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17th of October 2018


Hidden Stories of Chinese Migration and Culture Found in Giant Genetic Study


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Hidden Stories of Chinese Migration and Culture Found in Giant Genetic Study

Scientists reported an assortment of findings resulting from a sweeping and novel analysis of data from the prenatal tests of 141,431 participants.

ImagePeople of the Miao ethnic minority in Guizhou province, southwestern China. A sweeping study of Chinese DNA had more than 140,000 participants, representing nearly every Chinese province and 37 out of 56 officially recognized ethnic groups.CreditCreditAgence France-Presse — Getty Images

By Steph Yin

Oct. 5, 2018

Lamb stew, hearty and fragrant, cooked until meat falls off the bone and served alongside thick, chewy noodles — this is the type of food that cuts through northern China’s winter chill.

Further south, warmer climates support more crops. Fresh, stir-fried greens might accompany dim sum in Guangdong or punctuate a spicy meal in Sichuan. Lychee, durian and other fruits ripen the air.

Comb through the DNA of Chinese people and you’ll find a trace of this culinary story, according to the largest-scale genetic study of Chinese people to date, published Thursday in Cell. The authors reported that a mutation of FADS2, a gene involved in metabolizing fatty acids, is more common in northern than southern populations, indicating a diet richer in animal content. It is one of an assortment of findings resulting from a sweeping analysis of genetic information from 141,431 participants.

The approach — a novel one using data from prenatal blood tests — came with a trade-off. Though researchers were able to cheaply sequence a large number of genomes, they had access to a small fraction of each person’s genome, much less than what genome-wide studies typically look at.

Nevertheless, the study suggests that simple clinical tests can be an effective resource for surveying the genetics of large populations and generating hypotheses for study, said Ekta Khurana, an assistant professor of computational genomics at Weill Cornell Medicine in New York who was not involved in the research.

“This can be expanded to include not just mothers, but all different people,” she said.

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The authors used data from noninvasive prenatal testing for fetal trisomy, a condition that can cause Down syndrome. Pioneered in China, the test analyzes free-floating bits of fetal DNA in the mother’s blood and is administered for $100 or less throughout the country, said Xin Jin, a research scientist at BGI, a genome sequencing firm in Shenzhen, and an author of the paper. High-quality, whole genome sequencing, in comparison, costs about $1,000 per person.

The data set, which represented nearly every Chinese province and 37 out of 56 officially recognized ethnic groups, eclipsed many genome-wide studies, which often include only thousands, or tens of thousands, of participants.

But the team’s analysis covered a mere 10 percent or less of each person’s genome, while most rigorous genome-wide studies cover 80 percent or more, said Anders Albrechtsen, an associate professor at the University of Copenhagen and an author of the study.

To overcome this, the researchers relied on heavy computation and statistics, designing custom software that could infer missing DNA. They reported many preliminary but interesting insights.

For instance, the Han — comprising 92 percent of China’s population — were quite genetically homogeneous, mostly differing between the North and South.

This likely reflects governmental policies and job opportunities since 1949, which have largely driven migration eastward or westward, said Siyang Liu, a senior research scientist at BGI and lead author of the paper.

Her team identified several gene variants differing in frequency between northern and southern populations, related to immune response, bipolar disorder and earwax type.

Minority ethnic groups showed more genetic divergence than the Han, particularly Uyghurs and Kazakhs in Xinjiang and Mongols in Inner Mongolia.

This is noteworthy because sequencing studies are rarely done on ethnic minorities, even though findings can have important medical implications, said Charleston Chiang, an assistant professor at the University of Southern California’s Keck School of Medicine who was not involved in the research.

The researchers also diagnosed viruses in the mothers’ blood by checking DNA that did not align to the human genome against a database of viral sequences. They found a relatively high prevalence of hepatitis B and other viruses that can affect pregnancies, as well as a gene variant associated with roseola, which causes a high fever and rash in babies.

Last, to show that noninvasive pregnancy testing data can reveal associations between genes and specific traits, the scientists analyzed height and body mass index across their sample, finding 48 gene variants associated with height and 13 with body mass index. They also reported gene variants associated with maternal age and the likelihood of having twins.

Some of these associations had been reported in previous studies with Europeans, but the team also discovered new links, which underscores the importance of doing research in non-European populations, Dr. Jin said.

This study served as proof-of-concept, he added. His team is moving forward on evaluating prenatal testing data from more than 3.5 million Chinese people.

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