic characterization of blind patients is critical. Here, we evaluate the effects of comprehensive genetic analysis on the etiologic diagnosis of potentially hereditary vision loss and its impact on clinical management. METHODS We studied 100 non-syndromic and syndromic Spanish patients with a clinical diagnosis of blindness caused by alterations on the retina, choroid, vitreous and/or optic nerve. We used a next-generation sequencing (NGS) panel (OFTALMOgenics™), developed and validated within this study, including up to 362 genes previously associated with these conditions. RESULTS We identified the genetic cause of blindness in 45% of patients (45/100). A total of 28.9% of genetically diagnosed cases (13/45) were syndromic and, of those, in 30.8% (4/13) extraophthalmic features had been overlooked and/or not related to visual impairment before genetic testing, including cases with Mainzer-Saldino, Bardet-Biedl, mucolipidosis and MLCRD syndromes. In two additional cases-syndromic blindness had been proposed before, but not specifically diagnosed, and one patient with Heimler syndrome had been misdiagnosed as an Usher case before testing. 33.3% of the genetically diagnosed patients (15/45) had causative variants in genes targeted by clinical trials exploring the curative potential of gene therapy approaches. CONCLUSION Comprehensive genomic testing provided clinically relevant insights in a large proportion of blind patients, identifying potential therapeutic opportunities or previously undiagnosed syndromes in 42.2% of the genetically diagnosed cases (19/45).
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Affiliation(s)
- Marta Diñeiro
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Raquel Capín
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | | | - Eva Villota
- Instituto Oftalmológico Fernández‐Vega (IOFV)OviedoSpain
| | - Andrea Otero
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Adrián Santiago
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | - David Castillo
- Disease Research And Medicine (DREAMgenics) S. L.OviedoSpain
| | | | - Inés Hernando
- Hospital Universitario Central de AsturiasOviedoSpain
| | - Noelia S. Durán
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Rebeca Álvarez
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Claudia G. Lago
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | | | - Rubén Cabanillas
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
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31
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Gao G, Smith DI. Clinical Massively Parallel Sequencing. Clin Chem 2020; 66:77-88. [PMID: 31811004 DOI: 10.1373/clinchem.2019.303305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/24/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND The newest advances in DNA sequencing are based on technologies that perform massively parallel sequencing (MPS). Since 2006, the output from MPS platforms has increased from 20 Mb to >7 Tb. First-generation MPS platforms amplify individual DNA molecules to multiple copies and then interrogate the sequence of those molecules. Second-generation MPS analyzes single unamplified molecules to generate much longer sequence reads but with less output than first-generation MPS and lower first-pass accuracy. With MPS technologies, it is now possible to analyze genomes, exomes, a defined subset of genes, transcriptomes, and even methylation across the genome. These technologies have and will continue to completely transform the clinical practice. CONTENT The major first- and second-generation MPS platforms and how they are used in clinical practice are discussed. SUMMARY The ability to sequence terabases of DNA per run on an MPS platform will dramatically change how DNA sequencing is used in clinical practice. Currently, MPS of targeted gene panels is the most common use of this technology clinically, but as the cost for genome sequencing inches downward to $100, this may soon become the method of choice (with the caveat that, at least in the near term, clinical-grade genome sequencing with interpretation may cost much more than $100). Other uses of this technology include sequencing of a mixture of bacterial and viral species (metagenomics), as well as the characterization of methylation across the genome.
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Affiliation(s)
- Ge Gao
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - David I Smith
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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32
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Borges MG, Rocha CS, Carvalho BS, Lopes-Cendes I. Methodological differences can affect sequencing depth with a possible impact on the accuracy of genetic diagnosis. Genet Mol Biol 2020; 43:e20190270. [PMID: 32343762 PMCID: PMC7198014 DOI: 10.1590/1678-4685-gmb-2019-0270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/16/2020] [Indexed: 11/24/2022] Open
Abstract
For a better interpretation of variants, evidence-based databases, such as
ClinVar, compile data on the presumed relationships between variants and
phenotypes. In this study, we aimed to analyze the pattern of sequencing depth
in variants from whole-exome sequencing data in the 1000 Genomes project phase
3, focusing on the variants present in the ClinVar database that were predicted
to affect protein-coding regions. We demonstrate that the distribution of the
sequencing depth varies across different sequencing centers (pair-wise
comparison, p < 0.001). Most importantly, we found that the
distribution pattern of sequencing depth is specific to each facility, making it
possible to correctly assign 96.9% of the samples to their sequencing center.
