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Bąk A, Skonieczka K, Jaśkowiec A, Junkiert-Czarnecka A, Heise M, Pilarska-Deltow M, Potoczek S, Czyżewska M, Haus O. Germline mutations among Polish patients with acute myeloid leukemia. Hered Cancer Clin Pract 2021; 19:42. [PMID: 34641967 PMCID: PMC8507332 DOI: 10.1186/s13053-021-00200-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND A small but important proportion of patients (4-10 %) with AML have germline mutations. They can cause the development of AML at an earlier age, confer a higher risk of relapse or predispose to secondary leukemias, including therapy-related leukemias. The analysis of germline mutations in a patient and his/her family is also critical for the selection of suitable family donors if the patient is a candidate for hematopoietic stem cell transplantation (HSCT). METHODS 103 unrelated consecutive patients with de novo AML were enrolled in the study. Control group consisted of 103 persons from the general population. We performed NGS sequencing of bone marrow cells and buccal swabs DNA of six genes: CEBPA, DDX41, ETV6, TERT, GATA2, and IDH2 to detect germline pathogenic mutations. RESULTS In the investigated group, 49 variants were detected in six genes. 26 of them were somatic and 23 germline. Germline variants were detected in all six tested genes. Eight pathogenic germline mutations were detected in 7 AML patients, in three genes: CEBPA, ETV6, and IDH2. One patient had two pathogenic germinal mutations, one in ETV6 and one in CEBPA gene. We identified one novel pathogenic germline mutation in CEBPA gene. The difference in frequency of all pathogenic germline mutations between the tested (7.77 %) and control groups (0.97 %) was statistically significant (p = 0.046). In the tested group, the median age at AML diagnosis was 11 years lower in patients with pathogenic germline mutations than in patients without them (p = 0.028). CONCLUSIONS We showed higher frequency of CEBPA, ETV6, and IDH2 germline mutations in AML patients than in control group, which confirms the role of these mutations in the development of AML. We also showed that the median age at the onset of AML in patients with pathogenic germline mutations is significantly lower than in patients without them.
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Affiliation(s)
- Aneta Bąk
- Department of Clinical Genetics, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Toruń, Poland.
| | - Katarzyna Skonieczka
- Department of Clinical Genetics, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Toruń, Poland
| | - Anna Jaśkowiec
- Department of Hematology, Blood Neoplasms and Bone Marrow Transplantation, Medical University, Wrocław, Poland
| | - Anna Junkiert-Czarnecka
- Department of Clinical Genetics, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Toruń, Poland
| | - Marta Heise
- Department of Clinical Genetics, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Toruń, Poland
| | - Maria Pilarska-Deltow
- Department of Clinical Genetics, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Toruń, Poland
| | - Stanisław Potoczek
- Department of Hematology, Blood Neoplasms and Bone Marrow Transplantation, Medical University, Wrocław, Poland
| | | | - Olga Haus
- Department of Clinical Genetics, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Toruń, Poland
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2
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Guo X, Wang Y, Zhang R, Gu Z. STAMP: a multiplex sequencing method for simultaneous evaluation of mitochondrial DNA heteroplasmies and content. NAR Genom Bioinform 2020; 2:lqaa065. [PMID: 33134911 DOI: 10.1093/nargab/lqaa065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 08/04/2020] [Accepted: 10/09/2020] [Indexed: 01/25/2023] Open
Abstract
Human mitochondrial genome (mtDNA) variations, such as mtDNA heteroplasmies (the co-existence of mutated and wild-type mtDNA), have received increasing attention in recent years for their clinical relevance to numerous diseases. But large-scale population studies of mtDNA heteroplasmies have been lagging due to the lack of a labor- and cost-effective method. Here, we present a novel human mtDNA sequencing method called STAMP (sequencing by targeted amplification of multiplex probes) for measuring mtDNA heteroplasmies and content in a streamlined workflow. We show that STAMP has high-mapping rates to mtDNA, deep coverage of unique reads and high tolerance to sequencing and polymerase chain reaction errors when applied to human samples. STAMP also has high sensitivity and low false positive rates in identifying artificial mtDNA variants at fractions as low as 0.5% in genomic DNA samples. We further extend STAMP, by including nuclear DNA-targeting probes, to enable assessment of relative mtDNA content in the same assay. The high cost-effectiveness of STAMP, along with the flexibility of using it for measuring various aspects of mtDNA variations, will accelerate the research of mtDNA heteroplasmies and content in large population cohorts, and in the context of human diseases and aging.
