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In Print: Last Week's Microarray Papers of Note: Jan 29, 2013


Imputation across genotyping arrays for genome-wide association studies: assessment of bias and a correction strategy.
Hum Genet. 2013 Jan 22. [Epub ahead of print]
Johnson E, Hancock D, Levy J, et al.

Based on the idea that using differing genotyped SNP sets as inputs creates differential imputation errors and bias in the composite set of controls, the authors examined the degree to which imputation based on the union of genotyped SNPs results in bias, imputation based on the intersection of genotyped SNPs does not evidence such bias, and imputation quality varies by the size of the intersection of genotyped SNP sets.

DNA repair gene variants are associated with an increased risk of myelodysplastic syndromes in a Czech population.
J Hematol Oncol. 2013 Jan 22;6:9.
Belickova M, Merkerova M, Stara E, et al.

The authors used Illumina's SNP Cancer Panel to study the interactions between genetic variants and risk factors in myelodysplastic syndromes. They analyzed 1,421 SNPs in 408 genes involved in cancer-related pathways in 198 patients and 292 controls and identified genetic variants in the Czech population that they believe may serve as potential markers for myelodysplastic syndromes.

Use of the canonical discriminant analysis to select SNP markers for bovine breed assignment and traceability purposes.
Anim Genet. 2013 Jan 24. [Epub ahead of print]
Dimauro C, Cellesi M, Steri R, , et al.

In this study, a new method to discriminate among different bovine breeds and assign new individuals to groups was developed. Bulls of three cattle breeds farmed in Italy — Holstein, Brown, and Simmental — were genotyped using the 50K SNP Illumina BeadChip. The authors narrowed in on a set of 48 high discriminant SNPs that they claim can be used to routinely track monobreed products.

Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners.
Mol Ecol Resour. 2013 Jan 25. [Epub ahead of print]
Pavy N, Gagnon F, Rigault P, et al.

This paper details the design of two high-density Illumina Infinium iSelect SNP arrays for use in studying the conifer white spruce (Picea glauca). One array contains 7,338 segregating SNPs representative of 2,814 genes of various molecular functional classes and is intended for use in genetic association and population genetics studies. The other contains 9,559 segregating SNPs representative of 9,543 genes, and is intended for use in population genetics, linkage mapping of the genome and genomic prediction.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.