Experts from China, Singapore and the United States trawled through a genetic datamine of around 10,000 people of southern Chinese descent.
Half of the volunteers had been diagnosed with nasopharyngeal carcinoma, a cancer that forms in the lining of the upper throat lying behind the nose. The other half were otherwise healthy.
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What showed up in the cancer group were telltale variants in three genes, according to the research, reported in the journal Nature Genetics.
The three, named TNFRSF19, MDSIEVI1 and CDKN2A/2B, have been previously linked with leukaemia.
Another pointer in the cancer patients was a variation in the human leukocyte antigen (HLA) gene, which has previously been fingered in this disease.
The findings are important, says the study, as they could shed light on the molecular pathways of nasopharyngeal carcinoma and its high prevalence in southern China, especially Guangdong province.
In this region, the cancer occurs in about 25 cases per 100,000 people, which is 25 times higher than the rest of the world. As a result, nasopharyngeal carcinoma is sometimes called the "Cantonese cancer."
Only Alaska, parts of northern Africa and southeastern Asia have similarly high rates.
The research was led by the Genome Institute of Singapore and the Sun Yat-Sen University Cancer Centre in Guangzhou.
Nose and throat cancers have lifestyle as well as inherited factors. Smoking, in particular, is a major cause. In nasopharyngeal carcinoma, consumption of salted and pickled foods as well as high levels in the blood of Epstein-Barr virus are additionally in the spotlight.