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Affiliation(s)
- Xiaoxian Guo
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Yiqin Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Ruoyu Zhang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Zhenglong Gu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
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3
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Lee J, Lim H, Jang H, Hwang B, Lee JH, Cho J, Lee JH, Bang D. CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system. Nucleic Acids Res 2019; 47:e1. [PMID: 30215766 PMCID: PMC6326800 DOI: 10.1093/nar/gky820] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/04/2018] [Indexed: 12/26/2022] Open
Abstract
Existing methods to enrich target regions of genomic DNA based on PCR, hybridization capture, or molecular inversion probes have various drawbacks, including long experiment times and low throughput and/or enrichment quality. We developed CRISPR-Cap, a simple and scalable CRISPR-based method to enrich target regions of dsDNA, requiring only two short experimental procedures that can be completed within two hours. We used CRISPR-Cap to enrich 10 target genes 355.7-fold on average from Escherichia coli genomic DNA with a maximum on-target ratio of 81% and high enrichment uniformity. We also used CRISPR-Cap to measure gene copy numbers and detect rare alleles with frequencies as low as 1%. Finally, we enriched coding sequence regions of 20 genes from the human genome. We envision that CRISPR-Cap can be used as an alternative to other widely used target-enrichment methods, which will broaden the scope of CRISPR applications to the field of target enrichment field.
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Affiliation(s)
- Jeewon Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyeonseob Lim
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Hoon Jang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Byungjin Hwang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Joon Ho Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Junhyuk Cho
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea.,Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
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4
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Lim H, Cho N, Ahn J, Park S, Jang H, Kim H, Han H, Lee JH, Bang D. Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms. Nucleic Acids Res 2019; 46:e40. [PMID: 29361040 PMCID: PMC6283416 DOI: 10.1093/nar/gky016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/11/2018] [Indexed: 11/13/2022] Open
Abstract
Scalable and cost-effective production of error-free DNA is critical to meet the increased demand for such DNA in the field of biological science. Methods based on ‘Dial-out PCR’ have enabled the high-throughput error-free DNA synthesis from a microarray-synthesized DNA pool by labeling with retrieval PCR tags, and retrieving error-free DNA of which the sequence is identified via next generation sequencing (NGS). However, most of the retrieved products contain byproducts due to background amplification of redundantly labeled DNAs. Here, we present a highly selective retrieval method of desired DNA from a pool of millions of DNA clones from NGS platforms. Our strategy is based on replicating entire sequence-verified DNA molecules from NGS plates to obtain population-controlled DNA pool. Using the NGS-replica pool, we could perform improved and selective retrieval of desired DNA from the replicated DNA pool compared to other dial-out PCR based methods. To evaluate the method, we tested this strategy by using 454, Illumina, and Ion Torrent platforms for producing NGS-replica pool. As a result, we observed a highly selective retrieval yield of over 95%. We anticipate that applications based on this method will enable the preparation of high-fidelity sequenced DNA from heterogeneous collections of DNA molecules.
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Affiliation(s)
- Hyeonseob Lim
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Namjin Cho
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Jinwoo Ahn
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Sangun Park
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Hoon Jang
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Hwangbeom Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Hyojun Han
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
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Schwarz UI, Gulilat M, Kim RB. The Role of Next-Generation Sequencing in Pharmacogenetics and Pharmacogenomics. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a033027. [PMID: 29844222 DOI: 10.1101/cshperspect.a033027] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Inherited genetic variations in pharmacogenetic loci are widely acknowledged as important determinants of phenotypic differences in drug response, and may be actionable in the clinic. However, recent studies suggest that a considerable number of novel rare variants in pharmacogenes likely contribute to a still unexplained fraction of the observed interindividual variability. Next-generation sequencing (NGS) represents a rapid, relatively inexpensive, large-scale DNA sequencing technology with potential relevance as a comprehensive pharmacogenetic genotyping platform to identify genetic variation related to drug therapy. However, many obstacles remain before the clinical use of NGS-based test results, including technical challenges, functional interpretation, and strict requirements for diagnostic tests. Advanced computational analyses, high-throughput screening methodologies, and generation of shared resources with cell-based and clinical information will facilitate the integration of NGS data into candidate genotyping approaches, likely enhancing future drug phenotype predictions in patients.
