Allelic Imbalance (AI) / Loss of Heterozygosity (LOH)
To detect possible genetic changes in a tumour, we analyze polymorphic genetic markers from DNA isolated from both normal (e.g. blood) and tumour of the patient. The samples are fluorescently tagged by a standard PCR protocol, with fluorochromes in the 5 end of the primers. Only constitutional heterozygotes are scored for the presence of AI, as AI means a skewed intensity ratio between the two alleles in tumour DNA compared to blood DNA.
The PCR products are being run on an ABI PrismTM310 Genetic Analyzer (Applied Biosystems). For the analysis of the electropherograms, we use the softwares GeneScan®3.1 and Genotyper®. The allele peak heights are exported to Microsoft®Excel for further analysis.
Methodological evaluation:
Skotheim RI, Diep CB, Kraggerud SM, Jakobsen KS, and Lothe RA (2001). Evaluation of loss of heterozygosity/allelic imbalance scoring in tumor DNA. Cancer Genet.Cytogenet., 127(1): 64-70.
Publications using this methodology: Diep CB, Thorstensen L, Meling GI, Skovlund E, Rognum TO, and Lothe RA (2003). Genetic tumor markers with prognostic impact in Dukes' stages B and C colorectal cancer patients. J.Clin.Oncol., 21(5): 820-829.
Kraggerud SM, Åman P, Holm R, Stenwig AE, Fosså SD, Nesland JM, and Lothe RA (2002). Alterations of the fragile histidine triad gene, FHIT, and its encoded products contribute to testicular germ cell tumorigenesis. Cancer Res., 62(2): 512-517.
Smith-Sørensen B, Lind GE, Skotheim RI, Fosså SD, Fodstad Ø, Stenwig A-E, Jakobsen KS, and Lothe RA (2002). Frequent promoter hypermethylation of the O6-methylguanine-DNA methyltransferase (MGMT) gene in testicular cancer. Oncogene, 21(57): 8878-8884.
Skotheim RI, Kraggerud SM, Fosså SD, Stenwig AE, Gedde-Dahl T, Jr., Danielsen HE, Jakobsen KS, and Lothe RA (2001). Familial/bilateral and sporadic testicular germ cell tumors show frequent genetic changes at loci with suggestive linkage evidence. Neoplasia, 3(3): 196-203.
Thorstensen L, Qvist H, Nesland JM, Giercksky KE, and Lothe RA (2001). Identification of two potential suppressor gene regions on chromosome arm 14q that are commonly lost in advanced colorectal carcinomas. Scand.J.Gastroenterol., 36(12): 1327-1331.
Helland A, Kraggerud SM, Kristensen GB, Holm R, Abeler VM, Huebner K, Børresen-Dale AL, and Lothe RA (2000). Primary cervical carcinomas show 2 common regions of deletion at 3P, 1 within the FHIT gene: evaluation of allelic imbalance at FHIT, RB1 and TP53 in relation to survival. Int.J.Cancer, 88(2): 217-222.
Thorstensen L, Qvist H, Heim S, Liefers GJ, Nesland JM, Giercksky KE, and Lothe RA (2000). Evaluation of 1p losses in primary carcinomas, local recurrences and peripheral metastases from colorectal cancer patients. Neoplasia, 2(6): 514-522.
Bomme L, Heim S, Bardi G, Fenger C, Kronborg O, Brøgger A, and Lothe RA (1998). Allelic imbalance and cytogenetic deletion of 1p in colorectal adenomas: a target region identified between DIS199 and DIS234. Genes Chromosomes.Cancer, 21(3): 185-194.
Thorstensen L, Qvist H, Nesland JM, Giercksky KE, and Lothe RA (1996). Allelotype profiles of local recurrences and distant metastases from colorectal-cancer patients. Int.J.Cancer, 69(6): 452-456.
Lothe RA, Slettan A, Sæter G, Brøgger A, Børresen AL, and Nesland JM (1995). Alterations at chromosome 17 loci in peripheral nerve sheath tumors. J.Neuropathol.Exp.Neurol., 54(1): 65-73.
Lothe RA, Peltomäki P, Tommerup N, Fosså SD, Stenwig AE, Børresen AL, and Nesland JM (1995). Molecular genetic changes in human male germ cell tumors. Lab.Invest., 73(5): 606-614.
Lothe RA, Andersen SN, Hofstad B, Meling GI, Peltomäki P, Heim S, Brøgger A, Vatn M, Rognum TO, and Børresen AL (1995). Deletion of 1p loci and microsatellite instability in colorectal polyps. Genes Chromosomes.Cancer, 14(3): 182-188.
Lothe RA, Hastie N, Heimdal K, Fosså SD, Stenwig AE, and Børresen AL (1993). Frequent loss of 11p13 and 11p15 loci in male germ cell tumours. Genes Chromosomes.Cancer, 7(2): 96-101.
Lothe RA, Fossli T, Danielsen HE, Stenwig AE, Nesland JM, Gallie B, and Børresen AL (1992). Molecular genetic studies of tumor suppressor gene regions on chromosomes 13 and 17 in colorectal tumors. J.Natl.Cancer Inst., 84(14): 1100-1108.
Lothe RA, Fosså SD, Stenwig AE, Nakamura Y, White R, Børresen AL, and Brøgger A (1989). Loss of 3p or 11p alleles is associated with testicular cancer tumors. Genomics, 5(1): 134-138.
Lothe RA, Nakamura Y, Woodward S, Gedde-Dahl TJ, and White R (1988). VNTR (variable number of tandem repeats) markers show loss of chromosome 17p sequences in human colorectal carcinomas. Cytogenet.Cell Genet., 48(3): 167-169.
Lothe RA, Gedde-Dahl T, Jr., Lier ME, Aamdahl S, Bergan A, Stenwig AE, and Brøgger A (1987). Loss of one chromosome #13 during development of a polyposis tumor. Cancer Genet.Cytogenet., 28(2): 335-342.
Nunes L, Li F, Wu M, Luo T, Hammarström K, Torell E, Ljuslinder I, Mezheyeuski A, Edqvist PH, Löfgren-Burström A, Zingmark C, Edin S, Larsson C, Mathot L, Osterman E, Osterlund E, Ljungström V, Neves I, Yacoub N, Guðnadóttir U, Birgisson H, Enblad M, Ponten F, Palmqvist R, Xu Xet al.(2024) Prognostic genome and transcriptome signatures in colorectal cancers Nature, 633(8028), 137-146 DOI 10.1038/s41586-024-07769-3, PubMed 39112715
Bogaard M, Strømme JM, Kidd SG, Johannessen B, Bakken AC, Lothe RA, Axcrona K, Skotheim RI, Axcrona U(2024) GRIN3A: A biomarker associated with a cribriform pattern and poor prognosis in prostate cancer Neoplasia, 55, 101023 DOI 10.1016/j.neo.2024.101023, PubMed 38944914
Skotheim RI, Diep CB, Kraggerud SM, Jakobsen KS, and Lothe RA (2001). Evaluation of loss of heterozygosity/allelic imbalance scoring in tumor DNA. Cancer Genet.Cytogenet., 127(1): 64-70.