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Genomics In The Journals: Jun 23, 2011

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – In PLoS Genetics, a University of Texas Health Science Center at Houston-led team reports on copy number analyses of individuals with and without "thoracic aortic aneurisms and dissections," or TAAD, tears in part of the vessel that moves blood from the heart to other parts of the body.

Using SNP arrays, the team first looked for copy number changes in 765 TAAD patients and 4,569 unaffected controls, identifying a recurrent duplication in a chromosome 16 region previously linked to neuropsychiatric disease. The duplication — which affects nine genes, including one called MYH11 — was far more common in those with the condition in both discovery and follow-up experiments.

"The results of this study could affect clinical care because it appears patients with 16p13.1 duplications have an aggressive form of the thoracic aortic disease that causes aneurysms to dissect at smaller diameters," corresponding author Dianna Milewicz, a cardiovascular researcher with UTHealth, said in a statement.

Spanish and Italian researchers did whole-exome sequencing to find mutations behind hereditary pheochromocytoma, a rare, catecholamine hormone-producing tumor in part of the adrenal gland — work that they describe in the early, online edition of Nature Genetics.

After using the Illumina GAII to sequence coding regions captured with the Agilent SureSelect Human All Exon kits in three individuals with PCC, the team tracked down apparent disease-associated, germline mutations in MAX, which codes for a protein that works in cahoots with the transcription factors MYC and MXD1. Together with the group's follow-up experiments, the exome findings point to a role for MAX as a tumor suppressor that influences the formation of malignancies in the neural crest cells from which PCC tumors arise.

In a study in the early, online edition of the Proceedings of the National Academy of Sciences, an international research group explains how it used a physics-based approach called random matrix theory to scrutinize clade B HIV sequences from the Los Alamos HIV sequence database. The search, which focused on finding co-evolving residues and regions in which multiple mutations might make HIV less capable of compensatory mutations for escaping host immunity, yielded several sectors of residues that appear potentially vulnerable to immune attack. Among them: a group of amino acids in the protein Gag that also tends to undergo immune attack in individuals who naturally have an elevated ability to withstand HIV infection.

"Targeting such regions with higher order evolutionary constraints provides a novel approach to immunogen design for a vaccine against HIV and other rapidly mutating viruses," Massachusetts Institute of Technology researcher Arup Chakraborty, who was co-corresponding author on the study, and co-authors wrote.

In the Genetics Society of America's new journal G3, researchers present improved, high quality genome sequences for three yeast species in the Saccharomyces genus, known as S. sensu stricto. The team filled in published Sanger sequence data on the S. bayanus var. uvarum, S. kudriavzevii, and S. mikatae genomes using paired-end Illumina GAII and GAIIx reads before annotating the genomes and comparing them with those of S. cerevisiae and S. paradoxus. In the process, they found almost 5,300 Saccharomyces orthologs, got new clues about species-specific changes to the yeast gene repertoire, and garnered insights into evolution within the genus.

"Providing a complete catalog of diversity among this group of species will allow us to quickly test which changes are responsible for which functions in the laboratory with a level of precision and efficiency not possible in other organisms," senior author Chris Todd Hittinger, a biochemistry and molecular genetics researcher at the University of Colorado, said in a statement.

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