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In Print: Last Week's Microarray Papers of Note: Jan 28, 2014


Coverage and efficiency in current SNP chips.
Eur J Hum Genet. 2014 Jan 22. doi: 10.1038/ejhg.2013.304. [Epub ahead of print]
Ha NT, et al.

To answer the question as to which commercial high-density SNP chip covers most of the human genome given a fixed budget, the authors compared the performance of 12 chips of different sizes released by Affymetrix and Illumina for the European, Asian, and African populations. They identified the Affymetrix population-optimized arrays as offering the most cost-effective coverage for Asian and African populations. For European populations, they established the Illumina HumanOmni2.5-8 BeadChip as the preferred choice. Coverage estimates calculated for all chips proved much lower than those advertised by the vendors.

Chromosomal microarray analysis allows prenatal detection of low-level mosaic autosomal aneuploidy.
Prenat Diagn. 2014 Jan 26. [Epub ahead of print]
Hall G, et al.

The authors found chromosomal microarray analysis to be effective in detecting low-level mosaic autosomal aneuploidy in a prenatal setting which traditional methods may fail to detect. They argue that this detection of low-level mosaicism supports the use of chromosomal microarray analysis in prenatal diagnosis.

Who are the Okinawans? Ancestry, genome diversity, and implications for the genetic study of human longevity from a geographically isolated population..
J Gerontol A Biol Sci Med Sci. 2014 Jan 20. [Epub ahead of print]
Bendjilali N, et al.

The authors used Affymetrix SNP chips to assess Okinawans, a population isolate, recognized for longevity. Okinawans clustered almost exclusively with East Asians, they found. Following a sibling relative risk analysis, they also determined that siblings of Okinawan centenarians have 3.11 times (females) and 3.77 times (males) more likelihood of centenarianism.

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.