Deletion Analysis of the Imprinting Center Region in Patients with Angelman Syndrome and Prader-Willi Syndrome by Real-Time Quantitative PCR

Next-generation sequencing-based molecular diagnosis of neonatal hypotonia in Chinese Population

Neonatal hypotonia is extremely challenging to diagnose because numerous disorders present similar clinical manifestations. Two panels for diagnosing neonatal hypotonia were developed, which enriches 35 genes corresponding to 61 neonatal hypotonia-related disorders. A cohort of 214 neonates with hypotonia was recruited from 2012 to 2014 in China for this study. Of these subjects, twenty-eight neonates with hypotonia were eliminated according to exclusion criteria and 97 were confirmed using traditional detection methods. The clinical diagnoses of the remaining 89 neonates with hypotonia were approached by targeted next-generation sequencing (NGS). Among the 89 tested neonates, 25 potentially pathogenic variants in nine genes (RYR1, MECP2, MUT, CDKL5, MPZ, PMM2, MTM1, LAMA2 and DMPK) were identified in 22 patients. Six of these pathogenic variants were novel. Of the 186 neonates with hypotonia, we identified the genetic causes for 117 neonates by the traditional detection methods and targeted NGS, achieving a high solving rate of 62.9%. In addition, we found seven neonates with RETT syndrome carrying five mutations, thus expanding the mutation profiles in Chinese neonates with hypotonia. Our study highlights the utility of comprehensive molecular genetic testing, which provides the advantage of speed and diagnostic specificity without invasive procedures.

Detection of unknown deletions in beta-globin gene cluster using relative quantitative PCR methods

beta-Thalassemia is mainly caused by mutations involving single base substitution and small deletions. However, a considerable number of carriers are suspected to have large deletions in beta-globin gene cluster. Common strategy for identifying deletions with definite breakpoints is based on Gap PCR. There are, however, some cases with indefinite breakpoints which usually cannot be detected by this method. We developed and optimized a quantitative real-time PCR assay for copy number analysis of beta-globin gene cluster. The copy number of target fragments (i.e. beta, delta or (G)gamma-globin genes) was determined using comparative threshold cycle method. In addition, gene dosage was analyzed using multiplex ligation-dependent probe amplification (MLPA) method in all suspected carriers. Using these relative quantitative assays, normal or carrier statuses of all 26 unknown samples were successfully determined according to the ranges obtained from the ratios of normal and definite carrier samples. Interestingly, large deletions involving the entire beta-globin gene cluster were observed in six carrier individuals. This study showed that the MLPA as a preliminary screening test can be followed by SYBR Green real-time PCR for analysis of copy number variations in beta-globin gene cluster. Combination of these relative quantitative PCR methods could be an appropriate approach for accurate diagnosis of unknown beta-thalassemia deletions in routine diagnosis of beta-thalassemia mutations.

Genomic imprinting and imprinting defects in humans

In placental mammals some 100-200 genes are expressed only from the paternal or the maternal allele. This peculiar expression pattern is the result of genomic imprinting, an epigenetic process by which the male and the female germ line confer a parent-of-origin specific mark (imprint) on certain chromosomal regions. The size of imprinted regions ranges from several kilobases to several megabases. The process of genomic imprinting is controlled by cis-acting imprinting centers (IC) and trans-acting factors. IC mutations affect the establishment or maintenance of genomic imprints and hence the expression of all imprinted genes controlled by this IC. Imprinting defects play a causal role in several recognizable syndromes.

Highest accuracy of combined consensus clinical criteria and SNRPN gene molecular markers in diagnosis of Prader-Willi syndrome in Thai patients

BACKGROUND

Prader-Willi Syndrome (PWS) is a complex human genetic disease arising from a loss of paternal allele expression of imprinting genes on chromosome 15q11-q13. Normally the CpG islands at this site are heavily methylated in the maternal allele, but unmethylated in the paternal allele and therefore activated in gene expression. only the methylated allele should present in pws patients when methylation-specific pcr (msp) is analyzed.

