| 1. |
- Schaafsma, Gerard C.P., et al.
(author)
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BTKbase, Bruton Tyrosine Kinase Variant Database in X-Linked Agammaglobulinemia : Looking Back and Ahead
- 2023
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In: Human Mutation. - 1059-7794. ; 2023
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Journal article (peer-reviewed)abstract
- BTKbase is an international database for disease-causing variants in Bruton tyrosine kinase (BTK) leading to X-linked agammaglobulinemia (XLA), a rare primary immunodeficiency of antibody production. BTKbase was established in 1994 as one of the first publicly available variation databases. The number of cases has more than doubled since the last update; it now contains information for 2310 DNA variants in 2291 individuals. 1025 of the DNA variants are unique. The human genome contains more than 500 protein kinases, among which BTK has the largest number of unique disease-causing variants. The current version of BTKbase has numerous novel features: the database has been reformatted, it has moved to LOVD database management system, it has been internally harmonized, etc. Systematics and standardization have been increased, including Variation Ontology annotations for variation types. There are some regions with lower than expected variation frequency and some hotspots for variations. BTKbase contains, in addition to variant descriptions at DNA, RNA and protein levels, also laboratory parameters and clinical features for many patients. BTKbase has served clinical and research communities in the diagnosis of XLA cases and provides general insight into effects of variations, especially in signalling pathways. Amino acid substitutions and their effects were investigated, predicted, and visualized at 3D level in the protein domains. BTKbase is freely available.
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| 2. |
- Estupinan, HY, et al.
(author)
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BTK gatekeeper residue variation combined with cysteine 481 substitution causes super-resistance to irreversible inhibitors acalabrutinib, ibrutinib and zanubrutinib
- 2021
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In: Leukemia. - : Springer Science and Business Media LLC. - 1476-5551 .- 0887-6924. ; 35:85, s. 1317-1329
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Journal article (peer-reviewed)abstract
- Irreversible inhibitors of Bruton tyrosine kinase (BTK), pioneered by ibrutinib, have become breakthrough drugs in the treatment of leukemias and lymphomas. Resistance variants (mutations) occur, but in contrast to those identified for many other tyrosine kinase inhibitors, they affect less frequently the “gatekeeper” residue in the catalytic domain. In this study we carried out variation scanning by creating 11 substitutions at the gatekeeper amino acid, threonine 474 (T474). These variants were subsequently combined with replacement of the cysteine 481 residue to which irreversible inhibitors, such as ibrutinib, acalabrutinib and zanubrutinib, bind. We found that certain double mutants, such as threonine 474 to isoleucine (T474I) or methionine (T474M) combined with catalytically active cysteine 481 to serine (C481S), are insensitive to ≥16-fold the pharmacological serum concentration, and therefore defined as super-resistant to irreversible inhibitors. Conversely, reversible inhibitors showed a variable pattern, from resistance to no resistance, collectively demonstrating the structural constraints for different classes of inhibitors, which may affect their clinical application.
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| 3. |
- Schaafsma, Gerard C. P., et al.
(author)
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Genetic Variation in Bruton Tyrosine Kinase
- 2015
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In: Agammaglobulinemia. - Cham : Springer International Publishing. - 9783319227146 ; , s. 75-85
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Book chapter (peer-reviewed)abstract
- X-linked agammaglobulinemia (XLA) is a hereditary immunodeficiency caused by variations in the gene encoding for Bruton's tyrosine kinase (BTK). Patients with XLA have decreased numbers of mature B cells, lack all immunoglobulin isotypes, and therefore have susceptibility to severe bacterial infections. XLA-causing variations are collected into BTKbase freely available at http://structure.bmc.lu.se/idbase/BTKbase/. Details of the variations are provided at DNA, RNA, and protein levels, using standardized systematic names and a plain English description. In addition, clinical details from the patients are provided when available. BTKbase contains variation entries for 1362 patients from 1198 unrelated families altogether for 742 unique molecular events. The localization of the variations on the gene and protein for BTK can be analyzed by clicking sequences on web pages. The distribution of the variations in the five structural domains is approximately according to the length of the domains, except for the TH and SH3 domains. The most frequently affected sites are CpG dinucleotides. The majority of the amino acid substitutions are structural affecting protein fold or stability. Detailed statistics is provided highlighting variation types, affected domains, exons and introns, as well as structural consequences.
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| 4. |
- Schaafsma, Gerard C.P., et al.