Thus, indicating the presence of a systematic bias, related to the methods used
in the different facilities, which generates significant variations in breadth
and depth in whole-exome sequencing data in clinically relevant regions. Our
results show that methodological differences, leading to significant
heterogeneity in sequencing depth, may potentially influence the accuracy of
genetic diagnosis. Furthermore, our findings highlight how it is still
challenging to integrate results from different sequencing centers, which may
also have an impact on genomic research.
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Affiliation(s)
- Murilo G Borges
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP, Brazil.,Instituto Brasileiro de Neurociência e Neurotecnologia (BRAINN), Campinas, SP, Brazil.,Universidade Estadual de Campinas (UNICAMP), Instituto de Física "Gleb Wataghin". Campinas, SP, Brazil
| | - Cristiane S Rocha
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP, Brazil.,Instituto Brasileiro de Neurociência e Neurotecnologia (BRAINN), Campinas, SP, Brazil
| | - Benilton S Carvalho
- Instituto Brasileiro de Neurociência e Neurotecnologia (BRAINN), Campinas, SP, Brazil.,Universidade Estadual de Campinas (UNICAMP), Instituto de Matemática, Estatística e Computação Científica, Departamento de Estatística, Campinas, SP, Brazil
| | - Iscia Lopes-Cendes
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP, Brazil.,Instituto Brasileiro de Neurociência e Neurotecnologia (BRAINN), Campinas, SP, Brazil
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33
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Butz H, Nyírő G, Kurucz PA, Likó I, Patócs A. Molecular genetic diagnostics of hypogonadotropic hypogonadism: from panel design towards result interpretation in clinical practice. Hum Genet 2020; 140:113-134. [PMID: 32222824 PMCID: PMC7864839 DOI: 10.1007/s00439-020-02148-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/05/2020] [Indexed: 12/13/2022]
Abstract
Congenital hypogonadotropic hypogonadism (CHH) is a clinically and genetically heterogeneous congenital disease. Symptoms cover a wide spectrum from mild forms to complex phenotypes due to gonadotropin-releasing hormone (GnRH) deficiency. To date, more than 40 genes have been identified as pathogenic cause of CHH. These genes could be grouped into two major categories: genes controlling development and GnRH neuron migration and genes being responsible for neuroendocrine regulation and GnRH neuron function. High-throughput, next-generation sequencing (NGS) allows to analyze numerous gene sequences at the same time. Nowadays, whole exome or whole genome datasets could be investigated in clinical genetic diagnostics due to their favorable cost-benefit. The increasing genetic data generated by NGS reveal novel candidate genes and gene variants with unknown significance (VUSs). To provide clinically valuable genetic results, complex clinical and bioinformatics work are needed. The multifaceted genetics of CHH, the variable mode of inheritance, the incomplete penetrance, variable expressivity and oligogenic characteristics further complicate the interpretation of the genetic variants detected. The objective of this work, apart from reviewing the currently known genes associated with CHH, was to summarize the advantages and disadvantages of the NGS-based platforms and through the authors' own practice to guide through the whole workflow starting from gene panel design, performance analysis and result interpretation. Based on our results, a genetic diagnosis was clearly identified in 21% of cases tested (8/38).
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Affiliation(s)
- Henriett Butz
- Department of Laboratory Medicine, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary.,Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary.,Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Gábor Nyírő
- Department of Laboratory Medicine, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary.,Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Petra Anna Kurucz
- Department of Laboratory Medicine, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary
| | - István Likó
- Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Attila Patócs
- Department of Laboratory Medicine, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary. .,Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary. .,Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.
