Microarray Papers of Note Published December 2011
Journal: American Journal of Clinical Pathology. 2011 Dec;136(6):924-33.
Title: Clinical verification of the performance of the Pathwork Tissue of Origin Test: utility and limitations.
Authors: Dumur C, et al.
The authors aimed at verifying the analytic and clinical performance of Pathwork Diagnostics' Tissue of Origin Test on 43 poorly differentiated and undifferentiated tumor samples, including six off-panel cases and seven cancers of unknown primary. Their results showed 97 percent agreement between the Pathwork TOO Test result and the complete diagnosis, which included clinical correlations and immunohistochemical staining, after the original diagnosis. They concluded that for off-panel and CUP samples, the tissue type and the cell type may be confounded by the Pathwork TOO Test and argued that careful clinicopathologic assessment is needed when interpreting results from the test.
Journal: American Journal of Human Genetics. 2011 Dec 9;89(6):751-9.
Title: Genome-wide association of copy-number variation reveals an association between short stature and the presence of low-frequency genomic deletions.
Authors: Dauber A, et al.
The authors performed a genome-wide association study of copy-number variation and stature in a clinical cohort of children who had undergone comparative genomic hybridization microarray analysis for clinical indications. They found that subjects with short stature had a greater global burden of copy-number variants and a greater average CNV length than did controls. The authors suggest that in individuals undergoing copy-number analysis for clinical indications, short stature increases the odds that a low-frequency deletion will be found.
Journal: Developmental Biology. 2011 Dec 15;360(2):415-25.
Title: Integrated microarray and ChIP analysis identifies multiple Foxα2 dependent target genes in the notochord.
Authors: Tamplin O, et al.
The authors performed an extensive microarray-based gene expression screen using sorted embryonic notochord cells to identify early notochord-enriched genes. They validated their specificity to the node and notochord by whole mount in situ hybridization. Using existing Foxα2 ChIP-seq data from adult liver, they were able to identify a set of genes expressed in the notochord that had associated regions of Foxα2-bound chromatin. Candidate Foxα2-bound regions were tested for notochord-specific enhancer function in a zebrafish reporter assay and seven novel notochord enhancers were identified.
Journal: Gastroenterology. 2011 Dec 24. [Epub ahead of print]
Title: Integrative genomic identification of genes on 8p associated with hepatocellular carcinoma progression and patient survival.
Authors: Roessler S, et al.
The authors combined data from high-resolution, array-based comparative genomic hybridization and transcriptome analysis of hepatocellular carcinoma samples from 76 patients with hepatitis B virus infection with data on patient survival times. Candidate genes were functionally validated using in vitro and in vivo models. The authors ultimately identified 10 genes associated with HCC progression that might be used in assisting diagnosis and to stage tumors based on gene expression patterns.
Journal: Genes, Chromsomes and Cancer.
Title: CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material.
Authors: Krijgsman O, et al.
The authors compared commercially available array CGH platforms suitable for high-resolution copy number analysis using formalin-fixed, paraffin-embedded-derived DNA. Two dual-channel aCGH platforms, Agilent and Roche NimbleGen, and a single channel SNP-based platform, Affymetrix, were evaluated using seven FFPE colon cancer samples, and median absolute deviation, deflection, signal-to-noise ratio, and DNA input requirements were used as quality criteria. Large differences were observed between platforms: Agilent and NimbleGen showed better MAD values compared with Affymetrix, while Affymetrix showed a better deflection. This resulted in signal-to-nose ratios that were comparable between the three commercially available platforms.
Journal: Human Mutation.
Title: SgD-CNV, a database for common and rare copy number variants in three Asian populations.
Authors: Xu H, et al.
The authors performed an in-depth investigation of common and rare CNVs across 8,148 individuals from the three major Asian ethnic groups: Chinese, Malays, and Indians in Singapore. They detected about 16 CNVs per individual. The majority of the CNVs were of low frequency, and 40 percent were rare. In each population, about 20 percent of the CNVs were not previously catalogued in the Database of Genomic Variants. They also reported that the common CNVs found in the three Asian populations are "not well tagged" by SNPs in the Illumina 1M and 610K BeadChips, and noted that most disease-associated common CNVs previously reported in Europeans were rare in the studied populations.
Journal: Journal of Clinical Oncology. 2011 Dec 10;29(35):4620-6.
Title: Development and independent validation of a prognostic assay for stage II colon cancer using formalin-fixed paraffin-embedded tissue.
Authors: Kennedy R, et al.
The authors used arrays to develop a gene signature from a balanced set of 73 patients with recurrent disease and 142 patients with no recurrence within five years of surgery. The 634-probe set signature identified high-risk patients with a hazard ratio of 2.62 during cross validation of the training set. In an independent validation set of 144 samples, the signature identified high-risk patients with an HR of 2.53 for recurrence and an HR of 2.21 for cancer-related death.
BioArray News spoke with the authors about their work in November (BAN 11/15/2011).
