Analysis of Rare Variants in Genes Related to Lipid Metabolism in Patients with Familial Hypercholesterolemia in Western Siberia (Russia)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Patients
2.2. Isolation of Genomic DNA
2.3. Genome Library Preparation, Sequencing, and Bioinformatic Analysis
- −
- Big population frequency databases, such as gnomAD (available online: https://gnomad.broadinstitute.org/ [accessed on 4 October 2021]), with some help of databases on specific populations, like Greater Middle East (GME) Variome Project (available online: http://igm.ucsd.edu/gme/ [accessed on 4 October 2021]), AbraOM (Brazilian genomic variants) (available online: https://abraom.ib.usp.br/ [accessed on 4 October 2021]), and Korean Personal Genome Project (available online: http://opengenome.net/Main_Page [accessed on 4 October 2021]).
- −
- Databases representing in silico prediction tools, such as dbNSFP (available online: https://sites.google.com/site/jpopgen/dbNSFP [accessed on 4 October 2021]), which contains data from more than 30 pathogenicity prediction tools (e.g., MutationTaster2, SIFT, PROVEAN, and Polyphen2), and from 10 conservation prediction tools (e.g., phastCons, GERP++, and SiPhy). For pathogenicity prediction tools, we set thresholds according to respective authors’ recommendations; additionally, for conservation prediction tools, we used one common threshold, 0.7; therefore, we assumed a variant to be conserved if its conservation score was greater than the scores of ≥70% other variants. Additionally, we used databases dbscSNV and regSNP-intron for variants that may have an effect on splicing. Nevertheless, all these databases were only a supplementary tool, and they contributed little to the summary measure of pathogenicity.
- −
- Gene-based phenotype databases (e.g., OMIM).
- −
- Clinical significance databases: ClinVar (available online: https://www.ncbi.nlm.nih.gov/clinvar/ [accessed on 4 October 2021]), Human Gene Mutation Database (HGMD) (available online: http://www.hgmd.cf.ac.uk/ [accessed on 4 October 2021]), and Leiden Open Variation Database (available online: https://www.lovd.nl/ [accessed on 4 October 2021]); variants described as benign (B) or likely benign (LB) were also excluded from further analysis.
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- PubMed (available online: https://pubmed.ncbi.nlm.nih.gov/ [accessed on 4 October 2021]) and some other article databases as a source of information on specific clinical cases.
2.4. Verification of Findings
2.5. Multiplex Ligation-Dependent Probe Amplification (MLPA)
3. Results
3.1. LDLR
3.2. Identification of Deletions and Duplications in the LDLR Gene by MLPA
3.3. APOB
3.4. ABCG5
3.5. APOC3
3.6. LPL
3.7. SREBF1
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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M ± SD * | Minimum | Maximum | |
---|---|---|---|
Glucose, mmol/L | 5.7 ± 1.2 | 4.0 | 10.4 |
Total cholesterol, mmol/L (mg/dL) | 8.6 ± 3.4 (332.5 ± 131.4) | 3.4 (131.4) | 25.0 (966.5) |
Triglycerides, mmol/L (mg/dL) | 1.8 ± 1.4 (157.5 ± 122.5) | 0.4 (35.0) | 17.4 (1522.5) |
HDL-C, mmol/L (mg/dL) | 1.4 ± 0.4 (54.1 ± 15.5) | 0.54 (20.9) | 2.2 (85.1) |
LDL-C, mmol/L (mg/dL) | 5.6 ± 2.3 (216.5 ± 88.9) | 1.11 (42.9) | 11.94 (461.6) |
Body–mass index, m2/kg | 27.2 ± 4.6 | 19.0 | 39.0 |
Age, years | 46.0 ± 13.9 | 20 | 73 |
Patient ID | dbSNP ID | Position on Chromosome (GRCh38) | Nucleotide Substitution | Amino Acid Substitution | MAF According to Database GnomAD | Clinical Effect According to Database ClinVar | References for Russia |
---|---|---|---|---|---|---|---|
LDLR Gene | |||||||
P28, P40, P41, P42, P55, P56 | rs121908038 | 19:11113293 | c.1202T > A | p.Leu401His | ND | Likely Pathogenic | Zakharova et al., 2005 [26]; Shakhtshneider et al., 2017 [27]; Shakhtshneider et al., 2019 [28]; Vasilyev et al., 2020 [29]; Miroshnikova et al., 2021 [30] |
P45 | rs137853964 | 19:11129602 | c.2479G > A | p.Val827Ile | A = 0.001006 | Likely Pathogenic | Shakhtshneider et al., 2017 [27]; Shakhtshneider et al., 2019 [28]; Vasilyev et al., 2020 [29] |
