Prenatal diagnosis and neonatal phenotype of a de novo microdeletion of 17p11.2p12 associated with Smith–Magenis syndrome and external genital defects

Smith–Magenis syndrome (SMS, OMIM: 182290) is a multiple congenital anomalies and intellectual disability syndrome due to a 3.45 Mb microdeletion involving 17p11.2 and is estimated to occur about one in 25,000 births. Up to now, the ultrasound findings of the foetus with SMS and their external genital defects in patients are rarely reported. This case indicates that foetus with SMS may present polyhydramnios and ventriculomegaly in the second trimester. The newborn male patient had an abnormal phenotype in which he has micropenis and his anus is close to the perineal body. The identification of this case may further expand the phenotypic spectrum of this genetic disorder.

Genetic analysis of a case of 46, XX, SRY－ male syndrome / 中华男科学杂志

<p><b>Objective</b>To identify the etiology of chromosome abnormality in an infertile man and analyze the correlation between the genotype and phenotype.</p><p><b>METHODS</b>We analyzed the karyotype of an infertile male using the routine G-banding technique and then the chromosome abnormality of the patient by Illumina Human CytoSNP-12 Beadchip array.</p><p><b>RESULTS</b>Negative results were found in the examination of the sex-determining region Y (SRY) gene and the STR locus in the AZF zone of the patient. The karyotype of the patient was 46, XX. SNP array showed a 1.05 Mb 19p12 duplication and a 0.93 Mb Xq27.1 duplication.</p><p><b>CONCLUSIONS</b>The patient was confirmed as a case of 46,XX male syndrome. The increased copies of the FGF13 gene may be the major causes of abnormal sex determination and testis development.</p>

Effect of Combining Multiple CNV Defining Algorithms on the Reliability of CNV Calls from SNP Genotyping Data

In addition to single-nucleotide polymorphisms (SNP), copy number variation (CNV) is a major component of human genetic diversity. Among many whole-genome analysis platforms, SNP arrays have been commonly used for genomewide CNV discovery. Recently, a number of CNV defining algorithms from SNP genotyping data have been developed; however, due to the fundamental limitation of SNP genotyping data for the measurement of signal intensity, there are still concerns regarding the possibility of false discovery or low sensitivity for detecting CNVs. In this study, we aimed to verify the effect of combining multiple CNV calling algorithms and set up the most reliable pipeline for CNV calling with Affymetrix Genomewide SNP 5.0 data. For this purpose, we selected the 3 most commonly used algorithms for CNV segmentation from SNP genotyping data, PennCNV, QuantiSNP; and BirdSuite. After defining the CNV loci using the 3 different algorithms, we assessed how many of them overlapped with each other, and we also validated the CNVs by genomic quantitative PCR. Through this analysis, we proposed that for reliable CNV-based genomewide association study using SNP array data, CNV calls must be performed with at least 3 different algorithms and that the CNVs consistently called from more than 2 algorithms must be used for association analysis, because they are more reliable than the CNVs called from a single algorithm. Our result will be helpful to set up the CNV analysis protocols for Affymetrix Genomewide SNP 5.0 genotyping data.

A Case of Acute Myeloid Leukemia with Bone Marrow Basophilia and Dysmegakaryocytic Hyperplasia with Isochromosome 17q as a Sole Cytogenetic Abnormality: A Clinical Study with Literature Review

A new clinico-pathological entity in which isochromosome 17q is the sole abnormality has been reported in myelodysplastic syndrome and in myeloproliferative neoplasm with an aggressive course; In particular, myelodysplastic syndrome with the isolated i(17)(q10) chromosome has the unique features of male sex, severe anemia, dysmegakaryocytic hyperplasia, increased micromegakaryocytes, basophilia, eosinophila and high risk for progression to acute myeloid leukemia (AML). However, the isolated i(17)(q10) is occurring at a relatively low frequency in de novo AML, and only a few reports are available in the literature about the clinical features and molecular characteristics of the isolated i(17)(q10) in AML. Herein, we report both the clinico-pathological features and the results of high resolution single nucleotide polymorphism (SNP) array analysis in a case of AML with i(17)(q10) as the sole cytogenetic abnormality. This case showed marrow findings of basophilia and dysmegakaryocytic hyperplasia and aggressive clinical outcome and these findings were suggestive of the presence of underlying myelodysplastic syndrome. The breakpoint of i(17)(q10) was located within 17p11.2 sub-band, which is known as a genetically highly unstable region presenting a unique genomic architectural features of low copy repeats (LCRs); thus, LCRs within 17p11.2 might lead to genomic instability and facilitate somatic genetic rearrangements such as i(17) (q10) and could play an important pathogenetic role in presenting unique clinico-pathologic features as well as in tumor development and disease progression.