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Kozina AA, Shatalov PA, Baranich TI, Artemieva SB, Kupriyanova AG, Baryshnikova NV, Krasnenko AY, Ilinsky VV, Sukhorukov VS. Clinical and molecular-genetic profiles of patients with morphological indications of congenital multicore myopathy. BRSMU 2019. [DOI: 10.24075/brsmu.2019.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Congenital core myopathies are a clinically and genetically heterogenous group of congenital myopathies that share a specific histopathological feature: areas of reduced oxidative activity in muscle fibers. The relationship between clinical, genetic and morphological characteristics of this group of disorders remains understudied. The aim of this work was to compare clinical presentations and morphological phenotypes of patients with congenital myopathies/myodystrophy to the data yielded by massively parallel exome sequencing. Eight children were included in the study: 2 boys and 6 girls aged 3 to 14 years. Their biopsy material was analyzed by light and electron microscopy. Sequencing was performed on HiSeq2500. Mutations were detected in 7 (87.5%) of 8 participants. Six children had 8 mutations in the genes associated with congenital core myopathies; one patient had 2 mutations in the LAMA2 gene implicated in merosin-deficient muscular dystrophy. The proportions of patients with mutations in RYR1 and SEPN1 were equal (42.86%). Of 10 detected mutations, 3 had not been previously described, including c.7561G>A in RYR1, c.485C>A in SEPN1 and p.Cys1136Arg in LAMA2. The clinical and morphological features of core myopathies suggest that genetic causes of this group of disorders should not be limited to RYR1 and SEPN1 genes only. This necessitates the search for and the study of other genes implicated in congenital myopathies or myodystrophy using state-of-the-art molecular genetic tools.
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Affiliation(s)
- A. A. Kozina
- Pirogov Russian National Research Medical University, Moscow, Russia; Genotek Ltd., Moscow, Russia
| | - P. A. Shatalov
- Veltischev Research and Clinical Institute for Pediatrics, Pirogov Russian National Research Medical University, Moscow, Russia; Genotek Ltd., Moscow, Russia
| | - T. I. Baranich
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - S. B. Artemieva
- Veltischev Research and Clinical Institute for Pediatrics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - A. G. Kupriyanova
- Veltischev Research and Clinical Institute for Pediatrics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - N. V. Baryshnikova
- Pirogov Russian National Research Medical University, Moscow, Russia; Genotek Ltd., Moscow, Russia
| | - A. Yu. Krasnenko
- Pirogov Russian National Research Medical University, Moscow, Russia; Genotek Ltd., Moscow, Russia
| | - V. V. Ilinsky
- Pirogov Russian National Research Medical University, Moscow, Russia; Genotek Ltd., Moscow, Russia
| | - V. S. Sukhorukov
- Pirogov Russian National Research Medical University, Moscow, Russia; Research Center of Neurology, Moscow, Russia
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Tsukanov KY, Krasnenko AY, Plakhina DA, Korostin DO, Churov AV, Druzhilovskaya OS, Rebrikov DV, Ilinsky VV. [A bioinformatic pipeline for NGS data analysis and mutation calling in human solid tumors]. Biomed Khim 2019; 63:413-417. [PMID: 29080873 DOI: 10.18097/pbmc20176305413] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We aimed to develop a pipeline for the bioinformatic analysis and interpretation of NGS data and detection of a wide range of single-nucleotide somatic mutations within tumor DNA. Initially, the NGS reads were submitted to a quality control check by the Cutadapt program. Low-quality 3¢-nucleotides were removed. After that the reads were mapped to the reference genome hg19 (GRCh37.p13) by BWA. The SAMtools program was used for exclusion of duplicates. MuTect was used for SNV calling. The functional effect of SNVs was evaluated using the algorithm, including annotation and evaluation of SNV pathogenicity by SnpEff and analysis of such databases as COSMIC, dbNSFP, Clinvar, and OMIM. The effect of SNV on the protein function was estimated by SIFT and PolyPhen2. Mutation frequencies were obtained from 1000 Genomes and ExAC projects, as well as from our own databases with frequency data. In order to evaluate the pipeline we used 18 breast cancer tumor biopsies. The MYbaits Onconome KL v1.5 Panel ("MYcroarray") was used for targeted enrichment. NGS was performed on the Illumina HiSeq 2500 platform. As a result, we identified alterations in BRCA1, BRCA2, ATM, CDH1, CHEK2, TP53 genes that affected the sequence of encoded proteins. Our pipeline can be used for effective search and annotation of tumor SNVs. In this study, for the first time, we have tested this pipeline for NGS data analysis of samples from patients of the Russian population. However, further confirmation of efficiency and accuracy of the pipeline is required on NGS data from larger datasets as well as data from several types of solid tumors.