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34
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Laissue P, Vaiman D. Exploring the Molecular Aetiology of Preeclampsia by Massive Parallel Sequencing of DNA. Curr Hypertens Rep 2020; 22:31. [PMID: 32172383 DOI: 10.1007/s11906-020-01039-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW This manuscript aims to review (for the first time) studies describing NGS sequencing of preeclampsia (PE) women's DNA. RECENT FINDINGS Describing markers for the early detection of PE is an essential task because, although associated molecular dysfunction begins early on during pregnancy, the disease's clinical signs usually appear late in pregnancy. Although several biochemical biomarkers have been proposed, their use in clinical environments is still limited, thereby encouraging research into PE's genetic origin. Hundreds of genes involved in numerous implantation- and placentation-related biological processes may be coherent candidates for PE aetiology. Next-generation sequencing (NGS) offers new technical possibilities for PE studying, as it enables large genomic regions to be analysed at affordable cost. This technique has facilitated the description of genes contributing to the molecular origin of a significant amount of monogenic and complex diseases. Regarding PE, NGS of DNA has been used in familial and isolated cases, thereby enabling new genes potentially related to the phenotype to be proposed. For a better understanding of NGS, technical aspects, applications and limitations are presented initially. Thereafter, NGS studies of DNA in familial and non-familial cases are described, including pitfalls and positive findings. The information given here should enable scientists and clinicians to analyse and design new studies permitting the identification of novel clinically useful molecular PE markers.
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Affiliation(s)
- Paul Laissue
- Biopas Laboratoires, Biopas Group, Bogotá, Colombia. .,Inserm U1016, CNRS UMR8104, Institut Cochin, équipe FGTB, 24, rue du faubourg Saint-Jacques, 75014, Paris, France. .,CIGGUR Genetics Group, School of Medicine and Health Sciences, El Rosario University, Bogotá, Colombia.
| | - Daniel Vaiman
- Inserm U1016, CNRS UMR8104, Institut Cochin, équipe FGTB, 24, rue du faubourg Saint-Jacques, 75014, Paris, France
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35
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Hansen MC, Haferlach T, Nyvold CG. A decade with whole exome sequencing in haematology. Br J Haematol 2019; 188:367-382. [DOI: 10.1111/bjh.16249] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Marcus C. Hansen
- Hematology Pathology Research Laboratory Research Unit for Hematology and Research Unit for Pathology Odense University Hospital University of Southern Denmark Odense Denmark
| | | | - Charlotte G. Nyvold
- Hematology Pathology Research Laboratory Research Unit for Hematology and Research Unit for Pathology Odense University Hospital University of Southern Denmark Odense Denmark
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36
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Bailey CS, Moldenhauer HJ, Park SM, Keros S, Meredith AL. KCNMA1-linked channelopathy. J Gen Physiol 2019; 151:1173-1189. [PMID: 31427379 PMCID: PMC6785733 DOI: 10.1085/jgp.201912457] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/13/2019] [Indexed: 12/20/2022] Open
Abstract
Bailey et al. review a new neurological channelopathy associated with KCNMA1, encoding the BK voltage- and Ca2+-activated K+ channel. KCNMA1 encodes the pore-forming α subunit of the “Big K+” (BK) large conductance calcium and voltage-activated K+ channel. BK channels are widely distributed across tissues, including both excitable and nonexcitable cells. Expression levels are highest in brain and muscle, where BK channels are critical regulators of neuronal excitability and muscle contractility. A global deletion in mouse (KCNMA1−/−) is viable but exhibits pathophysiology in many organ systems. Yet despite the important roles in animal models, the consequences of dysfunctional BK channels in humans are not well characterized. Here, we summarize 16 rare KCNMA1 mutations identified in 37 patients dating back to 2005, with an array of clinically defined pathological phenotypes collectively referred to as “KCNMA1-linked channelopathy.” These mutations encompass gain-of-function (GOF) and loss-of-function (LOF) alterations in BK channel activity, as well as several variants of unknown significance (VUS). Human KCNMA1 mutations are primarily associated with neurological conditions, including seizures, movement disorders, developmental delay, and intellectual disability. Due to the recent identification of additional patients, the spectrum of symptoms associated with KCNMA1 mutations has expanded but remains primarily defined by brain and muscle dysfunction. Emerging evidence suggests the functional BK channel alterations produced by different KCNMA1 alleles may associate with semi-distinct patient symptoms, such as paroxysmal nonkinesigenic dyskinesia (PNKD) with GOF and ataxia with LOF. However, due to the de novo origins for the majority of KCNMA1 mutations identified to date and the phenotypic variability exhibited by patients, additional evidence is required to establish causality in most cases. The symptomatic picture developing from patients with KCNMA1-linked channelopathy highlights the importance of better understanding the roles BK channels play in regulating cell excitability. Establishing causality between KCNMA1-linked BK channel dysfunction and specific patient symptoms may reveal new treatment approaches with the potential to increase therapeutic efficacy over current standard regimens.