(author)
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Large differences in proportions of harmful and benign amino acid substitutions between proteins and diseases
- 2017
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In: Human Mutation. - : Hindawi Limited. - 1059-7794. ; 38:7, s. 839-848
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Journal article (peer-reviewed)abstract
- Genes and proteins are known to have differences in their sensitivity to alterations. Despite numerous sequencing studies, proportions of harmful and harmless substitutions are not known for proteins and groups of proteins. To address this question, we predicted the outcome for all possible single amino acid substitutions (AASs) in nine representative protein groups by using the PON-P2 method. The effects on 996 proteins were studied and vast differences were noticed. Proteins in the cancer group harbor the largest proportion of harmful variants (42.1%), whereas the non-disease group of proteins not known to have a disease association and not involved in the housekeeping functions had the lowest number of harmful variants (4.2%). Differences in the proportions of the harmful and benign variants are wide within each group, but they still show clear differences between the groups. Frequently appearing protein domains show a wide spectrum of variant frequencies, whereas no major protein structural class-specific differences were noticed. AAS types in the original and variant residues showed distinctive patterns, which are shared by all the protein groups. The observations are relevant for understanding genetic bases of diseases, variation interpretation, and for the development of methods for that purpose.
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| 5. |
- Schaafsma, Gerard C P, et al.
(author)
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Representativeness of variation benchmark datasets
- 2018
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In: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 19:1, s. 461-461
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Journal article (peer-reviewed)abstract
- BACKGROUND: Benchmark datasets are essential for both method development and performance assessment. These datasets have numerous requirements, representativeness being one. In the case of variant tolerance/pathogenicity prediction, representativeness means that the dataset covers the space of variations and their effects.RESULTS: We performed the first analysis of the representativeness of variation benchmark datasets. We used statistical approaches to investigate how proteins in the benchmark datasets were representative for the entire human protein universe. We investigated the distributions of variants in chromosomes, protein structures, CATH domains and classes, Pfam protein families, Enzyme Commission (EC) classifications and Gene Ontology annotations in 24 datasets that have been used for training and testing variant tolerance prediction methods. All the datasets were available in VariBench or VariSNP databases. We tested also whether the pathogenic variant datasets contained neutral variants defined as those that have high minor allele frequency in the ExAC database. The distributions of variants over the chromosomes and proteins varied greatly between the datasets.CONCLUSIONS: None of the datasets was found to be well representative. Many of the tested datasets had quite good coverage of the different protein characteristics. Dataset size correlates to representativeness but only weakly to the performance of methods trained on them. The results imply that dataset representativeness is an important factor and should be taken into account in predictor development and testing.
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| 6. |
- Schaafsma, Gerard C.P.
(author)
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Tools and annotations for variation
- 2017
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Doctoral thesis (other academic/artistic)abstract
- Since the finishing of the Human Genome Project, many next-generation (NGS) or high-throughput sequencing platforms have emerged. One of the applications of NGS technology, variant discovery, can serve as a basis for precision medicine. Large sequencing projects are generating huge amounts of genetic variation data, which are stored in databases, either large central databases such as dbSNP, or gene- or disease-centered locus-specific databases (LSDBs). There are many variation databases with many different formats and varying quality. Apart from storage and analysis pipeline capacity problems, the interpretation of the variation is also an issue. Computational methods for predicting the effects of variants have been and are being developed, since experimental assessment of variation effects is often not feasible. Benchmark datasets are needed for the development and for performance assessment of such prediction methods.We studied quality related aspects of variant databases and benchmark datasets. The online tool called VariOtator was developed to aid in the consistent use of the Variation Ontology, which was specifically developed to describe variation. Standardization is one aspect of database quality; the use of an ontology for variant annotation will contribute to the enhancement of it.BTKbase is a locus-specific database containing information on variants in BTK, the gene involved in X-linked agammaglobulinemia (XLA), a primary immunodeficiency. If available, phenotypic data, i.e. the variant effects, are also provided. Statistics on variants and variation types showed that there is a wide spectrum of variants and variation types, and that the distribution of protein variants in the different BTK domains is not even.The VariSNP database containing datasets with neutral (non-pathogenic) variants was generated by selecting variants from dbSNP and filtering for variants found in the ClinVar, PhenCode and SwissProt databases. Variants in these three databases are considered to be disease-related. The VariSNP database contains 13 datasets following the functional classification of dbSNP, and is updated on a regular basis.To study the sensitivity to variation in different protein and disease groups, we predicted the pathogenicity of all possible single amino acid substitutions (SAASs) in all proteins in these groups, using the well-performing prediction method PON P2. Large differences in the proportions of harmful, benign and unknown variants were found, and distinctive patterns of SAAS types were found, both in the original and variant amino acids.Representativeness is one quality aspect of variation benchmark datasets, and relates to the representation of the space of variants and their effects. We studied the coverage and distribution of protein features, including structure (CATH) and enzyme classification (EC), Pfam domains and Gene Ontology terms, in established benchmark datasets. None of the datasets is fully representative. Coverage of the features is in general better in the larger datasets, and better in the neutral datasets. At the higher levels of the CATH and EC classifications, all datasets were unbiased, but for the lower levels and other features, all datasets were biased.
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