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Archive - Jul 5, 2012

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Non-Invasive Sequencing of Fetal Genome from Mother’s Blood

Researchers at the Stanford University School of Medicine have for the first time sequenced the genome of an unborn baby using only a blood sample from the mother. The findings from the new approach, published online on July 4, 2012 in Nature, are related to research that was reported a month ago from the University of Washington. That research used a technique previously developed at Stanford to sequence a fetal genome using a blood sample from the mother, plus DNA samples from both the mother and father. The whole genome sequencing in the new Stanford study, however, did not require DNA from the father — a significant advantage when a child’s true paternity may not be known (a situation estimated to affect as many as one in 10 births in this country) or the father may be unavailable or unwilling to provide a sample. The technique brings fetal genetic testing one step closer to routine clinical use. “We’re interested in identifying conditions that can be treated before birth, or immediately after,” said Stephen Quake, Ph.D., the Lee Otterson Professor in the School of Engineering and professor of bioengineering and of applied physics. “Without such diagnoses, newborns with treatable metabolic or immune system disorders suffer until their symptoms become noticeable and the causes determined.” Dr. Quake is the senior author of the research. Former graduate student H. Christina Fan, Ph.D., now a senior scientist at ImmuMetrix, and current graduate student Wei Gu are co-first authors of the article. As the cost of such technology continues to drop, it will become increasingly common to diagnose genetic diseases within the first trimester of pregnancy, the researchers believe. In fact, they showed that sequencing just the exome, the coding portion of the genome, can provide clinically relevant information.

Yak Genome Sequence Provides Insights into High-Altitude Adaptation

An international team, led by Lanzhou University, and including BGI, the world's largest genomics organization, the Institute of Kunming Zoology, the Chinese Academy of Sciences, as well as twelve other institutes, has completed the genomic sequence and analyses of a female domestic yak, which provides important insights into understanding mammalian divergence and adaptation at high altitude. This study was published online on July 1, 2012 in Nature Genetics. As an iconic symbol of Tibet and of high altitude, the yak (Bos grunniens) is the most important domesticated species for Tibetans living at high altitude in China's Qinghai Province, which could provide meat and other basic resources, such as milk, transportation, dried dung for fuel, and hides for tented accommodation. Yaks have many anatomical and physiological traits that enable them to live at high altitude, including high metabolism, acute senses, impressive foraging ability, enlarged hearts and lungs, and a lack of blood vessel constriction in the lungs when faced with relatively low oxygen conditions. In the study, researchers sequenced the genome of a female domestic yak using high-throughput sequencing technology. The genomic data yielded a 2,657-Mb draft yak genome assembly that had 65-fold coverage. The researchers also conducted transcriptome sequencing on RNA samples derived from fresh heart, liver, brain, stomach, and lung tissues collected from the same yak. Based on the transcriptome data, researchers estimated that the yak genome contains 22,282 protein-coding genes and 2.2 million heterozygous SNPs. In order to understand evolutionary adaptation of yak to the high altitude, the team conducted comparative genomic analyses between yak and cattle, a closely related animal that typically lives at much lower altitudes.