scholarly journals From Clinical Diagnosis to the Discovery of Multigene Rare Sequence Variants in Pseudoxanthoma elasticum: A Case Report

2021 ◽  
Vol 8 ◽  
Author(s):  
Francesco Demetrio Lofaro ◽  
Dario Pasquale Mucciolo ◽  
Vittoria Murro ◽  
Laura Pavese ◽  
Daniela Quaglino ◽  
...  
Keyword(s):  
Rare Variants ◽  
Wide Spectrum ◽  
Personalised Medicine ◽  
Pseudoxanthoma Elasticum ◽  
Future Perspective ◽  
Sequence Variant ◽  
Sequence Variants ◽  
Generation Sequencing ◽  
Rare Autosomal Recessive Disease ◽  
Rare Sequence

Pseudoxanthoma elasticum (PXE) is a rare autosomal recessive disease clinically characterised by early cutaneous alterations, and by late clinically relevant ocular, and cardiovascular manifestations. ABCC6 genetic tests are used to confirm clinical PXE diagnosis, but this strategy may be rather challenging when only one ABCC6 pathogenic variant is found. A next-generation sequencing approach focusing on 362 genes related to the calcification process and/or to inherited retinal diseases was performed on a patient with clinical PXE diagnosis (skin papules and laxity, angioid streaks, and atrophy) who was carrier of only one ABCC6 rare sequence variant. Beside ABCC6, several rare sequence variants were detected which can contribute either to the occurrence of calcification (GGCX and SERPINF1 genes) and/or to ophthalmological manifestations (ABCA4, AGBL5, CLUAP1, and KCNV2 genes). This wide-spectrum analysis approach facilitates the identification of rare variants possibly involved in PXE, thus avoiding invasive skin biopsy as well as expensive and time-consuming diagnostic odyssey and allows to broaden and to deepen the knowledge on this complex rare disease and to improve patients' counselling, also with a future perspective of personalised medicine.

scholarly journals European External Quality Control Study on the Competence of Laboratories to Recognize Rare Sequence Variants Resulting in Unusual Genotyping Results

2009 ◽  
Vol 55 (4) ◽  
pp. 739-747 ◽  
Author(s):  
János Márki-Zay ◽  
Christoph L Klein ◽  
David Gancberg ◽  
Heinz G Schimmel ◽  
László Dux
Keyword(s):  
Quality Control ◽  
Error Rate ◽  
Rare Variants ◽  
Site Directed Mutagenesis ◽  
Sequence Variant ◽  
Sequence Variants ◽  
External Quality Control ◽  
External Quality ◽  
Quality Control Materials ◽  
Rare Sequence

Abstract Background: Depending on the method used, rare sequence variants adjacent to the single nucleotide polymorphism (SNP) of interest may cause unusual or erroneous genotyping results. Because such rare variants are known for many genes commonly tested in diagnostic laboratories, we organized a proficiency study to assess their influence on the accuracy of reported laboratory results. Methods: Four external quality control materials were processed and sent to 283 laboratories through 3 EQA organizers for analysis of the prothrombin 20210G>A mutation. Two of these quality control materials contained sequence variants introduced by site-directed mutagenesis. Results: One hundred eighty-nine laboratories participated in the study. When samples gave a usual result with the method applied, the error rate was 5.1%. Detailed analysis showed that more than 70% of the failures were reported from only 9 laboratories. Allele-specific amplification-based PCR had a much higher error rate than other methods (18.3% vs 2.9%). The variants 20209C>T and [20175T>G; 20179_20180delAC] resulted in unusual genotyping results in 67 and 85 laboratories, respectively. Eighty-three (54.6%) of these unusual results were not recognized, 32 (21.1%) were attributed to technical issues, and only 37 (24.3%) were recognized as another sequence variant. Conclusions: Our findings revealed that some of the participating laboratories were not able to recognize and correctly interpret unusual genotyping results caused by rare SNPs. Our study indicates that the majority of the failures could be avoided by improved training and careful selection and validation of the methods applied.

