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Article ; Online: Genebe.net: Implementation and validation of an automatic ACMG variant pathogenicity criteria assignment.

Stawiński, Piotr / Płoski, Rafał

2024

Abstract: We present GeneBe, an online platform streamlining the automated application of American College of Medical Genetics and Genomics (ACMG), Association for Molecular Pathology (AMP), and the College of American Pathologists (CAP) criteria for assessment of ...

Abstract	We present GeneBe, an online platform streamlining the automated application of American College of Medical Genetics and Genomics (ACMG), Association for Molecular Pathology (AMP), and the College of American Pathologists (CAP) criteria for assessment of pathogenicity of genetic variants. GeneBe utilizes automated algorithms that evaluate 17 criteria from 28, closely aligning with current guidelines and leveraging data from diverse sources, including ClinVar. The user-friendly web interface enables manual refinement of assignments for specific criteria based on site-collected data. Our algorithm demonstrates a high correlation (r = 0.90) of assigned pathogenicity scores compared to expert assessments from the ClinGen Evidence Repository and substantial concordance with ClinVar verdict assignments (κ = 0.69). Comparative analysis with other published tools reveals that GeneBe performs similarly to VarSome while being superior over TAPES and InterVar. In contrast to some other tools, GeneBe's web implementation is tracker-free and third-party request-free, safeguarding user privacy. Additionally, GeneBe offers an Application Programming Interface (API) for enhanced flexibility and integration into existing workflows and is provided free of charge for research purposes. GeneBe is available at https://genebe.net.
Language	English
Publishing date	2024-03-05
Publishing country	Denmark
Document type	Journal Article
ZDB-ID	221209-2
ISSN	1399-0004 ; 0009-9163
ISSN (online)	1399-0004
ISSN	0009-9163
DOI	10.1111/cge.14516
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Article: Prenatal Diagnosis of Jeune Syndrome Caused by Compound Heterozygous Variants in DYNC2H1 Gene—Case Report with Rapid WES Procedure and Differential Diagnosis of Lethal Skeletal Dysplasias

Stembalska, Agnieszka / Rydzanicz, Małgorzata / Klaniewska, Magdalena / Dudarewicz, Lech / Pollak, Agnieszka / Biela, Mateusz / Stawinski, Piotr / Ploski, Rafal / Smigiel, Robert

Genes. 2022 July 27, v. 13, no. 8

2022

Abstract: Skeletal dysplasias (SDs) are a large, heterogeneous group of mostly genetic disorders that affect the bones and cartilage, resulting in abnormal growth and development of skeletal structures. The high clinical and genetic diversity in SDs cause ... ...

Abstract	Skeletal dysplasias (SDs) are a large, heterogeneous group of mostly genetic disorders that affect the bones and cartilage, resulting in abnormal growth and development of skeletal structures. The high clinical and genetic diversity in SDs cause difficulties in prenatal diagnosis. To establish a correct prognosis and better management, it is very important to distinguish SDs with poor life-limiting prognosis or lethal SDs from other ones. Bad prognosis in foetuses is assessed on the basis of the size of the thorax, lung volumes, long bones’ length, bones’ echogenicity, bones’ angulation or presented fractures, and the concomitant presence of non-immune hydrops or visceral abnormalities. To confirm SD diagnosis and perform family genetic consultation, rapid molecular diagnostics are needed; therefore, the NGS method using a panel of genes corresponding to SD or whole-exome sequencing (WES) is commonly used. We report a case of a foetus showing long bones’ shortening and a narrow chest with short ribs, diagnosed prenatally with asphyxiating thoracic dystrophy, also known as Jeune syndrome (ATD; OMIM 208500), caused by compound heterozygous variants in the DYNC2H1 gene, identified by prenatally performed rapid-WES analysis. The missense variants in the DYNC2H1 gene were inherited from the mother (c.7289T>C; p.Ile2430Thr) and from the father (c.12716T>G; p.Leu4239Arg). The DYNC2H1 gene is one of at least 17 ATD-associated genes. This disorder belongs to the ninth group of SD, ciliopathies with major skeletal involvement. An extremely narrow, bell-shaped chest, and abnormalities of the kidneys, liver, and retinas were observed in most cases of ATD. Next to lethal and severe forms, clinically mild forms have also been reported. A diagnosis of ATD is important to establish the prognosis and management for the patient, as well as the recurrence risk for the family.
Keywords	cartilage ; chest ; diagnostic techniques ; edema ; fetus ; genes ; genetic variation ; growth and development ; heterozygosity ; liver ; lungs ; patients ; prognosis ; risk ; ultrasonography
Language	English
Dates of publication	2022-0727
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes13081339
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Article: WDR13: A Novel Gene Implicated in Non-Syndromic Intellectual Disability

