The Spectrum of Germline Nucleotide Variants in Gastric Cancer Patients in the Kyrgyz Republic
Abstract
:1. Introduction
2. Materials and Methods
2.1. DNA Extraction
2.2. Library Preparation and Sequencing
2.3. Variant Classification and Bioinformatics Analysis
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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SDHB, PTCH2, MUTYH, NTRK1, SDHC, CDC73, PARP1, FH, RET, BMPR1A, PTEN, SUFU, HRAS, CDKN1C, ABCC8, WT1, EXT2, SDHAF2, MEN1, MRE11A, ATM, SDHD, CDKN1B, CDK4, POLE, BRCA2, RB1, FANCM, MAX, RAD51B, MLH3, DICER1, GREM1, FANCI, BLM, NTHL1, TSC2, SLX4, PALB2, CDH1, FANCA, RPA1, TP53, FLCN, NF1, RAD51D, CDK12, ERBB2, SMARCE1, BRCA1, HOXB13, RAD51C, PPM1D, BRIP1, AXIN2, RHBDF2, RBBP8, SMAD4, STK11, SMARCA4, ERCC2, POLD1, GEN1, ALK, EPCAM, MSH2, MSH6, FANCL, TMEM127, PMS1, BARD1, SMARCB1, CHEK2, NF2, FANCD2, VHL, MLH1, BAP1, GATA2, ATR, PHOX2B, PDGFRA, KIT, FAM175A, SDHA, TERT, MSH3, APC, RAD50, CTNNA1, SPINK1, FANCE, PMS2, EGFR, RINT1, MET, POT1, PRSS1, XRCC2, PPP2R2A, RPS20, NBN, EXT1, RECQL4, CDKN2A, FANCG, FANCC, PTCH1, GALNT12, TSC1, FANCB. |
Characteristics | Number of Patients (%) | |
---|---|---|
Gender | Female | 35 (31%) |
Male | 78 (69%) | |
Histological types (Lauren) | Intestinal type | 77 (68.1%) |
Diffuse type | 21 (18.6%) | |
Mixed type | 15 (13.3%) | |
Helicobacter pylori | H. pylori + | 16 (14.2%) |
H. pylori − | 97 (85.8%) | |
Stage of cancer | I | 5 (4.4%) |
II | 16 (14.2%) | |
III | 61 (54%) | |
IV | 31 (27.4%) |
№ | Gender (Age) | Lauren Classification | Stage | Gene | Chromosomal Change | Coding | Protein | ACMG | Cancer Cases in Family History | Pathogenicity Scores * | GnomAD Exomes | Literature |
---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | Male (63) | D a | IIIB | TP53 | chr17:7675140G>A | c.472C>T | p.Arg158Cys | P d | No |
Pathogenic-22 Uncertai-9 Benign-1 | ƒ = 0.00000796 | [21,22] |
2 | Male (60) | D a | IIIB | RET | chr10:43119548G>A | c.2410G>A | p.Val804Met | P d | No |
Pathogenic-5 Uncertai-12 Benign-3 | ƒ = 0.000125 | [23,24] |
BRCA2 | chr13:32340763delA | c.6410del | p.Asn2137MetfsTer31 | P d | - | Not found | [25,26] | |||||
3 | Female (57) | M b | IIIB | POLD1 | chr19:50414912delT | c.2486del | p.Leu829ArgfsTer59 | LP e | No | - | Not found | - |
4 | Male (74) | I c | IIIB | POLD1 | chr19:50416486G>T | c.2911G>T | p.Glu971Ter | LP e | Yes |
Pathogenic-4 Uncertai-3 Benign-2 | Not found | - |
5 | Male (62) | I c | IIIB | PALB2 | chr16:23630456insACGACTT | c.1692_1698dup | p.His567LysfsTer13 | LP e | No | - | Not found | - |
6 | Male (70) | I c | IIIB | FANCA | chr16:89816550C>T | c.66G>A | p.Trp22Ter | P d | No |
Uncertai-3 Benign-7 | Not found | [27,28,29,30,31] |
7 | Male (58) | D a | III | FANCD2 | chr3:10081422delGC | c.3182_3183del | p.Cys1061LeufsTer21 | LP e | No | - | Not found | - |
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Bilyalov, A.; Nikolaev, S.; Danishevich, A.; Khatkov, I.; Makhmudov, K.; Isakova, Z.; Bakirov, N.; Omurbaev, E.; Osipova, A.; Ramaldanov, R.; et al. The Spectrum of Germline Nucleotide Variants in Gastric Cancer Patients in the Kyrgyz Republic. Curr. Issues Mol. Biol. 2023, 45, 6383-6394. https://doi.org/10.3390/cimb45080403
Bilyalov A, Nikolaev S, Danishevich A, Khatkov I, Makhmudov K, Isakova Z, Bakirov N, Omurbaev E, Osipova A, Ramaldanov R, et al. The Spectrum of Germline Nucleotide Variants in Gastric Cancer Patients in the Kyrgyz Republic. Current Issues in Molecular Biology. 2023; 45(8):6383-6394. https://doi.org/10.3390/cimb45080403
Chicago/Turabian StyleBilyalov, Airat, Sergey Nikolaev, Anastasiia Danishevich, Igor Khatkov, Komron Makhmudov, Zhainagul Isakova, Nurbek Bakirov, Ernis Omurbaev, Alena Osipova, Ramaldan Ramaldanov, and et al. 2023. "The Spectrum of Germline Nucleotide Variants in Gastric Cancer Patients in the Kyrgyz Republic" Current Issues in Molecular Biology 45, no. 8: 6383-6394. https://doi.org/10.3390/cimb45080403