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Affiliation(s)
- Ute I Schwarz
- Division of Clinical Pharmacology, Department of Medicine, Western University, London, Ontario N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, London, Ontario N6A 5A5, Canada
| | - Markus Gulilat
- Department of Physiology and Pharmacology, Western University, London, Ontario N6A 5A5, Canada
| | - Richard B Kim
- Division of Clinical Pharmacology, Department of Medicine, Western University, London, Ontario N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, London, Ontario N6A 5A5, Canada
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Pérez Millán MI, Vishnopolska SA, Daly AZ, Bustamante JP, Seilicovich A, Bergadá I, Braslavsky D, Keselman AC, Lemons RM, Mortensen AH, Marti MA, Camper SA, Kitzman JO. Next generation sequencing panel based on single molecule molecular inversion probes for detecting genetic variants in children with hypopituitarism. Mol Genet Genomic Med 2018; 6:514-525. [PMID: 29739035 PMCID: PMC6081231 DOI: 10.1002/mgg3.395] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/20/2018] [Accepted: 03/09/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Congenital Hypopituitarism is caused by genetic and environmental factors. Over 30 genes have been implicated in isolated and/or combined pituitary hormone deficiency. The etiology remains unknown for up to 80% of the patients, but most cases have been analyzed by limited candidate gene screening. Mutations in the PROP1 gene are the most common known cause, and the frequency of mutations in this gene varies greatly by ethnicity. We designed a custom array to assess the frequency of mutations in known hypopituitarism genes and new candidates, using single molecule molecular inversion probes sequencing (smMIPS). METHODS We used this panel for the first systematic screening for causes of hypopituitarism in children. Molecular inversion probes were designed to capture 693 coding exons of 30 known genes and 37 candidate genes. We captured genomic DNA from 51 pediatric patients with CPHD (n = 43) or isolated GH deficiency (IGHD) (n = 8) and their parents and conducted next generation sequencing. RESULTS We obtained deep coverage over targeted regions and demonstrated accurate variant detection by comparison to whole-genome sequencing in a control individual. We found a dominant mutation GH1, p.R209H, in a three-generation pedigree with IGHD. CONCLUSIONS smMIPS is an efficient and inexpensive method to detect mutations in patients with hypopituitarism, drastically limiting the need for screening individual genes by Sanger sequencing.
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Affiliation(s)
- María I. Pérez Millán
- Institute of Biomedical Investigations (INBIOMED‐UBA‐CONICET)University of Buenos AiresBuenos AiresArgentina
| | - Sebastian A. Vishnopolska
- Department of Biological Chemistry (IQUIBICEN‐UBA‐CONICET)Faculty of Exact and Natural SciencesUniversity of Buenos AiresBuenos AiresArgentina
| | | | - Juan P. Bustamante
- Department of Biological Chemistry (IQUIBICEN‐UBA‐CONICET)Faculty of Exact and Natural SciencesUniversity of Buenos AiresBuenos AiresArgentina
| | - Adriana Seilicovich
- Institute of Biomedical Investigations (INBIOMED‐UBA‐CONICET)University of Buenos AiresBuenos AiresArgentina
| | - Ignacio Bergadá
- División de EndocrinologíaHospital de Niños Ricardo GutiérrezCentro de Investigaciones Endocrinológicas ‘Dr César Bergadá’ (CEDIE) CONICET – FEIBuenos AiresArgentina
| | - Débora Braslavsky
- División de EndocrinologíaHospital de Niños Ricardo GutiérrezCentro de Investigaciones Endocrinológicas ‘Dr César Bergadá’ (CEDIE) CONICET – FEIBuenos AiresArgentina
| | - Ana C. Keselman
- División de EndocrinologíaHospital de Niños Ricardo GutiérrezCentro de Investigaciones Endocrinológicas ‘Dr César Bergadá’ (CEDIE) CONICET – FEIBuenos AiresArgentina
| | | | | | - Marcelo A. Marti
- Department of Biological Chemistry (IQUIBICEN‐UBA‐CONICET)Faculty of Exact and Natural SciencesUniversity of Buenos AiresBuenos AiresArgentina
| | - Sally A. Camper
- Department of Human GeneticsUniversity of MichiganAnn ArborMIUSA
| | - Jacob O. Kitzman
- Department of Human GeneticsUniversity of MichiganAnn ArborMIUSA
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7
