DNA Copy Number Changes in Thyroid Carcinoma

The genetic changes leading to thyroid cancer are poorly characterized. We studied DNA copy number changes by comparative genomic hybridization (CGH) in 69 primary thyroid carcinomas. In papillary carcinoma, DNA copy number changes were rare (3 of 26, 12%). The changes were all gains, and they were associated with old age (P = 0.01) and the presence of cervical lymph node metastases at presentation (P = 0.08). DNA copy number changes were much more frequent in follicular carcinoma (16 of 20, 80%) than in papillary carcinoma (P < 0.0001), and follicular carcinomas had more often deletions (13/20 versus 0/26, P < 0.0001). Loss of chromosome 22 was common in follicular carcinoma (n = 7, 35%), it was more often seen in widely invasive than in minimally invasive follicular carcinoma (54% versus 0%, P = 0.04), and it was associated with old age at presentation (P = 0.01). In three of the four patients with follicular carcinoma who died of cancer, the tumor had loss of chromosome 22. DNA copy number changes were found in 5 (50%) of the 10 medullary carcinomas studied. Four of these five carcinomas had deletions, and in two of them there was deletion of chromosome 22. Eleven (85%) of the thirteen anaplastic carcinomas investigated had DNA copy number changes, of which five had deletions, and one had deletion of chromosome 22. The most common gains in anaplastic carcinoma were in chromosomes 7p (p22-pter, 31%), 8q (q22-qter, 23%), and 9q (q34-qter, 23%). We conclude that DNA copy number changes are frequent in follicular, medullary, and anaplastic thyroid carcinoma but rare in papillary carcinoma when studied by CGH. Loss of chromosome 22 is particularly common in follicular carcinoma, and it is associated with the widely invasive type.     

DNA Copy Number Losses in Human Neoplasms

This review summarizes reports of recurrent DNA sequence copy number losses in human neoplasms detected by comparative genomic hybridization. Recurrent losses that affect each of the chromosome arms in 73 tumor types are tabulated from 169 reports. The tables are available online at http://www.amjpathol.org and http://www. helsinki.fi/ approximately lglvwww/CMG.html. The genes relevant to the lost regions are discussed for each of the chromosomes. The review is supplemented also by a list of known and putative tumor suppressor genes and DNA repair genes (see Table 1, online). Losses are found in all chromosome arms, but they seem to be relatively rare at 1q, 2p, 3q, 5p, 6p, 7p, 7q, 8q, 12p, and 20q. Losses and their minimal common overlapping areas that were present in a great proportion of the 73 tumor entities reported in Table 2 (see online) are (in descending order of frequency): 9p23-p24 (48%), 13q21 (47%), 6q16 (44%), 6q26-q27 (44%), 8p23 (37%), 18q22-q23 (37%), 17p12-p13 (34%), 1p36.1 (34%), 11q23 (33%), 1p22 (32%), 4q32-qter (31%), 14q22-q23 (25%), 10q23 (25%), 10q25-qter (25%),15q21 (23%), 16q22 (23%), 5q21 (23%), 3p12-p14 (22%), 22q12 (22%), Xp21 (21%), Xq21 (21%), and 10p12 (20%). The frequency of losses at chromosomes 7 and 20 was less than 10% in all tumors. The chromosomal regions in which the most frequent losses are found implicate locations of essential tumor suppressor genes and DNA repair genes that may be involved in the pathogenesis of several tumor types.     

