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This Week in Genome Biology: Nov 30, 2016

Researchers from the Murdoch Childrens Research Institute, the University of Melbourne, and elsewhere explore genetic factors associated with disorders of sex development (DSD) with targeted sequencing on hundreds of individuals with atypical chromosomal, gonadal, or phenotypic sex features. Based on sequences for more than 1,000 known of candidate genes in 278 XY individuals with DSD, four dozen XX individuals with DSD, and some of their family members, the team identified 28 genes associated with DSD, along with almost 100 variants not implicated in the conditions previously. The work "provided us with a better understanding of the underlying genetic etiology of this condition," authors say, noting that the their analysis "expanded the range of phenotypes associated with several DSD genes."

An international team led by investigators in Saudi Arabia present new candidate genes for primary cilium disorders, a broad group of conditions that are together known as ciliopathies. Using array-based genotyping, panel sequencing, and/or exome sequencing, the researchers assessed 371 ciliopathy-affected individuals from 265 families, uncovering potential causal mutations. Some 85 percent of the families tested had mutations in known ciliopathy genes, for example, including almost three-dozen alleles not implicated in the conditions in the past. The analysis also led to a new ciliopathy gene and seven more candidate genes, while shoring up a Mendelian inheritance model for ciliopathies.

Finally, investigators from Memorial Sloan Kettering report on findings from an expression-based analysis of immune cell microenvironment and T cell infiltration in 19 cancer types, including clear cell renal cell carcinoma (ccRCC). Based on expression patterns in almost 7,600 tumor samples and more than 600 normal samples assessed for the Cancer Genome Atlas Project, the team attempted to tease apart tumor infiltration by various immune cell types. In the ccRCC, for example, it identified three tumor subsets with distinct immune infiltration and T cell enrichment patterns, including groups of tumors that appeared to coincide with better or worse survival outcomes.