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In Print: Last Week's Papers of Note


Incidental copy-number variants identified by routine genome testing in a clinical population.

Genet Med. 2013 Jan;15(1):45-54.

Boone P, Soens Z, Campbell I, et al.

Mutational load of susceptibility variants has not been studied on a genomic scale in a clinical population, nor has the potential to identify these mutations as incidental findings during clinical testing been systematically ascertained, according to the authors. Array comparative genomic hybridization was performed clinically on DNA from 9,005 individuals. Copy-number variants encompassing or disrupting single genes were identified and analyzed for their potential to confer predisposition to dominant, adult-onset disease. They concluded that while copy-number variants potentially conferring susceptibility to adult-onset disease can be identified as incidental findings during routine genome-wide testing, and some of these mutations may be medically actionable, enabling disease surveillance or prevention, most incidentally observed single-gene copy-number variants are currently of unclear significance to the patient.

Molecular characteristics of a pancreatic adenocarcinoma associated with Shwachman-Diamond syndrome.

Pediatr Blood Cancer. 2013 Jan 9. [Epub ahead of print]

Dhanraj S, Manji A, Pinto D, et al.

Shwachman-Diamond syndrome is characterized by hypoplasia of the bone marrow and exocrine pancreas and a high risk of leukemia. According to the authors, it is unknown whether solid tumors are part of the disease phenotype. They analyzed copy number alterations using Affymetrix Human SNP 6.0 arrays and did direct sequencing of pancreatic cancer-related genes and immunohistochemical expression of selective proteins. Among the 41 patients with SDS who enrolled, the authors identified one male patient with a solid tumor, raising the possibility that solid tumors are associated with SDS and broadening the clinical phenotype of the disease.

Increased paternal age and the influence on burden of genomic copy number variation in the general population.

Hum Genet. 2013 Jan 13. [Epub ahead of print]

Buizer-Voskamp J, Blauw H, Boks M, et al.

The authors aimed to address the question of whether paternal age affects the burden of structural genomic deletions and duplications. They examined various types of copy number variation burden in a large population sample from the Netherlands. Healthy participants with parental age information were collected at different university medical centers and CNVs were called with the PennCNV algorithm using Illumina genome-wide SNP array data. They observed no evidence in support of a paternal age effect on CNV load in the offspring, and concluded that while recent studies suggest the de novo single nucleotide mutation rate to be dominated by the age of the father at conception, their results suggest that at the level of global CNV burden there is no influence of increased paternal age.

Contribution of domestic production records, Interbull estimated breeding values, and single nucleotide polymorphism genetic markers to the single-step genomic evaluation of milk production.

J Dairy Sci. 2013 Jan 9. [Epub ahead of print]

Přibyl J, Madsen P, Bauer J, et al.

Estimated breeding values for first-lactation milk production of Holstein cattle in the Czech Republic were calculated using a conventional animal model and by single-step prediction of the genomic enhanced breeding value. According to the authors, two overlapping data sets of milk production data were evaluated, global Interbull deregressed proofs were used in the analyses, and a total of 1,341 bulls were genotyped using the Illumina BovineSNP50 BeadChip. Based on the results of their analyses, they concluded that a combination of domestic and Interbull sources for both genotyped and nongenotyped animals is valuable for improving the accuracy of genetic prediction in small populations of dairy cattle.