scholarly journals A Case Report of Pseudoxanthoma Elasticum with Rare Sequence Variants in Genes Related to Inherited Retinal Diseases

Diagnostics ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1800
Author(s):  
Francesco Demetrio Lofaro ◽  
Dario Pasquale Mucciolo ◽  
Vittoria Murro ◽  
Laura Pavese ◽  
Daniela Quaglino ◽  
...  
Keyword(s):  
Wide Spectrum ◽  
Pseudoxanthoma Elasticum ◽  
Elastic Fibers ◽  
Sequence Variants ◽  
Retinal Diseases ◽  
Patient Counseling ◽  
Ocular Manifestations ◽  
Whole Exome ◽  
Rare Autosomal Recessive Disease

A case of a patient with an early and severe visual impairment is described. Due to the occurrence of skin papules a suspect of pseudoxanthoma elasticum (PXE) was posed. PXE is a rare autosomal recessive disease clinically characterized by skin, cardiovascular and ocular manifestations, these last being those that most severely affect patients’ quality of life. A whole exome sequencing approach focusing on 340 genes related to the calcification process and/or to inherited retinal diseases (IRDs) was performed. Rare monoallelic sequence variants in ABCA4, ABCC6, IMPG1, POC1B and RAX2 were found. The presence of calcified elastic fibers was assessed by ultrastructural analysis on a skin biopsy. Diagnosis of PXE was based on clinical, biomolecular and morphological results, although the additional involvement of several IRD genes is important to explain the unexpectedly severe ophthalmological phenotype of the patient also in prognostic and therapeutic perspectives. Data indicate that genetic screening using a wide-spectrum analysis approach is essential to assist ophthalmologists in improving patient counseling.

scholarly journals Pathogenic Effect of GDAP1 Gene Mutations in a Yeast Model

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 310 ◽  
Author(s):  
Weronika Rzepnikowska ◽  
Joanna Kaminska ◽  
Dagmara Kabzińska ◽  
Andrzej Kochański
Keyword(s):  
Gene Mutations ◽  
Causative Mutation ◽  
Mitochondrial Morphology ◽  
Clinical Genetics ◽  
Sequence Variant ◽  
Sequence Variants ◽  
Pathogenic Variants ◽  
Pathogenic Effect ◽  
And Function ◽  
Rare Sequence

The question of whether a newly identified sequence variant is truly a causative mutation is a central problem of modern clinical genetics. In the current era of massive sequencing, there is an urgent need to develop new tools for assessing the pathogenic effect of new sequence variants. In Charcot-Marie-Tooth disorders (CMT) with their extreme genetic heterogeneity and relatively homogenous clinical presentation, addressing the pathogenic effect of rare sequence variants within 80 CMT genes is extremely challenging. The presence of multiple rare sequence variants within a single CMT-affected patient makes selection for the strongest one, the truly causative mutation, a challenging issue. In the present study we propose a new yeast-based model to evaluate the pathogenic effect of rare sequence variants found within the one of the CMT-associated genes, GDAP1. In our approach, the wild-type and pathogenic variants of human GDAP1 gene were expressed in yeast. Then, a growth rate and mitochondrial morphology and function of GDAP1-expressing strains were studied. Also, the mutant GDAP1 proteins localization and functionality were assessed in yeast. We have shown, that GDAP1 was not only stably expressed but also functional in yeast cell, as it influenced morphology and function of mitochondria and altered the growth of a mutant yeast strain. What is more, the various GDAP1 pathogenic sequence variants caused the specific for them effect in the tests we performed. Thus, the proposed model is suitable for validating the pathogenic effect of known GDAP1 mutations and may be used for testing of unknown sequence variants found in CMT patients.

scholarly journals Expanding the Phenotype and Genotype of Female GnRH Deficiency