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Affiliation(s)
- Cole S Bailey
- Dept. of Physiology, University of Maryland School of Medicine, Baltimore, MD
| | - Hans J Moldenhauer
- Dept. of Physiology, University of Maryland School of Medicine, Baltimore, MD
| | - Su Mi Park
- Dept. of Physiology, University of Maryland School of Medicine, Baltimore, MD
| | - Sotirios Keros
- Department of Pediatrics, University of South Dakota Sanford School of Medicine, Sioux Falls, SD
| | - Andrea L Meredith
- Dept. of Physiology, University of Maryland School of Medicine, Baltimore, MD
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37
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Mendoza-Alvarez A, Guillen-Guio B, Baez-Ortega A, Hernandez-Perez C, Lakhwani-Lakhwani S, Maeso MDC, Lorenzo-Salazar JM, Morales M, Flores C. Whole-Exome Sequencing Identifies Somatic Mutations Associated With Mortality in Metastatic Clear Cell Kidney Carcinoma. Front Genet 2019; 10:439. [PMID: 31156702 PMCID: PMC6529576 DOI: 10.3389/fgene.2019.00439] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 04/29/2019] [Indexed: 11/16/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is among the most aggressive histologic subtypes of kidney cancer, representing about 3% of all human cancers. Patients at stage IV have nearly 60% of mortality in 2–3 years after diagnosis. To date, most ccRCC studies have used DNA microarrays and targeted sequencing of a small set of well-established, commonly altered genes. An exception is the large multi-omics study of The Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma (TCGA-KIRC), which identified new ccRCC genes based on whole exome-sequencing (WES) data, and molecular prognostic signatures based on transcriptomics, epigenetics and proteomics data. Applying WES to simultaneously interrogate virtually all exons in the human genome for somatic variation, here we analyzed the burden of coding somatic mutations in metastatic ccRCC primary tumors, and its association with patient mortality from cancer, in patients who received VEGF receptor-targeting drugs as the first-line therapy. To this end, we sequenced the exomes of ten tumor–normal pairs of ccRCC patient tissues from primary biopsies at >100× mean depth and called somatic coding variation. Mutation burden analysis prioritized 138 genes linked to patient mortality. A gene set enrichment analysis evidenced strong statistical support for the abundance of genes involved in the development of kidney cancer (p = 2.31 × 10−9) and carcinoma (p = 1.22 × 10−5), with 49 genes having direct links with kidney cancer according to the published records. Two of these genes, SIPA1L2 and EIF3A, demonstrated independent associations with mortality in TCGA-KIRC project data. Besides, three mutational signatures were found to be operative in the tumor exomes, one of which (COSMIC signature 12) has not been previously reported in ccRCC. Selection analysis yielded no detectable evidence of overall positive or negative selection, with the exome-wide number of nonsynonymous substitutions per synonymous site reflecting largely neutral tumor evolution. Despite the limited sample size, our results provide evidence for candidate genes where somatic mutation burden is tentatively associated with patient mortality in metastatic ccRCC, offering new potential pharmacological targets and a basis for further validation studies.