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Han SM, Park J, Lee JH, Lee SS, Kim H, Han H, Kim Y, Yi S, Cho JY, Jang IJ, Lee MG. Targeted Next-Generation Sequencing for Comprehensive Genetic Profiling of Pharmacogenes. Clin Pharmacol Ther 2016; 101:396-405. [PMID: 27727443 DOI: 10.1002/cpt.532] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 12/12/2022]
Abstract
Phenotypic differences in drug responses have been associated with known pharmacogenomic loci, but many remain to be characterized. Therefore, we developed next-generation sequencing (NGS) panels to enable broad and unbiased inspection of genes that are involved in pharmacokinetics (PKs) and pharmacodynamics (PDs). These panels feature repetitively optimized probes to capture up to 114 PK/PD-related genes with high coverage (99.6%) and accuracy (99.9%). Sequencing of a Korean cohort (n = 376) with the panels enabled profiling of actionable variants as well as rare variants of unknown functional consequences. Notably, variants that occurred at low frequency were enriched with likely protein-damaging variants and previously unreported variants. Furthermore, in vitro evaluation of four pharmacogenes, including cytochrome P450 2C19 (CYP2C19), confirmed that many of these rare variants have considerable functional impact. The present study suggests that targeted NGS panels are readily applicable platforms to facilitate comprehensive profiling of pharmacogenes, including common but also rare variants that warrant screening for personalized medicine.
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Affiliation(s)
- S M Han
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Korea
| | - J Park
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Korea
| | - J H Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, Korea
| | - S S Lee
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University College of Medicine, Busan, Korea
| | - H Kim
- Celemics Inc, Seoul, Korea
| | - H Han
- Celemics Inc, Seoul, Korea
| | - Y Kim
- Celemics Inc, Seoul, Korea
| | - S Yi
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | - J-Y Cho
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | - I-J Jang
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | - M G Lee
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Korea
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8
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Niedzicka M, Fijarczyk A, Dudek K, Stuglik M, Babik W. Molecular Inversion Probes for targeted resequencing in non-model organisms. Sci Rep 2016; 6:24051. [PMID: 27046329 PMCID: PMC4820773 DOI: 10.1038/srep24051] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/18/2016] [Indexed: 12/21/2022] Open
Abstract
Applications that require resequencing of hundreds or thousands of predefined genomic regions in numerous samples are common in studies of non-model organisms. However few approaches at the scale intermediate between multiplex PCR and sequence capture methods are available. Here we explored the utility of Molecular Inversion Probes (MIPs) for the medium-scale targeted resequencing in a non-model system. Markers targeting 112 bp of exonic sequence were designed from transcriptome of Lissotriton newts. We assessed performance of 248 MIP markers in a sample of 85 individuals. Among the 234 (94.4%) successfully amplified markers 80% had median coverage within one order of magnitude, indicating relatively uniform performance; coverage uniformity across individuals was also high. In the analysis of polymorphism and segregation within family, 77% of 248 tested MIPs were confirmed as single copy Mendelian markers. Genotyping concordance assessed using replicate samples exceeded 99%. MIP markers for targeted resequencing have a number of advantages: high specificity, high multiplexing level, low sample requirement, straightforward laboratory protocol, no need for preparation of genomic libraries and no ascertainment bias. We conclude that MIP markers provide an effective solution for resequencing targets of tens or hundreds of kb in any organism and in a large number of samples.
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Affiliation(s)
- M Niedzicka
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - A Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - K Dudek
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - M Stuglik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - W Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
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