Soft Copy versus Hard Copy Reading in Digital Mammography

The objective of this study was to compare soft copy reading at a mammography work station with hard copy reading of full-field digital mammographic images. Mammograms of 60 patients (n = 29 malignant, n = 31 benign) performed with full-field digital mammography (Senographe 2000D, GE, Buc, France) were evaluated. Reading was performed based on hard copy prints (Scopix, Agfa, Leverkusen, Germany) and on 2 k × 2.5 k high-resolution monitors (Sun Ultra 60, Sun Microsystems, Palo Alto, California, USA). Four readers with different levels of experience in mammography categorized the mammograms according to the BI-RADS classification. The comparative study was performed by four readers, and at least 2 months elapsed between the reading sessions. Postprocessing, of course, was available only at the work station (windowing and leveling, zooming, inversion). Sensitivity, specificity, and positive predictive value were evaluated. Diagnostic accuracy of the evaluation was determined. Sensitivity for malignant lesions in hard copy versus soft copy reading was 97% vs 90%, 97% vs 97%, 93% vs 97%, and 76% vs 76% for the four readers, respectively. Specificity was 52% vs 68%, 58% vs 74%, 65% vs 48%, and 61% vs 68%. Accuracy for the classification of malignant lesions according to the BI-RADS categories showed no difference between hard copy and soft copy reading. Soft copy reading is possible with the available system and enables radiologists to use the advantages of a digital system.     

Copy Number Variation in Tumor Cells and Extracellular DNA in Patients with Lung Adenocarcinoma

Bulletin of Experimental Biology and Medicine - Copy number variation of some gene loci in lung tumor cells extracted by laser capture microdissection and in cell-free DNA in the plasma of patients...     

拷贝数目变异研究进展

人类基因组中的DNA 拷贝数目变异Copy Number Variation（CNVs）一直以来都认为分布频率较低,并与疾病的发生以及不同个体对于疾病的易感性相关。随着Hapmap研究计划的顺利进行,研究者逐渐发现CNVs广泛分布于人基因组中。黑猩猩和实验室近交系的小鼠基因组也存在CNVs的广泛分布。目前已有多项研究证明了CNVs是人类基因组变异的主要原因,本综述将从CNVs的定义及其在健康人群的分布研究以及与疾病的相关性研究,CNVs的形成机制和CNVs的进化等方面对最新的CNVs研究进展做较为全面概述。     

Detection of Copy Number Variation by SNP-Allelotyping

Abstract

Charcot-Marie-Tooth disease type 1A (CMT1A) is caused by an abnormal copy number variation (CNV) with a trisomy of chromosome 17p12. The increase of the DNA-segment copy number is expected to alter the allele frequency of single nucleotide polymorphism (SNP) within the duplicated region. We tested whether SNP allele frequency determined by a Sequenom MassArray can be used to detect the CMT1A mutation. Our results revealed distinct patterns of SNP allele frequency distribution, which reliably differentiated CMT1A patients from controls. This finding suggests that this technique may serve as an alternative approach to identifying CNV in certain diseases, including CMT1A.     

Differences in Aggressive Behavior and DNA Copy Number Variants Between BALB/cJ and BALB/cByJ Substrains

Some BALB/c substrains exhibit different levels of aggression. We compared aggression levels between male BALB/cJ and BALB/cByJ substrains using the resident intruder paradigm. These substrains were also assessed in other tests of emotionality and information processing including the open field, forced swim, fear conditioning, and prepulse inhibition tests. We also evaluated single nucleotide polymorphisms (SNPs) previously reported between these BALB/c substrains. Finally, we compared BALB/cJ and BALB/cByJ mice for genomic deletions or duplications, collectively termed copy number variants (CNVs), to identify candidate genes that might underlie the observed behavioral differences. BALB/cJ mice showed substantially higher aggression levels than BALB/cByJ mice; however, only minor differences in other behaviors were observed. None of the previously reported SNPs were verified. Eleven CNV regions were identified between the two BALB/c substrains. Our findings identify a robust difference in aggressive behavior between BALB/cJ and BALB/cByJ substrains, which could be the result of the identified CNVs.     