METHODS

This paper reports an analysis of PWS in Thai patients using consensus diagnostic criteria based on a combination of clinical data, basic G-banding and fluorescence in situ hybridization (FISH) cytogenetics, PCR-based methylation assay, and bisulfite sequencing of the CpG islands of SNRPN to confirm 15q deletion or the methylation pattern of the SNRPN promoter and exon 1. Lack of complete clinical reports or inadequacy of the minimum laboratory support required had made it difficult to diagnose PWS, Angelman syndrome and other microdeletion disorders.

RESULTS

Accuracy of 100% was obtained for diagnosis of the PWS study patients using the minimum requirements necessary. A total of 20 patients were diagnosed as PWS based on clinical criteria and the scoring tool for PWS, and the same approach was applied to four separate patients with some unmatched criteria but phenotypic similarity to PWS. Findings showed that 70% of those clinically diagnosed as PWS patients (14/20) had a deletion at 15q11-q13 according to FISH, while all 20 patients showed MSP positive of SNRPN gene. Six cases (30%) without a paternal deletion were confirmed to have maternal uniparental disomy (mUPD) of PWS by MSP and methylation sequencing approaches. Noteworthy, two of the six cases with mUPD were 3.5 year-old twins. None of the five cases with scores lower than the reported consensus criteria showed positive G-band, FISH or MSP results.

CONCLUSIONS

We demonstrate here the high power of combining clinical findings, FISH and MSP in definitive diagnosis of PWS and in distinguishing between the two major different types of molecular mechanisms. No false positives or false negatives were observed in our analysis.

Robust, Easy, and Dose-Sensitive Methylation Test for the Diagnosis of Prader–Willi and Angelman Syndromes

We present a new method for differential diagnosis of Prader-Willi (PWS) and Angelman syndromes (AS) that requires only a small amount of DNA including that obtained from amniocentesis specimens. This method not only proved to be robust and rapid, but, most importantly, it can be dosage sensitive, supplying additional information useful for genetic counselling. After methylation-dependent digestion of DNA with HpaII or McrBC, exon 1 of the SNRPN gene is amplified together with a sequence in the CpG island of the H19 gene. Given the similarities in sequence composition and methylation status between the amplified sequences, their co-amplification under semiquantitative conditions allows an easy discrimination between single dosage (present in deletions or chromosomal translocations) and a double-dosage state (uniparental disomy or imprinting error), when the appropriate controls are included. The method we have developed in combination with standard cytogenetic studies and segregation analysis of microsatellite markers offers a rapid and easy procedure to resolve most suspected cases of PWS and AS, and consequently to provide accurate genetic counselling.

Investigação das causas de atraso no neurodesenvolvimento: recursos e desafios

Com o objetivo de verificar o alcance da investigação de causas do retardo no desenvolvimento neuromotor (RDNM), apresenta-se a experiência no atendimento em Pediatria, Neurologia Infantil e Genética Clínica, em nível terciário, de 73 crianças de 1 a 47 meses, do Programa de Estimulação da APAE de Batatais-SP, entre 1999 e 2001. Utilizando-se método transversal, prospectivo, inicialmente identificaram-se 6 grupos, segundo a semiologia clínica dominante - distúrbios motores, dismorfias, desnutrição, macrocefalia, microcefalia e unicamente atraso motor. Analisando-se a proporção com que os antecedentes e exames contribuíram para o diagnóstico, nos grupos "distúrbios motores" e "macrocefalia" destacaram-se os exames de imagem; nos demais grupos, o exame físico na criança e antecedentes maternos. As causas do RDNM foram detectadas em 48 crianças (66%), sendo de origem ambiental 38,4% e genética 24,6%. Ressalta-se a relevância da avaliação especializada e necessidade de fluxo adequado de informações na rede de saúde.