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Affiliation(s)
- Alejandro Mendoza-Alvarez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Adrian Baez-Ortega
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Carolina Hernandez-Perez
- Service of Medical Oncology, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Sita Lakhwani-Lakhwani
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Maria-Del-Carmen Maeso
- Department of Pathology, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Manuel Morales
- Service of Medical Oncology, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain.,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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38
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Bick D, Jones M, Taylor SL, Taft RJ, Belmont J. Case for genome sequencing in infants and children with rare, undiagnosed or genetic diseases. J Med Genet 2019; 56:783-791. [PMID: 31023718 PMCID: PMC6929710 DOI: 10.1136/jmedgenet-2019-106111] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/19/2019] [Indexed: 01/01/2023]
Abstract
Up to 350 million people worldwide suffer from a rare disease, and while the individual diseases are rare, in aggregate they represent a substantial challenge to global health systems. The majority of rare disorders are genetic in origin, with children under the age of five disproportionately affected. As these conditions are difficult to identify clinically, genetic and genomic testing have become the backbone of diagnostic testing in this population. In the last 10 years, next-generation sequencing technologies have enabled testing of multiple disease genes simultaneously, ranging from targeted gene panels to exome sequencing (ES) and genome sequencing (GS). GS is quickly becoming a practical first-tier test, as cost decreases and performance improves. A growing number of studies demonstrate that GS can detect an unparalleled range of pathogenic abnormalities in a single laboratory workflow. GS has the potential to deliver unbiased, rapid and accurate molecular diagnoses to patients across diverse clinical indications and complex presentations. In this paper, we discuss clinical indications for testing and historical testing paradigms. Evidence supporting GS as a diagnostic tool is supported by superior genomic coverage, types of pathogenic variants detected, simpler laboratory workflow enabling shorter turnaround times, diagnostic and reanalysis yield, and impact on healthcare.
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Affiliation(s)
- David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Marilyn Jones
- Rady Children's Hospital San Diego, San Diego, California, USA
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39
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Hwang KB, Lee IH, Li H, Won DG, Hernandez-Ferrer C, Negron JA, Kong SW. Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings. Sci Rep 2019; 9:3219. [PMID: 30824715 PMCID: PMC6397176 DOI: 10.1038/s41598-019-39108-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/16/2019] [Indexed: 12/30/2022] Open
Abstract
Comprehensive and accurate detection of variants from whole-genome sequencing (WGS) is a strong prerequisite for translational genomic medicine; however, low concordance between analytic pipelines is an outstanding challenge. We processed a European and an African WGS samples with 70 analytic pipelines comprising the combination of 7 short-read aligners and 10 variant calling algorithms (VCAs), and observed remarkable differences in the number of variants called by different pipelines (max/min ratio: 1.3~3.4). The similarity between variant call sets was more closely determined by VCAs rather than by short-read aligners. Remarkably, reported minor allele frequency had a substantial effect on concordance between pipelines (concordance rate ratio: 0.11~0.92; Wald tests, P < 0.001), entailing more discordant results for rare and novel variants. We compared the performance of analytic pipelines and pipeline ensembles using gold-standard variant call sets and the catalog of variants from the 1000 Genomes Project. Notably, a single pipeline using BWA-MEM and GATK-HaplotypeCaller performed comparable to the pipeline ensembles for ‘callable’ regions (~97%) of the human reference genome. While a single pipeline is capable of analyzing common variants in most genomic regions, our findings demonstrated the limitations and challenges in analyzing rare or novel variants, especially for non-European genomes.
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Affiliation(s)
- Kyu-Baek Hwang
- School of Computer Science and Engineering, Soongsil University, Seoul, 06978, Korea
| | - In-Hee Lee
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Honglan Li
- School of Computer Science and Engineering, Soongsil University, Seoul, 06978, Korea
| | - Dhong-Geon Won
- School of Computer Science and Engineering, Soongsil University, Seoul, 06978, Korea
| | - Carles Hernandez-Ferrer
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Jose Alberto Negron
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, 02115, USA
| | - 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.
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