Journal: Journal of Dairy Science. 2011 Dec;94(12):6153-61.
Title: Harmful recessive effects on fertility detected by absence of homozygous haplotypes.
Authors: Vanraden P, et al.
Genotypes from the Illumina BovineSNP50 BeadChip were examined for 58,453 Holsteins, 5,288 Jerseys, and 1,991 Brown Swiss with genotypes in the North American database. Haplotypes with a length of less than 75 markers were obtained and 11 candidate haplotypes were identified. The authors argue that haplotype tests can help breeders avoid carrier mating for certain defects and reduce future frequencies.
Journal: Journal of Human Genetics. 2011 Dec 1. [Epub ahead of print]
Title: Regions of homozygosity in three Southeast Asian populations.
Authors: Teo S, et al.
The authors aimed to identify and investigate the characteristics of regions of homozygosity in three Singapore populations. A total of 268 samples were genotyped on Illumina Human 1 M Beadchip and Affymetrix Genome-Wide Human SNP Array 6.0. They reported an abundance of ROHs with an average of more than one hundred regions per individual.
Journal: Nature Genetics. 2011 Dec 11;44(1):62-6.
Title: Genome-wide association study identifies five loci associated with susceptibility to pancreatic cancer in Chinese populations.
Authors: Wu C, et al.
The authors carried out a genome-wide association study on 981 individuals with pancreatic cancer and 1,991 cancer-free controls of Chinese descent using arrays containing 666,141 autosomal SNPs. Promising associations were replicated in an additional 2,603 pancreatic cancer cases and 2,877 controls recruited from 25 hospitals in 16 provinces or cities in China. The authors identified five new susceptibility loci.
Journal: Neuron. 2011 Dec 22;72(6):951-63.
Title: High frequencies of de novo CNVs in bipolar disorder and schizophrenia.
Authors: Malhotra D, et al.
The researchers used Roche NimbleGen HD2 arrays to look at the prevalence of de novo copy number changes in the genomes of 185 individuals with bipolar disorder and their parents, another 177 parent-child trios in which the child was diagnosed with schizophrenia, and 426 unaffected control trios. They found that rare CNVs occur more often in individuals with bipolar disorder than in those without. That pattern was particularly pronounced in individuals who developed bipolar disease before turning 18 years old.
Journal: Plastic and Reconstructive Surgery. 2011 Dec 16. [Epub ahead of print]
Title: DNA copy number variations at chromosome 7p14.1 and chromosome 14q11.2 are associated with Dupuytren's disease: potential role for MMP and Wnt signaling pathway.
Authors: Shih B, et al.
Array-based comparative genomic hybridization was used to survey samples from patients with Dupuytren's disease. Five common CNVs, on chromosome 17q12, 1p31.1, 20p13, 7p14.1 and 14q11.2 were identified by aCGH. Significantly higher copy numbers of CNVs at chromosome 7p14.1 and 14q11.2 in DD were confirmed in qPCR validation.
Journal: PLoS Biology. 2011 Dec;9(12):e1001214.
Title: MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates.
Authors: Somel M, et al.
The authors used arrays to compare gene expression throughout postnatal brain development in humans, chimpanzees, and macaques. They found that simple changes in gene expression levels, plausibly driven by mutations in cis-regulatory elements, accumulate at similar rates in all three evolutionary lineages. What sharply distinguishes humans from other species is change in the timing and shape of developmental expression patterns, according to the authors, particularly in the prefrontal cortex, where four-fold more genes showed more human-specific developmental changes than chimpanzee-specific ones. The authors argued that this massive developmental remodeling of the human cortex, which affects hundreds of genes, might be driven by expression changes of only a few key regulators, such as microRNAs.
Journal: PLoS One. 2011;6(12):e27894.
Title: Mutation screening of multiple genes in Spanish patients with autosomal recessive retinitis pigmentosa by targeted resequencing.
Authors: González-del Pozo M, et al.
The goal of this study was to develop and apply microarray-based resequencing technology capable of detecting both known and novel mutations associated with retinitis pigmentosa on a single high-throughput platform. The coding regions and exon/intron boundaries of 16 arRP genes were resequenced using microarrays in 102 Spanish patients with clinical diagnosis of autosomal recessive RP. All of the detected variations were confirmed by direct sequencing and potential pathogenicity was assessed by functional predictions and frequency in controls.
Journal: PLoS One. 2011;6(12):e28561.
Title: Copy number variation analysis of matched ovarian primary tumors and peritoneal metastasis.
Authors: Malek J, et al.
The authors used high-density SNP arrays to investigate copy number variations in matched primary and metastatic ovarian cancer from nine patients. They found that copy number variations acquired by ovarian tumors are significantly different between matched primary and metastatic tumors and these are likely due to different functional requirements. They also showed that these copy number variations clearly differentially affect specific pathways including the JAK/STAT and cytokine signaling pathways.