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Affiliation(s)
| | | | | | - D O Korostin
- Vavilov Institute of General Genetics, Moscow, Russia
| | - A V Churov
- Institute of Biology of Karelian Research Centre, Petrozavodsk, Russia
| | | | - D V Rebrikov
- Vavilov Institute of General Genetics, Moscow, Russia
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Okuneva EG, Kozina AA, Baryshnikova NV, Krasnenko AY, Tsukanov KY, Klimchuk OI, Surkova EI, Ilinsky VV. A novel elastin gene frameshift mutation in a Russian family with cutis laxa: a case report. BMC Dermatol 2019; 19:4. [PMID: 30704477 PMCID: PMC6357400 DOI: 10.1186/s12895-019-0084-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/28/2019] [Indexed: 12/30/2022]
Abstract
Background Cutis laxa (CL) is a rare connective tissue disorder characterized by loose, redundant, inelastic and wrinkled skin. Patients develop a prematurely aged appearance. Inheritance can be autosomal dominant or autosomal recessive. The X-linked form is now classified in the group of copper transport diseases. Autosomal dominant CL is characterized by wrinkled, redundant and sagging, inelastic skin and in some cases is associated with internal organ involvement. Case presentation We report a familial case of autosomal dominant CL, which includes a 33-year-old woman and her 11-year-old son with dry, thin and wrinkled skin that appeared prematurely aged. No serious involvement of internal organs was found. In both patients, we identified novel heterozygous mutation c.2323delG (p.Ala775fs) in exon 34 of elastin transcript NM_001278939.1. Similar frameshift mutations in the last exons of elastin gene were previously reported in patients with autosomal dominant CL. Conclusions Our results show a novel frameshift mutation that was found in patients with cutis laxa. Exome sequencing is effective and useful technology for properly diagnosis of diseases with similar phenotype to ensure proper treatment is provided.
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Affiliation(s)
- E G Okuneva
- Genotek Ltd., Nastavnicheskii pereulok 17/1, 105120, Moscow, Russia
| | - A A Kozina
- Institute of Biomedical Chemistry, Pogodinskaya street 10 building 8, 119121, Moscow, Russia
| | - N V Baryshnikova
- Genotek Ltd., Nastavnicheskii pereulok 17/1, 105120, Moscow, Russia.,Pirogov Russian National Research Medical University, Ostrovitianova street 1, 117997, Moscow, Russia
| | - A Yu Krasnenko
- Genotek Ltd., Nastavnicheskii pereulok 17/1, 105120, Moscow, Russia.,Pirogov Russian National Research Medical University, Ostrovitianova street 1, 117997, Moscow, Russia
| | - K Yu Tsukanov
- Genotek Ltd., Nastavnicheskii pereulok 17/1, 105120, Moscow, Russia
| | - O I Klimchuk
- Genotek Ltd., Nastavnicheskii pereulok 17/1, 105120, Moscow, Russia
| | - E I Surkova
- Genotek Ltd., Nastavnicheskii pereulok 17/1, 105120, Moscow, Russia.
| | - V V Ilinsky
- Pirogov Russian National Research Medical University, Ostrovitianova street 1, 117997, Moscow, Russia.,Vavilov Institute of General Genetics, Gubkina street 3, 119333, Moscow, Russia
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Krasnenko AY, Eliseev AY, Borisevich DI, Tsukanov KY, Davydova AI, Il'inskii VV. Library preparation for metagenomic sequencing with Illumina. Bulletin of RSMU 2017. [DOI: 10.24075/brsmu.2017-02-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Borisevich DI, Krasnenko AY, Stetsenko IF, Plakhina DA, Il'inskii VV. The impact of sequencing depth on accuracy of single nucleotide variant calls. Bulletin of RSMU 2017. [DOI: 10.24075/brsmu.2017-03-06] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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