Rzońca-Niewczas, Sylwia / Wierzba, Jolanta / Kaczorowska, Ewa / Poryszewska, Milena / Kosińska, Joanna / Stawiński, Piotr / Płoski, Rafał / Bal, Jerzy

Genes. 2021 Nov. 28, v. 12, no. 12

2021

Abstract: Investigating novel genetic variants involved in intellectual disability (ID) development is essential. X-linked intellectual disability (XLID) accounts for over 10% of all cases of ID in males. XLID genes are involved in many cellular pathways and ... ...

Abstract	Investigating novel genetic variants involved in intellectual disability (ID) development is essential. X-linked intellectual disability (XLID) accounts for over 10% of all cases of ID in males. XLID genes are involved in many cellular pathways and processes. Some of them are not specific to the development and functioning of the neural system. The implementation of exome sequencing simplifies the search for novel variants, especially those less expected. Here, we describe a nonsense variant of the XLID gene, WDR13. The mutation c.757C>T (p.Arg253Ter) was uncovered by X-chromosome exome sequencing in males with a familial form of intellectual disability. Quantitative PCR (qPCR) analysis showed that variant c.757C>T caused a significant decrease in WDR13 expression in the patient's fibroblast. Moreover, it dysregulated other genes linked to intellectual disability, such as FMR1, SYN1, CAMK2A, and THOC2. The obtained results indicate the pathogenic nature of the detected variant and suggest that the WDR13 gene interacts with other genes essential for the functioning of the nervous system, especially the synaptic plasticity process.
Keywords	X chromosome ; fibroblasts ; genes ; mutation ; nervous system ; neuroplasticity ; patients ; quantitative polymerase chain reaction
Language	English
Dates of publication	2021-1128
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12121911
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Article: Prenatal Versus Postnatal Diagnosis of Meckel–Gruber and Joubert Syndrome in Patients with TMEM67 Mutations

Stembalska, Agnieszka / Rydzanicz, Małgorzata / Pollak, Agnieszka / Kostrzewa, Grazyna / Stawinski, Piotr / Biela, Mateusz / Ploski, Rafal / Smigiel, Robert

Genes. 2021 July 16, v. 12, no. 7

2021

Abstract: Renal cystic diseases are characterized by genetic and phenotypic heterogeneity. Congenital renal cysts can be classified as developmental disorders and are commonly diagnosed prenatally using ultrasonography and magnetic resonance imaging. Progress in ... ...