Р22, P36, P58 | rs28942078 | 19:11113376 | c.1285G > A | p.Val429Met | A = 0.000012 | Pathogenic/Likely Pathogenic | - |
P65 | rs539080792 | 19:11221396 | c.1009G > A | p.Glu337Lys | A = 0.000104 | Uncertain Significance | Shakhtshneider et al., 2017 [27]; Shakhtshneider et al., 2019 [28]; Vasilyev et al., 2020 [29] |
P47 | rs570942190 | 19:11113337 | c.1246C > T | p.Arg416Trp | T = 0.000024 | Not reported in ClinVar | Shakhtshneider et al., 2017 [27]; Shakhtshneider et al., 2019 [28]; Vasilyev et al., 2020 [29] |
P67, P68 | rs755757866 | 19:11110730 | c.1019G > T | p.Cys340Tyr | T = 0.000008 | Likely Pathogenic | Shakhtshneider et al., 2017 [27]; Shakhtshneider et al., 2019 [28]; Vasilyev et al., 2020 [29] |
Р7 | rs761954844 | 19:11110697 | c.986G > A | p.Cys329Tyr | A = 0.000016 | Likely Pathogenic | Zakharova et al., 2005 [26]; Shakhtshneider et al., 2019 [28]; Semenova et al., 2020 [31]; Vasilyev et al., 2020 [29]; Miroshnikova et al., 2021 [30] |
P35 | rs879254566 | 19:11105440 | c.534TT > G | p.Asp178Glu | ND | Pathogenic/ Likely Pathogenic | Shakhtshneider et al., 2019 [28]; Vasilyev et al., 2020 [29] |
P38, P39 | rs879254721 | 19:11107496 | c.922G > A | p.Glu308Lys | ND | Pathogenic | Semenova et al., 2020 [31]; Vasilyev et al., 2020 [30]; |
P2 | rs879254980 | 19:11116179 | c.1672G > T | p.Glu558Ter | ND | Pathogenic | - |
P24, P25, P26, P81, P82 | rs879255191 | 19:11128090 | c.2389 + 5G > A | - | ND | Conflicting Interpretations of Pathogenicity | Meshkov et. Al. [32]; Shakhtshneider et al., 2019 [28]; Vasilyev et al., 2020 [29] |
P52 | rs875989907 | 19:11106666 | c.796G > A | p.Asp266Asn | A = 0.000012 | Pathogenic | Shakhtshneider et al., 2017 [27] |
rs879254769 | 19:11110765 | c.1054T > C | p.Cys352Ser | ND | Likely Pathogenic | Shakhtshneider et al., 2017 [27] | |
P10 | rs875989894 | 19:11213415 | c.266G > C | p.Cys89Ser | ND | Pathogenic/Likely Pathogenic | - |
ND | 19:11222252 | c.1123T > G | p.Tyr375Asp | ND | Novel variant | - | |
APOB Gene | |||||||
P11, P15, P71 | rs5742904 | 2:21006288 | c.10580G > A | p.Arg3527Gln | T = 0.000275 | Pathogenic | Voevoda et al. 2014 [33]; Shakhtshneider et al., 2019 [28]; Miroshnikova et al., 2021 [30] |
ABCG5 Gene | |||||||
P74 | rs145164937 | 2:43832056 | c.293C > G | p.Ala98Gly | C = 0.002223 | Conflicting interpretations of pathogenicity | - |
APOC3 Gene | |||||||
P59 | rs138326449 | 11:116830638 | c.55 + 1G > A | - | C = 0.002244 | Conflicting interpretations of pathogenicity | - |
LPL Gene | |||||||
P9 | rs118204077 | 8:19955873 | c.808C > T | p.Arg270Cys | C = 0.0001 | Pathogenic | - |
SREBF1 Gene | |||||||
P83, P84 | rs115855236 | 17:17820281 | c.422C > T | p.Pro141Leu | A = 0.001210 | Not reported in ClinVar | - |
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Shakhtshneider, E.; Ivanoshchuk, D.; Timoshchenko, O.; Orlov, P.; Semaev, S.; Valeev, E.; Goonko, A.; Ladygina, N.; Voevoda, M. Analysis of Rare Variants in Genes Related to Lipid Metabolism in Patients with Familial Hypercholesterolemia in Western Siberia (Russia). J. Pers. Med. 2021, 11, 1232. https://doi.org/10.3390/jpm11111232
Shakhtshneider E, Ivanoshchuk D, Timoshchenko O, Orlov P, Semaev S, Valeev E, Goonko A, Ladygina N, Voevoda M. Analysis of Rare Variants in Genes Related to Lipid Metabolism in Patients with Familial Hypercholesterolemia in Western Siberia (Russia). Journal of Personalized Medicine. 2021; 11(11):1232. https://doi.org/10.3390/jpm11111232
Chicago/Turabian StyleShakhtshneider, Elena, Dinara Ivanoshchuk, Olga Timoshchenko, Pavel Orlov, Sergey Semaev, Emil Valeev, Andrew Goonko, Nataliya Ladygina, and Mikhail Voevoda. 2021. "Analysis of Rare Variants in Genes Related to Lipid Metabolism in Patients with Familial Hypercholesterolemia in Western Siberia (Russia)" Journal of Personalized Medicine 11, no. 11: 1232. https://doi.org/10.3390/jpm11111232
APA StyleShakhtshneider, E., Ivanoshchuk, D., Timoshchenko, O., Orlov, P., Semaev, S., Valeev, E., Goonko, A., Ladygina, N., & Voevoda, M. (2021). Analysis of Rare Variants in Genes Related to Lipid Metabolism in Patients with Familial Hypercholesterolemia in Western Siberia (Russia). Journal of Personalized Medicine, 11(11), 1232. https://doi.org/10.3390/jpm11111232