Separation of Micronuclear DNA of Stylonychia lemnae by Pulsed-Field Electrophoresis and Identification of a DNA Molecule with a High Copy Number

DNA from the hypotrichous ciliatae Stylonychia lemnae was separated by PFGE. In addition to the separation of the macronuclear DNA molecules with a size up to approximately 40 kb, we were able to separate the micronuclear DNA with a size between approximately 90 kb and 2 Mb. One very prominent 90-kb DNA band appeared on the pulsed-field gels. We propose that this 90-kb DNA fragment represents a linear plasmid residing in the micronucleus in a very high copy number. About 10% of the micronuclear DNA consists of the 90-kb DNA molecule. It appears in the micronucleus as well as in the macronuclear anlagen during macronuclear development but not in the mature macronucleus. Thus, the multicopy DNA is eliminated during fragmentation of the macronuclear anlagen DNA in the course of macronuclear development. Therefore, this 90-kb DNA molecule might serve as an excellent tool to study the recognition and elimination of DNA during nuclear differentiation of hypotrichous ciliates.     

Robust Detection of EGFR Copy Number Changes and EGFR Variant III: Technical Aspects and Relevance for Glioma Diagnostics

Epidermal growth factor receptor (EGFR) is commonly affected in cancer, generally in the form of an increase in DNA copy number and/or as mutation variants [e.g., EGFR variant III (EGFRvIII), an in-frame deletion of exons 2–7]. While detection of EGFR aberrations can be expected to be relevant for glioma patients, such analysis has not yet been implemented in a routine setting, also because feasible and robust assays were lacking.
We evaluated multiplex ligation-dependent probe amplification (MLPA) for detection of EGFR amplification and EGFRvIII in DNA of a spectrum of 216 diffuse gliomas. EGFRvIII detection was verified at the protein level by immunohistochemistry and at the RNA level using the conventionally used endpoint RT-PCR as well as a newly developed quantitative RT-PCR. Compared to these techniques, the DNA-based MLPA assay for EGFR/EGFRvIII analysis tested showed 100% sensitivity and specificity. We conclude that MLPA is a robust assay for detection of EGFR/EGFRvIII aberrations. While the exact diagnostic, prognostic and predictive value of such EGFR testing remains to be seen, MLPA has great potential as it can reliably and relatively easily be performed on routinely processed (formalin-fixed, paraffin-embedded) tumor tissue in combination with testing for other relevant glioma markers.     

Image Quality Assurance of Soft Copy Display Systems

Image quality assurance has traditionally been a high priority in medical imaging departments. Recently, it has often been neglected with the transition from hard copy (film) to soft copy (computer) display systems, which could potentially result in difficulty in reading images or even misdiagnosis. This transition therefore requires careful management such that comparable image quality is achieved at a minimum. It is particularly difficult to maintain appropriate image quality in the clinical settings outside of medical imaging departments because of the volume of display systems and the financial restraints that prohibit the widespread use of dedicated computers and high-quality monitors. In this study, a protocol to test and calibrate display systems was developed and validated by using an inexpensive calibration tool. Using this protocol, monitors were identified in a hospital in which image quality was found to be inadequate for medical image viewing. It was also found that most monitors could achieve a substantial increase in image quality after calibration. For example, the 0 and 5% luminance difference was discernable on 30% of the piloted display systems before calibration, but it was discernable on 100% post calibration. In addition, about 50% of the piloted display systems did not have the maximum luminance (white level) suitably set, and 35% of them did not have the minimum luminance (dark level) suitably set. The results indicate that medical display systems must be carefully selected and strictly monitored, maintained, and calibrated to ensure adequate image quality.     

二维数字化超声软组织应变成像系统的研制

利用超声散射回波测量生物组织在静态压缩情况下弹性系数的超声弹性成像方法得到了很大的发展.利用国产高速数据采集卡以及商业线阵B型超声诊断仪,建立了一套二维数字化超声软组织应变成像系统.应用这一系统获得了数字化的射频组织超声散射回波信号,并对组织内的应变分布进行成像.实验结果表明,该应变成像系统在获得传统B型超声图像的同时,可以获得组织内部的应变分布图像,从而获取在B超图像上无法得到的组织弹性变化.这一系统的研制成功,不仅为超声弹性成像技术在医学临床上的应用研究打下了基础,同时也为扩宽普通商业B超的应用范围提供了途径.     

