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In Print: Last Week's Microarray Papers of Note: Mar 5, 2013


Comparison of whole-genome DNA methylation patterns in whole blood, saliva, and lymphoblastoid cell lines.
Behav Genet. 2013 Mar;43(2):168-76.
Thompson T, Sharfi D, Lee M, et al.

The authors performed comparative analyses of methylation patterns in whole blood, saliva, and lymphoblastoid cell lines derived from the same individuals, using Illumina HumanMethylation27 BeadChip arrays. The results showed that DNA methylation patterns in SL are relatively consistent with those in WB, whereas the patterns in LCLs are similarly distinct from both WB and SL. The results also indicated that due to multiple random and directed changes in DNA methylation throughout cell culturing, LCLs are not a reliable source of DNA for epigenetic studies and should be used with caution when investigating epigenetic mechanisms underlying biological processes.

Detection of copy-number variation in AUTS2 gene by targeted exonic array CGH in patients with developmental delay and autistic spectrum disorders.
Eur J Hum Genet. 2013 Mar;21(3):343-6.
Nagamani S, Erez A, Ben-Zeev B, et al.

The authors report four patients with small CNVs ranging in size between 133 and 319 kilobases that disrupt the autism susceptibility candidate 2, or AUTS2, gene. The CNVs were detected by an exon-targeted array CGH with dense oligonucleotide coverage in exons of genes known or hypothesized to be causative of multiple human phenotypes. The authors also show that disruption of AUTS2 results in a variety of neurobehavioral phenotypes, and describe the targeted exon array as a "highly sensitive clinical diagnostic tool for the detection of small genomic rearrangements in the clinically relevant regions of the human genome."

Modified array-based comparative genomic hybridization detects cryptic and variant PML-RARA rearrangements in Acute Promyelocytic Leukemia lacking classic translocations.
Diagn Mol Pathol. 2013 Mar;22(1):10-21.
Gruver AM, Rogers H, Cook J, et al.

The authors describe the detection of cryptic or variant promyelocytic leukemia-retinoic acid receptor α genes rearrangements by translocation-based comparative genomic hybridization, a modification of traditional CGH technology that facilitates the detection of balanced translocations by means of the linear amplification of a potential translocation breakpoint region, in two unusual cases of APL. One tumor lacked detectable t(15;17) by karyotype and FISH, and the other tumor lacked the typical morphologic and immunophenotypic features of APL and had a variant 3-way translocation involving PML and RARA. PML-RARA translocations were identified by tCGH in both cases providing confirmation of the diagnosis of APL.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.