Abstract	Renal cystic diseases are characterized by genetic and phenotypic heterogeneity. Congenital renal cysts can be classified as developmental disorders and are commonly diagnosed prenatally using ultrasonography and magnetic resonance imaging. Progress in molecular diagnostics and availability of exome sequencing procedures allows diagnosis of single-gene disorders in the prenatal period. Two patients with a prenatal diagnosis of polycystic kidney disease are presented in this article. TMEM67 mutations were identified in both fetuses using a whole-exome sequencing (WES) study. In one of them, the phenotypic syndrome diagnosed prenatally was different from that diagnosed in the postnatal period.
Keywords	diagnostic techniques ; magnetism ; phenotype ; phenotypic variation ; polycystic kidney diseases ; postpartum period ; prenatal development ; ultrasonography
Language	English
Dates of publication	2021-0716
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12071078
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Article ; Online: Prenatal Diagnosis of Jeune Syndrome Caused by Compound Heterozygous Variants in

Stembalska, Agnieszka / Rydzanicz, Małgorzata / Klaniewska, Magdalena / Dudarewicz, Lech / Pollak, Agnieszka / Biela, Mateusz / Stawinski, Piotr / Ploski, Rafal / Smigiel, Robert

Genes

2022 Volume 13, Issue 8

Abstract	Skeletal dysplasias (SDs) are a large, heterogeneous group of mostly genetic disorders that affect the bones and cartilage, resulting in abnormal growth and development of skeletal structures. The high clinical and genetic diversity in SDs cause difficulties in prenatal diagnosis. To establish a correct prognosis and better management, it is very important to distinguish SDs with poor life-limiting prognosis or lethal SDs from other ones. Bad prognosis in foetuses is assessed on the basis of the size of the thorax, lung volumes, long bones’ length, bones’ echogenicity, bones’ angulation or presented fractures, and the concomitant presence of non-immune hydrops or visceral abnormalities. To confirm SD diagnosis and perform family genetic consultation, rapid molecular diagnostics are needed; therefore, the NGS method using a panel of genes corresponding to SD or whole-exome sequencing (WES) is commonly used. We report a case of a foetus showing long bones’ shortening and a narrow chest with short ribs, diagnosed prenatally with asphyxiating thoracic dystrophy, also known as Jeune syndrome (ATD; OMIM 208500), caused by compound heterozygous variants in the DYNC2H1 gene, identified by prenatally performed rapid-WES analysis. The missense variants in the DYNC2H1 gene were inherited from the mother (c.7289T>C; p.Ile2430Thr) and from the father (c.12716T>G; p.Leu4239Arg). The DYNC2H1 gene is one of at least 17 ATD-associated genes. This disorder belongs to the ninth group of SD, ciliopathies with major skeletal involvement. An extremely narrow, bell-shaped chest, and abnormalities of the kidneys, liver, and retinas were observed in most cases of ATD. Next to lethal and severe forms, clinically mild forms have also been reported. A diagnosis of ATD is important to establish the prognosis and management for the patient, as well as the recurrence risk for the family.
MeSH term(s)	Cytoplasmic Dyneins/genetics ; Diagnosis, Differential ; Ellis-Van Creveld Syndrome ; Female ; Humans ; Mutation ; Pregnancy ; Prenatal Diagnosis ; Exome Sequencing
Chemical Substances	DYNC2H1 protein, human ; Cytoplasmic Dyneins (EC 3.6.4.2)
Language	English
Publishing date	2022-07-27
Publishing country	Switzerland
Document type	Case Reports ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes13081339
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Article ; Online: Postzygotic mosaicism of a novel PTPN11 mutation in monozygotic twins discordant for metachondromatosis.

Rydzanicz, Małgorzata / Glinkowski, Wojciech / Walczak, Anna / Koppolu, Agnieszka / Kostrzewa, Grażyna / Gasperowicz, Piotr / Pollak, Agnieszka / Stawiński, Piotr / Płoski, Rafał

American journal of medical genetics. Part A

2022 Volume 188, Issue 5, Page(s) 1482–1487

Abstract: Genetic mosaicism caused by postzygotic mutations is of a great interest due to its role in human disease. Monozygotic twins arising from a single zygote are considered as genetically identical, and any differences likely to be caused by postzygotic ... ...

