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Genomics In The Journals: Jul 5, 2012

NEW YORK (GenomeWeb News) – In Current Biology, researchers from Spain, Denmark, and Mexico offer evidence suggesting present-day Iberian populations are genetically different from hunter-gatherers who inhabited the region thousands of years ago.

The team generated mitochondrial and nuclear genomes sequences from the preserved, 7,000 year old remains of two individuals found at the La Braña-Arintero archaeological site in northwest Spain in 2006. Based on their analyses of sequences representing 0.53 percent and 1.34 percent of the individuals' nuclear genomes, combined with mitochondrial genome data, investigators concluded that the hunter-gatherers were not most closely related to current populations in the region but, instead, to hunter-gatherers who lived in what is now Northern and Central Europe at around the same time. The team eventually hopes to do whole-genome sequencing on the Mesolithic remains, which are far older than those of the famed Tyrolean Iceman, Ötzi, who is believed to have lived during the Neolithic or Stone Age about 5,300 years ago.

"[The] La Braña-Arintero site offers a unique opportunity to obtain pre-Neolithic genomes," senior author Carles Lalueza-Fox, a paleogenomics researcher with the Spanish National Research Council, or CSIC, said in a statement.

"The arrival of the Neolithic Period brought about a replacement of populations, and could cause genetic changes in genes associated with new infectious diseases, and in metabolic genes linked to changes in diet," he added. "Therefore, all the information extracted from this genome will be absolutely important."

A BMC Genetics study is highlighting the genetic diversity found in the rhesus macaque. Researchers at the National Institute on Alcohol Abuse and Alcoholism's neurogenetics lab and elsewhere used RNA sequencing and chromatin immunoprecipitation-sequencing to track down SNPs in post-mortem hippocampus brain samples from 14 humans and 14 rhesus macaques. When they looked at the variants patterns in each of the primates, investigators found that the rhesus macaque genome displays about three times as much genetic variation as the human genome.

Even so, their results indicate that the macaques have proportionally fewer alterations affecting coding regions. As a result of this pattern — believed to reflect selection pressure to preserve functional genes within very large macaque populations over time — the overall burden of potentially damaging mutations is comparable in rhesus macaques and humans despite their differences in diversity.

"Our comparative approach across primate species (human and macaques) gives us a genomic view of evolutionary selection and reaffirms the effects of population history on genetic variation," co-corresponding author Christina Barr, acting chief of the NIAAA's comparative behavioral genomics section, said in a statement. "Not very long ago, on an evolutionary timescale, there were more macaques than people, and the genomes of both species are a legacy of those times past."

Using a two-stage genome-wide association study approach, a team led by investigators in China has tracked down four new coronary artery disease risk loci in the Han Chinese population — work that's presented in Nature Genetics.

The researchers started with a meta-analysis involving 1,515 individuals with coronary artery disease and more than 5,000 unaffected controls, using data collected for the Beijing Atherosclerosis Study and the China Atherosclerosis Study. From information at some 2.2 million SNPs that were either imputed or directly genotyped in one of the two previous studies, the team settled on 96 SNPs to take forward for validation, progressively narrowing their set of suspicious SNPs further through testing in three replication groups representing another 15,460 cases and 11,472 controls. The search led to eight risk loci, including four previously linked to coronary artery disease in European populations and four newly detected sites in and around the TTC32-WDR35, GUCY1A3, C6orf10-BTNL2, and ATP2B1.

"These results suggest that both shared and unique genetic backgrounds of [coronary artery disease] susceptibility are present in different ancestry groups," Chinese Academy of Medical Sciences and Peking Union Medical College researcher Dongfeng Gu, the study's corresponding author, and colleagues noted, "and highlight the importance of fine-mapping efforts to pinpoint causal variants and mechanisms."

An international team led by researchers from Universitat de Barcelona has sequenced the melon (Cucumis melo) using 454 pyrosequencing. They reported their findings this week in the early edition of the Proceedings of the National Academy of Sciences.

Their approach produced 14.8 million single-shotgun and 7.7 million paired-end reads. The annotation of the assembled genome predicted 24,427 protein-coding genes, similar to other plant species. In addition, the researchers found that transposable elements have accumulated to a greater extent in the melon than in its close relative, the cucumber.

The researchers also collected data on disease resistance genes, accumulation of sugars, and carotenoid accumulation, which is responsible for the melon's flesh color. They also compared the melon genome with that of Arabidopsis, soybean, and Fragaria vesca.

Researchers from the Ludwig Institute for Cancer Research and the University of California, San Diego School of Medicine applied ChIP-Seq to a set of 19 tissues and cell types in the mouse to produce a map of nearly 300,000 murine cis-regulatory sequences.

The researchers, who published their study in this week's issue of Nature, said that the annotated sequences represent about 11 percent of the mouse genome and include more than 70 percent of the conserved non-coding sequences.

"The wide range of tissue and cell types examined in this study provides an unprecedented opportunity to detect tissue-specific and development-specific promoters and enhancers, analyses of which have yielded potential clues to transcription regulators of tissue-specific gene expression programs," the authors wrote.

Researchers from 23andMe have published the results of a genome-wide association study that has identified seven SNPs associated with breast size, three of which also correlated with breast cancer. The study, published online in BMC Medical Genetics, included data from 16,175 females of European ancestry who are customers of the direct-to-consumer genetics firm. In addition to genetic data, the participants filled out a survey that included questions regarding bra cup size and bra band size.

The loci associated with breast size are rs7816345 near ZNF703, rs4849887 and rs17625845 flanking INHBB, rs12173570 near ESR1, rs7089814 in ZNF365, rs12371778 near PTHLH, and rs62314947 near AREG.

Two of the SNPs, those near ESR1 and PTHLH, are strongly correlated with SNPs associated with breast cancer, and a third (ZNF365) is near another breast cancer SNP. The other three loci (ZNF703, INHBB, and AREG) have "strong links to estrogen regulation and breast development," 23andMe said in a statement.

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

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