Evidence-based genomic diagnosis characterized chromosomal and cryptic imbalances in 30 elderly patients with myelodysplastic syndrome and acute myeloid leukemia.

BACKGROUND: To evaluate the clinical validity of genome-wide oligonucleotide array comparative genomic hybridization (aCGH) for detecting somatic abnormalities, we have applied this genomic analysis to 30 cases (13 MDS and 17 AML) with clonal chromosomal abnormalities detected in more than 50% of analyzed metaphase cells. RESULTS: The aCGH detected all numerical chromosomal gains and losses from the mainline clones and 113 copy number alterations (CNAs) ranging from 0.257 to 102.519 megabases (Mb). Clinically significant recurrent deletions of 5q (involving the RPS14 gene), 12p12.3 (ETV6 gene), 17p13 (TP53 gene), 17q11.2 (NF1 gene) and 20q, double minutes containing the MYC gene and segmental amplification involving the MLL gene were further characterized with defined breakpoints and gene contents. Genomic features of microdeletions at 17q11.2 were confirmed by FISH using targeted BAC clones. The aCGH also defined break points in a derivative chromosome 6, der(6)t(3;6)(q21.3;p22.2), and an isodicentric X chromosome. However, chromosomally observed sideline clonal abnormalities in five cases were not detected by aCGH. CONCLUSIONS: Our data indicated that an integrated cytogenomic analysis will be a better diagnostic scheme to delineate genomic contents of chromosomal and cryptic abnormalities in patients with MDS and AML. An evidence-based approach to interpret somatic genomic findings was proposed

Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays

BACKGROUND: Gene expression profiling using microarrays has become an important genetic tool. Spotted arrays prepared in academic labs have the advantage of low cost and high design and content flexibility, but are often limited by their susceptibility to quality control (QC) issues. Previously, we have reported a novel 3-color microarray technology that enabled array fabrication QC. In this report we further investigated its advantage in spot-level data QC. RESULTS: We found that inadequate amount of bound probes available for hybridization led to significant, gene-specific compression in ratio measurements, increased data variability, and printing pin dependent heterogeneities. The impact of such problems can be captured through the definition of quality scores, and efficiently controlled through quality-dependent filtering and normalization. We compared gene expression measurements derived using our data processing pipeline with the known input ratios of spiked in control clones, and with the measurements by quantitative real time RT-PCR. In each case, highly linear relationships (R(2)>0.94) were observed, with modest compression in the microarray measurements (correction factor<1.17). CONCLUSION: Our microarray analytical and technical advancements enabled a better dissection of the sources of data variability and hence a more efficient QC. With that highly accurate gene expression measurements can be achieved using the cDNA microarray technology

Case report: Rare novel MIPEP compound heterozygous variants presenting with hypertrophic cardiomyopathy, severe lactic acidosis and hypotonia in a Chinese infant

BackgroundMitochondrial intermediate peptidase, encoded by the MIPEP gene, is involved in the processing of precursor mitochondrial proteins related to oxidative phosphorylation. Only a few studies have shown that mutations in MIPEP can cause combined oxidative phosphorylation deficiency-31 (COXPD31), an autosomal recessive multisystem disorder associated with mitochondrial dysfunction. We report herein a rare case of an 8-month-old boy in China with hypertrophic cardiomyopathy (HCM), severe lactic acidosis, and hypotonia caused by novel MIPEP compound heterozygous variants.MethodsTrio-whole-exome sequencing and copy number variation sequencing were performed to identify mutated genetic loci. Sanger sequencing and quantitative real-time PCR were used to validate the candidate single nucleotide variants and copy number variants, respectively.ResultsThe proband was an 8-month-old boy with HCM, severe lactic acidosis, and hypotonia who died 2 months after his first admission. Two novel compound heterozygous variants, c.1081T &gt; A (p. Tyr361Asn) and a whole deletion (Ex1-19 del), were found in the MIPEP gene, which were inherited from his healthy parents respectively. Additionally, his mitochondria DNA copy number was significantly reduced.ConclusionWe are the first to report a patient with rare MIPEP variants in China. Our findings expand the mutation spectrum of MIPEP, and provide insights into the genotype-phenotype relationship in COXPD31

Identification and Functional Clustering of Global Expression Differences Between Primary Thyroid Cancer and Lung Metastasis

A cDNA-microarray experiment was performed to study thyroid cancer metastasis. Follicular thyroid carcinoma cell lines from the primary (FTC-133) and lung metastasis (FTC-238) of the same patient were compared using a 19200 human cDNA micro array. Hybridizations were repeated with 3 separate cell passages, 3 repeats for each passage. Data were extracted and normalized for dye bias using commercial and house-developed software. Differential expression was determined by reference distribution method. Seven hundred seventy five genes and expressed sequence tags (ESTs) were identified as significantly over (393) /under (382) expressed (t test p \u3c 0.05) with respect to metastatic vs. primary thyroid carcinoma. Using both software and manual expert annotation with a threshold of log2 ratio IEijl \u3e2, 13119 over and 13/35 under expressed genes were associated with oncogenesis and/or metastatic processes. Six of the over expressed genes and four of the under expressed genes were further confirmed by realtime PCR. Western Blotting revealed protein over expression in 3 of3 genes tested. Several biological functional groups associated with the biological process (e.g. cell adhesion, cell migration, cell proliferation, apoptosis) of cancer metastasis were found to be affected. This study shows the feasibility of using high-throughput technologies for identifying genes and functional groups leading to metastatic follicular thyroid cancer. Further investigation is required to understand the precise relationship between the altered expression of these genes and the metastasis process of follicular thyroid cancer

Double-minute MYC amplification and deletion of MTAP, CDKN2A, CDKN2B, and ELAVL2 in an acute myeloid leukemia characterized by oligonucleotide-array comparative genomic hybridization.