Abstract	Genetic mosaicism caused by postzygotic mutations is of a great interest due to its role in human disease. Monozygotic twins arising from a single zygote are considered as genetically identical, and any differences likely to be caused by postzygotic events. Thus, phenotypically discordant monozygotic twins offer a unique opportunity to study genotype-phenotype correlation. Here, we present a three-generation family starting from a pair of monozygotic twins discordant for metachondromatosis due to postzygotic p.(Gln175His) variant in the PTPN11 gene. Both phenotypically discordant monozygotic twins harbor p.(Gln175His), however significant differences in mosaic ratio is observed not only between twins, but also within different tissue types within one individual. Phenotypic manifestation of p.(Gln175His) in examined family clearly depends on allele variant fraction (VAF). Individuals harboring constitutional mutation (VAF 50%) present typical metachondromatosis. Milder phenotype is observed in twin harboring high-level mosaicism in the tissue of ectodermal origin (VAF 45%), but not in a blood (VAF 5%). Finally, her twin sister harboring low-level mosaicism in blood (VAF 2%) and nonblood (VAF 12%) tissues is phenotypically normal. Our results provide insights into biological role of mosaicism in disease and further support the usefulness of nonblood tissues as an optimal source of DNA for the identification of postzygotic mutations in phenotypically discordant monozygotic twins.
MeSH term(s)	Bone Neoplasms ; Chondromatosis ; Diseases in Twins/diagnosis ; Diseases in Twins/genetics ; Exostoses, Multiple Hereditary ; Female ; Humans ; Mosaicism ; Mutation ; Phenotype ; Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics ; Twins, Monozygotic/genetics
Chemical Substances	PTPN11 protein, human (EC 3.1.3.48) ; Protein Tyrosine Phosphatase, Non-Receptor Type 11 (EC 3.1.3.48)
Language	English
Publishing date	2022-02-02
Publishing country	United States
Document type	Case Reports ; Journal Article ; Twin Study
ZDB-ID	2108614-X
ISSN	1552-4833 ; 0148-7299 ; 1552-4825
ISSN (online)	1552-4833
ISSN	0148-7299 ; 1552-4825
DOI	10.1002/ajmg.a.62670
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Article: Identification of New Copy Number Variation and the Evaluation of a CNV Detection Tool for NGS Panel Data in Polish Familial Hypercholesterolemia Patients

Rutkowska, Lena / Pinkier, Iwona / Sałacińska, Kinga / Kępczyński, Łukasz / Salachna, Dominik / Lewek, Joanna / Banach, Maciej / Matusik, Paweł / Starostecka, Ewa / Lewiński, Andrzej / Płoski, Rafał / Stawiński, Piotr / Gach, Agnieszka

Genes. 2022 Aug. 10, v. 13, no. 8

2022

Abstract: Familial hypercholesterolemia (FH) is an inherited, autosomal dominant metabolic disorder mostly associated with disease-causing variant in LDLR, APOB or PCSK9. Although the dominant changes are small-scale missense, frameshift and splicing variants, ... ...

