OBJECTIVETo investigate genomic variations of two Chinese Yersinia pestis isolates that were isolated from different plague foci obtained from vaccine strain EV76 from the Yunnan province of China.

METHODSA microarray containing 12 000 probes covering the entire genome of seven Yersinia pestis and two Yersinia pseudotuberculosis strains, was used. PCR assays were performed to confirm microarray results.

RESULTSThe gene variations detected included the absence of five genes related to the synthesis of betaine in both EV76 and another sequenced attenuated strain, KIM D27. Several genes related to phage-related membrane proteins were found to be absent in the Antiqua biovar Yunnan strain, 485, which was isolated from a rodent plague foci.

CONCLUSIONThese findings provide initial insight into the distinct strains isolated from natural foci, within their genomic context, including Yunnan Y. pestis strains. This information will be used therefore to establish subsequent comparisons of these sequences with published complete genomes of other strains.

China ; Comparative Genomic Hybridization ; methods ; Genome, Bacterial ; genetics ; Polymerase Chain Reaction ; Yersinia pestis ; genetics

Comparative Genomic Hybridization ; methods ; Female ; Humans ; Infant ; Wolf-Hirschhorn Syndrome ; diagnosis

Subchromosomal abnormalities can be positioned by the detection of copy number variation (CNV) using microarray comparative genomic hybridization (aCGH). aCGH has become a powerful tool in understanding the association between gene and genetic etiology in both research and clinical laboratories. Meanwhile as a new technique, controversies inevitably arose in its clinical application. As for the phenotype of CNV, little has been disclosed. For the clinicians, the difficulty in explanation of the CNV to the patients is obvious, which makes many doctors refuse to use aCGH for clinical diagnosis. Customized arrays have been exploited to decrease the uncertainty and efforts to search for a balance between overloaded information and insufficient information have been made. The purpose of this review is to discuss the current limitations and difficulties in application of aCGH in prenatal diagnosis and its application prospect from the point of a clinician.
Comparative Genomic Hybridization ; methods ; DNA Copy Number Variations ; Female ; Humans ; Oligonucleotide Array Sequence Analysis ; methods ; Pregnancy ; Prenatal Diagnosis ; methods

OBJECTIVETo measure the feasibility of application of comparative genomic hybridization technique in the prenatal diagnosis of fetus with mandibulofacial dysostosis.

METHODSA pregnant woman having a fetus with mandibulofacial dysostosis diagnosed by prenatal ultrasound test was selected. The amniotic fluid and blood of the pregnant and blood of her husband were collected and conventional cytogenetic analysis was performed. The whole genome was scanned by array comparative genomic hybridization assay (array-CGH). Reverse transcription fluorescence quantitative PCR (RT-qPCR) analysis was used to verify the result of array-CGH.

RESULTSNo abnormality was found in conventional cytogenetic analysis while a duplicated region in 1p36.33 was detected by array-CGH assay. The region spans 722 kb and contains two genes, VWA1 and PYGO2, which play roles in the development of cartilage. The result of array-CGH was confirmed by the RT-qPCR assay. The diagnosis of mandibulofacial dysostosis was confirmed after birth.

CONCLUSIONAuthor diagnosed a fetus with mandibulofacial dysostosis by array-CGH assay and found two candidate genes related to the development of craniofacial bone: VWA1 and PYGO2.

Adult ; Chromosome Aberrations ; Comparative Genomic Hybridization ; methods ; Female ; Fetus ; pathology ; Humans ; Karyotyping ; methods ; Mandibulofacial Dysostosis ; genetics ; Pregnancy ; Prenatal Diagnosis ; methods

OBJECTIVETo establish a single-cell whole genome amplification (WGA) technique, in combination with comparative genomic hybridization (CGH), for analyzing chromosomal copy number changes, and to explore its clinical application in preimplantation genetic diagnosis (PGD).

METHODSTwelve single-cell samples with known karyotypes, including 5 chorionic villus samples, 4 human embryonic stem cell (hESC) samples and 3 peripheral lymphocyte samples, and 4 single blastomere samples carrying chromosomal abnormalities detected by PGD, were collected for whole genome amplification by combining primer extension preamplification (PEP) with degenerate oligonucleotide primed-PCR (DOP-PCR) amplification. The amplified products labeled by red fluorescence were mixed with control DNA labeled by green fluorescence, and then the mixture was analyzed by CGH. As a comparison, 10 single cell samples were amplified by DOP-PCR only and then CGH analysis was performed.

RESULTSThe amplification using PEP-DOP-PCR was more stable than traditional DOP-PCR. The products of PEP-DOP-PCR range from 100 bp to 1000 bp, with the mean size being about 400 bp. The CGH results were consistent with analyses by other methods. However, only 6 out of 10 single cell samples were successfully amplified by DOP-PCR, and CGH analysis showed a high background and 2 samples showed inconsistent results from other methods.

