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In Print: Last Week's Microarray Papers of Note: Jun 4, 2013

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DNA methylation profiling of placental villi from karyotypically normal miscarriage and recurrent miscarriage.
Am J Pathol. 2013 Jun;182(6):2276-84.
Hanna C, McFadden D, Robinson W

Hypothesizing that aberrant DNA methylation may cause karyotypically normal miscarriage, the authors assessed DNA methylation in first-trimester chorionic villi in chromosomally normal miscarriages from women with recurrent miscarriage, isolated miscarriageand elective terminations using the Illumina Infinium HumanMethylation27 BeadChip array. They determined that altered DNA methylation in the placenta at specific loci, and global dysregulation in specific cases, may contribute to or be a consequence of poor placental function in karyotypically normal miscarriage.


Functional performance of aCGH design for clinical cytogenetics.
Comput Biol Med. 2013 Jul 1;43(6):775-85.
Gambin T, Stankiewicz P, Sykulski M, et al.

The authors of this paper propose a new approach to measure the quality of array CGH designs that measures the robustness of rearrangements detection to the noise. To accomplish this, they implemented the Monte Carlo method for testing noise robustness within DNAcopy software analysis procedure. This framework has been used to assess the functional quality of several array designs.


Gene copy number variations in breast cancer of Sub-Saharan African women.
Breast. 2013 Jun;22(3):295-300.
Ly M, Valent A, Diallo G, et al.

The authors carried out array comparative genomic hybridization profiling of breast cancer samples from Malian women and compared them with samples from American women. Six chromosomal regions were identified with a significant higher rate of copy number alterations. They concluded that breast cancers from African women contain biological differences with those occurring in the US.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.