Abstract	Familial hypercholesterolemia (FH) is an inherited, autosomal dominant metabolic disorder mostly associated with disease-causing variant in LDLR, APOB or PCSK9. Although the dominant changes are small-scale missense, frameshift and splicing variants, approximately 10% of molecularly defined FH cases are due to copy number variations (CNVs). The first-line strategy is to identify possible pathogenic SNVs (single nucleotide variants) using multiple PCR, Sanger sequencing, or with more comprehensive approaches, such as NGS (next-generation sequencing), WES (whole-exome sequencing) or WGS (whole-genome sequencing). The gold standard for CNV detection in genetic diagnostics are MLPA (multiplex ligation-dependent amplification) or aCGH (array-based comparative genome hybridization). However, faster and simpler analyses are needed. Therefore, it has been proposed that NGS data can be searched to analyze CNV variants. The aim of the study was to identify novel CNV changes in FH patients without detected pathogenic SNVs using targeted sequencing and evaluation of CNV calling tool (DECoN) working on gene panel NGS data; the study also assesses its suitability as a screening step in genetic diagnostics. A group of 136 adult and child patients were recruited for the present study. The inclusion criteria comprised at least “possible FH” according to the Simon Broome diagnostic criteria in children and the DLCN (Dutch Lipid Clinical Network) criteria in adults. NGS analysis revealed potentially pathogenic SNVs in 57 patients. Thirty selected patients without a positive finding from NGS were subjected to MLPA analysis; ten of these revealed possibly pathogenic CNVs. Nine patients were found to harbor exons 4–8 duplication, two harbored exons 6–8 deletion and one demonstrated exon 9–10 deletion in LDLR. To test the DECoN program, the whole study group was referred for bioinformatic analysis. The DECoN program detected duplication of exons 4–8 in the LDLR gene in two patients, whose genetic analysis was stopped after the NGS step. The integration of the two methods proved to be particularly valuable in a five-year-old girl presenting with extreme hypercholesterolemia, with both a pathogenic missense variant (c.1747C>T) and exons 9–10 deletion in LDLR. This is the first report of a heterozygous deletion of exons 9 and 10 co-occurring with SNV. Our results suggest that the NGS-based approach has the potential to identify large-scale variation in the LDLR gene and could be further applied to extend CNV screening in other FH-related genes. Nevertheless, the outcomes from the bioinformatic approach still need to be confirmed by MLPA; hence, the latter remains the reference method for assessing CNV in FH patients.
Keywords	adults ; bioinformatics ; children ; comparative genomic hybridization ; copy number variation ; diagnostic techniques ; exons ; genetic analysis ; girls ; heterozygosity ; hypercholesterolemia ; lipids
Language	English
Dates of publication	2022-0810
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes13081424
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Article ; Online: Cardiovascular involvement and prognosis in Loeys-Dietz syndrome.

Chmielewski, Przemysław / Ponińska, Joanna K / Michalak, Ewa / Michałowska, Ilona / Kowalik, Ilona / Truszkowska, Grażyna / Kugaudo, Monika / Minota, Ilona / Stawiński, Piotr / Płoski, Rafał / Bilińska, Zofia T

Kardiologia polska

2023 Volume 81, Issue 11, Page(s) 1096–1102

Abstract: Background: Loeys-Dietz syndrome (LDS) is an inherited connective tissue disorder associated with aortic root enlargement and risk of thoracic aortic dissection (AD). Genetic examination is essential for diagnosis.: Aims: The study aimed at analysis ... ...

Abstract	Background: Loeys-Dietz syndrome (LDS) is an inherited connective tissue disorder associated with aortic root enlargement and risk of thoracic aortic dissection (AD). Genetic examination is essential for diagnosis. Aims: The study aimed at analysis of clinical data on cardiovascular involvement and management of LDS patients. Methods: The study included carriers of LDS-associated genetic variants, identified between 2012 and 2022. Assessment of cardiovascular involvement was based on echocardiography and computed tomography angiography with quantitative assessment of arterial tortuosity. Involvement of other systems was also evaluated. We noted major cardiovascular events, including aortic events, defined as AD, elective aortic surgery, or otherwise unexplained sudden death. Results: Thirty-four patients from 15 families were included, and five identified variants were novel. Probands' mean age was 41 years. Cardiovascular abnormalities, aortic involvement, aortic tortuosity, and tortuosity of cervical arteries were present in 79%, 71%, 68%, and 100% of carriers, respectively. First aortic events (9 A-type AD, 6 elective thoracic aortic surgeries, and one sudden death) occurred in 16 (47%) patients at a median age of 35 years. The youngest age at AD was 16 years, and 7 years for elective aneurysm repair. Second and third aortic events occurred in 9 and 4 patients, respectively. Eight patients (24%) experienced other major cardiovascular events. Aortic event-free survival was shorter in the presence of skin striae (P = 0.03), tended to be shorter in the presence of Marfanoid features (P = 0.06), and longer with TGFB2 variants (P = 0.06). Conclusions: LDS is associated with high burden of cardiovascular complications at a young age.
MeSH term(s)	Humans ; Adult ; Loeys-Dietz Syndrome/genetics ; Loeys-Dietz Syndrome/surgery ; Aortic Dissection ; Arteries ; Prognosis ; Death, Sudden
Language	English
Publishing date	2023-10-12
Publishing country	Poland
Document type	Journal Article
ZDB-ID	411492-9
ISSN	1897-4279 ; 0022-9032
ISSN (online)	1897-4279
ISSN	0022-9032
DOI	10.33963/v.kp.97390
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Article ; Online: The Role of the Reanalysis of Genetic Test Results in the Diagnosis of Dysmorphic Syndrome Caused by Inherited xq24 Deletion including the