CONCLUSIONPEP-DOP-PCR can effectively amplify the whole genome DNA of single cell. Combined with CGH, this WGA method can successfully detect single-cell chromosomal copy number changes, while DOP-PCR was easy to fail to amplify and amplify inhomogeneously, and CGH analysis using this PCR product usually showed high background. These results suggest that PEP-DOP-CGH is a promising method for preimplantation genetic diagnosis.

Comparative Genomic Hybridization ; methods ; DNA Primers ; Genetic Testing ; methods ; Humans ; Karyotyping ; methods ; Nucleic Acid Amplification Techniques ; methods ; Nucleic Acid Hybridization ; methods ; Oligonucleotides ; chemistry ; Preimplantation Diagnosis ; methods

In recent years, significant progresses have been got in study on pathogenesis, treatment and prognosis of myelodysplastic syndromes (MDS), especially on use of new technology, that has great importance for cytogenetics of MDS. Recently, the progress of cytogenetic detection in MDS is very remarkable. Based on the metaphase cytogenetics (MC) method, prognostic significance of cytogenetics in MDS was clarified gradually. For example, people have known the prognostic significance of 12 p-, 11 q-, +21, t(11(q23)), although these genetic abnormalities are rare in the MDS. In addition, chromosome mutation emerged in the process of MDS may indicate the poor prognosis. On the other hand, with the use of SNP-A and aCGH in the study of genetics, MDS cytogenetic abnormality detection rate has been further improved and can reach to 78%. At the same time, some of MDS patients with the "normal karyotype" detected by MC have new hidden aberrations through the SNP or CGH detection, and these patients have a poorer prognosis. In this review, the advances of study on cytogenetic detection for MDS based on MC and SNP-A or aCGH methods are summarized.
Comparative Genomic Hybridization ; methods ; Cytogenetics ; methods ; Humans ; Karyotype ; Karyotyping ; Myelodysplastic Syndromes ; diagnosis ; genetics ; Polymorphism, Single Nucleotide ; Prognosis

OBJECTIVETo explore the genetic etiology for fetuses featuring intrauterine growth anomalies using array-based comparative genomic hybridization (aCGH).

METHODSForty-nine fetuses were enrolled in this study. Genomic DNA of the abortive tissues was analyzed with aCGH.

RESULTSFourteen (28.6%) samples were found with chromosomal aberrations, which included 8 chromosomal aneuploidies and 6 micro-aberrations (4 with known clinical pathogenecity and 2 with unknown clinical significance).

CONCLUSIONNumerical and structural chromosomal aberrations underlie a significant proportion of fetal growth anomalies. aCGH has provided an effective method for delineating their genetic cause.

Adult ; Chromosome Aberrations ; Comparative Genomic Hybridization ; methods ; Congenital Abnormalities ; genetics ; DNA Copy Number Variations ; Female ; Humans ; Pregnancy ; Prenatal Diagnosis ; methods

Comparative Genomic Hybridization ; methods ; DNA ; Gene Expression Profiling ; methods ; Genetics, Medical ; methods ; Humans ; In Situ Hybridization, Fluorescence ; Oligonucleotide Array Sequence Analysis ; methods

Breast Neoplasms ; genetics ; pathology ; Chromosome Aberrations ; Comparative Genomic Hybridization ; methods ; DNA, Neoplasm ; genetics ; Female ; Gene Dosage ; Humans ; Prognosis

BACKGROUNDPrimary ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 years. The etiology of primary ovarian insufficiency in human female patients is still unclear. The purpose of this study is to investigate the potential genetic causes in primary amenorrhea patients by high resolution array based comparative genomic hybridization (array-CGH) analysis.

METHODSFollowing the standard karyotyping analysis, genomic DNA from whole blood of 15 primary amenorrhea patients and 15 normal control women was hybridized with Affymetrix cytogenetic 2.7M arrays following the standard protocol. Copy number variations identified by array-CGH were confirmed by real time polymerase chain reaction.

RESULTSAll the 30 samples were negative by conventional karyotyping analysis. Microdeletions on chromosome 17q21.31-q21.32 with approximately 1.3 Mb were identified in four patients by high resolution array-CGH analysis. This included the female reproductive secretory pathway related factor N-ethylmaleimide-sensitive factor (NSF) gene.

CONCLUSIONSThe results of the present study suggest that there may be critical regions regulating primary ovarian insufficiency in women with a 17q21.31-q21.32 microdeletion. This effect might be due to the loss of function of the NSF gene/genes within the deleted region or to effects on contiguous genes.

Adult ; Comparative Genomic Hybridization ; methods ; Female ; Humans ; Karyotyping ; Polymerase Chain Reaction ; Primary Ovarian Insufficiency ; genetics ; Young Adult