2011 ◽  
Vol 32 (1) ◽  
pp. 156-157 ◽  
Author(s):  
Natalie D. Shaw ◽  
Stephanie B. Seminara ◽  
Corrine K. Welt ◽  
Margaret G. Au ◽  
Lacey Plummer ◽  
...  
Keyword(s):  
Clinical Presentation ◽  
Genetic Disorder ◽  
Pubertal Development ◽  
Academic Medical Center ◽  
Secretory Activity ◽  
Breast Development ◽  
Sequence Variant ◽  
Sequence Variants ◽  
Genetic Characteristics ◽  
Rare Sequence

Abstract Context: GnRH deficiency is a rare genetic disorder of absent or partial pubertal development. The clinical and genetic characteristics of GnRH-deficient women have not been well-described. Objective: To determine the phenotypic and genotypic spectrum of a large series of GnRH-deficient women. Design, Setting, and Subjects: Retrospective study of 248 females with GnRH deficiency evaluated at an academic medical center between 1980 and 2010. Main Outcome Measures: Clinical presentation, baseline endogenous GnRH secretory activity, and DNA sequence variants in 11 genes associated with GnRH deficiency. Results: Eighty-eight percent had undergone pubarche, 51% had spontaneous thelarche, and 10% had 1-2 menses. Women with spontaneous thelarche were more likely to demonstrate normal pubarche (P = 0.04). In 27% of women, neuroendocrine studies demonstrated evidence of some endogenous GnRH secretory activity. Thirty-six percent (a large excess relative to controls) harbored a rare sequence variant in a gene associated with GnRH deficiency (87% heterozygous and 13% biallelic), with variants in FGFR1 (15%), GNRHR (6.6%), and PROKR2 (6.6%) being most prevalent. One woman had a biallelic variant in the X-linked gene, KAL1, and nine women had heterozygous variants. Conclusions: The clinical presentation of female GnRH deficiency varies from primary amenorrhea and absence of any secondary sexual characteristics to spontaneous breast development and occasional menses. In this cohort, rare sequence variants were present in all of the known genes associated with GnRH deficiency, including the novel identification of GnRH-deficient women with KAL1 variants. The pathogenic mechanism through which KAL1 variants disrupt female reproductive development requires further investigation.

scholarly journals Phenotypic Features and Genetic Findings in a Cohort of Italian Pseudoxanthoma Elasticum Patients and Update of the Ophthalmologic Evaluation Score

2021 ◽  
Vol 10 (12) ◽  
pp. 2710
Author(s):  
Federica Boraldi ◽  
Vittoria Murro ◽  
Francesco Demetrio Lofaro ◽  
Dario Pasquale Mucciolo ◽  
Sonia Costa ◽  
...  
Keyword(s):  
Clinical Phenotype ◽  
Pseudoxanthoma Elasticum ◽  
Posterior Pole ◽  
Optic Disk ◽  
Ectopic Calcification ◽  
Sequence Variants ◽  
Number Of Patients ◽  
Optic Disk Drusen ◽  
Italian Origin ◽  
Rare Sequence

Background: Pseudoxanthoma elasticum (PXE) is a rare ectopic calcification genetic disease mainly caused by ABCC6 rare sequence variants. The clinical phenotype is characterized by typical dermatological, ophthalmological and cardiovascular manifestations, whose frequency and severity are differently reported in the literature. Methods: A retrospective study was performed on 377 PXE patients of Italian origin, clinically evaluated according to the Phenodex Index, who underwent ABCC6 biomolecular analyses. Moreover, 53 PXE patients were further characterized by in-depth ophthalmological examinations. Results: A total of 117 different ABCC6 rare sequence variants were detected as being spread through the whole gene. The severity of the clinical phenotype was dependent on age, but it was not influenced by gender or by the type of sequence variants. In-depth ophthalmological examinations focused on the incidences of coquille d’oeuf, comet lesions, pattern dystrophy-like lesions, optic disk drusen and posterior-pole atrophy. Conclusion: Given the large number of patients analyzed, we were able to better evaluate the occurrence of less frequent alterations (e.g., stroke, myocardial infarction, nephrolithiasis). A more detailed description of ophthalmological abnormalities allowed us to stratify patients and better evaluate disease progression, thus suggesting a further update of the PXE score system.