Wolańska, Ewelina / Pollak, Agnieszka / Rydzanicz, Małgorzata / Pesz, Karolina / Kłaniewska, Magdalena / Rozensztrauch, Anna / Skiba, Paweł / Stawiński, Piotr / Płoski, Rafał / Śmigiel, Robert

Genes

2021 Volume 12, Issue 3

Abstract: Psychomotor delay, hypotonia, and intellectual disability, as well as heart defects, urogenital malformations, and characteristic cranio-facial dysmorphism are the main symptoms of dysmorphic syndrome associated with intergenic deletion in the Xq24 ... ...

Abstract	Psychomotor delay, hypotonia, and intellectual disability, as well as heart defects, urogenital malformations, and characteristic cranio-facial dysmorphism are the main symptoms of dysmorphic syndrome associated with intergenic deletion in the Xq24 chromosome region including the
MeSH term(s)	Abnormalities, Multiple/genetics ; Abnormalities, Multiple/pathology ; Child ; Chromosome Deletion ; Chromosomes, Human, X/genetics ; Hemizygote ; Humans ; Intellectual Disability/genetics ; Intellectual Disability/pathology ; Male ; Nerve Tissue Proteins/genetics ; Nuclear Proteins/genetics ; Syndrome ; Ubiquitin-Conjugating Enzymes/genetics
Chemical Substances	Nerve Tissue Proteins ; Nuclear Proteins ; STEEP1 protein, human ; UBE2A protein, human (EC 2.3.2.23) ; Ubiquitin-Conjugating Enzymes (EC 2.3.2.23)
Language	English
Publishing date	2021-02-27
Publishing country	Switzerland
Document type	Case Reports
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12030350
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Article ; Online: WDR13

Rzońca-Niewczas, Sylwia / Wierzba, Jolanta / Kaczorowska, Ewa / Poryszewska, Milena / Kosińska, Joanna / Stawiński, Piotr / Płoski, Rafał / Bal, Jerzy

Genes

2021 Volume 12, Issue 12

Abstract	Investigating novel genetic variants involved in intellectual disability (ID) development is essential. X-linked intellectual disability (XLID) accounts for over 10% of all cases of ID in males. XLID genes are involved in many cellular pathways and processes. Some of them are not specific to the development and functioning of the neural system. The implementation of exome sequencing simplifies the search for novel variants, especially those less expected. Here, we describe a nonsense variant of the XLID gene,
MeSH term(s)	Adult ; Cell Cycle Proteins/genetics ; Female ; Gene Expression Regulation ; Genes, X-Linked ; Humans ; Intellectual Disability/genetics ; Intellectual Disability/metabolism ; Intellectual Disability/pathology ; Male ; Mental Retardation, X-Linked/genetics ; Mental Retardation, X-Linked/metabolism ; Mental Retardation, X-Linked/pathology ; Mutation ; Pedigree ; Whole Exome Sequencing/methods ; Young Adult
Chemical Substances	Cell Cycle Proteins ; WDR13 protein, human
Language	English
Publishing date	2021-11-28
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12121911
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