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In Print: Last Week's Microarray Papers of Note: Dec 11, 2012


Chromosomal microarray versus karyotyping for prenatal diagnosis.
N Engl J Med. 2012; 367:2175-2184
Wapner R, Martin C, Levy B, et al.

This study aimed to compare the amount of clinically relevant information that could be obtained from arrays versus karyotyping. Using arrays manufactured by Affymetrix and Agilent Technologies as well as karyotyping, the authors conducted a blinded trial of 4,400 patients at 29 centers across the US over a four-year period. Among fetuses in which a growth or structural anomaly had been detected with ultrasound, microarrays were able to detect clinically relevant chromosomal deletions or duplications in 6 percent of cases, changes that were not observed with karyotyping the same samples. And in cases sampled for advanced maternal age or positive screening results, array analysis identified an abnormality in one out of every 60 pregnancies, about 1.7 percent of all cases that had a normal karyotype (see related story, this issue).

Karyotype versus microarray testing for genetic abnormalities after stillbirth.
N Engl J Med. 2012; 367:2185-2193
Reddy U, Page G, Saade G, et al.

This study assessed the ability of chromsomal microarrays and karyotyping to detect clinically relevant results in stillbirth cases. The authors used karyotyping and Affymetrix SNP 6.0 arrays to survey CNVs of at least 500 kilobases in placental or fetal tissue in 532 cases and then compared the results. They found that arrays provided results 87 percent of the time, versus karyotyping, which yielded results 71 percent of the time. As compared with karyotype analysis, microarray analysis provided a relative increase in the diagnosis of genetic abnormalities of 42 percent in all stillbirths, 35 percent in antepartum stillbirths, and 54 percent in stillbirths with anomalies (see related story, this issue).

In vivo differentiated human embryonic stem cells can acquire chromosomal aberrations more frequently than in vitro during the same period.
Stem Cells Dev. 2012 Dec 10;21(18):3363-71.
Zucchelli M, Ström S, Holm F, et al.

The authors performed a comparative in vitro and in vivo study on three human embryonic stem cell lines to monitor changes during in vivo growth. In vivo differentiated cells and in vitro cultured hESCs were analyzed using a high-resolution Affymetrix SNP 6.0 array revealing DNA copy number variations. Based on the array results, the authors reported that, for the first time, they were able to identify chromosomal aberrations that had occurred in vivo in one out of the three hESC lines.

Prediction of breed composition in an admixed cattle population.
Anim Genet. 2012 Dec;43(6):696-703.
Frkonja A, Gredler B, Schnyder U, et al.

The authors used the Illumina BovineSNP50 Genotyping BeadChip to better understand the breed composition of Swiss Fleckvieh, a composite of the Simmental and Red Holstein Friesian breeds. They also compared the performance of hidden Markov models with methods conventionally used in genomic selection for predicting breed composition.

Chromosomal microarray analysis as a first-line test in pregnancies with a priori low risk for the detection of submicroscopic chromosomal abnormalities.
Eur J Hum Genet. 2012 Dec 5. [Epub ahead of print]
Fiorentino F, Napoletano S, Caiazzo F, et al.

The authors aimed to explore the use of chromosomal microarray analysis in groups of pregnancies with a priori low risk for detection of submicroscopic chromosome abnormalities, usually not considered an indication for testing, in order to assess whether CMA improves the detection rate of prenatal chromosomal aberrations. A total of 3,000 prenatal samples were processed in parallel using both whole-genome CMA and conventional karyotyping. The use of CMA resulted in an increased detection rate regardless of the indication for analysis, according to the authors.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.