Chromosomal analysis and fluorescence in situ hybridization (FISH) have been routinely used in detecting recurrent chromosomal abnormalities in patients with various hematological malignancies. However, the genomic imbalances underlying many recurrent abnormalities could not be delineated due to the low resolution of chromosome analysis. We have performed oligonucleotide-array comparative genomic hybridization (oaCGH) in an AML case with a 15p/17p translocation, a suspected 9p21 deletion, monosomies of chromosomes X and 9, and 2 to 60 double minutes. The oaCGH findings confirmed the chromosomal observations and further characterized a 21.338-Mb 17p deletion, a 3.916-Mb deletion at 9p21.3 containing the MTAP, CDKN2A, CDKN2B, and ELAVL2 genes, and a 3.981-Mb 8q24 double minute containing the TRIB1, FAM84B, MYC, and PVT1 genes, with an average of 30 double minutes in each cell. FISH using MYC probes and bacterial artificial chromosome clone probes confirmed the genomic findings and revealed a progressional pattern for the 9p21.3 deletion. These results demonstrate the potential of oaCGH as a powerful diagnostic tool for characterizing genomic imbalances for patients with hematological malignancies

Rapid Electrodeposition of Fe–Ni Alloy Foils from Chloride Baths Containing Trivalent Iron Ions

This work presents the rapid electrodeposition of Fe&ndash;Ni alloy foils from chloride baths containing trivalent iron ions at a low pH (&lt;0.0). The effect of the concentration of Ni2+ ions on the content, surface morphology, crystal structure, and tensile property of Fe&ndash;Ni alloys is studied in detail. The results show that the co-deposition of Fe and Ni is controlled by the adsorption of divalent nickel species at low current density and the ionic diffusion at high current density. The current density of preparing smooth and flexible Fe&ndash;Ni alloy foils is increased by increasing the concentration of Ni2+ ions, consequently the deposition rate of Fe&ndash;Ni alloy foils is increased. For example, at 0.6 M Ni2+ ions, the current density can be applied at 50 A&middot;dm&minus;2, along with a high deposition rate of ~288 &mu;m&middot;h&minus;1

Evidence-based genomic diagnosis characterized chromosomal and cryptic imbalances in 30 elderly patients with myelodysplastic syndrome and acute myeloid leukemia.

BACKGROUND: To evaluate the clinical validity of genome-wide oligonucleotide array comparative genomic hybridization (aCGH) for detecting somatic abnormalities, we have applied this genomic analysis to 30 cases (13 MDS and 17 AML) with clonal chromosomal abnormalities detected in more than 50% of analyzed metaphase cells. RESULTS: The aCGH detected all numerical chromosomal gains and losses from the mainline clones and 113 copy number alterations (CNAs) ranging from 0.257 to 102.519 megabases (Mb). Clinically significant recurrent deletions of 5q (involving the RPS14 gene), 12p12.3 (ETV6 gene), 17p13 (TP53 gene), 17q11.2 (NF1 gene) and 20q, double minutes containing the MYC gene and segmental amplification involving the MLL gene were further characterized with defined breakpoints and gene contents. Genomic features of microdeletions at 17q11.2 were confirmed by FISH using targeted BAC clones. The aCGH also defined break points in a derivative chromosome 6, der(6)t(3;6)(q21.3;p22.2), and an isodicentric X chromosome. However, chromosomally observed sideline clonal abnormalities in five cases were not detected by aCGH. CONCLUSIONS: Our data indicated that an integrated cytogenomic analysis will be a better diagnostic scheme to delineate genomic contents of chromosomal and cryptic abnormalities in patients with MDS and AML. An evidence-based approach to interpret somatic genomic findings was proposed

Interacting elevated CO \u3c inf\u3e 2 and tropospheric O \u3c inf\u3e 3 predisposes aspen (Populus tremuloides Michx.) to infection by rust (Melampsora medusae f. sp. tremuloidae)

We investigated the interaction of elevated CO2 and/or (Ozone) O3 on the occurrence and severity of aspen leaf rust (Melampsora medusae Thuem. f. sp. tremuloidae) on trembling aspen (Populus tremuloides Michx.), Furthermore, we examined the role of changes in leaf surface properties induced by elevated CO2 and/or O3 in this host-pathogen interaction. Three- to five-fold increases in levels of rust infection index were found in 2 consecutive years following growing-season-long exposures with either O3 alone or CO2 + O3 depending on aspen clone. Examination of leaf surface properties (wax appearance, wax amount, wax chemical composition, leaf surface and wettability) suggested significant effects by O3 and CO2 + O3. We conclude that elevated O3 is altering aspen leaf surfaces in such a way that it is likely predisposing the plants to increased infection by aspen leaf rust