Validity of Low Copy Number Typing and Applications to Forensic Science

Low copy number (LCN) typing, particularly for current short tandem repeat (STR) typing, refers to the analysis of any sample that contains less than 200 pg of template DNA. Generally, LCN typing simply can be defined as the analysis of any DNA sample where the results are below the stochastic threshold for reliable interpretation. There are a number of methodologies to increase sensitivity of detection to enable LCN typing. These approaches encompass modifications during the polymerase chain reaction (PCR) and/or post-PCR manipulations. Regardless of the manipulations, when processing a small number of starting templates during the PCR exaggerated stochastic sampling effects will occur. The result is that several phenomena can occur: a substantial imbalance of 2 alleles at a given heterozygous locus, allelic dropout, or increased stutter. With increased sensitivity of detection there is a concomitant increased risk of contamination. Recently, a commission reviewed LCN typing and found it to be “robust” and “fit for purpose.” Because LCN analysis by its nature is not reproducible, it cannot be considered as robust as that associated with conventional DNA typing. The findings of the commission seem inconsistent with the nature of LCN typing. While LCN typing is appropriate for identification of missing persons and human remains and for developing investigative leads, caution should be taken with its use in other endeavors until developments are made that overcome the vagaries of LCN typing. A more in-depth evaluation by the greater scientific community is warranted. The issues to consider include: training and education, evidence handling and collection procedures, the application or purpose for which the LCN result will be used, the reliability of current LCN methods, replicate analyses, interpretation and uncertainty, report writing, validation requirements, and alternate methodologies for better performance.     

Simulation of Mechanical and Thermal Wounds of Soft Tissues

Bulletin of Experimental Biology and Medicine - Millions of accidental and surgical injuries of soft tissues are registered annually around the world [5]. Untimely and insufficiently effective...     

No Association Between General Cognitive Ability and Rare Copy Number Variation

There is increasing evidence for the role of rare copy-number variation (CNV) in the development of neuropsychiatric disorders. It is likely that such variants also have an effect on the variation of cognition in what is considered the “normal” phenotypic range. The role of rare CNV (>20 KB in length; frequency <5 %) on general cognitive ability is investigated in a sample of 800 individuals (mean age = 16.5, SD = 1.2) using copy-number variants called from the Illumina 610K SNP genotyping array with the software QuantiSNP. We assessed three measures of CNV burden—total CNV length, number of CNV and average CNV length—for both deletions and duplications in combination and separately. No correlation was found between any of the measures of CNV burden and IQ, or when comparing the top and bottom 10 % of the sample for IQ, both on a genome-wide scale and at individual positions across the genome.     

一种能精确检测人间期细胞核中21号染色体拷贝数的DNA探针

目的制备能精确检测人类间期细胞核中２１号染色体拷贝数的ＦＩＳＨ探针。方法利用万能引物ＰＣＲ法,从定位于人２１ｑ１１的ＹＡＣ克隆８８１Ｄ２分离制备ＤＮＡ探针,并用于与８例正常人和５例２１三体患者的外周血淋巴细胞中期相和间期核,及经细胞松弛素Ｂ（ｃｙｔｏｃｈａｌａｓｉｎＢ）诱导的双核细胞进行ＦＩＳＨ分析。结果该探针具有以下特点：（１）长度集中于３５０～７５０ｂｐ;（２）其靶序列位于２１号染色体长臂上且紧靠着丝粒;（３）特异性强;（４）杂交信号明亮,容易辨认;（５）对中期相及间期细胞核中２１号染色体的检出率分别高达９９．６０％和９８．４０％。结论制备的ＤＮＡ探针能精确检测人类间期细胞核中２１号染色体的拷贝数,且适用于细胞分裂时２１号染色体分离情况的研究