Abstract
The majority of single nucleotide polymorphisms (SNPs) found in the coding region (cSNPs) are single base substitutions that may or may not lead to amino acid substitutions, most of which are related to diseases. Some cSNPs may prove useful for their potential links to functional cSNPs via linkage disequilibrium mapping. We have selected 48 cSNPs located in the coding regions of 25 genes to construct the cSNP chip. These genes are harbored in the high frequency loss regions of the chromosome 1p and 8p and related with apoptosis, cell cycles, signal transduction, oncogene, tumor suppressor genes and so on. All of the cSNPs can lead to amino acid substitutions except TP73 (rs1801174). The PCR products amplified from 31 hepatocellular carcinoma (HCC) specimens were labeled with Dig-dUTP and then hybridized with the cSNP chips. The results showed that there was no hybridization signal when there was more than one site of mutation in the amplification sequence, indicating that the cSNP chip had a high sensitivity. The statistic data of the SNP (MT, homozygous and HT, heterozygous) in the HCC patients with different phenotypes (HBV+/−, differentiation stage, family history positive or negative, tumor size) indicated that the number of MT was distinctly different between patients with positive HBV and negative HBV. The MT and HT numbers of all the 48 cSNPs were significantly different between low differentiation and high differentiation HCC patients. The numbers of MT and HT were not different between positived and negative family history groups and between tumor size >3 cm and ⩽ 3 cm groups. The study results provided useful information for understanding the molecular mechanisms of HCC development.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N, Shaw N, Lane C R, Lim E P, Kalyanaraman N, Nemesh J, Ziaugra L, Friedland L, Rolfe A, Warrington J, Lipshutz R, Daley G Q, Lander E S (1999). Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nature Genetics, 22(3): 231–238
Chan K L, Lee J M F, Guan X Y, Fan S T, Ng I O L (2002). High-density allelotyping of chromosome 8p in hepatocellular carcinoma and clinicopathologic correlation. Cancer, 94(12): 3179–3185
De B K, Srinivasan A (1989). Multiple primer pairs for the detection of HTLV-I by PCR. Nucleic Acids Research, 17(5): 2142.
Durigon E L, Erdman D D, Gary G W, Pallansch M A, Torok T J, Anderson L J (1993). Multiple primer pairs for polymerase chain reaction (PCR) amplification of human parvovirus B19 DNA. J Virol Methods, 44(2–3): 155–165
Farrand K, Delahunt B, Wang X L, McIver B, Hay I D, Goellner J R, Eberhardt N L, Grebe S K (2002). High resolution loss of heterozygosity mapping of 17p13 in thyroid cancer: Hurthle cell carcinomas exhibit a small 411-kilobase common region of allelic imbalance, probably containing a novel tumor suppressor gene. Journal of Clinical Endocrinology and Metabolism, 87(10): 4715–4721
Gao Y T, Chen R Y, Song W Q, Chen C B, Qi Z L, Jing L, Sun J Y, Qian S C (2003). DNA microarray for monitoring genetic variability of hepatitis B virus during lamivudine therapy. Chinese Journal of Virologica Sinica, 18: 523–529 (in Chinese)
Huber M, Mundlein A, Dornstauder E, Schneeberger C, Tempfer C B, Mueller M W, Schmidt W M (2002). Accessing single nucleotide polymorphisms in genomic DNA by direct multiplex polymerase chain reaction amplification on oligonucleotide microarrays. Analytical Biochemistry, 303(1): 25–33
Iwamoto K, Bundo M, Ueda J, Nakano Y, Ukai W, Hashimoto E, Saito T, Kato T (2007). Detection of chromosomal structural alterations in single cells by SNP arrays: a systematic survey of amplification bias and optimized workflow. Public of Library of Science, 2(12): e1306
Li S P, Wang H Y, Li J Q, Zhang C Q, Feng Q S, Huang P, Yu X J, Huang L X, Liang Q W, Zeng Y X (2001). Genome-wide analyses on loss of heterozygosity in hepatocellular carcinoma in Southern China. Journal of Hepatology, 34(6): 840–849
Lu T, Hano H, Meng C, Nagatsuma K, Chiba S, Ikegami M (2007). Frequent loss of heterozygosity in two distinct regions, 8p23.1 and 8p22, in hepatocellular carcinoma. World Journal of Gastroenterology, 13(7): 1090–1097
Midorikawa Y, Yamamoto S, Ishikawa S, Kamimura N, Igarashi H, Sugimura H, Makuuchi M, Aburatani H (2006). Molecular karyotyping of human hepatocellular carcinoma using single-nucleotide polymorphism arrays. Oncogene, 25 (40): 5581–5590
Monzon F A, Hagenkord J M, Lyons-Weiler M A, Balani J P, Parwani A V, Sciulli C M, Li J, Chandran U R, Bastacky S I, Dhir R (2008). Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors. Modern Pathology, Feb 8 [Epub ahead of print]
Niu J Y, Shen H B (2000). Application and purification of DNA from clotted blood. Journal of Nanjing Medical University, 20(5): 389–340 (in Chinese)
Pandya G A, Holmes M H, Sunkara S, Sparks A, Bai Y, Verratti K, Saeed K, Venepally P, Jarrahi B, Fleischmann R D, Peterson S N (2007). A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform. Nucleic Acids Research, 35(21): e148
Sambrook J, Russell D W (2003). Molecular Cloning: A Laboratory Manual, 3rd ed. Huang P T translation. Beijing: Science Press, 483–485 (in Chinese)
Shao J, Li H, Liew C T, Wu Q, Liang X, Hou J (1999). A preliminary study of loss of heterozygosity on chromosome 1p in primary hepatocellular carcinoma, Chinese Journal of Pathology, 28(1): 28–30 (in Chinese)
Tamura G (2006). Alterations of tumor suppressor and tumorrelated genes in the development and progression of gastric cancer. World Journal of Gastroenterology, 12(2): 192–198
Wang D G, Fan J B, Siao C J, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, Kruglyak L, Stein L, Hsie L, Topaloglou T, Hubbell E, Robinson E, Mittmann M, Morris M S, Shen N, Kilburn D, Rioux J, Nusbaum C, Rozen S, Hudson T J, Lipshutz R, Chee M, Lander E S (1998). Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science, 280: 1077–1082
Wang J, Ni H, Chen L, Liu Y X, Chen C B, Song W Q (2005). Preparation and analysis of cSNP chip on hepatocellular carcinoma-related genes. Hepatobiliary & Pancreatic Diseases International, 4: 398–402
Zhu G N, Zuo L, Zhou Q, Zhang S M, Zhu H Q, Gui S Y, Wang Y (2004). Loss of heterozygosity on chromosome 10q22–10q23 and 22q11.2–22q12.1 and p53 gene in primary hepatocellular carcinoma. World Journal of Gastroenterology, 10(13): 1975–1978
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Wang, J., Song, W. Analysis of genotype polymorphism of tumor-related genes harbored in chromosome arm 1p and 8p in hepatocellular carcinoma patients by cSNP chip. Front. Biol. China 4, 82–88 (2009). https://doi.org/10.1007/s11515-008-0075-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11515-008-0075-1