Molecular marker information from de novo assembled transcriptomes of chilli pepper (Capsicum annuum L.) varieties based on next-generation sequencing technology

2014 ◽  
Vol 12 (S1) ◽  
pp. S83-S86 ◽  
Author(s):  
Yul-Kyun Ahn ◽  
Swati Tripathi ◽  
Young-Il Cho ◽  
Jeong-Ho Kim ◽  
Hye-Eun Lee ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Sequence Variant ◽  
Nucleotide Polymorphisms ◽  
Next Generation ◽  
Chilli Pepper ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

scholarly journals Characterization of Coding/Noncoding Variants for SHROOM3 in Patients with CKD

2018 ◽  
Vol 29 (5) ◽  
pp. 1525-1535 ◽  
Author(s):  
Jeremy W. Prokop ◽  
Nan Cher Yeo ◽  
Christian Ottmann ◽  
Surya B. Chhetri ◽  
Kacie L. Florus ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Molecular Mechanisms ◽  
Rare Variants ◽  
Cultured Cells ◽  
Transcriptional Start Site ◽  
Hippo Pathway ◽  
Pdz Domain ◽  
Sequence Variant ◽  
Start Site ◽  
High Effect

Background Interpreting genetic variants is one of the greatest challenges impeding analysis of rapidly increasing volumes of genomic data from patients. For example, SHROOM3 is an associated risk gene for CKD, yet causative mechanism(s) of SHROOM3 allele(s) are unknown.Methods We used our analytic pipeline that integrates genetic, computational, biochemical, CRISPR/Cas9 editing, molecular, and physiologic data to characterize coding and noncoding variants to study the human SHROOM3 risk locus for CKD.Results We identified a novel SHROOM3 transcriptional start site, which results in a shorter isoform lacking the PDZ domain and is regulated by a common noncoding sequence variant associated with CKD (rs17319721, allele frequency: 0.35). This variant disrupted allele binding to the transcription factor TCF7L2 in podocyte cell nuclear extracts and altered transcription levels of SHROOM3 in cultured cells, potentially through the loss of repressive looping between rs17319721 and the novel start site. Although common variant mechanisms are of high utility, sequencing is beginning to identify rare variants involved in disease; therefore, we used our biophysical tools to analyze an average of 112,849 individual human genome sequences for rare SHROOM3 missense variants, revealing 35 high-effect variants. The high-effect alleles include a coding variant (P1244L) previously associated with CKD (P=0.01, odds ratio=7.95; 95% CI, 1.53 to 41.46) that we find to be present in East Asian individuals at an allele frequency of 0.0027. We determined that P1244L attenuates the interaction of SHROOM3 with 14–3-3, suggesting alterations to the Hippo pathway, a known mediator of CKD.Conclusions These data demonstrate multiple new SHROOM3-dependent genetic/molecular mechanisms that likely affect CKD.

Current Study Designs, Methods, and Future Directions of Genetic Association Mapping

2015 ◽  
pp. 323-358
Author(s):  
Jami Jackson ◽  
Alison Motsinger-Reif
Keyword(s):  
Association Mapping ◽  
Rare Variants ◽  
Disease Risk ◽  
Future Directions ◽  
Methods Development ◽  
Emerging Trends ◽  
Genome Wide ◽  
Study Designs ◽  
Genetic Association Mapping ◽  
Generation Sequencing

Rapid progress in genotyping technologies, including the scaling up of assay technologies to genome-wide levels and next generation sequencing, has motivated a burst in methods development and application to detect genotype-phenotype associations in a wide array of diseases and other phenotypes. In this chapter, the authors review the study design and genotyping options that are used in association mapping, along with the appropriate methods to perform mapping within these study designs. The authors discuss both candidate gene and genome-wide studies, focused on DNA level variation. Quality control, genotyping technologies, and single-SNP and multiple-SNP analyses have facilitated the successes in identifying numerous loci influence disease risk. However, variants identified have generally explained only a small fraction of the heritable component of disease risk. The authors discuss emerging trends and future directions in performing analysis for rare variants to detect these variants that predict these traits with more complex etiologies.

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